TATA box immunoglobulin like domain containing family: Difference between revisions

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|url=http://www.ncbi.nlm.nih.gov/gene/2209
|url=http://www.ncbi.nlm.nih.gov/gene/2209
|accessdate=2024-07-31 }}</ref> In version CR591922 there is an apparent TATA+ at -31 "TATGAGC" -25, with an INR- and MTE+ downstream, whereas version X14355 has an INR- and a MTE+ downstream, or an INR+ and a DPE+.<ref name=Jin/>
|accessdate=2024-07-31 }}</ref> In version CR591922 there is an apparent TATA+ at -31 "TATGAGC" -25, with an INR- and MTE+ downstream, whereas version X14355 has an INR- and a MTE+ downstream, or an INR+ and a DPE+.<ref name=Jin/>
===Gene ID: 2213===
"The protein encoded by this gene is a low affinity receptor for the Fc region of immunoglobulin gamma complexes. The encoded protein is involved in the phagocytosis of immune complexes and in the regulation of antibody production by B-cells. Variations in this gene may increase susceptibilty to systemic lupus erythematosus (SLE). Several transcript variants encoding different isoforms have been found for this gene."<ref name=RefSeq2213>{{ cite web
|author=RefSeq
|title=FCGR2B Fc gamma receptor IIb [ Homo sapiens ]
|publisher=ncbi.nlm.nih
|location=Bethsda, Maryland, USA
|date=June 2010
|url=http://www.ncbi.nlm.nih.gov/gene/2213
|accessdate=2024-07-31 }}</ref> This gene version CR592864 has an alleged TATA box at -35 "GAACATT" -29 with an INR- and MTE+ downstream, whereas version M90736 has an INR- and DPE-.<ref name=Jin/>


===Gene ID: 8483===
===Gene ID: 8483===

Revision as of 06:22, 1 August 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]

Human genes

Main article: Human genes

"TATA-containing genes are more often highly regulated, such as by biotic or stress stimuli."[4] Only "∼10% of these TATA-containing promoters have the canonical TATA box (TATAWAWR)."[4]

"SRF-regulated genes of the actin/cytoskeleton/contractile family tend to have a TATA box."[5]

Different "TATA box sequences have different abilities to convey the activating signals of certain enhancers and activators in mammalian cells [...] and in yeast [...]."[5]

"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 (...)."[5] "Global frequencies of core promoter types for human [9010 orthologous mouse-human promoter pairs with 1848 TATA-containing or 7162 TATA-less][6] genes with experimentally validated transcription start sites [are known from 2006]."[5] "The TATA box [...] has a consensus sequence of TATAWAAR [...]."[5] W = A or T and R = A or G. We "estimate that ~17% of promoters contain a TATA box".[6]

Gene ID: 2205

"The immunoglobulin epsilon receptor (IgE receptor) is the initiator of the allergic response. When two or more high-affinity IgE receptors are brought together by allergen-bound IgE molecules, mediators such as histamine that are responsible for allergy symptoms are released. This receptor is comprised of an alpha subunit, a beta subunit, and two gamma subunits. The protein encoded by this gene represents the alpha subunit."[7] In version AB059236 there is an INR-, whereas version L14075 has -34 "AAGCCTA" -28 as a TATA-, an INR- and a DPE+ downstream.[6]

Gene ID: 2209

"This gene encodes a protein that plays an important role in the immune response. This protein is a high-affinity Fc-gamma receptor. The gene is one of three related gene family members located on chromosome 1."[8] In version CR591922 there is an apparent TATA+ at -31 "TATGAGC" -25, with an INR- and MTE+ downstream, whereas version X14355 has an INR- and a MTE+ downstream, or an INR+ and a DPE+.[6]

Gene ID: 2213

"The protein encoded by this gene is a low affinity receptor for the Fc region of immunoglobulin gamma complexes. The encoded protein is involved in the phagocytosis of immune complexes and in the regulation of antibody production by B-cells. Variations in this gene may increase susceptibilty to systemic lupus erythematosus (SLE). Several transcript variants encoding different isoforms have been found for this gene."[9] This gene version CR592864 has an alleged TATA box at -35 "GAACATT" -29 with an INR- and MTE+ downstream, whereas version M90736 has an INR- and DPE-.[6]

Gene ID: 8483

"Major alterations in the composition of the cartilage extracellular matrix occur in joint disease, such as osteoarthrosis. This gene encodes the cartilage intermediate layer protein (CILP), which increases in early osteoarthrosis cartilage. The encoded protein was thought to encode a protein precursor for two different proteins; an N-terminal CILP and a C-terminal homolog of NTPPHase, however, later studies identified no nucleotide pyrophosphatase phosphodiesterase (NPP) activity. The full-length and the N-terminal domain of this protein was shown to function as an IGF-1 antagonist. An allelic variant of this gene has been associated with lumbar disc disease."[10] This gene has a TATA box at -30 "TATATAA" -24, INR- and MTE+.[6]

CILP and A1BG are in the HGNC gene group (Immunoglobulin like domain containing) of the Immunoglobulin superfamily domain containing.[11]

Gene ID: 9214

"Fc receptors specifically bind to the Fc region of immunoglobulins (Igs) to mediate the unique functions of each Ig class. FAIM3 encodes an Fc receptor for IgM (see MIM 147020) (Kubagawa et al., 2009 [PubMed 19858324]; Shima et al., 2010 [PubMed 20042454])."[12] In version BC006401, at the TATA box position there is no TATA box and downstream an INR- and a DPE-, whereas version NM_005449 has -29 "CTCTCTT" -23 as TATA- and an INR- downstream.[6]

Families of TATA box genes

Main article: 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 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.
  5. ↑ 5.0 5.1 5.2 5.3 5.4 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.
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 6.6 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.
  7. ↑ RefSeq (August 2011). "FCER1A Fc epsilon receptor Ia [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.
  8. ↑ RefSeq (July 2008). "FCGR1A Fc gamma receptor Ia [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.
  9. ↑ RefSeq (June 2010). "FCGR2B Fc gamma receptor IIb [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.
  10. ↑ RefSeq (September 2010). "CILP cartilage intermediate layer protein [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.
  11. ↑ HGNC (2024). "CILP cartilage intermediate layer protein [ Homo sapiens ]". Farmington, Connecticut, USA: genenames.org. Retrieved 2024-07-31.
  12. ↑ OMIM (July 2010). "FCMR Fc mu receptor [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.

External links


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