Sterol response element gene transcriptions: Difference between revisions

Latest revision as of 03:22, 1 March 2021

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

"These genomic sequences were analysed for the presence of sterol-response elements (SRE) motif (5'-TCGTATA-3') [...] using the NCBI BLAST tool."^[1]

Human genes

Consensus sequences

Consensus sequence for the sterol regulatory element is AGCAGATTGCG or CAGCAGATTGCG.^[2]

SRE (Branco) samplings

Copying the SRE consensus: TCGTATA and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG and no location between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TCGTATA (starting with SuccessablesSREB.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 TCGTATA, 0.
positive strand, negative direction, looking for TCGTATA, 0.
positive strand, positive direction, looking for TCGTATA, 0.
negative strand, positive direction, looking for TCGTATA, 0.
complement, negative strand, negative direction, looking for AGCATAT, 0.
complement, positive strand, negative direction, looking for AGCATAT, 0.
complement, positive strand, positive direction, looking for AGCATAT, 0.
complement, negative strand, positive direction, looking for AGCATAT, 0.
inverse complement, negative strand, negative direction, looking for TATACGA, 0.
inverse complement, positive strand, negative direction, looking for TATACGA, 0.
inverse complement, positive strand, positive direction, looking for TATACGA, 0.
inverse complement, negative strand, positive direction, looking for TATACGA, 0.
inverse negative strand, negative direction, looking for ATATGCT, 0.
inverse positive strand, negative direction, looking for ATATGCT, 0.
inverse positive strand, positive direction, looking for ATATGCT, 0.
inverse negative strand, positive direction, looking for ATATGCT, 0.

SRE (Yao) samplings

Copying the SRE consensus: NAGCAGATTGCG and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG and no location between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence NAGCAGATTGCG (starting with SuccessablesSREY.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 NAGCAGATTGCG, 0.
positive strand, negative direction, looking for NAGCAGATTGCG, 0.
positive strand, positive direction, looking for NAGCAGATTGCG, 0.
negative strand, positive direction, looking for NAGCAGATTGCG, 0.
complement, negative strand, negative direction, looking for NTCATCTAACGC, 0.
complement, positive strand, negative direction, looking for NTCATCTAACGC, 0.
complement, positive strand, positive direction, looking for NTCATCTAACGC, 0.
complement, negative strand, positive direction, looking for NTCATCTAACGC, 0.
inverse complement, negative strand, negative direction, looking for CGCAATCTACTN, 0.
inverse complement, positive strand, negative direction, looking for CGCAATCTACTN, 0.
inverse complement, positive strand, positive direction, looking for CGCAATCTACTN, 0.
inverse complement, negative strand, positive direction, looking for CGCAATCTACTN, 0.
inverse negative strand, negative direction, looking for GCGTTAGACGAN, 0.
inverse positive strand, negative direction, looking for GCGTTAGACGAN, 0.
inverse positive strand, positive direction, looking for GCGTTAGACGAN, 0.
inverse negative strand, positive direction, looking for GCGTTAGACGAN, 0.

Acknowledgements

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

References

↑ J. Branco, M. Ola, R. M. Silva, E. Fonseca, N. C. Gomes, C. Martins-Cruz, A. P. Silva, A. Silva-Dias, C. Pina-Vaz, C. Erraught, L. Brennan, A. G. Rodrigues, G. Butler and I. M. Miranda (August 2017). "Impact of ERG3 mutations and expression of ergosterol genes controlled by UPC2 and NDT80 in Candida parapsilosis azole resistance". Clinical Microbiology and Infection. 23 (8): 575.e1–575.e8. doi:10.1016/j.cmi.2017.02.002. PMID 28196695. Retrieved 5 September 2020.
↑ D. W. Yao, J. Luo, Q. Y. He, J. Li, H. Wang, H. B. Shi, H. F. Xu, M. Wang and J. J. Loor (May 2016). "Characterization of the liver X receptor-dependent regulatory mechanism of goat stearoyl-coenzyme A desaturase 1 gene by linoleic acid". Journal of Dairy Science. 99 (5): 3945–3957. doi:10.3168/jds.2015-10601. PMID 26947306. Retrieved 5 September 2020.

External links

[Branco-1] J. Branco, M. Ola, R. M. Silva, E. Fonseca, N. C. Gomes, C. Martins-Cruz, A. P. Silva, A. Silva-Dias, C. Pina-Vaz, C. Erraught, L. Brennan, A. G. Rodrigues, G. Butler and I. M. Miranda (August 2017). "Impact of ERG3 mutations and expression of ergosterol genes controlled by UPC2 and NDT80 in Candida parapsilosis azole resistance". Clinical Microbiology and Infection. 23 (8): 575.e1–575.e8. doi:10.1016/j.cmi.2017.02.002. PMID 28196695. Retrieved 5 September 2020.

[Yao2016-2] D. W. Yao, J. Luo, Q. Y. He, J. Li, H. Wang, H. B. Shi, H. F. Xu, M. Wang and J. J. Loor (May 2016). "Characterization of the liver X receptor-dependent regulatory mechanism of goat stearoyl-coenzyme A desaturase 1 gene by linoleic acid". Journal of Dairy Science. 99 (5): 3945–3957. doi:10.3168/jds.2015-10601. PMID 26947306. Retrieved 5 September 2020.

