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Aliases for BCL11B Gene

Aliases for BCL11B Gene

  • B Cell CLL/Lymphoma 11B 2 3 5
  • Radiation-Induced Tumor Suppressor Gene 1 Protein 3 4
  • B-Cell CLL/Lymphoma 11B (Zinc Finger Protein) 2 3
  • COUP-TF-Interacting Protein 2 3 4
  • BCL-11B 3 4
  • CTIP2 3 4
  • HRit1 3 4
  • RIT1 3 4
  • B-Cell CLL/Lymphoma 11B/T-Cell Receptor Delta Constant Region Fusion Protein 3
  • Zinc Finger Protein HRit1 Alpha 3
  • B-Cell Lymphoma/Leukaemia 11B 3
  • B-Cell Lymphoma/Leukemia 11B 3
  • B-Cell CLL/Lymphoma 11B 4
  • BCL11B/TRDC Fusion 3
  • HRIT1-Alpha 3
  • ATL1-Alpha 3
  • ATL1-Delta 3
  • ATL1-Gamma 3
  • ATL1-Beta 3
  • ZNF856B 3
  • CTIP-2 3
  • IMD49 3
  • ATL1 3

External Ids for BCL11B Gene

Previous HGNC Symbols for BCL11B Gene

  • ZNF856B

Previous GeneCards Identifiers for BCL11B Gene

  • GC14M097147
  • GC14M093451
  • GC14M097625
  • GC14M098705
  • GC14M099635
  • GC14M079819

Summaries for BCL11B Gene

Entrez Gene Summary for BCL11B Gene

  • This gene encodes a C2H2-type zinc finger protein and is closely related to BCL11A, a gene whose translocation may be associated with B-cell malignancies. Although the specific function of this gene has not been determined, the encoded protein is known to be a transcriptional repressor, and is regulated by the NURD nucleosome remodeling and histone deacetylase complex. Four alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Aug 2013]

GeneCards Summary for BCL11B Gene

BCL11B (B Cell CLL/Lymphoma 11B) is a Protein Coding gene. Diseases associated with BCL11B include Immunodeficiency 49 and Combined Immunodeficiency, X-Linked. Among its related pathways are NF-kappaB Signaling and Transcriptional misregulation in cancer. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is BCL11A.

UniProtKB/Swiss-Prot for BCL11B Gene

  • Key regulator of both differentiation and survival of T-lymphocytes during thymocyte development in mammals. Essential in controlling the responsiveness of hematopoietic stem cells to chemotactic signals by modulating the expression of the receptors CCR7 and CCR9, which direct the movement of progenitor cells from the bone marrow to the thymus (PubMed:27959755). Is a regulator of IL2 promoter and enhances IL2 expression in activated CD4(+) T-lymphocytes (PubMed:16809611). Tumor-suppressor that represses transcription through direct, TFCOUP2-independent binding to a GC-rich response element (By similarity). May also function in the P53-signaling pathway (By similarity).

Gene Wiki entry for BCL11B Gene

Additional gene information for BCL11B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BCL11B Gene

Genomics for BCL11B Gene

GeneHancer (GH) Regulatory Elements for BCL11B Gene

Promoters and enhancers for BCL11B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14J099255 Promoter/Enhancer 3.2 UCNEbase EPDnew FANTOM5 Ensembl ENCODE dbSUPER 676 +6.4 6393 19.8 PKNOX1 CLOCK NEUROD1 SIN3A FEZF1 ZNF2 ZBTB7B YY1 ZNF213 ZNF207 BCL11B RPL3P4 CCNK ENSG00000234648 YY1 ENSG00000235785
GH14J099239 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 33.5 +26.8 26769 11.5 KLF17 MZF1 SIN3A FEZF1 ZNF2 ZNF121 ZNF366 ZSCAN5C FOS OVOL3 BCL11B DEGS2 GC14M099236 GC14M099237 ENSG00000235785
GH14J099251 Enhancer 1.7 UCNEbase FANTOM5 ENCODE dbSUPER 18 +18.3 18328 3.4 PKNOX1 KLF17 MZF1 FEZF1 ZNF335 ZNF213 KLF7 EGR2 ZBTB11 OVOL3 BCL11B DEGS2 ENSG00000235785 GC14M099236 GC14M099237
GH14J099225 Enhancer 1.9 UCNEbase FANTOM5 Ensembl ENCODE dbSUPER 12.6 +40.4 40432 11.4 HDGF PKNOX1 INSM2 YBX1 FEZF1 BATF ZNF2 GLIS2 ZNF366 ZSCAN5C CCNK BCL11B ENSG00000234648 RPL3P4 SETD3 GC14M099236 GC14M099237 GC14P099215
GH14J099190 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 11 +79.8 79821 2.5 CTCF KLF1 RAD21 POLR2A ZNF366 ZBTB48 ZFP91 PRDM10 ZNF600 ZNF362 GC14M099192 GC14M099194 BCL11B C14orf177 GC14P099185
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around BCL11B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BCL11B gene promoter:

Genomic Locations for BCL11B Gene

Genomic Locations for BCL11B Gene
chr14:99,169,287-99,271,713
(GRCh38/hg38)
Size:
102,427 bases
Orientation:
Minus strand
chr14:99,635,624-99,737,861
(GRCh37/hg19)

Genomic View for BCL11B Gene

Genes around BCL11B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BCL11B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BCL11B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BCL11B Gene

Proteins for BCL11B Gene

  • Protein details for BCL11B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9C0K0-BC11B_HUMAN
    Recommended name:
    B-cell lymphoma/leukemia 11B
    Protein Accession:
    Q9C0K0
    Secondary Accessions:
    • Q9H162

    Protein attributes for BCL11B Gene

    Size:
    894 amino acids
    Molecular mass:
    95519 Da
    Quaternary structure:
    • Interacts with TFCOUP1, SIRT1, ARP1 and EAR2 (By similarity). Interacts with EP300; the interaction is detected in activated T-lymphocytes, but not under resting conditions (PubMed:27959755).

    Alternative splice isoforms for BCL11B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for BCL11B Gene

Post-translational modifications for BCL11B Gene

  • Sumoylated with SUMO1.
  • Ubiquitination at Lys875, Lys851, posLast=790790, Lys686, Lys617, Lys597, Lys591, and posLast=585585
  • Modification sites at PhosphoSitePlus

Other Protein References for BCL11B Gene

No data available for DME Specific Peptides for BCL11B Gene

Domains & Families for BCL11B Gene

Gene Families for BCL11B Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for BCL11B Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for BCL11B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with BCL11B: view

No data available for UniProtKB/Swiss-Prot for BCL11B Gene

Function for BCL11B Gene

Molecular function for BCL11B Gene

UniProtKB/Swiss-Prot Function:
Key regulator of both differentiation and survival of T-lymphocytes during thymocyte development in mammals. Essential in controlling the responsiveness of hematopoietic stem cells to chemotactic signals by modulating the expression of the receptors CCR7 and CCR9, which direct the movement of progenitor cells from the bone marrow to the thymus (PubMed:27959755). Is a regulator of IL2 promoter and enhances IL2 expression in activated CD4(+) T-lymphocytes (PubMed:16809611). Tumor-suppressor that represses transcription through direct, TFCOUP2-independent binding to a GC-rich response element (By similarity). May also function in the P53-signaling pathway (By similarity).

Phenotypes From GWAS Catalog for BCL11B Gene

Gene Ontology (GO) - Molecular Function for BCL11B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IBA --
GO:0003676 nucleic acid binding IEA --
GO:0003700 DNA binding transcription factor activity IBA --
genes like me logo Genes that share ontologies with BCL11B: view
genes like me logo Genes that share phenotypes with BCL11B: view

Human Phenotype Ontology for BCL11B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for BCL11B Gene

MGI Knock Outs for BCL11B:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for BCL11B Gene

Localization for BCL11B Gene

Subcellular locations from UniProtKB/Swiss-Prot for BCL11B Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for BCL11B gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for BCL11B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IBA --
GO:0043005 neuron projection IEA --
genes like me logo Genes that share ontologies with BCL11B: view

Pathways & Interactions for BCL11B Gene

genes like me logo Genes that share pathways with BCL11B: view

Pathways by source for BCL11B Gene

1 BioSystems pathway for BCL11B Gene
1 KEGG pathway for BCL11B Gene
1 Cell Signaling Technology pathway for BCL11B Gene

SIGNOR curated interactions for BCL11B Gene

Is activated by:

