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

Summary

Official Symbol: Prdm1provided by RGD
Official Full Name: PR/SET domain 1provided by RGD
Primary source: RGD:1311765
See related: Ensembl:ENSRNOG00000000323 AllianceGenome:RGD:1311765
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
Summary: Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; histone deacetylase binding activity; and promoter-specific chromatin binding activity. Predicted to be involved in cell fate commitment; regulation of lymphocyte differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including animal organ development; artery development; and regulation of B cell activation. Predicted to be active in cytoplasm and nucleus. Orthologous to human PRDM1 (PR/SET domain 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 47.1), Uterus (RPKM 34.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20q13

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (49542465..49564088, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (47959858..47981488, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (49464921..49556623, complement)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

RH128684 (e-PCR)
- UniSTS:211992

BI295453 (e-PCR)
- UniSTS:246647

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor 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 RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables histone methyltransferase binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables promoter-specific chromatin binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within aorta development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within artery morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cardiac septum development	ISO Inferred from Sequence Orthology more info
involved_in cell fate commitment	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell fate commitment	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within coronary vasculature development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic placenta development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within eye photoreceptor cell development	ISO Inferred from Sequence Orthology more info
involved_in gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within germ cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart valve development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within intestinal epithelial cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within kidney development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within maternal placenta development	ISO Inferred from Sequence Orthology more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within morphogenesis of a branching structure	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of gene expression	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
acts_upstream_of_or_within positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within post-embryonic development	ISO Inferred from Sequence Orthology more info
involved_in regulation of NK T cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of extrathymic T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of natural killer cell differentiation	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 regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within retinal bipolar neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sebum secreting cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within trophoblast giant cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ventricular septum development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	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
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: PR domain zinc finger protein 1

Names: PR domain 1; PR domain containing 1, with ZNF domain

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_001107639.3 → NP_001101109.2 PR domain zinc finger protein 1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000020

UniProtKB/TrEMBL

D4A1S2

Related

ENSRNOP00000040939.3, ENSRNOT00000048270.6

Conserved Domains (5) summary

smart00317
Location:100 → 206

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

COG5048
Location:405 → 687

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

sd00017
Location:576 → 596

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:574 → 596

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:616 → 641

zf-H2C2_2; Zinc-finger double domain

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_086038.1 Reference GRCr8

Range

49542465..49564088 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063279179.1 → XP_063135249.1 PR domain zinc finger protein 1 isoform X2

UniProtKB/TrEMBL

A0A096MJU6, A6K6V8
XM_039098772.2 → XP_038954700.1 PR domain zinc finger protein 1 isoform X1

Conserved Domains (4) summary

COG5048
Location:247 → 529

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

sd00017
Location:418 → 438

ZF_C2H2; C2H2 Zn finger [structural motif]

cl40432
Location:1 → 50

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

pfam13465
Location:458 → 483

zf-H2C2_2; Zinc-finger double domain