TATA box albumin family: Difference between revisions

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(Created page with "The '''TATA box''' (also called '''Goldberg-Hogness box''')<ref name=Lifton>{{ cite journal | author = R. P. Lifton, M. L. Goldberg, R. W. Karp, and D. S. Hogness | year = 1978 | title = The organization of the histone genes in Drosophila melanogaster: functional and evolutionary implications | url = https://symposium.cshlp.org/content/42/1047.extract | journal = Cold Spring Harbor Symposia on Quantitative Biology | volume = 42 | issue = | pages = 1047–51 | doi = 10.11...")
 
 
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|url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1955227/?tool=pubmed
|url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1955227/?tool=pubmed
| pmid = 17123746 }}</ref>
| pmid = 17123746 }}</ref>
==Atlantic salmon genes==
===Gene ID: 100136575===
"Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmoninae; Salmo"<ref name=RefSeq173>{{ cite web
|author=RefSeq
|title=alb1 serum albumin 1 [ Salmo salar (Atlantic salmon)
|publisher=ncbi.nlm.nih
|location=Bethsda, Maryland, USA
|date=30 November 2023
|url=http://www.ncbi.nlm.nih.gov/gene/173
|accessdate=2024-06-18 }}</ref>


==Human genes==
==Human genes==

Latest revision as of 19:48, 9 July 2024

The TATA box (also called Goldberg-Hogness box)[1] is a DNA sequence (cis-regulatory element) found in the promoter region of genes in archaea and eukaryotes;[2] approximately 24% of human genes contain a TATA box within the core promoter.[3]

Atlantic salmon genes

Gene ID: 100136575

"Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmoninae; Salmo"[4]

Human genes

"TATA-containing genes are more often highly regulated, such as by biotic or stress stimuli."[5] Only "∼10% of these TATA-containing promoters have the canonical TATA box (TATAWAWR)."[5]

"SRF-regulated genes of the actin/cytoskeleton/contractile family tend to have a TATA box."[6]

Different "TATA box sequences have different abilities to convey the activating signals of certain enhancers and activators in mammalian cells [...] and in yeast [...]."[6]

"SRF is a well established master regulator of the specific family of genes encoding the actin cytoskeleton and contractile apparatus [...], and we found that ~40% of the core promoters for these genes contain a TATA box, which is a significant enrichment compared to the low overall frequency of TATA-containing promoters in human and mouse genomes (...)."[6] "Global frequencies of core promoter types for human [9010 orthologous mouse-human promoter pairs with 1848 TATA-containing or 7162 TATA-less][7] genes with experimentally validated transcription start sites [are known from 2006]."[6] "The TATA box [...] has a consensus sequence of TATAWAAR [...]."[6] W = A or T and R = A or G. We "estimate that ~17% of promoters contain a TATA box".[7]

Gene ID: 173

"This gene is a member of the albumin gene family, which is comprised of four genes that localize to chromosome 4 in a tandem arrangement. These four genes encode structurally-related serum transport proteins that are known to be evolutionarily related. The protein encoded by this gene is regulated developmentally, expressed in the liver and secreted into the bloodstream."[4]

Families of TATA box genes

Acknowledgements

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

References

  1. R. P. Lifton, M. L. Goldberg, R. W. Karp, and D. S. Hogness (1978). "The organization of the histone genes in Drosophila melanogaster: functional and evolutionary implications". Cold Spring Harbor Symposia on Quantitative Biology. 42: 1047–51. doi:10.1101/SQB.1978.042.01.105. PMID 98262.
  2. Stephen T. Smale and James T. Kadonaga (July 2003). "The RNA Polymerase II Core Promoter" (PDF). Annual Review of Biochemistry. 72 (1): 449–79. doi:10.1146/annurev.biochem.72.121801.161520. PMID 12651739. Retrieved 2012-05-07.
  3. C Yang, E Bolotin, T Jiang, FM Sladek, E Martinez (March 2007). "Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters". Gene. 389 (1): 52–65. doi:10.1016/j.gene.2006.09.029. PMID 17123746.
  4. 4.0 4.1 RefSeq (30 November 2023). "alb1 serum albumin 1 [ Salmo salar (Atlantic salmon)". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-06-18.
  5. 5.0 5.1 Chuhu Yang, Eugene Bolotin, Tao Jiang, Frances M. Sladek, and Ernest Martinez (10 October 2006). "Prevalence of the Initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters". Gene. 389 (1): 52–65. doi:10.1016/j.gene.2006.09.029. PMID 17123746. Retrieved 2024-06-07.
  6. 6.0 6.1 6.2 6.3 6.4 Muyu Xu, Elsie Gonzalez-Hurtado, and Ernest Martinez (April 2016). "Core promoter-specific gene regulation: TATA box selectivity and Initiator-dependent bi-directionality of serum response factor-activated transcription". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1859 (4): 553–563. doi:10.1016/j.bbagrm.2016.01.005. Retrieved 2024-06-08.
  7. 7.0 7.1 Victor X Jin, Gregory AC Singer, Francisco J Agosto-Pérez, Sandya Liyanarachchi, and Ramana V Davuluri (2006). "Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs". BMC Bioinformatics. 7: 114. doi:10.1186/1471-2105-7-114. Retrieved 2024-06-09.

External links