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Prdm2 PR domain containing 2, with ZNF domain [ Mus musculus (house mouse) ]

Gene ID: 110593, updated on 28-Oct-2024

Summary

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Official Symbol
Prdm2provided by MGI
Official Full Name
PR domain containing 2, with ZNF domainprovided by MGI
Primary source
MGI:MGI:107628
See related
Ensembl:ENSMUSG00000057637 AllianceGenome:MGI:107628
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
Riz; KMT8; Riz1; Gm1033; Gm19732; Znfpr1c1; 4833427P12Rik; E330024L24Rik
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. Acts upstream of or within determination of adult lifespan. Predicted to be located in Golgi apparatus and nucleoplasm. Predicted to be active in nucleus. Is expressed in forelimb cartilage condensation; forelimb long bone; and tendon. Orthologous to human PRDM2 (PR/SET domain 2). [provided by Alliance of Genome Resources, Oct 2024]
Expression
Ubiquitous expression in testis adult (RPKM 8.9), limb E14.5 (RPKM 7.0) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Prdm2 in Genome Data Viewer
Location:
4 E1; 4 76.84 cM
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (142833961..142939560, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (143107391..143212769, complement)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene kazrin, periplakin interacting protein Neighboring gene STARR-seq mESC enhancer starr_11958 Neighboring gene predicted gene, 42342 Neighboring gene predicted gene, 42340 Neighboring gene predicted gene, 42341 Neighboring gene STARR-seq mESC enhancer starr_11959 Neighboring gene STARR-seq mESC enhancer starr_11960 Neighboring gene STARR-positive B cell enhancer ABC_E2723 Neighboring gene STARR-positive B cell enhancer ABC_E6253 Neighboring gene microRNA 7021 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:142809456-142809609 Neighboring gene STARR-seq mESC enhancer starr_11962 Neighboring gene STARR-seq mESC enhancer starr_11963 Neighboring gene ribosomal protein L7A pseudogene Neighboring gene eukaryotic translation elongation factor 2, pseudogene 2 Neighboring gene predicted gene, 22039 Neighboring gene predicted gene, 52493

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data 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

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Related articles in PubMed

  1. Retinoblastoma protein-interacting zinc finger 1, a tumor suppressor, augments lipopolysaccharide-induced proinflammatory cytokine production via enhancing nuclear factor-kappaB activation. Noman AS, et al. Cell Immunol, 2010. PMID 20557878
  2. Tumor suppressor RIZ1 in obesity and the PI3K/AKT/mTOR pathway. Xie X, et al. Obesity (Silver Spring), 2016 Feb. PMID 26709097
  3. Retinoblastoma protein-interacting zinc finger 1 (RIZ1) participates in RANKL-induced osteoclast formation via regulation of NFATc1 expression. Noman AS, et al. Immunol Lett, 2010 Jul 8. PMID 20417662
  4. Requirement of RIZ1 for cancer prevention by methyl-balanced diet. Zhou W, et al. PLoS One, 2008. PMID 18852888, Free PMC Article
  5. Riz maps to distal chromosome 4 near genes involved in tumorigenesis and nerve degeneration. Mock BA, et al. Mamm Genome, 1996 Aug. PMID 8679000

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RIZ1 is an important regulator of both Akt3 transcription and AKT phosphorylation and suggest a role for RIZ1 in HF-induced obesity and the AKT pathway
    Title: Tumor suppressor RIZ1 in obesity and the PI3K/AKT/mTOR pathway.
  2. RIZ1 might participate osteoclast formation through the regulation of NFATc1 expression.
    Title: Retinoblastoma protein-interacting zinc finger 1 (RIZ1) participates in RANKL-induced osteoclast formation via regulation of NFATc1 expression.
  3. prevents lipopolysaccharide-induced proinflammatory cytokine production via enhancing nuclear factor-kappaB activation
    Title: Retinoblastoma protein-interacting zinc finger 1, a tumor suppressor, augments lipopolysaccharide-induced proinflammatory cytokine production via enhancing nuclear factor-kappaB activation.
  4. Data suggest that the histone methyltransferase RIZ1 is required for estrogen response in female reproductive tissues and that estrogen-bound estrogen receptors may turn a transcriptional repressor into a coactivator.
    Title: A histone methyltransferase is required for maximal response to female sex hormones.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 
  • Targeted (2)  1 citation

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
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 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 ISO
Inferred from Sequence Orthology
more info
  
enables sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within determination of adult lifespan IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 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 ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
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
 PubMed 

General protein information

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Preferred Names
PR domain zinc finger protein 2
NP_001074824.3
NP_001243309.1
XP_006538549.1
XP_006538551.1
XP_011248476.1
XP_011248477.1
XP_017175407.1
XP_030108949.1
XP_030108950.1
XP_030108951.1
XP_030108952.1
XP_030108953.1
XP_036019478.1
XP_036019479.1
XP_036019480.1
XP_036019482.1

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_001081355.3 → NP_001074824.3  PR domain zinc finger protein 2 isoform a

