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    Prdm5 PR domain containing 5 [ Mus musculus (house mouse) ]

    Gene ID: 70779, updated on 27-Nov-2024

    Summary

    Official Symbol
    Prdm5provided by MGI
    Official Full Name
    PR domain containing 5provided by MGI
    Primary source
    MGI:MGI:1918029
    See related
    Ensembl:ENSMUSG00000029913 AllianceGenome:MGI:1918029
    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
    PFM2; 4432417F03Rik; 6530401I24Rik; E130112L17Rik
    Summary
    Predicted to enable DNA-binding transcription factor binding activity; DNA-binding transcription repressor activity, RNA polymerase II-specific; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in nuclear body and nucleolus. Is expressed in several structures, including central nervous system; early embryo; and genitourinary system. Human ortholog(s) of this gene implicated in brittle cornea syndrome 2. Orthologous to human PRDM5 (PR/SET domain 5). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in limb E14.5 (RPKM 2.9), CNS E11.5 (RPKM 1.9) and 20 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Prdm5 in Genome Data Viewer
    Location:
    6 C1; 6 30.32 cM
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (65754640..65914606)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (65777656..65937622)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 36144 Neighboring gene neuron-derived neurotrophic factor Neighboring gene STARR-seq mESC enhancer starr_16141 Neighboring gene STARR-seq mESC enhancer starr_16143 Neighboring gene STARR-seq mESC enhancer starr_16145 Neighboring gene RIKEN cDNA 4930544G11 gene Neighboring gene predicted gene, 23625

    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)
    • Endonuclease-mediated (2) 
    • Gene trapped (2) 

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription factor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription cis-regulatory region binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mitotic cell cycle ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in mitotic cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of extracellular matrix organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of extracellular matrix organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in nuclear body IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    PR domain zinc finger protein 5
    Names
    PR domain-containing protein 5
    NP_081823.2
    NP_083825.1
    XP_006506665.1
    XP_006506667.1
    XP_036008193.1
    XP_036008195.1

    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_027547.2NP_081823.2  PR domain zinc finger protein 5 isoform 1

      See identical proteins and their annotated locations for NP_081823.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK014501, BG070775, BX511446, BY014014
      Consensus CDS
      CCDS20208.1
      UniProtKB/Swiss-Prot
      B2RSK8, Q9CXE0
      Related
      ENSMUSP00000031976.8, ENSMUST00000031976.14
      Conserved Domains (4) summary
      smart00317
      Location:20123
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      COG5048
      Location:186590
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:460480
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:473496
      zf-H2C2_2; Zinc-finger double domain
    2. NM_029549.1NP_083825.1  PR domain zinc finger protein 5 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks multiple exons in the coding region but maintains the reading frame, compared to variant 1. These differences result in a shorter isoform (2), compared to isoform 1.
      Source sequence(s)
      AC154005, AC158677
      Consensus CDS
      CCDS85059.1
      UniProtKB/TrEMBL
      E9Q707, Q9D364
      Related
      ENSMUSP00000031973.7, ENSMUST00000031973.13

    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_000072.7 Reference GRCm39 C57BL/6J

      Range
      65754640..65914606
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006506604.4XP_006506667.1  PR domain zinc finger protein 5 isoform X4

      Conserved Domains (4) summary
      COG5048
      Location:258621
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:491511
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam15909
      Location:172222
      zf-C2H2_8; C2H2-type zinc ribbon
      cd19190
      Location:2128
      PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins
    2. XM_036152300.1XP_036008193.1  PR domain zinc finger protein 5 isoform X1

      UniProtKB/TrEMBL
      G3UWU3
      Related
      ENSMUSP00000133423.2, ENSMUST00000172638.2
      Conserved Domains (3) summary
      COG5048
      Location:168365
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:319339
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd19190
      Location:2128
      PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins
    3. XM_006506602.4XP_006506665.1  PR domain zinc finger protein 5 isoform X2

      Conserved Domains (3) summary
      COG5048
      Location:163325
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:195215
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl40432
      Location:2100
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    4. XM_036152302.1XP_036008195.1  PR domain zinc finger protein 5 isoform X3

      Conserved Domains (3) summary
      COG5048
      Location:188318
      COG5048; FOG: Zn-finger [General function prediction only]
      COG5189
      Location:2296
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:188208
      ZF_C2H2; C2H2 Zn finger [structural motif]

    RNA

    1. XR_004933621.1 RNA Sequence

    2. XR_377492.4 RNA Sequence

    3. XR_377493.4 RNA Sequence