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    Prdm6 PR/SET domain 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 307305, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Prdm6provided by RGD
    Official Full Name
    PR/SET domain 6provided by RGD
    Primary source
    RGD:1559594
    See related
    EnsemblRapid:ENSRNOG00000030486 AllianceGenome:RGD:1559594
    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
    Also known as
    RGD1559594
    Summary
    Predicted to enable identical protein binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of DNA-templated transcription; negative regulation of smooth muscle cell differentiation; and neurogenesis. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in patent ductus arteriosus. Orthologous to human PRDM6 (PR/SET domain 6). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 73.9), Heart (RPKM 9.8) and 3 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Prdm6 in Genome Data Viewer
    Location:
    18q11
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 18 NC_086036.1 (49102290..49206763)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 18 NC_051353.1 (46904115..47008482)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (48433747..48538834)

    Chromosome 18 - NC_086036.1Genomic Context describing neighboring genes Neighboring gene sorting nexin 24 Neighboring gene peptidylprolyl isomerase C Neighboring gene U6 spliceosomal RNA Neighboring gene centrosomal protein 120 Neighboring gene uncharacterized LOC134483022

    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. PRISM/PRDM6, a transcriptional repressor that promotes the proliferative gene program in smooth muscle cells. Davis CA, et al. Mol Cell Biol, 2006 Apr. PMID 16537907, Free PMC Article
    2. Prdm proto-oncogene transcription factor family expression and interaction with the Notch-Hes pathway in mouse neurogenesis. Kinameri E, et al. PLoS One, 2008. PMID 19050759, Free PMC Article
    3. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Black JC, et al. Mol Cell, 2012 Nov 30. PMID 23200123, Free PMC Article
    4. 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 histone methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of smooth muscle cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neurogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    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/SET domain 6; putative histone-lysine N-methyltransferase PRDM6
    Names
    PR domain 6
    PR domain containing 6

    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_001432439.1 → NP_001419368.1  PR/SET domain 6 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000018
      UniProtKB/TrEMBL
      D3ZQA6

    2. NM_001432440.1 → NP_001419369.1  PR/SET domain 6 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000018

    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_086036.1 Reference GRCr8

      Range
      49102290..49206763
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039097239.2 → XP_038953167.1  putative histone-lysine N-methyltransferase PRDM6 isoform X4

      Conserved Domains (1) summary
      cl40432
      Location:246 → 302
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

    2. XM_039097238.2 → XP_038953166.1  putative histone-lysine N-methyltransferase PRDM6 isoform X3

      Conserved Domains (1) summary
      cl40432
      Location:246 → 302
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

    3. XM_008772191.3 → XP_008770413.1  putative histone-lysine N-methyltransferase PRDM6 isoform X2

      Related
      ENSRNOP00000041369.3, ENSRNOT00000047755.7
      Conserved Domains (5) summary
      COG5048
      Location:402 → 587
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:506 → 526
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:504 → 526
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:262 → 367
      SET; SET domain
      pfam13465
      Location:547 → 571
      zf-H2C2_2; Zinc-finger double domain

    4. XM_008772189.3 → XP_008770411.1  putative histone-lysine N-methyltransferase PRDM6 isoform X1

      Related
      ENSRNOP00000099549.1, ENSRNOT00000148772.1
      Conserved Domains (5) summary
      COG5048
      Location:402 → 534
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:478 → 498
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:532 → 554
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:262 → 367
      SET; SET domain
      pfam13465
      Location:518 → 542
      zf-H2C2_2; Zinc-finger double domain
    Nucleotide Protein Strain
    Heading Accession and Version

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