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BCL11A B-cell CLL/lymphoma 11A [ Homo sapiens (human) ]

Gene ID: 53335, updated on 17-Sep-2017
Official Symbol
BCL11Aprovided by HGNC
Official Full Name
B-cell CLL/lymphoma 11Aprovided by HGNC
Primary source
HGNC:HGNC:13221
See related
Ensembl:ENSG00000119866 MIM:606557; Vega:OTTHUMG00000129420
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
EVI9; CTIP1; DILOS; ZNF856; HBFQTL5; BCL11A-L; BCL11A-S; BCL11a-M; BCL11A-XL
Summary
This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. The corresponding mouse gene is a common site of retroviral integration in myeloid leukemia, and may function as a leukemia disease gene, in part, through its interaction with BCL6. During hematopoietic cell differentiation, this gene is down-regulated. It is possibly involved in lymphoma pathogenesis since translocations associated with B-cell malignancies also deregulates its expression. Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Orthologs
Location:
2p16.1
Exon count:
8
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 2 NC_000002.12 (60451167..60553498, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (60678302..60780633, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene MIR4432 host gene Neighboring gene uncharacterized LOC102724142 Neighboring gene microRNA 4432 Neighboring gene uncharacterized LOC107985887 Neighboring gene RNA, 7SL, cytoplasmic 361, pseudogene Neighboring gene interferon induced transmembrane protein 3 pseudogene

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Intellectual developmental disorder with persistence of fetal hemoglobin
MedGen: C4310833 OMIM: 617101 GeneReviews: Not available
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2017-04-13)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2017-04-13)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association identified the common genetic variants influence disease severity in beta0-thalassemia/hemoglobin E.
NHGRI GWA Catalog
A QTL influencing F cell production maps to a gene encoding a zinc-finger protein on chromosome 2p15.
NHGRI GWA Catalog
Fetal hemoglobin in sickle cell anemia: genome-wide association studies suggest a regulatory region in the 5' olfactory receptor gene cluster.
NHGRI GWA Catalog
Genetic and clinical correlates of early-outgrowth colony-forming units.
NHGRI GWA Catalog
Genetic determinants of haemolysis in sickle cell anaemia.
NHGRI GWA Catalog
Genome wide association study of fetal hemoglobin in sickle cell anemia in Tanzania.
NHGRI GWA Catalog
Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients.
NHGRI GWA Catalog
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
NHGRI GWA Catalog
Genome-wide association study in German patients with attention deficit/hyperactivity disorder.
NHGRI GWA Catalog
Genome-wide association study of HLA-DQB1*06:02 negative essential hypersomnia.
NHGRI GWA Catalog
Genome-wide association study shows BCL11A associated with persistent fetal hemoglobin and amelioration of the phenotype of beta-thalassemia.
NHGRI GWA Catalog
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
NHGRI GWA Catalog
Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.
NHGRI GWA Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
NHGRI GWA Catalog
Seventy-five genetic loci influencing the human red blood cell.
NHGRI GWA Catalog
The Genetics of Hemoglobin A2 Regulation in Sickle Cell Anemia.
NHGRI GWA Catalog
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
NHGRI GWA Catalog

Replication interactions

Interaction Pubs
Knockdown of B-cell CLL/lymphoma 11A (zinc finger protein, BCL11A) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ10173, FLJ34997, KIAA1809

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cellular response to L-glutamate IEA
Inferred from Electronic Annotation
more info
 
negative regulation of branching morphogenesis of a nerve IEA
Inferred from Electronic Annotation
more info
 
negative regulation of dendrite development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of dendrite extension IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron remodeling IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
neurogenesis IBA
Inferred from Biological aspect of Ancestor
more info
 
positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
protein sumoylation ISS
Inferred from Sequence or Structural Similarity
more info
 
signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
postsynaptic density IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
B-cell lymphoma/leukemia 11A
Names
B-cell CLL/lymphoma 11A (zinc finger protein) isoform 2
BCL-11A
BCL11A B-cell CLL/lymphoma 11A (zinc finger protein) isoform 1
C2H2-type zinc finger protein
COUP-TF-interacting protein 1
EVI-9
ecotropic viral integration site 9 homolog
ecotropic viral integration site 9 protein homolog
zinc finger protein 856

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_011968.1 RefSeqGene

    Range
    5001..107332
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_018014.3NP_060484.2  B-cell lymphoma/leukemia 11A isoform 2

    See identical proteins and their annotated locations for NP_060484.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is also known as B-cell lymphoma/leukaemia 11A long form (BCL11A-L). It has a different 3' end coding and UTR region when compared to variant 1, and thus encodes an isoform (2) that contains a different and shorter C-terminus, as compared to isoform 1.
    Source sequence(s)
    AF080216, AJ404611, AJ404612, BC021098
    Consensus CDS
    CCDS1861.1
    UniProtKB/Swiss-Prot
    Q9H165
    UniProtKB/TrEMBL
    D9YZV9
    Related
    ENSP00000349300.4, OTTHUMP00000159788, ENST00000356842.8, OTTHUMT00000251578
    Conserved Domains (3) summary
    sd00017
    Location:379399
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:378399
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:391416
    zf-H2C2_2; Zinc-finger double domain
  2. NM_022893.3NP_075044.2  B-cell lymphoma/leukemia 11A isoform 1

    See identical proteins and their annotated locations for NP_075044.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is also known as B-cell lymphoma/leukaemia 11A extra long form (BCL11A-XL). It encodes the longest isoform (1).
    Source sequence(s)
    AB058712, AF080216, AJ404611, AK001035, BG393787
    Consensus CDS
    CCDS1862.1
    UniProtKB/Swiss-Prot
    Q9H165
    UniProtKB/TrEMBL
    D6W5D9
    Related
    ENSP00000338774.6, OTTHUMP00000159789, ENST00000335712.10, OTTHUMT00000251579
    Conserved Domains (3) summary
    sd00017
    Location:744764
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:743764
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:391416
    zf-H2C2_2; Zinc-finger double domain
  3. NM_138559.1NP_612569.1  B-cell lymphoma/leukemia 11A isoform 3

    See identical proteins and their annotated locations for NP_612569.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) is also known as B-cell lymphoma/leukaemia 11A short form (BCL11A-S). It lacks a large portion of the 3' coding region which introduces a frameshift, and it contains a different 3' UTR region when compared to variant 1. The encoded isoform (3) has a truncated and distinct C-terminus, as compared to isoform 1.
    Source sequence(s)
    AJ404613
    Consensus CDS
    CCDS46295.1
    UniProtKB/Swiss-Prot
    Q9H165
    Related
    ENSP00000352648.5, OTTHUMP00000201250, ENST00000359629.9, OTTHUMT00000325349

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p7 Primary Assembly

    Range
    60451167..60553498 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532912.1XP_011531214.1  B-cell lymphoma/leukemia 11A isoform X6

    See identical proteins and their annotated locations for XP_011531214.1

    Conserved Domains (4) summary
    sd00017
    Location:345365
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:710730
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:709730
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:722747
    zf-H2C2_2; Zinc-finger double domain
  2. XM_011532910.1XP_011531212.1  B-cell lymphoma/leukemia 11A isoform X3

    See identical proteins and their annotated locations for XP_011531212.1

    Conserved Domains (4) summary
    sd00017
    Location:379399
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:744764
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:743764
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:756781
    zf-H2C2_2; Zinc-finger double domain
  3. XM_011532909.1XP_011531211.1  B-cell lymphoma/leukemia 11A isoform X1

    See identical proteins and their annotated locations for XP_011531211.1

    UniProtKB/Swiss-Prot
    Q9H165
    UniProtKB/TrEMBL
    D6W5D9
    Conserved Domains (3) summary
    sd00017
    Location:744764
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:743764
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:391416
    zf-H2C2_2; Zinc-finger double domain
  4. XM_017004334.1XP_016859823.1  B-cell lymphoma/leukemia 11A isoform X4

    UniProtKB/Swiss-Prot
    Q9H165
    Related
    ENSP00000351307.4, OTTHUMP00000202084, ENST00000358510.5, OTTHUMT00000327043
    Conserved Domains (3) summary
    sd00017
    Location:710730
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:709730
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:722747
    zf-H2C2_2; Zinc-finger double domain
  5. XM_017004335.1XP_016859824.1  B-cell lymphoma/leukemia 11A isoform X5

    Conserved Domains (3) summary
    sd00017
    Location:708728
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:707728
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:720745
    zf-H2C2_2; Zinc-finger double domain
  6. XM_017004333.1XP_016859822.1  B-cell lymphoma/leukemia 11A isoform X2

    Conserved Domains (3) summary
    sd00017
    Location:742762
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:741762
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:754779
    zf-H2C2_2; Zinc-finger double domain
  7. XM_017004336.1XP_016859825.1  B-cell lymphoma/leukemia 11A isoform X7

    Conserved Domains (3) summary
    sd00017
    Location:633653
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:632653
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:645670
    zf-H2C2_2; Zinc-finger double domain
  8. XM_017004338.1XP_016859827.1  B-cell lymphoma/leukemia 11A isoform X8

    Conserved Domains (3) summary
    sd00017
    Location:592612
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:591612
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:604629
    zf-H2C2_2; Zinc-finger double domain
  9. XM_017004337.1XP_016859826.1  B-cell lymphoma/leukemia 11A isoform X8

    Conserved Domains (3) summary
    sd00017
    Location:592612
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:591612
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:604629
    zf-H2C2_2; Zinc-finger double domain

Alternate CHM1_1.1

Genomic

  1. NC_018913.2 Alternate CHM1_1.1

    Range
    60608322..60710989 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_138553.1: Suppressed sequence

    Description
    NM_138553.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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