Wdhd1 WD repeat and HMG-box DNA binding protein 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Wdhd1provided by RGD
Official Full Name: WD repeat and HMG-box DNA binding protein 1provided by RGD
Primary source: RGD:1310200
See related: EnsemblRapid:ENSRNOG00000011167 AllianceGenome:RGD:1310200
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
Summary: Predicted to enable RNA binding activity; RNA polymerase binding activity; and chromatin binding activity. Predicted to be involved in DNA repair; DNA-templated DNA replication; and mitotic cell cycle. Predicted to act upstream of or within RNA processing; pericentric heterochromatin organization; and regulation of chromosome organization. Predicted to be located in chromosome, centromeric region and nucleoplasm. Predicted to be active in nuclear replication fork. Human ortholog(s) of this gene implicated in cholangiocarcinoma. Orthologous to human WDHD1 (WD repeat and HMG-box DNA binding protein 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 160.5), Spleen (RPKM 123.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 15p14

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	15	NC_086033.1 (22957492..23002820, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	15	NC_051350.1 (20478310..20523106, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	15	NC_005114.4 (24021674..24056073, complement)

Chromosome 15 - NC_086033.1 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA-templated DNA replication	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within RNA processing	ISO Inferred from Sequence Orthology more info
involved_in mitotic cell cycle	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within pericentric heterochromatin organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of chromosome organization	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromosome, centromeric region	ISO Inferred from Sequence Orthology more info
is_active_in nuclear replication fork	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: WD repeat and HMG-box DNA-binding 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_001107255.1 → NP_001100725.1 WD repeat and HMG-box DNA-binding protein 1 isoform 3

See identical proteins and their annotated locations for NP_001100725.1

Status: PROVISIONAL

Source sequence(s)

CH474040

UniProtKB/TrEMBL

A0A8I6A4W0, A6KE41

Conserved Domains (4) summary

smart00398
Location:1005 → 1058

HMG; high mobility group

cd00200
Location:10 → 289

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 ...

sd00039
Location:21 → 54

7WD40; WD40 repeat [structural motif]

pfam12341
Location:423 → 706

Mcl1_mid; Minichromosome loss protein, Mcl1, middle region
NM_001431411.1 → NP_001418340.1 WD repeat and HMG-box DNA-binding protein 1 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000015

UniProtKB/TrEMBL

A0A8I6A4W0, D3ZN63
NM_001431412.1 → NP_001418341.1 WD repeat and HMG-box DNA-binding protein 1 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000015

UniProtKB/TrEMBL

A0A8I6A4W0

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

NC_086033.1 Reference GRCr8

Range

22957492..23002820 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039093262.2 → XP_038949190.1 WD repeat and HMG-box DNA-binding protein 1 isoform X2

Related

ENSRNOP00000101557.1, ENSRNOT00000157066.1

Conserved Domains (4) summary

smart00398
Location:1007 → 1058

HMG; high mobility group

cd00200
Location:10 → 289

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 ...

sd00039
Location:21 → 54

7WD40; WD40 repeat [structural motif]

pfam12341
Location:423 → 706

Mcl1_mid; Minichromosome loss protein, Mcl1, middle region
XM_006251795.5 → XP_006251857.1 WD repeat and HMG-box DNA-binding protein 1 isoform X1

Related

ENSRNOP00000015100.6, ENSRNOT00000015100.7

Conserved Domains (5) summary

smart00398
Location:1007 → 1060

HMG; high mobility group

COG2319
Location:11 → 297

WD40; WD40 repeat [General function prediction only]

cd00200
Location:10 → 289

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 ...

pfam12341
Location:424 → 706

Mcl1_mid; Minichromosome loss protein, Mcl1, middle region

sd00039
Location:21 → 54

7WD40; WD40 repeat [structural motif]