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

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; AllianceGenome:HGNC:9346
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; BLIMP-1; 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: mouse all
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Genomic context

Location:: 6q21

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (105992690..106109938)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (107168603..107285801)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (106534211..106557813)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PRDM1 promotes nucleus pulposus cell pyroptosis leading to intervertebral disc degeneration via activating CASP1 transcription.
Title: PRDM1 promotes nucleus pulposus cell pyroptosis leading to intervertebral disc degeneration via activating CASP1 transcription.
PTIP epigenetically regulates DNA damage-induced cell cycle arrest by upregulating PRDM1.
Title: PTIP epigenetically regulates DNA damage-induced cell cycle arrest by upregulating PRDM1.
Human split hand/foot variants are not as functional as wildtype human PRDM1 in the rescue of craniofacial defects.
Title: Human split hand/foot variants are not as functional as wildtype human PRDM1 in the rescue of craniofacial defects.
Pro-Inflammatory of PRDM1/SIRT2/NLRP3 Axis in Monosodium Urate-Induced Acute Gouty Arthritis.
Title: Pro-Inflammatory of PRDM1/SIRT2/NLRP3 Axis in Monosodium Urate-Induced Acute Gouty Arthritis.
Exploring the putative role of PRDM1 and PRDM2 transcripts as mediators of T lymphocyte activation.
Title: Exploring the putative role of PRDM1 and PRDM2 transcripts as mediators of T lymphocyte activation.
Expression of B lymphocyte-induced maturation protein 1 (Blimp-1) in keratinocyte and cytokine signalling drives human Th17 response in psoriasis.
Title: Expression of B lymphocyte-induced maturation protein 1 (Blimp-1) in keratinocyte and cytokine signalling drives human Th17 response in psoriasis.
BLIMP1 and NR4A3 transcription factors reciprocally regulate antitumor CAR T cell stemness and exhaustion.
Title: BLIMP1 and NR4A3 transcription factors reciprocally regulate antitumor CAR T cell stemness and exhaustion.
The role of PRDM1 gene polymorphism in the progression of hepatocellular carcinoma in Egyptian patients.
Title: The role of PRDM1 gene polymorphism in the progression of hepatocellular carcinoma in Egyptian patients.
Regulatory network of BLIMP1, IRF4, and XBP1 triad in plasmacytic differentiation and multiple myeloma pathogenesis.
Title: Regulatory network of BLIMP1, IRF4, and XBP1 triad in plasmacytic differentiation and multiple myeloma pathogenesis.
Blimp-1 is a prognostic indicator for progression of cervical intraepithelial neoplasia grade 2.
Title: Blimp-1 is a prognostic indicator for progression of cervical intraepithelial neoplasia grade 2.

Submit: New GeneRIF Correction See all GeneRIFs (169)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6S1217E (e-PCR)
- UniSTS:26944

PRDM1_1073 (e-PCR)
- UniSTS:277614

D6S1410 (e-PCR)
- UniSTS:21387

Clone Names

MGC118922, MGC118923, MGC118924, MGC118925

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables histone methyltransferase binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables promoter-specific chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
involved_in aorta development	IEA Inferred from Electronic Annotation more info
involved_in artery morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cell fate commitment	IBA Inferred from Biological aspect of Ancestor more info
involved_in coronary vasculature development	IEA Inferred from Electronic Annotation more info
involved_in eye photoreceptor cell development	IEA Inferred from Electronic Annotation more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in germ cell development	IEA Inferred from Electronic Annotation more info
involved_in heart valve development	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in intestinal epithelial cell development	IEA Inferred from Electronic Annotation more info
involved_in kidney development	IEA Inferred from Electronic Annotation more info
involved_in maternal placenta development	IEA Inferred from Electronic Annotation more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in morphogenesis of a branching structure	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in post-embryonic development	IEA Inferred from Electronic Annotation more info
involved_in regulation of NK T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in regulation of extrathymic T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of natural killer cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in retinal bipolar neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in sebum secreting cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in trophoblast giant cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in ventricular septum development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: PR domain zinc finger protein 1

Names: B-lymphocyte-induced maturation protein 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)

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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

NG_029115.2 RefSeqGene

Range

98648..122250

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001198.4 → NP_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

B2REA6, E1P5E0, O75626, Q86WM7

UniProtKB/TrEMBL

A8K0J1

Related

ENSP00000358092.4, ENST00000369096.9

Conserved Domains (5) summary

smart00317
Location:100 → 206

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

COG5048
Location:570 → 688

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:577 → 597

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:575 → 597

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:617 → 642

zf-H2C2_2; Zinc-finger double domain
NM_182907.3 → NP_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)

AY198415

Consensus CDS

CCDS34505.1

UniProtKB/TrEMBL

Q3SYG0

Related

ENSP00000358085.3, ENST00000369089.3

Conserved Domains (4) summary

smart00317
Location:5 → 72

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

COG5189
Location:371 → 544

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

sd00017
Location:443 → 463

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:483 → 508

zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

105992690..106109938

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047419246.1 → XP_047275202.1 PR domain zinc finger protein 1 isoform X3

UniProtKB/TrEMBL

Q5T4E8

Related

ENSP00000498580.1, ENST00000652320.1
XM_017011187.2 → XP_016866676.1 PR domain zinc finger protein 1 isoform X3

UniProtKB/TrEMBL

A8K0J1, Q5T4E8

Related

ENSP00000498716.1, ENST00000651185.1

Conserved Domains (5) summary

smart00317
Location:64 → 170

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

COG5048
Location:534 → 652

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:541 → 561

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:539 → 561

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:581 → 606

zf-H2C2_2; Zinc-finger double domain
XM_047419247.1 → XP_047275203.1 PR domain zinc finger protein 1 isoform X4
XM_011536062.4 → XP_011534364.1 PR domain zinc finger protein 1 isoform X1

UniProtKB/TrEMBL

A0A3B3IU23, A8K0J1

Related

ENSP00000498029.1, ENST00000648754.1

Conserved Domains (5) summary

smart00317
Location:114 → 220

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

COG5048
Location:584 → 702

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:591 → 611

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:589 → 611

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:631 → 656

zf-H2C2_2; Zinc-finger double domain
XM_006715550.4 → XP_006715613.1 PR domain zinc finger protein 1 isoform X2

UniProtKB/TrEMBL

A8K0J1

Conserved Domains (3) summary

smart00317
Location:114 → 220

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

sd00017
Location:605 → 624

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:616 → 641

zf-H2C2_2; Zinc-finger double domain
XM_011536064.4 → XP_011534366.1 PR domain zinc finger protein 1 isoform X5

See identical proteins and their annotated locations for XP_011534366.1

UniProtKB/TrEMBL

Q3SYG0

Conserved Domains (5) summary

smart00317
Location:1 → 48

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

COG5048
Location:412 → 530

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:419 → 439

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:417 → 439

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:459 → 484

zf-H2C2_2; Zinc-finger double domain
XM_047419248.1 → XP_047275204.1 PR domain zinc finger protein 1 isoform X6