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

Gene ID: 231712, updated on 5-Mar-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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See Trafd1 in Genome Data Viewer
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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