Calcineurin-responsive transcription factor gene transcriptions: Difference between revisions

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For the Basic programs testing consensus sequence 5'-TG(A/C)GCCNC-3' (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:
For the Basic programs testing consensus sequence 5'-TG(A/C)GCCNC-3' (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 5'-TG(A/C)GCCNC-3', 0.
# negative strand, negative direction, looking for 5'-TG(A/C)GCCNC-3', 0.
# negative strand, positive direction, looking for 5'-TG(A/C)GCCNC-3', 0.
# negative strand, positive direction, looking for 5'-TG(A/C)GCCNC-3', 2, 5'-TGAGCCAC-3' at 2560, 5'-TGAGCCAC-3' at 1291.
# positive strand, negative direction, looking for 5'-TG(A/C)GCCNC-3', 0.
# positive strand, negative direction, looking for 5'-TG(A/C)GCCNC-3', 0.
# positive strand, positive direction, looking for 5'-TG(A/C)GCCNC-3', 0.
# positive strand, positive direction, looking for 5'-TG(A/C)GCCNC-3', 0.
# complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# complement, negative strand, negative direction, looking for 5'-AC(G/T)CGGNG-3', 0.
# complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# complement, negative strand, positive direction, looking for 5'-AC(G/T)CGGNG-3', 0.
# complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# complement, positive strand, negative direction, looking for 5'-AC(G/T)CGGNG-3', 0.
# complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# complement, positive strand, positive direction, looking for 5'-AC(G/T)CGGNG-3', 2, 5'-ACTCGGTG-3' at 2560, 5'-ACTCGGTG-3' at 1291, and complements.
# inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, negative strand, negative direction, looking for 5'-GNGGC(G/T)CA-3', 0.
# inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, negative strand, positive direction, looking for 5'-GNGGC(G/T)CA-3', 0.
# inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, positive strand, negative direction, looking for 5'-GNGGC(G/T)CA-3', 8, 5'-GTGGCTCA-3' at 4114, 5'-GTGGCTCA-3' at 3963, 5'-GTGGCTCA-3' at 3054, 5'-GTGGCTCA-3' at 2531, 5'-GTGGCTCA-3' at 2204, 5'-GTGGCTCA-3' at 1769, 5'-GTGGCTCA-3' at 1124, 5'-GTGGCTCA-3' at 660.
# inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, positive strand, positive direction, looking for 5'-GNGGC(G/T)CA-3', 3, 5'-GCGGCTCA-3' at 1166, 5'-GCGGCTCA-3' at 1082, 5'-GGGGCTCA-3' at 578.
# inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# inverse negative strand, negative direction, looking for 5'-CNCCG(A/C)GT-3', 8, 5'-CACCGAGT-3' at 4114, 5'-CACCGAGT-3' at 3963, 5'-CACCGAGT-3' at 3054, 5'-CACCGAGT-3' at 2531, 5'-CACCGAGT-3' at 2204, 5'-CACCGAGT-3' at 1769, 5'-CACCGAGT-3' at 1124, 5'-CACCGAGT-3' at 660.
# inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# inverse negative strand, positive direction, looking for 5'-CNCCG(A/C)GT-3', 3, 5'-CGCCGAGT-3' at 1166, 5'-CGCCGAGT-3' at 1082, 5'-CCCCGAGT-3' at 578.
# inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, negative direction, looking for 5'-CNCCG(A/C)GT-3', 0.
# inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, positive direction, looking for 5'-CNCCG(A/C)GT-3', 0.


===AAA core promoters===
===CRT distal promoters===
{{main|Core promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}
Positive strand, negative direction: 5'-GTGGCTCA-3' at 4114, 5'-GTGGCTCA-3' at 3963, 5'-GTGGCTCA-3' at 3054, 5'-GTGGCTCA-3' at 2531, 5'-GTGGCTCA-3' at 2204, 5'-GTGGCTCA-3' at 1769, 5'-GTGGCTCA-3' at 1124, 5'-GTGGCTCA-3' at 660, and complements.


===AAA proximal promoters===
Negative strand, positive direction: 5'-TGAGCCAC-3' at 2560, 5'-TGAGCCAC-3' at 1291, and complements.
{{main|Proximal promoter gene transcriptions}}


===AAA distal promoters===
Positive strand, positive direction: 5'-GCGGCTCA-3' at 1166, 5'-GCGGCTCA-3' at 1082, 5'-GGGGCTCA-3' at 578, and complements.
{{main|Distal promoter gene transcriptions}}


==See also==
==See also==

Revision as of 04:16, 7 November 2020

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

Human genes

Gene ID: 1827 is RCAN1 regulator of calcineurin 1 on 21q22.12: "The protein encoded by this gene interacts with calcineurin A and inhibits calcineurin-dependent signaling pathways, possibly affecting central nervous system development. This gene is located in the minimal candidate region for the Down syndrome phenotype, and is overexpressed in the brain of Down syndrome fetuses. Chronic overexpression of this gene may lead to neurofibrillary tangles such as those associated with Alzheimer disease. Alternative splicing results in multiple transcript variants."[1]

