TMEM50A
| TMEM50A | |||||||||||||||||||||||||||||||||||||||||||||||||||
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| Aliases | TMEM50A, IFNRC, SMP1, transmembrane protein 50A | ||||||||||||||||||||||||||||||||||||||||||||||||||
| External IDs | OMIM: 605348; MGI: 1919067; HomoloGene: 4469; GeneCards: TMEM50A; OMA:TMEM50A - orthologs | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Transmembrane protein 50A is a protein that in humans is encoded by the TMEM50A gene.[5][6][7]
This gene is located in the RH gene locus, between the RHD and RHCE genes. The function of its protein product is unknown; however, its sequence has potential transmembrane domains suggesting that it may be an integral membrane protein. Its position between the RH genes suggests that polymorphisms in this gene may be tightly linked to RH haplotypes and may contribute to selective pressure for or against certain RH haplotypes.[7]
Gene
The TMEM50A gene is located on chromosome 1 p36.11 in the human (homo sapiens) genome. Its mRNA sequence is 2284 base pairs in length and includes seven exons. The coding sequence is from base pairs 151 to 624.
Protein
The TMEM50A protein is 157 amino acids in length.
Cellular Location
PSORT II predicts that TMEM50A is most likely found in the cells plasma membrane or the endoplasmic reticulum.
Predicted properties
Through bioinformatic analysis several of TMEM50A's protein properties were predicted.
- Molecular Weight: 17.4 KDal[8]
- Isoelectric point: 5.483[9]
- Post-translational modification: Several post-translational modifications are predicted:
- Two serine phosphorylation sites found at amino acids 82 and 84 Residue[10]
- One possibleN-Linked Glycosylation Site located at amino acid 74 [10]
- One possible Tyrosine phosphorylation site
Structure
The exact structure of TMEM50A is unknown but through the use of several prediction programs, some of its most likely structural components can be assumed.
- TMHMM shows that TMEM50A has four transmembrane regions. This was further confirmed by similar results found in TMEM50A orthologs and the neutral charge found in these regions using SAPS program in Biology Workbench
- By using the PELE program in Biology Workbench along with comparing the results of known protein structures, it can be predicted that TMEM50A has:
- Two Alpha Helix structures
- Five Beta Sheets
Splice Sites
Alternative Splice sites were found by BLAT on the UCSC genome browser
TMEM50A has several alternative splices including:
- Removal of exon 2
- Removal of exons 2 and 3
- Removal of exons 2, 3, and 5
- Removal of exon 3
- Removal of exon 5
These alternative splice sites don't affect the reading frame of the sequence and thus may not alter the function of the protein.
Expression
TMEM50A is expressed in almost all human tissues, but evidence from EST profiles through NCBI, suggests that its expression may be slightly higher in parathyroid tissues and brain tissues. It also seems to be expressed higher during the neonate and juvenile development stages.
Interacting Proteins
There is one predicted protein that interacts with TMEM50A, C7orf43. This proteins gene is located on chromosome 7 open reading frame 43. Its function is also unknown.
Future Medical Applications
Investigation of several GEO profiles showed that TMEM50A is highly upregulated in late stage cervical cancer. This may suggest that TMEM50A has some function that may be causing or is caused directly by cervical cancer. Although few studies are available to confirm this idea, more studies may offer suggestions that use TMEM50A for treatment of late stage cervical cancer.
References
- ^ a b c GRCh38: Ensembl release 89: ENSG00000183726 – Ensembl, May 2017
- ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000028822 – Ensembl, May 2017
- ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ Flegel WA, Wagner FF (Dec 2000). "Molecular genetics of RH". Vox Sang. 78 Suppl 2: 109–15. PMID 10938938.
- ^ Wagner FF, Flegel WA (Aug 2000). "RHD gene deletion occurred in the Rhesus box". Blood. 95 (12): 3662–8. doi:10.1182/blood.V95.12.3662. PMID 10845894.
- ^ a b "Entrez Gene: TMEM50A transmembrane protein 50A".
- ^ Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S (March 1992). "Methods and algorithms for statistical analysis of protein sequences". Proceedings of the National Academy of Sciences of the United States of America. 89 (6): 2002–6. Bibcode:1992PNAS...89.2002B. doi:10.1073/pnas.89.6.2002. PMC 48584. PMID 1549558.
- ^ "PI Program (Isoelectric Point Prediction)". Archived from the original on 2008-10-26.
- ^ a b "UniProt Database".
Further reading
- Mehrle A, Rosenfelder H, Schupp I, et al. (2006). "The LIFEdb database in 2006". Nucleic Acids Res. 34 (Database issue): D415–8. doi:10.1093/nar/gkj139. PMC 1347501. PMID 16381901.
- Tao WA, Wollscheid B, O'Brien R, et al. (2005). "Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry". Nat. Methods. 2 (8): 591–8. doi:10.1038/nmeth776. PMID 16094384. S2CID 20475874.
- Wiemann S, Arlt D, Huber W, et al. (2004). "From ORFeome to Biology: A Functional Genomics Pipeline". Genome Res. 14 (10B): 2136–44. doi:10.1101/gr.2576704. PMC 528930. PMID 15489336.
- Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121–7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334.
- Clark HF, Gurney AL, Abaya E, et al. (2003). "The Secreted Protein Discovery Initiative (SPDI), a Large-Scale Effort to Identify Novel Human Secreted and Transmembrane Proteins: A Bioinformatics Assessment". Genome Res. 13 (10): 2265–70. doi:10.1101/gr.1293003. PMC 403697. PMID 12975309.
- Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. Bibcode:2002PNAS...9916899M. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
- Wagner FF, Flegel WA (2002). "RHCE represents the ancestral RH position, while RHD is the duplicated gene". Blood. 99 (6): 2272–3. doi:10.1182/blood-2001-12-0153. PMID 11902138.
- Simpson JC, Wellenreuther R, Poustka A, et al. (2001). "Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing". EMBO Rep. 1 (3): 287–92. doi:10.1093/embo-reports/kvd058. PMC 1083732. PMID 11256614.
- Wiemann S, Weil B, Wellenreuther R, et al. (2001). "Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs". Genome Res. 11 (3): 422–35. doi:10.1101/gr.GR1547R. PMC 311072. PMID 11230166.
- Hartley JL, Temple GF, Brasch MA (2001). "DNA Cloning Using In Vitro Site-Specific Recombination". Genome Res. 10 (11): 1788–95. doi:10.1101/gr.143000. PMC 310948. PMID 11076863.