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

Gene ID: 100366024, updated on 4-Jan-2025

Summary

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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, Jan 2025]
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

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See Prdm16 in Genome Data Viewer
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_086023.1Genomic Context describing neighboring genes Neighboring gene multiple EGF-like-domains 6 Neighboring gene Rho guanine nucleotide exchange factor 16 Neighboring gene uncharacterized LOC102555433 Neighboring gene uncharacterized LOC120103049 Neighboring gene actin-related protein T2 Neighboring gene uncharacterized LOC102555491

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. Aberrant expression of the MEL1S gene identified in association with hypomethylation in adult T-cell leukemia cells. Yoshida M, et al. Blood, 2004 Apr 1. PMID 14656887
  2. A novel EVI1 gene family, MEL1, lacking a PR domain (MEL1S) is expressed mainly in t(1;3)(p36;q21)-positive AML and blocks G-CSF-induced myeloid differentiation. Nishikata I, et al. Blood, 2003 Nov 1. PMID 12816872
  3. Transcriptional control of brown fat determination by PRDM16. Seale P, et al. Cell Metab, 2007 Jul. PMID 17618855, Free PMC Article
  4. Ablation of PRDM16 and beige adipose causes metabolic dysfunction and a subcutaneous to visceral fat switch. Cohen P, et al. Cell, 2014 Jan 16. PMID 24439384, Free PMC Article
  5. Cold-inducible Zfp516 activates UCP1 transcription to promote browning of white fat and development of brown fat. Dempersmier J, et al. Mol Cell, 2015 Jan 22. PMID 25578880, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

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
XP_038967290.1
XP_038967291.1
XP_038967293.1
XP_038967294.1
XP_038967295.1
XP_038967296.1
XP_038967298.1
XP_063143113.1
XP_063143114.1
XP_063143115.1

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_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

  1. NC_086023.1 Reference GRCr8

    Range
    170162275..170486371 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. XM_063287045.1 → XP_063143115.1  histone-lysine N-methyltransferase PRDM16 isoform X10

    UniProtKB/TrEMBL
    A6IUL8

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

    UniProtKB/TrEMBL
    A6IUL8

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

    UniProtKB/TrEMBL
    A6IUL8

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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
Nucleotide Protein Strain
Heading Accession and Version

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