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Aliases for PRDM1 Gene

Aliases for PRDM1 Gene

  • PR/SET Domain 1 2 3 5
  • PR Domain Containing 1, With ZNF Domain 2 3
  • PR Domain 1 2 3
  • PRDI-BF1 3 4
  • BLIMP-1 3 4
  • BLIMP1 3 4
  • Beta-Interferon Gene Positive-Regulatory Domain I Binding Factor 3
  • Beta-Interferon Gene Positive Regulatory Domain I-Binding Factor 4
  • Positive Regulatory Domain I-Binding Factor 1 4
  • B-Lymphocyte-Induced Maturation Protein 1 3
  • PR Domain Zinc Finger Protein 1 3
  • PR Domain-Containing Protein 1 4
  • PRDI-Binding Factor-1 3
  • PRDI-Binding Factor 1 4
  • EC 2.1.1.- 4

External Ids for PRDM1 Gene

Previous HGNC Symbols for PRDM1 Gene

  • BLIMP1

Previous GeneCards Identifiers for PRDM1 Gene

  • GC06P106371
  • GC06P106557
  • GC06P106579
  • GC06P106640
  • GC06P103981
  • GC06P106534

Summaries for PRDM1 Gene

Entrez Gene Summary for PRDM1 Gene

  • This gene encodes a protein that acts as a repressor of beta-interferon gene expression. The protein binds specifically to the PRDI (positive regulatory domain I element) of the beta-IFN gene promoter. Transcription of this gene increases upon virus induction. Two alternatively spliced transcript variants that encode different isoforms have been reported. [provided by RefSeq, Jul 2008]

CIViC summary for PRDM1 Gene

GeneCards Summary for PRDM1 Gene

PRDM1 (PR/SET Domain 1) is a Protein Coding gene. Diseases associated with PRDM1 include Adult Lymphoma and Central Nervous System Lymphoma. Among its related pathways are Gene Expression and Direct p53 effectors. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is ZNF683.

UniProtKB/Swiss-Prot for PRDM1 Gene

  • Transcription factor that mediates a transcriptional program in various innate and adaptive immune tissue-resident lymphocyte T cell types such as tissue-resident memory T (Trm), natural killer (trNK) and natural killer T (NKT) cells and negatively regulates gene expression of proteins that promote the egress of tissue-resident T-cell populations from non-lymphoid organs. Plays a role in the development, retention and long-term establishment of adaptive and innate tissue-resident lymphocyte T cell types in non-lymphoid organs, such as the skin and gut, but also in other nonbarrier tissues like liver and kidney, and therefore may provide immediate immunological protection against reactivating infections or viral reinfection (By similarity). Binds specifically to the PRDI element in the promoter of the beta-interferon gene (PubMed:1851123). Drives the maturation of B-lymphocytes into Ig secreting cells (PubMed:12626569). Associates with the transcriptional repressor ZNF683 to chromatin at gene promoter regions (By similarity).

Gene Wiki entry for PRDM1 Gene

Additional gene information for PRDM1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRDM1 Gene

Genomics for PRDM1 Gene

GeneHancer (GH) Regulatory Elements for PRDM1 Gene

Promoters and enhancers for PRDM1 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
GH06J106082 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 673.2 +0.1 109 8.1 SIN3A ZNF2 IRF4 ZNF766 ZNF207 ZNF143 FOS SP3 JUNB REST PRDM1 RNU6-344P ENSG00000269919 ATG5
GH06J106096 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 668.1 +14.1 14120 7.5 PKNOX1 ATF1 SMAD1 ARNT IRF4 YY1 ZNF766 ZNF143 ZFP91 ATF7 PRDM1 ENSG00000269919 PIR35075 ATG5
GH06J105991 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE 690.7 -91.2 -91223 7 ARID4B SIN3A ZNF2 ZNF766 ZNF207 ZNF143 SP3 NFYC MXD4 REST PRDM1 GC06M106046 GC06M105873 GC06M105874
GH06J106044 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 661.2 -35.5 -35463 13.2 HDAC1 ATF1 FOXA2 ZFP64 ATF7 CEBPB ZEB2 ZNF148 SP1 SMARCA4 PRDM1 ATG5 GC06M106046
GH06J106162 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 39.1 +77.7 77687 3 HDGF PKNOX1 SMAD1 BATF IRF4 ATF7 ETV6 IKZF2 RUNX3 CREM PRDM1 ENSG00000269919 PIR35075 ATG5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PRDM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRDM1 gene promoter:
  • STAT3
  • IRF-1
  • p53
  • GR

Genomic Locations for PRDM1 Gene

Genomic Locations for PRDM1 Gene
chr6:106,086,320-106,109,939
(GRCh38/hg38)
Size:
23,620 bases
Orientation:
Plus strand
chr6:106,534,195-106,557,814
(GRCh37/hg19)
Size:
23,620 bases
Orientation:
Plus strand

