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

    Gene ID: 110593, updated on 27-Nov-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, Nov 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
    • 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 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
    Heading Accession and Version

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