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

Gene ID: 55254, updated on 3-Oct-2020

Summary

Official Symbol
TMEM39Aprovided by HGNC
Official Full Name
transmembrane protein 39Aprovided by HGNC
Primary source
HGNC:HGNC:25600
See related
Ensembl:ENSG00000176142
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
Expression
Ubiquitous expression in thyroid (RPKM 7.9), placenta (RPKM 6.8) and 25 other tissues See more
Orthologs

Genomic context

See TMEM39A in Genome Data Viewer
Location:
3q13.33
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (119428949..119463632, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (119147807..119182529, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Rho GTPase activating protein 31 Neighboring gene ARHGAP31 antisense RNA 1 Neighboring gene RNA, U6 small nuclear 1127, pseudogene Neighboring gene protein O-glucosyltransferase 1 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

Associated conditions

Description Tests
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
GeneReviews: Not available
Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10902, FLJ34745

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
autophagy IEA
Inferred from Electronic Annotation
more info
 
negative regulation of autophagosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of autophagosome maturation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of autophagosome maturation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of viral genome replication IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
membrane IBA
Inferred from Biological aspect of Ancestor
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)

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
    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: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    119428949..119463632 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017006788.2XP_016862277.1  transmembrane protein 39A isoform X1

    Conserved Domains (1) summary
    pfam10271
    Location:42449
    Tmp39; Putative transmembrane protein
  2. XM_005247578.2XP_005247635.1  transmembrane protein 39A isoform X2

    Conserved Domains (1) summary
    pfam10271
    Location:42371
    Tmp39; Putative transmembrane protein
  3. XM_006713687.2XP_006713750.1  transmembrane protein 39A isoform X3

    See identical proteins and their annotated locations for XP_006713750.1

    UniProtKB/Swiss-Prot
    Q9NV64
    Conserved Domains (1) summary
    pfam10271
    Location:42477
    Tmp39; Putative transmembrane protein
  4. XM_011512958.3XP_011511260.1  transmembrane protein 39A isoform X4

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

RNA

  1. XR_001740198.2 RNA Sequence

  2. XR_001740197.2 RNA Sequence

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