Adenylate–uridylate rich element gene transcriptions

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Associate Editor(s)-in-Chief: Henry A. Hoff

"Functionally defined and derived adenylate–uridylate rich element (ARE) consensus sequences have been shown to exist in the 3′UTR of selected mRNAs belonging to interferons, cytokines and proto-oncogenes ( 1 ). A 13-bp ARE motif was computationally derived from a list of functionally labile ARE-mRNAs and was the basis of the ARE-mRNA database (ARED) which contains GenBank entries where the 3′UTR matches the motif ( 2 )."[1]

Human genes

Main article: Human genes

The ARE-mRNA database (ARED) "demonstrated that ARE-mRNAs represent as much as 5–8% of human genes and encode functionally diverse proteins that are important in many transient biological processes including cell growth and differentiation, signal transduction, transcriptional and translational control, hematopoiesis, apoptosis, nutrient transport, and metabolism ( 2 )."[1]

"The 3′UTRs were searched for the 13-bp pattern WWWUAUUUAUWW with mismatch=−1 which was computationally derived as previously described ( 2 ). The pattern was further statistically validated against larger sets of mRNA data (10 872 mRNA with 3′UTR; GenBank 119) showing occurrence of the motif in 6.8% of human mRNA."[1]

"The ARED website ( http://rc.kfshrc.edu.sa/ared ) offers a query search engine that allows searches for ARE-genes using multiple identifier numbers or descriptions such as UniGene IDs, UniGene definition, RefSeq IDs, accession numbers, alternative names, official Gene symbols and mouse homologs (MGD) ( 10 )."[1]

Gene expressions

Main article: Gene expressions

"3′ untranslated regions play an important role in regulating mRNA fate by complexing with RNA binding proteins that help control mRNA localization, translation, and stability [1, 2, 3]. Identification of a consensus UUAUUUAU sequence in the 3′ UTRs of human and mouse mRNAs encoding tumor necrosis factor (TNF-α) and a variety of other inflammatory mediators led to the suggestion that these AU-rich elements AREs) could be important for regulating gene expression [4]. Subsequent studies confirmed that these and other AREs interact with ARE-binding proteins such as AUF1 (also known as hnRNPD), HuR and other Hu family proteins, and the CCCH zinc finger-containing RBPs ZFP36 (tristetraprolin), ZFP36L1, and ZFP36L2 [5], to alter mRNA degradation and protein expression [6]. In most cases, AREs have been reported to destabilize mRNAs, although in some cellular contexts certain AREs and ARE-binding proteins have been shown to stabilize mRNAs [6, 7]. Subsequent analyses of the human genome concluded that as many as 58% of human genes code for mRNAs that contain AREs [8, 9, 10], suggesting that these elements play a major role in regulating expression of a large group of genes."[2]

Interactions

Main article: Interaction gene transcriptions

"Chen and Shyu[3] divided AREs into two classes of AUUUA-containing AREs and a third class of non-AUUUA AREs. Class I AUUUA-containing AREs had 1-3 copies of scattered AUUUA motifs coupled with a nearby U-rich region or U stretch, whereas class II AUUUA-containing AREs had at least two overlapping copies of the nonamer UUAUUUA(U/A)(U/A) in a U-rich region. Non-AUUUA AREs had a U-rich region and other unknown features, and the relationship of these sequences to AUUUA-containing AREs remains poorly understood. Subsequent studies based on analyses of a set of 4884 AUUUA-containing AREs led to a new classification based primarily on the number of overlapping AUUUA-repeats [8, 9, 10]. This classification system, with five clusters distinguished by the number of repeats, was used to identify AUUUA-containing AREs in the human genome. AREs identified using this classification were found to be abundant in 3′ UTRs of human genes."[2]

Consensus sequences

Main article: Consensus sequence gene transcriptions

WWWUAUUUAUWW=(A/T)(A/T)(A/T)TATTTAT(A/T)(A/T).[1]

Binding site for stem loop motifs

Constitutive "decay elements (CDEs) [4, 18][...] are conserved stem loop motifs that bind to the proteins Roquin and Roquin2, resulting in increased mRNA decay [18]. CDEs include an upper stem-loop sequence of the form UUCYRYGAA flanked by lower stem sequences. Lower stem sequences are formed by 2-5 nt pairs of reverse-complementary sequences (e.g. CCUUCYRYGAAGG has a lower stem length of 2)."[2]

CCUUCYRYGAAGG is CCTTC(C/T)(A/G)(C/T)GAAGG, and UUCYRYGAA is TTC(C/T)(A/G)(C/T)GAA.

Adenylate–uridylate rich element (Bakheet) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) (starting with SuccessablesAURE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 1, TTTTATTTATTA at 4076.
  2. positive strand, negative direction, looking for (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 0.
  3. positive strand, positive direction, looking for (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 0.
  4. negative strand, positive direction, looking for (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 0.
  5. complement, negative strand, negative direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 0.
  6. complement, positive strand, negative direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 1, AAAATAAATAAT at 4076.
  7. complement, positive strand, positive direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 0.
  8. complement, negative strand, positive direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 0.
  9. inverse complement, negative strand, negative direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 0.
  10. inverse complement, positive strand, negative direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 1, AAATAAATAATA at 4077.
  11. inverse complement, positive strand, positive direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 0.
  12. inverse complement, negative strand, positive direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 0.
  13. inverse negative strand, negative direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 1, TTTATTTATTAT at 4077.
  14. inverse positive strand, negative direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 0.
  15. inverse positive strand, positive direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 0.
  16. inverse negative strand, positive direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 0.

Adenylate–uridylate rich element (Bakheet) UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: TTTTATTTATTA at 4076.

Positive strand, negative direction: AAATAAATAATA at 4077.

Adenylate–uridylate rich element (Bakheet) random dataset samplings

  1. AUREr0: 0.
  2. AUREr1: 0.
  3. AUREr2: 0.
  4. AUREr3: 0.
  5. AUREr4: 0.
  6. AUREr5: 1, AATTATTTATTT at 859.
  7. AUREr6: 0.
  8. AUREr7: 0.
  9. AUREr8: 0.
  10. AUREr9: 0.
  11. AUREr0ci: 1, TAATAAATAAAA at 1499.
  12. AUREr1ci: 0.
  13. AUREr2ci: 0.
  14. AUREr3ci: 0.
  15. AUREr4ci: 0.
  16. AUREr5ci: 0.
  17. AUREr6ci: 0.
  18. AUREr7ci: 0.
  19. AUREr8ci: 0.
  20. AUREr9ci: 0.

AUREr arbitrary negative direction (evens) (2596-1) distal promoters

  1. AUREr0ci: TAATAAATAAAA at 1499.

AUREr alternate negative direction (odds) (2596-1) distal promoters

  1. AUREr5: AATTATTTATTT at 859.

AUREr arbitrary positive direction (odds) (4050-1) distal promoters

  1. AUREr5: AATTATTTATTT at 859.

AUREr alternate positive direction (evens) (4050-1) distal promoters

  1. AUREr0ci: TAATAAATAAAA at 1499.

Adenylate–uridylate rich element (Bakheet) analysis and results

Main article: Complex locus A1BG and ZNF497 § AUREs

"The 3′UTRs were searched for the 13-bp pattern WWWUAUUUAUWW with mismatch=−1 which was computationally derived as previously described ( 2 ). The pattern was further statistically validated against larger sets of mRNA data (10 872 mRNA with 3′UTR; GenBank 119) showing occurrence of the motif in 6.8% of human mRNA."[1] WWWUAUUUAUWW=(A/T)(A/T)(A/T)TATTTAT(A/T)(A/T).[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 1 10 0.1 0.1
Randoms Distal alternate negative 1 10 0.1 0.1
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 1 10 0.1 0.1
Randoms Distal alternate positive 1 10 0.1 0.1

Comparison:

The occurrences of real adenylate–uridylate rich element consensus sequences are greater than the randoms. This suggests that the real adenylate–uridylate rich element consensus sequences are likely active or activable.

ATTTA (Chen and Shyu, Class I) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence ATTTA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence ATTTA (starting with SuccessablesAURS.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for ATTTA, 3, ATTTA at 4073, ATTTA at 2636, ATTTA at 1698.
  2. positive strand, negative direction, looking for ATTTA, 1, ATTTA at 4535.
  3. positive strand, positive direction, looking for ATTTA, 1, ATTTA at 3428.
  4. negative strand, positive direction, looking for ATTTA, 1, ATTTA at 4135.
  5. inverse complement, negative strand, negative direction, looking for TAAAT, 1, TAAAT at 4535.
  6. inverse complement, positive strand, negative direction, looking for TAAAT, 3, TAAAT at 4073, TAAAT at 2636, TAAAT at 1698.
  7. inverse complement, positive strand, positive direction, looking for TAAAT, 1, TAAAT at 4135.
  8. inverse complement, negative strand, positive direction, looking for TAAAT, 1, TAAAT at 3428.

AURS (4560-2846) UTRs

  1. Negative strand, negative direction: ATTTA at 4073.
  2. Positive strand, negative direction: ATTTA at 4535.

AURS negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: ATTTA at 2636.

AURS positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: ATTTA at 4135.

AURS negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: ATTTA at 1698.

AURS positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: ATTTA at 3428.

AURS random dataset samplings

  1. AURSr0: 2, ATTTA at 2391, ATTTA at 752.
  2. AURSr1: 4, ATTTA at 3611, ATTTA at 3096, ATTTA at 1872, ATTTA at 1004.
  3. AURSr2: 9, ATTTA at 4144, ATTTA at 3617, ATTTA at 3485, ATTTA at 2895, ATTTA at 2520, ATTTA at 2131, ATTTA at 1771, ATTTA at 996, ATTTA at 129.
  4. AURSr3: 7, ATTTA at 4287, ATTTA at 4027, ATTTA at 2327, ATTTA at 1559, ATTTA at 1088, ATTTA at 797, ATTTA at 359.
  5. AURSr4: 8, ATTTA at 3863, ATTTA at 3723, ATTTA at 3027, ATTTA at 1676, ATTTA at 1300, ATTTA at 560, ATTTA at 403, ATTTA at 121.
  6. AURSr5: 8, ATTTA at 4055, ATTTA at 3718, ATTTA at 3629, ATTTA at 2630, ATTTA at 1313, ATTTA at 1110, ATTTA at 856, ATTTA at 490.
  7. AURSr6: 11, ATTTA at 4372, ATTTA at 3761, ATTTA at 3748, ATTTA at 3622, ATTTA at 2763, ATTTA at 2729, ATTTA at 1144, ATTTA at 1140, ATTTA at 916, ATTTA at 483, ATTTA at 187.
  8. AURSr7: 5, ATTTA at 3914, ATTTA at 2978, ATTTA at 2766, ATTTA at 1527, ATTTA at 330.
  9. AURSr8: 5, ATTTA at 2244, ATTTA at 1043, ATTTA at 828, ATTTA at 729, ATTTA at 195.
  10. AURSr9: 5, ATTTA at 3116, ATTTA at 1101, ATTTA at 968, ATTTA at 809, ATTTA at 623.

The complement inverse is the same as the complement which means the above results would repeat as their complements in the real sequences.

AURSr arbitrary (evens) (4560-2846) UTRs

  1. AURSr2: ATTTA at 4144, ATTTA at 3617, ATTTA at 3485, ATTTA at 2895.
  2. AURSr4: ATTTA at 3863, ATTTA at 3723, ATTTA at 3027.
  3. AURSr6: ATTTA at 4372, ATTTA at 3761, ATTTA at 3748, ATTTA at 3622.

AURSr alternate (odds) (4560-2846) UTRs

  1. AURSr1: ATTTA at 3611, ATTTA at 3096.
  2. AURSr3: ATTTA at 4287, ATTTA at 4027.
  3. AURSr5: ATTTA at 4055, ATTTA at 3718, ATTTA at 3629.
  4. AURSr7: ATTTA at 3914, ATTTA at 2978.
  5. AURSr9: ATTTA at 3116.

AURSr arbitrary positive direction (odds) (4445-4265) core promoters

  1. AURSr3: ATTTA at 4287.

AURSr alternate positive direction (evens) (4445-4265) core promoters

  1. AURSr6: ATTTA at 4372.

AURSr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. AURSr6: ATTTA at 2763, ATTTA at 2729.

AURSr alternate negative direction (odds) (2811-2596) proximal promoters

  1. AURSr5: ATTTA at 2630.
  2. AURSr7: ATTTA at 2766.

AURSr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. AURSr5: ATTTA at 4055.

AURSr alternate positive direction (evens) (4265-4050) proximal promoters

  1. AURSr2: ATTTA at 4144.

AURSr arbitrary negative direction (evens) (2596-1) distal promoters

  1. AURSr0: ATTTA at 2391, ATTTA at 752.
  2. AURSr2: ATTTA at 2520, ATTTA at 2131, ATTTA at 1771, ATTTA at 996, ATTTA at 129.
  3. AURSr4: ATTTA at 1676, ATTTA at 1300, ATTTA at 560, ATTTA at 403, ATTTA at 121.
  4. AURSr6: ATTTA at 1144, ATTTA at 1140, ATTTA at 916, ATTTA at 483, ATTTA at 187.
  5. AURSr8: ATTTA at 2244, ATTTA at 1043, ATTTA at 828, ATTTA at 729, ATTTA at 195.

