FAM71D

Last updated
GARIN2
Identifiers
Aliases GARIN2 , C14orf54, family with sequence similarity 71 member D, golgi associated RAB2 interactor family member 2, GARI-L1, FAM71D, GARI-L2
External IDs MGI: 1918147 HomoloGene: 49887 GeneCards: GARIN2
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_173526
NM_001395907

NM_027597
NM_029069

RefSeq (protein)

NP_775797

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

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

Gene Neighbors.png [23]

Homology

[24]

Genus and SpeciesCommon NameAccession NumberSeq. LengthSeq. IdentitySeq. Similarity
Pan troglodytesChimpanzeeXP_0011335797.2422 a97%98%
Chlorocebus SabaeusGreen MonkeyXP_007985246.1422 a94%97%
Macaca mulattaRhesus macaqueXP_001102828.2422 a94%96%
Camelus dromedariusDromedaryXP_5010975019.1476 a70%81%
Vicogna pacosAlpacaXP_006207055.1573 a70%80%
Bos taurusCattleXP_010807832.1400 a68%79%
Odobenus rosmarus divergensWalrusXP_004397632.1412 a70%81%
Pteropus vampyrusLarge flying foxXP_011384479.1527 a73%80%
Felis catusCatXP_011281587.1398 a74%82%
Mus musculusMouseNP_083345.1440 a59%74%
Oryctolagus cuniculusEuropean rabbitXP_008270069.1397 a75%84%
Capra hircusGoatXP_005686047.1397 a72%82%
Pantholops hodgsoniiTibetan antelopeXP_005961615.1397 a71%82%
Ornicus orcaKiller whaleXP_004262188.1391 a72%81%
Tursiops trucatusBottlenose dolphinXP_004322689.1391 a72%81%
Phseter catodonSperm whaleXP_007119740.1397 a72%82%
Equus caballusHorseXP_005605311.1386 a69%79%
Ailuropoda melanoleucaGiant pandaXP_0112304461.1417 a71%81%
Fukomys demarensisDimaraland mole-ratXP_010643626.1412 a74%83%

Protein

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

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

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

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

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]

Expression FAM71D.png [36]

Clinical Relevance

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.

Related Research Articles

<span class="mw-page-title-main">CCDC113</span> Protein-coding gene in the species Homo sapiens

Coiled-coil domain-containing protein 113 also known as HSPC065, GC16Pof6842 and GC16P044152, is a protein that in humans is encoded by the CCDC113 gene. The human CCDC113 gene is located on chromosome 16q21 and encodes 5,304 base pairs of mRNA and 377 amino acids.

<span class="mw-page-title-main">FAM107B</span> Protein-coding gene in the species Homo sapiens

FAM107B is a gene found in humans. It is located on the minus strand of chromosome 10, p13, which is on the short arm of the chromosome. It has other alias names, such as C10orf45, FLJ45505, MGC11034 and MGC90261. The gene contains a conserved domain, DUF1151, which is a family that consists of several eukaryotic proteins of unknown function. FAM107B is expressed in most tissues in the human body without there being a high frequency in any one tissue. It is found in all stages of human development.

<span class="mw-page-title-main">Fam158a</span> Protein-coding gene in the species Homo sapiens

UPF0172 protein FAM158A, also known as c14orf122 or CGI112, is a protein that in humans is encoded by the FAM158A gene located on chromosome 14q11.2.

<span class="mw-page-title-main">Ccdc78</span> Protein-coding gene in the species Homo sapiens

Coiled-coil domain-containing 78 (CCDC78) is a protein in humans encoded by the CCDC78 gene. It has several aliases including C16orf25, FLJ34512, CNM4, and JFP10. It is located on the (-) strand on chromosome 16 (16p13.3). Its gene neighborhood includes NARFL, HAGHL, FAM173A, and METRN. The CCDC78 gene is 10,892 base pairs long, and the protein contains 438 amino acids. The protein weighs approximately 4.852 KDal. There are several isoforms, including one indicated with a unique congenital myopathy. Several expression profiles show it has ubiquitous expression at moderate levels. Although no paralogs exist several orthologs do.

<span class="mw-page-title-main">FAM185A</span> Gene of the species Homo sapiens

The FAM185A is a protein that in humans is encoded by the FAM185A gene. The FAM185A gene is found on the positive strand of Chromosome 7 at 7q22.1. The gene begins 102,389,399bp from the p-terminus of the chromosome and ends at 102,449,672bp from the p-terminus; it covers a total of 73,308 basepairs. The protein encoded by this gene is characterized by the presence of multiple copies of DUF4098 near its C-terminus. It is described as a Long Interspersed Nuclear Element (LINE), a subclass of penaeid repetitive elements (PREs).

<span class="mw-page-title-main">FAM214A</span>

Protein FAM214A, also known as protein family with sequence similarity 214, A (FAM214A) is a protein that, in humans, is encoded by the FAM214A gene. FAM214A is a gene with unknown function found at the q21.2-q21.3 locus on Chromosome 15 (human). The protein product of this gene has two conserved domains, one of unknown function (DUF4210) and another one called Chromosome_Seg. Although the function of the FAM214A protein is uncharacterized, both DUF4210 and Chromosome_Seg have been predicted to play a role in chromosome segregation during meiosis.

<span class="mw-page-title-main">FAM167A</span> Protein-coding gene in the species Homo sapiens

Family with sequence similarity 167, member A is a protein in humans that is encoded by the FAM167A gene located on chromosome 8. FAM167A and its paralogs are protein encoding genes containing the conserved domain DUF3259, a protein of unknown function. FAM167A has many orthologs in which the domain of unknown function is highly conserved.

