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    Prdm2 PR/SET domain 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313678, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Prdm2provided by RGD
    Official Full Name
    PR/SET domain 2provided by RGD
    Primary source
    RGD:1594531
    See related
    EnsemblRapid:ENSRNOG00000033522 AllianceGenome:RGD:1594531
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Riz
    Summary
    Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; DNA-binding transcription repressor activity, RNA polymerase II-specific; and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in response to estradiol. Predicted to be located in Golgi apparatus and nucleoplasm. Predicted to be active in nucleus. Orthologous to human PRDM2 (PR/SET domain 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 61.3), Kidney (RPKM 56.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Prdm2 in Genome Data Viewer
    Location:
    5q36
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (160704396..160815184, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (155421066..155531884, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (161769587..161879150, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene kazrin, periplakin interacting protein Neighboring gene uncharacterized LOC102556543 Neighboring gene uncharacterized LOC120103134 Neighboring gene large ribosomal subunit protein uL5-like Neighboring gene uncharacterized LOC103692503 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene ribosomal protein S20, pseudogene 11 Neighboring gene tubulin, alpha 1A, pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Dependence-induced increase of alcohol self-administration and compulsive drinking mediated by the histone methyltransferase PRDM2. Barbier E, et al. Mol Psychiatry, 2017 Dec. PMID 27573876, Free PMC Article
    2. Transcriptional repression mediated by the PR domain zinc finger gene RIZ. Xie M, et al. J Biol Chem, 1997 Oct 17. PMID 9334209
    3. cDNA cloning of a novel protein containing two zinc-finger domains that may function as a transcription factor for the human heme-oxygenase-1 gene. Muraosa Y, et al. Eur J Biochem, 1996 Feb 1. PMID 8654390
    4. The retinoblastoma-interacting zinc-finger protein RIZ is a downstream effector of estrogen action. Abbondanza C, et al. Proc Natl Acad Sci U S A, 2000 Mar 28. PMID 10706618, Free PMC Article
    5. The retinoblastoma protein binds to RIZ, a zinc-finger protein that shares an epitope with the adenovirus E1A protein. Buyse IM, et al. Proc Natl Acad Sci U S A, 1995 May 9. PMID 7538672, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    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 transcription regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K9 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in determination of adult lifespan IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within determination of adult lifespan ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    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
    		  
    involved_in positive regulation of transcription by RNA polymerase II 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
    		  
    involved_in response to estradiol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    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
    		  

    General protein information

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    Preferred Names
    PR domain zinc finger protein 2
    Names
    PR domain 2
    PR domain containing 2, with ZNF domain
    PR domain-containing protein 2
    retinoblastoma interacting zinc finger protein
    retinoblastoma protein-binding zinc finger protein
    retinoblastoma protein-interacting zinc finger protein
    zinc finger protein RIZ
    NP_001071116.2
    XP_017448915.1
    XP_038966015.1
    XP_038966018.1
    XP_063143890.1
    XP_063143891.1
    XP_063143892.1

    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_001077648.2 → NP_001071116.2  PR domain zinc finger protein 2

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/Swiss-Prot
      Q63755
      UniProtKB/TrEMBL
      F1LQ66
      Related
      ENSRNOP00000046011.3, ENSRNOT00000041175.6
      Conserved Domains (4) summary
      sd00017
      Location:1125 → 1145
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd19188
      Location:22 → 144
      PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
      pfam00096
      Location:355 → 377
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:476 → 499
      zf-C2H2_4; C2H2-type zinc finger

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      160704396..160815184 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063287822.1 → XP_063143892.1  PR domain zinc finger protein 2 isoform X5

    2. XM_039110087.2 → XP_038966015.1  PR domain zinc finger protein 2 isoform X1

      UniProtKB/Swiss-Prot
      Q63755
      UniProtKB/TrEMBL
      F1LQ66
      Conserved Domains (4) summary
      sd00017
      Location:1125 → 1145
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd19188
      Location:22 → 144
      PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
      pfam00096
      Location:355 → 377
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:476 → 499
      zf-C2H2_4; C2H2-type zinc finger

    3. XM_017593426.3 → XP_017448915.1  PR domain zinc finger protein 2 isoform X1

      UniProtKB/Swiss-Prot
      Q63755
      UniProtKB/TrEMBL
      F1LQ66
      Conserved Domains (4) summary
      sd00017
      Location:1125 → 1145
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd19188
      Location:22 → 144
      PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
      pfam00096
      Location:355 → 377
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:476 → 499
      zf-C2H2_4; C2H2-type zinc finger

    4. XM_063287821.1 → XP_063143891.1  PR domain zinc finger protein 2 isoform X3

      UniProtKB/Swiss-Prot
      Q63755
      Related
      ENSRNOP00000106619.1, ENSRNOT00000124287.1

    5. XM_039110090.2 → XP_038966018.1  PR domain zinc finger protein 2 isoform X4

      UniProtKB/Swiss-Prot
      Q63755
      Conserved Domains (2) summary
      sd00017
      Location:925 → 945
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:155 → 177
      zf-C2H2; Zinc finger, C2H2 type

    6. XM_063287820.1 → XP_063143890.1  PR domain zinc finger protein 2 isoform X2

      UniProtKB/Swiss-Prot
      Q63755
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q63755.1 GenPept UniProtKB/Swiss-Prot:Q63755

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