FAM71E1
GARIN5A | |||||||||||||||||||||||||||||||||||||||||||||||||||
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Aliases | GARIN5A, family with sequence similarity 71 member E1, GARIL5, golgi associated RAB2 interactor 5A, FAM71E1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
External IDs | MGI: 1922788; HomoloGene: 19259; GeneCards: GARIN5A; OMA:GARIN5A - orthologs | ||||||||||||||||||||||||||||||||||||||||||||||||||
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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.
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 Neighbohood
In humans, the gene is flanked by the following genes:[5][6]
- SPIB: putative oncogene that is active in hematopoietic cells [7]
- MYBPC2: encodes a structural protein and is actively expressed in striated muscle cells [8]
- EMC10: encodes a protein of unknown function [9]
- JOSD2: encodes a protein involved in de-ubiquitination [10]
![](http://upload.wikimedia.org/wikipedia/commons/thumb/9/90/FAM71E1_Gene_Location.png/220px-FAM71E1_Gene_Location.png)
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
![](http://upload.wikimedia.org/wikipedia/commons/thumb/f/f6/FAM71E1_Paralogs.png/220px-FAM71E1_Paralogs.png)
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]
Paralog | Accession number | Sequence length (aa) | Sequence Identity (%) | Sequence Similarity (%) |
FAM71E1 | NM_001308429 | 247 | 100 | 100 |
FAM71C | NP_699195.1 | 241 | 20.1 | 28.0 |
FAM71F1 | NP_115988.1 | 344 | 16.3 | 24.2 |
FAM71F2 | NP_001012457.3 | 309 | 15.4 | 23.8 |
FAM71D | NP_775797.2 | 422 | 12.0 | 16.5 |
AC020922.1 | Unavailable | 472 | 11.1 | 16.3 |
FAM71A | NP_705834.2 | 594 | 10.8 | 14.5 |
FAM71B | NP_570969.2 | 605 | 10.2 | 13.9 |
FAM71E2 | NP_001138874.1 | 922 | 6.8 | 9.0 |
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]
Genus and species | Common Name | Accession number | Length (aa) | Identity (%) | Similarity (%) |
Homo sapiens | Human | NP_001295358 | 247 | 100 | 100 |
Pan troglodytes | Chimpanzee | XP_009434364 | 247 | 98 | 97 |
Microcebus murinus | Gray mouse lemur | XP_012609669.1 | 233 | 79 | 82 |
Mus musculus | House mouse | NP_082445.1 | 212 | 68 | 72 |
Equus caballus | Horse | XP_023505998.1 | 192 | 76 | 79 |
Bos taurus | Cattle | XP_010813399 | 227 | 75 | 79 |
Panthera pardus | Leopard | XP_019281103 | 217 | 71 | 76 |
Trichechus manatus latirostris | Florida manatee | XP_004381904 | 219 | 73 | 76 |
Phascolarctos cinereus | Koala | XP_020827525 | 231 | 68 | 75 |
Python bivittatus | Burmese python | XP_007423163 | 167 | 50 | 64 |
Anolis carolinensis | Green anole | XP_016850131 | 131 | 37 | 48 |
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]
References
- ^ a b c GRCh38: Ensembl release 89: ENSG00000142530 – Ensembl, May 2017
- ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000051113 – Ensembl, May 2017
- ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ a b c "Human Gene FAM71E1 (ENST00000600100.5) Description and Page Index". genome.ucsc.edu. Retrieved 2018-02-20.
- ^ a b c "FAM71E1 family with sequence similarity 71 member E1 [ Homo sapiens (human) ]". NCBI Gene.
- ^ "SPIB Gene". www.genecards.org. Retrieved 2018-05-06.
- ^ "MYBPC2 Gene". www.genecards.org. Retrieved 2018-05-06.
- ^ "EMC10 Gene". www.genecards.org. Retrieved 2018-05-06.
- ^ "JOSD2 Gene". www.genecards.org. Retrieved 2018-05-06.
- ^ "Genomatix - NGS Data Analysis & Personalized Medicine". www.genomatix.de. Retrieved 2018-05-07.
- ^ "FAM71E1- Multiple normal tissues". www.ncbi.nlm.nih.gov. Retrieved 2018-05-06.
- ^ "FAM71E1- Normal tissues of diverse types (SHBW)". www.ncbi.nlm.nih.gov. Retrieved 2018-05-06.
- ^ a b mieg@ncbi.nlm.nih.gov, Danielle Thierry-Mieg and Jean Thierry-Mieg, NCBI/NLM/NIH. "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.
{{cite web}}
: CS1 maint: multiple names: authors list (link) - ^ 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.
{{cite journal}}
: CS1 maint: unflagged free DOI (link) - ^ "Gene: FAM71E1 - ENSG00000142530". bgee.org. Retrieved 2018-05-06.
- ^ "Expression Atlas entry on FAM71E1". www.ebi.ac.uk. Retrieved 2018-05-06.
- ^ "Genevisible entry on FAM71E1". Genevisible.
- ^ "Tissue expression of FAM71E1 - Summary - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2018-05-06.
- ^ Group, Schuler. "EST Profile - Hs.448941". www.ncbi.nlm.nih.gov. Retrieved 2018-05-06.
{{cite web}}
:|last=
has generic name (help) - ^ "FAM71E1- Age effect on the skeletal muscle". www.ncbi.nlm.nih.gov. Retrieved 2018-05-07.
- ^ "FAM71E1- Pancreatic islet-like cell clusters derived from T3 embryonic stem cells". www.ncbi.nlm.nih.gov. Retrieved 2018-05-07.
- ^ "Homo sapiens family with sequence similarity 71 member E1 (FAM71E1), t - Nucleotide - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2018-02-20.
- ^ a b "Transcript Summary on FAM71E1". Vega.
- ^ "miRNA entry on FAM71E1". 34.236.212.39. Retrieved 2018-05-07.
- ^ "Results for pfam12480". bioinf.umbc.edu. Retrieved 2018-05-07.
- ^ "CALIPHO Bioinformatics". www.nextprot.org. SIB Swiss Institute of Bioinformatics.
- ^ Kyoto University Bioinformatics Center. "Multiple Sequence Alignment - CLUSTALW". www.genome.jp. Retrieved 2018-05-06.
- ^ a b "Ensembl entry on FAM71E1 Gene Tree".
- ^ a b EMBL-EBI. "Clustal Omega < Multiple Sequence Alignment < EMBL-EBI". www.ebi.ac.uk. Retrieved 2018-05-06.
- ^ "Kann Laboratory- Domain Mapping of Disease Mutations entry on FAM71E1".
- ^ "ExAC entry on FAM71E1". exac.broadinstitute.org. Retrieved 2018-05-06.
- ^ "FAM71E1- Type 2 diabetes and role of hepatokines". www.ncbi.nlm.nih.gov.
- ^ a b 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.
{{cite journal}}
: CS1 maint: unflagged free DOI (link) - ^ Brown, John (2016). Immunohistochemical and genomic analysis of ductal carcinoma in situ of the human breast (PDF) (Ph.D.). Kings College London.
{{cite thesis}}
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ignored (|name-list-style=
suggested) (help) - ^ Nisha, Kanwar (March 2017). Early Genomic Events Associated with Dissemination of Breast Cancer Cells (Ph.D.). University of Toronto. hdl:1807/77456.
{{cite thesis}}
: Unknown parameter|name-list-format=
ignored (|name-list-style=
suggested) (help) - ^ 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.