CAT box gene transcriptions: Difference between revisions

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Based on the mismatching occurrences the real CAT boxes are likely active or activable.
Based on the mismatching occurrences the real CAT boxes are likely active or activable.
==CAT-box-like element samplings==
Copying a responsive elements consensus sequence AAAAAAAA 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 AAAAAAAA (starting with SuccessablesAAA.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, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
===AAA UTRs===
{{main|UTR promoter gene transcriptions}}
===AAA core promoters===
{{main|Core promoter gene transcriptions}}
===AAA proximal promoters===
{{main|Proximal promoter gene transcriptions}}
===AAA distal promoters===
{{main|Distal promoter gene transcriptions}}
==CAT-box-like element random dataset samplings==
# RDr0: 0.
# RDr1: 0.
# RDr2: 0.
# RDr3: 0.
# RDr4: 0.
# RDr5: 0.
# RDr6: 0.
# RDr7: 0.
# RDr8: 0.
# RDr9: 0.
# RDr0ci: 0.
# RDr1ci: 0.
# RDr2ci: 0.
# RDr3ci: 0.
# RDr4ci: 0.
# RDr5ci: 0.
# RDr6ci: 0.
# RDr7ci: 0.
# RDr8ci: 0.
# RDr9ci: 0.
===RDr UTRs===
{{main|UTR promoter gene transcriptions}}
===RDr core promoters===
{{main|Core promoter gene transcriptions}}
===RDr proximal promoters===
{{main|Proximal promoter gene transcriptions}}
===RDr distal promoters===
{{main|Distal promoter gene transcriptions}}
==Response element analysis and results==
{{main|Complex locus A1BG and ZNF497#CAT-box-like elements}}


==Acknowledgements==
==Acknowledgements==

Revision as of 04:37, 26 January 2022

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

Human genes

Main article: Human genes

The "four cystatin genes [GeneID: 1469 CST1, GeneID: 1470 CST2, GeneID: 1471 CST3, and GeneID: 1472 CST4] contain the ATA-box sequence (ATAAA) in their 5'-flanking regions; however, the CAT-box sequence (CAT), a binding site of the transcription factor, CTF, is found only in the 5'-flanking region of the S-type cystatin genes."[1]

Gene expressions

Main article: Gene expressions

The "5‘ flanking region of the rat acetylcholine receptor (AChR) β subunit gene [with] regulatory elements that confer muscle specificity [includes] a minimal TATA-box-less promoter region containing an initiator motif. An 85-bp fragment [promotes] high muscle-specific expression of a chloramphenicol acetyltransferase (CAT) reporter construct upon transfection in primary muscle cells. This sequence can be functionally dissected in a basal muscle-specific promoter element carrying a M-CAT box that is flanked at the 5’ end by an enhancer element with two binding sites for myogenic factors. Point mutations in the M-CAT box cause the loss of transcriptional activity of the basal promoter fragment. The enhancer activity depends on the presence of both E boxes that cooperate in a synergistic fashion. [The] control of muscle-specific and developmental expression of the rat AChR β subunit gene requires both regulatory elements, the M-CAT box and two adjacent E boxes, located in close proximity to each other."[2]

Interactions

Main article: Interaction gene transcriptions

The "minimal regulatory region of the 5’ flanking sequence contains E box elements that are defined by the nucleotides CANNTG [26, 271. E boxes are shown to provide binding sites for helix-loop-helix proteins of the MyoDl family including MyoDl [28], myogenin [29, 301, MRF4/ herculin [31] and myf5 [32]."[2]

Enhancer activity

"Partial sequence of the 5' flanking region of the rat AChR β subunit gene [contains] putative E box element [CAGGTG], putative Sp1 element [GGGGCGGGT at -85 nts], putative Shue box element [CCCTGGCCTGG at -15 nts], M-CAT box element [GCGGCCTC at -8 nts]."[2]

"Within the first 140bp of the 5’ flanking region the position and sequence of three other putative regulatory elements, the Spl [43, 44], M-CAT [34] and Shue box [45], are conserved between mouse and rat".[2]

Consensus sequences

Main article: Consensus sequence gene transcriptions

"The M-CAT consensus sequence [is] CATTCCT".[2]

Promoter occurrences

"A CAT-box-like element, GCCATT [34], adjacent to the GC-box, is conserved in the three promoters."[2]

Hypotheses

Main article: Hypotheses
  1. A1BG has no CAT boxes in either promoter.
  2. A1BG is not transcribed by a CAT box.
  3. CAT box does not participate in the transcription of A1BG.