Genomic View for PRDM1 Gene

Genes around PRDM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRDM1 Gene

Proteins for PRDM1 Gene

  • Protein details for PRDM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75626-PRDM1_HUMAN
    Recommended name:
    PR domain zinc finger protein 1
    Protein Accession:
    O75626
    Secondary Accessions:
    • B2REA6
    • E1P5E0
    • Q86WM7

    Protein attributes for PRDM1 Gene

    Size:
    825 amino acids
    Molecular mass:
    91771 Da
    Quaternary structure:
    • Interacts with PRMT5 (By similarity). Interacts with FBXO10 (PubMed:24613396). Interacts with FBXO11 (PubMed:24613396, PubMed:24968003).
    SequenceCaution:
    • Sequence=AAO45623.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PRDM1 Gene

    Alternative splice isoforms for PRDM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PRDM1 Gene

Post-translational modifications for PRDM1 Gene

  • Sumoylation at Lys-816 by PIAS1 augments transcriptional repressor activity, and is critical for plasma cell differentiation.
  • Ubiquitinated by the SCF(FBXO11) complex, leading to its degradation by the proteasome.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PRDM1 Gene

Domains & Families for PRDM1 Gene

Gene Families for PRDM1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for PRDM1 Gene

Graphical View of Domain Structure for InterPro Entry

O75626

UniProtKB/Swiss-Prot:

PRDM1_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 PRDM1: view

Function for PRDM1 Gene

Molecular function for PRDM1 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor that mediates a transcriptional program in various innate and adaptive immune tissue-resident lymphocyte T cell types such as tissue-resident memory T (Trm), natural killer (trNK) and natural killer T (NKT) cells and negatively regulates gene expression of proteins that promote the egress of tissue-resident T-cell populations from non-lymphoid organs. Plays a role in the development, retention and long-term establishment of adaptive and innate tissue-resident lymphocyte T cell types in non-lymphoid organs, such as the skin and gut, but also in other nonbarrier tissues like liver and kidney, and therefore may provide immediate immunological protection against reactivating infections or viral reinfection (By similarity). Binds specifically to the PRDI element in the promoter of the beta-interferon gene (PubMed:1851123). Drives the maturation of B-lymphocytes into Ig secreting cells (PubMed:12626569). Associates with the transcriptional repressor ZNF683 to chromatin at gene promoter regions (By similarity).
GENATLAS Biochemistry:
PR domain containing 1,B-lymphocyte maturation promoting transcription factor,repressing the expression of IFNB promoter,and the transcription by recruiting a complex of Groucho family proteins to DNA,deleted in several B-cell non Hodgkin lymphoma and other cancers

Enzyme Numbers (IUBMB) for PRDM1 Gene

Phenotypes From GWAS Catalog for PRDM1 Gene

Gene Ontology (GO) - Molecular Function for PRDM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 1851123
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001078 transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding IDA 1851123
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with PRDM1: view
genes like me logo Genes that share phenotypes with PRDM1: view

Animal Models for PRDM1 Gene

MGI Knock Outs for PRDM1:

Animal Model Products

CRISPR Products

Targeted motifs for PRDM1 Gene
HOMER Transcription Factor Regulatory Elements motif PRDM1
  • Consensus sequence: ACTTTCACTTTC Submotif: canonical Cell Type: Hela GEO ID: GSE31477

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM1

Clone Products

  • Addgene plasmids for PRDM1

No data available for Human Phenotype Ontology and Transcription Factor Targets for PRDM1 Gene

Localization for PRDM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM1 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 PRDM1 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PRDM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA,IDA 21421998
genes like me logo Genes that share ontologies with PRDM1: view

Pathways & Interactions for PRDM1 Gene

genes like me logo Genes that share pathways with PRDM1: view

Pathways by source for PRDM1 Gene

SIGNOR curated interactions for PRDM1 Gene

Inactivates:
Is activated by:

Gene Ontology (GO) - Biological Process for PRDM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 1851123
GO:0001701 in utero embryonic development IEA --
GO:0001763 morphogenesis of a branching structure IEA --
GO:0001892 embryonic placenta development IEA --
GO:0001893 maternal placenta development IEA --
genes like me logo Genes that share ontologies with PRDM1: view

Drugs & Compounds for PRDM1 Gene

(3) Drugs for PRDM1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with PRDM1: view

Transcripts for PRDM1 Gene

Unigene Clusters for PRDM1 Gene

PR domain containing 1, with ZNF domain:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM1

Clone Products

  • Addgene plasmids for PRDM1

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c · 3d ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b · 11c
SP1: - - - - - - - -
SP2: - - - - - - -
SP3: -
SP4: - -
SP5: - - - - -
SP6:
SP7: -
SP8: - -
SP9: -
SP10: -

Relevant External Links for PRDM1 Gene

GeneLoc Exon Structure for
PRDM1
ECgene alternative splicing isoforms for
PRDM1

Expression for PRDM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PRDM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PRDM1 Gene

This gene is overexpressed in Esophagus - Mucosa (x7.8) and Whole Blood (x4.2).