Gene Ontology (GO) - Biological Process for BCL11B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003334 keratinocyte development IEA --
GO:0003382 epithelial cell morphogenesis IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IBA,IEA --
GO:0006366 transcription by RNA polymerase II IEA --
genes like me logo Genes that share ontologies with BCL11B: view

Drugs & Compounds for BCL11B Gene

No Compound Related Data Available

Transcripts for BCL11B Gene

mRNA/cDNA for BCL11B Gene

Unigene Clusters for BCL11B Gene

B-cell CLL/lymphoma 11B (zinc finger protein):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for BCL11B Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4
SP1:
SP2: -

Relevant External Links for BCL11B Gene

GeneLoc Exon Structure for
BCL11B
ECgene alternative splicing isoforms for
BCL11B

Expression for BCL11B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BCL11B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for BCL11B Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x6.6), Brain - Putamen (basal ganglia) (x5.8), Skin - Sun Exposed (Lower leg) (x5.6), Skin - Not Sun Exposed (Suprapubic) (x5.5), and Brain - Caudate (basal ganglia) (x5.3).

Protein differential expression in normal tissues from HIPED for BCL11B Gene

This gene is overexpressed in CD8 Tcells (19.7), Adipocyte (17.7), CD4 Tcells (8.9), Pancreatic juice (7.9), and Peripheral blood mononuclear cells (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for BCL11B Gene



Protein tissue co-expression partners for BCL11B Gene

NURSA nuclear receptor signaling pathways regulating expression of BCL11B Gene:

BCL11B

SOURCE GeneReport for Unigene cluster for BCL11B Gene:

Hs.709690

mRNA Expression by UniProt/SwissProt for BCL11B Gene:

Q9C0K0-BC11B_HUMAN
Tissue specificity: Highly expressed in brain and in malignant T-cell lines derived from patients with adult T-cell leukemia/lymphoma.

Evidence on tissue expression from TISSUES for BCL11B Gene

  • Liver(4)
  • Nervous system(2.2)
  • Blood(2.1)
genes like me logo Genes that share expression patterns with BCL11B: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for BCL11B Gene

Orthologs for BCL11B Gene

This gene was present in the common ancestor of animals.

Orthologs for BCL11B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia BCL11B 34 33
  • 99.74 (n)
OneToOne
dog
(Canis familiaris)
Mammalia BCL11B 34 33
  • 96.31 (n)
OneToOne
cow
(Bos Taurus)
Mammalia BCL11B 34 33
  • 94.33 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Bcl11b 16 34 33
  • 89.08 (n)
rat
(Rattus norvegicus)
Mammalia Bcl11b 33
  • 88.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia BCL11B 34
  • 82 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia BCL11B 34
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves -- 34
  • 85 (a)
OneToMany
-- 34
  • 82 (a)
OneToMany
BCL11B 33
  • 76.66 (n)
lizard
(Anolis carolinensis)
Reptilia BCL11B 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia bcl11b 33
  • 70.58 (n)
Str.12510 33
zebrafish
(Danio rerio)
Actinopterygii bcl11ba 34
  • 76 (a)
OneToMany
LOC100330974 33
  • 70.2 (n)
BCL11B (2 of 2) 34
  • 60 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG9650 34 35
  • 17 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea F13H6.1 34 35
  • 16 (a)
OneToMany
Species where no ortholog for BCL11B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 BCL11B Gene

ENSEMBL:
Gene Tree for BCL11B (if available)
TreeFam:
Gene Tree for BCL11B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for BCL11B: view image

Paralogs for BCL11B Gene

Paralogs for BCL11B Gene

genes like me logo Genes that share paralogs with BCL11B: view

Variants for BCL11B Gene

Sequence variations from dbSNP and Humsavar for BCL11B Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs750610248 pathogenic, Combined immunodeficiency, Immunodeficiency 49, Immunodeficiency 49 (IMD49) [MIM:617237] 99,175,513(-) A/C/G coding_sequence_variant, missense_variant, synonymous_variant
VAR_035554 A colorectal cancer sample p.Ser331Pro
rs1057524045 uncertain-significance, not specified 99,257,609(-) T/G coding_sequence_variant, missense_variant
rs760277241 benign, not specified 99,174,930(-) CGTCGCC/CGTCGCCGTCGCC coding_sequence_variant, inframe_insertion
rs1000005471 -- 99,250,592(-) A/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for BCL11B Gene

