Wdfy1 WD repeat and FYVE domain containing 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Wdfy1provided by MGI
Official Full Name: WD repeat and FYVE domain containing 1provided by MGI
Primary source: MGI:MGI:1916618
See related: Ensembl:ENSMUSG00000073643 AllianceGenome:MGI:1916618
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: Jr1; WDF1; FENS-1; ZFYVE17; mKIAA1435; 1700013B03Rik; 1700120F24Rik
Summary: Predicted to enable 1-phosphatidylinositol binding activity. Involved in positive regulation of toll-like receptor 3 signaling pathway and positive regulation of toll-like receptor 4 signaling pathway. Located in early endosome. Is expressed in extraembryonic component; placenta; and skin. Orthologous to human WDFY1 (WD repeat and FYVE domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in testis adult (RPKM 34.1), whole brain E14.5 (RPKM 7.6) and 25 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 40.94 cM; 1 C4

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (79679979..79753764, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (79702262..79776143, complement)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

WDFY1, a WD40 repeat protein, is not essential for spermatogenesis and male fertility in mice.
Title: WDFY1, a WD40 repeat protein, is not essential for spermatogenesis and male fertility in mice.
miR-511 Deficiency Protects Mice from Experimental Colitis by Reducing TLR3 and TLR4 Responses via WD Repeat and FYVE-Domain-Containing Protein 1.
Title: miR-511 Deficiency Protects Mice from Experimental Colitis by Reducing TLR3 and TLR4 Responses via WD Repeat and FYVE-Domain-Containing Protein 1.
Wdfy1 deficiency impairs Tlr3-mediated immune responses in vivo.
Title: Wdfy1 deficiency impairs Tlr3-mediated immune responses in vivo.
Genome-wide assessment of Hes1 occupancy revealed that suppression of WDFY1 was secondary to direct binding and thus enhancement of expression of VEGF-C by Hes1
Title: Hes1 attenuates type I IFN responses via VEGF-C and WDFY1.
PRDX6 inhibits the neurogenesis of neural precursor cells through TLR4-dependent downregulation of WDFY1.
Title: PRDX6 Inhibits Neurogenesis through Downregulation of WDFY1-Mediated TLR4 Signal.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4)
Gene trapped (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Wdfy1 (e-PCR), detects polymorphism
- UniSTS:532247

MARC_16705-16706:1018020718:3 (e-PCR)
- UniSTS:268080

BE197290 (e-PCR)
- UniSTS:207178

D10Mit157.2 (e-PCR), detects polymorphism
- UniSTS:126061

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables 1-phosphatidylinositol binding	ISO Inferred from Sequence Orthology more info
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 positive regulation of toll-like receptor 3 signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of toll-like receptor 3 signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of toll-like receptor 3 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of toll-like receptor 4 signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of toll-like receptor 4 signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of toll-like receptor 4 signaling pathway	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in cell junction	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
is_active_in early endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome	ISO Inferred from Sequence Orthology more info
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: WD repeat and FYVE domain-containing protein 1

Names: WD40 and FYVE domain containing 1; WD40- and FYVE domain-containing protein 1

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)

NM_001111279.1 → NP_001104749.1 WD repeat and FYVE domain-containing protein 1 isoform 1

See identical proteins and their annotated locations for NP_001104749.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer protein (isoform 1).

Source sequence(s)

AC083910, AK007215, AK159710, AK165554, AK220391, BQ031098

Consensus CDS

CCDS48296.1

UniProtKB/Swiss-Prot

E9Q4P1, Q5DTX9

Related

ENSMUSP00000109140.2, ENSMUST00000113512.8

Conserved Domains (3) summary

cd15756
Location:279 → 354

FYVE_WDFY1; FYVE domain found in WD40 repeat and FYVE domain-containing protein 1 (WDFY1) and similar proteins

sd00039
Location:28 → 67

7WD40; WD40 repeat [structural motif]

cl29593
Location:16 → 272

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_027057.3 → NP_081333.1 WD repeat and FYVE domain-containing protein 1 isoform 2

See identical proteins and their annotated locations for NP_081333.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks multiple exons and uses an alternate splice site in the 3' coding region, compared to variant 1, that results in a frameshift. It encodes isoform 2 which has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AK005937, AK007215, BE197290

Consensus CDS

CCDS15090.1

UniProtKB/TrEMBL

D3Z057, Q9DAD3

Related

ENSMUSP00000040224.8, ENSMUST00000048820.14

Conserved Domains (2) summary

sd00039
Location:27 → 64

7WD40; WD40 repeat [structural motif]

cl29593
Location:20 → 138

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

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

NC_000067.7 Reference GRCm39 C57BL/6J

Range

79679979..79753764 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036153456.1 → XP_036009349.1 WD repeat and FYVE domain-containing protein 1 isoform X4

UniProtKB/Swiss-Prot

E9Q4P1, Q5DTX9

Conserved Domains (3) summary

cd15756
Location:279 → 354

FYVE_WDFY1; FYVE domain found in WD40 repeat and FYVE domain-containing protein 1 (WDFY1) and similar proteins

sd00039
Location:28 → 67

7WD40; WD40 repeat [structural motif]

cl29593
Location:16 → 272

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_006496543.3 → XP_006496606.1 WD repeat and FYVE domain-containing protein 1 isoform X1

UniProtKB/TrEMBL

Q8R3I5

Conserved Domains (3) summary

sd00039
Location:14 → 51

7WD40; WD40 repeat [structural motif]

cl28890
Location:176 → 251

FYVE_like_SF; FYVE domain like superfamily

cl29593
Location:4 → 169

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_030242794.1 → XP_030098654.1 WD repeat and FYVE domain-containing protein 1 isoform X2

Conserved Domains (2) summary

sd00039
Location:27 → 64

7WD40; WD40 repeat [structural motif]

cl29593
Location:16 → 207

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_030242799.1 → XP_030098659.1 WD repeat and FYVE domain-containing protein 1 isoform X2

Conserved Domains (2) summary

sd00039
Location:27 → 64

7WD40; WD40 repeat [structural motif]

cl29593
Location:16 → 207

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_017322387.1 → XP_017177876.1 WD repeat and FYVE domain-containing protein 1 isoform X2

Conserved Domains (2) summary

sd00039
Location:27 → 64

7WD40; WD40 repeat [structural motif]

cl29593
Location:16 → 207

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_030242801.1 → XP_030098661.1 WD repeat and FYVE domain-containing protein 1 isoform X3

UniProtKB/TrEMBL

D3Z057, Q9DAD3

Conserved Domains (2) summary

sd00039
Location:27 → 64

7WD40; WD40 repeat [structural motif]

cl29593
Location:20 → 138

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...