AURSr alternate negative direction (odds) (2596-1) distal promoters

  1. AURSr1: ATTTA at 1872, ATTTA at 1004.
  2. AURSr3: ATTTA at 2327, ATTTA at 1559, ATTTA at 1088, ATTTA at 797, ATTTA at 359.
  3. AURSr5: ATTTA at 1313, ATTTA at 1110, ATTTA at 856, ATTTA at 490.
  4. AURSr7: ATTTA at 1527, ATTTA at 330.
  5. AURSr9: ATTTA at 1101, ATTTA at 968, ATTTA at 809, ATTTA at 623.

AURSr arbitrary positive direction (odds) (4050-1) distal promoters

  1. AURSr1: ATTTA at 3611, ATTTA at 3096, ATTTA at 1872, ATTTA at 1004.
  2. AURSr3: ATTTA at 4027, ATTTA at 2327, ATTTA at 1559, ATTTA at 1088, ATTTA at 797, ATTTA at 359.
  3. AURSr5: ATTTA at 3718, ATTTA at 3629, ATTTA at 2630, ATTTA at 1313, ATTTA at 1110, ATTTA at 856, ATTTA at 490.
  4. AURSr7: ATTTA at 3914, ATTTA at 2978, ATTTA at 2766, ATTTA at 1527, ATTTA at 330.
  5. AURSr9: ATTTA at 3116, ATTTA at 1101, ATTTA at 968, ATTTA at 809, ATTTA at 623.

AURSr alternate positive direction (evens) (4050-1) distal promoters

  1. AURSr2: ATTTA at 3617, ATTTA at 3485, ATTTA at 2895, ATTTA at 2520, ATTTA at 2131, ATTTA at 1771, ATTTA at 996, ATTTA at 129.
  2. AURSr4: ATTTA at 3863, ATTTA at 3723, ATTTA at 3027, ATTTA at 1676, ATTTA at 1300, ATTTA at 560, ATTTA at 403, ATTTA at 121.
  3. AURSr6: ATTTA at 3761, ATTTA at 3748, ATTTA at 3622, ATTTA at 2763, ATTTA at 2729, ATTTA at 1144, ATTTA at 1140, ATTTA at 916, ATTTA at 483, ATTTA at 187.
  4. AURSr8: ATTTA at 2244, ATTTA at 1043, ATTTA at 828, ATTTA at 729, ATTTA at 195.

Adenylate–uridylate rich element (Chen and Shyu, Class I) analysis and results

Main article: Complex locus A1BG and ZNF497 § Adenylate–uridylate rich elements (Chen and Shyu, Class I)

"Class I AUUUA-containing AREs had 1-3 copies of scattered AUUUA motifs coupled with a nearby U-rich region or U stretch".[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1
Randoms UTR arbitrary negative 11 10 1.1 1.05
Randoms UTR alternate negative 10 10 1.0 1.05
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 1 10 0.1 0.1
Randoms Core alternate positive 1 10 0.1 0.1
Reals Proximal negative 1 2 0.5 0.5
Randoms Proximal arbitrary negative 2 10 0.1 0.1
Randoms Proximal alternate negative 2 10 0.1 0.1
Reals Proximal positive 1 2 0.5 0.5
Randoms Proximal arbitrary positive 1 10 0.1 0.1
Randoms Proximal alternate positive 1 10 0.1 0.1
Reals Distal negative 1 2 0.5 0.5
Randoms Distal arbitrary negative 22 10 2.2 1.95
Randoms Distal alternate negative 17 10 1.7 1.95
Reals Distal positive 1 2 0.5 0.5
Randoms Distal arbitrary positive 27 10 2.7 2.9
Randoms Distal alternate positive 31 10 3.1 2.9

Comparison:

The occurrences of real AURS UTRs are the same as the lower end of the randoms, the proximals are greater than the randoms and the distals are less than the randoms. This suggests that the real AURSs are likely active or activable.

UUAUUUA(U/A)(U/A) (Chen and Shyu, Class II) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence TTATTTATT and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or one between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TTATTTA(A/T)(A/T) (starting with SuccessablesUUA.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for TTATTTA(A/T)(A/T), 1, TTATTTATT at 4075.
  2. positive strand, negative direction, looking for TTATTTA(A/T)(A/T), 0.
  3. positive strand, positive direction, looking for TTATTTA(A/T)(A/T), 0.
  4. negative strand, positive direction, looking for TTATTTA(A/T)(A/T), 0.
  5. complement, negative strand, negative direction, looking for AATAAAT(A/T)(A/T), 0.
  6. complement, positive strand, negative direction, looking for AATAAAT(A/T)(A/T), 1, AATAAATAA at 4075.
  7. complement, positive strand, positive direction, looking for AATAAAT(A/T)(A/T), 0.
  8. complement, negative strand, positive direction, looking for AATAAAT(A/T)(A/T), 0.
  9. inverse complement, negative strand, negative direction, looking for (A/T)(A/T)TAAATAA, 0.
  10. inverse complement, positive strand, negative direction, looking for (A/T)(A/T)TAAATAA, 1, AATAAATAA at 4075.
  11. inverse complement, positive strand, positive direction, looking for (A/T)(A/T)TAAATAA, 0.
  12. inverse complement, negative strand, positive direction, looking for (A/T)(A/T)TAAATAA, 0.
  13. inverse negative strand, negative direction, looking for (A/T)(A/T)ATTTATT, 1, TTATTTATT at 4075.
  14. inverse positive strand, negative direction, looking for (A/T)(A/T)ATTTATT, 0.
  15. inverse positive strand, positive direction, looking for (A/T)(A/T)ATTTATT, 0.
  16. inverse negative strand, positive direction, looking for (A/T)(A/T)ATTTATT, 0.

UUA UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: TTATTTATT at 4075.

UUA random dataset samplings

  1. UUAr0: 0.
  2. UUAr1: 0.
  3. UUAr2: 0.
  4. UUAr3: 0.
  5. UUAr4: 0.
  6. UUAr5: 2, TTATTTAAT at 3631, TTATTTATT at 858.
  7. UUAr6: 0.
  8. UUAr7: 0.
  9. UUAr8: 0.
  10. UUAr9: 0.
  11. UUAr0ci: 1, AATAAATAA at 1497.
  12. UUAr1ci: 0.
  13. UUAr2ci: 0.
  14. UUAr3ci: 0.
  15. UUAr4ci: 0.
  16. UUAr5ci: 0.
  17. UUAr6ci: 0.
  18. UUAr7ci: 1, TATAAATAA at 3632.
  19. UUAr8ci: 0.
  20. UUAr9ci: 0.

UUAr alternate (odds) (4560-2846) UTRs

  1. UUAr5: TTATTTAAT at 3631.
  2. UUAr7ci: TATAAATAA at 3632.

UUAr arbitrary negative direction (evens) (2596-1) distal promoters

  1. UUAr0ci: AATAAATAA at 1497.

UUAr alternate negative direction (odds) (2596-1) distal promoters

  1. UUAr5: TTATTTATT at 858.

UUAr arbitrary positive direction (odds) (4050-1) distal promoters

  1. UUAr5: TTATTTAAT at 3631, TTATTTATT at 858.
  2. UUAr7ci: TATAAATAA at 3632.

UUAr alternate positive direction (evens) (4050-1) distal promoters

  1. UUAr0ci: AATAAATAA at 1497.

UUAUUUA(U/A)(U/A) (Chen and Shyu, Class II) analysis and results

Main article: Complex locus A1BG and ZNF497 § Adenylate–uridylate rich elements (Chen and Shyu, Class II)

class II AUUUA-containing AREs had at least two overlapping copies of the nonamer UUAUUUA(U/A)(U/A) in a U-rich region.[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5
Randoms UTR arbitrary negative 0 10 0 0.1
Randoms UTR alternate negative 2 10 0.2 0.1
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 1 10 0.1 0.1
Randoms Distal alternate negative 1 10 0.1 0.1
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 3 10 0.3 0.2
Randoms Distal alternate positive 1 10 0.1 0.2

Comparison:

The occurrences of real UUAs are greater than the randoms. This suggests that the real UUAs are likely active or activable.

ATTT (Chen and Shyu, Class III)

Copying a responsive elements consensus sequence ATTT and putting the sequence in "⌘F" finds 3-25 between ZNF497 and A1BG or 3-25 between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence ATTT (starting with SuccessablesAURIII.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for ATTT, 26, ATTT at 4514, ATTT at 4072, ATTT at 3481, ATTT at 3438, ATTT at 3362, ATTT at 3352, ATTT at 3335, ATTT at 3170, ATTT at 3162, ATTT at 3023, ATTT at 3014, ATTT at 3009, ATTT at 2874, ATTT at 2856, ATTT at 2635, ATTT at 2298, ATTT at 2173, ATTT at 1871, ATTT at 1736, ATTT at 1697, ATTT at 1547, ATTT at 762, ATTT at 628, ATTT at 221, ATTT at 182, ATTT at 65.
  2. positive strand, negative direction, looking for ATTT, 11, ATTT at 4534, ATTT at 4510, ATTT at 3687, ATTT at 2883, ATTT at 2852, ATTT at 1726, ATTT at 1602, ATTT at 1379, ATTT at 363, ATTT at 189, ATTT at 21.
  3. positive strand, positive direction, looking for ATTT, 3, ATTT at 3427, ATTT at 2444, ATTT at 2136.
  4. negative strand, positive direction, looking for ATTT, 7, ATTT at 4134, ATTT at 4119, ATTT at 2869, ATTT at 2644, ATTT at 2448, ATTT at 2440, ATTT at 1977.
  5. inverse complement, negative strand, negative direction, looking for AAAT, 11, AAAT at 4535, AAAT at 4512, AAAT at 3350, AAAT at 3021, AAAT at 2854, AAAT at 1734, AAAT at 1728, AAAT at 348, AAAT at 217, AAAT at 191, AAAT at 48.
  6. inverse complement, positive strand, negative direction, looking for AAAT, 36, AAAT at 4219, AAAT at 4088, AAAT at 4073, AAAT at 4069, AAAT at 3768, AAAT at 3498, AAAT at 3355, AAAT at 3332, AAAT at 3314, AAAT at 3173, AAAT at 3011, AAAT at 2930, AAAT at 2867, AAAT at 2747, AAAT at 2646, AAAT at 2636, AAAT at 2301, AAAT at 2185, AAAT at 2158, AAAT at 2061, AAAT at 1884, AAAT at 1874, AAAT at 1738, AAAT at 1698, AAAT at 1661, AAAT at 1631, AAAT at 1578, AAAT at 1562, AAAT at 1231, AAAT at 774, AAAT at 765, AAAT at 640, AAAT at 631, AAAT at 496, AAAT at 488, AAAT at 40.
  7. inverse complement, positive strand, positive direction, looking for AAAT, 8, AAAT at 4140, AAAT at 4135, AAAT at 4121, AAAT at 4110, AAAT at 2586, AAAT at 2442, AAAT at 2345, AAAT at 148.
  8. inverse complement, negative strand, positive direction, looking for AAAT, 6, AAAT at 4092, AAAT at 3795, AAAT at 3428, AAAT at 3166, AAAT at 2624, AAAT at 2446.

AURIII (4560-2846) UTRs

  1. Negative strand, negative direction: AAAT at 4535, ATTT at 4514, AAAT at 4512, ATTT at 4072, ATTT at 3481, ATTT at 3438, ATTT at 3362, ATTT at 3352, AAAT at 3350, ATTT at 3335, ATTT at 3170, ATTT at 3162, ATTT at 3023, AAAT at 3021, ATTT at 3014, ATTT at 3009, ATTT at 2874, ATTT at 2856, AAAT at 2854.
  2. Positive strand, negative direction: ATTT at 4534, ATTT at 4510, AAAT at 4219, AAAT at 4088, AAAT at 4073, AAAT at 4069, AAAT at 3768, ATTT at 3687, AAAT at 3498, AAAT at 3355, AAAT at 3332, AAAT at 3314, AAAT at 3173, AAAT at 3011, AAAT at 2930, ATTT at 2883, AAAT at 2867, ATTT at 2852.

AURIII negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: ATTT at 2635.
  2. Positive strand, negative direction: AAAT at 2747, AAAT at 2646, AAAT at 2636.

AURIII positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: ATTT at 4134, ATTT at 4119, AAAT at 4092.
  2. Positive strand, positive direction: AAAT at 4140, AAAT at 4135, AAAT at 4121, AAAT at 4110.

AURIII negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: ATTT at 2298, ATTT at 2173, ATTT at 1871, ATTT at 1736, AAAT at 1734, AAAT at 1728, ATTT at 1697, ATTT at 1547, ATTT at 762, ATTT at 628, AAAT at 348, ATTT at 221, AAAT at 217, AAAT at 191, ATTT at 182, ATTT at 65, AAAT at 48.
  2. Positive strand, negative direction: AAAT at 2301, AAAT at 2185, AAAT at 2158, AAAT at 2061, AAAT at 1884, AAAT at 1874, AAAT at 1738, ATTT at 1726, AAAT at 1698, AAAT at 1661, AAAT at 1631, ATTT at 1602, AAAT at 1578, AAAT at 1562, ATTT at 1379, AAAT at 1231, AAAT at 774, AAAT at 765, AAAT at 640, AAAT at 631, AAAT at 496, AAAT at 488, ATTT at 363, ATTT at 189, AAAT at 40, ATTT at 21.

AURIII positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: AAAT at 3795, AAAT at 3428, AAAT at 3166, ATTT at 2869, ATTT at 2644, AAAT at 2624, ATTT at 2448, AAAT at 2446, ATTT at 2440, ATTT at 1977.
  2. Positive strand, positive direction: ATTT at 3427, AAAT at 2586, ATTT at 2444, AAAT at 2442, AAAT at 2345, ATTT at 2136, AAAT at 148.

