N box gene transcriptions: Difference between revisions
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# inverse negative strand, positive direction, looking for AAGGCC, 10, AAGGCC at 1513, AAGGCC at 1429, AAGGCC at 1329, AAGGCC at 1261, AAGGCC at 1009, AAGGCC at 925, AAGGCC at 825, AAGGCC at 673, AAGGCC at 589, AAGGCC at 212. | # inverse negative strand, positive direction, looking for AAGGCC, 10, AAGGCC at 1513, AAGGCC at 1429, AAGGCC at 1329, AAGGCC at 1261, AAGGCC at 1009, AAGGCC at 925, AAGGCC at 825, AAGGCC at 673, AAGGCC at 589, AAGGCC at 212. | ||
===N-box UTRs=== | ===N-box (Lee) UTRs=== | ||
{{main|UTR promoter gene transcriptions}} | {{main|UTR promoter gene transcriptions}} | ||
Negative strand, negative direction: TTCCGG at 4167, CCGGAA at 3569. | Negative strand, negative direction: TTCCGG at 4167, CCGGAA at 3569. | ||
===N-box proximal promoters=== | ===N-box (Lee) proximal promoters=== | ||
{{main|Proximal promoter gene transcriptions}} | {{main|Proximal promoter gene transcriptions}} | ||
Negative strand, positive direction: TTCCGG at 4244. | Negative strand, positive direction: TTCCGG at 4244. | ||
===N-box distal promoters=== | ===N-box (Lee) distal promoters=== | ||
{{main|Distal promoter gene transcriptions}} | {{main|Distal promoter gene transcriptions}} | ||
Positive strand, positive direction: CCGGAA at 1797, CCGGAA at 1515, TTCCGG at 1513, CCGGAA at 1431, TTCCGG at 1429, CCGGAA at 1331, TTCCGG at 1329, CCGGAA at 1263, TTCCGG at 1261, CCGGAA at 1011, TTCCGG at 1009, CCGGAA at 927, TTCCGG at 925, CCGGAA at 827, TTCCGG at 825, CCGGAA at 675, TTCCGG at 673, CCGGAA at 591, TTCCGG at 589, TTCCGG at 212. | Positive strand, positive direction: CCGGAA at 1797, CCGGAA at 1515, TTCCGG at 1513, CCGGAA at 1431, TTCCGG at 1429, CCGGAA at 1331, TTCCGG at 1329, CCGGAA at 1263, TTCCGG at 1261, CCGGAA at 1011, TTCCGG at 1009, CCGGAA at 927, TTCCGG at 925, CCGGAA at 827, TTCCGG at 825, CCGGAA at 675, TTCCGG at 673, CCGGAA at 591, TTCCGG at 589, TTCCGG at 212. | ||
Revision as of 17:28, 20 March 2021
Associate Editor(s)-in-Chief: Henry A. Hoff
"Human pColQ1a carries consensus sequences for transcriptional factors E-protein (E-box, CANNTG), NFAT (GGAAA), c-Ets transcription factor [c-Ets, (C/A)GGA(A/T)], Elk-1, N-box (CCGGAA), and MEF2 (CTAAAAATAA), which play essential roles in muscle-specific and NMJ-specific transcriptional activities (Lee et al., 2004)."[1]
Human genes
Gene expressions
Interactions
Consensus sequences
CCGGAA[1]
Binding site for
"The [basic helix–loop–helix] bHLH proteins from group E were usually bound to the CACGCG [Coupling element] or CACGAG (N-box) motif."[2]
"Group E comprises two families in which the proteins have a conserved Pro or Gly residue within the basic region that mediates preferential binding to the N-box sequences CACGGC or CACGAC."[3]
Promoter occurrences
"Transcriptional upregulation of pColQ1a at the [neuromuscular junction] NMJ is mediated by the N-box (CCGGAA; Lee et al., 2004). The N-box (CGGAA) is also the neuregulin-response element in mouse Chrnd encoding the δ subunit of acetylcholine receptor (AChR; Fromm and Burden, 1998) and in rat Chrne encoding the AChR ε subunit (Sapru et al., 1998). Similar involvement of the neuregulin-responsive N-box in the NMJ-specific transcription of ColQ in mouse have also been reported (Lee et al., 2004; Ting et al., 2005). Also, specific activation of pColQ1 and pColQ1a in slow- and fast-twitch muscles, respectively, is mediated by a slow upstream regulatory element (SURE) in pColQ1 and a fast intronic regulatory element (FIRE) in pColQ1a (Lee et al., 2004; Ting et al., 2005)."[1]
Hypotheses
- A1BG has no regulatory elements in either promoter.
- A1BG is not transcribed by a regulatory element.
- No regulatory element participates in the transcription of A1BG.
N-box (Lee) samplings
Copying a responsive elements consensus sequence CCGGAA 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 CCGGAA (starting with SuccessablesN-box.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 CCGGAA, 1, CCGGAA at 3569.
