PRDM11 PR/SET domain 11 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PRDM11provided by HGNC
Official Full Name: PR/SET domain 11provided by HGNC
Primary source: HGNC:HGNC:13996
See related: Ensembl:ENSG00000019485 MIM:616347; AllianceGenome:HGNC:13996
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PFM8
Summary: Predicted to enable chromatin binding activity. Involved in several processes, including negative regulation of cell growth; positive regulation of fibroblast apoptotic process; and regulation of DNA-templated transcription. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in thyroid (RPKM 2.3), ovary (RPKM 1.9) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11p11.2

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (45094159..45235109)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (45251156..45392625)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (45115710..45256660)

Chromosome 11 - NC_000011.10 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: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

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.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis identifies six new loci associated with forced vital capacity. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S3626 (e-PCR)
- UniSTS:152863

SHGC-57630 (e-PCR)
- UniSTS:43308

SHGC-141727 (e-PCR)
- UniSTS:171053

G02149 (e-PCR)
- UniSTS:16186

SHGC-31737 (e-PCR)
- UniSTS:12604

G20711 (e-PCR)
- UniSTS:59724

A006C44 (e-PCR)
- UniSTS:59725

RH48405 (e-PCR)
- UniSTS:19030

G02301 (e-PCR)
- UniSTS:68963

RH48132 (e-PCR)
- UniSTS:18827

D11S4633 (e-PCR)
- UniSTS:54683

NoName (e-PCR)
- UniSTS:492446

D11S2322E (e-PCR)
- UniSTS:9160

SHGC-53097 (e-PCR)
- UniSTS:57801

SHGC-56565 (e-PCR)
- UniSTS:51150

D1Bda2 (e-PCR)
- UniSTS:240336

RH46268 (e-PCR)
- UniSTS:44274

SHGC-79552 (e-PCR)
- UniSTS:103675

SHGC-36809 (e-PCR)
- UniSTS:17919

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell growth	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of fibroblast apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of MAPK cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: PR domain-containing protein 11

Names: PR-domain containing protein 11

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_001256695.2 → NP_001243624.1 PR domain-containing protein 11 isoform 1

See identical proteins and their annotated locations for NP_001243624.1

Status: VALIDATED

Source sequence(s)

AC103681

Consensus CDS

CCDS73277.1

UniProtKB/TrEMBL

A0A087WWZ6

Related

ENSP00000480626.1, ENST00000622142.5

Conserved Domains (1) summary

cd19195
Location:109 → 235

PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
NM_001256696.2 → NP_001243625.1 PR domain-containing protein 11 isoform 2

See identical proteins and their annotated locations for NP_001243625.1

Status: VALIDATED

Source sequence(s)

AC103681

Consensus CDS

CCDS58130.1

UniProtKB/Swiss-Prot

Q8N9F1, Q9NQV5

Related

ENSP00000394314.2, ENST00000424263.6

Conserved Domains (1) summary

cd19195
Location:109 → 235

PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
NM_001359633.2 → NP_001346562.2 PR domain-containing protein 11 isoform 2

Status: VALIDATED

Source sequence(s)

AC103681, AC103682

Consensus CDS

CCDS58130.1

UniProtKB/Swiss-Prot

Q8N9F1, Q9NQV5

Related

ENSP00000435976.2, ENST00000530656.5

Conserved Domains (1) summary

cd19195
Location:109 → 235

PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
NM_001384648.1 → NP_001371577.1 PR domain-containing protein 11 isoform 1

Status: VALIDATED

Source sequence(s)

AC103681

Consensus CDS

CCDS73277.1

UniProtKB/TrEMBL

A0A087WWZ6

Related

ENSP00000507575.1, ENST00000683152.1

Conserved Domains (1) summary

cd19195
Location:109 → 235

PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
NM_001384649.1 → NP_001371578.1 PR domain-containing protein 11 isoform 4

Status: VALIDATED

Source sequence(s)

AC103681

Consensus CDS

CCDS91463.1

UniProtKB/TrEMBL

H3BSZ2

Related

ENSP00000456942.2, ENST00000534751.3

Conserved Domains (2) summary

PHA03247
Location:334 → 404

PHA03247; large tegument protein UL36; Provisional

cl40432
Location:109 → 235

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
NM_001384650.1 → NP_001371579.1 PR domain-containing protein 11 isoform 4

Status: VALIDATED

Source sequence(s)

AC103681

Consensus CDS

CCDS91463.1

UniProtKB/TrEMBL

H3BSZ2

Conserved Domains (2) summary

PHA03247
Location:334 → 404

PHA03247; large tegument protein UL36; Provisional

cl40432
Location:109 → 235

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
NM_001384651.1 → NP_001371580.1 PR domain-containing protein 11 isoform 4

Status: VALIDATED

Source sequence(s)

AC103681

Consensus CDS

CCDS91463.1

UniProtKB/TrEMBL

H3BSZ2

Conserved Domains (2) summary

PHA03247
Location:334 → 404

PHA03247; large tegument protein UL36; Provisional

cl40432
Location:109 → 235

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

45094159..45235109

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011520225.3 → XP_011518527.1 PR domain-containing protein 11 isoform X1

See identical proteins and their annotated locations for XP_011518527.1

UniProtKB/TrEMBL

A0A087WWZ6

Conserved Domains (1) summary

cd19195
Location:109 → 235

PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
XM_011520222.3 → XP_011518524.1 PR domain-containing protein 11 isoform X1

See identical proteins and their annotated locations for XP_011518524.1

UniProtKB/TrEMBL

A0A087WWZ6

Conserved Domains (1) summary

cd19195
Location:109 → 235

PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
XM_011520228.4 → XP_011518530.1 PR domain-containing protein 11 isoform X3

Conserved Domains (1) summary

smart00317
Location:129 → 230

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
XM_011520224.4 → XP_011518526.1 PR domain-containing protein 11 isoform X1

See identical proteins and their annotated locations for XP_011518526.1

UniProtKB/TrEMBL

A0A087WWZ6

Conserved Domains (1) summary

cd19195
Location:109 → 235

PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
XM_047427314.1 → XP_047283270.1 PR domain-containing protein 11 isoform X5
XM_047427313.1 → XP_047283269.1 PR domain-containing protein 11 isoform X4

UniProtKB/TrEMBL

H3BSZ2
XM_011520226.3 → XP_011518528.1 PR domain-containing protein 11 isoform X2

See identical proteins and their annotated locations for XP_011518528.1

Conserved Domains (2) summary

pfam09306
Location:195 → 327

Phage-scaffold; Bacteriophage, scaffolding protein

cl02566
Location:1 → 47

SET; SET domain

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

45251156..45392625

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054369438.1 → XP_054225413.1 PR domain-containing protein 11 isoform X1

UniProtKB/TrEMBL

A0A087WWZ6
XM_054369436.1 → XP_054225411.1 PR domain-containing protein 11 isoform X1

UniProtKB/TrEMBL

A0A087WWZ6
XM_054369440.1 → XP_054225415.1 PR domain-containing protein 11 isoform X3
XM_054369437.1 → XP_054225412.1 PR domain-containing protein 11 isoform X1

UniProtKB/TrEMBL

A0A087WWZ6
XM_054369442.1 → XP_054225417.1 PR domain-containing protein 11 isoform X5
XM_054369441.1 → XP_054225416.1 PR domain-containing protein 11 isoform X4
XM_054369439.1 → XP_054225414.1 PR domain-containing protein 11 isoform X2