Pribnow box gene transcriptions

Editor-In-Chief: Henry A. Hoff

"Although the first five bases of the conserved sequence are identical to the first five bases of the Pribnow box (TATAA), the sixth base of the Pribnow box is a 100 per cent conserved T (refs 15-17) while the 100 per cent conserved A found here is actually more similar to eukaryotic promoter sequences²⁰."^[1]

"Two domains upstream of the start site of transcription have been identified for which a consensus sequence has been formulated(1-5). These domains are the -35 sequence (5'-T-T-G-A-C-A) and the Pribnow box (5'-T-A-T-A-A-T) in the -10 region. Both domains are in close contact with the RNA polymerase during initiation of RNAsynthesis (2,6)."^[2]

Pribnow box samplings

For the Basic programs (starting with SuccessablesPrib.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:

negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesPrib--.bas, looking for 3'-TATAAT-5', 2, 3'-TATAAT-5', 3454, 3'-TATAAT-5', 3468,
negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesPrib-+.bas, looking for 3'-TATAAT-5', 1, 3'-TATAAT-5', 729,
positive strand in the negative direction is SuccessablesPrib+-.bas, looking for 3'-TATAAT-5', 0,
positive strand in the positive direction is SuccessablesPrib++.bas, looking for 3'-TATAAT-5', 0,
complement, negative strand, negative direction is SuccessablesPribc--.bas, looking for 3'-ATATTA-5', 0,
complement, negative strand, positive direction is SuccessablesPribc-+.bas, looking for 3'-ATATTA-5', 0,
complement, positive strand, negative direction is SuccessablesPribc+-.bas, looking for 3'-ATATTA-5', 2, 3'-ATATTA-5', 3454, 3'-ATATTA-5', 3468,
complement, positive strand, positive direction is SuccessablesPribc++.bas, looking for 3'-ATATTA-5', 1, 3'-ATATTA-5', 729,
inverse complement, negative strand, negative direction is SuccessablesPribci--.bas, looking for 3'-ATTATA-5', 2, 3'-ATTATA-5', 272, 3'-ATTATA-5', 603,
inverse complement, negative strand, positive direction is SuccessablesPribci-+.bas, looking for 3'-ATTATA-5', 1, 3'-ATTATA-5', 727,
inverse complement, positive strand, negative direction is SuccessablesPribci+-.bas, looking for 3'-ATTATA-5', 0,
inverse complement, positive strand, positive direction is SuccessablesPribci++.bas, looking for 3'-ATTATA-5', 0,
inverse, negative strand, negative direction, is SuccessablesPribi--.bas, looking for 3'-TAATAT-5', 0,
inverse, negative strand, positive direction, is SuccessablesPribi-+.bas, looking for 3'-TAATAT-5', 0,
inverse, positive strand, negative direction, is SuccessablesPribi+-.bas, looking for 3'-TAATAT-5', 2, 3'-TAATAT-5', 272, 3'-TAATAT-5', 603,
inverse, positive strand, positive direction, is SuccessablesPribi++.bas, looking for 3'-TAATAT-5', 1, 3'-TAATAT-5', 727.

Prib (4560-2846) UTRs

Negative strand, negative direction: TATAAT at 3468, TATAAT at 3454.

Prib negative direction (2596-1) distal promoters

Negative strand, negative direction: ATTATA at 603, ATTATA at 272.

Prib positive direction (4050-1) distal promoters

Negative strand, positive direction: TATAAT at 729.
Negative strand, positive direction: ATTATA at 727.

Pribnow box random dataset samplings

Pribr0: 1, TATAAT at 3603.
Pribr1: 1, TATAAT at 4335.
Pribr2: 1, TATAAT at 240.
Pribr3: 2, TATAAT at 3274, TATAAT at 784.
Pribr4: 2, TATAAT at 3892, TATAAT at 775.
Pribr5: 1, TATAAT at 3518.
Pribr6: 0.
Pribr7: 2, TATAAT at 4084, TATAAT at 2454.
Pribr8: 2, TATAAT at 3983, TATAAT at 3071.
Pribr9: 0.
Pribr0ci: 0.
Pribr1ci: 5, ATTATA at 1265, ATTATA at 1233, ATTATA at 364, ATTATA at 338, ATTATA at 252.
Pribr2ci: 1, ATTATA at 1781.
Pribr3ci: 0.
Pribr4ci: 0.
Pribr5ci: 1, ATTATA at 1561.
Pribr6ci: 1, ATTATA at 3867.
Pribr7ci: 0.
Pribr8ci: 1, ATTATA at 2187.
Pribr9ci: 0.

Pribr arbitrary (evens) (4560-2846) UTRs

Pribr0: TATAAT at 3603.
Pribr4: TATAAT at 3892.
Pribr6ci: ATTATA at 3867.

