Free for academic non-profit institutions. Other users need a Commercial license

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]

GeneCards Summary for PRDM1 Gene

PRDM1 (PR/SET Domain 1) is a Protein Coding gene. Diseases associated with PRDM1 include Central Nervous System Lymphoma and Adult Lymphoma. Among its related pathways are IL6-mediated signaling events and IgA-Producing B Cells in the Intestine. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and RNA polymerase II core promoter proximal region 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

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

Genomics for PRDM1 Gene

Regulatory Elements for PRDM1 Gene

Enhancers for PRDM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F105991 1.3 FANTOM5 Ensembl ENCODE 40.7 -91.2 -91224 7.0 ARNT SIN3A ARID4B ZNF2 YY1 ZNF143 ZNF207 FOS DEK ZNF263 PRDM1 GC06M106046 GC06M105873 GC06M105874
GH06F106162 1.4 FANTOM5 Ensembl ENCODE 39.1 +77.7 77724 3.1 HDGF PKNOX1 TBL1XR1 ZBTB40 ETV6 CREM EGR2 CEBPB JUNB TBX21 PRDM1 ENSG00000269919 PIR35075
GH06F105986 0.7 FANTOM5 33.6 -100.1 -100109 0.3 CBX8 RNF2 SUZ12 CBX2 CTBP2 EZH2 PRDM1 GC06M105873 GC06M105874 GC06M106046
GH06F105791 1.4 FANTOM5 Ensembl ENCODE 28.1 -291.0 -290962 8.5 HDGF RAD21 ZBTB40 RARA YY1 SCRT2 SMARCC2 RCOR1 FOS SMARCC1 PRDM1 HACE1 GC06M105786 LOC105377923
GH06F105879 1.3 FANTOM5 Ensembl ENCODE 27.7 -205.9 -205920 1.6 MTA2 BHLHE40 MAX TRIM22 BMI1 TBX21 IKZF1 TARDBP NBN MLLT1 PRDM1 QRSL1 LOC105377923 GC06M105786
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PRDM1 on UCSC Golden Path with GeneCards custom track

Promoters for PRDM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001223452 1880 5201 CREB3L1 SIN3A GLIS2 FOS SP3 JUNB REST SMARCB1 SMARCA4 NBN

Genomic Location for PRDM1 Gene

Chromosome:
6
Start:
106,086,320 bp from pter
End:
106,109,939 bp from pter
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

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PRDM1 (PRDM1)
  • Cloud-Clone Corp. Antibodies for PRDM1

No data available for DME Specific Peptides for PRDM1 Gene

Domains & Families for PRDM1 Gene

Gene Families for PRDM1 Gene

Graphical View of Domain Structure for InterPro Entry

O75626

UniProtKB/Swiss-Prot:

PRDM1_HUMAN :
  • Contains 1 SET domain.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
  • Contains 4 C2H2-type zinc fingers.
Domain:
  • Contains 1 SET domain.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Similarity:
  • Contains 4 C2H2-type zinc fingers.
genes like me logo Genes that share domains with PRDM1: view

Function for PRDM1 Gene

Molecular function for PRDM1 Gene

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
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).

Enzyme Numbers (IUBMB) for PRDM1 Gene

Gene Ontology (GO) - Molecular Function for PRDM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA 1851123
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding IDA 1851123
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding IEA,TAS 1851123
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

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

Flow Cytometry Products

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
Jensen Localization Image for PRDM1 Gene COMPARTMENTS Subcellular localization image for PRDM1 gene
Compartment Confidence
nucleus 5
cytosol 1
endoplasmic reticulum 1
extracellular 1
plasma membrane 1

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 from RNA polymerase II promoter 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:

Inhibitory RNA Products

Flow Cytometry Products

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 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, PaxDb, 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
genes like me logo Genes that share expression patterns with PRDM1: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt 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 35
  • 99.6 (n)
mouse
(Mus musculus)
Mammalia Prdm1 34 16 35
  • 86.94 (n)
rat
(Rattus norvegicus)
Mammalia Prdm1 34
  • 86.92 (n)
cow
(Bos Taurus)
Mammalia PRDM1 34 35
  • 86.37 (n)
dog
(Canis familiaris)
Mammalia PRDM1 34 35
  • 84.44 (n)
oppossum
(Monodelphis domestica)
Mammalia PRDM1 35
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PRDM1 35
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRDM1 34
  • 77.38 (n)
BLIMP-1 35
  • 73 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PRDM1 35
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm1 34
  • 70.42 (n)
African clawed frog
(Xenopus laevis)
Amphibia prdm1-prov 34
zebrafish
(Danio rerio)
Actinopterygii prdm1a 34 35
  • 62.2 (n)
ubo 34
fruit fly
(Drosophila melanogaster)
Insecta CG5249 36
  • 72 (a)
Blimp-1 35
  • 19 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea odd-3 36
  • 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)

Paralogs for PRDM1 Gene

Variants for PRDM1 Gene

Sequence variations from dbSNP and Humsavar for PRDM1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs139718143 untested 106,107,241(+) AGGAC(A/G)TGGAG reference, missense
rs141465160 untested 106,105,508(+) GCAAT(C/T)TCCTC reference, missense
rs143040512 untested 106,105,221(+) TCACA(A/G)CAGCC reference, missense
rs144524449 untested 106,105,382(+) ACAAC(C/G/T)CTCAC reference, missense
rs149024185 untested 106,104,971(+) CTAAC(A/G)TTTCA reference, missense

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

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

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)

Relevant External Links for PRDM1 Gene

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

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: DISEASES, Novoseek, and GeneCards

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

Relevant External Links for PRDM1

Genetic Association Database (GAD)
PRDM1
Human Genome Epidemiology (HuGE) Navigator
PRDM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PRDM1
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 A.D. … Maniatis T. (Genes Dev. 1991) 2 3 4 22 64
  2. Lack of evidence of a role of XBP1 and PRDM1 polymorphisms in Spanish patients with immunoglobulin A deficiency. (PMID: 19735688) del Pozo N. … NA_A+ez C. (Hum. Immunol. 2009) 3 22 46 64
  3. Identification of a functionally impaired positive regulatory domain I binding factor 1 transcription repressor in myeloma cell lines. (PMID: 12626569) Gyory I. … Wright K.L. (J. Immunol. 2003) 3 4 22 64
  4. SUMOylation of Blimp-1 is critical for plasma cell differentiation. (PMID: 22555612) Ying H.Y. … Lin K.I. (EMBO Rep. 2012) 3 4 64
  5. NANOS3 function in human germ cell development. (PMID: 21421998) Julaton V.T. … Reijo Pera R.A. (Hum. Mol. Genet. 2011) 3 4 64

Products for PRDM1 Gene

Sources for PRDM1 Gene

Content
Loading form....