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BCL11B B cell CLL/lymphoma 11B [ Homo sapiens (human) ]

Gene ID: 64919, updated on 12-Aug-2018

Summary

Official Symbol
BCL11Bprovided by HGNC
Official Full Name
B cell CLL/lymphoma 11Bprovided by HGNC
Primary source
HGNC:HGNC:13222
See related
Ensembl:ENSG00000127152 MIM:606558; Vega:OTTHUMG00000028967
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
ATL1; RIT1; CTIP2; IMD49; CTIP-2; ZNF856B; ATL1-beta; ATL1-alpha; ATL1-delta; ATL1-gamma; hRIT1-alpha
Summary
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]
Expression
Biased expression in skin (RPKM 7.8), lymph node (RPKM 5.6) and 13 other tissues See more
Orthologs

Genomic context

See BCL11B in Genome Data Viewer
Location:
14q32.2
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (99169287..99271713, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (99635624..99738514, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984696 Neighboring gene VISTA enhancer hs622 Neighboring gene uncharacterized LOC105370659 Neighboring gene uncharacterized LOC105370660 Neighboring gene SET domain containing 3 Neighboring gene RNA, U6 small nuclear 91, 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Immunodeficiency 49
MedGen: C4310656 OMIM: 617237 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
NHGRI GWA Catalog
Common genetic variation in the 3'-BCL11B gene desert is associated with carotid-femoral pulse wave velocity and excess cardiovascular disease risk: the AortaGen Consortium.
NHGRI GWA Catalog
Genetic variants near PDGFRA are associated with corneal curvature in Australians.
NHGRI GWA Catalog
Genome wide association study of SNP-, gene-, and pathway-based approaches to identify genes influencing susceptibility to Staphylococcus aureus infections.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat LSD1 interacts with CTIP2 and co-localizes with HIV-1 Tat. LSD1 is required for CTIP2 recruitment at the HIV-1 proximal promoter to repress HIV-1 replication and transcription PubMed
tat BCL11B and metastasis associated 1 protein (MTA1) inhibits HIV-1 Tat-mediated LTR transactivation by association with the integrated HIV-LTR PubMed
tat CTIP2 forms a complex with HIV-1 Tat and HP1alpha resulting in relocalization of Tat and inactivation of Tat-mediated transactivation of the HIV-1 LTR promoter PubMed
tat CTIP2 harbors two HIV-1 Tat interaction interfaces (amino acids 145-434 and 717-813) and binds to the N-terminus (amino acids 1-48) of Tat PubMed
Vpr vpr COUP-TF-interacting protein 2 (CTIP2) abolishes Vpr-mediated stimulation of p21 by cooperating with SUV39H1 and HDAC1/HDAC2 to silence the p21 gene transcription PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

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 
RNA polymerase II proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
T cell differentiation in thymus IEA
Inferred from Electronic Annotation
more info
 
T cell receptor V(D)J recombination IEA
Inferred from Electronic Annotation
more info
 
alpha-beta T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
commitment of neuronal cell to specific neuron type in forebrain IEA
Inferred from Electronic Annotation
more info
 
epithelial cell morphogenesis IEA
Inferred from Electronic Annotation
more info
 
hematopoietic stem cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
keratinocyte development IEA
Inferred from Electronic Annotation
more info
 
lymphoid lineage cell migration into thymus IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
odontogenesis of dentin-containing tooth IEA
Inferred from Electronic Annotation
more info
 
olfactory bulb axon guidance IEA
Inferred from Electronic Annotation
more info
 
positive T cell selection IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
post-embryonic camera-type eye development IEA
Inferred from Electronic Annotation
more info
 
regulation of keratinocyte proliferation IEA
Inferred from Electronic Annotation
more info
 
regulation of lipid metabolic process IEA
Inferred from Electronic Annotation
more info
 
regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
striatal medium spiny neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
thymus development IEA
Inferred from Electronic Annotation
more info
 
transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
neuron projection IEA
Inferred from Electronic Annotation
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
B-cell lymphoma/leukemia 11B
Names
B-cell CLL/lymphoma 11B (zinc finger protein)
B-cell CLL/lymphoma 11B/T-cell receptor delta constant region fusion protein
B-cell lymphoma/leukaemia 11B
BCL-11B
BCL11B/TRDC fusion
COUP-TF-interacting protein 2
hRit1
radiation-induced tumor suppressor gene 1 protein
zinc finger protein hRit1 alpha

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_027894.1 RefSeqGene

    Range
    4773..107199
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001282237.1NP_001269166.1  B-cell lymphoma/leukemia 11B isoform 3

    See identical proteins and their annotated locations for NP_001269166.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.
    Source sequence(s)
    AB057668, AJ404614, AL109767
    UniProtKB/Swiss-Prot
    Q9C0K0
    UniProtKB/TrEMBL
    L8B8F6
    Conserved Domains (4) summary
    sd00017
    Location:797817
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:428448
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:796817
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:809834
    zf-H2C2_2; Zinc-finger double domain
  2. NM_001282238.1NP_001269167.1  B-cell lymphoma/leukemia 11B isoform 4

    See identical proteins and their annotated locations for NP_001269167.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice junction at the 5' end of an exon and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AB057670, AJ404614, AL109767
    UniProtKB/Swiss-Prot
    Q9C0K0
    UniProtKB/TrEMBL
    L8B862
    Conserved Domains (3) summary
    sd00017
    Location:726746
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:725746
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:738763
    zf-H2C2_2; Zinc-finger double domain
  3. NM_022898.2NP_075049.1  B-cell lymphoma/leukemia 11B isoform 2

    See identical proteins and their annotated locations for NP_075049.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AB057669, AJ404614
    Consensus CDS
    CCDS9949.1
    UniProtKB/Swiss-Prot
    Q9C0K0
    UniProtKB/TrEMBL
    L8B567
    Related
    ENSP00000280435.6, OTTHUMP00000067187, ENST00000345514.2, OTTHUMT00000072333
    Conserved Domains (4) summary
    sd00017
    Location:727747
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:358378
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:726747
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:739764
    zf-H2C2_2; Zinc-finger double domain
  4. NM_138576.3NP_612808.1  B-cell lymphoma/leukemia 11B isoform 1

    See identical proteins and their annotated locations for NP_612808.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AB041218, AB043584, AJ404614
    Consensus CDS
    CCDS9950.1
    UniProtKB/Swiss-Prot
    Q9C0K0
    UniProtKB/TrEMBL
    L8B7P7
    Related
    ENSP00000349723.3, OTTHUMP00000067186, ENST00000357195.7, OTTHUMT00000072332
    Conserved Domains (4) summary
    sd00017
    Location:798818
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:429449
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:797818
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:810835
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    99169287..99271713 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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