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    Prdm13 PR domain containing 13 [ Mus musculus (house mouse) ]

    Gene ID: 230025, updated on 9-Dec-2024

    Summary

    Official Symbol
    Prdm13provided by MGI
    Official Full Name
    PR domain containing 13provided by MGI
    Primary source
    MGI:MGI:2448528
    See related
    Ensembl:ENSMUSG00000040478 AllianceGenome:MGI:2448528
    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
    Summary
    Enables RNA polymerase II-specific DNA-binding transcription factor binding activity; chromatin binding activity; and histone methyltransferase activity. Involved in GABAergic neuron differentiation and hypothalamus cell differentiation. Acts upstream of or within negative regulation of transcription by RNA polymerase II and neurogenesis. Located in nucleus. Is expressed in several structures, including central nervous system and retina. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia. Orthologous to human PRDM13 (PR/SET domain 13). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Prdm13 in Genome Data Viewer
    Location:
    4 A3; 4 8.78 cM
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (21675865..21685963, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (21675865..21685963, complement)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene predicted gene 11875 Neighboring gene predicted gene, 57726 Neighboring gene STARR-seq mESC enhancer starr_09725 Neighboring gene STARR-seq mESC enhancer starr_09729 Neighboring gene STARR-seq mESC enhancer starr_09730 Neighboring gene cyclin C Neighboring gene STARR-positive B cell enhancer ABC_E3481 Neighboring gene STARR-seq mESC enhancer starr_09732 Neighboring gene STARR-seq mESC enhancer starr_09733 Neighboring gene thiosulfate sulfurtransferase (rhodanese)-like domain containing 3 Neighboring gene ubiquitin specific petidase 45

    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

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    General gene information

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase II-specific DNA-binding transcription factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    PR domain zinc finger protein 13
    Names
    PR domain-containing protein 13

    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_001080771.1NP_001074240.1  PR domain zinc finger protein 13

      See identical proteins and their annotated locations for NP_001074240.1

      Status: VALIDATED

      Source sequence(s)
      BB665287, BC017632
      Consensus CDS
      CCDS38699.1
      UniProtKB/Swiss-Prot
      B1AV74, E9PZZ1
      Related
      ENSMUSP00000092761.4, ENSMUST00000095141.4
      Conserved Domains (6) summary
      sd00017
      Location:622642
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00018
      Location:185208
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:622642
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:62159
      SET; SET domain
      pfam13465
      Location:635657
      zf-H2C2_2; Zinc-finger double domain
      pfam13894
      Location:677700
      zf-C2H2_4; C2H2-type zinc finger

    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_000070.7 Reference GRCm39 C57BL/6J

      Range
      21675865..21685963 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006537807.2XP_006537870.1  PR domain zinc finger protein 13 isoform X1

      See identical proteins and their annotated locations for XP_006537870.1

      Conserved Domains (6) summary
      COG5189
      Location:527602
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:524544
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00018
      Location:87110
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:524544
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:537555
      zf-H2C2_2; Zinc-finger double domain
      cl40432
      Location:169
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    2. XM_006537806.2XP_006537869.1  PR domain zinc finger protein 13 isoform X1

      See identical proteins and their annotated locations for XP_006537869.1

      Conserved Domains (6) summary
      COG5189
      Location:527602
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:524544
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00018
      Location:87110
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:524544
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:537555
      zf-H2C2_2; Zinc-finger double domain
      cl40432
      Location:169
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily