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Aliases for PRDM1 Gene

Aliases for PRDM1 Gene

  • PR Domain 1 2 3
  • PR Domain Containing 1, With ZNF Domain 2 3 5
  • 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-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 Domain 1) is a Protein Coding gene. Diseases associated with PRDM1 include Central Nervous System Lymphoma and Hodgkin Lymphoma. Among its related pathways are Gene Expression and NF-kappaB Signaling. 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

  • Transcriptional repressor that 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).

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 Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

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

ENSRs around PRDM1 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the PRDM1 gene promoter:

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 and FBXO11.
    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

Proteomics data for PRDM1 Gene at MOPED

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

Other Protein References for PRDM1 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PRDM1 (PRDM1)

No data available for DME Specific Peptides for PRDM1 Gene

Domains & Families for PRDM1 Gene

Gene Families for PRDM1 Gene

Protein Domains 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:
Transcriptional repressor that 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).

Enzyme Numbers (IUBMB) for PRDM1 Gene

Gene Ontology (GO) - Molecular Function for PRDM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA,IPI 22555612
GO:0008168 methyltransferase activity 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

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

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

No data available for Gene Ontology (GO) - Cellular Components for PRDM1 Gene

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:0001763 morphogenesis of a branching structure IEA --
GO:0003279 cardiac septum development IEA --
GO:0003281 ventricular septum development IEA --
GO:0007281 germ cell 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:

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 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



SOURCE GeneReport for Unigene cluster for PRDM1 Gene Hs.436023

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

Protein tissue co-expression partners for PRDM1 Gene

- Elite partner

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
cow
(Bos Taurus)
Mammalia PRDM1 35
  • 86.37 (n)
  • 88.11 (a)
PRDM1 36
  • 88 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PRDM1 35
  • 84.44 (n)
  • 83.91 (a)
PRDM1 36
  • 84 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Prdm1 35
  • 86.94 (n)
  • 89.17 (a)
Prdm1 16
Prdm1 36
  • 89 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PRDM1 35
  • 99.6 (n)
  • 99.15 (a)
PRDM1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Prdm1 35
  • 86.92 (n)
  • 88.58 (a)
oppossum
(Monodelphis domestica)
Mammalia PRDM1 36
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PRDM1 36
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRDM1 35
  • 77.38 (n)
  • 79.68 (a)
BLIMP-1 36
  • 73 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PRDM1 36
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm1 35
  • 70.42 (n)
  • 70.68 (a)
African clawed frog
(Xenopus laevis)
Amphibia prdm1-prov 35
zebrafish
(Danio rerio)
Actinopterygii prdm1a 35
  • 62.2 (n)
  • 62.43 (a)
ubo 35
prdm1a 36
  • 54 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG5249 37
  • 72 (a)
Blimp-1 36
  • 19 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea odd-3 37
  • 60 (a)
Species with no ortholog for PRDM1:
  • 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

Paralogs for PRDM1 Gene

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

Variants for PRDM1 Gene

Sequence variations from dbSNP and Humsavar for PRDM1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs2185379 - 106,088,378(+) ATGGC(A/G)GTACT reference, missense
rs811925 - 106,099,497(-) GCAAA(C/G)TCCCG reference, missense
rs1010273 -- 106,107,150(+) GCCCC(A/G)GCGCC reference, synonymous-codon
rs4946722 -- 106,084,571(+) TGATT(A/C)TAAAA upstream-variant-2KB
rs4946723 -- 106,087,381(+) TGAGG(A/G)CTCCT intron-variant, upstream-variant-2KB

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

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

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

Disorders for PRDM1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
central nervous system lymphoma
  • microglioma
hodgkin lymphoma
  • hodgkin's lymphoma
adult lymphoma
b-cell lymphomas
  • b-cell lymphoma
primary central nervous system lymphoma
  • primary cns lymphoma
- 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 23 67
  2. Blimp-1: a marker of terminal differentiation but not of sebocytic progenitor cells. (PMID: 19788443) Sellheyer K. … Krahl D. (J. Cutan. Pathol. 2010) 3 23
  3. Blimp-1 is a tumor suppressor gene in lymphoid malignancies. (PMID: 20047096) Hangaishi A. … Kurokawa M. (Int. J. Hematol. 2010) 3 23
  4. Involvement of histone demethylase LSD1 in Blimp-1-mediated gene repression during plasma cell differentiation. (PMID: 19124609) Su S.T. … Lin K.I. (Mol. Cell. Biol. 2009) 3 23
  5. Blimp-1/PRDM1 mediates transcriptional suppression of the NLR gene NLRP12/Monarch-1. (PMID: 19234190) Lord C.A. … Williams K.L. (J. Immunol. 2009) 3 23

Products for PRDM1 Gene

Sources for PRDM1 Gene

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