Human Gene BCL11A (ENST00000642384.2_9) from GENCODE V47lift37
  Description: BAF chromatin remodeling complex subunit BCL11A, transcript variant 1 (from RefSeq NM_022893.4)
Gencode Transcript: ENST00000642384.2_9
Gencode Gene: ENSG00000119866.22_20
Transcript (Including UTRs)
   Position: hg19 chr2:60,684,329-60,780,789 Size: 96,461 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr2:60,687,539-60,780,405 Size: 92,867 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:60,684,329-60,780,789)mRNA (may differ from genome)Protein (835 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: BC11A_HUMAN
DESCRIPTION: RecName: Full=B-cell lymphoma/leukemia 11A; Short=BCL-11A; AltName: Full=B-cell CLL/lymphoma 11A; AltName: Full=COUP-TF-interacting protein 1; AltName: Full=Ecotropic viral integration site 9 protein homolog; Short=EVI-9; AltName: Full=Zinc finger protein 856;
FUNCTION: Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis, is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity).
SUBUNIT: Interacts with TFCOUP1, PIAS3, ARP1 and EAR2 (By similarity).
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Associates with the nuclear body. Colocalizes with SUMO1 and SENP2 in nuclear speckles (By similarity).
TISSUE SPECIFICITY: Expressed at high levels in brain, spleen thymus, bone marrow and testis. Expressed in CD34-positive myeloid precursor cells, B-cells, monocytes and megakaryocytes. Expression is tightly regulated during B-cell development.
PTM: Sumoylated with SUMO1 (By similarity).
POLYMORPHISM: Genetic variation in BCL11A underlies the fetal hemoglobin quantitative trait locus 5 [MIM:142335]. It is associated with quantitative variation in the production of F cells, that is erythrocytes containing measurable amounts of fetal hemoglobin (HbF). In healthy adults, HbF is present at residual levels (less than 0.6% of total hemoglobin) with over twenty-fold variation. Ten to fifteen percent of adults in the upper tail of the distribution have HbF levels between 0.8% and 5.0%, a condition referred to as heterocellular hereditary persistence of fetal hemoglobin (hHPFH). Although these HbF levels are modest in otherwise healthy individuals, interaction of hHPFH with beta thalassemia or sickle cell disease can increase HbF output in these individuals to levels that are clinically beneficial.
DISEASE: Note=Chromosomal aberrations involving BCL11A may be a cause of lymphoid malignancies. Translocation t(2;14)(p13;q32.3) causes BCL11A deregulation and amplification.
SIMILARITY: Contains 6 C2H2-type zinc fingers.
SEQUENCE CAUTION: Sequence=BAB47438.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/BCL11AID391.html";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: BCL11A
Diseases sorted by gene-association score: dias-logan syndrome* (1300), sickle cell anemia (19), lymphoma (16), sickle cell disease (12), thalassemia (12), hereditary persistence of fetal hemoglobin-sickle cell disease syndrome* (11), gray zone lymphoma (9), mediastinal malignant lymphoma (7), chromosome 2p16.1-p15 deletion syndrome (7), alpha thalassemia-intellectual disability syndrome type 1 (7), mediastinal gray zone lymphoma (6), composite lymphoma (5), hypersomnia (5), thalassemia, hispanic gamma-delta-beta (4), intellectual disability (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -87.50384-0.228 Picture PostScript Text
3' UTR -725.103210-0.226 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

Pfam Domains:
PF00096 - Zinc finger, C2H2 type

SCOP Domains:
48371 - ARM repeat
57667 - beta-beta-alpha zinc fingers

ModBase Predicted Comparative 3D Structure on Q9H165
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003676 nucleic acid binding
GO:0005515 protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007165 signal transduction
GO:0010976 positive regulation of neuron projection development
GO:0010977 negative regulation of neuron projection development
GO:0016925 protein sumoylation
GO:0022008 neurogenesis
GO:0030517 negative regulation of axon extension
GO:0032463 negative regulation of protein homooligomerization
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048671 negative regulation of collateral sprouting
GO:0048672 positive regulation of collateral sprouting
GO:0050773 regulation of dendrite development
GO:2000171 negative regulation of dendrite development

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AJ404612 - Homo sapiens mRNA for B-cell lymphoma/leukaemia 11A long form (BCL11A-L gene).
AJ404613 - Homo sapiens mRNA for B-cell lymphoma/leukaemia 11A short form (BCL11A-S gene).
AF080216 - Homo sapiens C2H2-type zinc-finger protein mRNA, complete cds.
BC021098 - Homo sapiens B-cell CLL/lymphoma 11A (zinc finger protein), mRNA (cDNA clone MGC:31810 IMAGE:5087967), complete cds.
AB058712 - Homo sapiens KIAA1809 mRNA for KIAA1809 protein.
AK055251 - Homo sapiens cDNA FLJ30689 fis, clone FCBBF2000566, highly similar to B-cell lymphoma/leukemia 11A.
AK297507 - Homo sapiens cDNA FLJ58516 complete cds, highly similar to B-cell lymphoma/leukemia 11A.
AK300012 - Homo sapiens cDNA FLJ57865 complete cds, highly similar to B-cell lymphoma/leukemia 11A.
JN852960 - Homo sapiens BCL11a-M (BCL11A) mRNA, partial cds, alternatively spliced.
AB384297 - Synthetic construct DNA, clone: pF1KSDA1809, Homo sapiens BCL11A gene for B-cell lymphoma/leukemia 11A, complete cds, without stop codon, in Flexi system.
EU446622 - Synthetic construct Homo sapiens clone IMAGE:100070203; IMAGE:100011831; FLH258223.01L B-cell CLL/lymphoma 11A (zinc finger protein) (BCL11A) gene, encodes complete protein.
EU446808 - Synthetic construct Homo sapiens clone IMAGE:100070306; IMAGE:100012017; FLH262799.01L B-cell CLL/lymphoma 11A (zinc finger protein) (BCL11A) gene, encodes complete protein.
AJ404611 - Homo sapiens mRNA for B-cell lymphoma/leukaemia 11A extra long form (BCL11A-XL gene).
AK001035 - Homo sapiens cDNA FLJ10173 fis, clone HEMBA1003953.
JD091396 - Sequence 72420 from Patent EP1572962.
JD092702 - Sequence 73726 from Patent EP1572962.
JD036456 - Sequence 17480 from Patent EP1572962.
JD301119 - Sequence 282143 from Patent EP1572962.
JD561908 - Sequence 542932 from Patent EP1572962.
JD197187 - Sequence 178211 from Patent EP1572962.
JD083017 - Sequence 64041 from Patent EP1572962.
JD449068 - Sequence 430092 from Patent EP1572962.
JD504162 - Sequence 485186 from Patent EP1572962.
JD173933 - Sequence 154957 from Patent EP1572962.
JD509458 - Sequence 490482 from Patent EP1572962.
JD263101 - Sequence 244125 from Patent EP1572962.
JD237137 - Sequence 218161 from Patent EP1572962.
JD231017 - Sequence 212041 from Patent EP1572962.
JD101296 - Sequence 82320 from Patent EP1572962.
JD038631 - Sequence 19655 from Patent EP1572962.
JD225907 - Sequence 206931 from Patent EP1572962.
JD327334 - Sequence 308358 from Patent EP1572962.
JD305713 - Sequence 286737 from Patent EP1572962.
JD510872 - Sequence 491896 from Patent EP1572962.
AK092316 - Homo sapiens cDNA FLJ34997 fis, clone OCBBF2011625, highly similar to B-cell lymphoma/leukemia 11A.
AX747478 - Sequence 1003 from Patent EP1308459.
JD110654 - Sequence 91678 from Patent EP1572962.
AY228763 - Homo sapiens B-cell CLL/lymphoma 11A isoform 6 (BCL11A) mRNA, complete cds.
CU676818 - Synthetic construct Homo sapiens gateway clone IMAGE:100021976 5' read BCL11A mRNA.
AY692278 - Homo sapiens B-cell lymphoma/leukaemia 11A extra-short form (BCL11A) mRNA, complete cds, alternatively spliced.
JD458488 - Sequence 439512 from Patent EP1572962.
JD271292 - Sequence 252316 from Patent EP1572962.
JD458514 - Sequence 439538 from Patent EP1572962.
JD458513 - Sequence 439537 from Patent EP1572962.
JD056229 - Sequence 37253 from Patent EP1572962.
JD458511 - Sequence 439535 from Patent EP1572962.
JD458512 - Sequence 439536 from Patent EP1572962.
JD271291 - Sequence 252315 from Patent EP1572962.
JD458510 - Sequence 439534 from Patent EP1572962.
JD406055 - Sequence 387079 from Patent EP1572962.
JD057274 - Sequence 38298 from Patent EP1572962.
JD406801 - Sequence 387825 from Patent EP1572962.
JD461601 - Sequence 442625 from Patent EP1572962.
JD056228 - Sequence 37252 from Patent EP1572962.
JD458352 - Sequence 439376 from Patent EP1572962.
JD258038 - Sequence 239062 from Patent EP1572962.
JD377121 - Sequence 358145 from Patent EP1572962.
JD465208 - Sequence 446232 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BC11A_HUMAN, CTIP1, D6W5D7, ENST00000642384.1, EVI9, KIAA1809, NM_022893, Q66LN6, Q86W14, Q8WU92, Q96JL6, Q9H163, Q9H164, Q9H165, Q9H3G9, Q9NWA7, uc328iqv.1, uc328iqv.2, ZNF856
UCSC ID: ENST00000642384.2_9
RefSeq Accession: NM_022893.4
Protein: Q9H165 (aka BC11A_HUMAN or BC1A_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene BCL11A:
bcl11a-id (BCL11A-Related Intellectual Disability)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.