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TMEM239 transmembrane protein 239 [ Homo sapiens (human) ]

Gene ID: 100288797, updated on 27-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
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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
  • 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)

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

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