Format

Send to:

Choose Destination

PRDM1 PR/SET domain 1 [ Homo sapiens (human) ]

Gene ID: 639, updated on 15-Apr-2019

Summary

Official Symbol
PRDM1provided by HGNC
Official Full Name
PR/SET domain 1provided by HGNC
Primary source
HGNC:HGNC:9346
See related
Ensembl:ENSG00000057657 MIM:603423
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BLIMP1; PRDI-BF1
Summary
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]
Expression
Broad expression in esophagus (RPKM 16.3), endometrium (RPKM 7.2) and 17 other tissues See more
Orthologs

Genomic context

See PRDM1 in Genome Data Viewer
Location:
6q21
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (106046729..106109939)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (106534195..106557814)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377923 Neighboring gene RN7SK pseudogene 211 Neighboring gene autophagy related 5 Neighboring gene RNA, 7SL, cytoplasmic 47, pseudogene Neighboring gene RNA, U6 small nuclear 344, pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus.
NHGRI GWA Catalog
Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
NHGRI GWA Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
NHGRI GWA Catalog
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 reduces expression of PRDM1 (BLIMP1) expression and inversely correlates with HIV-1 viral load and TP53 (Ki67) expression in activated B cells from HIV-1-infected treatment naive individuals PubMed
Knockdown of PR domain containing 1, with ZNF domain (PRDM1; BLIMP1) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat upregulates the expression of T-bet, Eomesdermin, Blimp-1, Bcl-6, and Bcl-2 in stimulated but not in unstimulated CD8+T lymphocytes PubMed
tat BLIMP-1 inhibits basal HIV-1 transcription as well as transcription in the presence of HIV-1 Tat in Jurkat cells and primary human CD4+ T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Direct p53 effectors, organism-specific biosystem (from Pathway Interaction Database)
    Direct p53 effectors, organism-specific biosystem
    Direct p53 effectors
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • IL-6 signaling pathway, organism-specific biosystem (from WikiPathways)
    IL-6 signaling pathway, organism-specific biosystemIL-6 is a pleiotropic cytokine with important role in immune regulation, hematopoiesis, inflammation and oncogenesis. IL-6-type cytokines exert their action via the signal transducer gp130 that assoc...
  • Nucleotide-binding Oligomerization Domain (NOD) pathway, organism-specific biosystem (from WikiPathways)
    Nucleotide-binding Oligomerization Domain (NOD) pathway, organism-specific biosystemThe NOD (nucleotide-binding oligomerization domain) proteins NOD1 and NOD2 have important roles in innate immunity as sensors of microbial components derived from bacterial peptidoglycan. The importa...
  • Regulation of TP53 Activity, organism-specific biosystem (from REACTOME)
    Regulation of TP53 Activity, organism-specific biosystemProtein stability and transcriptional activity of TP53 (p53) tumor suppressor are regulated by post-translational modifications that include ubiquitination, phosphorylation, acetylation, methylation,...
  • Regulation of TP53 Expression, organism-specific biosystem (from REACTOME)
    Regulation of TP53 Expression, organism-specific biosystemTranscription of the TP53 (p53) gene is negatively regulated by the TP53 transcriptional target PRDM1 (BLIMP1), which binds to the promoter region of TP53 and probably induces repressive methylation ...
  • Regulation of TP53 Expression and Degradation, organism-specific biosystem (from REACTOME)
    Regulation of TP53 Expression and Degradation, organism-specific biosystemTP53 (p53) tumor suppressor protein is a transcription factor that functions as a homotetramer (Jeffrey et al. 1995). The protein levels of TP53 are low in unstressed cells due to MDM2-mediated ubiqu...
  • Transcriptional Regulation by TP53, organism-specific biosystem (from REACTOME)
    Transcriptional Regulation by TP53, organism-specific biosystemThe tumor suppressor TP53 (encoded by the gene p53) is a transcription factor. Under stress conditions, it recognizes specific responsive DNA elements and thus regulates the transcription of many gen...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC118922, MGC118923, MGC118924, MGC118925

