Prdm5 PR domain containing 5 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Prdm5provided by MGI
Official Full Name: PR domain containing 5provided by MGI
Primary source: MGI:MGI:1918029
See related: Ensembl:ENSMUSG00000029913 AllianceGenome:MGI:1918029
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: PFM2; 4432417F03Rik; 6530401I24Rik; E130112L17Rik
Summary: Predicted to enable DNA-binding transcription factor binding activity; DNA-binding transcription repressor activity, RNA polymerase II-specific; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in nuclear body and nucleolus. Is expressed in several structures, including central nervous system; early embryo; and genitourinary system. Human ortholog(s) of this gene implicated in brittle cornea syndrome 2. Orthologous to human PRDM5 (PR/SET domain 5). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Broad expression in limb E14.5 (RPKM 2.9), CNS E11.5 (RPKM 1.9) and 20 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 C1; 6 30.32 cM

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (65754640..65914606)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (65777656..65937622)

Chromosome 6 - NC_000072.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Endocannabinoid signaling regulates the reinforcing and psychostimulant effects of ketamine in mice.
Title: Endocannabinoid signaling regulates the reinforcing and psychostimulant effects of ketamine in mice.
PRDM5 promotes the proliferation and invasion of murine melanoma cells through up-regulating JNK expression and strategies targeting PRDM5 may be promising for the therapy of melanoma.
Title: PRDM5 promotes the proliferation and invasion of murine melanoma cells through up-regulating JNK expression.
Data provide the first causal link between Prdm5 loss and intestinal carcinogenesis, and uncover an extensive and novel PRDM5 target repertoire likely facilitating the tumor-suppressive functions of PRDM5.
Title: Prdm5 suppresses Apc(Min)-driven intestinal adenomas and regulates monoacylglycerol lipase expression.
These data indicate how Prdm5 modulates transcription by interacting with factors involved in genome organization in mouse embryonic stem cells.
Title: Genomic and proteomic analyses of Prdm5 reveal interactions with insulator binding proteins in embryonic stem cells.
we show that Prdm5 controls both Collagen I transcription and fibrillogenesis by binding inside the Col1a1 gene body and maintaining RNA polymerase II occupancy
Title: Prdm5 regulates collagen gene transcription by association with RNA polymerase II in developing bone.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)
Gene trapped (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH135956 (e-PCR)
- UniSTS:209952

BE335543 (e-PCR)
- UniSTS:207971

NoName (e-PCR)
- UniSTS:235461

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor binding	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation 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	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 metal ion binding	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in mitotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in mitotic cell cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation 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
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of extracellular matrix organization	IEA Inferred from Electronic Annotation more info
involved_in regulation of extracellular matrix organization	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

Component	Evidence Code	Pubs
located_in nuclear body	IEA Inferred from Electronic Annotation more info
located_in nuclear body	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	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: PR domain zinc finger protein 5

Names: PR domain-containing protein 5

NP_081823.2

EC 2.1.1.-

NP_083825.1

EC 2.1.1.-

XP_006506665.1

EC 2.1.1.-

XP_006506667.1

EC 2.1.1.-

XP_036008193.1

EC 2.1.1.-

XP_036008195.1

EC 2.1.1.-

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)

NM_027547.2 → NP_081823.2 PR domain zinc finger protein 5 isoform 1

See identical proteins and their annotated locations for NP_081823.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK014501, BG070775, BX511446, BY014014

Consensus CDS

CCDS20208.1

UniProtKB/Swiss-Prot

B2RSK8, Q9CXE0

Related

ENSMUSP00000031976.8, ENSMUST00000031976.14

Conserved Domains (4) summary

smart00317
Location:20 → 123

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

COG5048
Location:186 → 590

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

sd00017
Location:460 → 480

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:473 → 496

zf-H2C2_2; Zinc-finger double domain
NM_029549.1 → NP_083825.1 PR domain zinc finger protein 5 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks multiple exons in the coding region but maintains the reading frame, compared to variant 1. These differences result in a shorter isoform (2), compared to isoform 1.

Source sequence(s)

AC154005, AC158677

Consensus CDS

CCDS85059.1

UniProtKB/TrEMBL

E9Q707, Q9D364

Related

ENSMUSP00000031973.7, ENSMUST00000031973.13

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000072.7 Reference GRCm39 C57BL/6J

Range

65754640..65914606

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006506604.4 → XP_006506667.1 PR domain zinc finger protein 5 isoform X4

Conserved Domains (4) summary

COG5048
Location:258 → 621

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

sd00017
Location:491 → 511

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam15909
Location:172 → 222

zf-C2H2_8; C2H2-type zinc ribbon

cd19190
Location:2 → 128

PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins
XM_036152300.1 → XP_036008193.1 PR domain zinc finger protein 5 isoform X1

UniProtKB/TrEMBL

G3UWU3

Related

ENSMUSP00000133423.2, ENSMUST00000172638.2

Conserved Domains (3) summary

COG5048
Location:168 → 365

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

sd00017
Location:319 → 339

ZF_C2H2; C2H2 Zn finger [structural motif]

cd19190
Location:2 → 128

PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins
XM_006506602.4 → XP_006506665.1 PR domain zinc finger protein 5 isoform X2

Conserved Domains (3) summary

COG5048
Location:163 → 325

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

sd00017
Location:195 → 215

ZF_C2H2; C2H2 Zn finger [structural motif]

cl40432
Location:2 → 100

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
XM_036152302.1 → XP_036008195.1 PR domain zinc finger protein 5 isoform X3

Conserved Domains (3) summary

COG5048
Location:188 → 318

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

COG5189
Location:22 → 96

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

sd00017
Location:188 → 208

ZF_C2H2; C2H2 Zn finger [structural motif]