- positive strand, negative direction, looking for CCGGAA, 0.
- positive strand, positive direction, looking for CCGGAA, 10, CCGGAA at 1797, CCGGAA at 1515, CCGGAA at 1431, CCGGAA at 1331, CCGGAA at 1263, CCGGAA at 1011, CCGGAA at 927, CCGGAA at 827, CCGGAA at 675, CCGGAA at 591.
- negative strand, positive direction, looking for CCGGAA, 0.
- complement, negative strand, negative direction, looking for GGCCTT, 0.
- complement, positive strand, negative direction, looking for GGCCTT, 1, GGCCTT at 3569.
- complement, positive strand, positive direction, looking for GGCCTT, 0.
- complement, negative strand, positive direction, looking for GGCCTT, 10, GGCCTT at 1797, GGCCTT at 1515, GGCCTT at 1431, GGCCTT at 1331, GGCCTT at 1263, GGCCTT at 1011, GGCCTT at 927, GGCCTT at 827, GGCCTT at 675, GGCCTT at 591.
- inverse complement, negative strand, negative direction, looking for TTCCGG, 1, TTCCGG at 4167.
- inverse complement, positive strand, negative direction, looking for TTCCGG, 0.
- inverse complement, positive strand, positive direction, looking for TTCCGG, 10, TTCCGG at 1513, TTCCGG at 1429, TTCCGG at 1329, TTCCGG at 1261, TTCCGG at 1009, TTCCGG at 925, TTCCGG at 825, TTCCGG at 673, TTCCGG at 589, TTCCGG at 212.
- inverse complement, negative strand, positive direction, looking for TTCCGG, 1, TTCCGG at 4244.
- inverse negative strand, negative direction, looking for AAGGCC, 0.
- inverse positive strand, negative direction, looking for AAGGCC, 1, AAGGCC at 4167.
- inverse positive strand, positive direction, looking for AAGGCC, 1, AAGGCC at 4244.
- inverse negative strand, positive direction, looking for AAGGCC, 10, AAGGCC at 1513, AAGGCC at 1429, AAGGCC at 1329, AAGGCC at 1261, AAGGCC at 1009, AAGGCC at 925, AAGGCC at 825, AAGGCC at 673, AAGGCC at 589, AAGGCC at 212.
N-box (Lee) UTRs
Negative strand, negative direction: TTCCGG at 4167, CCGGAA at 3569.
N-box (Lee) proximal promoters
Negative strand, positive direction: TTCCGG at 4244.
N-box (Lee) distal promoters
Positive strand, positive direction: CCGGAA at 1797, CCGGAA at 1515, TTCCGG at 1513, CCGGAA at 1431, TTCCGG at 1429, CCGGAA at 1331, TTCCGG at 1329, CCGGAA at 1263, TTCCGG at 1261, CCGGAA at 1011, TTCCGG at 1009, CCGGAA at 927, TTCCGG at 925, CCGGAA at 827, TTCCGG at 825, CCGGAA at 675, TTCCGG at 673, CCGGAA at 591, TTCCGG at 589, TTCCGG at 212.
N-box (Bai) samplings
Copying a responsive elements consensus sequence CACGAG and putting the sequence in "⌘F" finds one 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 CACGAG (starting with SuccessablesN-boxB.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.
N-box (Bai) UTRs
N-box (Bai) core promoters
N-box (Bai) proximal promoters
N-box (Bai) distal promoters
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
- ↑ 1.0 1.1 1.2 Kun Huang, Jin Li, Mikako Ito, Jun-Ichi Takeda, Bisei Ohkawara, Tomoo Ogi, Akio Masuda, and Kinji Ohno (8 September 2020). "Gene Expression Profile at the Motor Endplate of the Neuromuscular Junction of Fast-Twitch Muscle". Frontiers in Molecular Neuroscience. 13: 154–165. doi:10.3389/fnmol.2020.00154. PMID 33117128 Check
|pmid=value (help). Retrieved 19 March 2021. - ↑ Ge Bai, Da-Hai Yang, Peijian Chao, Heng Yao, MingLiang Fei, Yihan Zhang, Xuejun Chen, Bingguang Xiao, Feng Li, Zhen-Yu Wang, Jun Yang and He Xie (19 December 2020). "Genome-wide identification and expression analysis of NtbHLH gene family in tobacco (Nicotiana tabacum L.) and the role of NtbHLH86 in drought adaptation". Plant Diversity. 10: 4. doi:10.1016/j.pld.2020.10.004. Retrieved 19 March 2021.
- ↑ Min Gao, Yanxun Zhu, Jinhua Yang, Hongjing Zhang, Chenxia Cheng, Yucheng Zhang, Ran Wan, Zhangjun Fei & Xiping Wang (18 March 2019). "Identification of the grape basic helix–loop–helix transcription factor family and characterization of expression patterns in response to different stresses". Plant Growth Regulation. 88: 19–39. Retrieved 20 March 2021.