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Prdm1 PR/SET domain 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 309871, updated on 18-Apr-2019

Summary

Official Symbol
Prdm1provided by RGD
Official Full Name
PR/SET domain 1provided by RGD
Primary source
RGD:1311765
See related
Ensembl:ENSRNOG00000000323
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Expression
Biased expression in Lung (RPKM 47.1), Uterus (RPKM 34.4) and 9 other tissues See more
Orthologs

Genomic context

See Prdm1 in Genome Data Viewer
Location:
20q13
Exon count:
10
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (49464921..49556623, complement)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 20 NC_005119.3 (51096616..51118240, complement)

Chromosome 20 - NC_005119.4Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC103694450 Neighboring gene uncharacterized LOC102554933 Neighboring gene cation transport regulator-like protein 2 pseudogene Neighboring gene uncharacterized LOC102555236 Neighboring gene uncharacterized LOC102555144

Genomic regions, transcripts, and products

Expression

  • 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

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone deacetylase binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone deacetylase binding ISO
Inferred from Sequence Orthology
more info
PubMed 
promoter-specific chromatin binding IEA
Inferred from Electronic Annotation
more info
 
promoter-specific chromatin binding ISO
Inferred from Sequence Orthology
more info
PubMed 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
PubMed 
Process Evidence Code Pubs
aorta development IEA
Inferred from Electronic Annotation
more info
 
aorta development ISO
Inferred from Sequence Orthology
more info
PubMed 
artery morphogenesis IEA
Inferred from Electronic Annotation
more info
 
artery morphogenesis ISO
Inferred from Sequence Orthology
more info
PubMed 
cardiac septum development ISO
Inferred from Sequence Orthology
more info
PubMed 
cell fate commitment IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell fate commitment ISO
Inferred from Sequence Orthology
more info
PubMed 
coronary vasculature development IEA
Inferred from Electronic Annotation
more info
 
coronary vasculature development ISO
Inferred from Sequence Orthology
more info
PubMed 
embryonic placenta development ISO
Inferred from Sequence Orthology
more info
PubMed 
eye photoreceptor cell development IEA
Inferred from Electronic Annotation
more info
 
eye photoreceptor cell development ISO
Inferred from Sequence Orthology
more info
PubMed 
germ cell development IEA
Inferred from Electronic Annotation
more info
 
germ cell development ISO
Inferred from Sequence Orthology
more info
PubMed 
heart valve development IEA
Inferred from Electronic Annotation
more info
 
heart valve development ISO
Inferred from Sequence Orthology
more info
PubMed 
in utero embryonic development ISO
Inferred from Sequence Orthology
more info
PubMed 
intestinal epithelial cell development IEA
Inferred from Electronic Annotation
more info
 
intestinal epithelial cell development ISO
Inferred from Sequence Orthology
more info
PubMed 
maternal placenta development IEA
Inferred from Electronic Annotation
more info
 
maternal placenta development ISO
Inferred from Sequence Orthology
more info
PubMed 
morphogenesis of a branching structure IEA
Inferred from Electronic Annotation
more info
 
morphogenesis of a branching structure ISO
Inferred from Sequence Orthology
more info
PubMed 
negative regulation of B cell proliferation ISO
Inferred from Sequence Orthology
more info
PubMed 
negative regulation of gene expression ISO
Inferred from Sequence Orthology
more info
PubMed 
negative regulation of lipopolysaccharide-mediated signaling pathway ISO
Inferred from Sequence Orthology
more info
PubMed 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of B cell differentiation ISO
Inferred from Sequence Orthology
more info
PubMed 
NOT positive regulation of B cell differentiation ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
positive regulation of gene expression ISO
Inferred from Sequence Orthology
more info
PubMed 
post-embryonic development IEA
Inferred from Electronic Annotation
more info
 
post-embryonic development ISO
Inferred from Sequence Orthology
more info
PubMed 
regulation of NK T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of NK T cell differentiation ISO
Inferred from Sequence Orthology
more info
PubMed 
regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
regulation of cell proliferation ISO
Inferred from Sequence Orthology
more info
PubMed 
regulation of extrathymic T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of extrathymic T cell differentiation ISO
Inferred from Sequence Orthology
more info
PubMed 
regulation of natural killer cell differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of natural killer cell differentiation ISO
Inferred from Sequence Orthology
more info
PubMed 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
sebum secreting cell proliferation IEA
Inferred from Electronic Annotation
more info
 
sebum secreting cell proliferation ISO
Inferred from Sequence Orthology
more info
PubMed 
trophoblast giant cell differentiation IEA
Inferred from Electronic Annotation
more info
 
trophoblast giant cell differentiation ISO
Inferred from Sequence Orthology
more info
PubMed 
ventricular septum development IEA
Inferred from Electronic Annotation
more info
 
ventricular septum development ISO
Inferred from Sequence Orthology
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm ISO
Inferred from Sequence Orthology
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
PubMed 

General protein information

Preferred Names
PR domain zinc finger protein 1
Names
PR domain 1
PR domain containing 1, with ZNF domain

NCBI Reference Sequences (RefSeq)

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_001107639.2NP_001101109.2  PR domain zinc finger protein 1

    Status: PROVISIONAL

    Source sequence(s)
    AABR07045503
    UniProtKB/TrEMBL
    D4A1S2
    Related
    ENSRNOP00000040939.3, ENSRNOT00000048270.5
    Conserved Domains (5) summary
    smart00317
    Location:100206
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:405687
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:576596
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:574596
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:616641
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005119.4 Reference Rnor_6.0 Primary Assembly

    Range
    49464921..49556623 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017601664.1XP_017457153.1  PR domain zinc finger protein 1 isoform X1

  2. XM_017601663.1XP_017457152.1  PR domain zinc finger protein 1 isoform X1

  3. XM_017601662.1XP_017457151.1  PR domain zinc finger protein 1 isoform X1

  4. XM_008772991.2XP_008771213.1  PR domain zinc finger protein 1 isoform X2

    See identical proteins and their annotated locations for XP_008771213.1

    UniProtKB/TrEMBL
    A0A096MJU6
    Related
    ENSRNOP00000068267.1, ENSRNOT00000076541.1
    Conserved Domains (5) summary
    smart00317
    Location:133239
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:438720
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:609629
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:607629
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:649674
    zf-H2C2_2; Zinc-finger double domain

Alternate Rn_Celera

Genomic

  1. AC_000088.1 Alternate Rn_Celera

    Range
    52026331..52047919
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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