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

Summary

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 DNA-templated transcription; negative regulation of smooth muscle cell differentiation; 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, Oct 2024]
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

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_000084.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
identified Prdm6 as a factor that is essential for the physiological control of cardiovascular development
Title: Prdm6 is essential for cardiovascular development in vivo.
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.
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.

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Variation

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Alleles

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

Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D18Mit54 (e-PCR), detects polymorphism
- UniSTS:128275

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables histone H4K20 monomethyltransferase 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

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in 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	IEA Inferred from Electronic Annotation 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	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

EC 2.1.1.361

XP_011245206.1

EC 2.1.1.361

XP_011245207.1

EC 2.1.1.361

XP_017173378.1

EC 2.1.1.361

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)

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

NC_000084.7 Reference GRCm39 C57BL/6J

Range

53597027..53708976

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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