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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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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

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