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

    Gene ID: 110593, updated on 9-Dec-2024

    Summary

    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, Dec 2024]
    Expression
    Ubiquitous expression in testis adult (RPKM 8.9), limb E14.5 (RPKM 7.0) and 28 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    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

    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 (1) 
    • Targeted (2)  1 citation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    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

    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)

    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_001081355.3NP_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:11281148
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:358378
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd19188
      Location:22144
      PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
      pfam00096
      Location:356378
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:477500
      zf-C2H2_4; C2H2-type zinc finger
    2. NM_001256380.1NP_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:34146
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      sd00017
      Location:11281148
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:356378
      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_011250175.3XP_011248477.1  PR domain zinc finger protein 2 isoform X7

      Conserved Domains (1) summary
      cd19188
      Location:22144
      PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
    2. XM_036163585.1XP_036019478.1  PR domain zinc finger protein 2 isoform X1

      UniProtKB/TrEMBL
      A2A7B5
      Conserved Domains (5) summary
      sd00017
      Location:11281148
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:358378
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd19188
      Location:22144
      PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
      pfam00096
      Location:356378
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:477500
      zf-C2H2_4; C2H2-type zinc finger
    3. XM_006538486.4XP_006538549.1  PR domain zinc finger protein 2 isoform X3

      Conserved Domains (5) summary
      sd00017
      Location:10551075
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:285305
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl40432
      Location:171
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
      pfam00096
      Location:283305
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:404427
      zf-C2H2_4; C2H2-type zinc finger
    4. XM_017319918.3XP_017175407.1  PR domain zinc finger protein 2 isoform X1

      UniProtKB/TrEMBL
      A2A7B5
      Conserved Domains (5) summary
      sd00017
      Location:11281148
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:358378
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd19188
      Location:22144
      PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
      pfam00096
      Location:356378
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:477500
      zf-C2H2_4; C2H2-type zinc finger
    5. XM_036163587.1XP_036019480.1  PR domain zinc finger protein 2 isoform X5

      Conserved Domains (3) summary
      sd00017
      Location:928948
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:158178
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:156178
      zf-C2H2; Zinc finger, C2H2 type
    6. XM_030253090.1XP_030108950.1  PR domain zinc finger protein 2 isoform X4

      Conserved Domains (4) summary
      sd00017
      Location:10441064
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:274294
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:272294
      zf-C2H2; Zinc finger, C2H2 type
      cl40432
      Location:160
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    7. XM_030253092.1XP_030108952.1  PR domain zinc finger protein 2 isoform X5

      Conserved Domains (3) summary
      sd00017
      Location:928948
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:158178
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:156178
      zf-C2H2; Zinc finger, C2H2 type
    8. XM_030253091.1XP_030108951.1  PR domain zinc finger protein 2 isoform X5

      Conserved Domains (3) summary
      sd00017
      Location:928948
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:158178
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:156178
      zf-C2H2; Zinc finger, C2H2 type
    9. XM_030253089.2XP_030108949.1  PR domain zinc finger protein 2 isoform X4

      Conserved Domains (4) summary
      sd00017
      Location:10441064
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:274294
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:272294
      zf-C2H2; Zinc finger, C2H2 type
      cl40432
      Location:160
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    10. XM_036163586.1XP_036019479.1  PR domain zinc finger protein 2 isoform X3

      Conserved Domains (5) summary
      sd00017
      Location:10551075
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:285305
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl40432
      Location:171
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
      pfam00096
      Location:283305
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:404427
      zf-C2H2_4; C2H2-type zinc finger
    11. XM_006538488.4XP_006538551.1  PR domain zinc finger protein 2 isoform X5

      Conserved Domains (3) summary
      sd00017
      Location:928948
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:158178
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:156178
      zf-C2H2; Zinc finger, C2H2 type
    12. XM_030253093.2XP_030108953.1  PR domain zinc finger protein 2 isoform X5

      Conserved Domains (3) summary
      sd00017
      Location:928948
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:158178
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:156178
      zf-C2H2; Zinc finger, C2H2 type
    13. XM_011250174.2XP_011248476.1  PR domain zinc finger protein 2 isoform X2

      Conserved Domains (4) summary
      sd00017
      Location:11281148
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:358378
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:356378
      zf-C2H2; Zinc finger, C2H2 type
      cd19188
      Location:22144
      PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
    14. XM_036163589.1XP_036019482.1  PR domain zinc finger protein 2 isoform X6

      Conserved Domains (3) summary
      sd00017
      Location:928948
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:158178
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:156178
      zf-C2H2; Zinc finger, C2H2 type