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FAM71E1

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GARIN5A
Identifiers
AliasesGARIN5A, family with sequence similarity 71 member E1, GARIL5, golgi associated RAB2 interactor 5A, FAM71E1
External IDsMGI: 1922788; HomoloGene: 19259; GeneCards: GARIN5A; OMA:GARIN5A - orthologs
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 MbChr 7: 44.15 – 44.15 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/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.

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]

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[28]

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]
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]

Overview of FAM71E1 Orthologs[30]
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

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000142530 – Ensembl, May 2017
  2. ^ a b c 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. ^ a b c "Human Gene FAM71E1 (ENST00000600100.5) Description and Page Index". genome.ucsc.edu. Retrieved 2018-02-20.
  6. ^ a b c "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. ^ a b 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. ^ a b "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. ^ a b "Ensembl entry on FAM71E1 Gene Tree".
  30. ^ a b "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. ^ 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.
  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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