U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

BCL11A BAF chromatin remodeling complex subunit BCL11A [ Homo sapiens (human) ]

Gene ID: 53335, updated on 13-Aug-2022

Summary

Official Symbol
BCL11Aprovided by HGNC
Official Full Name
BAF chromatin remodeling complex subunit BCL11Aprovided by HGNC
Primary source
HGNC:HGNC:13221
See related
Ensembl:ENSG00000119866 MIM:606557; AllianceGenome:HGNC:13221
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; SMARCM1
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]
Annotation information
Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
Expression
Broad expression in skin (RPKM 2.8), lymph node (RPKM 2.2) and 17 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See BCL11A in Genome Data Viewer
Location:
2p16.1
Exon count:
10
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (60450520..60553654, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (60456325..60559492, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (60677655..60780789, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724142 Neighboring gene uncharacterized LOC124906010 Neighboring gene VISTA enhancer hs957 Neighboring gene VISTA enhancer hs1142 Neighboring gene RNA, 7SL, cytoplasmic 361, 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
Dias-Logan syndrome Compare labs

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

EBI GWAS Catalog

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

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10173, FLJ34997, KIAA1809

Gene Ontology Provided by GOA

Component Evidence Code Pubs
part_of SWI/SNF complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in nuclear matrix IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in postsynaptic density IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
B-cell lymphoma/leukemia 11A
Names
B cell CLL/lymphoma 11A
B-cell CLL/lymphoma 11A (zinc finger protein)
BCL11A B-cell CLL/lymphoma 11A (zinc finger protein)
BCL11A, BAF complex component
C2H2-type zinc finger protein
COUP-TF-interacting protein 1
ecotropic viral integration site 9 homolog
ecotropic viral integration site 9 protein homolog
zinc finger protein 856

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_011968.1 RefSeqGene

    Range
    4845..107979
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001363864.1NP_001350793.1  B-cell lymphoma/leukemia 11A isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple differences in the coding region and 3' UTR, compared to variant 1. It encodes an isoform (4) with a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC007381, AC009970
    Consensus CDS
    CCDS86845.1
    UniProtKB/TrEMBL
    A0A2U3TZJ5
    Related
    ENSP00000351307.5, ENST00000358510.6
    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:357382
    zf-H2C2_2; Zinc-finger double domain
  2. NM_001365609.1NP_001352538.1  B-cell lymphoma/leukemia 11A isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC007381, AF080216, AJ404611, AY228763
    Related
    ENSP00000338774.7, ENST00000335712.11
    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:357382
    zf-H2C2_2; Zinc-finger double domain
  3. NM_001405708.1NP_001392637.1  B-cell lymphoma/leukemia 11A isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
    UniProtKB/Swiss-Prot
    Q9NWA7
    UniProtKB/TrEMBL
    D6W5D9
  4. NM_001405709.1NP_001392638.1  B-cell lymphoma/leukemia 11A isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
    UniProtKB/Swiss-Prot
    Q9NWA7
    UniProtKB/TrEMBL
    D6W5D9
  5. NM_001405710.1NP_001392639.1  B-cell lymphoma/leukemia 11A isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  6. NM_001405711.1NP_001392640.1  B-cell lymphoma/leukemia 11A isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  7. NM_001405712.1NP_001392641.1  B-cell lymphoma/leukemia 11A isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  8. NM_001405713.1NP_001392642.1  B-cell lymphoma/leukemia 11A isoform 15

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  9. NM_001405714.1NP_001392643.1  B-cell lymphoma/leukemia 11A isoform 15

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  10. NM_001405715.1NP_001392644.1  B-cell lymphoma/leukemia 11A isoform 15

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  11. NM_001405716.1NP_001392645.1  B-cell lymphoma/leukemia 11A isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  12. NM_001405717.1NP_001392646.1  B-cell lymphoma/leukemia 11A isoform 16

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  13. NM_001405718.1NP_001392647.1  B-cell lymphoma/leukemia 11A isoform 16

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  14. NM_001405719.1NP_001392648.1  B-cell lymphoma/leukemia 11A isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  15. NM_001405720.1NP_001392649.1  B-cell lymphoma/leukemia 11A isoform 17

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  16. NM_001405721.1NP_001392650.1  B-cell lymphoma/leukemia 11A isoform 17

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  17. NM_001405722.1NP_001392651.1  B-cell lymphoma/leukemia 11A isoform 18

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  18. NM_001405723.1NP_001392652.1  B-cell lymphoma/leukemia 11A isoform 18

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  19. NM_001405724.1NP_001392653.1  B-cell lymphoma/leukemia 11A isoform 9

