FAM40A
| STRIP1 | |||||||||||||||||||||||||||||||||||||||||||||||||||
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| Aliases | STRIP1, FAM40A, FAR11A, striatin interacting protein 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| External IDs | OMIM: 617918; MGI: 2443884; HomoloGene: 35064; GeneCards: STRIP1; OMA:STRIP1 - orthologs | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Protein FAM40A is a protein that is located on chromosome 1 in humans and is encoded by the FAM40A gene.[5][6][7]
Characteristics and secondary structure
[edit]FAM40A has an isoelectric point of 5.92 and a molecular weight of 95,575 daltons.[8] It is predicted to have three transmembrane domains, making it a transmembrane protein.[9] FAM40A does not contain a signal peptide and is also predicted to bind to DNA, possibly making it a membrane protein in the nuclear membrane.[10][11]
The secondary structure of FAM40A is predicted to contain twenty-six alpha helices and two beta sheets.[12] The 5' untranslated region of FAM40A is predicted to contain one stem-loop and the 3' untranslated region is predicted to contain eight stem-loop structures.[13] Two miRNAs are predicted to bind to two of the stem-loop structures present in the 3' UTR region.[14]
Homology
[edit]FAM40A has no paralogs. However, it does have orthologs stretching all the way back to yeast. It has been suggested that FAM40A is a homolog to the yeast gene FAR11, which is involved in the recovery from cell cycle arrest.[15][16]
The following table represents a small selection of orthologs found using searches in BLAST[17] and BLAT.[18] This is by no means a comprehensive list, however it does show the vast diversity of species where FAM40A orthologs are found.
| Scientific Name | Common Name | Accession number (from NCBI [16]) | Sequence Length | Percent Identity | Percent Similarity |
|---|---|---|---|---|---|
| Homo sapiens | Human | NP_149079 | 837 | - | - |
| Pongo abelii | Sumatran orangutan | XP_002810520 | 837 | 99.6% | 100% |
| Sus scrofa | Pig | XP_003125904 | 837 | 98.8% | 100% |
| Equus caballus | Horse | XP_001493762 | 837 | 98.8% | 100% |
| Mus musculus | Mouse | NP_705791 | 837 | 98% | 100% |
| Rattus norvegicus | Rat | XP_001068288 | 837 | 97.8% | 100% |
| Monodelphis domestica | Gray short-tailed opossum | XP_001372588 | 843 | 95.4% | 100% |
| Danio rerio | Zebra fish | XP_001918929 | 813 | 83.4% | 98% |
| Canis lupus familiaris | Dog | From BLAT [18] | 812 | 96.1% | 100% |
| Ailuropoda melanoleuca | Panda | From BLAT [18] | 823 | $96.2 | 100% |
| Oryzias latipes | Medaka | From BLAT [18] | 751 | 78.4% | 96% |
| Xenopus (Silurana) tropicalis | Western clawed frog | NP_001027483 | 819 | 86.4% | 96% |
| Aedes aegypti | Yellow-fever mosquito | XP_001658692 | 829 | 51.2% | 97% |
| Tribolium castaneum | Red flour beetle | XP_001815164 | 817 | 57.4% | 97% |
| Hydra magnipapillata | Hydra hydrozoan | XP_002164866 | 830 | 44% | 97% |
| Ciona intestinalis | Sea squirt | XP_002130558 | 867 | 46.4% | 97% |
| Pediculus humanus corporis | Human lice | XP_002425964 | 808 | 52.7% | 97% |
| Nasonia vitripennis | Jewel wasp | XP_001603859 | 802 | 52.7% | 97% |
| Drosophila erecta | Fruit fly | XP_001971743 | 882 | 45.2% | 97% |
| Saccharomyces cerevisiae | Bakers yeast | NP_014272 | 953 | 18.9% | 97% |
Expression
[edit]FAM40A is expressed in high levels during the blastocyst, eight-cell stage, and fetal stages of development.[19] FAM40A has also been shown to be expressed in high levels in the mammary glands, brain, thymus, mouth and the testes.[20] It has also been shown to be expressed in high levels in mammary gland tumors, leukemia cells, and germ cell tumors.[20]
Transcription Regulation
[edit]FAM40A is predicted to have a promoter region 789 base pairs upstream of the start of transcription.[21] The SOX transcription factors are predicted to bind to the promoter region of the FAM40A gene, possibly indicating a role in sex determination.[21]
Interactions
[edit]FAM40A has been shown to interact with RP6-213H19.1,[22] STRN,[22] PDCD10,[22] TRAF3IP3,[22] STRN3,[22] PPP2R1A,[22] MOBKL3,[22] CTTNBP2NL,[22] STK24[22][23] and PPP2CA.[22]
References
[edit]- ^ a b c GRCh38: Ensembl release 89: ENSG00000143093 – Ensembl, May 2017
- ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000014601 – 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.
