FAM40A

STRIP1
Identifiers
Aliases	STRIP1 , FAM40A, FAR11A, striatin interacting protein 1
External IDs	OMIM: 617918 MGI: 2443884 HomoloGene: 35064 GeneCards: STRIP1
Gene location (Human) Chr. Chromosome 1 (human) [1] Band 1p13.3 Start 110,031,577 bp [1] End 110,074,641 bp [1]
Gene location (Mouse) Chr. Chromosome 3 (mouse) [2] Band 3|3 F2.3 Start 107,519,848 bp [2] End 107,539,010 bp [2]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in pancreatic ductal cell ganglionic eminence bone marrow cells tibialis anterior muscle stromal cell of endometrium canal of the cervix smooth muscle tissue spleen prefrontal cortex germinal epithelium Top expressed in hand lens ganglionic eminence neural tube secondary oocyte lip superior cervical ganglion cerebellar cortex otolith organ foot More reference expression data BioGPS n/a
Gene ontology Molecular function protein binding molecular function protein kinase binding Cellular component extracellular exosome nucleus cytoplasm cytosol Biological process regulation of cell morphogenesis cortical actin cytoskeleton organization Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 85369 229707 Ensembl ENSG00000143093 ENSMUSG00000014601 UniProt Q5VSL9 Q8C079 RefSeq (mRNA) NM_001270768 NM_033088 NM_153563 RefSeq (protein) NP_001257697 NP_149079 NP_705791 Location (UCSC) Chr 1: 110.03 – 110.07 Mb Chr 3: 107.52 – 107.54 Mb PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

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

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]}

Prediction of the orientation of the transmembrane domains of FAM40A

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

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

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]

Predicted FAM40A expression in different tissues of the body

Transcription Regulation

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

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

1. GRCh38: Ensembl release 89: ENSG00000143093 - Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000014601 - Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. 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.
6. 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.
7. "Entrez Gene: FAM40A family with sequence similarity 40, member A".
8. pI/MW Tool
9. Transmembrane domain prediction
10. SignalP 3.0 Server
11. SOSUI System
12. Phyre v. 2.0 ^{[ permanent dead link ]}
13. "RNA Folding Form". Archived from the original on 2015-08-18. Retrieved 2019-04-29.
14. miRBase
15. Yeast Gene FAR11 from Saccharomyces Genome Database
16. National Center for Biotechnology Information (NCBI) Protein
17. NCBI BLAST: Basic Local Alignment Search Tool
18. BLAT Search Genome ^{[ permanent dead link ]}
19. European Bioinformatics Institute
20. EST Profile for FAM40A
21. Genomatix
22. 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.
23. 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

• 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.