Prdm16 PR/SET domain 16 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Prdm16provided by RGD
Full Name: PR/SET domain 16provided by RGD
Primary source: RGD:2324431
See related: EnsemblRapid:ENSRNOG00000045913 AllianceGenome:RGD:2324431
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
Summary: Predicted to enable several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; histone H3K9 methyltransferase activity; and transcription coactivator activity. Predicted to be involved in several processes, including negative regulation of granulocyte differentiation; positive regulation of cold-induced thermogenesis; and regulation of DNA-templated transcription. Predicted to act 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 regulation of DNA-templated transcription. Predicted to be located in aggresome; cytosol; and nucleoplasm. Predicted to be part of transcription repressor complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in dilated cardiomyopathy 1LL. Orthologous to human PRDM16 (PR/SET domain 16). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 29.4), Heart (RPKM 18.9) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (170162275..170486371, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (164879864..165203986, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (171662277..171711561, complement)

Chromosome 5 - NC_086023.1 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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
enables histone H3K9 methyltransferase activity	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
acts_upstream_of brown fat cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in brown fat cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin organization	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
NOT involved_in negative regulation of transforming growth factor beta receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transforming growth factor beta receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transforming growth factor beta receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neurogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cold-induced thermogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of cellular respiration	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within somatic stem cell population maintenance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within stem cell population maintenance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within tongue development	ISO Inferred from Sequence Orthology more info
involved_in white fat cell differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in aggresome	IEA Inferred from Electronic Annotation more info
located_in aggresome	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation 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	ISO Inferred from Sequence Orthology more info
part_of transcription repressor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: histone-lysine N-methyltransferase PRDM16

Names: PR domain 16; PR domain containing 16; PR domain zinc finger protein 16; PR domain zinc finger protein 16-like

NP_001414232.1

EC 2.1.1.367

XP_038967290.1

EC 2.1.1.367

XP_038967291.1

EC 2.1.1.367

XP_038967293.1

EC 2.1.1.367

XP_038967294.1

EC 2.1.1.367

XP_038967295.1

EC 2.1.1.367

XP_038967296.1

EC 2.1.1.367

XP_038967298.1

EC 2.1.1.367

XP_063143113.1

EC 2.1.1.367

XP_063143114.1

EC 2.1.1.367

XP_063143115.1

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_001427303.2 → NP_001414232.1 histone-lysine N-methyltransferase PRDM16

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A6IUL8

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

NC_086023.1 Reference GRCr8

Range

170162275..170486371 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039111366.2 → XP_038967294.1 histone-lysine N-methyltransferase PRDM16 isoform X4

UniProtKB/TrEMBL

A6IUL8

Conserved Domains (5) summary

sd00017
Location:954 → 974

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:952 → 974

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:966 → 990

zf-H2C2_2; Zinc-finger double domain

cd20908
Location:982 → 1016

SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
XM_063287045.1 → XP_063143115.1 histone-lysine N-methyltransferase PRDM16 isoform X10

UniProtKB/TrEMBL

A6IUL8
XM_063287044.1 → XP_063143114.1 histone-lysine N-methyltransferase PRDM16 isoform X9

UniProtKB/TrEMBL

A6IUL8
XM_063287043.1 → XP_063143113.1 histone-lysine N-methyltransferase PRDM16 isoform X6

UniProtKB/TrEMBL

A6IUL8
XM_039111367.2 → XP_038967295.1 histone-lysine N-methyltransferase PRDM16 isoform X5

UniProtKB/TrEMBL

A6IUL8

Related

ENSRNOP00000068441.3, ENSRNOT00000076044.3

Conserved Domains (5) summary

sd00017
Location:938 → 958

ZF_C2H2; C2H2 Zn finger [structural motif]

cd19213
Location:61 → 206

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

pfam00096
Location:936 → 958

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:950 → 974

zf-H2C2_2; Zinc-finger double domain

cd20908
Location:966 → 1000

SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
XM_039111365.2 → XP_038967293.1 histone-lysine N-methyltransferase PRDM16 isoform X3

UniProtKB/TrEMBL

A6IUL8

Conserved Domains (5) summary

sd00017
Location:952 → 972

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:950 → 972

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:964 → 988

zf-H2C2_2; Zinc-finger double domain

cd20908
Location:980 → 1014

SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
XM_039111363.2 → XP_038967291.1 histone-lysine N-methyltransferase PRDM16 isoform X2

UniProtKB/TrEMBL

A6IUL8

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_039111368.2 → XP_038967296.1 histone-lysine N-methyltransferase PRDM16 isoform X7

UniProtKB/TrEMBL

A0A096MJ70

Conserved Domains (5) summary

sd00017
Location:954 → 974

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:952 → 974

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:966 → 990

zf-H2C2_2; Zinc-finger double domain

cd20908
Location:982 → 1016

SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
XM_039111362.2 → XP_038967290.1 histone-lysine N-methyltransferase PRDM16 isoform X1

UniProtKB/TrEMBL

A0A096MKA6, A6IUL8

Related

ENSRNOP00000068014.3, ENSRNOT00000077015.4

Conserved Domains (5) summary

sd00017
Location:954 → 974

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:952 → 974

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:966 → 990

zf-H2C2_2; Zinc-finger double domain

cd20908
Location:982 → 1016

SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
XM_039111370.2 → XP_038967298.1 histone-lysine N-methyltransferase PRDM16 isoform X8

UniProtKB/TrEMBL

A0A096MJ70

Conserved Domains (5) summary

sd00017
Location:954 → 974

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:952 → 974

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:966 → 990

zf-H2C2_2; Zinc-finger double domain

cd20908
Location:982 → 1016

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