ATTT (Chen and Shyu, Class III) random dataset samplings

  1. AURIIIr0: 29, ATTT at 4228, ATTT at 4201, ATTT at 4128, ATTT at 4002, ATTT at 3694, ATTT at 3664, ATTT at 3513, ATTT at 3353, ATTT at 3310, ATTT at 3023, ATTT at 2825, ATTT at 2616, ATTT at 2494, ATTT at 2415, ATTT at 2390, ATTT at 2144, ATTT at 1910, ATTT at 1819, ATTT at 1814, ATTT at 1642, ATTT at 1568, ATTT at 1459, ATTT at 1450, ATTT at 1192, ATTT at 1166, ATTT at 751, ATTT at 493, ATTT at 474, ATTT at 129.
  2. AURIIIr1: 22, ATTT at 4219, ATTT at 4050, ATTT at 4034, ATTT at 3781, ATTT at 3610, ATTT at 3605, ATTT at 3584, ATTT at 3452, ATTT at 3408, ATTT at 3095, ATTT at 2565, ATTT at 2425, ATTT at 2140, ATTT at 1871, ATTT at 1493, ATTT at 1291, ATTT at 1243, ATTT at 1003, ATTT at 827, ATTT at 788, ATTT at 766, ATTT at 306.
  3. AURIIIr2: 29, ATTT at 4483, ATTT at 4413, ATTT at 4202, ATTT at 4143, ATTT at 4072, ATTT at 3951, ATTT at 3616, ATTT at 3557, ATTT at 3484, ATTT at 3404, ATTT at 3380, ATTT at 3299, ATTT at 3115, ATTT at 3002, ATTT at 2921, ATTT at 2894, ATTT at 2626, ATTT at 2519, ATTT at 2130, ATTT at 1886, ATTT at 1770, ATTT at 1373, ATTT at 1245, ATTT at 1118, ATTT at 995, ATTT at 808, ATTT at 261, ATTT at 128, ATTT at 33.
  4. AURIIIr3: 28, ATTT at 4349, ATTT at 4295, ATTT at 4286, ATTT at 4194, ATTT at 4093, ATTT at 4064, ATTT at 4050, ATTT at 4026, ATTT at 3969, ATTT at 3779, ATTT at 3756, ATTT at 3688, ATTT at 3164, ATTT at 2615, ATTT at 2538, ATTT at 2504, ATTT at 2326, ATTT at 2018, ATTT at 1784, ATTT at 1558, ATTT at 1087, ATTT at 924, ATTT at 919, ATTT at 796, ATTT at 408, ATTT at 402, ATTT at 358, ATTT at 169.
  5. AURIIIr4: 22, ATTT at 3862, ATTT at 3722, ATTT at 3672, ATTT at 3663, ATTT at 3514, ATTT at 3353, ATTT at 3026, ATTT at 3017, ATTT at 2904, ATTT at 2886, ATTT at 2767, ATTT at 2546, ATTT at 2254, ATTT at 1675, ATTT at 1299, ATTT at 841, ATTT at 835, ATTT at 559, ATTT at 539, ATTT at 402, ATTT at 240, ATTT at 120.
  6. AURIIIr5: 29, ATTT at 4468, ATTT at 4195, ATTT at 4054, ATTT at 3877, ATTT at 3717, ATTT at 3703, ATTT at 3655, ATTT at 3628, ATTT at 3492, ATTT at 3459, ATTT at 3353, ATTT at 3280, ATTT at 2789, ATTT at 2704, ATTT at 2629, ATTT at 2600, ATTT at 1608, ATTT at 1447, ATTT at 1312, ATTT at 1203, ATTT at 1174, ATTT at 1109, ATTT at 995, ATTT at 859, ATTT at 855, ATTT at 489, ATTT at 293, ATTT at 272, ATTT at 110.
  7. AURIIIr6: 29, ATTT at 4525, ATTT at 4371, ATTT at 4265, ATTT at 3857, ATTT at 3811, ATTT at 3760, ATTT at 3747, ATTT at 3621, ATTT at 3264, ATTT at 2974, ATTT at 2798, ATTT at 2762, ATTT at 2741, ATTT at 2728, ATTT at 2649, ATTT at 2230, ATTT at 2020, ATTT at 1878, ATTT at 1654, ATTT at 1648, ATTT at 1305, ATTT at 1143, ATTT at 1139, ATTT at 915, ATTT at 815, ATTT at 482, ATTT at 402, ATTT at 186, ATTT at 94.
  8. AURIIIr7: 21, ATTT at 4380, ATTT at 4223, ATTT at 3913, ATTT at 3452, ATTT at 3241, ATTT at 2977, ATTT at 2765, ATTT at 2516, ATTT at 2445, ATTT at 2395, ATTT at 2253, ATTT at 2242, ATTT at 1893, ATTT at 1808, ATTT at 1526, ATTT at 1341, ATTT at 1176, ATTT at 708, ATTT at 488, ATTT at 329, ATTT at 110.
  9. AURIIIr8: 28, ATTT at 4541, ATTT at 4354, ATTT at 4309, ATTT at 3488, ATTT at 3334, ATTT at 3001, ATTT at 2540, ATTT at 2525, ATTT at 2427, ATTT at 2331, ATTT at 2288, ATTT at 2243, ATTT at 2221, ATTT at 2119, ATTT at 1811, ATTT at 1801, ATTT at 1479, ATTT at 1157, ATTT at 1042, ATTT at 930, ATTT at 871, ATTT at 827, ATTT at 739, ATTT at 728, ATTT at 482, ATTT at 266, ATTT at 194, ATTT at 165.
  10. AURIIIr9: 27, ATTT at 4270, ATTT at 3801, ATTT at 3618, ATTT at 3578, ATTT at 3492, ATTT at 3476, ATTT at 3329, ATTT at 3115, ATTT at 2926, ATTT at 2782, ATTT at 2562, ATTT at 2524, ATTT at 2510, ATTT at 2341, ATTT at 2139, ATTT at 2125, ATTT at 1741, ATTT at 1652, ATTT at 1447, ATTT at 1350, ATTT at 1100, ATTT at 967, ATTT at 833, ATTT at 808, ATTT at 622, ATTT at 466, ATTT at 158.
  11. AURIIIr0ci: 29, AAAT at 4126, AAAT at 4022, AAAT at 3925, AAAT at 3914, AAAT at 3566, AAAT at 3172, AAAT at 2807, AAAT at 2696, AAAT at 2558, AAAT at 2334, AAAT at 2259, AAAT at 2172, AAAT at 2156, AAAT at 1987, AAAT at 1812, AAAT at 1788, AAAT at 1705, AAAT at 1556, AAAT at 1495, AAAT at 1448, AAAT at 861, AAAT at 797, AAAT at 770, AAAT at 749, AAAT at 544, AAAT at 504, AAAT at 195, AAAT at 142, AAAT at 114.
  12. AURIIIr1ci: 25, AAAT at 3970, AAAT at 3883, AAAT at 3591, AAAT at 3489, AAAT at 3440, AAAT at 3371, AAAT at 3363, AAAT at 3168, AAAT at 3072, AAAT at 2914, AAAT at 2502, AAAT at 2423, AAAT at 2362, AAAT at 1941, AAAT at 1933, AAAT at 1869, AAAT at 1669, AAAT at 1619, AAAT at 1491, AAAT at 1422, AAAT at 1254, AAAT at 1001, AAAT at 311, AAAT at 262, AAAT at 166.
  13. AURIIIr2ci: 22, AAAT at 4309, AAAT at 3949, AAAT at 3828, AAAT at 3798, AAAT at 3786, AAAT at 3441, AAAT at 3427, AAAT at 2919, AAAT at 2730, AAAT at 2665, AAAT at 2517, AAAT at 2382, AAAT at 2128, AAAT at 2083, AAAT at 1768, AAAT at 1589, AAAT at 1551, AAAT at 1332, AAAT at 426, AAAT at 369, AAAT at 348, AAAT at 185.
  14. AURIIIr3ci: 27, AAAT at 4343, AAAT at 4231, AAAT at 4192, AAAT at 4174, AAAT at 4020, AAAT at 3967, AAAT at 3940, AAAT at 3362, AAAT at 3267, AAAT at 3011, AAAT at 2935, AAAT at 2847, AAAT at 2764, AAAT at 2386, AAAT at 1835, AAAT at 1782, AAAT at 1644, AAAT at 1201, AAAT at 1054, AAAT at 1041, AAAT at 875, AAAT at 794, AAAT at 763, AAAT at 537, AAAT at 444, AAAT at 157, AAAT at 97.
  15. AURIIIr4ci: 17, AAAT at 4483, AAAT at 4471, AAAT at 4385, AAAT at 4371, AAAT at 4184, AAAT at 3860, AAAT at 3629, AAAT at 2815, AAAT at 2515, AAAT at 2444, AAAT at 1808, AAAT at 1777, AAAT at 1613, AAAT at 1362, AAAT at 1323, AAAT at 1073, AAAT at 477.
  16. AURIIIr5ci: 24, AAAT at 4284, AAAT at 4166, AAAT at 4017, AAAT at 3963, AAAT at 3928, AAAT at 3875, AAAT at 3781, AAAT at 3715, AAAT at 3108, AAAT at 3045, AAAT at 2766, AAAT at 2372, AAAT at 2283, AAAT at 2104, AAAT at 1885, AAAT at 1564, AAAT at 1288, AAAT at 1270, AAAT at 1172, AAAT at 1063, AAAT at 993, AAAT at 753, AAAT at 487, AAAT at 133.
  17. AURIIIr6ci: 22, AAAT at 4559, AAAT at 4523, AAAT at 3863, AAAT at 3714, AAAT at 3697, AAAT at 3681, AAAT at 3526, AAAT at 3335, AAAT at 3188, AAAT at 3152, AAAT at 3077, AAAT at 2739, AAAT at 2661, AAAT at 2370, AAAT at 2235, AAAT at 1980, AAAT at 1781, AAAT at 901, AAAT at 747, AAAT at 726, AAAT at 362, AAAT at 71.
  18. AURIIIr7ci: 34, AAAT at 4500, AAAT at 4362, AAAT at 4049, AAAT at 3962, AAAT at 3919, AAAT at 3634, AAAT at 3630, AAAT at 3322, AAAT at 3307, AAAT at 3206, AAAT at 3033, AAAT at 3014, AAAT at 2955, AAAT at 2512, AAAT at 2502, AAAT at 2393, AAAT at 2282, AAAT at 2149, AAAT at 2064, AAAT at 1951, AAAT at 1833, AAAT at 1506, AAAT at 1425, AAAT at 1409, AAAT at 1210, AAAT at 1184, AAAT at 1141, AAAT at 1112, AAAT at 1035, AAAT at 660, AAAT at 564, AAAT at 507, AAAT at 430, AAAT at 142.
  19. AURIIIr8ci: 30, AAAT at 4552, AAAT at 4522, AAAT at 4044, AAAT at 3994, AAAT at 3876, AAAT at 3714, AAAT at 3608, AAAT at 3594, AAAT at 3497, AAAT at 3425, AAAT at 3104, AAAT at 2979, AAAT at 2947, AAAT at 2523, AAAT at 2502, AAAT at 2495, AAAT at 2341, AAAT at 2286, AAAT at 2081, AAAT at 1957, AAAT at 1477, AAAT at 1375, AAAT at 1299, AAAT at 1225, AAAT at 962, AAAT at 928, AAAT at 389, AAAT at 283, AAAT at 212, AAAT at 139.
  20. AURIIIr9ci: 22, AAAT at 4499, AAAT at 4401, AAAT at 4325, AAAT at 4300, AAAT at 4053, AAAT at 3799, AAAT at 3785, AAAT at 3576, AAAT at 3465, AAAT at 3234, AAAT at 2910, AAAT at 2623, AAAT at 2093, AAAT at 2076, AAAT at 1377, AAAT at 1165, AAAT at 937, AAAT at 496, AAAT at 406, AAAT at 330, AAAT at 273, AAAT at 221.

AURIIIr arbitrary (evens) (4560-2846) UTRs

  1. AURIIIr0: ATTT at 4228, ATTT at 4201, ATTT at 4128, ATTT at 4002, ATTT at 3694, ATTT at 3664, ATTT at 3513, ATTT at 3353, ATTT at 3310, ATTT at 3023.
  2. AURIIIr2: ATTT at 4483, ATTT at 4413, ATTT at 4202, ATTT at 4143, ATTT at 4072, ATTT at 3951, ATTT at 3616, ATTT at 3557, ATTT at 3484, ATTT at 3404, ATTT at 3380, ATTT at 3299, ATTT at 3115, ATTT at 3002, ATTT at 2921, ATTT at 2894.
  3. AURIIIr4: ATTT at 3862, ATTT at 3722, ATTT at 3672, ATTT at 3663, ATTT at 3514, ATTT at 3353, ATTT at 3026, ATTT at 3017, ATTT at 2904, ATTT at 2886.
  4. AURIIIr6: ATTT at 4525, ATTT at 4371, ATTT at 4265, ATTT at 3857, ATTT at 3811, ATTT at 3760, ATTT at 3747, ATTT at 3621, ATTT at 3264, ATTT at 2974.
  5. AURIIIr8: ATTT at 4541, ATTT at 4354, ATTT at 4309, ATTT at 3488, ATTT at 3334, ATTT at 3001.
  6. AURIIIr0ci: AAAT at 4126, AAAT at 4022, AAAT at 3925, AAAT at 3914, AAAT at 3566, AAAT at 3172.
  7. AURIIIr2ci: AAAT at 4309, AAAT at 3949, AAAT at 3828, AAAT at 3798, AAAT at 3786, AAAT at 3441, AAAT at 3427, AAAT at 2919.
  8. AURIIIr4ci: AAAT at 4483, AAAT at 4471, AAAT at 4385, AAAT at 4371, AAAT at 4184, AAAT at 3860, AAAT at 3629.
  9. AURIIIr6ci: AAAT at 4559, AAAT at 4523, AAAT at 3863, AAAT at 3714, AAAT at 3697, AAAT at 3681, AAAT at 3526, AAAT at 3335, AAAT at 3188, AAAT at 3152, AAAT at 3077.
  10. AURIIIr8ci: AAAT at 4552, AAAT at 4522, AAAT at 4044, AAAT at 3994, AAAT at 3876, AAAT at 3714, AAAT at 3608, AAAT at 3594, AAAT at 3497, AAAT at 3425, AAAT at 3104, AAAT at 2979, AAAT at 2947.

