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

    Gene ID: 55116, updated on 17-Jun-2024

    Summary

    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
    NEW
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    Try the new Transcript table

    Genomic context

    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

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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
     

    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_001319677.2NP_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:1351
      Tmp39; Putative transmembrane protein
    2. NM_001319678.2NP_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:1279
      Tmp39; Putative transmembrane protein
    3. NM_001319679.2NP_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:1279
      Tmp39; Putative transmembrane protein
    4. NM_018056.4NP_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:51478
      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_047423840.1XP_047279796.1  transmembrane protein 39B isoform X1

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

      See identical proteins and their annotated locations for XP_006710788.1

      Conserved Domains (1) summary
      pfam10271
      Location:51414
      Tmp39; Putative transmembrane protein
    3. XM_006710724.3XP_006710787.1  transmembrane protein 39B isoform X2

      Conserved Domains (1) summary
      pfam10271
      Location:51414
      Tmp39; Putative transmembrane protein
    4. XM_047423846.1XP_047279802.1  transmembrane protein 39B isoform X4

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

    6. XM_005270988.3XP_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:1351
      Tmp39; Putative transmembrane protein
    7. XM_047423852.1XP_047279808.1  transmembrane protein 39B isoform X8

    8. XM_011541683.2XP_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:1351
      Tmp39; Putative transmembrane protein
    9. XM_017001595.2XP_016857084.1  transmembrane protein 39B isoform X5

      UniProtKB/TrEMBL
      B3KRL9
      Conserved Domains (1) summary
      pfam10271
      Location:3363
      Tmp39; Putative transmembrane protein
    10. XM_047423851.1XP_047279807.1  transmembrane protein 39B isoform X7

      UniProtKB/TrEMBL
      B3KRL9

    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_054337330.1XP_054193305.1  transmembrane protein 39B isoform X1

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

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

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

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

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

      UniProtKB/TrEMBL
      B3KRL9, Q9NW51
    7. XM_054337339.1XP_054193314.1  transmembrane protein 39B isoform X8

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

      UniProtKB/TrEMBL
      B3KRL9, Q9NW51
    9. XM_054337335.1XP_054193310.1  transmembrane protein 39B isoform X5

      UniProtKB/TrEMBL
      B3KRL9
    10. XM_054337338.1XP_054193313.1  transmembrane protein 39B isoform X7

      UniProtKB/TrEMBL
      B3KRL9