[1]

[2]

@@ Line 20: / Line 20: @@
 ==Consensus sequences==
-Consensus sequence for the sterol regulatory element is AGCAGATTGCG or CAGCAGATTGCG.<ref name=Yao2016/>
+Consensus sequence for the sterol regulatory element is AGCAGATTGCG or CAGCAGATTGCG.<ref name=Yao2016>{{ cite journal
+|author=D. W. Yao, J. Luo, Q. Y. He, J. Li, H. Wang, H. B. Shi, H. F. Xu, M. Wang and J. J. Loor
+|title=Characterization of the liver X receptor-dependent regulatory mechanism of goat stearoyl-coenzyme A desaturase 1 gene by linoleic acid
+|journal=Journal of Dairy Science
+|date=May 2016
+|volume=99
+|issue=5
+|pages=3945-3957
+|url=https://www.sciencedirect.com/science/article/pii/S0022030216300273
+|arxiv=
+|bibcode=
+|doi=10.3168/jds.2015-10601
+|pmid=26947306
+|accessdate=5 September 2020 }}</ref>
-==Samplings==
+==SRE (Branco) samplings==
-Copying the SRE consensus: 5'-TCGTATA-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG and no location between ZSCAN22 and A1BG as can be found by the computer programs.
+Copying the SRE consensus: TCGTATA and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG and no location between ZSCAN22 and A1BG as can be found by the computer programs.
-Copying the SRE consensus: 5'-CAGCAGATTGCG-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG and no location between ZSCAN22 and A1BG as can be found by the computer programs.
+For the Basic programs testing consensus sequence TCGTATA (starting with SuccessablesSREB.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 TCGTATA, 0.
+# positive strand, negative direction, looking for TCGTATA, 0.
+# positive strand, positive direction, looking for TCGTATA, 0.
+# negative strand, positive direction, looking for TCGTATA, 0.
+# complement, negative strand, negative direction, looking for AGCATAT, 0.
+# complement, positive strand, negative direction, looking for AGCATAT, 0.
+# complement, positive strand, positive direction, looking for AGCATAT, 0.
+# complement, negative strand, positive direction, looking for AGCATAT, 0.
+# inverse complement, negative strand, negative direction, looking for TATACGA, 0.
+# inverse complement, positive strand, negative direction, looking for TATACGA, 0.
+# inverse complement, positive strand, positive direction, looking for TATACGA, 0.
+# inverse complement, negative strand, positive direction, looking for TATACGA, 0.
+# inverse negative strand, negative direction, looking for ATATGCT, 0.
+# inverse positive strand, negative direction, looking for ATATGCT, 0.
+# inverse positive strand, positive direction, looking for ATATGCT, 0.
+# inverse negative strand, positive direction, looking for ATATGCT, 0.
+==SRE (Yao) samplings==
+Copying the SRE consensus: NAGCAGATTGCG and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG and no location between ZSCAN22 and A1BG as can be found by the computer programs.
+For the Basic programs testing consensus sequence NAGCAGATTGCG (starting with SuccessablesSREY.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 NAGCAGATTGCG, 0.
+# positive strand, negative direction, looking for NAGCAGATTGCG, 0.
+# positive strand, positive direction, looking for NAGCAGATTGCG, 0.
+# negative strand, positive direction, looking for NAGCAGATTGCG, 0.
+# complement, negative strand, negative direction, looking for NTCATCTAACGC, 0.
+# complement, positive strand, negative direction, looking for NTCATCTAACGC, 0.
+# complement, positive strand, positive direction, looking for NTCATCTAACGC, 0.
+# complement, negative strand, positive direction, looking for NTCATCTAACGC, 0.
+# inverse complement, negative strand, negative direction, looking for CGCAATCTACTN, 0.
+# inverse complement, positive strand, negative direction, looking for CGCAATCTACTN, 0.
+# inverse complement, positive strand, positive direction, looking for CGCAATCTACTN, 0.
+# inverse complement, negative strand, positive direction, looking for CGCAATCTACTN, 0.
+# inverse negative strand, negative direction, looking for GCGTTAGACGAN, 0.
+# inverse positive strand, negative direction, looking for GCGTTAGACGAN, 0.
+# inverse positive strand, positive direction, looking for GCGTTAGACGAN, 0.
+# inverse negative strand, positive direction, looking for GCGTTAGACGAN, 0.
+==Acknowledgements==
+The content on this page was first contributed by: Henry A. Hoff.
 ==See also==
 {{div col|colwidth=20em}}
+* [[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]]
 * [[Complex locus A1BG and ZNF497]]
-* [[Transcription factor]]
 {{Div col end}}
@@ Line 38: / Line 98: @@
 ==External links==
+* [http://www.genome.jp/ GenomeNet KEGG database]
+* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI]
+* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search]
+* [http://www.ncbi.nlm.nih.gov/ncbisearch/ NCBI Site Search]
+* [http://www.ncbi.nlm.nih.gov/pccompound PubChem Public Chemical Database]
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@@ Line 43: / Line 108: @@
 <!-- footer categories -->
-[[Category:Resources last modified in September 2020]]
+[[Category:Resources last modified in February 2021]]

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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 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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 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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