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    TMEM129 transmembrane protein 129, E3 ubiquitin ligase [ Homo sapiens (human) ]

    Gene ID: 92305, updated on 27-Nov-2024

    Summary

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    Official Symbol
    TMEM129provided by HGNC
    Official Full Name
    transmembrane protein 129, E3 ubiquitin ligaseprovided by HGNC
    Primary source
    HGNC:HGNC:25137
    See related
    Ensembl:ENSG00000168936 MIM:615975; AllianceGenome:HGNC:25137
    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
    D4S2561E
    Summary
    Enables ubiquitin protein ligase activity. Involved in protein polyubiquitination; retrograde protein transport, ER to cytosol; and ubiquitin-dependent protein catabolic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 11.0), thyroid (RPKM 10.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMEM129 in Genome Data Viewer
    Location:
    4p16.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (1715952..1721323, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (1713779..1719151, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (1717679..1723050, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 53 member A Neighboring gene uncharacterized LOC105374349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1648945-1649446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15137 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1686561-1687180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1687181-1687800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1707982-1708482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21155 Neighboring gene stem-loop histone mRNA binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1723083-1724078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1732480-1732980 Neighboring gene uncharacterized LOC112268460 Neighboring gene transforming acidic coiled-coil containing protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1755043-1755650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1767895-1768754 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1769833-1770398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1770399-1770964 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15143 Neighboring gene uncharacterized LOC124900648

    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. Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk. Brumwell A, et al. Arthritis Res Ther, 2022 Aug 8. PMID 35941660, Free PMC Article
    2. The E3 Ubiquitin Ligase TMEM129 Is a Tri-Spanning Transmembrane Protein. van de Weijer ML, et al. Viruses, 2016 Nov 15. PMID 27854284, Free PMC Article
    3. Identifying the ERAD ubiquitin E3 ligases for viral and cellular targeting of MHC class I. van den Boomen DJ, et al. Mol Immunol, 2015 Dec. PMID 26210183, Free PMC Article
    4. Human cytomegalovirus evades antibody-mediated immunity through endoplasmic reticulum-associated degradation of the FcRn receptor. Liu X, et al. Nat Commun, 2019 Jul 9. PMID 31289263, Free PMC Article
    5. TMEM129 is a Derlin-1 associated ERAD E3 ligase essential for virus-induced degradation of MHC-I. van den Boomen DJ, et al. Proc Natl Acad Sci U S A, 2014 Aug 5. PMID 25030448, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk.
      Title: Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk.
    2. This insertion in the endoplasmic reticulum membrane positions the C-terminal really interesting new gene (RING) domain of TMEM129 in the cytosol, making it available to catalyze ubiquitination reactions that are required for cytosolic degradation of secretory proteins.
      Title: The E3 Ubiquitin Ligase TMEM129 Is a Tri-Spanning Transmembrane Protein.
    3. TRC8 and TMEM129 are endoplasmic reticulum-associated degradation ubiquitin E3 ligases for viral and cellular targeting of MHC class I. (Review)
      Title: Identifying the ERAD ubiquitin E3 ligases for viral and cellular targeting of MHC class I.
    4. TMEM129 is an integral part of the Endoplasmic Reticulum-resident dislocation complex mediating US11-induced HLA class I degradation.
      Title: A high-coverage shRNA screen identifies TMEM129 as an E3 ligase involved in ER-associated protein degradation.
    5. TMEM129 contains an unusual cysteine-only RING with intrinsic E3 ligase activity and is recruited to US11 via Derlin-1.
      Title: TMEM129 is a Derlin-1 associated ERAD E3 ligase essential for virus-induced degradation of MHC-I.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci.
    EBI GWAS Catalog
    A sequence variant at 4p16.3 confers susceptibility to urinary bladder cancer.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple loci associated with bladder cancer risk.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ25600

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin protein ligase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in ERAD pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein polyubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein ubiquitination TAS
    Traceable Author Statement
    more info
    		  
    involved_in response to unfolded protein IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde protein transport, ER to cytosol IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase TM129
    Names
    RING-type E3 ubiquitin transferase TM129
    transmembrane protein 129, E3 ubiquitin protein ligase
    NP_001120738.1
    NP_612394.1

    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_001127266.2 → NP_001120738.1  E3 ubiquitin-protein ligase TM129 isoform a

      See identical proteins and their annotated locations for NP_001120738.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      BC009331, BC126370
      Consensus CDS
      CCDS46998.1
      UniProtKB/Swiss-Prot
      A0AVI4, A6NH49, A6NI98, D3DVP8
      Related
      ENSP00000372394.3, ENST00000382936.8
      Conserved Domains (1) summary
      pfam10272
      Location:17 → 359
      Tmpp129; Putative transmembrane protein precursor

    2. NM_138385.4 → NP_612394.1  E3 ubiquitin-protein ligase TM129 isoform b

      See identical proteins and their annotated locations for NP_612394.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the coding region compared to variant 1, that causes a frameshift. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
      Source sequence(s)
      BC009331, BC126370
      Consensus CDS
      CCDS3351.1
      UniProtKB/Swiss-Prot
      A0AVI4
      Related
      ENSP00000305243.2, ENST00000303277.6
      Conserved Domains (1) summary
      pfam10272
      Location:17 → 226
      Tmpp129; Putative transmembrane protein precursor

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      1715952..1721323 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      1713779..1719151 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A0AVI4.1 GenPept UniProtKB/Swiss-Prot:A0AVI4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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