Prdm11 PR domain containing 11 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Prdm11provided by MGI
Official Full Name: PR domain containing 11provided by MGI
Primary source: MGI:MGI:2685553
See related: Ensembl:ENSMUSG00000075028 AllianceGenome:MGI:2685553
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: Gm707; Gm29694; 8030443D09Rik
Summary: Enables chromatin binding activity. Predicted to be involved in several processes, including negative regulation of cell growth; positive regulation of fibroblast apoptotic process; and regulation of DNA-templated transcription. Predicted to be located in cytosol. Predicted to be active in nucleus. Is expressed in embryo and head. Orthologous to human PRDM11 (PR/SET domain 11). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in limb E14.5 (RPKM 2.4), adrenal adult (RPKM 2.0) and 26 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2; 2 E1

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (92795496..92876825, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (92965151..93046165, complement)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

We characterize PRDM11 as a putative novel tumor suppressor that controls the expression of key oncogenes, and we add new mechanistic insight into B-cell lymphomagenesis.
Title: Loss of PRDM11 promotes MYC-driven lymphomagenesis.
PRDM11, in contrast to PRDM3 and PRDM16, is not directly involved in regulation of HSPCs in mice.
Title: PRDM11 is dispensable for the maintenance and function of hematopoietic stem and progenitor cells.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Endonuclease-mediated (1)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell fate commitment	IBA Inferred from Biological aspect of Ancestor more info
involved_in methylation	IEA Inferred from Electronic Annotation 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 cell growth	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell growth	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of fibroblast apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of fibroblast apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of MAPK cascade	ISO Inferred from Sequence Orthology more info
involved_in regulation of MAPK cascade	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell cycle	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity 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
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: PR domain-containing protein 11

Names: zinc finger protein 862 pseudogene

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_001177536.2 → NP_001171007.1 PR domain-containing protein 11 isoform 3

See identical proteins and their annotated locations for NP_001171007.1

Status: VALIDATED

Source sequence(s)

AL713913

Consensus CDS

CCDS50647.1

UniProtKB/Swiss-Prot

A2AGX2, A2AGX3, A2AGX4

Related

ENSMUSP00000136795.2, ENSMUST00000178666.8

Conserved Domains (1) summary

smart00317
Location:129 → 230

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
NM_001368848.1 → NP_001355777.1 PR domain-containing protein 11 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AL713913

Consensus CDS

CCDS89522.1

UniProtKB/TrEMBL

A0A5F8MPE3

Related

ENSMUSP00000158933.2, ENSMUST00000238863.2

Conserved Domains (2) summary

pfam18445
Location:75 → 101

zf_PR_Knuckle; PR zinc knuckle motif

cd19195
Location:109 → 235

PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
NM_001368849.1 → NP_001355778.1 PR domain-containing protein 11 isoform 2

Status: VALIDATED

Source sequence(s)

AL713913

Conserved Domains (1) summary

smart00317
Location:129 → 230

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

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_000068.8 Reference GRCm39 C57BL/6J

Range

92795496..92876825 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030245942.2 → XP_030101802.1 PR domain-containing protein 11 isoform X2

UniProtKB/TrEMBL

A0A5F8MPE3

Conserved Domains (2) summary

pfam18445
Location:75 → 101

zf_PR_Knuckle; PR zinc knuckle motif

cd19195
Location:109 → 235

PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
XM_030245934.2 → XP_030101794.1 PR domain-containing protein 11 isoform X1

Conserved Domains (2) summary

pfam18445
Location:101 → 127

zf_PR_Knuckle; PR zinc knuckle motif

cd19195
Location:135 → 261

PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
XM_030245944.2 → XP_030101804.1 PR domain-containing protein 11 isoform X2

UniProtKB/TrEMBL

A0A5F8MPE3

Conserved Domains (2) summary

pfam18445
Location:75 → 101

zf_PR_Knuckle; PR zinc knuckle motif

cd19195
Location:109 → 235

PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
XM_030245943.1 → XP_030101803.1 PR domain-containing protein 11 isoform X3

Conserved Domains (1) summary

cl40432
Location:52 → 104

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
XM_030245948.1 → XP_030101808.1 PR domain-containing protein 11 isoform X4