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

    Gene ID: 100366024, updated on 9-Dec-2024

    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, 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

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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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