FAM71E1

Last updated
GARIN5A
Identifiers
Aliases GARIN5A , family with sequence similarity 71 member E1, GARIL5, golgi associated RAB2 interactor 5A, FAM71E1
External IDs MGI: 1922788 HomoloGene: 19259 GeneCards: GARIN5A
Orthologs
SpeciesHumanMouse
Entrez

112703

75538

Ensembl

ENSG00000142530

ENSMUSG00000051113

UniProt

Q6IPT2

A1L3C1

RefSeq (mRNA)

NM_001308429
NM_138411

RefSeq (protein)

NP_001295358
NP_612420

Location (UCSC) Chr 19: 50.47 – 50.48 Mb Chr 7: 44.15 – 44.15 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

FAM71E1, also known as Family With Sequence Similarity 71 Member E1, is a protein that in humans is encoded by the FAM71E1 gene. [5] [6] It is thought to be ubiquitously expressed at low levels throughout the body, and it is conserved in vertebrates, particularly mammals and some reptiles. The protein is localized to the nucleus and can be exported to the cytoplasm.

Contents

Gene

Location

The gene is located on the minus strand at 19q13.33 and spans from 50,466,643 to 50,476,753. It is 10,070 bp long. [5] [6]

Gene Neighborhood

In humans, the gene is flanked by the following genes: [5] [6]

Location of FAM71E1 on minus f Chromstrand oosome 19 at q13.33. FAM71E1 Gene Location.png
Location of FAM71E1 on minus f Chromstrand oosome 19 at q13.33.

Promoter

The promoter of FAM71E1 is located on the minus strand from 50,476,094 to 50,477,946 . It is 1,853 bp long. [11]

Expression

The gene seems to be ubiquitously expressed at low levels throughout the body [12] [13] [14] but has prominent expression in the adult human testis, [15] followed by lower expression levels in the sperm, oocyte, and brain. [16] [17] [18] [19] [20] Age does not have an effect on its expression in the skeletal muscle of males or females. [21] Its expression is elevated prior to the differentiation of embryonic stem cells into pancreatic islet-like cells. [22]

Transcript

Isoforms

The FAM71E1 gene produces two isoforms from alternative splicing. Isoform 1 is 1281 bp long, and isoform 2 is slightly shorter at 1233 bp long. [23] Both transcript variants have 5 exons, 4 of which are coding exons. The third intron for the isoform 2 transcript is longer than the one found in isoform 1. [24]

Regulation

The FAM71E1 transcript is regulated by micro-RNAs, such as miR-149, miR-7, miR-125b, miR-125a-5p, miR192-5p, and miR-215. [25]

Protein

Properties

The protein from isoform 1 is 247 amino acids long with a molecular weight of 27.6 kDa. It has a charge of 5.0 and an isoelectric point of 8.9. [24] It has a domain of unknown function (DUF3699), which is conserved in eukaryotes and has no known pairwise interactions with other domains. [26] The structure of the protein has 3 alpha helices and 5 beta strands.

Localization

The protein is predicted to localize to the nucleus and thought to be mainly associated with the nucleoli fibrillar center. [27] It can also be exported to the cytoplasm. [14]

Homologs

Evolutionary tree of FAM71E1 paralogs and their associated peptide length FAM71E1 Paralogs.png
Evolutionary tree of FAM71E1 paralogs and their associated peptide length

Paralogs

The FAM71E1 gene is fast evolving. It has the following 8 paralogs: FAM71A, FAM71B, FAM71C, FAM71D, FAM71E2, FAM71F1, FAM71F2, and AC020922.1. FAM71D, FAM71E2 and AC0209221.1 are found in Amniotes and their last common ancestor with FAM71E1 was likely in the ancestor of the Sauria taxon, which includes reptiles and birds. The remaining paralogs are found in mammals and are expressed in organisms from the evolutionary descendants of the lobe-finned fish (Sarcopterygii). Their last common ancestor with FAM71E1 was Coelacanth ( Latimeria chalumnae ). [29]

