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    Tmem39a transmembrane protein 39a [ Mus musculus (house mouse) ]

    Gene ID: 67846, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Tmem39aprovided by MGI
    Official Full Name
    transmembrane protein 39aprovided by MGI
    Primary source
    MGI:MGI:1915096
    See related
    Ensembl:ENSMUSG00000002845 AllianceGenome:MGI:1915096
    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
    2610033C09Rik
    Summary
    Predicted to be involved in negative regulation of autophagosome assembly; negative regulation of autophagosome maturation; and positive regulation of viral genome replication. Predicted to act upstream of or within autophagy. Predicted to be located in endoplasmic reticulum. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum membrane. Orthologous to human TMEM39A (transmembrane protein 39A). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in limb E14.5 (RPKM 30.5), placenta adult (RPKM 15.8) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Tmem39a in Genome Data Viewer
    Location:
    16 26.87 cM; 16 B4
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (38379060..38412524)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (38558698..38592162)

    Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene translocase of inner mitochondrial membrane domain containing 1 Neighboring gene STARR-seq mESC enhancer starr_40830 Neighboring gene ubiquitin-like, containing PHD and RING finger domains, 1 pseudogene Neighboring gene predicted gene, 53953 Neighboring gene protein O-glucosyltransferase 1 Neighboring gene STARR-seq mESC enhancer starr_40832 Neighboring gene STARR-seq mESC enhancer starr_40833 Neighboring gene Rho GTPase activating protein 31 Neighboring gene predicted gene, 36482 Neighboring gene anaphase promoting complex subunit 10 pseudogene

    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. Isolation of novel tissue-specific genes from cDNA libraries representing the individual tissue constituents of the gastrulating mouse embryo. Harrison SM, et al. Development, 1995 Aug. PMID 7671812
    2. EUCOMM--the European conditional mouse mutagenesis program. Friedel RH, et al. Brief Funct Genomic Proteomic, 2007 Sep. PMID 17967808
    3. A large-scale, gene-driven mutagenesis approach for the functional analysis of the mouse genome. Hansen J, et al. Proc Natl Acad Sci U S A, 2003 Aug 19. PMID 12904583, Free PMC Article
    4. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Stryke D, et al. Nucleic Acids Res, 2003 Jan 1. PMID 12520002, 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 (17) 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)
    • Gene trapped (1) 

    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
    acts_upstream_of_or_within autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of autophagosome maturation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of viral genome replication ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    transmembrane protein 39A

    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_001205286.1 → NP_001192215.1  transmembrane protein 39A isoform 1

      See identical proteins and their annotated locations for NP_001192215.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate 5' UTR exon, compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AK160576, AK169127
      Consensus CDS
      CCDS28171.1
      UniProtKB/Swiss-Prot
      Q3TFJ2, Q9CYC3
      Related
      ENSMUSP00000132515.2, ENSMUST00000163884.8
      Conserved Domains (1) summary
      pfam10271
      Location:42 → 475
      Tmp39; Putative transmembrane protein

    2. NM_001205287.1 → NP_001192216.1  transmembrane protein 39A isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame segment in the CDS, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AK160576, AK169127
      Consensus CDS
      CCDS57029.1
      UniProtKB/Swiss-Prot
      Q9CYC3
      Related
      ENSMUSP00000126218.2, ENSMUST00000171687.8
      Conserved Domains (1) summary
      pfam10271
      Location:46 → 407
      Tmp39; Putative transmembrane protein

    3. NM_026407.3 → NP_080683.2  transmembrane protein 39A isoform 1

      See identical proteins and their annotated locations for NP_080683.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) and variant 2 encode the same isoform (1).
      Source sequence(s)
      AK017817, AK133638, BY072316
      Consensus CDS
      CCDS28171.1
      UniProtKB/Swiss-Prot
      Q3TFJ2, Q9CYC3
      Related
      ENSMUSP00000002924.9, ENSMUST00000002924.15
      Conserved Domains (1) summary
      pfam10271
      Location:42 → 475
      Tmp39; Putative transmembrane protein

    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_000082.7 Reference GRCm39 C57BL/6J

      Range
      38379060..38412524
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006522496.4 → XP_006522559.1  transmembrane protein 39A isoform X1

      Conserved Domains (1) summary
      pfam10271
      Location:42 → 447
      Tmp39; Putative transmembrane protein

    2. XM_006522497.4 → XP_006522560.1  transmembrane protein 39A isoform X2

      Conserved Domains (1) summary
      pfam10271
      Location:42 → 311
      Tmp39; Putative transmembrane protein

    RNA

    1. XR_001781854.2 RNA Sequence

    2. XR_384596.4 RNA Sequence

    3. XR_003951823.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9CYC3.1 GenPept UniProtKB/Swiss-Prot:Q9CYC3

    Gene LinkOut

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

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