AURIIIr alternate (odds) (4560-2846) UTRs

  1. AURIIIr1: ATTT at 4219, ATTT at 4050, ATTT at 4034, ATTT at 3781, ATTT at 3610, ATTT at 3605, ATTT at 3584, ATTT at 3452, ATTT at 3408, ATTT at 3095.
  2. AURIIIr3: ATTT at 4349, ATTT at 4295, ATTT at 4286, ATTT at 4194, ATTT at 4093, ATTT at 4064, ATTT at 4050, ATTT at 4026, ATTT at 3969, ATTT at 3779, ATTT at 3756, ATTT at 3688, ATTT at 3164.
  3. AURIIIr5: ATTT at 4468, ATTT at 4195, ATTT at 4054, ATTT at 3877, ATTT at 3717, ATTT at 3703, ATTT at 3655, ATTT at 3628, ATTT at 3492, ATTT at 3459, ATTT at 3353, ATTT at 3280.
  4. AURIIIr7: ATTT at 4380, ATTT at 4223, ATTT at 3913, ATTT at 3452, ATTT at 3241, ATTT at 2977.
  5. AURIIIr9: ATTT at 4270, ATTT at 3801, ATTT at 3618, ATTT at 3578, ATTT at 3492, ATTT at 3476, ATTT at 3329, ATTT at 3115, ATTT at 2926.
  6. AURIIIr1ci: AAAT at 3970, AAAT at 3883, AAAT at 3591, AAAT at 3489, AAAT at 3440, AAAT at 3371, AAAT at 3363, AAAT at 3168, AAAT at 3072, AAAT at 2914.
  7. AURIIIr3ci: AAAT at 4343, AAAT at 4231, AAAT at 4192, AAAT at 4174, AAAT at 4020, AAAT at 3967, AAAT at 3940, AAAT at 3362, AAAT at 3267, AAAT at 3011, AAAT at 2935, AAAT at 2847.
  8. AURIIIr5ci: AAAT at 4284, AAAT at 4166, AAAT at 4017, AAAT at 3963, AAAT at 3928, AAAT at 3875, AAAT at 3781, AAAT at 3715, AAAT at 3108, AAAT at 3045.
  9. AURIIIr7ci: AAAT at 4500, AAAT at 4362, AAAT at 4049, AAAT at 3962, AAAT at 3919, AAAT at 3634, AAAT at 3630, AAAT at 3322, AAAT at 3307, AAAT at 3206, AAAT at 3033, AAAT at 3014, AAAT at 2955.
  10. AURIIIr9ci: AAAT at 4499, AAAT at 4401, AAAT at 4325, AAAT at 4300, AAAT at 4053, AAAT at 3799, AAAT at 3785, AAAT at 3576, AAAT at 3465, AAAT at 3234, AAAT at 2910.

AURIIIr arbitrary negative direction (evens) (2846-2811) core promoters

  1. AURIIIr0: ATTT at 2825.
  2. AURIIIr4ci: AAAT at 2815.

AURIIIr arbitrary positive direction (odds) (4445-4265) core promoters

  1. AURIIIr3: ATTT at 4349, ATTT at 4295, ATTT at 4286.
  2. AURIIIr7: ATTT at 4380.
  3. AURIIIr9: ATTT at 4270.
  4. AURIIIr3ci: AAAT at 4343.
  5. AURIIIr5ci: AAAT at 4284.
  6. AURIIIr7ci: AAAT at 4362.
  7. AURIIIr9ci: AAAT at 4401, AAAT at 4325, AAAT at 4300.

AURIIIr alternate positive direction (evens) (4445-4265) core promoters

  1. AURIIIr2: ATTT at 4413.
  2. AURIIIr6: ATTT at 4371, ATTT at 4265.
  3. AURIIIr8: ATTT at 4354, ATTT at 4309.
  4. AURIIIr2ci: AAAT at 4309.
  5. AURIIIr4ci: AAAT at 4385, AAAT at 4371.

AURIIIr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. AURIIIr0: ATTT at 2616.
  2. AURIIIr2: ATTT at 2626.
  3. AURIIIr4: ATTT at 2767.
  4. AURIIIr6: ATTT at 2798, ATTT at 2762, ATTT at 2741, ATTT at 2728, ATTT at 2649.
  5. AURIIIr0ci: AAAT at 2807, AAAT at 2696.
  6. AURIIIr2ci: AAAT at 2730, AAAT at 2665.
  7. AURIIIr6ci: AAAT at 2739, AAAT at 2661.

AURIIIr alternate negative direction (odds) (2811-2596) proximal promoters

  1. AURIIIr3: ATTT at 2615.
  2. AURIIIr5: ATTT at 2789, ATTT at 2704, ATTT at 2629, ATTT at 2600.
  3. AURIIIr7: ATTT at 2765.
  4. AURIIIr9: ATTT at 2782.
  5. AURIIIr3ci: AAAT at 2764.
  6. AURIIIr5ci: AAAT at 2766.
  7. AURIIIr9ci: AAAT at 2623.

AURIIIr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. AURIIIr1: ATTT at 4219, ATTT at 4050.
  2. AURIIIr3: ATTT at 4194, ATTT at 4093, ATTT at 4064, ATTT at 4050.
  3. AURIIIr5: ATTT at 4195, ATTT at 4054.
  4. AURIIIr7: ATTT at 4223.
  5. AURIIIr3ci: AAAT at 4231, AAAT at 4192, AAAT at 4174.
  6. AURIIIr5ci: AAAT at 4166.
  7. AURIIIr9ci: AAAT at 4053.

AURIIIr alternate positive direction (evens) (4265-4050) proximal promoters

  1. AURIIIr0: ATTT at 4228, ATTT at 4201, ATTT at 4128.
  2. AURIIIr2: ATTT at 4202, ATTT at 4143, ATTT at 4072.
  3. AURIIIr6: ATTT at 4265.
  4. AURIIIr0ci: AAAT at 4126.
  5. AURIIIr4ci: AAAT at 4184.

AURIIIr arbitrary negative direction (evens) (2596-1) distal promoters

  1. AURIIIr0: ATTT at 2494, ATTT at 2415, ATTT at 2390, ATTT at 2144, ATTT at 1910, ATTT at 1819, ATTT at 1814, ATTT at 1642, ATTT at 1568, ATTT at 1459, ATTT at 1450, ATTT at 1192, ATTT at 1166, ATTT at 751, ATTT at 493, ATTT at 474, ATTT at 129.
  2. AURIIIr2: ATTT at 2519, ATTT at 2130, ATTT at 1886, ATTT at 1770, ATTT at 1373, ATTT at 1245, ATTT at 1118, ATTT at 995, ATTT at 808, ATTT at 261, ATTT at 128, ATTT at 33.
  3. AURIIIr4: ATTT at 2546, ATTT at 2254, ATTT at 1675, ATTT at 1299, ATTT at 841, ATTT at 835, ATTT at 559, ATTT at 539, ATTT at 402, ATTT at 240, ATTT at 120.
  4. AURIIIr6: ATTT at 2230, ATTT at 2020, ATTT at 1878, ATTT at 1654, ATTT at 1648, ATTT at 1305, ATTT at 1143, ATTT at 1139, ATTT at 915, ATTT at 815, ATTT at 482, ATTT at 402, ATTT at 186, ATTT at 94.
  5. AURIIIr8: ATTT at 2540, ATTT at 2525, ATTT at 2427, ATTT at 2331, ATTT at 2288, ATTT at 2243, ATTT at 2221, ATTT at 2119, ATTT at 1811, ATTT at 1801, ATTT at 1479, ATTT at 1157, ATTT at 1042, ATTT at 930, ATTT at 871, ATTT at 827, ATTT at 739, ATTT at 728, ATTT at 482, ATTT at 266, ATTT at 194, ATTT at 165.
  6. AURIIIr0ci: AAAT at 2558, AAAT at 2334, AAAT at 2259, AAAT at 2172, AAAT at 2156, AAAT at 1987, AAAT at 1812, AAAT at 1788, AAAT at 1705, AAAT at 1556, AAAT at 1495, AAAT at 1448, AAAT at 861, AAAT at 797, AAAT at 770, AAAT at 749, AAAT at 544, AAAT at 504, AAAT at 195, AAAT at 142, AAAT at 114.
  7. AURIIIr2ci: AAAT at 2517, AAAT at 2382, AAAT at 2128, AAAT at 2083, AAAT at 1768, AAAT at 1589, AAAT at 1551, AAAT at 1332, AAAT at 426, AAAT at 369, AAAT at 348, AAAT at 185.
  8. AURIIIr4ci: AAAT at 2515, AAAT at 2444, AAAT at 1808, AAAT at 1777, AAAT at 1613, AAAT at 1362, AAAT at 1323, AAAT at 1073, AAAT at 477.
  9. AURIIIr6ci: AAAT at 2370, AAAT at 2235, AAAT at 1980, AAAT at 1781, AAAT at 901, AAAT at 747, AAAT at 726, AAAT at 362, AAAT at 71.
  10. AURIIIr8ci: AAAT at 2523, AAAT at 2502, AAAT at 2495, AAAT at 2341, AAAT at 2286, AAAT at 2081, AAAT at 1957, AAAT at 1477, AAAT at 1375, AAAT at 1299, AAAT at 1225, AAAT at 962, AAAT at 928, AAAT at 389, AAAT at 283, AAAT at 212, AAAT at 139.

AURIIIr alternate negative direction (odds) (2596-1) distal promoters

  1. AURIIIr1: ATTT at 2565, ATTT at 2425, ATTT at 2140, ATTT at 1871, ATTT at 1493, ATTT at 1291, ATTT at 1243, ATTT at 1003, ATTT at 827, ATTT at 788, ATTT at 766, ATTT at 306.
  2. AURIIIr3: ATTT at 2538, ATTT at 2504, ATTT at 2326, ATTT at 2018, ATTT at 1784, ATTT at 1558, ATTT at 1087, ATTT at 924, ATTT at 919, ATTT at 796, ATTT at 408, ATTT at 402, ATTT at 358, ATTT at 169.
  3. AURIIIr5: ATTT at 1608, ATTT at 1447, ATTT at 1312, ATTT at 1203, ATTT at 1174, ATTT at 1109, ATTT at 995, ATTT at 859, ATTT at 855, ATTT at 489, ATTT at 293, ATTT at 272, ATTT at 110.
  4. AURIIIr7: ATTT at 2516, ATTT at 2445, ATTT at 2395, ATTT at 2253, ATTT at 2242, ATTT at 1893, ATTT at 1808, ATTT at 1526, ATTT at 1341, ATTT at 1176, ATTT at 708, ATTT at 488, ATTT at 329, ATTT at 110.
  5. AURIIIr9: ATTT at 2562, ATTT at 2524, ATTT at 2510, ATTT at 2341, ATTT at 2139, ATTT at 2125, ATTT at 1741, ATTT at 1652, ATTT at 1447, ATTT at 1350, ATTT at 1100, ATTT at 967, ATTT at 833, ATTT at 808, ATTT at 622, ATTT at 466, ATTT at 158.
  6. AURIIIr1ci: AAAT at 2502, AAAT at 2423, AAAT at 2362, AAAT at 1941, AAAT at 1933, AAAT at 1869, AAAT at 1669, AAAT at 1619, AAAT at 1491, AAAT at 1422, AAAT at 1254, AAAT at 1001, AAAT at 311, AAAT at 262, AAAT at 166.
  7. AURIIIr3ci: AAAT at 2386, AAAT at 1835, AAAT at 1782, AAAT at 1644, AAAT at 1201, AAAT at 1054, AAAT at 1041, AAAT at 875, AAAT at 794, AAAT at 763, AAAT at 537, AAAT at 444, AAAT at 157, AAAT at 97.
  8. AURIIIr5ci: AAAT at 2372, AAAT at 2283, AAAT at 2104, AAAT at 1885, AAAT at 1564, AAAT at 1288, AAAT at 1270, AAAT at 1172, AAAT at 1063, AAAT at 993, AAAT at 753, AAAT at 487, AAAT at 133.
  9. AURIIIr7ci: AAAT at 2512, AAAT at 2502, AAAT at 2393, AAAT at 2282, AAAT at 2149, AAAT at 2064, AAAT at 1951, AAAT at 1833, AAAT at 1506, AAAT at 1425, AAAT at 1409, AAAT at 1210, AAAT at 1184, AAAT at 1141, AAAT at 1112, AAAT at 1035, AAAT at 660, AAAT at 564, AAAT at 507, AAAT at 430, AAAT at 142.
  10. AURIIIr9ci: AAAT at 2093, AAAT at 2076, AAAT at 1377, AAAT at 1165, AAAT at 937, AAAT at 496, AAAT at 406, AAAT at 330, AAAT at 273, AAAT at 221.

