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    TMEM39A transmembrane protein 39A [ Homo sapiens (human) ]

    Gene ID: 55254, updated on 9-Dec-2024

    Summary

    Official Symbol
    TMEM39Aprovided by HGNC
    Official Full Name
    transmembrane protein 39Aprovided by HGNC
    Primary source
    HGNC:HGNC:25600
    See related
    Ensembl:ENSG00000176142 AllianceGenome:HGNC:25600
    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
    Also known as
    SUSR2
    Summary
    Involved in negative regulation of autophagosome assembly; negative regulation of autophagosome maturation; and positive regulation of viral genome replication. Located in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 7.9), placenta (RPKM 6.8) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TMEM39A in Genome Data Viewer
    Location:
    3q13.33
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (119428949..119463615, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (122148660..122183326, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (119147796..119182462, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Rho GTPase activating protein 31 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20299 Neighboring gene RNA, U6 small nuclear 1127, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:119068069-119068893 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:119070415-119071112 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:119079699-119080370 Neighboring gene uncharacterized LOC124906273 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20302 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:119187474-119187974 Neighboring gene protein O-glucosyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20304 Neighboring gene MPRA-validated peak4782 silencer Neighboring gene translocase of inner mitochondrial membrane domain containing 1 Neighboring gene CD80 molecule

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
    EBI GWAS Catalog
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10902, FLJ34745

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    transmembrane protein 39A
    Names
    suppressor of SQST-1 aggregates in rpl-43 mutants

    NCBI Reference Sequences (RefSeq)

    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_018266.3NP_060736.1  transmembrane protein 39A

      See identical proteins and their annotated locations for NP_060736.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.
      Source sequence(s)
      AC074271, AK001764, BC003192
      Consensus CDS
      CCDS2987.1
      UniProtKB/Swiss-Prot
      D3DN80, Q53FN4, Q53GI1, Q6PKB5, Q9NV64
      Related
      ENSP00000326063.5, ENST00000319172.10
      Conserved Domains (1) summary
      pfam10271
      Location:42477
      Tmp39; Putative transmembrane protein

    RNA

    1. NR_073506.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC074271, BC003192
      Related
      ENST00000438581.6

    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
      119428949..119463615 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448511.1XP_047304467.1  transmembrane protein 39A isoform X2

    2. XM_047448512.1XP_047304468.1  transmembrane protein 39A isoform X3

    3. XM_006713687.3XP_006713750.1  transmembrane protein 39A isoform X1

      See identical proteins and their annotated locations for XP_006713750.1

      UniProtKB/Swiss-Prot
      D3DN80, Q53FN4, Q53GI1, Q6PKB5, Q9NV64
      Conserved Domains (1) summary
      pfam10271
      Location:42477
      Tmp39; Putative transmembrane protein
    4. XM_047448513.1XP_047304469.1  transmembrane protein 39A isoform X4

    5. XM_017006788.3XP_016862277.1  transmembrane protein 39A isoform X2

      Conserved Domains (1) summary
      pfam10271
      Location:42449
      Tmp39; Putative transmembrane protein
    6. XM_005247578.3XP_005247635.1  transmembrane protein 39A isoform X3

      Conserved Domains (1) summary
      pfam10271
      Location:42371
      Tmp39; Putative transmembrane protein
    7. XM_011512958.4XP_011511260.1  transmembrane protein 39A isoform X5

      Conserved Domains (1) summary
      pfam10271
      Location:42313
      Tmp39; Putative transmembrane protein

    RNA

    1. XR_007095705.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      122148660..122183326 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347165.1XP_054203140.1  transmembrane protein 39A isoform X2

    2. XM_054347167.1XP_054203142.1  transmembrane protein 39A isoform X3

    3. XM_054347163.1XP_054203138.1  transmembrane protein 39A isoform X1

      UniProtKB/Swiss-Prot
      D3DN80, Q53FN4, Q53GI1, Q6PKB5, Q9NV64
    4. XM_054347168.1XP_054203143.1  transmembrane protein 39A isoform X4

    5. XM_054347164.1XP_054203139.1  transmembrane protein 39A isoform X2

    6. XM_054347166.1XP_054203141.1  transmembrane protein 39A isoform X3

    7. XM_054347169.1XP_054203144.1  transmembrane protein 39A isoform X5

    RNA

    1. XR_008486747.1 RNA Sequence