TATA box immunoglobulin like domain containing family: Difference between revisions

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|date=July 2008
|date=July 2008
|url=http://www.ncbi.nlm.nih.gov/gene/3383
|url=http://www.ncbi.nlm.nih.gov/gene/3383
|accessdate=2024-06-27 }}</ref> This gene has a TATA box at -14 "TATAAAG" -8 and a MTE+.<ref name=Jin/>
|accessdate=2024-08-01 }}</ref> This gene has a TATA box at -14 "TATAAAG" -8 and a MTE+.<ref name=Jin/>
 
===Gene ID: 3386===
 
"This gene encodes the Landsteiner-Wiener (LW) blood group antigen(s) that belongs to the immunoglobulin (Ig) superfamily, and that shares similarity with the intercellular adhesion molecule (ICAM) protein family. This ICAM protein contains 2 Ig-like C2-type domains and binds to the leukocyte adhesion LFA-1 protein. The molecular basis of the LW(A)/LW(B) blood group antigens is a single aa variation at position 100; Gln-100=LW(A) and Arg-100=LW(B). Alternative splicing results in multiple transcript variants encoding distinct isoforms."<ref name=RefSeq3386>{{ cite web
|author=RefSeq
|title=ICAM4 intercellular adhesion molecule 4 (Landsteiner-Wiener blood group) [ Homo sapiens ]
|publisher=National Center for Biotechnology Information, U.S. National Library of Medicine
|location=8600 Rockville Pike, Bethesda MD, 20894 USA
|date=July 2008
|url=http://www.ncbi.nlm.nih.gov/gene/3386
|accessdate=2024-08-01 }}</ref> This gene has no TATA box in its core promoter but has an INR+ and a MTE-.<ref name=Jin/>


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

Revision as of 02:43, 2 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: 1

"The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins."[7]

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."[8] 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."[9] 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."[10] 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: 3383

"This gene encodes a cell surface glycoprotein which is typically expressed on endothelial cells and cells of the immune system. It binds to integrins of type CD11a / CD18, or CD11b / CD18 and is also exploited by Rhinovirus as a receptor."[11] This gene has a TATA box at -14 "TATAAAG" -8 and a MTE+.[6]

Gene ID: 3386

"This gene encodes the Landsteiner-Wiener (LW) blood group antigen(s) that belongs to the immunoglobulin (Ig) superfamily, and that shares similarity with the intercellular adhesion molecule (ICAM) protein family. This ICAM protein contains 2 Ig-like C2-type domains and binds to the leukocyte adhesion LFA-1 protein. The molecular basis of the LW(A)/LW(B) blood group antigens is a single aa variation at position 100; Gln-100=LW(A) and Arg-100=LW(B). Alternative splicing results in multiple transcript variants encoding distinct isoforms."[12] This gene has no TATA box in its core promoter but has an INR+ and a MTE-.[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."[13] 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.[14]

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])."[15] 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]

Gene ID: 10223

"The glycoprotein encoded by this gene is a cell surface antigen that is expressed in greater than 95% of human colon cancers. The open reading frame encodes a 319-amino acid polypeptide having a putative secretory signal sequence and 3 potential glycosylation sites. The predicted mature protein has a 213-amino acid extracellular region, a single transmembrane domain, and a 62-amino acid intracellular tail. The sequence of the extracellular region contains 2 domains characteristic of the CD2 subgroup of the immunoglobulin (Ig) superfamily."[16] In version BC069789 there is no TATA box, but there is an INR-, a MTE+ and DPE+.[6] In another version of the same version, there is an apparent TATA box at -34 "TATTATT" -28 with an INR+ and MTE- downstream.

Gene ID: 84824

"This gene encodes a protein similar to receptors for the Fc fragment of gamma immunoglobulin (IgG). These receptors, referred to as FCGRs, mediate the destruction of IgG-coated antigens and of cells induced by antibodies. This encoded protein is selectively expressed in B cells, and may be involved in their development. This protein may also be involved in the development of lymphomas. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene."[17] This gene has no TATA box in its core promoter but it does have an INR-, MTE+ and a DPE+.[6]

Gene ID: 115350

"This gene encodes a member of the immunoglobulin receptor superfamily and is one of several Fc receptor-like glycoproteins clustered on the long arm of chromosome 1. The encoded protein contains three extracellular C2-like immunoglobulin domains, a transmembrane domain and a cytoplasmic domain with two immunoreceptor-tyrosine activation motifs. This protein may play a role in the regulation of cancer cell growth. Alternative splicing results in multiple transcript variants."[18] This gene has an INR+ and a MTE+.[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. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 6.11 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 (July 2008). "A1BG alpha-1-B glycoprotein [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.
  8. ↑ RefSeq (August 2011). "FCER1A Fc epsilon receptor Ia [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.
  9. ↑ RefSeq (July 2008). "FCGR1A Fc gamma receptor Ia [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.
  10. ↑ RefSeq (June 2010). "FCGR2B Fc gamma receptor IIb [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.
  11. ↑ RefSeq (July 2008). "ICAM1 intercellular adhesion molecule 1 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2024-08-01.
  12. ↑ RefSeq (July 2008). "ICAM4 intercellular adhesion molecule 4 (Landsteiner-Wiener blood group) [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2024-08-01.
  13. ↑ RefSeq (September 2010). "CILP cartilage intermediate layer protein [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.
  14. ↑ HGNC (2024). "CILP cartilage intermediate layer protein [ Homo sapiens ]". Farmington, Connecticut, USA: genenames.org. Retrieved 2024-07-31.
  15. ↑ OMIM (July 2010). "FCMR Fc mu receptor [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.
  16. ↑ RefSeq (July 2008). "GPA33 glycoprotein A33 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-08-01.
  17. ↑ RefSeq (August 2011). "FCRLA Fc receptor like A [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.
  18. ↑ RefSeq (April 2009). "FCRL1 Fc receptor like 1 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-31.

External links


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