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

Gene ID: 304054, updated on 17-Aug-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 RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and promoter-specific chromatin binding activity. Predicted to be involved in 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 nucleus. Orthologous to human PRDM15 (PR/SET domain 15). [provided by Alliance of Genome Resources, Apr 2022]
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 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 DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
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 methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables promoter-specific chromatin binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in cell fate commitment IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in methylation IEA
Inferred from Electronic Annotation
more info
  
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 stem cell division 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
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
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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