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    Prdm15 PR/SET domain 15 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304054, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Prdm15provided by RGD
    Official Full Name
    PR/SET domain 15provided by RGD
    Primary source
    RGD:1310055
    See related
    EnsemblRapid:ENSRNOG00000001620 AllianceGenome:RGD:1310055
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA-binding transcription factor activity; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and promoter-specific chromatin binding activity. Predicted to be involved in several processes, including positive regulation of transcription by RNA polymerase II; regulation of signal transduction; and regulation of stem cell division. Predicted to be located in nuclear body. Predicted to be active in cytoplasm and nucleus. Orthologous to human PRDM15 (PR/SET domain 15). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 41.4), Spleen (RPKM 37.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Prdm15 in Genome Data Viewer
    Location:
    11q12
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (50633973..50691624, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (37164608..37225172, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (38294040..38354648, complement)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108352390 Neighboring gene receptor-interacting serine-threonine kinase 4 Neighboring gene C2 calcium-dependent domain containing 2 Neighboring gene uncharacterized LOC134480980 Neighboring gene ribosomal protein S17, pseudogene 5

    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. Identification of a novel zinc finger protein gene (ZNF298) in the GAP2 of human chromosome 21q. Shibuya K, et al. Biochem Biophys Res Commun, 2005 Jul 1. PMID 15904895
    2. PRDM15 safeguards naive pluripotency by transcriptionally regulating WNT and MAPK-ERK signaling. Mzoughi S, et al. Nat Genet, 2017 Sep. PMID 28740264
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables promoter-specific chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of MAPK cascade ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of canonical Wnt signaling pathway 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 gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of stem cell division ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear body 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
    		  

    General protein information

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    Preferred Names
    PR domain zinc finger protein 15
    Names
    PR domain 15
    PR domain containing 15

    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_001427299.1 → NP_001414228.1  PR domain zinc finger protein 15

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000011
      UniProtKB/TrEMBL
      A6IQH4

    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_086029.1 Reference GRCr8

      Range
      50633973..50691624 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063270570.1 → XP_063126640.1  PR domain zinc finger protein 15 isoform X7

      UniProtKB/TrEMBL
      A6IQH4
      Related
      ENSRNOP00000084210.2, ENSRNOT00000114092.2

    2. XM_063270569.1 → XP_063126639.1  PR domain zinc finger protein 15 isoform X4

      UniProtKB/TrEMBL
      A6IQH4

    3. XM_017598097.3 → XP_017453586.1  PR domain zinc finger protein 15 isoform X2

      UniProtKB/TrEMBL
      A6IQH4
      Related
      ENSRNOP00000041592.6, ENSRNOT00000046318.7

    4. XM_039088807.2 → XP_038944735.1  PR domain zinc finger protein 15 isoform X1

      UniProtKB/TrEMBL
      A6IQH4, D3ZQ99
      Conserved Domains (5) summary
      COG5048
      Location:665 → 834
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:701 → 721
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam18445
      Location:12 → 37
      zf_PR_Knuckle; PR zinc knuckle motif
      cd19199
      Location:41 → 166
      PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
      NF033909
      Location:221 → 338
      opacity_OapA; opacity-associated protein OapA

    5. XM_039088802.2 → XP_038944730.1  PR domain zinc finger protein 15 isoform X1

      UniProtKB/TrEMBL
      A6IQH4, D3ZQ99
      Conserved Domains (5) summary
      COG5048
      Location:665 → 834
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:701 → 721
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam18445
      Location:12 → 37
      zf_PR_Knuckle; PR zinc knuckle motif
      cd19199
      Location:41 → 166
      PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
      NF033909
      Location:221 → 338
      opacity_OapA; opacity-associated protein OapA

    6. XM_039088805.2 → XP_038944733.1  PR domain zinc finger protein 15 isoform X5

      UniProtKB/TrEMBL
      A6IQH4
      Conserved Domains (5) summary
      COG3087
      Location:221 → 317
      FtsN; Cell division protein FtsN [Cell cycle control, cell division, chromosome partitioning]
      COG5048
      Location:631 → 800
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:667 → 687
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam18445
      Location:12 → 37
      zf_PR_Knuckle; PR zinc knuckle motif
      cd19199
      Location:41 → 166
      PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins

    7. XM_039088803.2 → XP_038944731.1  PR domain zinc finger protein 15 isoform X3

      UniProtKB/TrEMBL
      A6IQH4
      Conserved Domains (5) summary
      COG5048
      Location:368 → 829
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:696 → 716
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam18445
      Location:12 → 37
      zf_PR_Knuckle; PR zinc knuckle motif
      cd19199
      Location:41 → 166
      PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
      NF033909
      Location:221 → 338
      opacity_OapA; opacity-associated protein OapA

    8. XM_063270572.1 → XP_063126642.1  PR domain zinc finger protein 15 isoform X9

      UniProtKB/TrEMBL
      A6IQH4

    9. XM_039088804.2 → XP_038944732.1  PR domain zinc finger protein 15 isoform X6

      UniProtKB/TrEMBL
      A6IQH4
      Conserved Domains (5) summary
      COG5048
      Location:631 → 800
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:667 → 687
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam18445
      Location:12 → 37
      zf_PR_Knuckle; PR zinc knuckle motif
      cd19199
      Location:41 → 166
      PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
      NF033909
      Location:187 → 304
      opacity_OapA; opacity-associated protein OapA

    10. XM_063270571.1 → XP_063126641.1  PR domain zinc finger protein 15 isoform X8

      UniProtKB/TrEMBL
      A0A8I5ZYR1, A6IQH4

    11. XM_017598100.3 → XP_017453589.1  PR domain zinc finger protein 15 isoform X10

      UniProtKB/TrEMBL
      A6IQH4

    12. XM_039088808.2 → XP_038944736.1  PR domain zinc finger protein 15 isoform X11

      Conserved Domains (2) summary
      COG5048
      Location:162 → 331
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:198 → 218
      ZF_C2H2; C2H2 Zn finger [structural motif]

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001107104.1: Suppressed sequence

      Description
      NM_001107104.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from human: PRDM15 (GeneID:63977).
    Nucleotide Protein Strain
    Heading Accession and Version

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