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

Gene ID: 361980, updated on 4-Jan-2025

Summary

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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, Jan 2025]
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

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See Khdc4 in Genome Data Viewer
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_086020.1Genomic Context describing neighboring genes Neighboring gene Rho/Rac guanine nucleotide exchange factor 2 Neighboring gene U6 spliceosomal RNA Neighboring gene relaxin family peptide/INSL5 receptor 4 Neighboring gene small Cajal body-specific RNA 4 Neighboring gene RNA, U6 small nuclear 632 Neighboring gene Ras-like without CAAX 1 Neighboring gene synaptotagmin 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
  • 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. Inhibition of pre-mRNA splicing by a synthetic Blom7α-interacting small RNA. Löscher M, et al. PLoS One, 2012. PMID 23144703, Free PMC Article
  2. Blom7alpha is a novel heterogeneous nuclear ribonucleoprotein K homology domain protein involved in pre-mRNA splicing that interacts with SNEVPrp19-Pso4. Grillari J, et al. J Biol Chem, 2009 Oct 16. PMID 19641227, Free PMC Article
  3. The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity. Rapicavoli NA, et al. Neural Dev, 2011 Sep 21. PMID 21936910, Free PMC Article
  4. 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
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

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)

  1. 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

  1. NC_086020.1 Reference GRCr8

    Range
    176446895..176475405
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A6J697

  2. XM_063282125.1 → XP_063138195.1  KH homology domain-containing protein 4 isoform X3

  3. XM_063282126.1 → XP_063138196.1  KH homology domain-containing protein 4 isoform X4

  4. 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

  5. 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
Nucleotide Protein Strain
Heading Accession and Version

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