- ^ Nagase T, Kikuno R, Hattori A, Kondo Y, Okumura K, Ohara O (Feb 2001). "Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 7 (6): 347–55. doi:10.1093/dnares/7.6.347. PMID 11214970.
- ^ Kemp HA, Sprague GF Jr (Feb 2003). "Far3 and five interacting proteins prevent premature recovery from pheromone arrest in the budding yeast Saccharomyces cerevisiae". Mol Cell Biol. 23 (5): 1750–63. doi:10.1128/MCB.23.5.1750-1763.2003. PMC 151714. PMID 12588993.
- ^ "Entrez Gene: FAM40A family with sequence similarity 40, member A".
- ^ pI/MW Tool
- ^ Transmembrane domain prediction
- ^ SignalP 3.0 Server
- ^ SOSUI System
- ^ Phyre v. 2.0[permanent dead link]
- ^ "RNA Folding Form". Archived from the original on 2015-08-18. Retrieved 2019-04-29.
- ^ miRBase
- ^ Yeast Gene FAR11 from Saccharomyces Genome Database
- ^ a b National Center for Biotechnology Information (NCBI) Protein
- ^ NCBI BLAST: Basic Local Alignment Search Tool
- ^ a b c d BLAT Search Genome[permanent dead link]
- ^ European Bioinformatics Institute
- ^ a b EST Profile for FAM40A
- ^ a b "Genomatix". Archived from the original on 2021-12-02. Retrieved 2011-05-10.
- ^ a b c d e f g h i j Goudreault M, D'Ambrosio Lisa M, Kean Michelle J, Mullin Michael J, Larsen Brett G, Sanchez Amy, Chaudhry Sidharth, Chen Ginny I, Sicheri Frank, Nesvizhskii Alexey I, Aebersold Ruedi, Raught Brian, Gingras Anne-Claude (Jan 2009). "A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein". Mol. Cell. Proteomics. 8 (1): 157–71. doi:10.1074/mcp.M800266-MCP200. PMC 2621004. PMID 18782753.
- ^ Ewing RM, Chu Peter, Elisma Fred, Li Hongyan, Taylor Paul, Climie Shane, McBroom-Cerajewski Linda, Robinson Mark D, O'Connor Liam, Li Michael, Taylor Rod, Dharsee Moyez, Ho Yuen, Heilbut Adrian, Moore Lynda, Zhang Shudong, Ornatsky Olga, Bukhman Yury V, Ethier Martin, Sheng Yinglun, Vasilescu Julian, Abu-Farha Mohamed, Lambert Jean-Philippe, Duewel Henry S, Stewart Ian I, Kuehl Bonnie, Hogue Kelly, Colwill Karen, Gladwish Katharine, Muskat Brenda, Kinach Robert, Adams Sally-Lin, Moran Michael F, Morin Gregg B, Topaloglou Thodoros, Figeys Daniel (2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931.
Further reading
[edit]- 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.
- Ota T, Suzuki Y, Nishikawa T, et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40–5. doi:10.1038/ng1285. PMID 14702039.
- Beausoleil SA, Jedrychowski M, Schwartz D, et al. (2004). "Large-scale characterization of HeLa cell nuclear phosphoproteins". Proc. Natl. Acad. Sci. U.S.A. 101 (33): 12130–5. Bibcode:2004PNAS..10112130B. doi:10.1073/pnas.0404720101. PMC 514446. PMID 15302935.
- 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.
- Gregory SG, Barlow KF, McLay KE, et al. (2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315–21. Bibcode:2006Natur.441..315G. doi:10.1038/nature04727. PMID 16710414.
- Beausoleil SA, Villén J, Gerber SA, et al. (2006). "A probability-based approach for high-throughput protein phosphorylation analysis and site localization". Nat. Biotechnol. 24 (10): 1285–92. doi:10.1038/nbt1240. PMID 16964243. S2CID 14294292.
- Olsen JV, Blagoev B, Gnad F, et al. (2006). "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks". Cell. 127 (3): 635–48. doi:10.1016/j.cell.2006.09.026. PMID 17081983. S2CID 7827573.
- Ewing RM, Chu P, Elisma F, et al. (2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931.