N box gene transcriptions

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 CACGAG, 1, CACGAG at 4403.
positive strand, negative direction, looking for CACGAG, 6, CACGAG at 4472, CACGAG at 3232, CACGAG at 1182, CACGAG at 708, CACGAG at 572, CACGAG at 435.
positive strand, positive direction, looking for CACGAG, 2, CACGAG at 3152, CACGAG at 2090.
negative strand, positive direction, looking for CACGAG, 1, CACGAG at 243.
complement, negative strand, negative direction, looking for GTGCTC, 6, GTGCTC at 4472, GTGCTC at 3232, GTGCTC at 1182, GTGCTC at 708, GTGCTC at 572, GTGCTC at 435.
complement, positive strand, negative direction, looking for GTGCTC, 1, GTGCTC at 4403.
complement, positive strand, positive direction, looking for GTGCTC, 1, GTGCTC at 243.
complement, negative strand, positive direction, looking for GTGCTC, 2, GTGCTC at 3152, GTGCTC at 2090.
inverse complement, negative strand, negative direction, looking for CTCGTG, 1, CTCGTG at 3914.
inverse complement, positive strand, negative direction, looking for CTCGTG, 0.
inverse complement, positive strand, positive direction, looking for CTCGTG, 5, CTCGTG at 3739, CTCGTG at 1627, CTCGTG at 1207, CTCGTG at 955, CTCGTG at 855.
inverse complement, negative strand, positive direction, looking for CTCGTG, 1, CTCGTG at 4376.
inverse negative strand, negative direction, looking for GAGCAC, 0.
inverse positive strand, negative direction, looking for GAGCAC, 1, GAGCAC at 3914.
inverse positive strand, positive direction, looking for GAGCAC, 1, GAGCAC at 4376.
inverse negative strand, positive direction, looking for GAGCAC, 5, GAGCAC at 3739, GAGCAC at 1627, GAGCAC at 1207, GAGCAC at 955, GAGCAC at 855.

N-box (Bai) UTRs

Negative strand, negative direction: CACGAG at 4403, CTCGTG at 3914.

Positive strand, negative direction: CACGAG at 4472, CACGAG at 3232.

N-box (Bai) core promoters

Negative strand, positive direction: CTCGTG at 4376.

N-box (Bai) distal promoters

Positive strand, negative direction: CACGAG at 1182, CACGAG at 708, CACGAG at 572, CACGAG at 435.

Negative strand, positive direction: CACGAG at 243.

Positive strand, positive direction: CTCGTG at 3739, CACGAG at 3152, CACGAG at 2090, CTCGTG at 1627, CTCGTG at 1207, CTCGTG at 955, CTCGTG at 855.

Acknowledgements

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

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.

External links

[Huang-1] 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.

[Bai-2] 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.

[Gao-3] 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.

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[2]

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Transcription resources	A1BG gene transcription core promoters A1BG gene transcriptions A1BG regulatory elements and regions A1BG response element gene transcriptions A1BG response element negative results A1BG response element positive results ABA-response element gene transcriptions Abf1 regulatory factor gene transcriptions A box gene transcriptions ACGT-containing element gene transcriptions Activating protein gene transcriptions Activating transcription factor gene transcriptions Adenylate–uridylate rich element gene transcriptions Adr1p gene transcriptions Aft1p gene transcriptions AGC box gene transcriptions AGCE gene transcriptions Alpha-amylase conserved element gene transcriptions Amino acid response element gene transcriptions AARE-like Androgen response element gene transcriptions Angiotensinogen core promoter element gene transcriptions Antioxidant-electrophile responsive element gene transcriptions ATA box gene transcriptions Auxin response factor gene transcriptions B box gene transcriptions Bioinformatics tool gene transcriptions Box gene transcriptions Bridge gene transcriptions CAAT box gene transcriptions CadC binding domain gene transcriptions Calcineurin-responsive transcription factor gene transcriptions Calcium-response element gene transcriptions cAMP response element gene transcriptions C and D boxes gene transcriptions Carbohydrate response element gene transcriptions Carbon source-responsive element gene transcriptions Carcinoembryonic antigen gene family CARE gene transcriptions CArG box gene transcriptions CAT box gene transcriptions Cat8p gene transcriptions Cbf1 regulatory factor gene transcriptions C box gene transcriptions CCCTC-binding factor gene transcriptions C-EBP box gene transcriptions Cell-cycle box gene transcriptions Cell cycle regulation gene transcriptions CENP-B box gene transcriptions CGCG box gene transcriptions Circadian control element gene transcriptions Cold-responsive element gene transcriptions Complement copy gene transcriptions Complement-inverse copy gene transcriptions Consensus sequence gene transcriptions Copper response element gene transcriptions Core promoter gene transcriptions Coupling element gene transcriptions CRE box gene transcriptions Cytokinin response regulator gene transcriptions Cytoplasmic polyadenylation element gene transcriptions DAF-16-associated element gene transcriptions DAF-16 binding element gene transcriptions D box gene transcriptions Defense and stress-responsive element gene transcriptions Degenerate nucleotide gene transcriptions Dispersed promoter gene transcriptions Distal promoter gene transcriptions DNA melting gene transcriptions DNA damage response element gene transcriptions DNA replication-related element gene transcriptions Downstream core element gene transcriptions Downstream promoter element gene transcriptions Downstream TFIIB recognition element gene transcriptions DREB box gene transcriptions E2 box gene transcriptions EIF4E basal element gene transcriptions EIN3 binding site gene transcriptions Enhancer activity copy gene transcriptions E box gene transcriptions Element gene transcriptions Endoplasmic reticulum stress response element gene transcriptions Endosperm expression gene transcriptions Enhancer box gene transcriptions Estrogen response element gene transcriptions Ethylene responsive element gene transcriptions Factor II B recognition element gene transcriptions F box gene transcriptions Focused promoter gene transcriptions Forkhead box gene transcriptions Fur box gene transcriptions GAAC element gene transcriptions Gal4p gene transcriptions Γ-interferon activated sequence gene transcriptions GARE gene transcriptions GA responsive complex gene transcriptions GATA gene transcriptions G box gene transcriptions GC box gene transcriptions GCC box gene transcriptions Gcn4p gene transcriptions Gcr1p gene transcriptions Gene 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 Hex sequence gene transcriptions HMG box gene transcriptions HNF gene transcriptions Homeobox gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle 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 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 gene transcriptions 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 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