Variant ID Type Subtype PubMed ID
dgv385n67 CNV gain 20364138
dgv386n67 CNV gain 20364138
dgv3879n54 CNV loss 21841781
dgv387n67 CNV gain 20364138
dgv3880n54 CNV gain+loss 21841781
dgv3881n54 CNV gain 21841781
dgv3882n54 CNV loss 21841781
dgv3883n54 CNV loss 21841781
dgv3884n54 CNV loss 21841781
esv23236 CNV loss 19812545
esv2658925 CNV deletion 23128226
esv2671501 CNV deletion 23128226
esv275067 CNV gain+loss 21479260
esv3552038 CNV deletion 23714750
esv3581404 CNV loss 25503493
esv3635480 CNV gain 21293372
nsv1071166 CNV deletion 25765185
nsv470666 CNV gain 18288195
nsv476798 CNV novel sequence insertion 20440878
nsv528741 CNV loss 19592680
nsv565706 CNV loss 21841781
nsv565707 CNV loss 21841781
nsv565708 CNV loss 21841781
nsv565709 CNV gain+loss 21841781
nsv565714 CNV loss 21841781
nsv827039 CNV gain 20364138
nsv827040 CNV gain 20364138
nsv827049 CNV gain 20364138
nsv832871 CNV gain 17160897
nsv832872 CNV loss 17160897

Variation tolerance for BCL11B Gene

Residual Variation Intolerance Score: 10.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.93; 19.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BCL11B Gene

Human Gene Mutation Database (HGMD)
BCL11B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
BCL11B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for BCL11B Gene

Disorders for BCL11B Gene

MalaCards: The human disease database

(7) MalaCards diseases for BCL11B Gene - From: HGMD, OMIM, ClinVar, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
immunodeficiency 49
  • imd49
combined immunodeficiency, x-linked
  • cidx
lymphoma
  • lymphoid cancer
adult t-cell leukemia
  • adult t-cell leukemia/lymphoma
spastic quadriplegia
  • quadriplegic infantile cerebral palsy
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

BC11B_HUMAN
  • Immunodeficiency 49 (IMD49) [MIM:617237]: A form of severe combined immunodeficiency characterized by severe T-cell lymphopenia, no detectable T-cell receptor excision circles, no naive helper CD4+ T-cells, and impaired T-cell proliferative response. In addition to primary immunodeficiency, affected individuals manifest multiple abnormal systemic features, including severe delayed psychomotor development, intellectual disability, spastic quadriplegia, and craniofacial abnormalities. {ECO:0000269 PubMed:27959755}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for BCL11B

genes like me logo Genes that share disorders with BCL11B: view

No data available for Genatlas for BCL11B Gene

Publications for BCL11B Gene

  1. Homozygous deletions and point mutations of the Rit1/Bcl11b gene in gamma-ray induced mouse thymic lymphomas. (PMID: 12565905) Wakabayashi Y … Kominami R (Biochemical and biophysical research communications 2003) 3 4 22 58
  2. The BCL11 gene family: involvement of BCL11A in lymphoid malignancies. (PMID: 11719382) Satterwhite E … Dyer MJ (Blood 2001) 2 3 4 58
  3. Multisystem Anomalies in Severe Combined Immunodeficiency with Mutant BCL11B. (PMID: 27959755) Punwani D … Puck JM (The New England journal of medicine 2016) 3 4 58
  4. Expression of COUP-TF-interacting protein 2 (CTIP2) in human atopic dermatitis and allergic contact dermatitis skin. (PMID: 19366371) Ganguli-Indra G … Indra AK (Experimental dermatology 2009) 3 22 58
  5. Functional roles for the striatal-enriched transcription factor, Bcl11b, in the control of striatal gene expression and transcriptional dysregulation in Huntington's disease. (PMID: 18595722) Desplats PA … Thomas EA (Neurobiology of disease 2008) 3 22 58

Products for BCL11B Gene

Sources for BCL11B Gene

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