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    TRAFD1 TRAF-type zinc finger domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 10906, updated on 3-Nov-2024

    Summary

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    Official Symbol
    TRAFD1provided by HGNC
    Official Full Name
    TRAF-type zinc finger domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:24808
    See related
    Ensembl:ENSG00000135148 MIM:613197; AllianceGenome:HGNC:24808
    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
    FLN29
    Summary
    The innate immune system confers host defense against viral and microbial infection, and TRAFD1 is a negative feedback regulator that controls excessive immune responses (Sanada et al., 2008 [PubMed 18849341]).[supplied by OMIM, Dec 2009]
    Expression
    Ubiquitous expression in testis (RPKM 18.8), lymph node (RPKM 16.4) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See TRAFD1 in Genome Data Viewer
    Location:
    12q24.13
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (112125560..112153604)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (112102466..112130510)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (112563364..112591408)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903022 Neighboring gene N-alpha-acetyltransferase 25, NatB auxiliary subunit Neighboring gene microRNA 3657 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:112540436-112540936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:112544255-112544756 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4881 Neighboring gene Sharpr-MPRA regulatory region 5940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7045 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7046 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:112603752-112604358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:112616819-112617320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:112617321-112617820 Neighboring gene Sharpr-MPRA regulatory region 5198 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:112621798-112622366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:112622367-112622936 Neighboring gene microRNA 6861 Neighboring gene HECT domain E3 ubiquitin protein ligase 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:112630491-112630990 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4882 Neighboring gene RN7SK pseudogene 71

    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 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. TRAFD1 (FLN29) Interacts with Plekhm1 and Regulates Osteoclast Acidification and Resorption. Witwicka H, et al. PLoS One, 2015. PMID 25992615, Free PMC Article
    2. Integrative Multiomics and Regulatory Network Analyses Uncovers the Role of OAS3, TRAFD1, miR-222-3p, and miR-125b-5p in Hepatitis E Virus Infection. Gupta S, et al. Genes (Basel), 2022 Dec 23. PMID 36672782, Free PMC Article
    3. FLN29, a novel interferon- and LPS-inducible gene acting as a negative regulator of toll-like receptor signaling. Mashima R, et al. J Biol Chem, 2005 Dec 16. PMID 16221674
    4. FLN29 deficiency reveals its negative regulatory role in the Toll-like receptor (TLR) and retinoic acid-inducible gene I (RIG-I)-like helicase signaling pathway. Sanada T, et al. J Biol Chem, 2008 Dec 5. PMID 18849341, Free PMC Article
    5. Cytosolic quality control of mislocalized proteins requires RNF126 recruitment to Bag6. Rodrigo-Brenni MC, et al. Mol Cell, 2014 Jul 17. PMID 24981174, Free PMC Article

    See all (76) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Integrative Multiomics and Regulatory Network Analyses Uncovers the Role of OAS3, TRAFD1, miR-222-3p, and miR-125b-5p in Hepatitis E Virus Infection.
      Title: Integrative Multiomics and Regulatory Network Analyses Uncovers the Role of OAS3, TRAFD1, miR-222-3p, and miR-125b-5p in Hepatitis E Virus Infection.
    2. FLN29, in addition to playing a negative regulatory role in the TLR4 signaling pathway, negatively regulates the RIG-I-like helicase signaling pathway at the level of IPS-1/TRAF6 and IPS-1/TRAF3 complexes
      Title: FLN29 deficiency reveals its negative regulatory role in the Toll-like receptor (TLR) and retinoic acid-inducible gene I (RIG-I)-like helicase signaling pathway.
    3. FLN29 is a new negative feedback regulator of TLR signaling
      Title: FLN29, a novel interferon- and LPS-inducible gene acting as a negative regulator of toll-like receptor signaling.
    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
    Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    EBI GWAS Catalog
    Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.
    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)

    Genotypes

    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

    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 
    Process Evidence Code Pubs
    involved_in negative regulation of innate immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of innate immune response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    TRAF-type zinc finger domain-containing protein 1
    Names
    FLN29 gene product

    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_001143906.2 → NP_001137378.1  TRAF-type zinc finger domain-containing protein 1

      See identical proteins and their annotated locations for NP_001137378.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AK122620, BC003553, BG828961, CA314188
      Consensus CDS
      CCDS9160.1
      UniProtKB/Swiss-Prot
      A8K5L6, B4DI89, O14545
      Related
      ENSP00000257604.5, ENST00000257604.9
      Conserved Domains (2) summary
      cl26464
      Location:406 → 543
      Atrophin-1; Atrophin-1 family
      cl27293
      Location:7 → 131
      UFD1; Ubiquitin fusion degradation protein UFD1

    2. NM_006700.3 → NP_006691.1  TRAF-type zinc finger domain-containing protein 1

      See identical proteins and their annotated locations for NP_006691.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AK312601, BC003553, CA314188
      Consensus CDS
      CCDS9160.1
      UniProtKB/Swiss-Prot
      A8K5L6, B4DI89, O14545
      Related
      ENSP00000396526.2, ENST00000412615.7
      Conserved Domains (2) summary
      cl26464
      Location:406 → 543
      Atrophin-1; Atrophin-1 family
      cl27293
      Location:7 → 131
      UFD1; Ubiquitin fusion degradation protein UFD1

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      112125560..112153604
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      112102466..112130510
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O14545.1 GenPept UniProtKB/Swiss-Prot:O14545

    Gene LinkOut

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

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