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Prdm6 PR domain containing 6 [ Mus musculus (house mouse) ]

Gene ID: 225518, updated on 9-Aug-2024

Summary

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Official Symbol
Prdm6provided by MGI
Official Full Name
PR domain containing 6provided by MGI
Primary source
MGI:MGI:2684938
See related
Ensembl:ENSMUSG00000069378 AllianceGenome:MGI:2684938
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Gm92; PRISM
Summary
Enables identical protein binding activity. Acts upstream of or within negative regulation of smooth muscle cell differentiation; negative regulation of transcription, DNA-templated; and neurogenesis. Located in nucleus. Is expressed in several structures, including arterial system; central nervous system; genitourinary system; heart; and respiratory system. 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, Apr 2022]
Expression
Biased expression in lung adult (RPKM 4.6), bladder adult (RPKM 3.1) and 9 other tissues See more
Orthologs
human all
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Genomic context

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See Prdm6 in Genome Data Viewer
Location:
18 D1; 18 29.04 cM
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (53597027..53708976)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (53463955..53575904)

Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_44622 Neighboring gene STARR-seq mESC enhancer starr_44623 Neighboring gene peptidylprolyl isomerase C Neighboring gene predicted gene, 41726 Neighboring gene STARR-seq mESC enhancer starr_44624 Neighboring gene predicted gene, 19466 Neighboring gene STARR-seq mESC enhancer starr_44626 Neighboring gene centrosomal protein 120 Neighboring gene STARR-positive B cell enhancer ABC_E966 Neighboring gene STARR-positive B cell enhancer ABC_E8978 Neighboring gene STARR-seq mESC enhancer starr_44627 Neighboring gene predicted gene, 41728

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. PRDM6 is enriched in vascular precursors during development and inhibits endothelial cell proliferation, survival, and differentiation. Wu Y, et al. J Mol Cell Cardiol, 2008 Jan. PMID 17662997, Free PMC Article
  2. Acetaminophen-induced liver damage in mice is associated with gender-specific adduction of peroxiredoxin-6. Mohar I, et al. Redox Biol, 2014. PMID 24563856, Free PMC Article
  3. Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus. Li N, et al. Am J Hum Genet, 2016 Jun 2. PMID 27181681, Free PMC Article
  4. Prdm6 drives ductus arteriosus closure by promoting ductus arteriosus smooth muscle cell identity and contractility. Zou M, et al. JCI Insight, 2023 Mar 8. PMID 36749647, Free PMC Article
  5. Prdm6 is essential for cardiovascular development in vivo. Gewies A, et al. PLoS One, 2013. PMID 24278461, Free PMC Article

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Prdm6 drives ductus arteriosus closure by promoting ductus arteriosus smooth muscle cell identity and contractility.
    Title: Prdm6 drives ductus arteriosus closure by promoting ductus arteriosus smooth muscle cell identity and contractility.
  2. Prdm6 controls heart development by regulating neural crest cell differentiation and migration.
    Title: Prdm6 controls heart development by regulating neural crest cell differentiation and migration.
  3. identified Prdm6 as a factor that is essential for the physiological control of cardiovascular development
    Title: Prdm6 is essential for cardiovascular development in vivo.
  4. These data indicate that PRDM6 is expressed by vascular precursors, has differential effects in endothelial cells and smooth muscle cells, and may play a role in vascular precursor differentiation and survival.
    Title: PRDM6 is enriched in vascular precursors during development and inhibits endothelial cell proliferation, survival, and differentiation.
  5. PRISM acts as a novel epigenetic regulator of Smooth Muscle Cells (SMC) phenotypic plasticity by suppressing differentiation and maintaining the proliferative potential of vascular SMCs.
    Title: PRISM/PRDM6, a transcriptional repressor that promotes the proliferative gene program in smooth muscle cells.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables histone H4K20 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables identical protein 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 transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within negative regulation of smooth muscle cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within neurogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
putative histone-lysine N-methyltransferase PRDM6
Names
PR domain-containing protein 6
PR domain-containing protein in smooth muscle
PR-domain zinc finger protein 6
NP_001028453.1
XP_011245206.1
XP_011245207.1
XP_017173378.1

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_001033281.3 → NP_001028453.1  putative histone-lysine N-methyltransferase PRDM6

    See identical proteins and their annotated locations for NP_001028453.1

    Status: PROVISIONAL

    Source sequence(s)
    AC116597, AC164620
    Consensus CDS
    CCDS29253.1
    UniProtKB/Swiss-Prot
    B9EIB0, Q2I2X0, Q2I2X1, Q3UX75, Q3UZD5
    Related
    ENSMUSP00000089513.4, ENSMUST00000091900.11
    Conserved Domains (4) summary
    sd00017
    Location:504 → 524
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:530 → 552
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:545 → 569
    zf-H2C2_2; Zinc-finger double domain
    cd19191
    Location:245 → 373
    PR-SET_PRDM6; PR-SET domain found in PR domain zinc finger protein 6 (PRDM6) and similar proteins

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_000084.7 Reference GRCm39 C57BL/6J

    Range
    53597027..53708976
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017317889.2 → XP_017173378.1  putative histone-lysine N-methyltransferase PRDM6 isoform X2

    UniProtKB/Swiss-Prot
    B9EIB0, Q2I2X0, Q2I2X1, Q3UX75, Q3UZD5
    Conserved Domains (4) summary
    sd00017
    Location:504 → 524
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:530 → 552
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:545 → 569
    zf-H2C2_2; Zinc-finger double domain
    cd19191
    Location:245 → 373
    PR-SET_PRDM6; PR-SET domain found in PR domain zinc finger protein 6 (PRDM6) and similar proteins

  2. XM_011246904.2 → XP_011245206.1  putative histone-lysine N-methyltransferase PRDM6 isoform X1

    See identical proteins and their annotated locations for XP_011245206.1

    Conserved Domains (4) summary
    sd00017
    Location:476 → 496
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:530 → 552
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:516 → 540
    zf-H2C2_2; Zinc-finger double domain
    cd19191
    Location:245 → 373
    PR-SET_PRDM6; PR-SET domain found in PR domain zinc finger protein 6 (PRDM6) and similar proteins

  3. XM_011246905.3 → XP_011245207.1  putative histone-lysine N-methyltransferase PRDM6 isoform X3

    Conserved Domains (1) summary
    cl40432
    Location:245 → 304
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q3UZD5.1 GenPept UniProtKB/Swiss-Prot:Q3UZD5

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