Overview of FAM71E1 Paralogs [30]
ParalogAccession numberSequence length (aa)Sequence Identity (%)Sequence Similarity (%)
FAM71E1NM_001308429247100100
FAM71CNP_699195.124120.128.0
FAM71F1NP_115988.134416.324.2
FAM71F2NP_001012457.330915.423.8
FAM71DNP_775797.242212.016.5
AC020922.1Unavailable47211.116.3
FAM71ANP_705834.259410.814.5
FAM71BNP_570969.260510.213.9
FAM71E2NP_001138874.19226.89.0

Orthologs

Orthologs of FAM71E1 can be found only in vertebrates, primarily in placental mammals in the Boreoeutheria group and occasionally in a few reptilian species. Reptiles and marsupials are included in the distant homologs, while orthologs in placental animals such as rodents and primates are more closely related to FAM71E1. The gene history contains 27 duplication events and 1 splitting event. [29]

Overview of FAM71E1 Orthologs [30]
Genus and speciesCommon NameAccession numberLength (aa)Identity (%)Similarity (%)
Homo sapiensHumanNP_001295358247100100
Pan troglodytesChimpanzeeXP_0094343642479897
Microcebus murinusGray mouse lemurXP_012609669.12337982
Mus musculusHouse mouseNP_082445.12126872
Equus caballusHorseXP_023505998.11927679
Bos taurusCattleXP_0108133992277579
Panthera pardusLeopardXP_0192811032177176
Trichechus manatus latirostrisFlorida manateeXP_0043819042197376
Phascolarctos cinereusKoalaXP_0208275252316875
Python bivittatusBurmese pythonXP_0074231631675064
Anolis carolinensisGreen anoleXP_0168501311313748

Clinical Significance

Mutations

There are no disease-causing mutations associated with this gene, [31] and it is tolerant towards loss-of-function variants. [32]

Disease Associations

FAM71E1 has reduced expression in Type 2 diabetes patients and is likely not involved in the disease's pathophysiology. [33] Its expression is also altered in Parkinson's disease [34] and several cancers, such as non-triple negative ductal carcinoma in situ, [35] breast cancer, [36] pancreatic adenocarcinoma, and colorectal carcinoma. [34] It is a gene of interest in predicting susceptibility to pneumonia. [37]

Related Research Articles

<span class="mw-page-title-main">ITFG3</span> Protein-coding gene in the species Homo sapiens

Protein ITFG3 also known as family with sequence similarity 234 member A (FAM234A) is a protein that in humans is encoded by the ITFG3 gene. Here, the gene is explored as encoded by mRNA found in Homo sapiens. The FAM234A gene is conserved in mice, rats, chickens, zebrafish, dogs, cows, frogs, chimpanzees, and rhesus monkeys. Orthologs of the gene can be found in at least 220 organisms including the tropical clawed frog, pandas, and Chinese hamsters. The gene is located at 16p13.3 and has a total of 19 exons. The mRNA has a total of 3224 bp and the protein has 552 aa. The molecular mass of the protein produced by this gene is 59660 Da. It is expressed in at least 27 tissue types in humans, with the greatest presence in the duodenum, fat, small intestine, and heart.

<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">FAM63A</span> Protein-coding gene in the species Homo sapiens

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.

TMEM156 is a gene that encodes the transmembrane protein 156 (TMEM156) in Homo sapiens. It has the clone name of FLJ23235.

<span class="mw-page-title-main">TMEM176B</span> Protein-coding gene in the species Homo sapiens

Transmembrane Protein 176B, or TMEM176B is a transmembrane protein that in humans is encoded by the TMEM176B gene. It is thought to play a role in the process of maturation of dendritic cells.

Uncharacterized protein Chromosome 16 Open Reading Frame 71 is a protein in humans, encoded by the C16orf71 gene. The gene is expressed in epithelial tissue of the respiratory system, adipose tissue, and the testes. Predicted associated biological processes of the gene include regulation of the cell cycle, cell proliferation, apoptosis, and cell differentiation in those tissue types. 1357 bp of the gene are antisense to spliced genes ZNF500 and ANKS3, indicating the possibility of regulated alternate expression.

<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">C21orf58</span> Protein-coding gene in the species Homo sapiens

Chromosome 21 Open Reading Frame 58 (C21orf58) is a protein that in humans is encoded by the C21orf58 gene.