    See identical proteins and their annotated locations for NP_001074824.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform .
    Source sequence(s)
    AI850024, AK087820, AL606915, BY232351, CN537770
    Consensus CDS
    CCDS38942.2
    UniProtKB/TrEMBL
    A2A7B5
    Related
    ENSMUSP00000101404.2, ENSMUST00000105778.8
    Conserved Domains (5) summary
    sd00017
    Location:1128 → 1148
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:358 → 378
    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:356 → 378
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:477 → 500
    zf-C2H2_4; C2H2-type zinc finger

  2. NM_001256380.1 → NP_001243309.1  PR domain zinc finger protein 2 isoform b

    See identical proteins and their annotated locations for NP_001243309.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two exons in the 3' CDS and UTR, compared to variant 1. It encodes isoform b, which is shorter than isoform a.
    Source sequence(s)
    AL606915
    UniProtKB/TrEMBL
    B9EKQ3
    Conserved Domains (3) summary
    smart00317
    Location:34 → 146
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    sd00017
    Location:1128 → 1148
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:356 → 378
    zf-C2H2; Zinc finger, C2H2 type

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
    142833961..142939560 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011250175.3 → XP_011248477.1  PR domain zinc finger protein 2 isoform X7

    Conserved Domains (1) summary
    cd19188
    Location:22 → 144
    PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins

  2. XM_036163585.1 → XP_036019478.1  PR domain zinc finger protein 2 isoform X1

    UniProtKB/TrEMBL
    A2A7B5
    Conserved Domains (5) summary
    sd00017
    Location:1128 → 1148
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:358 → 378
    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:356 → 378
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:477 → 500
    zf-C2H2_4; C2H2-type zinc finger

  3. XM_006538486.4 → XP_006538549.1  PR domain zinc finger protein 2 isoform X3

    Conserved Domains (5) summary
    sd00017
    Location:1055 → 1075
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:285 → 305
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cl40432
    Location:1 → 71
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    pfam00096
    Location:283 → 305
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:404 → 427
    zf-C2H2_4; C2H2-type zinc finger

  4. XM_017319918.3 → XP_017175407.1  PR domain zinc finger protein 2 isoform X1

    UniProtKB/TrEMBL
    A2A7B5
    Conserved Domains (5) summary
    sd00017
    Location:1128 → 1148
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:358 → 378
    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:356 → 378
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:477 → 500
    zf-C2H2_4; C2H2-type zinc finger

  5. XM_036163587.1 → XP_036019480.1  PR domain zinc finger protein 2 isoform X5

    Conserved Domains (3) summary
    sd00017
    Location:928 → 948
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:158 → 178
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:156 → 178
    zf-C2H2; Zinc finger, C2H2 type

  6. XM_030253090.1 → XP_030108950.1  PR domain zinc finger protein 2 isoform X4

    Conserved Domains (4) summary
    sd00017
    Location:1044 → 1064
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:274 → 294
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:272 → 294
    zf-C2H2; Zinc finger, C2H2 type
    cl40432
    Location:1 → 60
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

  7. XM_030253092.1 → XP_030108952.1  PR domain zinc finger protein 2 isoform X5

    Conserved Domains (3) summary
    sd00017
    Location:928 → 948
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:158 → 178
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:156 → 178
    zf-C2H2; Zinc finger, C2H2 type

  8. XM_030253091.1 → XP_030108951.1  PR domain zinc finger protein 2 isoform X5

    Conserved Domains (3) summary
    sd00017
    Location:928 → 948
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:158 → 178
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:156 → 178
    zf-C2H2; Zinc finger, C2H2 type

  9. XM_030253089.2 → XP_030108949.1  PR domain zinc finger protein 2 isoform X4

    Conserved Domains (4) summary
    sd00017
    Location:1044 → 1064
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:274 → 294
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:272 → 294
    zf-C2H2; Zinc finger, C2H2 type
    cl40432
    Location:1 → 60
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

  10. XM_036163586.1 → XP_036019479.1  PR domain zinc finger protein 2 isoform X3

    Conserved Domains (5) summary
    sd00017
    Location:1055 → 1075
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:285 → 305
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cl40432
    Location:1 → 71
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    pfam00096
    Location:283 → 305
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:404 → 427
    zf-C2H2_4; C2H2-type zinc finger

  11. XM_006538488.4 → XP_006538551.1  PR domain zinc finger protein 2 isoform X5

    Conserved Domains (3) summary
    sd00017
    Location:928 → 948
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:158 → 178
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:156 → 178
    zf-C2H2; Zinc finger, C2H2 type

  12. XM_030253093.2 → XP_030108953.1  PR domain zinc finger protein 2 isoform X5

    Conserved Domains (3) summary
    sd00017
    Location:928 → 948
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:158 → 178
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:156 → 178
    zf-C2H2; Zinc finger, C2H2 type

  13. XM_011250174.2 → XP_011248476.1  PR domain zinc finger protein 2 isoform X2

    Conserved Domains (4) summary
    sd00017
    Location:1128 → 1148
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:358 → 378
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:356 → 378
    zf-C2H2; Zinc finger, C2H2 type
    cd19188
    Location:22 → 144
    PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins

  14. XM_036163589.1 → XP_036019482.1  PR domain zinc finger protein 2 isoform X6

    Conserved Domains (3) summary
    sd00017
    Location:928 → 948
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:158 → 178
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:156 → 178
    zf-C2H2; Zinc finger, C2H2 type
Nucleotide Protein Strain
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