CAT box samplings

Main article: Model samplings

Copying a CAT box consensus sequence 5'-CATTCCT-3' and putting the sequence in "⌘F" finds one 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 5'-CATTCCT-3' (starting with SuccessablesCAT.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 5'-CATTCCT-3', 0.
  2. negative strand, positive direction, looking for 5'-CATTCCT-3', 1, 5'-CATTCCT-3' at 2209, and complement.
  3. positive strand, negative direction, looking for 5'-CATTCCT-3', 0.
  4. positive strand, positive direction, looking for 5'-CATTCCT-3', 1, 5'-CATTCCT-3' at 2458, and complement.
  5. complement, negative strand, negative direction, looking for 5'-GTAAGGA-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-GTAAGGA-3', 1, 5'-GTAAGGA-3' at 2458.
  7. complement, positive strand, negative direction, looking for 5'-GTAAGGA-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-GTAAGGA-3', 1, 5'-GTAAGGA-3' at 2209.
  9. inverse complement, negative strand, negative direction, looking for 5'-AGGAATG-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-AGGAATG-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-AGGAATG-3', 1, 5'-AGGAATG-3' at 4554.
  12. inverse complement, positive strand, positive direction, looking for 5'-AGGAATG-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-TCCTTAC-3', 1, 5'-TCCTTAC-3' at 4554.
  14. inverse negative strand, positive direction, looking for 5'-TCCTTAC-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-TCCTTAC-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-TCCTTAC-3', 0.

CAT box UTR promoters

  1. Negative strand, negative direction: TCCTTAC at 4554.

CAT box distal promoters

Main article: Distal promoter gene transcriptions
  1. Negative strand, positive direction: CATTCCT at 2209.
  2. Positive strand, positive direction: CATTCCT at 2458.

CAT box random dataset samplings

  1. CATr0: 0.
  2. CATr1: 0.
  3. CATr2: 0.
  4. CATr3: 1, CATTCCT at 3089.
  5. CATr4: 1, CATTCCT at 1553.
  6. CATr5: 1, CATTCCT at 985.
  7. CATr6: 0.
  8. CATr7: 0.
  9. CATr8: 0.
  10. CATr9: 0.
  11. CATr0ci: 0.
  12. CATr1ci: 0.
  13. CAT2ci: 1, AGGAATG at 4356.
  14. CATr3ci: 0.
  15. CATr4ci: 1, AGGAATG at 2701.
  16. CATr5ci: 0.
  17. CATr6ci: 0.
  18. CATr7ci: 0.
  19. CATr8ci: 1, AGGAATG at 157.
  20. CATr9ci: 1, AGGAATG at 3677.

CATr UTRs

Main article: UTR promoter gene transcriptions
  1. CAT2ci: AGGAATG at 4356.

CATr proximal promoters

Main article: Proximal promoter gene transcriptions
  1. CATr4ci: AGGAATG at 2701.

CATr distal promoters

Main article: Distal promoter gene transcriptions
  1. CATr4: CATTCCT at 1553.
  2. CATr8ci: AGGAATG at 157.


  1. CATr3: CATTCCT at 3089.
  2. CATr5: CATTCCT at 985.
  3. CATr9ci: AGGAATG at 3677.

CAT box analysis and results

Main article: Complex locus A1BG and ZNF497 § CAT boxes

The real promoters have one consensus sequence in the ZSCAN22-side UTR to A1BG (occurrence 0.5), none in the core promoter or proximal promoter and two in the positive direction only in the distal promoter (occurrence 1).

The random datasets had one consensus sequence in the ZSCAN22-side UTR of A1BG (occurrence 0.1), no core promoter sequences, one in the promoter in the negative direction (occurrence 0.1) and five in the distal promoters (occurrence 0.2 in the negative direction) and (occurrence 0.3 in the positive direction).

Based on the mismatching occurrences the real CAT boxes are likely active or activable.

CAT-box-like element samplings

Copying a responsive elements consensus sequence AAAAAAAA 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 AAAAAAAA (starting with SuccessablesAAA.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 AAAAAAAA, 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. positive strand, positive direction, looking for AAAAAAAA, 0.
  4. negative strand, positive direction, looking for AAAAAAAA, 0.
  5. complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  8. complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  10. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  11. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  12. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  13. inverse negative strand, negative direction, looking for AAAAAAAA, 0.
  14. inverse positive strand, negative direction, looking for AAAAAAAA, 0.
  15. inverse positive strand, positive direction, looking for AAAAAAAA, 0.
  16. inverse negative strand, positive direction, looking for AAAAAAAA, 0.

AAA UTRs

Main article: UTR promoter gene transcriptions

AAA core promoters

Main article: Core promoter gene transcriptions

AAA proximal promoters

Main article: Proximal promoter gene transcriptions

AAA distal promoters

Main article: Distal promoter gene transcriptions

CAT-box-like element random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr UTRs

Main article: UTR promoter gene transcriptions

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

RDr distal promoters

Main article: Distal promoter gene transcriptions

Response element analysis and results

Main article: Complex locus A1BG and ZNF497 § CAT-box-like elements

Acknowledgements

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

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

See also

References

  1. ↑ Eiichi Saitoh and Satoko Isemura (January 1, 1993). "Molecular Biology of Human Salivary Cysteine Proteinase Inhibitors" (PDF). Critical Reviews in Oral Biology and Medicine. 4 (3/4): 487–93. doi:10.1177/10454411930040033301. Retrieved 2013-06-28.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Christof Berberich, Ingolf Dürr, Michael Koenen and Veit Witzemann (September 1993). "Two adjacent E box elements and a M‐CAT box are involved in the muscle‐specific regulation of the rat acetylcholine receptor β subunit gene". European Journal of Biochemistry. 216 (2): 395–404. doi:10.1111/j.1432-1033.1993.tb18157.x. Retrieved 27 December 2019.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=CAT_box_gene_transcriptions&oldid=1718962"