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FAM71D

From Wikipedia, the free encyclopedia
GARIN2
Identifiers
AliasesGARIN2, C14orf54, family with sequence similarity 71 member D, golgi associated RAB2 interactor family member 2, GARI-L1, FAM71D, GARI-L2
External IDsMGI: 1918147; HomoloGene: 49887; GeneCards: GARIN2; OMA:GARIN2 - orthologs
Orthologs
SpeciesHumanMouse
Entrez

161142

70897

Ensembl

ENSG00000172717

ENSMUSG00000056987

UniProt

Q8N9W8

D3YV92

RefSeq (mRNA)

NM_173526
NM_001395907

NM_027597
NM_029069

RefSeq (protein)

NP_775797

Location (UCSC)Chr 14: 67.19 – 67.23 MbChr 12: 78.69 – 78.73 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

FAM71D, also known as chromosome 14 open reading frame 54 (C14orf54), is a protein that in humans is encoded by the FAM71D gene on Chromosome 14.[5] Orthologs of FAM71D reach as far back in evolution to Reptiles, however, it is closer in homology to primates than any other orthologs. FAM71D has 6 paralogs: FAM71A, FAM71B, FAM71C, FAM71E1, FAM71F1, and FAM71F2[6] which encode a protein of unknown function.

Gene

[edit]

In humans, FAM71D is located at 14q23.3 and stretches between positions 67189393 and 67228550 (span 39157 bp).[7] It codes for at least 10 unique human protein isoforms: the primary isoform (422 aa; also denoted X1),[8][9][10][11] isoform X2 (417 aa),[12] isoform X3 (413 aa),[13] isoform X4 (400 aa),[14] isoform X5 (399 aa),[15] isoform X6 (398 aa),[16] isoform X7 (392 aa),[17][18] isoform X8 (389 aa),[19] isoform X9 (347 aa),[20] isoform X10 (336 aa)[21] In humans, FAM71D codes for an mRNA strand that is 1790 base pairs long. The human mRNA is composed of a 5' untranslated region that is 290 bases long and a 3' untranslated region that is 231 bases long[22] The gene has the following neighbours on the same chromosome:

MPP5: MAGUK p55 subfamily member 5 plays a role in tumour suppression and receptor clustering
GPHN: Gephyrin plays a role in anchoring inhibitory neurotransmitter receptors to postsynaptic cytoskeleton
AT6V1D: V-type proton ATPase subunit D, an enzyme that mediates acidifcation of eukaryotic intracellular organelles
SF3B44P1: Splicing Factor 3b, Subunit 4 Pseudogene 1
LOC101927920: Probable Ribosome Biogenesis Protein RLP24-Like
LOC105370538: Uncharacterized protein
LOC105370541: Uncharacterized protein

[23]

Homology

[edit]

[24]

Genus and Species Common Name Accession Number Seq. Length Seq. Identity Seq. Similarity
Pan troglodytes Chimpanzee XP_0011335797.2 422 a 97% 98%
Chlorocebus Sabaeus Green Monkey XP_007985246.1 422 a 94% 97%
Macaca mulatta Rhesus macaque XP_001102828.2 422 a 94% 96%
Camelus dromedarius Dromedary XP_5010975019.1 476 a 70% 81%
Vicogna pacos Alpaca XP_006207055.1 573 a 70% 80%
Bos taurus Cattle XP_010807832.1 400 a 68% 79%
Odobenus rosmarus divergens Walrus XP_004397632.1 412 a 70% 81%
Pteropus vampyrus Large flying fox XP_011384479.1 527 a 73% 80%
Felis catus Cat XP_011281587.1 398 a 74% 82%
Mus musculus Mouse NP_083345.1 440 a 59% 74%
Oryctolagus cuniculus European rabbit XP_008270069.1 397 a 75% 84%
Capra hircus Goat XP_005686047.1 397 a 72% 82%
Pantholops hodgsonii Tibetan antelope XP_005961615.1 397 a 71% 82%
Ornicus orca Killer whale XP_004262188.1 391 a 72% 81%
Tursiops trucatus Bottlenose dolphin XP_004322689.1 391 a 72% 81%
Phseter catodon Sperm whale XP_007119740.1 397 a 72% 82%
Equus caballus Horse XP_005605311.1 386 a 69% 79%
Ailuropoda melanoleuca Giant panda XP_0112304461.1 417 a 71% 81%
Fukomys demarensis Dimaraland mole-rat XP_010643626.1 412 a 74% 83%

