Prdm16 PR domain containing 16 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Prdm16provided by MGI
Official Full Name: PR domain containing 16provided by MGI
Primary source: MGI:MGI:1917923
See related: Ensembl:ENSMUSG00000039410 AllianceGenome:MGI:1917923
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: csp1; mel1; 5730557K01Rik
Summary: Enables several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; histone methyltransferase activity (H3-K9 specific); and transcription coactivator activity. Involved in several processes, including brown fat cell differentiation; positive regulation of cold-induced thermogenesis; and regulation of transcription, DNA-templated. Acts upstream of or within several processes, including negative regulation of transforming growth factor beta receptor signaling pathway; positive regulation of brown fat cell differentiation; and tongue development. Located in nucleus. Part of transcription repressor complex. Is expressed in several structures, including alimentary system; branchial arch; central nervous system; embryo mesenchyme; and sensory organ. Orthologous to human PRDM16 (PR/SET domain 16). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in duodenum adult (RPKM 4.8), lung adult (RPKM 4.0) and 23 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 E2; 4 83.96 cM

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (154400579..154721851, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (154316122..154637360, complement)

Chromosome 4 - NC_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nonsense Variant PRDM16-Q187X Causes Impaired Myocardial Development and TGF-beta Signaling Resulting in Noncompaction Cardiomyopathy in Humans and Mice.
Title: Nonsense Variant PRDM16-Q187X Causes Impaired Myocardial Development and TGF-β Signaling Resulting in Noncompaction Cardiomyopathy in Humans and Mice.
Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators.
Title: Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators.
Discovery of PRDM16-Mediated TRPA1 Induction as the Mechanism for Low Tubulo-Interstitial Fibrosis in Diabetic Kidney Disease.
Title: Discovery of PRDM16-Mediated TRPA1 Induction as the Mechanism for Low Tubulo-Interstitial Fibrosis in Diabetic Kidney Disease.
PRDM16 Deletion Is Associated With Sex-dependent Cardiomyopathy and Cardiac Mortality: A Translational, Multi-Institutional Cohort Study.
Title: PRDM16 Deletion Is Associated With Sex-dependent Cardiomyopathy and Cardiac Mortality: A Translational, Multi-Institutional Cohort Study.
PRDM16 exerts critical role in myocardial metabolism and energetics in type 2 diabetes induced cardiomyopathy.
Title: PRDM16 exerts critical role in myocardial metabolism and energetics in type 2 diabetes induced cardiomyopathy.
Androgen Receptor is a Negative Regulator of PRDM16 in Beige Adipocyte.
Title: Androgen Receptor is a Negative Regulator of PRDM16 in Beige Adipocyte.
PRDM16 deficiency in vascular smooth muscle cells aggravates abdominal aortic aneurysm.
Title: PRDM16 deficiency in vascular smooth muscle cells aggravates abdominal aortic aneurysm.
Antagonism between Prdm16 and Smad4 specifies the trajectory and progression of pancreatic cancer.
Title: Antagonism between Prdm16 and Smad4 specifies the trajectory and progression of pancreatic cancer.
PRDM16 expression and function in mammalian cochlear development.
Title: PRDM16 expression and function in mammalian cochlear development.
Post-translational control of beige fat biogenesis by PRDM16 stabilization.
Title: Post-translational control of beige fat biogenesis by PRDM16 stabilization.

Submit: New GeneRIF Correction See all GeneRIFs (73)

Variation

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Alleles

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

Gene trapped (1)
Targeted (9) 1 citation
Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW743053 (e-PCR)
- UniSTS:207739

RH132707 (e-PCR)
- UniSTS:215990

D4Mit209 (e-PCR), detects polymorphism
- UniSTS:129990

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables SMAD binding	IPI Inferred from Physical Interaction more info	PubMed
enables histone H3K9 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 monomethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in brown fat cell differentiation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of brown fat cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in brown fat cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of granulocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	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 negative regulation of transforming growth factor beta receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neurogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of brown fat cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cold-induced thermogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cellular respiration	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within roof of mouth development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within somatic stem cell population maintenance	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within stem cell population maintenance	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within stem cell population maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within tongue development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in white fat cell differentiation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in aggresome	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytosol	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	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	IC Inferred by Curator more info	PubMed
part_of transcription repressor complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone-lysine N-methyltransferase PRDM16

