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

    Gene ID: 74200, updated on 9-Dec-2024

    Summary

    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 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
    Ubiquitous expression in limb E14.5 (RPKM 32.4), CNS E14 (RPKM 30.0) and 28 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Khdc4 in Genome Data Viewer
    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

    Expression

    • 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

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 RNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in mRNA splice site recognition ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in mRNA splice site recognition ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    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
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of spliceosomal complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of spliceosomal complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    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)

    NEW Try the new Transcript table

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

      Status: VALIDATED

      Source sequence(s)
      AC134246
    2. NM_028814.5NP_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:234324
      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_017319752.3XP_017175241.1  KH homology domain-containing protein 4 isoform X1

      Conserved Domains (1) summary
      cl00098
      Location:234324
      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