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TMEM40 transmembrane protein 40 [ Homo sapiens (human) ]

Gene ID: 55287, updated on 5-Mar-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 integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in esophagus (RPKM 20.2), skin (RPKM 12.3) and 2 other tissues See more
Orthologs
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Genomic context

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Location:
3p25.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (12733528..12769457, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (12735046..12770993, complement)
105.20220307 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. ∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis. Pankow S, et al. Nature, 2015 Dec 24. PMID 26618866, Free PMC Article

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

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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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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NEW Try the new Transcript table

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_2023_10

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

Gene LinkOut

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