BCL6 BCL6 transcription repressor [Homo sapiens (human)] - Gene

Summary

Official Symbol: BCL6provided by HGNC
Official Full Name: BCL6 transcription repressorprovided by HGNC
Primary source: HGNC:HGNC:1001
See related: Ensembl:ENSG00000113916 MIM:109565; AllianceGenome:HGNC:1001
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: BCL5; LAZ3; BCL6A; ZNF51; ZBTB27
Summary: The protein encoded by this gene is a zinc finger transcription factor and contains an N-terminal POZ domain. This protein acts as a sequence-specific repressor of transcription, and has been shown to modulate the transcription of STAT-dependent IL-4 responses of B cells. This protein can interact with a variety of POZ-containing proteins that function as transcription corepressors. This gene is found to be frequently translocated and hypermutated in diffuse large-cell lymphoma (DLCL), and may be involved in the pathogenesis of DLCL. Alternatively spliced transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, Aug 2015]
Expression: Ubiquitous expression in fat (RPKM 29.2), bone marrow (RPKM 20.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q27.3

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (187721377..187745468, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (190538887..190562977, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (187439165..187463256, complement)

Chromosome 3 - NC_000003.12 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?

B Cell Lymphoma 6 (BCL6): A Conserved Regulator of Immunity and Beyond.
Title: B Cell Lymphoma 6 (BCL6): A Conserved Regulator of Immunity and Beyond.
Deficiency of CBL and CBLB ubiquitin ligases leads to hyper T follicular helper cell responses and lupus by reducing BCL6 degradation.
Title: Deficiency of CBL and CBLB ubiquitin ligases leads to hyper T follicular helper cell responses and lupus by reducing BCL6 degradation.
Delineating the mechanism of fragility at BCL6 breakpoint region associated with translocations in diffuse large B cell lymphoma.
Title: Delineating the mechanism of fragility at BCL6 breakpoint region associated with translocations in diffuse large B cell lymphoma.
Alternative genetic alterations of MYC, BCL2, and/or BCL6 in high-grade B-cell lymphoma (HGBL) and diffuse large B-cell lymphoma (DLBCL): Can we identify different prognostic subgroups?
Title: Alternative genetic alterations of MYC, BCL2, and/or BCL6 in high-grade B-cell lymphoma (HGBL) and diffuse large B-cell lymphoma (DLBCL): Can we identify different prognostic subgroups?
Bcl6 is a subset-defining transcription factor of lymphoid tissue inducer-like ILC3.
Title: Bcl6 is a subset-defining transcription factor of lymphoid tissue inducer-like ILC3.
Identification of mutation gene prognostic biomarker in multiple myeloma through gene panel exome sequencing and transcriptome analysis in Chinese population.
Title: Identification of mutation gene prognostic biomarker in multiple myeloma through gene panel exome sequencing and transcriptome analysis in Chinese population.
B-cell lymphoma 6 expression significantly differs by the uterine preparation method used for frozen embryo transfer.
Title: B-cell lymphoma 6 expression significantly differs by the uterine preparation method used for frozen embryo transfer.
Clinical course and features of persistent polyclonal B-cell lymphocytosis with BCL-6 amplification during pregnancy.
Title: Clinical course and features of persistent polyclonal B-cell lymphocytosis with BCL-6 amplification during pregnancy.
Bcl6 drives stem-like memory macrophages differentiation to foster tumor progression.
Title: Bcl6 drives stem-like memory macrophages differentiation to foster tumor progression.
BCL6-SPECC1L: A Novel Fusion Gene in Nasopharyngeal Carcinoma.
Title: BCL6-SPECC1L: A Novel Fusion Gene in Nasopharyngeal Carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (322)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of B cell non-Hodgkin lymphoma identifies 3q27 as a susceptibility locus in the Chinese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization. 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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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120 upregulates the expression of B-cell CLL/lymphoma 6 (BCL6) in human B cells	PubMed
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	HIV-1 Tat upregulates the expression of BCL-6 in Kaposi's sarcoma cells and human primary 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

SHGC-77640 (e-PCR)
- UniSTS:58625

SHGC-64334 (e-PCR)
- UniSTS:34563

RH70520 (e-PCR)
- UniSTS:64302

STS-W46183 (e-PCR)
- UniSTS:74552

SHGC-77610 (e-PCR)
- UniSTS:82745

RH47862 (e-PCR)
- UniSTS:18348

BCL6 (e-PCR)
- UniSTS:505525

PMC309637P2 (e-PCR)
- UniSTS:272596

RH69801 (e-PCR)
- UniSTS:61681

PMC137537P1 (e-PCR)
- UniSTS:270834

SHGC-34056 (e-PCR)
- UniSTS:19451

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	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 chromatin DNA binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables intronic transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in B cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in DNA damage response	IDA Inferred from Direct Assay more info	PubMed
involved_in Rho protein signal transduction	IEA Inferred from Electronic Annotation more info
involved_in T-helper 2 cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in actin cytoskeleton organization	IEA Inferred from Electronic Annotation more info
involved_in cell morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cell motility	IEA Inferred from Electronic Annotation more info
involved_in cell-matrix adhesion	IEA Inferred from Electronic Annotation more info
involved_in erythrocyte development	IEA Inferred from Electronic Annotation more info
involved_in germinal center formation	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin formation	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in isotype switching to IgE isotypes	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of B cell apoptotic process	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of Notch signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of Rho protein signal transduction	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of T-helper 2 cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell growth	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cell-matrix adhesion	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cellular senescence	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of isotype switching to IgE isotypes	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of mast cell cytokine production	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of mitotic cell cycle DNA replication	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of mononuclear cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of plasma cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in plasma cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of B cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell motility	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of regulatory T cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization	IEA Inferred from Electronic Annotation more info
involved_in pyramidal neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in regulation of T cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cell population proliferation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cytokine production	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of germinal center formation	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of immune response	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of immune system process	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of memory T cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in type 2 immune response	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
located_in nucleolus	IDA Inferred from Direct Assay more info
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in paraspeckles	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with replication fork	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: B-cell lymphoma 6 protein