Names: MDS1/EVI1-like gene 1; PR domain zinc finger protein 16; PR domain-containing protein 16; line 27; transcription factor MEL1

NP_001171466.1

EC 2.1.1.367

NP_001277955.1

EC 2.1.1.367

NP_001277958.1

EC 2.1.1.367

NP_081780.3

EC 2.1.1.367

XP_006539234.1

EC 2.1.1.367

XP_006539235.1

EC 2.1.1.367

XP_006539236.1

EC 2.1.1.367

XP_006539237.1

EC 2.1.1.367

XP_006539238.1

EC 2.1.1.367

XP_036020313.1

EC 2.1.1.367

XP_036020315.1

EC 2.1.1.367

XP_036020316.1

EC 2.1.1.367

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_001177995.2 → NP_001171466.1 histone-lysine N-methyltransferase PRDM16 isoform 2

Status: VALIDATED

Source sequence(s)

AL611950, AL627123, AL627127, AL627226

Consensus CDS

CCDS51400.1

UniProtKB/TrEMBL

A2A930, A2A934

Related

ENSMUSP00000101261.2, ENSMUST00000105636.8

Conserved Domains (6) summary

smart00317
Location:84 → 210

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

COG5048
Location:932 → 1004

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:954 → 974

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:952 → 974

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:966 → 990

zf-H2C2_2; Zinc-finger double domain

pfam15909
Location:371 → 452

zf-C2H2_8; C2H2-type zinc ribbon
NM_001291026.2 → NP_001277955.1 histone-lysine N-methyltransferase PRDM16 isoform 3

Status: VALIDATED

Source sequence(s)

AL611950, AL627123, AL627127, AL627226

Consensus CDS

CCDS71530.1

UniProtKB/TrEMBL

A2A930, A2A931

Related

ENSMUSP00000101262.2, ENSMUST00000105637.8

Conserved Domains (6) summary

smart00317
Location:84 → 208

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

COG5048
Location:930 → 1002

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:952 → 972

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:950 → 972

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:964 → 988

zf-H2C2_2; Zinc-finger double domain

pfam15909
Location:369 → 450

zf-C2H2_8; C2H2-type zinc ribbon
NM_001291029.2 → NP_001277958.1 histone-lysine N-methyltransferase PRDM16 isoform 4

See identical proteins and their annotated locations for NP_001277958.1

Status: VALIDATED

Source sequence(s)

AL611950, AL627123, AL627127, AL627226

Consensus CDS

CCDS71532.1

UniProtKB/TrEMBL

A2A930

Related

ENSMUSP00000064546.8, ENSMUST00000070313.14

Conserved Domains (6) summary

smart00317
Location:84 → 210

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

COG5048
Location:933 → 1005

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:955 → 975

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:953 → 975

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:967 → 991

zf-H2C2_2; Zinc-finger double domain

pfam15909
Location:371 → 452

zf-C2H2_8; C2H2-type zinc ribbon
NM_027504.4 → NP_081780.3 histone-lysine N-methyltransferase PRDM16 isoform 1

See identical proteins and their annotated locations for NP_081780.3

Status: VALIDATED

Source sequence(s)

AL611950, AL627123, AL627127, AL627226

Consensus CDS

CCDS38989.1

UniProtKB/Swiss-Prot

A2A935, Q69ZD6, Q6PB79, Q7TPF4

UniProtKB/TrEMBL

A2A930

Related

ENSMUSP00000030902.7, ENSMUST00000030902.13

Conserved Domains (6) summary

smart00317
Location:84 → 209

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

COG5048
Location:931 → 1003

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:953 → 973

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:951 → 973

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:965 → 989

zf-H2C2_2; Zinc-finger double domain

pfam15909
Location:370 → 451

zf-C2H2_8; C2H2-type zinc ribbon

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_000070.7 Reference GRCm39 C57BL/6J