Protein

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The primary protein encoded by FAM71D in humans is 422 amino acids long with a molecular weight of 47076 Da.[25] The protein is part of a functionally uncharacterized family of proteins (pfam 12480) with a domain of unknown function DUF3699.[26]

Structure

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Several tools are available to predict the secondary structure of a protein. One tool that combines the results of few of them is PELE on SDSC Biology WorkBench.[27] According to this tool, the protein's secondary structure is mostly alpha helices, beta stands and coiled-coiled domains.

Post Translational Modifications

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Like any other protein, this protein undergoes post-translational modifications. FAM71D is predicted to contain 2 nuclear export signals,[28] and lacks both a signal peptide[29] and transmembrane domains.[30]

Interactions

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FAM71D interacts with PGK2,[31] TUBA3C,[31] and HSPB1.[32] FAM71D is also predicted to interact with the following proteins using STRING:[33]

THUMPD3: THUMP domain containing 3
CCDC170: Coiled-coil domain containing 170
KLH10: Kelch-like 10
TMEM48: Transmembrane protein 48
SHCBP1L: SHC SH2-domain binding protein
ASNA1: arsA arsenite transporter
PPP1R16A: Protein Phosphate 1, regulatory subunit 16A
IZUMO1: izumo sperm-egg fusion 1
SF3B2: Splicing factor 3b, submit 2
TUBB4B: Tubulin, beta 4B class IVb

Expression

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FAM71D is primarily expressed in the testis of humans only expressed during the adult developmental stage.[34] GEO microarray data also supports the expression of FAM71D in humans[35]

[36]

Clinical Relevance

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No studies have directly associated FAM71D protein with certain diseases. However, using NCBI GEO Profiles, FAM71D was found to be over-expressed in patients with unruptured intracranial aneurysms.

References

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  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000172717 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000056987 – 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. ^ "NCBI Protein".
  6. ^ "NCBI BLAST (National Center for Biotechnology Information)".
  7. ^ "NCBI Gene".
  8. ^ "NCBI Protein (National Center for Biotechnology Information)".
  9. ^ "NCBI Protein (National Center for Biotechnology Information)".
  10. ^ "NCBI Protein (National Center for Biotechnology Information)".
  11. ^ "NCBI Protein (National Center for Biotechnology Information)".
  12. ^ "NCBI Protein (National Center for Biotechnology Information)".
  13. ^ "NCBI Protein (National Center for Biotechnology Information)".
  14. ^ "NCBI Protein (National Center for Biotechnology Information)".
  15. ^ "NCBI Protein (National Center for Biotechnology Information)".
  16. ^ "NCBI Protein (National Center for Biotechnology Information)".
  17. ^ "NCBI Protein (National Center for Biotechnology Information)".
  18. ^ "NCBI Protein (National Center for Biotechnology Information)".
  19. ^ "NCBI Protein (National Center for Biotechnology Information)".
  20. ^ "NCBI Protein (National Center for Biotechnology Information)".
  21. ^ "NCBI Protein (National Center for Biotechnology Information)".
  22. ^ "NCBI Nucleotide (National Center for Biotechnology Information)". 4 May 2019.
  23. ^ "NCBI Gene (National Center for Biotechnology Information)".
  24. ^ "NCBI Blast (National Center for Biotechnology Information)".
  25. ^ "PhosphositePlus".
  26. ^ "NCBI Conserved Domains (National Center for Biotechnology Information)".
  27. ^ "Biology Workbench".[permanent dead link‍]
  28. ^ "CBS (Center of Biological Sequence Analysis)".
  29. ^ "CBS (Center of Biological Sequence Analysis)".
  30. ^ "CBS (Center of Biological Sequence Analysis)".
  31. ^ a b "BioGrid3.3".
  32. ^ "Mentha".
  33. ^ "STRING 10".
  34. ^ "NCBI UniGene (National Center for Biotechnology Information)".
  35. ^ "NCBI UniGene (National Center for Biotechnology Information)".
  36. ^ "NCBI Gene (National Center for Biotechnology Information)".

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