Khdc4 KH domain containing 4, pre-mRNA splicing factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Khdc4provided by RGD
Official Full Name: KH domain containing 4, pre-mRNA splicing factorprovided by RGD
Primary source: RGD:1565775
See related: EnsemblRapid:ENSRNOG00000020139 AllianceGenome:RGD:1565775
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: Blom7; RGD1565775
Summary: Predicted to enable RNA binding activity. Predicted to be involved in mRNA splice site recognition. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be part of spliceosomal complex. Predicted to be active in nucleus. Orthologous to human KHDC4 (KH domain containing 4, pre-mRNA splicing factor). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 252.2), Lung (RPKM 199.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q34

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (176446895..176475405)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (174149059..174177816)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (188051657..188080280)

Chromosome 2 - NC_086020.1 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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General gene information

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Markers

RH129213 (e-PCR)
- UniSTS:212521

RH139154 (e-PCR)
- UniSTS:221240

RH136040 (e-PCR)
- UniSTS:210035

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in mRNA splice site recognition	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of spliceosomal complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: KH homology domain-containing protein 4

Names: nuclear ribonucleoprotein K homology domain protein

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_001399238.1 → NP_001386167.1 KH homology domain-containing protein 4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/TrEMBL

A6J698, F1LM38, Q56A23

Related

ENSRNOP00000027385.7, ENSRNOT00000027385.10

Conserved Domains (2) summary

cd22385
Location:100 → 183

KH-I_KHDC4_rpt1; first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins

cd22386
Location:230 → 331

KH-I_KHDC4_rpt2; first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins

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_086020.1 Reference GRCr8

Range

176446895..176475405

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063282124.1 → XP_063138194.1 KH homology domain-containing protein 4 isoform X1

UniProtKB/TrEMBL

A6J697
XM_063282125.1 → XP_063138195.1 KH homology domain-containing protein 4 isoform X3
XM_063282126.1 → XP_063138196.1 KH homology domain-containing protein 4 isoform X4
XM_039103757.2 → XP_038959685.1 KH homology domain-containing protein 4 isoform X2

Conserved Domains (1) summary

cd22386
Location:2 → 103

KH-I_KHDC4_rpt2; first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins
XM_039103756.2 → XP_038959684.1 KH homology domain-containing protein 4 isoform X2

Conserved Domains (1) summary

cd22386
Location:2 → 103

KH-I_KHDC4_rpt2; first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins