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    BCL11B BCL11 transcription factor B [ Homo sapiens (human) ]

    Gene ID: 64919, updated on 3-Dec-2024

    Summary

    Official Symbol
    BCL11Bprovided by HGNC
    Official Full Name
    BCL11 transcription factor Bprovided by HGNC
    Primary source
    HGNC:HGNC:13222
    See related
    Ensembl:ENSG00000127152 MIM:606558; AllianceGenome:HGNC:13222
    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; IDDFSTA; SMARCM2; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See BCL11B in Genome Data Viewer
    Location:
    14q32.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (99169287..99272197, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (93400844..93503767, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (99635624..99738534, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs622 Neighboring gene uncharacterized LOC107984696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99496427-99496927 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:99504757-99505257 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99559873-99560872 Neighboring gene uncharacterized LOC105370659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99600505-99601228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99608696-99609604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99640571-99641086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99658267-99658828 Neighboring gene uncharacterized LOC124903412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99677677-99678177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99695676-99696574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99703507-99704031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99713148-99714044 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:99723824-99724098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99734631-99735236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99735237-99735841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6061 Neighboring gene uncharacterized LOC105370660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99750257-99750979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99784572-99785298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99786594-99787222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99787223-99787850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99788913-99789673 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99798343-99799050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99799051-99799757 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99814550-99815224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99815225-99815898 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:99827260-99827481 Neighboring gene Sharpr-MPRA regulatory region 7827 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99849405-99850263 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99860795-99861575 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99874757-99875323 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:99878378-99879044 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99879711-99880376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99890523-99891386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99891387-99892249 Neighboring gene SET domain containing 3, actin N3(tau)-histidine methyltransferase 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Immunodeficiency 49
    MedGen: C4310656 OMIM: 617237 GeneReviews: Not available
    Compare labs
    Intellectual developmental disorder with speech delay, dysmorphic facies, and t-cell abnormalities
    MedGen: C4748152 OMIM: 618092 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS 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.
    EBI GWAS Catalog
    Genetic variants near PDGFRA are associated with corneal curvature in Australians.
    EBI GWAS Catalog
    Genome wide association study of SNP-, gene-, and pathway-based approaches to identify genes influencing susceptibility to Staphylococcus aureus infections.
    EBI GWAS 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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA-binding transcription factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    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 double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in T cell differentiation in thymus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in T cell receptor V(D)J recombination IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in alpha-beta T cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in commitment of neuronal cell to specific neuron type in forebrain IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in epithelial cell morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in hematopoietic stem cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in keratinocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lymphoid lineage cell migration into thymus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of thymocyte apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in odontogenesis of dentin-containing tooth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in olfactory bulb axon guidance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive T cell selection IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in post-embryonic camera-type eye development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of keratinocyte proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in striatal medium spiny neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in thymocyte apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in thymus development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of SWI/SNF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in neuron projection IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    B-cell lymphoma/leukemia 11B
    Names
    B cell CLL/lymphoma 11B
    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
    BAF chromatin remodeling complex subunit BCL11B
    BCL-11B
    BCL11B, BAF complex component
    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)

    NEW Try the new Transcript table

    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
      4289..107199
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001282237.2NP_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/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_001282238.2NP_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/TrEMBL
      D3YTK1, L8B862
      Conserved Domains (4) summary
      sd00017
      Location:726746
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:357377
      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_022898.3NP_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, AL109767
      Consensus CDS
      CCDS9949.1
      UniProtKB/TrEMBL
      D3YTK1, L8B567
      Related
      ENSP00000280435.6, ENST00000345514.2
      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_138576.4NP_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, AL109767
      Consensus CDS
      CCDS9950.1
      UniProtKB/Swiss-Prot
      Q9C0K0, Q9H162
      UniProtKB/TrEMBL
      L8B7P7
      Related
      ENSP00000349723.3, ENST00000357195.8
      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: 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

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      99169287..99272197 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431708.1XP_047287664.1  B-cell lymphoma/leukemia 11B isoform X2

      UniProtKB/TrEMBL
      D3YTK1
    2. XM_047431707.1XP_047287663.1  B-cell lymphoma/leukemia 11B isoform X1

      UniProtKB/TrEMBL
      D3YTK1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      93400844..93503767 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376624.1XP_054232599.1  B-cell lymphoma/leukemia 11B isoform X2

      UniProtKB/TrEMBL
      D3YTK1
    2. XM_054376623.1XP_054232598.1  B-cell lymphoma/leukemia 11B isoform X1

      UniProtKB/TrEMBL
      D3YTK1