Protein differential expression in normal tissues from HIPED for PRDM1 Gene

This gene is overexpressed in Serum (37.1) and Pancreas (27.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PRDM1 Gene



Protein tissue co-expression partners for PRDM1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PRDM1 Gene:

PRDM1

SOURCE GeneReport for Unigene cluster for PRDM1 Gene:

Hs.436023

Evidence on tissue expression from TISSUES for PRDM1 Gene

  • Bone marrow(3)
  • Blood(2.7)
  • Lymph node(2.7)
  • Spleen(2.4)
  • Intestine(2)
genes like me logo Genes that share expression patterns with PRDM1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRDM1 Gene

Orthologs for PRDM1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRDM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PRDM1 34 33
  • 99.6 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Prdm1 16 34 33
  • 86.94 (n)
rat
(Rattus norvegicus)
Mammalia Prdm1 33
  • 86.92 (n)
cow
(Bos Taurus)
Mammalia PRDM1 34 33
  • 86.37 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PRDM1 34 33
  • 84.44 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PRDM1 34
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PRDM1 34
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRDM1 33
  • 77.38 (n)
BLIMP-1 34
  • 73 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PRDM1 34
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm1 33
  • 70.42 (n)
African clawed frog
(Xenopus laevis)
Amphibia prdm1-prov 33
zebrafish
(Danio rerio)
Actinopterygii prdm1a 34 33
  • 62.2 (n)
OneToOne
ubo 33
fruit fly
(Drosophila melanogaster)
Insecta CG5249 35
  • 72 (a)
Blimp-1 34
  • 19 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea odd-3 35
  • 60 (a)
Species where no ortholog for PRDM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)

Evolution for PRDM1 Gene

ENSEMBL:
Gene Tree for PRDM1 (if available)
TreeFam:
Gene Tree for PRDM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRDM1: view image

Paralogs for PRDM1 Gene

Variants for PRDM1 Gene

Sequence variations from dbSNP and Humsavar for PRDM1 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs139718143 not-provided, not specified 106,107,241(+) G/A coding_sequence_variant, missense_variant
rs141465160 not-provided, not specified 106,105,508(+) C/G/T coding_sequence_variant, missense_variant
rs143040512 not-provided, not specified 106,105,221(+) G/A coding_sequence_variant, missense_variant
rs144524449 not-provided, not specified 106,105,382(+) G/C/T coding_sequence_variant, missense_variant
rs149024185 not-provided, not specified 106,104,971(+) A/G coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for PRDM1 Gene

Variant ID Type Subtype PubMed ID
nsv830755 CNV loss 17160897
nsv5429 CNV insertion 18451855
nsv1025231 CNV gain 25217958
dgv6134n100 CNV gain 25217958

Variation tolerance for PRDM1 Gene

Residual Variation Intolerance Score: 55.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.10; 84.51% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRDM1 Gene

Human Gene Mutation Database (HGMD)
PRDM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRDM1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM1 Gene

Disorders for PRDM1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for PRDM1 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
adult lymphoma
central nervous system lymphoma
  • microglioma
oral hairy leukoplakia
  • hairy leukoplakia
plasmablastic lymphoma
  • pbl
b-cell lymphomas
  • b-cell lymphoma
- elite association - COSMIC cancer census association via MalaCards
Search PRDM1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PRDM1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PRDM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PRDM1 Gene

Publications for PRDM1 Gene

  1. Identification and characterization of a novel repressor of beta-interferon gene expression. (PMID: 1851123) Keller AD … Maniatis T (Genes & development 1991) 2 3 4 22 58
  2. Lack of evidence of a role of XBP1 and PRDM1 polymorphisms in Spanish patients with immunoglobulin A deficiency. (PMID: 19735688) del Pozo N … Núñez C (Human immunology 2009) 3 22 44 58
  3. Identification of a functionally impaired positive regulatory domain I binding factor 1 transcription repressor in myeloma cell lines. (PMID: 12626569) Györy I … Wright KL (Journal of immunology (Baltimore, Md. : 1950) 2003) 3 4 22 58
  4. SUMOylation of Blimp-1 is critical for plasma cell differentiation. (PMID: 22555612) Ying HY … Lin KI (EMBO reports 2012) 3 4 58
  5. NANOS3 function in human germ cell development. (PMID: 21421998) Julaton VT … Reijo Pera RA (Human molecular genetics 2011) 3 4 58

Products for PRDM1 Gene

Sources for PRDM1 Gene

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