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

Gene ID: 114635, updated on 2-Nov-2024

Summary

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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
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

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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

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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

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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_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.

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