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

Gene ID: 313678, updated on 10-Oct-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. Located in nucleus. Orthologous to human PRDM2 (PR/SET domain 2). [provided by Alliance of Genome Resources, Apr 2022]
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 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 IBA
Inferred from Biological aspect of Ancestor
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

    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

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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