PRDM11 Gene (Protein Coding)

PR/SET Domain 11

GC11P045072
GIFtS:
32

Aliases for PRDM11 Gene

Aliases for PRDM11 Gene

  • PR/SET Domain 11 2 3 5
  • PR Domain-Containing Protein 11 3 4
  • PR-Domain Containing Protein 11 2 3
  • PFM8 3 4
  • PR Domain Containing 11 2
  • PR Domain 11 2
  • EC 2.1.1.- 4

External Ids for PRDM11 Gene

Previous GeneCards Identifiers for PRDM11 Gene

  • GC11P046892
  • GC11M045834
  • GC11P045147
  • GC11P045079
  • GC11P044914

Summaries for PRDM11 Gene

GeneCards Summary for PRDM11 Gene

PRDM11 (PR/SET Domain 11) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and methyltransferase activity. An important paralog of this gene is PRDM7.

UniProtKB/Swiss-Prot Summary for PRDM11 Gene

Additional gene information for PRDM11 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRDM11 Gene

Genomics for PRDM11 Gene

GeneHancer (GH) Regulatory Elements for PRDM11 Gene

Promoters and enhancers for PRDM11 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH11J045333 Enhancer 0.8 ENCODE dbSUPER 18.9 +239.6 239558 1.8 CTCF USF2 NFYC ELF1 RAD21 ZNF148 JUND USF1 SMC3 STAT1 PRDM11 ENSG00000254497 CHST1 SYT13 lnc-PRDM11-8 LINC02696
GH11J044936 Enhancer 1.1 Ensembl ENCODE CraniofacialAtlas dbSUPER 12.2 -157.0 -157012 1.6 CTCF CC2D1A RAD21 REST ZNF7 TRIM22 RUNX3 DEK SMC3 SMARCA5 lnc-SYT13-6 lnc-SYT13-7 PRDM11 TP53I11
GH11J045025 Enhancer 1.1 FANTOM5 Ensembl ENCODE dbSUPER 11.9 -67.8 -67829 2.9 RFX1 SP1 ZNF623 NR2F2 BCOR ADNP ZMYM3 MAX SRF PRDM11 TP53I11 TSPAN18 piR-38352-078 lnc-PRDM11-2 RF00017-904 ENSG00000287984 LOC105376650
GH11J044942 Promoter/Enhancer 1.1 Ensembl ENCODE dbSUPER 11.6 -150.7 -150744 1.7 MAX RELA ZIC2 ZBTB8A TARDBP OSR2 RUNX3 ZFHX2 EBF1 SIN3A PRDM11 TP53I11 lnc-SYT13-6
GH11J044939 Promoter/Enhancer 1 Ensembl ENCODE dbSUPER 12.3 -154.2 -154246 1 ATF1 CREM ATF2 CTCF ATF7 PRDM11 lnc-SYT13-6 TP53I11
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRDM11 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRDM11 gene promoter:
  • C/EBPalpha
  • CP2
  • MZF-1
  • NRSF form 1
  • NRSF form 2
  • RFX1
  • SRF
  • SRF (504 AA)

Genomic Locations for PRDM11 Gene

Genomic Locations for PRDM11 Gene
chr11:45,094,013-45,235,124
(GRCh38/hg38)
Size:
141,112 bases
Orientation:
Plus strand
chr11:45,115,564-45,247,734
(GRCh37/hg19)
Size:
132,171 bases
Orientation:
Plus strand

Genomic View for PRDM11 Gene

Genes around PRDM11 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM11 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM11 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PRDM11 Gene

Proteins for PRDM11 Gene

Products:

  1. Antibody
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  • Protein details for PRDM11 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQV5-PRD11_HUMAN
    Recommended name:
    PR domain-containing protein 11
    Protein Accession:
    Q9NQV5
    Secondary Accessions:
    • Q8N9F1

