FAM40A

FAM40A

FAM40A

Protein-coding gene in the species Homo sapiens

Protein FAM40A is a protein that is located on chromosome 1 in humans and is encoded by the FAM40A gene.[5][6][7]

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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.

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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. [1]
    GRCh38: Ensembl release 89: ENSG00000143093 – Ensembl, May 2017
  2. [2]
    GRCm38: Ensembl release 89: ENSMUSG00000014601 – Ensembl, May 2017
  3. [3]
    "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. [4]
    "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. [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. [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. [7]
    "Entrez Gene: FAM40A family with sequence similarity 40, member A".
  8. [8]
    pI/MW Tool
  9. [9]
    Transmembrane domain prediction
  10. [10]
    SignalP 3.0 Server
  11. [11]
    SOSUI System
  12. [12]
    Phyre v. 2.0[permanent dead link]
  13. [13]
    "RNA Folding Form". Archived from the original on 2015-08-18. Retrieved 2019-04-29.
  14. [14]
    miRBase
  15. [15]
    Yeast Gene FAR11 from Saccharomyces Genome Database
  16. [16]
    National Center for Biotechnology Information (NCBI) Protein
  17. [17]
    NCBI BLAST: Basic Local Alignment Search Tool
  18. [18]
    BLAT Search Genome[permanent dead link]
  19. [19]
    European Bioinformatics Institute
  20. [20]
    EST Profile for FAM40A
  21. [21]
    "Genomatix". Archived from the original on 2021-12-02. Retrieved 2011-05-10.
  22. [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. [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.

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