<span class="mw-page-title-main">C16orf46</span> Human gene

Chromosome 16 open reading frame 46 is a protein of yet to be determined function in Homo sapiens. It is encoded by the C16orf46 gene with NCBI accession number of NM_001100873. It is a protein-coding gene with an overlapping locus.

<span class="mw-page-title-main">Chromosome 9 open reading frame 43</span> Protein-coding gene in the species Homo sapiens

Chromosome 9 open reading frame 43 is a protein that in humans is encoded by the C9orf43 gene. The gene is also known as MGC17358 and LOC257169. C9orf43 contains DUF 4647 and a polyglutamine repeat region although protein function is not well understood.

<span class="mw-page-title-main">C9orf25</span> Protein-coding gene in the species Homo sapiens

Chromosome 9 open reading frame 25 (C9orf25) is a domain that encodes the FAM219A gene. The terms FAM219A and C9orf25 are aliases and can be used interchangeably. The function of this gene is not yet completely understood.

<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.

FAM71E2, also known as Family With Sequence Similarity 71 Member E2, is a protein that, in humans, is encoded by the FAM71E2 gene. Aliases include C19orf16, Protein FAM71E2, Chromosome 19 open reading frame 16, and Putative Protein FAM71E2. The gene is primarily conserved in mammals, but it is also conserved in two reptile species.

<span class="mw-page-title-main">C12orf24</span> Protein-coding gene in the species Homo sapiens

C12orf24 is a gene in humans that encodes a protein known as FAM216A. This gene is primarily expressed in the testis and brain, but has constitutive expression in 25 other tissues. FAM216A is an intracellular protein that has been predicted to reside within the nucleus of cells. The exact function of C12orf24 is unknown. FAM216A is highly expressed in Sertoli cells of the testis as well as different stage spermatids.

<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">FAM120AOS</span> Protein-coding gene in the species Homo sapiens

FAM120AOS, or family with sequence similarity 120A opposite strand, codes for uncharacterized protein FAM120AOS, which currently has no known function. The gene ontology describes the gene to be protein binding. Overall, it appears that the thyroid and the placenta are the two tissues with the highest expression levels of FAM120AOS across a majority of datasets.

<span class="mw-page-title-main">FAM98C</span> Gene

Family with sequence 98, member C or FAM98C is a gene that encodes for FAM98C has two aliases FLJ44669 and hypothetical protein LOC147965. FAM98C has two paralogs in humans FAM98A and FAM98B. FAM98C can be characterized for being a Leucine-rich protein. The function of FAM98C is still not defined. FAM98C has orthologs in mammals, reptiles, and amphibians and has a distant orhtologs in Rhinatrema bivittatum and Nanorana parkeri.

<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">TEKTIP1</span> Gene

TEKTIP1, also known as tektin-bundle interacting protein 1, is a protein that in humans is encoded by the TEKTIP1 gene.

<span class="mw-page-title-main">Chromosome 5 open reading frame 47</span> Human C5ORF47 Gene

Chromosome 5 Open Reading Frame 47, or C5ORF47, is a protein which, in humans, is encoded by the C5ORF47 gene. It also goes by the alias LOC133491. The human C5ORF47 gene is primarily expressed in the testis.

