Prdm4 PR/SET domain 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Prdm4provided by RGD
Official Full Name: PR/SET domain 4provided by RGD
Primary source: RGD:619929
See related: EnsemblRapid:ENSRNOG00000004962 AllianceGenome:RGD:619929
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
Also known as: SC-1
Summary: Enables death receptor binding activity. Involved in several processes, including negative regulation of cell growth; regulation of neural precursor cell proliferation; and regulation of stem cell differentiation. Predicted to be located in cytosol and nucleoplasm. Predicted to be part of histone methyltransferase complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human PRDM4 (PR/SET domain 4). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Heart (RPKM 89.0), Thymus (RPKM 74.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q13

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (19841560..19868224)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (17953832..17980489)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (23959932..23986535)

Chromosome 7 - NC_086025.1 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

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?

We investigated the potential mechanism of nuclear shuttling of PRDM4 via the importin alpha/beta-mediated pathway and find that PRDM4 nuclear targeting is independent of alpha/beta-mediated nuclear import.
Title: Zinc fingers 1, 2, 5 and 6 of transcriptional regulator, PRDM4, are required for its nuclear localisation.
SC1 and PRMT5 are components of an epigenetic regulatory complex that maintains the "stem-like" cellular state of the neural stem cells.
Title: Transcription factor positive regulatory domain 4 (PRDM4) recruits protein arginine methyltransferase 5 (PRMT5) to mediate histone arginine methylation and control neural stem cell proliferation and differentiation.

Submit: New GeneRIF Correction

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	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables death receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables histone methyltransferase binding	IEA Inferred from Electronic Annotation 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 sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cellular response to growth factor stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to nutrient	IEP Inferred from Expression Pattern more info	PubMed
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell growth	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of neural precursor cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	TAS Traceable Author Statement more info
part_of histone methyltransferase complex	IEA Inferred from Electronic Annotation more info
part_of histone methyltransferase complex	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement 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

General protein information

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Preferred Names: PR domain zinc finger protein 4

Names: PR domain 4; PR domain containing 4; PR domain-containing protein 4

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_133312.2 → NP_579846.2 PR domain zinc finger protein 4

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000007

UniProtKB/Swiss-Prot

Q9QZP2

UniProtKB/TrEMBL

A6IFD2

Conserved Domains (4) summary

sd00017
Location:616 → 636

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:361 → 398

zf_PR_Knuckle; PR zinc knuckle motif

cd19189
Location:401 → 533

PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins

pfam13465
Location:628 → 653

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_086025.1 Reference GRCr8

Range

19841560..19868224

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063262939.1 → XP_063119009.1 PR domain zinc finger protein 4 isoform X2

UniProtKB/Swiss-Prot

Q9QZP2

UniProtKB/TrEMBL

A6IFD2
XM_039078328.1 → XP_038934256.1 PR domain zinc finger protein 4 isoform X1

UniProtKB/Swiss-Prot

Q9QZP2

UniProtKB/TrEMBL

F1LPR7

Conserved Domains (4) summary

sd00017
Location:623 → 643

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:361 → 398

zf_PR_Knuckle; PR zinc knuckle motif

cd19189
Location:401 → 540

PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins

pfam13465
Location:635 → 660

zf-H2C2_2; Zinc-finger double domain
XM_006241161.4 → XP_006241223.1 PR domain zinc finger protein 4 isoform X2

See identical proteins and their annotated locations for XP_006241223.1

UniProtKB/Swiss-Prot

Q9QZP2

UniProtKB/TrEMBL

A6IFD2

Related

ENSRNOP00000006886.7, ENSRNOT00000006886.8

Conserved Domains (4) summary

sd00017
Location:616 → 636

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:361 → 398

zf_PR_Knuckle; PR zinc knuckle motif

cd19189
Location:401 → 533

PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins

pfam13465
Location:628 → 653

zf-H2C2_2; Zinc-finger double domain
XM_006241160.3 → XP_006241222.1 PR domain zinc finger protein 4 isoform X1

UniProtKB/Swiss-Prot

Q9QZP2

UniProtKB/TrEMBL

F1LPR7

Conserved Domains (4) summary

sd00017
Location:623 → 643

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:361 → 398

zf_PR_Knuckle; PR zinc knuckle motif

cd19189
Location:401 → 540

PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins

pfam13465
Location:635 → 660

zf-H2C2_2; Zinc-finger double domain
XM_063262940.1 → XP_063119010.1 PR domain zinc finger protein 4 isoform X3
XM_039078330.1 → XP_038934258.1 PR domain zinc finger protein 4 isoform X4

Conserved Domains (2) summary

pfam18445
Location:361 → 398

zf_PR_Knuckle; PR zinc knuckle motif

cl40432
Location:401 → 468

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
XM_039078331.1 → XP_038934259.1 PR domain zinc finger protein 4 isoform X5

UniProtKB/TrEMBL

A0A8I6AA47

Conserved Domains (2) summary

pfam18445
Location:361 → 398

zf_PR_Knuckle; PR zinc knuckle motif

cl40432
Location:401 → 461

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