Names: B cell CLL/lymphoma 6; B-cell lymphoma 5 protein; B-cell lymphoma 6 protein transcript; BCL-5; BCL-6; cys-his2 zinc finger transcription factor; lymphoma-associated zinc finger gene on chromosome 3; protein LAZ-3; zinc finger and BTB domain-containing protein 27; zinc finger protein 51; zinc finger transcription factor BCL6S

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_007149.1 RefSeqGene

Range

5068..29155

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001130845.2 → NP_001124317.1 B-cell lymphoma 6 protein isoform 1

See identical proteins and their annotated locations for NP_001124317.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has a downstream and alternate 5' UTR exon, as compared to variant 1.

Source sequence(s)

AC072022, BC146796, BC150184, CN401512

Consensus CDS

CCDS3289.1

UniProtKB/Swiss-Prot

A7E241, B8PSA7, D3DNV5, P41182

UniProtKB/TrEMBL

A5PL18

Related

ENSP00000232014.4, ENST00000232014.8

Conserved Domains (4) summary

smart00225
Location:33 → 126

BTB; Broad-Complex, Tramtrack and Bric a brac

sd00017
Location:576 → 596

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00651
Location:22 → 126

BTB; BTB/POZ domain

pfam13465
Location:588 → 613

zf-H2C2_2; Zinc-finger double domain
NM_001134738.1 → NP_001128210.1 B-cell lymphoma 6 protein isoform 2

See identical proteins and their annotated locations for NP_001128210.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks a coding exon, as compared to variant 1. The reading frame is not affected and the resulting isoform (2) lacks an internal segment, as compared to isoform 2.

Source sequence(s)

AW337942, BC146796, BC150184, EU883531, Z21943

Consensus CDS

CCDS46975.1

UniProtKB/TrEMBL

B5B0A5

Related

ENSP00000413122.2, ENST00000450123.6

Conserved Domains (5) summary

smart00225
Location:33 → 126

BTB; Broad-Complex, Tramtrack and Bric a brac

sd00017
Location:520 → 540

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:518 → 540

zf-C2H2; Zinc finger, C2H2 type

pfam00651
Location:22 → 126

BTB; BTB/POZ domain

pfam13465
Location:532 → 557

zf-H2C2_2; Zinc-finger double domain
NM_001706.5 → NP_001697.2 B-cell lymphoma 6 protein isoform 1

See identical proteins and their annotated locations for NP_001697.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) and variant 2 encode the same isoform (1).

Source sequence(s)

BC146796, BC150184, DB079847

Consensus CDS

CCDS3289.1

UniProtKB/Swiss-Prot

A7E241, B8PSA7, D3DNV5, P41182

UniProtKB/TrEMBL

A5PL18

Related

ENSP00000384371.2, ENST00000406870.7

Conserved Domains (4) summary

smart00225
Location:33 → 126

BTB; Broad-Complex, Tramtrack and Bric a brac

sd00017
Location:576 → 596

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00651
Location:22 → 126

BTB; BTB/POZ domain

pfam13465
Location:588 → 613

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_000003.12 Reference GRCh38.p14 Primary Assembly

Range

187721377..187745468 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011513062.4 → XP_011511364.1 B-cell lymphoma 6 protein isoform X2

See identical proteins and their annotated locations for XP_011511364.1

UniProtKB/TrEMBL

B5B0A5

Related

ENSP00000479784.1, ENST00000621333.4

Conserved Domains (5) summary

smart00225
Location:33 → 126

BTB; Broad-Complex, Tramtrack and Bric a brac

sd00017
Location:520 → 540

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:518 → 540

zf-C2H2; Zinc finger, C2H2 type

pfam00651
Location:22 → 126

BTB; BTB/POZ domain

pfam13465
Location:532 → 557

zf-H2C2_2; Zinc-finger double domain
XM_047448655.1 → XP_047304611.1 B-cell lymphoma 6 protein isoform X1

UniProtKB/Swiss-Prot

A7E241, B8PSA7, D3DNV5, P41182
XM_005247694.5 → XP_005247751.1 B-cell lymphoma 6 protein isoform X1

See identical proteins and their annotated locations for XP_005247751.1

UniProtKB/Swiss-Prot

A7E241, B8PSA7, D3DNV5, P41182

UniProtKB/TrEMBL

A5PL18

Conserved Domains (4) summary

smart00225
Location:33 → 126

BTB; Broad-Complex, Tramtrack and Bric a brac

sd00017
Location:576 → 596

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00651
Location:22 → 126

BTB; BTB/POZ domain

pfam13465
Location:588 → 613

zf-H2C2_2; Zinc-finger double domain

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

190538887..190562977 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054347430.1 → XP_054203405.1 B-cell lymphoma 6 protein isoform X2
XM_054347429.1 → XP_054203404.1 B-cell lymphoma 6 protein isoform X1
XM_054347428.1 → XP_054203403.1 B-cell lymphoma 6 protein isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_138931.1: Suppressed sequence

Description

NM_138931.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.