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    Trafd1 TRAF type zinc finger domain containing 1 [ Mus musculus (house mouse) ]

    Gene ID: 231712, updated on 21-Apr-2024

    Summary

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    Official Symbol
    Trafd1provided by MGI
    Official Full Name
    TRAF type zinc finger domain containing 1provided by MGI
    Primary source
    MGI:MGI:1923551
    See related
    Ensembl:ENSMUSG00000042726 AllianceGenome:MGI:1923551
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Fln29; 1110008K06Rik
    Summary
    Predicted to enable zinc ion binding activity. Involved in negative regulation of innate immune response. Is expressed in central nervous system; neural retinal epithelium; retina inner nuclear layer; retina nuclear layer; and retina outer nuclear layer. Orthologous to human TRAFD1 (TRAF-type zinc finger domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis adult (RPKM 91.2), CNS E14 (RPKM 38.2) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    5 F; 5 61.78 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (121509788..121524543, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (121371725..121386570, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_14255 Neighboring gene STARR-positive B cell enhancer ABC_E4784 Neighboring gene predicted gene, 26205 Neighboring gene ribosomal protein L6 Neighboring gene HECT domain E3 ubiquitin protein ligase 4 Neighboring gene STARR-positive B cell enhancer mm9_chr5:121780251-121780552 Neighboring gene predicted gene, 24671 Neighboring gene STARR-positive B cell enhancer ABC_E1688 Neighboring gene predicted gene, 42020 Neighboring gene N(alpha)-acetyltransferase 25, NatB auxiliary subunit Neighboring gene STARR-seq mESC enhancer starr_14257 Neighboring gene STARR-positive B cell enhancer ABC_E6373 Neighboring gene STARR-positive B cell enhancer ABC_E6374 Neighboring gene endoplasmic reticulum protein 29

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    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. 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
    3. 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
    4. Genomic analysis of mouse retinal development. Blackshaw S, et al. PLoS Biol, 2004 Sep. PMID 15226823, Free PMC Article
    5. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TRAFD1, in association with Plekhm1/Rab7-positive late endosomes-early lysosomes, has a previously unknown role in vesicle trafficking, acidification, and resorption in osteoclasts
      Title: TRAFD1 (FLN29) Interacts with Plekhm1 and Regulates Osteoclast Acidification and Resorption.
    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

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (2)  1 citation
    • Endonuclease-mediated (2) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    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 zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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_001163470.1 → NP_001156942.1  TRAF-type zinc finger domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001156942.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AA168469, AK150038, BU613615
      Consensus CDS
      CCDS51638.1
      UniProtKB/Swiss-Prot
      Q3UDK1, Q8CFI8
      Related
      ENSMUSP00000047475.8, ENSMUST00000042312.14
      Conserved Domains (1) summary
      PLN03086
      Location:7 → 131
      PLN03086; PRLI-interacting factor K; Provisional

    2. NM_001359947.1 → NP_001346876.1  TRAF-type zinc finger domain-containing protein 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, that results in a protein (isoform 2) with a shorter C-terminus, compared to isoform 1. Variants 2 and 3 both encode the same isoform (2).
      Source sequence(s)
      AC126938
      Consensus CDS
      CCDS51639.1
      Conserved Domains (1) summary
      PLN03086
      Location:7 → 131
      PLN03086; PRLI-interacting factor K; Provisional

    3. NM_172275.2 → NP_758479.2  TRAF-type zinc finger domain-containing protein 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, that results in a protein (isoform 2) with a shorter C-terminus, compared to isoform 1. Variants 2 and 3 both encode the same isoform (2).
      Source sequence(s)
      AA168469, AK003586, AK150038, BU613615
      Consensus CDS
      CCDS51639.1
      UniProtKB/Swiss-Prot
      Q3UDK1
      Related
      ENSMUSP00000113910.2, ENSMUST00000120784.8
      Conserved Domains (1) summary
      PLN03086
      Location:7 → 131
      PLN03086; PRLI-interacting factor K; Provisional

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      121509788..121524543 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017320867.3 → XP_017176356.2  TRAF-type zinc finger domain-containing protein 1 isoform X2

      Conserved Domains (1) summary
      PLN03086
      Location:73 → 197
      PLN03086; PRLI-interacting factor K; Provisional

    2. XM_017320864.2 → XP_017176353.1  TRAF-type zinc finger domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q3UDK1, Q8CFI8
      Conserved Domains (1) summary
      PLN03086
      Location:7 → 131
      PLN03086; PRLI-interacting factor K; Provisional

    3. XM_017320865.2 → XP_017176354.1  TRAF-type zinc finger domain-containing protein 1 isoform X3

      UniProtKB/Swiss-Prot
      Q3UDK1
      Conserved Domains (1) summary
      PLN03086
      Location:7 → 131
      PLN03086; PRLI-interacting factor K; Provisional

    4. XM_011248197.4 → XP_011246499.1  TRAF-type zinc finger domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_011246499.1

      UniProtKB/Swiss-Prot
      Q3UDK1, Q8CFI8
      Conserved Domains (1) summary
      PLN03086
      Location:7 → 131
      PLN03086; PRLI-interacting factor K; Provisional

    5. XM_006530302.4 → XP_006530365.1  TRAF-type zinc finger domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006530365.1

      UniProtKB/Swiss-Prot
      Q3UDK1, Q8CFI8
      Conserved Domains (1) summary
      PLN03086
      Location:7 → 131
      PLN03086; PRLI-interacting factor K; Provisional

    6. XM_030254429.1 → XP_030110289.1  TRAF-type zinc finger domain-containing protein 1 isoform X4

      Conserved Domains (1) summary
      PLN03086
      Location:7 → 131
      PLN03086; PRLI-interacting factor K; Provisional

    7. XM_030254428.1 → XP_030110288.1  TRAF-type zinc finger domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q3UDK1, Q8CFI8
      Conserved Domains (1) summary
      PLN03086
      Location:7 → 131
      PLN03086; PRLI-interacting factor K; Provisional
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3UDK1.1 GenPept UniProtKB/Swiss-Prot:Q3UDK1

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