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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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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