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  20. NM_001405725.1NP_001392654.1  B-cell lymphoma/leukemia 11A isoform 19

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
    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:239264
    zf-H2C2_2; Zinc-finger double domain
  21. NM_001405726.1NP_001392655.1  B-cell lymphoma/leukemia 11A isoform 19

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
    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:239264
    zf-H2C2_2; Zinc-finger double domain
  22. NM_001405727.1NP_001392656.1  B-cell lymphoma/leukemia 11A isoform 19

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
    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:239264
    zf-H2C2_2; Zinc-finger double domain
  23. NM_001405728.1NP_001392657.1  B-cell lymphoma/leukemia 11A isoform 19

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
    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:239264
    zf-H2C2_2; Zinc-finger double domain
  24. NM_001405729.1NP_001392658.1  B-cell lymphoma/leukemia 11A isoform 10

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  25. NM_001405730.1NP_001392659.1  B-cell lymphoma/leukemia 11A isoform 11

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  26. NM_001405731.1NP_001392660.1  B-cell lymphoma/leukemia 11A isoform 12

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
    UniProtKB/TrEMBL
    B4DT16
  27. NM_001405732.1NP_001392661.1  B-cell lymphoma/leukemia 11A isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  28. NM_001405733.1NP_001392662.1  B-cell lymphoma/leukemia 11A isoform 13

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
    UniProtKB/TrEMBL
    A0A2R8Y2E8
  29. NM_001405734.1NP_001392663.1  B-cell lymphoma/leukemia 11A isoform 20

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  30. NM_001405735.1NP_001392664.1  B-cell lymphoma/leukemia 11A isoform 20

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  31. NM_001405736.1NP_001392665.1  B-cell lymphoma/leukemia 11A isoform 14

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970
  32. NM_018014.4NP_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)
    AC007381, AC009970, AF080216, AJ404611, AJ404612, BC021098
    Consensus CDS
    CCDS1861.1
    UniProtKB/Swiss-Prot
    Q9H165
    UniProtKB/TrEMBL
    D9YZV9
    Related
    ENSP00000349300.4, ENST00000356842.9
    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
  33. NM_022893.4NP_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, AC009970, AF080216, AJ404611, AK001035, BG393787
    Consensus CDS
    CCDS1862.1
    UniProtKB/Swiss-Prot
    Q9H165, Q9NWA7
    UniProtKB/TrEMBL
    D6W5D9
    Related
    ENSP00000496168.1, ENST00000642384.2
    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
  34. NM_138559.2NP_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)
    AC007381, AC009970
    Consensus CDS
    CCDS46295.1
    UniProtKB/Swiss-Prot
    Q9H165
    Related
    ENSP00000352648.5, ENST00000359629.10

RNA

  1. NR_175964.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC007381, AC009970

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    60450520..60553654 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047444758.1XP_047300714.1  B-cell lymphoma/leukemia 11A isoform X7

  2. XM_011532910.2XP_011531212.1  B-cell lymphoma/leukemia 11A isoform X2

    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:391416
    zf-H2C2_2; Zinc-finger double domain
  3. XM_047444760.1XP_047300716.1  B-cell lymphoma/leukemia 11A isoform X10

  4. XM_047444759.1XP_047300715.1  B-cell lymphoma/leukemia 11A isoform X8

  5. XM_047444757.1XP_047300713.1  B-cell lymphoma/leukemia 11A isoform X6

  6. XM_047444756.1XP_047300712.1  B-cell lymphoma/leukemia 11A isoform X3

  7. XM_024452962.2XP_024308730.1  B-cell lymphoma/leukemia 11A isoform X5

    Conserved Domains (3) summary
    sd00017
    Location:692712
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:691712
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:339364
    zf-H2C2_2; Zinc-finger double domain
  8. XM_017004335.2XP_016859824.1  B-cell lymphoma/leukemia 11A isoform X4

    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:355380
    zf-H2C2_2; Zinc-finger double domain
  9. XM_017004333.2XP_016859822.1  B-cell lymphoma/leukemia 11A isoform X1

    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:389414
    zf-H2C2_2; Zinc-finger double domain
  10. XM_024452963.2XP_024308731.1  B-cell lymphoma/leukemia 11A isoform X5

    Conserved Domains (3) summary
    sd00017
    Location:692712
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:691712
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:339364
    zf-H2C2_2; Zinc-finger double domain
  11. XM_017004336.2XP_016859825.1  B-cell lymphoma/leukemia 11A isoform X9

    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
  12. XM_047444761.1XP_047300717.1  B-cell lymphoma/leukemia 11A isoform X11

    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:239264
    zf-H2C2_2; Zinc-finger double domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    60456325..60559492 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.