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Khdc4 KH domain containing 4, pre-mRNA splicing factor [ Mus musculus (house mouse) ]

Gene ID: 74200, updated on 20-Apr-2024

Summary

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Official Symbol
Khdc4provided by MGI
Official Full Name
KH domain containing 4, pre-mRNA splicing factorprovided by MGI
Primary source
MGI:MGI:1921450
See related
Ensembl:ENSMUSG00000028060 AllianceGenome:MGI:1921450
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
Blom7; Kiaa0907; 2810403A07Rik; A430106P18Rik
Summary
Enables RNA binding activity. Predicted to be involved in mRNA splice site selection. Predicted to act upstream of or within RNA splicing and mRNA processing. 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, Apr 2022]
Expression
Ubiquitous expression in limb E14.5 (RPKM 32.4), CNS E14 (RPKM 30.0) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
3 F1; 3 38.93 cM
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (88593087..88620240)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (88685428..88712933)

Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene Rho/Rac guanine nucleotide exchange factor 2 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:88425928-88426111 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:88426160-88426313 Neighboring gene predicted gene 20652 Neighboring gene STARR-seq mESC enhancer starr_08213 Neighboring gene STARR-seq mESC enhancer starr_08214 Neighboring gene relaxin family peptide receptor 4 Neighboring gene STARR-positive B cell enhancer ABC_E2077 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:88490214-88490323 Neighboring gene predicted gene, 25820 Neighboring gene STARR-positive B cell enhancer ABC_E2669 Neighboring gene Ras-like without CAAX 1 Neighboring gene STARR-seq mESC enhancer starr_08216 Neighboring gene predicted gene 10253

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. 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
  2. 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
  3. Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins. Crisci A, et al. Nucleic Acids Res, 2015 Dec 2. PMID 26420826, Free PMC Article
  4. Prediction of the coding sequences of mouse homologues of KIAA gene: IV. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, et al. DNA Res, 2004 Jun 30. PMID 15368895
  5. BioID screening of biotinylation sites using the avidin-like protein Tamavidin 2-REV identifies global interactors of stimulator of interferon genes (STING). Motani K, et al. J Biol Chem, 2020 Aug 7. PMID 32554809, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding ISO
Inferred from Sequence Orthology
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
  
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 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
brings lots of money 7
pre-mRNA splicing factor protein Khdc4
protein BLOM7

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_001429209.1 → NP_001416138.1  KH homology domain-containing protein 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC134246

  2. NM_028814.5 → NP_083090.2  KH homology domain-containing protein 4 isoform 1

    See identical proteins and their annotated locations for NP_083090.2

    Status: VALIDATED

    Source sequence(s)
    AC134246
    Consensus CDS
    CCDS17483.1
    UniProtKB/Swiss-Prot
    Q3TCX3, Q69ZW1, Q8BUQ0, Q923C9, Q9CZ63, Q9D207
    Related
    ENSMUSP00000029696.7, ENSMUST00000029696.11
    Conserved Domains (1) summary
    cl00098
    Location:234 → 324
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

RNA

  1. NR_151825.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC134246
    Related
    ENSMUST00000199684.5

  2. NR_151826.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC134246
    Related
    ENSMUST00000198042.5

  3. NR_151827.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC134246

  4. NR_190694.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC134246

  5. NR_190695.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC134246

  6. NR_190696.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC134246

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_000069.7 Reference GRCm39 C57BL/6J

    Range
    88593087..88620240
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017319752.3 → XP_017175241.1  KH homology domain-containing protein 4 isoform X1

    Conserved Domains (1) summary
    cl00098
    Location:234 → 324
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

RNA

  1. XR_003954405.2 RNA Sequence

  2. XR_375591.3 RNA Sequence

  3. XR_003954406.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q3TCX3.1 GenPept UniProtKB/Swiss-Prot:Q3TCX3

Gene LinkOut

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