FAM40A

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Template:Short description Template:Cs1 config Template:Infobox gene Protein FAM40A is a protein that is located on chromosome 1 in humans and is encoded by the FAM40A gene.[1][2][3]

Characteristics and secondary structure

FAM40A has an isoelectric point of 5.92 and a molecular weight of 95,575 daltons.[4] It is predicted to have three transmembrane domains, making it a transmembrane protein.[5] 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.[6][7]

File:Transmembrane.png
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.[8] 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.[9] Two miRNAs are predicted to bind to two of the stem-loop structures present in the 3' UTR region.[10]

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.[11][12]

The following table represents a small selection of orthologs found using searches in BLAST[13] and BLAT.[14] 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 [12]) 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 [14] 812 96.1% 100%
Ailuropoda melanoleuca Panda From BLAT [14] 823 $96.2 100%
Oryzias latipes Medaka From BLAT [14] 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.[15] FAM40A has also been shown to be expressed in high levels in the mammary glands, brain, thymus, mouth and the testes.[16] It has also been shown to be expressed in high levels in mammary gland tumors, leukemia cells, and germ cell tumors.[16]

File:Expression data.png
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.[17] The SOX transcription factors are predicted to bind to the promoter region of the FAM40A gene, possibly indicating a role in sex determination.[17]

Interactions

FAM40A has been shown to interact with RP6-213H19.1,[18] STRN,[18] PDCD10,[18] TRAF3IP3,[18] STRN3,[18] PPP2R1A,[18] MOBKL3,[18] CTTNBP2NL,[18] STK24[18][19] and PPP2CA.[18]

References

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  1. ↑ Script error: No such module "Citation/CS1".
  2. ↑ Script error: No such module "Citation/CS1".
  3. ↑ Script error: No such module "citation/CS1".
  4. ↑ pI/MW Tool
  5. ↑ Transmembrane domain prediction
  6. ↑ SignalP 3.0 Server
  7. ↑ SOSUI System
  8. ↑ Phyre v. 2.0Script error: No such module "Unsubst".
  9. ↑ Script error: No such module "citation/CS1".
  10. ↑ miRBase
  11. ↑ Yeast Gene FAR11 from Saccharomyces Genome Database
  12. ↑ a b National Center for Biotechnology Information (NCBI) Protein
  13. ↑ NCBI BLAST: Basic Local Alignment Search Tool
  14. ↑ a b c d BLAT Search GenomeScript error: No such module "Unsubst".
  15. ↑ European Bioinformatics Institute
  16. ↑ a b EST Profile for FAM40A
  17. ↑ a b Script error: No such module "citation/CS1".
  18. ↑ a b c d e f g h i j Script error: No such module "Citation/CS1".
  19. ↑ Script error: No such module "Citation/CS1".

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Further reading

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