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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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