    Protein attributes for PRDM11 Gene

    Size:
    511 amino acids
    Molecular mass:
    57863 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for PRDM11 Gene

    Alternative splice isoforms for PRDM11 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PRDM11 Gene

Protein Expression for PRDM11 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PRDM11 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PRDM11 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for PRDM11

No data available for DME Specific Peptides for PRDM11 Gene

Domains & Families for PRDM11 Gene

Gene Families for PRDM11 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for PRDM11 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PRDM11 Gene

GenScript: Design optimal peptide antigens:
  • PR domain-containing protein 11 (PRD11_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NQV5

UniProtKB/Swiss-Prot:

PRD11_HUMAN :
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with PRDM11: view

Function for PRDM11 Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for PRDM11 Gene

UniProtKB/Swiss-Prot Function:
May be involved in transcription regulation.

Enzyme Numbers (IUBMB) for PRDM11 Gene

Phenotypes From GWAS Catalog for PRDM11 Gene

Gene Ontology (GO) - Molecular Function for PRDM11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0001047 core promoter binding IDA 25499759
GO:0003682 chromatin binding ISS --
GO:0003700 DNA-binding transcription factor activity IBA 21873635
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with PRDM11: view
genes like me logo Genes that share phenotypes with PRDM11: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM11

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PRDM11 Gene

Localization for PRDM11 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM11 Gene

Nucleus. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PRDM11 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 0

Gene Ontology (GO) - Cellular Components for PRDM11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 25499759
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA 25499759
genes like me logo Genes that share ontologies with PRDM11: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PRDM11 Gene

Pathways & Interactions for PRDM11 Gene

PathCards logo

SuperPathways for PRDM11 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PRDM11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030308 negative regulation of cell growth IDA 25499759
GO:0032259 methylation IEA --
GO:0043408 regulation of MAPK cascade IMP 25499759
GO:0045892 negative regulation of transcription, DNA-templated IMP 25499759
GO:0045893 positive regulation of transcription, DNA-templated IMP 25499759
genes like me logo Genes that share ontologies with PRDM11: view

No data available for Pathways by source and SIGNOR curated interactions for PRDM11 Gene

Drugs & Compounds for PRDM11 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for PRDM11 Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PRDM11 Gene

(3) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(39) Selected AceView cDNA sequences:
(6) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM11

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM11 Gene

No ASD Table

Relevant External Links for PRDM11 Gene

GeneLoc Exon Structure for
PRDM11
ECgene alternative splicing isoforms for
PRDM11

Expression for PRDM11 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PRDM11 Gene

mRNA expression in normal human tissues for PRDM11 Gene
mRNA expression by GTEx for PRDM11 GenemRNA expression by BioGPS for PRDM11 Gene

Protein differential expression in normal tissues from HIPED for PRDM11 Gene

This gene is overexpressed in Fetal gut (67.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PRDM11 Gene



Protein tissue co-expression partners for PRDM11 Gene

NURSA nuclear receptor signaling pathways regulating expression of PRDM11 Gene:

PRDM11

SOURCE GeneReport for Unigene cluster for PRDM11 Gene:

Hs.178715

mRNA Expression by UniProt/SwissProt for PRDM11 Gene:

Q9NQV5-PRD11_HUMAN
Tissue specificity: Highly expressed in lung, including bronchial epithelial cells and airway smooth muscle cells, as well as in peripheral blood mononuclear cells. In tonsils, expressed in B-cell types, including naive B-cells, centroblasts, centrocytes and memory B-cells (at protein level). In benign hyperplastic lymph nodes, expressed in germinal center cells in both the dark and light zones, as well as in scattered cells in the mantle zone and the interfollicular area (at protein level).