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000142530 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000051113 - 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. 1 2 3 "Human Gene FAM71E1 (ENST00000600100.5) Description and Page Index". genome.ucsc.edu. Retrieved 2018-02-20.
  6. 1 2 3 "FAM71E1 family with sequence similarity 71 member E1 [ Homo sapiens (human) ]". NCBI Gene.
  7. ↑ "SPIB Gene". www.genecards.org. Retrieved 2018-05-06.
  8. ↑ "MYBPC2 Gene". www.genecards.org. Retrieved 2018-05-06.
  9. ↑ "EMC10 Gene". www.genecards.org. Retrieved 2018-05-06.
  10. ↑ "JOSD2 Gene". www.genecards.org. Retrieved 2018-05-06.
  11. ↑ "Genomatix - NGS Data Analysis & Personalized Medicine". www.genomatix.de. Retrieved 2018-05-07.
  12. ↑ "FAM71E1- Multiple normal tissues". www.ncbi.nlm.nih.gov. Retrieved 2018-05-06.
  13. ↑ "FAM71E1- Normal tissues of diverse types (SHBW)". www.ncbi.nlm.nih.gov. Retrieved 2018-05-06.
  14. 1 2 Thierry-Mieg, Danielle; Thierry-Mieg, Jean. "AceView: Gene:FAM71E1, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView". www.ncbi.nlm.nih.gov. Retrieved 2018-02-20.
  15. ↑ Kwon JT, Ham S, Jeon S, Kim Y, Oh S, Cho C (2017-07-25). "Expression of uncharacterized male germ cell-specific genes and discovery of novel sperm-tail proteins in mice". PLOS ONE. 12 (7): e0182038. Bibcode:2017PLoSO..1282038K. doi: 10.1371/journal.pone.0182038 . PMC   5526581 . PMID   28742876.
  16. ↑ "Gene: FAM71E1 - ENSG00000142530". bgee.org. Retrieved 2018-05-06.
  17. ↑ "Expression Atlas entry on FAM71E1". www.ebi.ac.uk. Retrieved 2018-05-06.
  18. ↑ "Genevisible entry on FAM71E1". Genevisible.
  19. ↑ "Tissue expression of FAM71E1 - Summary - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2018-05-06.
  20. ↑ "EST Profile - Hs.448941". www.ncbi.nlm.nih.gov. Retrieved 2018-05-06.
  21. ↑ "FAM71E1- Age effect on the skeletal muscle". www.ncbi.nlm.nih.gov. Retrieved 2018-05-07.
  22. ↑ "FAM71E1- Pancreatic islet-like cell clusters derived from T3 embryonic stem cells". www.ncbi.nlm.nih.gov. Retrieved 2018-05-07.
  23. ↑ "Homo sapiens family with sequence similarity 71 member E1 (FAM71E1), t - Nucleotide - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2018-02-20.
  24. 1 2 "Transcript Summary on FAM71E1". Vega.
  25. ↑ "miRNA entry on FAM71E1". 34.236.212.39. Retrieved 2018-05-07.
  26. ↑ "Results for pfam12480". bioinf.umbc.edu. Retrieved 2018-05-07.
  27. ↑ "CALIPHO Bioinformatics". www.nextprot.org. SIB Swiss Institute of Bioinformatics.
  28. ↑ "Multiple Sequence Alignment - CLUSTALW". www.genome.jp. Kyoto University Bioinformatics Center. Retrieved 2018-05-06.
  29. 1 2 "Ensembl entry on FAM71E1 Gene Tree".
  30. 1 2 "Clustal Omega < Multiple Sequence Alignment < EMBL-EBI". www.ebi.ac.uk. Retrieved 2018-05-06.
  31. ↑ "Kann Laboratory- Domain Mapping of Disease Mutations entry on FAM71E1".
  32. ↑ "ExAC entry on FAM71E1". exac.broadinstitute.org. Retrieved 2018-05-06.
  33. ↑ "FAM71E1- Type 2 diabetes and role of hepatokines". www.ncbi.nlm.nih.gov.
  34. 1 2 Momcilovic O, Sivapatham R, Oron TR, Meyer M, Mooney S, Rao MS, Zeng X (May 2016). "Derivation, Characterization, and Neural Differentiation of Integration-Free Induced Pluripotent Stem Cell Lines from Parkinson's Disease Patients Carrying SNCA, LRRK2, PARK2, and GBA Mutations". PLOS ONE. 11 (5): e0154890. Bibcode:2016PLoSO..1154890M. doi: 10.1371/journal.pone.0154890 . PMC   4871453 . PMID   27191603.
  35. ↑ Brown J (2016). Immunohistochemical and genomic analysis of ductal carcinoma in situ of the human breast (PDF) (Ph.D.). King's College London.
  36. ↑ Nisha K (March 2017). Early Genomic Events Associated with Dissemination of Breast Cancer Cells (Ph.D.). University of Toronto. hdl:1807/77456.
  37. ↑ Hayden LP, Cho MH, McDonald MN, Crapo JD, Beaty TH, Silverman EK, Hersh CP (January 2017). "Susceptibility to Childhood Pneumonia: A Genome-Wide Analysis". American Journal of Respiratory Cell and Molecular Biology. 56 (1): 20–28. doi:10.1165/rcmb.2016-0101oc. PMC   5248961 . PMID   27508494.
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