<span class="mw-page-title-main">FAM63A</span>

Family with sequence similarity 63, member A is a protein that, in humans, is encoded by the FAM63A gene. It is located on the minus strand of chromosome 1 at locus 1q21.3.

<span class="mw-page-title-main">C7orf31</span>

Chromosome Seven Open Reading Frame 31 (C7orf31) is a protein that in humans is encoded by the C7orf31 gene on chromosome seven.

<span class="mw-page-title-main">FAM71F2</span> Protein-coding gene in the species Homo sapiens

FAM71F2 or Family with Sequence Similarity 71 member F2 is a protein that in humans is encoded by the Family with Sequence Similarity 71 member F2 gene. This gene is highly active in the reproductive tissues, specifically the testis, and may serve as a potential biomarker for determining metastatic testicular cancer.

<span class="mw-page-title-main">C12orf60</span>

Uncharacterized protein C12orf60 is a protein that in humans is encoded by the C12orf60 gene. The gene is also known as LOC144608 or MGC47869. The protein lacks transmembrane domains and helices, but it is rich in alpha-helices. It is predicted to localize in the nucleus.

<span class="mw-page-title-main">C19orf44</span> Mammalian protein found in Homo sapiens

Chromosome 19 open reading frame 44 is a protein that in humans is encoded by the C19orf44 gene. C19orf44 is an uncharacterized protein with an unknown function in humans. C19orf44 is non-limiting implying that the protein exists in other species besides human. The protein contains one domain of unknown function (DUF) that is highly conserved throughout its orthologs. This protein is most highly expressed in the testis and ovary, but also has significant expression in the thyroid and parathyroid. Other names for this protein include: LOC84167.

LOC101928193 is a protein which in humans is encoded by the LOC101928193 gene. There are no known aliases for this gene or protein. Similar copies of this gene, called orthologs, are known to exist in several different species across mammals, amphibians, fish, mollusks, cnidarians, fungi, and bacteria. The human LOC101928193 gene is located on the long (q) arm of chromosome 9 with a cytogenic location at 9q34.2. The molecular location of the gene is from base pair 133,189,767 to base pair 133,192,979 on chromosome 9 for an mRNA length of 3213 nucleotides. The gene and protein are not yet well understood by the scientific community, but there is data on its genetic makeup and expression. The LOC101928193 protein is targeted for the cytoplasm and has the highest level of expression in the thyroid, ovary, skin, and testes in humans.

<span class="mw-page-title-main">SMCO3</span>

Single-pass membrane and coiled-coil domain-containing protein 3 is a protein that is encoded in humans by the SMCO3 gene.

<span class="mw-page-title-main">C7orf50</span>

C7orf50 is a gene in humans that encodes a protein known as C7orf50. This gene is ubiquitously expressed in the kidneys, brain, fat, prostate, spleen, among 22 other tissues and demonstrates low tissue specificity. C7orf50 is conserved in chimpanzees, Rhesus monkeys, dogs, cows, mice, rats, and chickens, along with 307 other organisms from mammals to fungi. This protein is predicted to be involved with the import of ribosomal proteins into the nucleus to be assembled into ribosomal subunits as a part of rRNA processing. Additionally, this gene is predicted to be a microRNA (miRNA) protein coding host gene, meaning that it may contain miRNA genes in its introns and/or exons.

<span class="mw-page-title-main">FAM214B</span> Protein-coding gene in the species Homo sapiens

The FAM214B, also known as protein family with sequence similarity 214, B (FAM214B) is a protein that, in humans, is encoded by the FAM214B gene located on the human chromosome 9. The protein has 538 amino acids. The gene contain 9 exon. There has been studies that there are low expression of this gene in patients with major depression disorder. In most organisms such as mammals, amphibians, reptiles, and birds, there are high levels of gene expression in the bone marrow and blood. For humans in fetal development, FAM214B is mostly expressed in the brains and bone marrow.

<span class="mw-page-title-main">FAM166C</span>

Family with Sequence Similarity 166, member C (FAM166C), is a protein encoded by the FAM166C gene. The protein FAM166C is localized in the nucleus. It has a calculated molecular weight of 23.29 kDa. It also contains DUF2475, a protein of unknown function from amino acid 19–85. The FAM166C protein is nominally expressed in the testis, stomach, and thyroid.

<span class="mw-page-title-main">C12orf50</span> Protein encoding gene C12orf50

Chromosome 12 Open Reading Frame 50 (C12orf50) is a protein-encoding gene which in humans encodes for the C12orf50 protein. The accession id for this gene is NM_152589. The location of C12orf50 is 12q21.32. It covers 55.42 kb, from 88429231 to 88373811, on the reverse strand. Some of the neighboring genes to C12orf50 are RPS4XP15, LOC107984542, and C12orf29. RPS4XP15 is upstream C12orf50 and is on the same strand. LOC107984542 and C12orf29 are both downstream. LOC107984542 is on the opposite strand while C12orf29 is on the same strand. C12orf50 has six isoforms. This page is focusing on isoform X1. C12orf50 isoform X1 is 1711 nucleotides long and has a protein with a length of 414 aa.

<span class="mw-page-title-main">CXorf65</span> Gene on human chromosome X

Human uncharacterized protein CXorf65 is encoded by the gene CXorf65, which is located on the minus strand of chromosome X. Its transcript is 834 nucleotides long and consists of 6 exons. The translated protein is 183 amino acids in length. with a molecular weight of 21.3 kDa

<span class="mw-page-title-main">C13orf46</span> C13of46 Gene and Protein

Chromosome 13 Open Reading Frame 46 is a protein which in humans is encoded by the C13orf46 gene. In humans, C13orf46 is ubiquitously expressed at low levels in tissues, including the lungs, stomach, prostate, spleen, and thymus. This gene encodes eight alternatively spliced mRNA transcript, which produce five different protein isoforms.

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