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TMEM87A transmembrane protein 87A [ Homo sapiens (human) ]

Gene ID: 25963, updated on 7-Apr-2024

Summary

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Official Symbol
TMEM87Aprovided by HGNC
Official Full Name
transmembrane protein 87Aprovided by HGNC
Primary source
HGNC:HGNC:24522
See related
Ensembl:ENSG00000103978 AllianceGenome:HGNC:24522
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ELKIN1
Summary
Involved in retrograde transport, endosome to Golgi. Located in Golgi cisterna membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 20.9), prostate (RPKM 20.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
15q15.1
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (42210447..42273584, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (40016476..40079617, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (42502645..42565782, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42438231-42438731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42441913-42442700 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:42442839-42442991 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42446257-42446767 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42448559-42449274 Neighboring gene phospholipase A2 group IVF Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42451565-42452064 Neighboring gene VPS39 subunit of HOPS complex Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9296 Neighboring gene microRNA 627 Neighboring gene VPS39 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9297 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9298 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:42565593-42566792 Neighboring gene glucosidase alpha, neutral C Neighboring gene BCL2 interacting protein 3 pseudogene 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42652107-42652607 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:42655654-42656620 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:42676684-42677239 Neighboring gene uncharacterized LOC105370794 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:42677734-42678933 Neighboring gene calpain 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. TMEM87a/Elkin1, a component of a novel mechanoelectrical transduction pathway, modulates melanoma adhesion and migration. Patkunarajah A, et al. Elife, 2020 Apr 1. PMID 32228863, Free PMC Article
  2. Post-Golgi anterograde transport requires GARP-dependent endosome-to-TGN retrograde transport. Hirata T, et al. Mol Biol Cell, 2015 Sep 1. PMID 26157166, Free PMC Article
  3. Large genomic duplicons map to sites of instability in the Prader-Willi/Angelman syndrome chromosome region (15q11-q13). Christian SL, et al. Hum Mol Genet, 1999 Jun. PMID 10332034
  4. Structure of the GOLD-domain seven-transmembrane helix protein family member TMEM87A. Hoel CM, et al. Elife, 2022 Nov 14. PMID 36373655, Free PMC Article
  5. Congenital dyserythropoietic anemia type I is caused by mutations in codanin-1. Dgany O, et al. Am J Hum Genet, 2002 Dec. PMID 12434312, Free PMC Article

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Touch sensation requires the mechanically gated ion channel ELKIN1.
    Title: Touch sensation requires the mechanically gated ion channel ELKIN1.
  2. TMEM87a/Elkin1, a component of a novel mechanoelectrical transduction pathway, modulates melanoma adhesion and migration.
    Title: TMEM87a/Elkin1, a component of a novel mechanoelectrical transduction pathway, modulates melanoma adhesion and migration.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ13507, DKFZp564G2022

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cellular response to mechanical stimulus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrograde transport, endosome to Golgi IGI
Inferred from Genetic Interaction
more info
 PubMed 
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in Golgi cisterna membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi cisterna membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in ruffle IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
transmembrane protein 87A

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001110503.3 → NP_001103973.1  transmembrane protein 87A isoform 2 precursor

    See identical proteins and their annotated locations for NP_001103973.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks multiple 3' coding exons and contains an alternate 3' terminal exon, resulting in a distinct 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC022468, BC005335, N63753
    Consensus CDS
    CCDS45243.1
    UniProtKB/Swiss-Prot
    Q8NBN3
    Related
    ENSP00000305894.6, ENST00000307216.10

  2. NM_001286487.1 → NP_001273416.1  transmembrane protein 87A isoform 3

    See identical proteins and their annotated locations for NP_001273416.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 5' coding region and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AF129927, AI434902, BC069240, HY036655
    UniProtKB/TrEMBL
    A8K369
    Conserved Domains (1) summary
    pfam06814
    Location:145 → 406
    Lung_7-TM_R; Lung seven transmembrane receptor

  3. NM_015497.5 → NP_056312.2  transmembrane protein 87A isoform 1 precursor

    See identical proteins and their annotated locations for NP_056312.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC036103, AF129927, AI434902, AK074870
    Consensus CDS
    CCDS32205.1
    UniProtKB/Swiss-Prot
    Q6NT77, Q8NBN3, Q8NCA4, Q9BS46, Q9P103, Q9Y3Y7
    UniProtKB/TrEMBL
    A0A994J4W5, A0A994J7M5, A8K0M6, A8K285
    Related
    ENSP00000374484.4, ENST00000389834.9
    Conserved Domains (1) summary
    pfam06814
    Location:206 → 467
    Lung_7-TM_R; Lung seven transmembrane receptor

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    42210447..42273584 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011521443.4 → XP_011519745.1  transmembrane protein 87A isoform X2

    UniProtKB/TrEMBL
    A8K369
    Conserved Domains (1) summary
    pfam06814
    Location:145 → 407
    Lung_7-TM_R; Lung seven transmembrane receptor

  2. XM_005254287.3 → XP_005254344.1  transmembrane protein 87A isoform X1

    UniProtKB/TrEMBL
    A0A994J4W5, A0A994J7M5, A8K0M6, A8K285, H3BTS6
    Related
    ENSP00000457308.2, ENST00000566014.2
    Conserved Domains (1) summary
    pfam06814
    Location:206 → 468
    Lung_7-TM_R; Lung seven transmembrane receptor

  3. XM_006720468.3 → XP_006720531.1  transmembrane protein 87A isoform X3

    UniProtKB/TrEMBL
    A8K369
    Conserved Domains (1) summary
    pfam06814
    Location:65 → 327
    Lung_7-TM_R; Lung seven transmembrane receptor

  4. XM_011521444.4 → XP_011519746.1  transmembrane protein 87A isoform X4

    Conserved Domains (1) summary
    cl21735
    Location:206 → 354
    Lung_7-TM_R; Lung seven transmembrane receptor

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    40016476..40079617 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377699.1 → XP_054233674.1  transmembrane protein 87A isoform X2

  2. XM_054377698.1 → XP_054233673.1  transmembrane protein 87A isoform X1

  3. XM_054377700.1 → XP_054233675.1  transmembrane protein 87A isoform X3

  4. XM_054377701.1 → XP_054233676.1  transmembrane protein 87A isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NBN3.3 GenPept UniProtKB/Swiss-Prot:Q8NBN3

Gene LinkOut

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