  1. NP_001272318.1 calcipressin-1 isoform d: "Transcript Variant: This variant (4) uses an alternate 5' exon compared to variant 1. The resulting isoform (d) has a distinct N-terminus compared to isoform a."[1]
  2. NP_001272320.2 calcipressin-1 isoform e: "Transcript Variant: This variant (5) uses an alternate promoter and 5' exon compared to variant 1. The resulting isoform (e) has a distinct N-terminus compared to isoform a."[1]
  3. NP_001272321.1 calcipressin-1 isoform b: "Transcript Variant: This variant (6) uses an alternate promoter and 5' exon compared to variant 1. The resulting isoform (b) has a shorter N-terminus compared to isoform a."[1]
  4. NP_001272322.1 calcipressin-1 isoform b: "Transcript Variant: This variant (7) uses an alternate promoter and 5' exon compared to variant 1. The resulting isoform (b) has a shorter N-terminus compared to isoform a."[1]
  5. NP_001317945.1 calcipressin-1 isoform f.[1]
  6. NP_004405.3 calcipressin-1 isoform a: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a)."[1]
  7. NP_981962.1 calcipressin-1 isoform b: "Transcript Variant: This variant (2) uses an alternate 5' exon compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a."[1]
  8. NP_981963.1 calcipressin-1 isoform c: "Transcript Variant: This variant (3) uses an alternate 5' exon compared to variant 1. The resulting isoform (c) has a distinct N-terminus compared to isoform a."[1]

Interactions

Consensus sequences

The upstream activating sequence for the calcineurin-responsive transcription factor (Crz1p) is 5'-TG(A/C)GCCNC-3'.[2]

Hypotheses

Main article: Hypotheses
  1. A1BG has no Calcineurin-responsive transcription factors in either promoter.
  2. A1BG is not transcribed by a Calcineurin-responsive transcription factor.
  3. Calcineurin-responsive transcription factor does not participate in the transcription of A1BG.

Samplings

Copying 5'-TGCGCCCC-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-TG(A/C)GCCNC-3' (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 5'-TG(A/C)GCCNC-3', 0.
  2. negative strand, positive direction, looking for 5'-TG(A/C)GCCNC-3', 2, 5'-TGAGCCAC-3' at 2560, 5'-TGAGCCAC-3' at 1291.
  3. positive strand, negative direction, looking for 5'-TG(A/C)GCCNC-3', 0.
  4. positive strand, positive direction, looking for 5'-TG(A/C)GCCNC-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-AC(G/T)CGGNG-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-AC(G/T)CGGNG-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-AC(G/T)CGGNG-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-AC(G/T)CGGNG-3', 2, 5'-ACTCGGTG-3' at 2560, 5'-ACTCGGTG-3' at 1291, and complements.
  9. inverse complement, negative strand, negative direction, looking for 5'-GNGGC(G/T)CA-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-GNGGC(G/T)CA-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-GNGGC(G/T)CA-3', 8, 5'-GTGGCTCA-3' at 4114, 5'-GTGGCTCA-3' at 3963, 5'-GTGGCTCA-3' at 3054, 5'-GTGGCTCA-3' at 2531, 5'-GTGGCTCA-3' at 2204, 5'-GTGGCTCA-3' at 1769, 5'-GTGGCTCA-3' at 1124, 5'-GTGGCTCA-3' at 660.
  12. inverse complement, positive strand, positive direction, looking for 5'-GNGGC(G/T)CA-3', 3, 5'-GCGGCTCA-3' at 1166, 5'-GCGGCTCA-3' at 1082, 5'-GGGGCTCA-3' at 578.
  13. inverse negative strand, negative direction, looking for 5'-CNCCG(A/C)GT-3', 8, 5'-CACCGAGT-3' at 4114, 5'-CACCGAGT-3' at 3963, 5'-CACCGAGT-3' at 3054, 5'-CACCGAGT-3' at 2531, 5'-CACCGAGT-3' at 2204, 5'-CACCGAGT-3' at 1769, 5'-CACCGAGT-3' at 1124, 5'-CACCGAGT-3' at 660.
  14. inverse negative strand, positive direction, looking for 5'-CNCCG(A/C)GT-3', 3, 5'-CGCCGAGT-3' at 1166, 5'-CGCCGAGT-3' at 1082, 5'-CCCCGAGT-3' at 578.
  15. inverse positive strand, negative direction, looking for 5'-CNCCG(A/C)GT-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-CNCCG(A/C)GT-3', 0.

CRT distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, negative direction: 5'-GTGGCTCA-3' at 4114, 5'-GTGGCTCA-3' at 3963, 5'-GTGGCTCA-3' at 3054, 5'-GTGGCTCA-3' at 2531, 5'-GTGGCTCA-3' at 2204, 5'-GTGGCTCA-3' at 1769, 5'-GTGGCTCA-3' at 1124, 5'-GTGGCTCA-3' at 660, and complements.

Negative strand, positive direction: 5'-TGAGCCAC-3' at 2560, 5'-TGAGCCAC-3' at 1291, and complements.

Positive strand, positive direction: 5'-GCGGCTCA-3' at 1166, 5'-GCGGCTCA-3' at 1082, 5'-GGGGCTCA-3' at 578, and complements.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 RefSeq (November 2013). "RCAN1 regulator of calcineurin 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 6 November 2020.
  2. ↑ Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling (6 August 2020). "Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae". Metabolites. 10 (8): 320–39. doi:10.3390/metabo10080320. PMID 32781665 Check |pmid= value (help). Retrieved 18 September 2020.

External links

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