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TMEM39B transmembrane protein 39B [ Homo sapiens (human) ]

Gene ID: 55116, updated on 3-Apr-2024

Summary

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Official Symbol
TMEM39Bprovided by HGNC
Official Full Name
transmembrane protein 39Bprovided by HGNC
Primary source
HGNC:HGNC:25510
See related
Ensembl:ENSG00000121775 AllianceGenome:HGNC:25510
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
Summary
Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in placenta (RPKM 2.8), testis (RPKM 2.8) and 25 other tissues See more
Orthologs
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Genomic context

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See TMEM39B in Genome Data Viewer
Location:
1p35.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (32072031..32102863)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31929980..31960816)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32537632..32568464)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC128031832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32389035-32389578 Neighboring gene protein tyrosine phosphatase 4A2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 660 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32403472-32403643 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 581 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 661 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32409768-32410302 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32419864-32420642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32420643-32421419 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32421420-32422197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 667 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:32473819-32474378 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32479704-32480274 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 583 Neighboring gene KH RNA binding domain containing, signal transduction associated 1 Neighboring gene VISTA enhancer hs645 Neighboring gene NANOG hESC enhancer GRCh37_chr1:32526442-32527054 Neighboring gene Sharpr-MPRA regulatory region 15509 Neighboring gene Sharpr-MPRA regulatory region 7843 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32532900-32533694 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32537939-32538544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32557367-32557892 Neighboring gene microRNA 5585 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32573351-32573869 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32573870-32574387 Neighboring gene Sharpr-MPRA regulatory region 5670 Neighboring gene karyopherin subunit alpha 6 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32644454-32645213 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32645214-32645972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 671 Neighboring gene taxilin alpha Neighboring gene coiled-coil domain containing 28B

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Image-based genome-wide siRNA screen identifies selective autophagy factors. Orvedahl A, et al. Nature, 2011 Dec 1. PMID 22020285, Free PMC Article
  2. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Wagner SA, et al. Mol Cell Proteomics, 2011 Oct. PMID 21890473, Free PMC Article
  3. Large-scale analysis of the human ubiquitin-related proteome. Matsumoto M, et al. Proteomics, 2005 Nov. PMID 16196087
  4. Quantitative Lys-ϵ-Gly-Gly (diGly) proteomics coupled with inducible RNAi reveals ubiquitin-mediated proteolysis of DNA damage-inducible transcript 4 (DDIT4) by the E3 ligase HUWE1. Thompson JW, et al. J Biol Chem, 2014 Oct 17. PMID 25147182, Free PMC Article
  5. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Wiemann S, et al. Genome Res, 2001 Mar. PMID 11230166, Free PMC Article

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10315

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
transmembrane protein 39B

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_001319677.2 → NP_001306606.1  transmembrane protein 39B isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon, resulting in a different 5' UTR and use of a downstream in-frame start codon, compared to variant 1. It encodes isoform 2, which is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AK091861, AK300293
    UniProtKB/TrEMBL
    B3KRL9, Q9NW51
    Related
    ENST00000487305.5
    Conserved Domains (1) summary
    pfam10271
    Location:1 → 351
    Tmp39; Putative transmembrane protein

  2. NM_001319678.2 → NP_001306607.1  transmembrane protein 39B isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstream in-frame start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AK298766, AL136695, DA614559
    UniProtKB/TrEMBL
    B3KRL9
    Conserved Domains (1) summary
    pfam10271
    Location:1 → 279
    Tmp39; Putative transmembrane protein

  3. NM_001319679.2 → NP_001306608.1  transmembrane protein 39B isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstream in-frame start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    BC004364, DA614559
    UniProtKB/TrEMBL
    B3KRL9
    Conserved Domains (1) summary
    pfam10271
    Location:1 → 279
    Tmp39; Putative transmembrane protein

  4. NM_018056.4 → NP_060526.2  transmembrane protein 39B isoform 1

    See identical proteins and their annotated locations for NP_060526.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK023331, BC004364
    Consensus CDS
    CCDS351.2
    UniProtKB/Swiss-Prot
    B4DKN8, B4DQE6, B4DTN8, D3DPP4, Q6IA44, Q9GZU3
    Related
    ENSP00000338165.5, ENST00000336294.10
    Conserved Domains (1) summary
    pfam10271
    Location:51 → 478
    Tmp39; Putative transmembrane protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    32072031..32102863
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423840.1 → XP_047279796.1  transmembrane protein 39B isoform X1

  2. XM_006710725.5 → XP_006710788.1  transmembrane protein 39B isoform X3

    See identical proteins and their annotated locations for XP_006710788.1

    Conserved Domains (1) summary
    pfam10271
    Location:51 → 414
    Tmp39; Putative transmembrane protein

  3. XM_006710724.3 → XP_006710787.1  transmembrane protein 39B isoform X2

    Conserved Domains (1) summary
    pfam10271
    Location:51 → 414
    Tmp39; Putative transmembrane protein

  4. XM_047423846.1 → XP_047279802.1  transmembrane protein 39B isoform X4

  5. XM_047423842.1 → XP_047279798.1  transmembrane protein 39B isoform X4

  6. XM_005270988.3 → XP_005271045.1  transmembrane protein 39B isoform X6

    See identical proteins and their annotated locations for XP_005271045.1

    UniProtKB/TrEMBL
    B3KRL9, Q9NW51
    Conserved Domains (1) summary
    pfam10271
    Location:1 → 351
    Tmp39; Putative transmembrane protein

  7. XM_047423852.1 → XP_047279808.1  transmembrane protein 39B isoform X8

  8. XM_011541683.2 → XP_011539985.1  transmembrane protein 39B isoform X6

    See identical proteins and their annotated locations for XP_011539985.1

    UniProtKB/TrEMBL
    B3KRL9, Q9NW51
    Conserved Domains (1) summary
    pfam10271
    Location:1 → 351
    Tmp39; Putative transmembrane protein

  9. XM_017001595.2 → XP_016857084.1  transmembrane protein 39B isoform X5

    UniProtKB/TrEMBL
    B3KRL9
    Conserved Domains (1) summary
    pfam10271
    Location:3 → 363
    Tmp39; Putative transmembrane protein

  10. XM_047423851.1 → XP_047279807.1  transmembrane protein 39B isoform X7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    31929980..31960816
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337330.1 → XP_054193305.1  transmembrane protein 39B isoform X1

  2. XM_054337332.1 → XP_054193307.1  transmembrane protein 39B isoform X3

  3. XM_054337331.1 → XP_054193306.1  transmembrane protein 39B isoform X2

  4. XM_054337334.1 → XP_054193309.1  transmembrane protein 39B isoform X4

  5. XM_054337333.1 → XP_054193308.1  transmembrane protein 39B isoform X4

  6. XM_054337336.1 → XP_054193311.1  transmembrane protein 39B isoform X6

    UniProtKB/TrEMBL
    Q9NW51

  7. XM_054337339.1 → XP_054193314.1  transmembrane protein 39B isoform X8

  8. XM_054337337.1 → XP_054193312.1  transmembrane protein 39B isoform X6

    UniProtKB/TrEMBL
    Q9NW51

  9. XM_054337335.1 → XP_054193310.1  transmembrane protein 39B isoform X5

  10. XM_054337338.1 → XP_054193313.1  transmembrane protein 39B isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9GZU3.1 GenPept UniProtKB/Swiss-Prot:Q9GZU3

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