Evidence on tissue expression from TISSUES for PRDM11 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with PRDM11: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRDM11 Gene

Orthologs for PRDM11 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRDM11 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PRDM11 33 32
  • 99.42 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia PRDM11 32
  • 91.39 (n)
cow
(Bos Taurus)
 Mammalia PRDM11 33 32
  • 91.14 (n)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia PRDM11 33
  • 89 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Prdm11 32
  • 87.63 (n)
mouse
(Mus musculus)
 Mammalia Prdm11 17 33 32
  • 86.5 (n)
oppossum
(Monodelphis domestica)
 Mammalia PRDM11 33
  • 31 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves PRDM11 33 32
  • 78.26 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia PRDM11 33
  • 62 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia prdm11 32
  • 73.3 (n)
zebrafish
(Danio rerio)
 Actinopterygii prdm11 33 32
  • 65.04 (n)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta CG43347 33
  • 2 (a)
 OneToMany
Species where no ortholog for PRDM11 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PRDM11 Gene

ENSEMBL:
Gene Tree for PRDM11 (if available)
TreeFam:
Gene Tree for PRDM11 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRDM11: view image

Paralogs for PRDM11 Gene

Paralogs for PRDM11 Gene

genes like me logo Genes that share paralogs with PRDM11: view

Variants for PRDM11 Gene

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  1. SNP Genotyping and Copy Number Assay

Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM11 Gene

PRD11_HUMAN-Q9NQV5
A genome-wide association analysis shows PRDM11 association with forced vital capacity (FVC), a spirometric measure of pulmonary function, that reflects lung volume and is used to diagnose and monitor lung diseases.

Sequence variations from dbSNP and Humsavar for PRDM11 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs111724149 A patient with diffuse large B-cell lymphoma 45,204,720(+) A/G 5_prime_UTR_variant, coding_sequence_variant, missense_variant
rs35090414 A patient with diffuse large B-cell lymphoma 45,224,227(+) G/A/T coding_sequence_variant, intron_variant, missense_variant, synonymous_variant
rs1000004841 -- 45,145,279(+) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000044787 -- 45,162,821(+) T/A genic_upstream_transcript_variant, intron_variant
rs1000045409 -- 45,166,677(+) G/A/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PRDM11 Gene

Variant ID Type Subtype PubMed ID
dgv137e201 CNV deletion 23290073
dgv631n106 CNV deletion 24896259
esv1665387 CNV insertion 17803354
esv1954118 CNV deletion 18987734
esv2676978 CNV deletion 23128226
esv2744423 CNV deletion 23290073
esv2744424 CNV deletion 23290073
esv2744425 CNV deletion 23290073
esv2744426 CNV deletion 23290073
esv2744427 CNV deletion 23290073
esv2744428 CNV deletion 23290073
esv3547690 CNV deletion 23714750
esv3626171 CNV loss 21293372
nsv1069578 CNV deletion 25765185
nsv1070447 CNV deletion 25765185
nsv1120653 CNV deletion 24896259
nsv1131025 CNV deletion 24896259
nsv513314 CNV insertion 21212237
nsv523057 CNV loss 19592680
nsv825852 CNV gain 20364138
nsv825854 CNV gain 20364138
nsv825855 CNV gain 20364138
nsv951607 CNV duplication 24416366

Variation tolerance for PRDM11 Gene

Residual Variation Intolerance Score: 30.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.90; 59.29% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRDM11 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRDM11

Disorders for PRDM11 Gene

Additional Disease Information for PRDM11

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PRDM11 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PRDM11 Gene

Publications for PRDM11 Gene

  1. Loss of PRDM11 promotes MYC-driven lymphomagenesis. (PMID: 25499759) Fog CK … Lund AH (Blood 2015) 3 4 56
  2. Genome-wide association analysis identifies six new loci associated with forced vital capacity. (PMID: 24929828) Loth DW … London SJ (Nature genetics 2014) 3 4 56
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56
  4. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3 56
  5. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. (PMID: 28112733) Hendriks IA … Nielsen ML (Nature structural & molecular biology 2017) 4 56

ExternalLinks

View latest publications for PRDM11 gene in Mastermind

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