FAM40A

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

STRIP1
Identifiers
AliasesSTRIP1, FAM40A, FAR11A, striatin interacting protein 1
External IDsOMIM: 617918 MGI: 2443884 HomoloGene: 35064 GeneCards: STRIP1
Gene location (Human)
Chr.Chromosome 1 (human)[1]
Band1p13.3Start110,031,577 bp[1]
End110,074,641 bp[1]
Orthologs
SpeciesHumanMouse
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 MbChr 3: 107.61 – 107.63 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

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 NameCommon NameAccession number (from NCBI [16])Sequence LengthPercent IdentityPercent Similarity
Homo sapiensHumanNP_149079837--
Pongo abeliiSumatran orangutanXP_00281052083799.6%100%
Sus scrofaPigXP_00312590483798.8%100%
Equus caballusHorseXP_00149376283798.8%100%
Mus musculusMouseNP_70579183798%100%
Rattus norvegicusRatXP_00106828883797.8%100%
Monodelphis domesticaGray short-tailed opossumXP_00137258884395.4%100%
Danio rerioZebra fishXP_00191892981383.4%98%
Canis lupus familiarisDogFrom BLAT [18]81296.1%100%
Ailuropoda melanoleucaPandaFrom BLAT [18]823$96.2100%
Oryzias latipesMedakaFrom BLAT [18]75178.4%96%
Xenopus (Silurana) tropicalisWestern clawed frogNP_00102748381986.4%96%
Aedes aegyptiYellow-fever mosquitoXP_00165869282951.2%97%
Tribolium castaneumRed flour beetleXP_00181516481757.4%97%
Hydra magnipapillataHydra hydrozoanXP_00216486683044%97%
Ciona intestinalisSea squirtXP_00213055886746.4%97%
Pediculus humanus corporisHuman liceXP_00242596480852.7%97%
Nasonia vitripennisJewel waspXP_00160385980252.7%97%
Drosophila erectaFruit flyXP_00197174388245.2%97%
Saccharomyces cerevisiaeBakers yeastNP_01427295318.9%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]

gollark: `<**~` - REAL HASKELL OPERATOR
gollark: `<**->` you.
gollark: See? Random.
gollark: Best RNG.
gollark: ```c#include <stdio.h>int main() { int i; printf("%d", i);}```

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
  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
  19. European Bioinformatics Institute
  20. EST Profile for FAM40A
  21. Genomatix
  22. Goudreault, Marilyn; 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, Rob M; 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
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