Pribr alternate (odds) (4560-2846) UTRs

Pribr1: TATAAT at 4335.
Pribr3: TATAAT at 3274.
Pribr5: TATAAT at 3518.
Pribr7: TATAAT at 4084.

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

Pribr1: TATAAT at 4335.

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

Pribr7: TATAAT at 4084.

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

Pribr4: TATAAT at 775.
Pribr2ci: ATTATA at 1781.
Pribr8ci: ATTATA at 2187.

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

Pribr3: TATAAT at 784.
Pribr7: TATAAT at 2454.
Pribr1ci: ATTATA at 1265, ATTATA at 1233, ATTATA at 364, ATTATA at 338, ATTATA at 252.
Pribr5ci: ATTATA at 1561.

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

Pribr3: TATAAT at 3274, TATAAT at 784.
Pribr5: TATAAT at 3518.
Pribr7: TATAAT at 2454.
Pribr1ci: ATTATA at 1265, ATTATA at 1233, ATTATA at 364, ATTATA at 338, ATTATA at 252.
Pribr5ci: ATTATA at 1561.

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

Pribr0: TATAAT at 3603.
Pribr4: TATAAT at 3892, TATAAT at 775.
Pribr2ci: ATTATA at 1781.
Pribr6ci: ATTATA at 3867.
Pribr8ci: ATTATA at 2187.

Pribnow box analysis and results

The Pribnow box (5'-T-A-T-A-A-T) is in the -10 region.^[2]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	2	2	1	1 ± 1 (--2,+-0)
Randoms	UTR	arbitrary negative	3	10	0.3	0.35
Randoms	UTR	alternate negative	4	10	0.4	0.35
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	0.05
Randoms	Core	alternate positive	0	10	0	0.05
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	1	10	0.1	0.05
Randoms	Proximal	alternate positive	0	10	0	0.05
Reals	Distal	negative	2	2	1	1 ± 1 (--2,+-0)
Randoms	Distal	arbitrary negative	3	10	0.3	0.55
Randoms	Distal	alternate negative	8	10	0.8	0.55
Reals	Distal	positive	2	2	1	1 ± 1 (-+2,++0)
Randoms	Distal	arbitrary positive	10	10	1	0.8
Randoms	Distal	alternate positive	6	10	0.6	0.8

Comparison:

The occurrences of real Prib UTRs and distals are greater than the randoms. This suggests that the real Pribs are likely active or activable.

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

References

↑ Alan C. Christensen & Elton T. Young (1982). "T4 late transcripts are initiated near a conserved DNA sequence". Nature. 299 (5881): 369–71. doi:10.1038/299369a0. Retrieved 2017-02-19. Unknown parameter |month= ignored (help)
↑ ^2.0 ^2.1 Herman A. de Boer, Lisa J. Comstock, and Mark Vasser (1983). "The tac promoter: A functional hybrid derived from the trpand lac promoters" (PDF). Proceedings of the National Academy of Sciences USA. 80 (1): 21–5. Retrieved 2017-02-19. Unknown parameter |month= ignored (help)

External links

Template:Sisterlinks

[Christensen-1] Alan C. Christensen & Elton T. Young (1982). "T4 late transcripts are initiated near a conserved DNA sequence". Nature. 299 (5881): 369–71. doi:10.1038/299369a0. Retrieved 2017-02-19. Unknown parameter |month= ignored (help)

[Boer-2] 2.0 ^2.1 Herman A. de Boer, Lisa J. Comstock, and Mark Vasser (1983). "The tac promoter: A functional hybrid derived from the trpand lac promoters" (PDF). Proceedings of the National Academy of Sciences USA. 80 (1): 21–5. Retrieved 2017-02-19. Unknown parameter |month= ignored (help)

[1]

[2]

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expressions General factor II D gene transcriptions General regulatory factors General transcription factor II A gene transcriptions General transcription factor II B gene transcriptions General transcription factor II D gene transcriptions General transcription factor II F gene transcriptions General transcription factor II H gene transcriptions General transcription factor gene transcriptions Gene transcriptions GGC triplet gene transcriptions Gibberellin responsive element gene transcriptions GLM box gene transcriptions Glucocorticoid response element gene transcriptions Grainy head gene transcriptions Grainy head transcription factor gene transcriptions Growth hormone response element gene transcriptions GT boxes Hac1p gene transcriptions Hair color gene expressions H and ACA box gene transcriptions H box gene transcriptions Heat-responsive element gene transcriptions Heat shock elements Hex sequence gene transcriptions HMG box gene transcriptions HNF gene transcriptions Homeobox 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sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Nanos/Pumilio response element Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions Tryptophan residue U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions