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    TMEM239 transmembrane protein 239 [ Homo sapiens (human) ]

    Gene ID: 100288797, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TMEM239provided by HGNC
    Official Full Name
    transmembrane protein 239provided by HGNC
    Primary source
    HGNC:HGNC:40044
    See related
    Ensembl:ENSG00000198326 AllianceGenome:HGNC:40044
    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
    Summary
    Predicted to be located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward testis (RPKM 4.0) See more
    Orthologs
    mouse all
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    Genomic context

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    See TMEM239 in Genome Data Viewer
    Location:
    20p13
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (2815784..2820284)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (2846368..2850756)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (2796948..2800930)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2778855-2779842 Neighboring gene ribosomal protein L19 pseudogene 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2779843-2780830 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2780831-2781816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12607 Neighboring gene carboxypeptidase X, M14 family member 1 Neighboring gene CRISPRi-validated cis-regulatory element chr20.196 Neighboring gene chromosome 20 open reading frame 141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2812614-2813114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17472 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2820603-2821134 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:2821668-2822199 Neighboring gene PC-esterase domain containing 1A Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:2840338-2840838 Neighboring gene VPS16 core subunit of CORVET and HOPS complexes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2852243-2852874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2852875-2853504 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2853505-2854136 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:2854137-2854766 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60029 Neighboring gene protein tyrosine phosphatase receptor type A Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:2903375-2903875 Neighboring gene Sharpr-MPRA regulatory region 1396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17473 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:3007535-3008734

    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 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. White matter integrity as an intermediate phenotype: exploratory genome-wide association analysis in individuals at high risk of bipolar disorder. Sprooten E, et al. Psychiatry Res, 2013 Apr 30. PMID 23218918
    2. Widespread macromolecular interaction perturbations in human genetic disorders. Sahni N, et al. Cell, 2015 Apr 23. PMID 25910212, Free PMC Article
    3. Assessment of community efforts to advance network-based prediction of protein-protein interactions. Wang XW, et al. Nat Commun, 2023 Mar 22. PMID 36949045, Free PMC Article
    4. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Yang X, et al. Cell, 2016 Feb 11. PMID 26871637, Free PMC Article
    5. Sequential genome-wide CRISPR-Cas9 screens identify genes regulating cell-surface expression of tetraspanins. Yang J, et al. Cell Rep, 2023 Feb 28. PMID 36724073

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    EBI GWAS Catalog

    Description
    White matter integrity as an intermediate phenotype: exploratory genome-wide association analysis in individuals at high risk of bipolar disorder.
    EBI GWAS Catalog

    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

    • FLJ26142, FLJ44045

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    transmembrane protein 239

    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_001167670.3 → NP_001161142.1  transmembrane protein 239 isoform 2

      See identical proteins and their annotated locations for NP_001161142.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate 3' terminal exon, resulting in a distinct 5' UTR and the use of a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AI383461, AL035460, BC021178, DB337508
      Consensus CDS
      CCDS54444.1
      UniProtKB/Swiss-Prot
      Q8WW34
      Related
      ENSP00000369959.1, ENST00000380585.2
      Conserved Domains (1) summary
      pfam15841
      Location:2 → 150
      TMEM239; Transmembrane protein 239 family

    2. NM_001318207.1 → NP_001305136.1  transmembrane protein 239 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK126033, AL035460, AL161656
      Consensus CDS
      CCDS82595.1
      UniProtKB/Swiss-Prot
      Q5JY54, Q6ZU23, Q8WW34
      Related
      ENSP00000354312.1, ENST00000361033.1
      Conserved Domains (1) summary
      pfam15841
      Location:45 → 193
      TMEM239; Transmembrane protein 239 family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      2815784..2820284
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439814.1 → XP_047295770.1  transmembrane protein 239 isoform X2

    2. XM_011529128.3 → XP_011527430.1  transmembrane protein 239 isoform X1

      Conserved Domains (1) summary
      pfam15841
      Location:28 → 176
      TMEM239; Transmembrane protein 239 family

    RNA

    1. XR_001754107.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      2846368..2850756
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322814.1 → XP_054178789.1  transmembrane protein 239 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WW34.3 GenPept UniProtKB/Swiss-Prot:Q8WW34

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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