AURIIIr arbitrary positive direction (odds) (4050-1) distal promoters

  1. AURIIIr1: ATTT at 4050, ATTT at 4034, ATTT at 3781, ATTT at 3610, ATTT at 3605, ATTT at 3584, ATTT at 3452, ATTT at 3408, ATTT at 3095, ATTT at 2565, ATTT at 2425, ATTT at 2140, ATTT at 1871, ATTT at 1493, ATTT at 1291, ATTT at 1243, ATTT at 1003, ATTT at 827, ATTT at 788, ATTT at 766, ATTT at 306.
  2. AURIIIr3: ATTT at 4050, ATTT at 4026, ATTT at 3969, ATTT at 3779, ATTT at 3756, ATTT at 3688, ATTT at 3164, ATTT at 2615, ATTT at 2538, ATTT at 2504, ATTT at 2326, ATTT at 2018, ATTT at 1784, ATTT at 1558, ATTT at 1087, ATTT at 924, ATTT at 919, ATTT at 796, ATTT at 408, ATTT at 402, ATTT at 358, ATTT at 169.
  3. AURIIIr5: ATTT at 3877, ATTT at 3717, ATTT at 3703, ATTT at 3655, ATTT at 3628, ATTT at 3492, ATTT at 3459, ATTT at 3353, ATTT at 3280, ATTT at 2789, ATTT at 2704, ATTT at 2629, ATTT at 2600, ATTT at 1608, ATTT at 1447, ATTT at 1312, ATTT at 1203, ATTT at 1174, ATTT at 1109, ATTT at 995, ATTT at 859, ATTT at 855, ATTT at 489, ATTT at 293, ATTT at 272, ATTT at 110.
  4. AURIIIr7: ATTT at 3913, ATTT at 3452, ATTT at 3241, ATTT at 2977, ATTT at 2765, ATTT at 2516, ATTT at 2445, ATTT at 2395, ATTT at 2253, ATTT at 2242, ATTT at 1893, ATTT at 1808, ATTT at 1526, ATTT at 1341, ATTT at 1176, ATTT at 708, ATTT at 488, ATTT at 329, ATTT at 110.
  5. AURIIIr9: ATTT at 3801, ATTT at 3618, ATTT at 3578, ATTT at 3492, ATTT at 3476, ATTT at 3329, ATTT at 3115, ATTT at 2926, ATTT at 2782, ATTT at 2562, ATTT at 2524, ATTT at 2510, ATTT at 2341, ATTT at 2139, ATTT at 2125, ATTT at 1741, ATTT at 1652, ATTT at 1447, ATTT at 1350, ATTT at 1100, ATTT at 967, ATTT at 833, ATTT at 808, ATTT at 622, ATTT at 466, ATTT at 158.
  6. AURIIIr1ci: AAAT at 3970, AAAT at 3883, AAAT at 3591, AAAT at 3489, AAAT at 3440, AAAT at 3371, AAAT at 3363, AAAT at 3168, AAAT at 3072, AAAT at 2914, AAAT at 2502, AAAT at 2423, AAAT at 2362, AAAT at 1941, AAAT at 1933, AAAT at 1869, AAAT at 1669, AAAT at 1619, AAAT at 1491, AAAT at 1422, AAAT at 1254, AAAT at 1001, AAAT at 311, AAAT at 262, AAAT at 166.
  7. AURIIIr3ci: AAAT at 4020, AAAT at 3967, AAAT at 3940, AAAT at 3362, AAAT at 3267, AAAT at 3011, AAAT at 2935, AAAT at 2847, AAAT at 2764, AAAT at 2386, AAAT at 1835, AAAT at 1782, AAAT at 1644, AAAT at 1201, AAAT at 1054, AAAT at 1041, AAAT at 875, AAAT at 794, AAAT at 763, AAAT at 537, AAAT at 444, AAAT at 157, AAAT at 97.
  8. AURIIIr5ci: AAAT at 4017, AAAT at 3963, AAAT at 3928, AAAT at 3875, AAAT at 3781, AAAT at 3715, AAAT at 3108, AAAT at 3045, AAAT at 2766, AAAT at 2372, AAAT at 2283, AAAT at 2104, AAAT at 1885, AAAT at 1564, AAAT at 1288, AAAT at 1270, AAAT at 1172, AAAT at 1063, AAAT at 993, AAAT at 753, AAAT at 487, AAAT at 133.
  9. AURIIIr7ci: AAAT at 4049, AAAT at 3962, AAAT at 3919, AAAT at 3634, AAAT at 3630, AAAT at 3322, AAAT at 3307, AAAT at 3206, AAAT at 3033, AAAT at 3014, AAAT at 2955, AAAT at 2512, AAAT at 2502, AAAT at 2393, AAAT at 2282, AAAT at 2149, AAAT at 2064, AAAT at 1951, AAAT at 1833, AAAT at 1506, AAAT at 1425, AAAT at 1409, AAAT at 1210, AAAT at 1184, AAAT at 1141, AAAT at 1112, AAAT at 1035, AAAT at 660, AAAT at 564, AAAT at 507, AAAT at 430, AAAT at 142.
  10. AURIIIr9ci: AAAT at 3799, AAAT at 3785, AAAT at 3576, AAAT at 3465, AAAT at 3234, AAAT at 2910, AAAT at 2623, AAAT at 2093, AAAT at 2076, AAAT at 1377, AAAT at 1165, AAAT at 937, AAAT at 496, AAAT at 406, AAAT at 330, AAAT at 273, AAAT at 221.

AURIIIr alternate positive direction (evens) (4050-1) distal promoters

  1. AURIIIr0: ATTT at 4002, ATTT at 3694, ATTT at 3664, ATTT at 3513, ATTT at 3353, ATTT at 3310, ATTT at 3023, ATTT at 2825, ATTT at 2616, ATTT at 2494, ATTT at 2415, ATTT at 2390, ATTT at 2144, ATTT at 1910, ATTT at 1819, ATTT at 1814, ATTT at 1642, ATTT at 1568, ATTT at 1459, ATTT at 1450, ATTT at 1192, ATTT at 1166, ATTT at 751, ATTT at 493, ATTT at 474, ATTT at 129.
  2. AURIIIr2: ATTT at 3951, ATTT at 3616, ATTT at 3557, ATTT at 3484, ATTT at 3404, ATTT at 3380, ATTT at 3299, ATTT at 3115, ATTT at 3002, ATTT at 2921, ATTT at 2894, ATTT at 2626, ATTT at 2519, ATTT at 2130, ATTT at 1886, ATTT at 1770, ATTT at 1373, ATTT at 1245, ATTT at 1118, ATTT at 995, ATTT at 808, ATTT at 261, ATTT at 128, ATTT at 33.
  3. AURIIIr4: ATTT at 3862, ATTT at 3722, ATTT at 3672, ATTT at 3663, ATTT at 3514, ATTT at 3353, ATTT at 3026, ATTT at 3017, ATTT at 2904, ATTT at 2886, ATTT at 2767, ATTT at 2546, ATTT at 2254, ATTT at 1675, ATTT at 1299, ATTT at 841, ATTT at 835, ATTT at 559, ATTT at 539, ATTT at 402, ATTT at 240, ATTT at 120.
  4. AURIIIr6: ATTT at 3857, ATTT at 3811, ATTT at 3760, ATTT at 3747, ATTT at 3621, ATTT at 3264, ATTT at 2974, ATTT at 2798, ATTT at 2762, ATTT at 2741, ATTT at 2728, ATTT at 2649, ATTT at 2230, ATTT at 2020, ATTT at 1878, ATTT at 1654, ATTT at 1648, ATTT at 1305, ATTT at 1143, ATTT at 1139, ATTT at 915, ATTT at 815, ATTT at 482, ATTT at 402, ATTT at 186, ATTT at 94.
  5. AURIIIr8: ATTT at 3488, ATTT at 3334, ATTT at 3001, ATTT at 2540, ATTT at 2525, ATTT at 2427, ATTT at 2331, ATTT at 2288, ATTT at 2243, ATTT at 2221, ATTT at 2119, ATTT at 1811, ATTT at 1801, ATTT at 1479, ATTT at 1157, ATTT at 1042, ATTT at 930, ATTT at 871, ATTT at 827, ATTT at 739, ATTT at 728, ATTT at 482, ATTT at 266, ATTT at 194, ATTT at 165.
  6. AURIIIr0ci: AAAT at 4022, AAAT at 3925, AAAT at 3914, AAAT at 3566, AAAT at 3172, AAAT at 2807, AAAT at 2696, AAAT at 2558, AAAT at 2334, AAAT at 2259, AAAT at 2172, AAAT at 2156, AAAT at 1987, AAAT at 1812, AAAT at 1788, AAAT at 1705, AAAT at 1556, AAAT at 1495, AAAT at 1448, AAAT at 861, AAAT at 797, AAAT at 770, AAAT at 749, AAAT at 544, AAAT at 504, AAAT at 195, AAAT at 142, AAAT at 114.
  7. AURIIIr2ci: AAAT at 3949, AAAT at 3828, AAAT at 3798, AAAT at 3786, AAAT at 3441, AAAT at 3427, AAAT at 2919, AAAT at 2730, AAAT at 2665, AAAT at 2517, AAAT at 2382, AAAT at 2128, AAAT at 2083, AAAT at 1768, AAAT at 1589, AAAT at 1551, AAAT at 1332, AAAT at 426, AAAT at 369, AAAT at 348, AAAT at 185.
  8. AURIIIr4ci: AAAT at 3860, AAAT at 3629, AAAT at 2815, AAAT at 2515, AAAT at 2444, AAAT at 1808, AAAT at 1777, AAAT at 1613, AAAT at 1362, AAAT at 1323, AAAT at 1073, AAAT at 477.
  9. AURIIIr6ci: AAAT at 3863, AAAT at 3714, AAAT at 3697, AAAT at 3681, AAAT at 3526, AAAT at 3335, AAAT at 3188, AAAT at 3152, AAAT at 3077, AAAT at 2739, AAAT at 2661, AAAT at 2370, AAAT at 2235, AAAT at 1980, AAAT at 1781, AAAT at 901, AAAT at 747, AAAT at 726, AAAT at 362, AAAT at 71.
  10. AURIIIr8ci: AAAT at 4044, AAAT at 3994, AAAT at 3876, AAAT at 3714, AAAT at 3608, AAAT at 3594, AAAT at 3497, AAAT at 3425, AAAT at 3104, AAAT at 2979, AAAT at 2947, AAAT at 2523, AAAT at 2502, AAAT at 2495, AAAT at 2341, AAAT at 2286, AAAT at 2081, AAAT at 1957, AAAT at 1477, AAAT at 1375, AAAT at 1299, AAAT at 1225, AAAT at 962, AAAT at 928, AAAT at 389, AAAT at 283, AAAT at 212, AAAT at 139.

AURIII (Chen and Shyu, Class III) analysis and results

Main article: Complex locus A1BG and ZNF497 § Adenylate–uridylate rich elements (Chen and Shyu, Class III)

"Chen and Shyu[3] divided AREs into [...] a third class of non-AUUUA AREs. [...] Non-AUUUA AREs had a U-rich region and other unknown features, and the relationship of these sequences to AUUUA-containing AREs remains poorly understood."[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 37 2 18.5 18.5 ± 0.5 (--19,+-18)
Randoms UTR arbitrary negative 97 10 9.7 10.15 ± 0.45
Randoms UTR alternate negative 106 10 10.6 10.15 ± 0.45
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 2 10 0.2 0.1
Randoms Core alternate negative 0 10 0 0.1
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 11 10 1.1 0.95 ± 0.15
Randoms Core alternate positive 8 10 0.8 0.95 ± 0.15
Reals Proximal negative 4 2 20 2 ± 1 (--1,+-3)
Randoms Proximal arbitrary negative 14 10 1.4 1.2
Randoms Proximal alternate negative 10 10 1.0 1.2
Reals Proximal positive 7 2 3.5 3.5 ± 0.5 (-+3,++4)
Randoms Proximal arbitrary positive 14 10 1.4 1.15 ± 0.25
Randoms Proximal alternate positive 9 10 0.9 1.15 ± 0.25
Reals Distal negative 43 2 21.5 21.5 ± 4.5 (--17,+-26)
Randoms Distal arbitrary negative 144 10 14.4 14.35
Randoms Distal alternate negative 143 10 14.3 14.35
Reals Distal positive 17 2 8.5 8.5 ± 1.5 (-+10,++7)
Randoms Distal arbitrary positive 233 10 23.3 23.25
Randoms Distal alternate positive 232 10 23.2 23.25

Comparison:

The occurrences of real AURIII UTRs, positive direction proximals and negative direction distals are greater than the randoms, the low occurrence negative direction proximals overlap the randoms, the positive direction distals are less than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

Both the sequence ATTT and its inverse complement AAAT were searched on both sides of A1BG. An overlap would occur e.g. as follows ATTT occurs on the negative strand in the negative direction at 4514, i.e. ATTT ends at 4514, ATT ends at 4513, AT ends at 4512, and the A occurs at 4511. A first overlap would be ATTTATTT beginning at 4510, but the next ATTT ends at 4072. In order to overlap an occurrence near A1BG would need to end at -4 before the specific occurrence. For example, ATTT ends at 3014, but the further away ARE is ATTT at 3009, which is -5 rather than -4 so there is no overlapping repeat. For the negative strand in the negative direction there are no ATTTATTT overlapping repeats. For each of the direct sequences there are no overlapping repeats. However, for the inverse complements, there is an overlapping sequence positive strand, negative direction: AAAT at 4073 and AAAT at 4069, yielding AAATAAAT at 4073.

For the twenty random datasets, there are (1) AURIIIr5: ATTT at 859 and ATTT at 855 for ATTTATTT at 859, (2) AURIIIr6: ATTT at 1143 and ATTT at 1139 for ATTTATTT at 1143, and (3) AURIIIr7ci: AAAT at 3634 and AAAT at 3630 for AAATAAAT at 3634. This yields a probability of 0.15 for direct and inverse complement whereas the real promoters have one occurrence. The sequence AAATAAAT at 4073 in the UTR of A1BG (negative direction) is likely active or activable. The two that did occur in the random datasets were both in the arbitrary positive direction. Choosing the other datasets would put one in the UTR and the other in the distal promoter.

Overlapping (Siegel) mers

"Cluster 1 and 2 motifs total 13 nucleotides, with AU-rich segments flanking one or two AUUUA core motifs, respectively. Clusters 3, 4 and 5 include 3, 4, or 5 exact AUUUA repeats respectively."[2] "Naive Effective Length Pentamers: Pentamers classified by the “effective length” according to the formula floor((length(nt) + registration − 2)/4). “Registration” refers to the starting nucleotides of the ARE within the initial AUUUA pentamer: an ARE that starts AUUU*=0, UUUA*=1, UUAU*=2, and UAUU*=3. No mismatches allowed."[2]

To find possible ATTT regions within the promoters an algorithm was written to look for sequences of "(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)" so that an ATTTA can occur at least once for each of the first five nts. Only the negative strand, negative direction need be considered as the positive strand contains the complements. Possible ATTT regions with overlaps appear to exist such as "TTTATTATT at 4224" but continued examination shows that "TTTTATTAT at 4223" it is not. Another "ATTTATTAT at 4077" upon continuation shows "ATTTATTAT at 4077, TATTTATTA at 4076, TTATTTATT at 4075, TTTATTTAT at 4074, TTTTATTTA at 4073, TTTTTATTT at 4072" that an "ATTTA" is present but overlapping is unlikely. No other such "ATTTA" sequence wa found in either direction or side of A1BG.

These nucleotide sequences can have as few as five ATTTA, or continual sequences such as ATTTA, TTTATT, TATTTA, TTTAT. Using the various results so far it may be possible to find all of the AREs in each strand. Starting with nucleotides between ZN497 and A1BG approached from the positive direction yields TATTTA and TTATTT where the second is TTATTTA at the only ATTTA. Nucleotides between ZNF497 and A1BG approached from ZNF497 on the negative strand yields ATTTA (1), TATTT has two but no additional A or T. Nucleotides between ZSCAN22 and A1BG approached from ZSCAN22 on the negative strand yields three CTTAATTTAC, GATTTATATG and GTTTTTTATTTATTATCTTTCTTTTTAC. Nucleotides between ZSCAN22 and A1BG approached from ZSCAN22 on the positive strand yields zero for ATTTA, but many without ATTTA or just TTT.

Using each of the random datasets, there are a number of ATTTAs between two and eleven but none are close enough to overlap, say within. The closest number of nucleotides is 13 nts except random6 has ATTTA at 1144, ATTTA at 1140 or ATTTATTTA at 1144. The optimal way to look may be (A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T) so that an ATTTA can occur at least once for each of the first five.

  1. Negative strand, negative direction: 96, AATAATTAA at 4541, AAATAATTA at 4540, TAAATAATT at 4539, ATTATTAAT at 4227, TATTATTAA at 4226, TTATTATTA at 4225, TTTATTATT at 4224, TTTTATTAT at 4223, TTTTTATTA at 4222, TTTTTTATT at 4221, ATTTATTAT at 4077, TATTTATTA at 4076, TTATTTATT at 4075, TTTATTTAT at 4074, TTTTATTTA at 4073, TTTTTATTT at 4072, TTTTTTATT at 4071, AATTTTTAA at 3356, AAATTTTTA at 3355, AAAATTTTT at 3354, ATTTTTAAT at 3175, TATTTTTAA at 3174, AAATTTTTT at 3026, AAAATTTTT at 3025, AAAAATTTT at 3024, ATTTTATTT at 3014, TATATATTT at 2874, TTATATATT at 2873, TTTATATAT at 2872, TTTTATATA at 2871, ATAAAATTT at 2856, TATAAAATT at 2855, TTATAAAAT at 2854, TTTTTTTTT at 2470, TTTTTTTTT at 2469, TTTTTTTTT at 2468, TTTTTTTTT at 2467, TTTTTTTTT at 2466, TTTTTTTTT at 2465, TTTTTTTTT at 2464, TTTTTTTTA at 2061, TTTTTTTTT at 2051, TTTTTTTTT at 2050, TTTTTTTTT at 2049, TTTTTTTTT at 2048, TTTTTTTTT at 2047, TTTTTTTTT at 2046, TTTTTTTTT at 2045, TTTTTTTTT at 2044, TTTTTTTTT at 2043, TTTTTTTTT at 2042, TTTTTTTTT at 2041, TTTTTTAAT at 1886, TTTTTTTAA at 1885, AATTTTATA at 1740, AAATTTTAT at 1739, AATAAAATA at 1729, TAATAAAAT at 1728, TTAATAAAA at 1727, ATATATAAA at 1602, TATATATAA at 1601, AAAAAAAAA at 1432, AAAAAAAAA at 1431, AAAAAAAAA at 1430, AAAAAAAAA at 1429, AAAAAAAAA at 1428, AAAAAAAAA at 1427, AAAAAAAAA at 1426, AAAAAAAAA at 1425, AAAAAAAAA at 1424, TTTTTTAAT at 1233, TTTTTTTTT at 1105, TTTTTTTTT at 1104, TTTTTTTTT at 1103, TTTTTTTTT at 1102, TTTTTTTTT at 1101, TTTTTTTTT at 1100, TTTTTTTTT at 1099, TTTTTTTTT at 1098, TTTTTTTTT at 1097, TTTTTTTTT at 942, TTTTTTTTT at 941, TTTTTTTTT at 940, TTTTTTTTT at 939, TTTTTTTTT at 938, TTTTTTTTT at 937, TTTTTTTTT at 936, TTTTTTTTT at 935, TTTTTTTTT at 934, TTTTTTTTT at 933, TTTTTTTTT at 932, TTTTTTTTT at 931, TTTTTTAAT at 776, AAATATTTT at 222, AAAATATTT at 221, AAAAATATT at 220.
  2. Positive strand, negative direction: 96, TTATTAATT at 4541, TTTATTAAT at 4540, ATTTATTAA at 4539, TAATAATTA at 4227, ATAATAATT at 4226, AATAATAAT at 4225, AAATAATAA at 4224, AAAATAATA at 4223, AAAAATAAT at 4222, AAAAAATAA at 4221, TAAATAATA at 4077, ATAAATAAT at 4076, AATAAATAA at 4075, AAATAAATA at 4074, AAAATAAAT at 4073, AAAAATAAA at 4072, AAAAAATAA at 4071, TTAAAAATT at 3356, TTTAAAAAT at 3355, TTTTAAAAA at 3354, TAAAAATTA at 3175, ATAAAAATT at 3174, TTTAAAAAA at 3026, TTTTAAAAA at 3025, TTTTTAAAA at 3024, TAAAATAAA at 3014, ATATATAAA at 2874, AATATATAA at 2873, AAATATATA at 2872, AAAATATAT at 2871, TATTTTAAA at 2856, ATATTTTAA at 2855, AATATTTTA at 2854, AAAAAAAAA at 2470, AAAAAAAAA at 2469, AAAAAAAAA at 2468, AAAAAAAAA at 2467, AAAAAAAAA at 2466, AAAAAAAAA at 2465, AAAAAAAAA at 2464, AAAAAAAAT at 2061, AAAAAAAAA at 2051, AAAAAAAAA at 2050, AAAAAAAAA at 2049, AAAAAAAAA at 2048, AAAAAAAAA at 2047, AAAAAAAAA at 2046, AAAAAAAAA at 2045, AAAAAAAAA at 2044, AAAAAAAAA at 2043, AAAAAAAAA at 2042, AAAAAAAAA at 2041, AAAAAATTA at 1886, AAAAAAATT at 1885, TTAAAATAT at 1740, TTTAAAATA at 1739, TTATTTTAT at 1729, ATTATTTTA at 1728, AATTATTTT at 1727, TATATATTT at 1602, ATATATATT at 1601, TTTTTTTTT at 1432, TTTTTTTTT at 1431, TTTTTTTTT at 1430, TTTTTTTTT at 1429, TTTTTTTTT at 1428, TTTTTTTTT at 1427, TTTTTTTTT at 1426, TTTTTTTTT at 1425, TTTTTTTTT at 1424, AAAAAATTA at 1233, AAAAAAAAA at 1105, AAAAAAAAA at 1104, AAAAAAAAA at 1103, AAAAAAAAA at 1102, AAAAAAAAA at 1101, AAAAAAAAA at 1100, AAAAAAAAA at 1099, AAAAAAAAA at 1098, AAAAAAAAA at 1097, AAAAAAAAA at 942, AAAAAAAAA at 941, AAAAAAAAA at 940, AAAAAAAAA at 939, AAAAAAAAA at 938, AAAAAAAAA at 937, AAAAAAAAA at 936, AAAAAAAAA at 935, AAAAAAAAA at 934, AAAAAAAAA at 933, AAAAAAAAA at 932, AAAAAAAAA at 931, AAAAAATTA at 776, TTTATAAAA at 222, TTTTATAAA at 221, TTTTTATAA at 220.
  3. Positive strand, positive direction: 11, TAATATTAA at 4169, AAATAATTA at 4145, TTTAAAAAA at 2451, TTTTAAAAA at 2450, ATTTTAAAA at 2449, AATTTTAAA at 2448, AAATTTTAA at 2447, AAAATTTTA at 2446, TAAAATTTT at 2445, TTAAAATTT at 2444, ATTAAAATT at 2443.
  4. Negative strand, positive direction: 11, ATTATAATT at 4169, TTTATTAAT at 4145, AAATTTTTT at 2451, AAAATTTTT at 2450, TAAAATTTT at 2449, TTAAAATTT at 2448, TTTAAAATT at 2447, TTTTAAAAT at 2446, ATTTTAAAA at 2445, AATTTTAAA at 2444, TAATTTTAA at 2443.

MERS (4560-2846) UTRs

  1. Negative strand, negative direction: AATAATTAA at 4541, AAATAATTA at 4540, TAAATAATT at 4539, ATTATTAAT at 4227, TATTATTAA at 4226, TTATTATTA at 4225, TTTATTATT at 4224, TTTTATTAT at 4223, TTTTTATTA at 4222, TTTTTTATT at 4221, ATTTATTAT at 4077, TATTTATTA at 4076, TTATTTATT at 4075, TTTATTTAT at 4074, TTTTATTTA at 4073, TTTTTATTT at 4072, TTTTTTATT at 4071, AATTTTTAA at 3356, AAATTTTTA at 3355, AAAATTTTT at 3354, ATTTTTAAT at 3175, TATTTTTAA at 3174, AAATTTTTT at 3026, AAAATTTTT at 3025, AAAAATTTT at 3024, ATTTTATTT at 3014, TATATATTT at 2874, TTATATATT at 2873, TTTATATAT at 2872, TTTTATATA at 2871, ATAAAATTT at 2856, TATAAAATT at 2855, TTATAAAAT at 2854.

MERS positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: ATTATAATT at 4169, TTTATTAAT at 4145.

MERS negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TTTTTTTTT at 2470, TTTTTTTTT at 2469, TTTTTTTTT at 2468, TTTTTTTTT at 2467, TTTTTTTTT at 2466, TTTTTTTTT at 2465, TTTTTTTTT at 2464, TTTTTTTTA at 2061, TTTTTTTTT at 2051, TTTTTTTTT at 2050, TTTTTTTTT at 2049, TTTTTTTTT at 2048, TTTTTTTTT at 2047, TTTTTTTTT at 2046, TTTTTTTTT at 2045, TTTTTTTTT at 2044, TTTTTTTTT at 2043, TTTTTTTTT at 2042, TTTTTTTTT at 2041, TTTTTTAAT at 1886, TTTTTTTAA at 1885, AATTTTATA at 1740, AAATTTTAT at 1739, AATAAAATA at 1729, TAATAAAAT at 1728, TTAATAAAA at 1727, ATATATAAA at 1602, TATATATAA at 1601, AAAAAAAAA at 1432, AAAAAAAAA at 1431, AAAAAAAAA at 1430, AAAAAAAAA at 1429, AAAAAAAAA at 1428, AAAAAAAAA at 1427, AAAAAAAAA at 1426, AAAAAAAAA at 1425, AAAAAAAAA at 1424, TTTTTTAAT at 1233, TTTTTTTTT at 1105, TTTTTTTTT at 1104, TTTTTTTTT at 1103, TTTTTTTTT at 1102, TTTTTTTTT at 1101, TTTTTTTTT at 1100, TTTTTTTTT at 1099, TTTTTTTTT at 1098, TTTTTTTTT at 1097, TTTTTTTTT at 942, TTTTTTTTT at 941, TTTTTTTTT at 940, TTTTTTTTT at 939, TTTTTTTTT at 938, TTTTTTTTT at 937, TTTTTTTTT at 936, TTTTTTTTT at 935, TTTTTTTTT at 934, TTTTTTTTT at 933, TTTTTTTTT at 932, TTTTTTTTT at 931, TTTTTTAAT at 776, AAATATTTT at 222, AAAATATTT at 221, AAAAATATT at 220.

MERS positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: AAATTTTTT at 2451, AAAATTTTT at 2450, TAAAATTTT at 2449, TTAAAATTT at 2448, TTTAAAATT at 2447, TTTTAAAAT at 2446, ATTTTAAAA at 2445, AATTTTAAA at 2444, TAATTTTAA at 2443.

ARES random dataset samplings

  1. ARESr0: 30, AAATTTTTA at 4131, ATATAATTA at 3605, AAATATATA at 2701, AAAATATAT at 2700, AAAAATATA at 2699, TAAAAATAT at 2698, TTAAAAATA at 2697, ATTTAAAAA at 2395, AAAATAATA at 2263, AAAAATAAT at 2262, TAAAAATAA at 2261, TTATATTTT at 2145, TAAATAAAA at 1499, ATAAATAAA at 1498, AATAAATAA at 1497, TAATAAATA at 1496, ATAATAAAT at 1495, AATAATAAA at 1494, AATTTTTTT at 1454, AAATTTTTT at 1453, TTTTATAAA at 499, ATTTTATAA at 498, TATTTTATA at 497, TTTAATAAA at 412, TTTTTTATT at 227, TTTTTTTAT at 226, AAATAAAAA at 200, AAAATAAAA at 199, AATAATAAT at 148, AAATAATAA at 147.
  2. ARESr1: 21, TTTTATTTA at 3611, ATTTTATTT at 3610, TTTTTTAAT at 3458, ATTTTTTAA at 3457, AAAAAAAAA at 3064, TAAAAAAAA at 3063, ATTAAAAAA at 2855, TTTTAAATT at 1670, TTTTTAAAT at 1669, TTTTTTAAA at 1668, TATTATATA at 1267, TTATTATAT at 1266, ATTATTATA at 1265, AATTTAATT at 1007, AAATTTAAT at 1006, AAAATTTAA at 1005, ATTATATTA at 367, TTTTAAATT at 312, ATTTTAAAT at 311, ATAAAATAT at 168, TATATATTA at 141.
  3. ARESr2: 10, TAAATTTTT at 3953, ATAAATTTT at 3952, AATAAATTT at 3951, TAATAAATT at 3950, ATAATAAAT at 3949, TTAAATTTA at 1771, AAATTAATT at 1556, TAAATTAAT at 1555, TAAAAAAAA at 939, TTTTAAAAA at 250.
  4. ARESr3: 16, ATTAATTTT at 4350, AATTAATTT at 4349, AAATTAATT at 4348, AAAATTAAT at 4347, AAAAATTAA at 4346, TAAATTTTA at 4196, TTAAATTTT at 4195, TTTAAATTT at 4194, TTTTAAATT at 4193, TTTTTAAAT at 4192, TAATATATA at 3803, ATAATATAT at 3802, ATAATTTTT at 2617, TTTAAAAAT at 537, TTTTAATTT at 408, ATTTTAATT at 407.
  5. ARESr4: 11, ATATTAATA at 4166, AATATTAAT at 4165, TAATATTAA at 4164, TTAATATTA at 4163, TTTAATATT at 4162, TAAATTTAT at 3864, TATATTTAA at 3724, TTATATTTA at 3723, TTAATAAAT at 2444, TTTAATAAA at 2443, ATTTTTTTT at 846.
  6. ARESr5: 22, TAAAATTAT at 3784, TTATTTAAT at 3631, ATTATTTAA at 3630, TTTTTTAAA at 3360, TTTTTTTAA at 3359, ATTTTTTTA at 3358, ATTATAAAT at 1564, AATTATAAA at 1563, TAATTTATT at 1112, ATTTATTTT at 860, TATTTATTT at 859, TTATTTATT at 858, ATTATTTAT at 857, AATTATTTA at 856, TAATTATTT at 855, TTAATTATT at 854, TTTAATTAT at 853, TTTTAATTA at 852, TTTTTAATT at 851, AAATTTATT at 492, TTTTATTTT at 273, TATTTTAAT at 114.
  7. ARESr6: 17, AAAATTATA at 3867, TAAATATAA at 2239, TTAAATATA at 2238, TTTAAATAT at 2237, TTTTAAATA at 2236, ATTTTAAAT at 2235, AATTTTAAA at 2234, TTTAATTTT at 1655, TTTTAATTT at 1654, ATTTTAATT at 1653, AATTTTAAT at 1652, ATTTATTTA at 1144, TATTTATTT at 1143, ATATTTATT at 1142, TATATTTAT at 1141, TATTTATTA at 919, AATTATTTA at 187.
  8. ARESr7: 22, TTAAAAATA at 3920, TTTAAAAAT at 3919, ATTTAAAAA at 3918, AATTTAAAA at 3917, TAATTTAAA at 3916, AAATAAATT at 3635, TAAATAAAT at 3634, ATAAATAAA at 3633, TATAAATAA at 3632, TTTTTTTTT at 3459, TTTTTTTTT at 3458, ATTTTTTTT at 3457, AATTTTTTT at 3456, TAATTTTTT at 3455, AAATATTTT at 2517, AAAATATTT at 2516, AAAAATATT at 2515, TAAAAATAT at 2514, TTAAAAATA at 2513, TTTATAATT at 2455, ATAATTTTT at 2244, AATAATTTT at 2243.
  9. ARESr8: 10, TTTTAAATA at 3609, AATATTATT at 3508, ATTTTTTAT at 2293, AATTTTTTA at 2292, AAATTTTTT at 2291, AAAAAATTT at 1479, TAAAAATTT at 930, ATAAAAATT at 929, AATAAAAAT at 928, TAATAAAAA at 927.
  10. ARESr9: 13, AAAAAAAAA at 1304, TAAAAATTA at 1167, TTAAAAATT at 1166, ATTAAAAAT at 1165, TATTAAAAA at 1164, TTATTAAAA at 1163, ATTATTAAA at 1162, ATTTTTTAA at 838, TATTTTTTA at 837, ATTATTTAA at 810, AATTATTTA at 809, AAAAAAATA at 407, TATTTTATA at 162.

ARESr arbitrary (evens) (4560-2846) UTRs

  1. ARESr0: AAATTTTTA at 4131, ATATAATTA at 3605.
  2. ARESr2: TAAATTTTT at 3953, ATAAATTTT at 3952, AATAAATTT at 3951, TAATAAATT at 3950, ATAATAAAT at 3949.
  3. ARESr4: ATATTAATA at 4166, AATATTAAT at 4165, TAATATTAA at 4164, TTAATATTA at 4163, TTTAATATT at 4162, TAAATTTAT at 3864, TATATTTAA at 3724, TTATATTTA at 3723.
  4. ARESr6: AAAATTATA at 3867.
  5. ARESr8: TTTTAAATA at 3609, AATATTATT at 3508.

ARESr alternate (odds) (4560-2846) UTRs

  1. ARESr1: TTTTATTTA at 3611, ATTTTATTT at 3610, TTTTTTAAT at 3458, ATTTTTTAA at 3457, AAAAAAAAA at 3064, TAAAAAAAA at 3063, ATTAAAAAA at 2855.
  2. ARESr3: ATTAATTTT at 4350, AATTAATTT at 4349, AAATTAATT at 4348, AAAATTAAT at 4347, AAAAATTAA at 4346, TAAATTTTA at 4196, TTAAATTTT at 4195, TTTAAATTT at 4194, TTTTAAATT at 4193, TTTTTAAAT at 4192, TAATATATA at 3803, ATAATATAT at 3802.
  3. ARESr5: TAAAATTAT at 3784, TTATTTAAT at 3631, ATTATTTAA at 3630, TTTTTTAAA at 3360, TTTTTTTAA at 3359, ATTTTTTTA at 3358.
  4. ARESr7: TTAAAAATA at 3920, TTTAAAAAT at 3919, ATTTAAAAA at 3918, AATTTAAAA at 3917, TAATTTAAA at 3916, AAATAAATT at 3635, TAAATAAAT at 3634, ATAAATAAA at 3633, TATAAATAA at 3632, TTTTTTTTT at 3459, TTTTTTTTT at 3458, ATTTTTTTT at 3457, AATTTTTTT at 3456, TAATTTTTT at 3455.

ARESr arbitrary positive direction (odds) (4445-4265) core promoters

  1. ARESr3: ATTAATTTT at 4350, AATTAATTT at 4349, AAATTAATT at 4348, AAAATTAAT at 4347, AAAAATTAA at 4346.

ARESr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. ARESr0: AAATATATA at 2701, AAAATATAT at 2700, AAAAATATA at 2699, TAAAAATAT at 2698, TTAAAAATA at 2697.

ARESr alternate negative direction (odds) (2811-2596) proximal promoters

  1. ARESr3: ATAATTTTT at 2617.

ARESr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. ARESr3: TAAATTTTA at 4196, TTAAATTTT at 4195, TTTAAATTT at 4194, TTTTAAATT at 4193, TTTTTAAAT at 4192.

ARESr alternate positive direction (evens) (4265-4050) proximal promoters

  1. ARESr0: AAATTTTTA at 4131.
  2. ARESr4: ATATTAATA at 4166, AATATTAAT at 4165, TAATATTAA at 4164, TTAATATTA at 4163, TTTAATATT at 4162.

ARESr arbitrary negative direction (evens) (2596-1) distal promoters

  1. ARESr0: ATTTAAAAA at 2395, AAAATAATA at 2263, AAAAATAAT at 2262, TAAAAATAA at 2261, TTATATTTT at 2145, TAAATAAAA at 1499, ATAAATAAA at 1498, AATAAATAA at 1497, TAATAAATA at 1496, ATAATAAAT at 1495, AATAATAAA at 1494, AATTTTTTT at 1454, AAATTTTTT at 1453, TTTTATAAA at 499, ATTTTATAA at 498, TATTTTATA at 497, TTTAATAAA at 412, TTTTTTATT at 227, TTTTTTTAT at 226, AAATAAAAA at 200, AAAATAAAA at 199, AATAATAAT at 148, AAATAATAA at 147.
  2. ARESr2: TTAAATTTA at 1771, AAATTAATT at 1556, TAAATTAAT at 1555, TAAAAAAAA at 939, TTTTAAAAA at 250.
  3. ARESr4: TTAATAAAT at 2444, TTTAATAAA at 2443, ATTTTTTTT at 846.
  4. ARESr6: TAAATATAA at 2239, TTAAATATA at 2238, TTTAAATAT at 2237, TTTTAAATA at 2236, ATTTTAAAT at 2235, AATTTTAAA at 2234, TTTAATTTT at 1655, TTTTAATTT at 1654, ATTTTAATT at 1653, AATTTTAAT at 1652, ATTTATTTA at 1144, TATTTATTT at 1143, ATATTTATT at 1142, TATATTTAT at 1141, TATTTATTA at 919, AATTATTTA at 187.
  5. ARESr8: ATTTTTTAT at 2293, AATTTTTTA at 2292, AAATTTTTT at 2291, AAAAAATTT at 1479, TAAAAATTT at 930, ATAAAAATT at 929, AATAAAAAT at 928, TAATAAAAA at 927.

ARESr alternate negative direction (odds) (2596-1) distal promoters

  1. ARESr1: TTTTAAATT at 1670, TTTTTAAAT at 1669, TTTTTTAAA at 1668, TATTATATA at 1267, TTATTATAT at 1266, ATTATTATA at 1265, AATTTAATT at 1007, AAATTTAAT at 1006, AAAATTTAA at 1005, ATTATATTA at 367, TTTTAAATT at 312, ATTTTAAAT at 311, ATAAAATAT at 168, TATATATTA at 141.
  2. ARESr3: TTTAAAAAT at 537, TTTTAATTT at 408, ATTTTAATT at 407.
  3. ARESr5: ATTATAAAT at 1564, AATTATAAA at 1563, TAATTTATT at 1112, ATTTATTTT at 860, TATTTATTT at 859, TTATTTATT at 858, ATTATTTAT at 857, AATTATTTA at 856, TAATTATTT at 855, TTAATTATT at 854, TTTAATTAT at 853, TTTTAATTA at 852, TTTTTAATT at 851, AAATTTATT at 492, TTTTATTTT at 273, TATTTTAAT at 114.
  4. ARESr7: AAATATTTT at 2517, AAAATATTT at 2516, AAAAATATT at 2515, TAAAAATAT at 2514, TTAAAAATA at 2513, TTTATAATT at 2455, ATAATTTTT at 2244, AATAATTTT at 2243.
  5. ARESr9: AAAAAAAAA at 1304, TAAAAATTA at 1167, TTAAAAATT at 1166, ATTAAAAAT at 1165, TATTAAAAA at 1164, TTATTAAAA at 1163, ATTATTAAA at 1162, ATTTTTTAA at 838, TATTTTTTA at 837, ATTATTTAA at 810, AATTATTTA at 809, AAAAAAATA at 407, TATTTTATA at 162.