Range

154400579..154721851 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006539175.5 → XP_006539238.1 histone-lysine N-methyltransferase PRDM16 isoform X5

UniProtKB/TrEMBL

A2A930

Conserved Domains (4) summary

sd00017
Location:953 → 973

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:951 → 973

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:965 → 989

zf-H2C2_2; Zinc-finger double domain

cd19213
Location:61 → 221

PR-SET_PRDM16; PR-SET domain found in PR domain zinc finger protein 16 (PRDM16) and similar proteins
XM_006539173.5 → XP_006539236.1 histone-lysine N-methyltransferase PRDM16 isoform X3

UniProtKB/TrEMBL

A2A930

Conserved Domains (4) summary

sd00017
Location:954 → 974

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:952 → 974

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:966 → 990

zf-H2C2_2; Zinc-finger double domain

cd19213
Location:61 → 222

PR-SET_PRDM16; PR-SET domain found in PR domain zinc finger protein 16 (PRDM16) and similar proteins
XM_036164423.1 → XP_036020316.1 histone-lysine N-methyltransferase PRDM16 isoform X8

UniProtKB/TrEMBL

A2A930

Conserved Domains (5) summary

sd00017
Location:953 → 973

ZF_C2H2; C2H2 Zn finger [structural motif]

cd19213
Location:61 → 222

PR-SET_PRDM16; PR-SET domain found in PR domain zinc finger protein 16 (PRDM16) and similar proteins

pfam00096
Location:951 → 973

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:965 → 989

zf-H2C2_2; Zinc-finger double domain

cd20908
Location:981 → 1015

SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
XM_006539172.5 → XP_006539235.1 histone-lysine N-methyltransferase PRDM16 isoform X2

UniProtKB/TrEMBL

A2A930, A2A933

Related

ENSMUSP00000101263.3, ENSMUST00000105638.9

Conserved Domains (4) summary

sd00017
Location:954 → 974

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:952 → 974

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:966 → 990

zf-H2C2_2; Zinc-finger double domain

cd19213
Location:61 → 222

PR-SET_PRDM16; PR-SET domain found in PR domain zinc finger protein 16 (PRDM16) and similar proteins
XM_006539174.5 → XP_006539237.1 histone-lysine N-methyltransferase PRDM16 isoform X4

UniProtKB/TrEMBL

A2A930

Conserved Domains (4) summary

sd00017
Location:954 → 974

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:952 → 974

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:966 → 990

zf-H2C2_2; Zinc-finger double domain

cd19213
Location:61 → 223

PR-SET_PRDM16; PR-SET domain found in PR domain zinc finger protein 16 (PRDM16) and similar proteins
XM_006539171.5 → XP_006539234.1 histone-lysine N-methyltransferase PRDM16 isoform X1

UniProtKB/TrEMBL

A2A930

Conserved Domains (4) summary

sd00017
Location:955 → 975

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:953 → 975

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:967 → 991

zf-H2C2_2; Zinc-finger double domain

cd19213
Location:61 → 223

PR-SET_PRDM16; PR-SET domain found in PR domain zinc finger protein 16 (PRDM16) and similar proteins
XM_036164420.1 → XP_036020313.1 histone-lysine N-methyltransferase PRDM16 isoform X6

UniProtKB/TrEMBL

A2A930

Conserved Domains (5) summary

sd00017
Location:953 → 973

ZF_C2H2; C2H2 Zn finger [structural motif]

cd19213
Location:61 → 221

PR-SET_PRDM16; PR-SET domain found in PR domain zinc finger protein 16 (PRDM16) and similar proteins

pfam00096
Location:951 → 973

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:965 → 989

zf-H2C2_2; Zinc-finger double domain

cd20908
Location:981 → 1015

SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
XM_036164422.1 → XP_036020315.1 histone-lysine N-methyltransferase PRDM16 isoform X7

Conserved Domains (4) summary

sd00017
Location:665 → 685

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:663 → 685

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:677 → 701

zf-H2C2_2; Zinc-finger double domain

cd20908
Location:693 → 727

SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins