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    TMEM40 transmembrane protein 40 [ Homo sapiens (human) ]

    Gene ID: 55287, updated on 27-Nov-2024

    Summary

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    Official Symbol
    TMEM40provided by HGNC
    Official Full Name
    transmembrane protein 40provided by HGNC
    Primary source
    HGNC:HGNC:25620
    See related
    Ensembl:ENSG00000088726 AllianceGenome:HGNC:25620
    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
    Biased expression in esophagus (RPKM 20.2), skin (RPKM 12.3) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMEM40 in Genome Data Viewer
    Location:
    3p25.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (12733528..12769457, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (12735046..12770993, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (12775027..12810956, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Raf-1 proto-oncogene, serine/threonine kinase Neighboring gene small nucleolar RNA U13 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:12684584-12684794 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12698025-12698668 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12704698-12705308 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12705309-12705920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19449 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12711892-12712473 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12712474-12713054 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12715375-12716244 Neighboring gene cysteine rich protein 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12735645-12736146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19450 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12779747-12780569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19451 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14067 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19453 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12800761-12801346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14069 Neighboring gene keratin 18 pseudogene 17 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12845071-12845571 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14070 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:12855381-12855561 Neighboring gene cullin associated and neddylation dissociated 2 (putative) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12871622-12872570 Neighboring gene ribosomal protein L32

    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. High expression of TMEM40 contributes to progressive features of tongue squamous cell carcinoma. Zhang Q, et al. Oncol Rep, 2019 Jan. PMID 30320346, Free PMC Article
    2. High expression of TMEM40 is associated with the malignant behavior and tumorigenesis in bladder cancer. Zhang ZF, et al. J Transl Med, 2018 Jan 19. PMID 29351801, Free PMC Article
    3. Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins. Macaulay IC, et al. Blood, 2007 Apr 15. PMID 17192395, Free PMC Article
    4. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Gevaert K, et al. Nat Biotechnol, 2003 May. PMID 12665801
    5. CFTR interactome mapping using the mammalian membrane two-hybrid high-throughput screening system. Lim SH, et al. Mol Syst Biol, 2022 Feb. PMID 35156780, Free PMC Article

    See all (12) 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

    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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    Homology

    Clone Names

    • FLJ11036

    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 40

    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_001284406.2 → NP_001271335.1  transmembrane protein 40 isoform a

      See identical proteins and their annotated locations for NP_001271335.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC034198, AI452552, AK001898, AK092470, AK301984
      UniProtKB/TrEMBL
      B4DXI0
      Conserved Domains (1) summary
      pfam15817
      Location:129 → 248
      TMEM40; Transmembrane protein 40 family

    2. NM_001284407.2 → NP_001271336.1  transmembrane protein 40 isoform c

      See identical proteins and their annotated locations for NP_001271336.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, initiates translation at a downstream in-frame start codon, and lacks an alternate in-frame exon in the central coding region, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AC034198, AI452552, AK092470, BC020658
      Consensus CDS
      CCDS68348.1
      UniProtKB/Swiss-Prot
      Q8WWA1
      Related
      ENSP00000405740.2, ENST00000435218.6
      Conserved Domains (1) summary
      pfam15817
      Location:83 → 202
      TMEM40; Transmembrane protein 40 family

    3. NM_001284408.2 → NP_001271337.1  transmembrane protein 40 isoform d

      See identical proteins and their annotated locations for NP_001271337.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, initiates translation at a downstream in-frame start codon, and lacks two alternate in-frame exons in the central coding region, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AC034198, AI452552, AK001898, AK092470, BG335433
      Consensus CDS
      CCDS68347.1
      UniProtKB/Swiss-Prot
      Q8WWA1
      Related
      ENSP00000396895.1, ENST00000435575.5
      Conserved Domains (1) summary
      pfam15817
      Location:37 → 156
      TMEM40; Transmembrane protein 40 family

    4. NM_018306.4 → NP_060776.2  transmembrane protein 40 isoform b

      See identical proteins and their annotated locations for NP_060776.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AC034198, AI452552, AK001898, AK092470
      Consensus CDS
      CCDS2613.1
      UniProtKB/Swiss-Prot
      C9JID5, Q8NAL4, Q8WWA1, Q9NUZ4
      Related
      ENSP00000322837.7, ENST00000314124.12
      Conserved Domains (1) summary
      pfam15817
      Location:113 → 232
      TMEM40; Transmembrane protein 40 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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      12733528..12769457 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011533937.3 → XP_011532239.1  transmembrane protein 40 isoform X1

      See identical proteins and their annotated locations for XP_011532239.1

      UniProtKB/Swiss-Prot
      C9JID5, Q8NAL4, Q8WWA1, Q9NUZ4
      Conserved Domains (1) summary
      pfam15817
      Location:113 → 232
      TMEM40; Transmembrane protein 40 family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      12735046..12770993 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347174.1 → XP_054203149.1  transmembrane protein 40 isoform X1

      UniProtKB/Swiss-Prot
      C9JID5, Q8NAL4, Q8WWA1, Q9NUZ4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WWA1.2 GenPept UniProtKB/Swiss-Prot:Q8WWA1

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