ARESr arbitrary positive direction (odds) (4050-1) distal promoters

  1. ARESr1: TTTTATTTA at 3611, ATTTTATTT at 3610, TTTTTTAAT at 3458, ATTTTTTAA at 3457, AAAAAAAAA at 3064, TAAAAAAAA at 3063, ATTAAAAAA at 2855, TTTTAAATT at 1670, TTTTTAAAT at 1669, TTTTTTAAA at 1668, TATTATATA at 1267, TTATTATAT at 1266, ATTATTATA at 1265, AATTTAATT at 1007, AAATTTAAT at 1006, AAAATTTAA at 1005, ATTATATTA at 367, TTTTAAATT at 312, ATTTTAAAT at 311, ATAAAATAT at 168, TATATATTA at 141.
  2. ARESr3: TAATATATA at 3803, ATAATATAT at 3802, ATAATTTTT at 2617, TTTAAAAAT at 537, TTTTAATTT at 408, ATTTTAATT at 407.
  3. ARESr5: TAAAATTAT at 3784, TTATTTAAT at 3631, ATTATTTAA at 3630, TTTTTTAAA at 3360, TTTTTTTAA at 3359, ATTTTTTTA at 3358, ATTATAAAT at 1564, AATTATAAA at 1563, TAATTTATT at 1112, ATTTATTTT at 860, TATTTATTT at 859, TTATTTATT at 858, ATTATTTAT at 857, AATTATTTA at 856, TAATTATTT at 855, TTAATTATT at 854, TTTAATTAT at 853, TTTTAATTA at 852, TTTTTAATT at 851, AAATTTATT at 492, TTTTATTTT at 273, TATTTTAAT at 114.
  4. ARESr7: TTAAAAATA at 3920, TTTAAAAAT at 3919, ATTTAAAAA at 3918, AATTTAAAA at 3917, TAATTTAAA at 3916, AAATAAATT at 3635, TAAATAAAT at 3634, ATAAATAAA at 3633, TATAAATAA at 3632, TTTTTTTTT at 3459, TTTTTTTTT at 3458, ATTTTTTTT at 3457, AATTTTTTT at 3456, TAATTTTTT at 3455, AAATATTTT at 2517, AAAATATTT at 2516, AAAAATATT at 2515, TAAAAATAT at 2514, TTAAAAATA at 2513, TTTATAATT at 2455, ATAATTTTT at 2244, AATAATTTT at 2243.
  5. ARESr9: AAAAAAAAA at 1304, TAAAAATTA at 1167, TTAAAAATT at 1166, ATTAAAAAT at 1165, TATTAAAAA at 1164, TTATTAAAA at 1163, ATTATTAAA at 1162, ATTTTTTAA at 838, TATTTTTTA at 837, ATTATTTAA at 810, AATTATTTA at 809, AAAAAAATA at 407, TATTTTATA at 162.

ARESr alternate positive direction (evens) (4050-1) distal promoters

  1. ARESr0: ATATAATTA at 3605, AAATATATA at 2701, AAAATATAT at 2700, AAAAATATA at 2699, TAAAAATAT at 2698, TTAAAAATA at 2697, ATTTAAAAA at 2395, AAAATAATA at 2263, AAAAATAAT at 2262, TAAAAATAA at 2261, TTATATTTT at 2145, TAAATAAAA at 1499, ATAAATAAA at 1498, AATAAATAA at 1497, TAATAAATA at 1496, ATAATAAAT at 1495, AATAATAAA at 1494, AATTTTTTT at 1454, AAATTTTTT at 1453, TTTTATAAA at 499, ATTTTATAA at 498, TATTTTATA at 497, TTTAATAAA at 412, TTTTTTATT at 227, TTTTTTTAT at 226, AAATAAAAA at 200, AAAATAAAA at 199, AATAATAAT at 148, AAATAATAA at 147.
  2. ARESr2: TAAATTTTT at 3953, ATAAATTTT at 3952, AATAAATTT at 3951, TAATAAATT at 3950, ATAATAAAT at 3949, TTAAATTTA at 1771, AAATTAATT at 1556, TAAATTAAT at 1555, TAAAAAAAA at 939, TTTTAAAAA at 250.
  3. ARESr4: TAAATTTAT at 3864, TATATTTAA at 3724, TTATATTTA at 3723, TTAATAAAT at 2444, TTTAATAAA at 2443, ATTTTTTTT at 846.
  4. ARESr6: AAAATTATA at 3867, TAAATATAA at 2239, TTAAATATA at 2238, TTTAAATAT at 2237, TTTTAAATA at 2236, ATTTTAAAT at 2235, AATTTTAAA at 2234, TTTAATTTT at 1655, TTTTAATTT at 1654, ATTTTAATT at 1653, AATTTTAAT at 1652, ATTTATTTA at 1144, TATTTATTT at 1143, ATATTTATT at 1142, TATATTTAT at 1141, TATTTATTA at 919, AATTATTTA at 187.
  5. ARESr8: TTTTAAATA at 3609, AATATTATT at 3508, ATTTTTTAT at 2293, AATTTTTTA at 2292, AAATTTTTT at 2291, AAAAAATTT at 1479, TAAAAATTT at 930, ATAAAAATT at 929, AATAAAAAT at 928, TAATAAAAA at 927.

Overlapping (Siegel) mers analysis and results

Main article: Complex locus A1BG and ZNF497 § MERs

Subsequent studies based on analyses of a set of 4884 AUUUA-containing AREs led to a new classification based primarily on the number of overlapping AUUUA-repeats [8, 9, 10]. This classification system, with five clusters distinguished by the number of repeats, was used to identify AUUUA-containing AREs in the human genome. AREs identified using this classification were found to be abundant in 3′ UTRs of human genes."[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 33 2 16.5 16.5 ± 16.5 (--33,+-0)
Randoms UTR arbitrary negative 18 10 1.8 2.85
Randoms UTR alternate negative 39 10 3.9 2.85
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 5 10 0.5 0.25
Randoms Core alternate positive 0 10 0 0.25
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 5 10 0.5 0.3
Randoms Proximal alternate negative 1 10 0.1 0.3
Reals Proximal positive 2 2 1 1 ± 1 (-+2,++0)
Randoms Proximal arbitrary positive 5 10 0.5 0.55
Randoms Proximal alternate positive 6 10 0.6 0.55
Reals Distal negative 63 2 31.5 31.5 ± 31.5 (--63,+-0)
Randoms Distal arbitrary negative 55 10 5.5 5.45
Randoms Distal alternate negative 54 10 5.4 5.45
Reals Distal positive 9 2 4.5 4.5 ± 4.5 (-+9,++0)
Randoms Distal arbitrary positive 84 10 8.4 7.8
Randoms Distal alternate positive 72 10 7.2 7.8

Comparison:

The occurrences of real MER UTRs, positive direction proximals and distals are greater than the randoms. This suggests that the real overlapping mers are likely active or activable.

In the random datasets an "ATTTAAAAA at 2395" was found in ARESr0, as was a complement "TAAATAAAA at 1499, ATAAATAAA at 1498, AATAAATAA at 1497, TAATAAATA at 1496, ATAATAAAT at 1495, AATAATAAA at 1494". Others were found "TTTTATTTA at 3611, ATTTTATTT at 3610" and "AATTTAATT at 1007, AAATTTAAT at 1006, AAAATTTAA at 1005" in ARESr1, "TAAATTTTT at 3953, ATAAATTTT at 3952, AATAAATTT at 3951, TAATAAATT at 3950, ATAATAAAT at 3949", "AAATTAATT at 1556, TAAATTAAT at 1555" and "TTAAATTTA at 1771" in ARESr2, "TAAATTTTA at 4196, TTAAATTTT at 4195, TTTAAATTT at 4194, TTTTAAATT at 4193, TTTTTAAAT at 4192" in ARESr3, "TATATTTAA at 3724, TTATATTTA at 3723" and "TTAATAAAT at 2444, TTTAATAAA at 2443" in ARESr4, "ATTATAAAT at 1564, AATTATAAA at 1563" and "AAATTTATT at 492" in ARESr5, "TAAATATAA at 2239, TTAAATATA at 2238, TTTAAATAT at 2237, TTTTAAATA at 2236, ATTTTAAAT at 2235, AATTTTAAA at 2234" and "ATTTATTTA at 1144, TATTTATTT at 1143, ATATTTATT at 1142, TATATTTAT at 1141", "TATTTATTA at 919" and "AATTATTTA at 187" in ARESr6, "TTAAAAATA at 3920, TTTAAAAAT at 3919, ATTTAAAAA at 3918, AATTTAAAA at 3917, TAATTTAAA at 3916" and "AAATAAATT at 3635, TAAATAAAT at 3634, ATAAATAAA at 3633, TATAAATAA at 3632" in ARESr7, "TTTTAAATA at 3609" in ARESr8, and "ATTATTTAA at 810, AATTATTTA at 809" in ARESr9; for an occurrence of nineteen possible overlaps in ten datasets for 1.9 per dataset compared with one for two or 0.5 for the real promoters which suggests that the occurrence is likely active or activable but insufficient when two or more are needed.

Constitutive decay element (Siegel) samplings

Copying a responsive elements consensus sequence TTC(C/T)(A/G)(C/T)GAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TTC(C/T)(A/G)(C/T)GAA (starting with SuccessablesCDE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for TTC(C/T)(A/G)(C/T)GAA, 0.
  2. positive strand, negative direction, looking for TTC(C/T)(A/G)(C/T)GAA, 0.
  3. positive strand, positive direction, looking for TTC(C/T)(A/G)(C/T)GAA, 1, TTCCATGAA at 128.
  4. negative strand, positive direction, looking for TTC(C/T)(A/G)(C/T)GAA, 0.
  5. complement, negative strand, negative direction, looking for AAG(A/G)(C/T)(A/G)CTT, 0.
  6. complement, positive strand, negative direction, looking for AAG(A/G)(C/T)(A/G)CTT, 0.
  7. complement, positive strand, positive direction, looking for AAG(A/G)(C/T)(A/G)CTT, 0.
  8. complement, negative strand, positive direction, looking for AAG(A/G)(C/T)(A/G)CTT, 1, AAGGTACTT at 128.
  9. inverse complement, negative strand, negative direction, looking for TTC(A/G)(C/T)(A/G)GAA, 0.
  10. inverse complement, positive strand, negative direction, looking for TTC(A/G)(C/T)(A/G)GAA, 0.
  11. inverse complement, positive strand, positive direction, looking for TTC(A/G)(C/T)(A/G)GAA, 0.
  12. inverse complement, negative strand, positive direction, looking for TTC(A/G)(C/T)(A/G)GAA, 0.
  13. inverse negative strand, negative direction, looking for AAG(C/T)(A/G)(C/T)CTT, 0.
  14. inverse positive strand, negative direction, looking for AAG(C/T)(A/G)(C/T)CTT, 0.
  15. inverse positive strand, positive direction, looking for AAG(C/T)(A/G)(C/T)CTT, 0.
  16. inverse negative strand, positive direction, looking for AAG(C/T)(A/G)(C/T)CTT, 0.

CDE distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, positive direction: TTCCATGAA at 128.

CDE random dataset samplings

  1. CDEr0: 0.
  2. CDEr1: 0.
  3. CDEr2: 0.
  4. CDEr3: 0.
  5. CDEr4: 0.
  6. CDEr5: 0.
  7. CDEr6: 0.
  8. CDEr7: 0.
  9. CDEr8: 1, TTCCATGAA at 1472.
  10. CDEr9: 1, TTCTATGAA at 2350.
  11. CDEr0ci: 0.
  12. CDEr1ci: 0.
  13. CDEr2ci: 0.
  14. CDEr3ci: 0.
  15. CDEr4ci: 1, TTCGCGGAA at 2553.
  16. CDEr5ci: 1, TTCGTGGAA at 633.
  17. CDEr6ci: 0.
  18. CDEr7ci: 0.
  19. CDEr8ci: 0.
  20. CDEr9ci: 0.

CDEr arbitrary negative direction (evens) (2596-1) distal promoters

  1. CDEr8: TTCCATGAA at 1472.
  2. CDEr4ci: TTCGCGGAA at 2553.

CDEr alternate negative direction (odds) (2596-1) distal promoters

  1. CDEr9: TTCTATGAA at 2350.
  2. CDEr5ci: TTCGTGGAA at 633.

CDEr arbitrary positive direction (odds) (4050-1) distal promoters

  1. CDEr9: TTCTATGAA at 2350.
  2. CDEr5ci: TTCGTGGAA at 633.

CDEr alternate positive direction (evens) (4050-1) distal promoters

  1. CDEr8: TTCCATGAA at 1472.
  2. CDEr4ci: TTCGCGGAA at 2553.

Constitutive decay element analysis and results

Main article: Complex locus A1BG and ZNF497 § Constitutive decay elements

Constitutive "decay elements (CDEs) [4, 18][...] are conserved stem loop motifs that bind to the proteins Roquin and Roquin2, resulting in increased mRNA decay [18]. CDEs include an upper stem-loop sequence of the form UUCYRYGAA flanked by lower stem sequences. Lower stem sequences are formed by 2-5 nt pairs of reverse-complementary sequences (e.g. CCUUCYRYGAAGG has a lower stem length of 2)."[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 2 10 0.2 0.2
Randoms Distal alternate negative 2 10 0.2 0.2
Reals Distal positive 1 2 0.5 0.5
Randoms Distal arbitrary positive 2 10 0.2 0.2
Randoms Distal alternate positive 2 10 0.2 0.2

Comparison:

The occurrence of real CDE is greater than the randoms. This suggests that the real CDE is likely active or activable.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Tala Bakheet, Bryan R. G. Williams, and Khalid S. A. Khabar (1 January 2003). "ARED 2.0: an update of AU-rich element mRNA database". Nucleic Acids Research. 31 (1): 421–423. doi:10.1093/nar/gkg023. Retrieved 23 March 2021.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 David A. Siegel, Olivier Le Tonqueze, Anne Biton, Noah Zaitlen, and David J. Erle (12 February 2020). "Massively Parallel Analysis of Human 3′ UTRs Reveals that AU-Rich Element Length and Registration Predict mRNA Destabilization" (PDF). bioRxiv. doi:10.1101/2020.02.12.945063. Retrieved 23 March 2021.
  3. ↑ 3.0 3.1 3.2 Chyi-Ying A. Chen and Ann-Bin Shyu (November 1995). "AU-rich elements: characterization and importance in mRNA degradation" (PDF). Trends in Biochemical Sciences. 20 (11): 465–470. doi:10.1016/S0968-0004(00)89102-1. Retrieved 2 October 2022.

External links

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