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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
    mouse all
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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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