Calcineurin-responsive transcription factor gene transcriptions

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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.

CRT 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 SuccessablesCRT.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: 2, TGAGCCAC at 2560, TGAGCCAC 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. inverse complement, negative strand, negative direction, looking for 5'-GNGGC(G/T)CA-3', 0.
  6. inverse complement, negative strand, positive direction, looking for 5'-GNGGC(G/T)CA-3', 0.
  7. inverse complement, positive strand, negative direction: 8, GTGGCTCA at 4114, GTGGCTCA at 3963, GTGGCTCA at 3054, GTGGCTCA at 2531, GTGGCTCA at 2204, GTGGCTCA at 1769, GTGGCTCA at 1124, GTGGCTCA at 660.
  8. inverse complement, positive strand, positive direction: 3, GCGGCTCA at 1166, GCGGCTCA at 1082, GGGGCTCA at 578.

CRT (4560-2846) UTRs

  1. Positive strand, negative direction: GTGGCTCA at 4114, GTGGCTCA at 3963, GTGGCTCA at 3054.

CRT negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: GTGGCTCA at 2531, GTGGCTCA at 2204, GTGGCTCA at 1769, GTGGCTCA at 1124, GTGGCTCA at 660.

CRT positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TGAGCCAC at 2560, TGAGCCAC at 1291.
  2. Positive strand, positive direction: GCGGCTCA at 1166, GCGGCTCA at 1082, GGGGCTCA at 578.

CRT random dataset samplings

  1. CRTr0: 0.
  2. CRTr1: 1, TGCGCCTC at 2284.
  3. CRTr2: 1, TGCGCCCC at 708.
  4. CRTr3: 1, TGAGCCGC at 4137.
  5. CRTr4: 0.
  6. CRTr5: 0.
  7. CRTr6: 3, TGCGCCAC at 3907, TGCGCCCC at 3315, TGAGCCCC at 2451.
  8. CRTr7: 2, TGAGCCCC at 2175, TGAGCCCC at 1840.
  9. CRTr8: 1, TGAGCCAC at 3710.
  10. CRTr9: 0.
  11. CRTr0ci: 1, GTGGCTCA at 2847.
  12. CRTr1ci: 0.
  13. CRTr2ci: 0.
  14. CRTr3ci: 0.
  15. CRTr4ci: 0.
  16. CRTr5ci: 0.
  17. CRTr6ci: 0.
  18. CRTr7ci: 1, GCGGCTCA at 3618.
  19. CRTr8ci: 0.
  20. CRTr9ci: 3, GAGGCTCA at 2983, GGGGCTCA at 1719, GAGGCTCA at 766.

CRTr arbitrary (evens) (4560-2846) UTRs

  1. CRTr6: TGCGCCAC at 3907, TGCGCCCC at 3315.
  2. CRTr8: TGAGCCAC at 3710.
  3. CRTr0ci: GTGGCTCA at 2847.

CRTr alternate (odds) (4560-2846) UTRs

  1. CRTr3: TGAGCCGC at 4137.
  2. CRTr7ci: GCGGCTCA at 3618.
  3. CRTr9ci: GAGGCTCA at 2983.

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

  1. CRTr3: TGAGCCGC at 4137.

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

  1. CRTr2: TGCGCCCC at 708.
  2. CRTr6: TGAGCCCC at 2451.

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

  1. CRTr1: TGCGCCTC at 2284.
  2. CRTr7: TGAGCCCC at 2175, TGAGCCCC at 1840.
  3. CRTr9ci: GGGGCTCA at 1719, GAGGCTCA at 766.

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

  1. CRTr1: TGCGCCTC at 2284.
  2. CRTr7: TGAGCCCC at 2175, TGAGCCCC at 1840.
  3. CRTr7ci: GCGGCTCA at 3618.
  4. CRTr9ci: GAGGCTCA at 2983, GGGGCTCA at 1719, GAGGCTCA at 766.

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

  1. CRTr2: TGCGCCCC at 708.
  2. CRTr6: TGCGCCAC at 3907, TGCGCCCC at 3315, TGAGCCCC at 2451.
  3. CRTr8: TGAGCCAC at 3710.
  4. CRTr0ci: GTGGCTCA at 2847.

Calcineurin-responsive transcription factor analysis and results

Main article: Complex locus A1BG and ZNF497 § Calcineurin-responsive transcription factors

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

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 3 2 1.5 1.5
Randoms UTR arbitrary negative 4 10 0.4 0.35
Randoms UTR alternate negative 3 10 0.3 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 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 1 10 0.1 0.05
Randoms Proximal alternate positive 0 10 0 0.05
Reals Distal negative 5 2 2.5 2.5
Randoms Distal arbitrary negative 2 10 0.2 0.35
Randoms Distal alternate negative 5 10 0.5 0.35
Reals Distal positive 5 2 2.5 2.5 ± 0.5 (-+2,++3)
Randoms Distal arbitrary positive 7 10 0.7 0.65
Randoms Distal alternate positive 6 10 0.6 0.65

Comparison:

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

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. ↑ 2.0 2.1 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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