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone deacetylase binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
promoter-specific chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
aorta development IEA
Inferred from Electronic Annotation
more info
 
artery morphogenesis IEA
Inferred from Electronic Annotation
more info
 
cell fate commitment IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
coronary vasculature development IEA
Inferred from Electronic Annotation
more info
 
eye photoreceptor cell development IEA
Inferred from Electronic Annotation
more info
 
germ cell development IEA
Inferred from Electronic Annotation
more info
 
heart valve development IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
intestinal epithelial cell development IEA
Inferred from Electronic Annotation
more info
 
maternal placenta development IEA
Inferred from Electronic Annotation
more info
 
methylation IEA
Inferred from Electronic Annotation
more info
 
morphogenesis of a branching structure IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
post-embryonic development IEA
Inferred from Electronic Annotation
more info
 
regulation of NK T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
regulation of extrathymic T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of natural killer cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
sebum secreting cell proliferation IEA
Inferred from Electronic Annotation
more info
 
trophoblast giant cell differentiation IEA
Inferred from Electronic Annotation
more info
 
ventricular septum development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
PR domain zinc finger protein 1
Names
B-lymphocyte-induced maturation protein 1
BLIMP-1
PR domain 1
PR domain containing 1, with ZNF domain
PRDI-binding factor-1
beta-interferon gene positive-regulatory domain I binding factor

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_029115.1 RefSeqGene

    Range
    5001..28620
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001198.4NP_001189.2  PR domain zinc finger protein 1 isoform 1

    See identical proteins and their annotated locations for NP_001189.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as PRDM1alpha, encodes the longer isoform (1). The protein encoded by this transcript has also been named PRDI-BF1alpha.
    Source sequence(s)
    AY198414
    Consensus CDS
    CCDS5054.2
    UniProtKB/Swiss-Prot
    O75626
    Related
    ENSP00000358092.4, ENST00000369096.9
    Conserved Domains (5) summary
    smart00317
    Location:100206
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:570688
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:577597
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:575597
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:617642
    zf-H2C2_2; Zinc-finger double domain
  2. NM_182907.2NP_878911.1  PR domain zinc finger protein 1 isoform 2

    See identical proteins and their annotated locations for NP_878911.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as PRDM1beta, contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (2) has a shorter N-terminus when compared to isoform 1. The protein encoded by this transcript has also been named PRDI-BF1beta.
    Source sequence(s)
    AK301341, AY198415
    Consensus CDS
    CCDS34505.1
    UniProtKB/Swiss-Prot
    O75626
    UniProtKB/TrEMBL
    B4DW27
    Related
    ENSP00000358085.3, ENST00000369089.3
    Conserved Domains (4) summary
    smart00317
    Location:572
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5189
    Location:371544
    SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
    sd00017
    Location:443463
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:483508
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    106046729..106109939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011187.1XP_016866676.1  PR domain zinc finger protein 1 isoform X3

    UniProtKB/Swiss-Prot
    O75626
    UniProtKB/TrEMBL
    Q5T4E8
    Related
    ENSP00000498580.1, ENST00000652320.1
    Conserved Domains (5) summary
    smart00317
    Location:64170
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:534652
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:541561
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:539561
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:581606
    zf-H2C2_2; Zinc-finger double domain
  2. XM_006715550.3XP_006715613.1  PR domain zinc finger protein 1 isoform X2

    Conserved Domains (3) summary
    smart00317
    Location:114220
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    sd00017
    Location:605624
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:616641
    zf-H2C2_2; Zinc-finger double domain
  3. XM_011536062.3XP_011534364.1  PR domain zinc finger protein 1 isoform X1

    Related
    ENSP00000498029.1, ENST00000648754.1
    Conserved Domains (5) summary
    smart00317
    Location:114220
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:584702
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:591611
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:589611
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:631656
    zf-H2C2_2; Zinc-finger double domain
  4. XM_011536063.2XP_011534365.1  PR domain zinc finger protein 1 isoform X3

    See identical proteins and their annotated locations for XP_011534365.1

    UniProtKB/Swiss-Prot
    O75626
    UniProtKB/TrEMBL
    Q5T4E8
    Conserved Domains (5) summary
    smart00317
    Location:64170
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:534652
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:541561
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:539561
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:581606
    zf-H2C2_2; Zinc-finger double domain
  5. XM_011536064.3XP_011534366.1  PR domain zinc finger protein 1 isoform X4

    See identical proteins and their annotated locations for XP_011534366.1

    Conserved Domains (5) summary
    smart00317
    Location:148
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:412530
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:419439
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:417439
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:459484
    zf-H2C2_2; Zinc-finger double domain
Support Center