U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Trafd1 TRAF type zinc finger domain containing 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 114635, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Trafd1provided by RGD
    Official Full Name
    TRAF type zinc finger domain containing 1provided by RGD
    Primary source
    RGD:620171
    See related
    EnsemblRapid:ENSRNOG00000001351 AllianceGenome:RGD:620171
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Fln29
    Summary
    Predicted to enable zinc ion binding activity. Involved in response to cytokine. Predicted to be active in mitochondrion. Orthologous to human TRAFD1 (TRAF-type zinc finger domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 229.2), Testes (RPKM 222.7) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Trafd1 in Genome Data Viewer
    Location:
    12q16
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (40826251..40840169)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (35165606..35179525)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (40695520..40709438)

    Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene N(alpha)-acetyltransferase 25, NatB auxiliary subunit Neighboring gene 40S ribosomal protein S27-like Neighboring gene 40S ribosomal protein S20-like Neighboring gene HECT domain E3 ubiquitin protein ligase 4 Neighboring gene small nucleolar RNA SNORA42/SNORA80 family Neighboring gene ribosomal protein L6 Neighboring gene protein tyrosine phosphatase, non-receptor type 11

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Cytokine-induced down-regulation of zfm1/splicing factor-1 promotes smooth muscle cell proliferation. Cattaruzza M, et al. J Biol Chem, 2002 Feb 22. PMID 11748220
    2. 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
    3. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Gibbs RA, et al. Nature, 2004 Apr 1. PMID 15057822
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of innate immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of innate immune response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in response to cytokine IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    TRAF-type zinc finger domain-containing protein 1
    Names
    FLN29 gene product

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_053760.2 → NP_446212.2  TRAF-type zinc finger domain-containing protein 1

      See identical proteins and their annotated locations for NP_446212.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000012
      UniProtKB/Swiss-Prot
      Q5M806, Q99MM4
      UniProtKB/TrEMBL
      A6J1F4, G3V959
      Related
      ENSRNOP00000036651.5, ENSRNOT00000033984.7
      Conserved Domains (1) summary
      PLN03086
      Location:12 → 131
      PLN03086; PRLI-interacting factor K; Provisional

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086030.1 Reference GRCr8

      Range
      40826251..40840169
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006249376.5 → XP_006249438.1  TRAF-type zinc finger domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006249438.1

      UniProtKB/Swiss-Prot
      Q5M806, Q99MM4
      UniProtKB/TrEMBL
      A6J1F4, G3V959
      Conserved Domains (1) summary
      PLN03086
      Location:12 → 131
      PLN03086; PRLI-interacting factor K; Provisional
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99MM4.2 GenPept UniProtKB/Swiss-Prot:Q99MM4

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools