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    Tmem40 transmembrane protein 40 [ Mus musculus (house mouse) ]

    Gene ID: 94346, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Tmem40provided by MGI
    Official Full Name
    transmembrane protein 40provided by MGI
    Primary source
    MGI:MGI:2137870
    See related
    Ensembl:ENSMUSG00000059900 AllianceGenome:MGI:2137870
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    9030407H20Rik
    Summary
    Predicted to be located in membrane. Is expressed in lens; lens vesicle; and liver lobe. Orthologous to human TMEM40 (transmembrane protein 40). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in bladder adult (RPKM 8.7), stomach adult (RPKM 6.9) and 14 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Tmem40 in Genome Data Viewer
    Location:
    6 E3; 6 53.68 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (115706092..115739427, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (115729131..115762466, complement)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 38879 Neighboring gene STARR-positive B cell enhancer ABC_E10402 Neighboring gene predicted gene, 24008 Neighboring gene STARR-seq mESC enhancer starr_17094 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:115724212-115724399 Neighboring gene predicted gene, 44180 Neighboring gene microRNA 7660 Neighboring gene cullin associated and neddylation dissociated 2 (putative)

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. A large-scale in situ screen provides molecular evidence for the induction of eye anterior segment structures by the developing lens. Thut CJ, et al. Dev Biol, 2001 Mar 1. PMID 11180952
    2. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Carninci P, et al. Genome Res, 2003 Jun. PMID 12819125, Free PMC Article
    3. USP7 represses lineage differentiation genes in mouse embryonic stem cells by both catalytic and noncatalytic activities. Liu C, et al. Sci Adv, 2023 May 19. PMID 37196079, Free PMC Article
    4. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article
    5. Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Hansen GM, et al. Genome Res, 2008 Oct. PMID 18799693, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (1) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    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_001168256.1 → NP_001161728.1  transmembrane protein 40 isoform a

      See identical proteins and their annotated locations for NP_001161728.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode isoform a.
      Source sequence(s)
      AC109169, BY279100, CV561368, CX564997
      Consensus CDS
      CCDS39601.1
      UniProtKB/Swiss-Prot
      Q4FJU9, Q8C5D2, Q8VCR5
      UniProtKB/TrEMBL
      E9QN39
      Related
      ENSMUSP00000131697.2, ENSMUST00000166254.7
      Conserved Domains (1) summary
      pfam15817
      Location:105 → 224
      TMEM40; Transmembrane protein 40 family

    2. NM_001168257.1 → NP_001161729.1  transmembrane protein 40 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AC109169, BY279100, CV561368
      Consensus CDS
      CCDS51879.1
      UniProtKB/TrEMBL
      E9Q6I9
      Related
      ENSMUSP00000130407.2, ENSMUST00000170625.8
      Conserved Domains (1) summary
      pfam15817
      Location:80 → 199
      TMEM40; Transmembrane protein 40 family

    3. NM_144805.2 → NP_659054.2  transmembrane protein 40 isoform a

      See identical proteins and their annotated locations for NP_659054.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode isoform a.
      Source sequence(s)
      AC109169, BY104106, BY767648, CV561368, CX564997
      Consensus CDS
      CCDS39601.1
      UniProtKB/Swiss-Prot
      Q4FJU9, Q8C5D2, Q8VCR5
      UniProtKB/TrEMBL
      E9QN39
      Related
      ENSMUSP00000072704.7, ENSMUST00000072933.13
      Conserved Domains (1) summary
      pfam15817
      Location:105 → 224
      TMEM40; Transmembrane protein 40 family

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      115706092..115739427 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036152415.1 → XP_036008308.1  transmembrane protein 40 isoform X5

      Conserved Domains (1) summary
      pfam15817
      Location:36 → 155
      TMEM40; Transmembrane protein 40 family

    2. XM_036152416.1 → XP_036008309.1  transmembrane protein 40 isoform X5

      Conserved Domains (1) summary
      pfam15817
      Location:36 → 155
      TMEM40; Transmembrane protein 40 family

    3. XM_006506819.5 → XP_006506882.1  transmembrane protein 40 isoform X2

      See identical proteins and their annotated locations for XP_006506882.1

      UniProtKB/Swiss-Prot
      Q4FJU9, Q8C5D2, Q8VCR5
      UniProtKB/TrEMBL
      E9QN39
      Conserved Domains (1) summary
      pfam15817
      Location:105 → 224
      TMEM40; Transmembrane protein 40 family

    4. XM_011241511.3 → XP_011239813.1  transmembrane protein 40 isoform X2

      See identical proteins and their annotated locations for XP_011239813.1

      UniProtKB/Swiss-Prot
      Q4FJU9, Q8C5D2, Q8VCR5
      UniProtKB/TrEMBL
      E9QN39
      Conserved Domains (1) summary
      pfam15817
      Location:105 → 224
      TMEM40; Transmembrane protein 40 family

    5. XM_011241510.3 → XP_011239812.1  transmembrane protein 40 isoform X1

      UniProtKB/TrEMBL
      E9QN39
      Conserved Domains (1) summary
      pfam15817
      Location:121 → 240
      TMEM40; Transmembrane protein 40 family

    6. XM_011241512.4 → XP_011239814.1  transmembrane protein 40 isoform X3

      UniProtKB/TrEMBL
      E9QN39
      Conserved Domains (1) summary
      pfam15817
      Location:102 → 221
      TMEM40; Transmembrane protein 40 family

    7. XM_011241513.4 → XP_011239815.1  transmembrane protein 40 isoform X4

      Conserved Domains (1) summary
      pfam15817
      Location:77 → 196
      TMEM40; Transmembrane protein 40 family

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001168258.1: Suppressed sequence

      Description
      NM_001168258.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.

    2. NM_001168259.1: Suppressed sequence

      Description
      NM_001168259.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q4FJU9.1 GenPept UniProtKB/Swiss-Prot:Q4FJU9

    Gene LinkOut

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

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