Bcl11a BCL11 transcription factor A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Bcl11aprovided by MGI
Official Full Name: BCL11 transcription factor Aprovided by MGI
Primary source: MGI:MGI:106190
See related: Ensembl:ENSMUSG00000000861 AllianceGenome:MGI:106190
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Evi9; Ctip1; Evi9a; Evi9b; Evi9c; BCL-11A; mKIAA1809; 2810047E18Rik; D930021L15Rik
Summary: Enables transcription corepressor activity. Involved in negative regulation of transcription by RNA polymerase II and protein sumoylation. Acts upstream of or within B cell differentiation; T cell differentiation; and negative regulation of gene expression. Located in nuclear body. Is expressed in several structures, including alimentary system; branchial arch; genitourinary system; nervous system; and sensory organ. Human ortholog(s) of this gene implicated in autism spectrum disorder; beta thalassemia; schizophrenia; and sickle cell anemia. Orthologous to human BCL11A (BAF chromatin remodeling complex subunit BCL11A). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in CNS E14 (RPKM 11.6), CNS E18 (RPKM 11.0) and 13 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 A3.2; 11 14.41 cM

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (24026498..24123558)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (24076564..24173558)

Chromosome 11 - NC_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Transcription factors Bcl11a and Bcl11b are required for the production and differentiation of cortical projection neurons.
Title: Transcription factors Bcl11a and Bcl11b are required for the production and differentiation of cortical projection neurons.
Selective Ablation of BCL11A in Epidermal Keratinocytes Alters Skin Homeostasis and Accelerates Excisional Wound Healing In Vivo.
Title: Selective Ablation of BCL11A in Epidermal Keratinocytes Alters Skin Homeostasis and Accelerates Excisional Wound Healing In Vivo.
The transcription factor BCL11A defines distinct subsets of midbrain dopaminergic neurons.
Title: The transcription factor BCL11A defines distinct subsets of midbrain dopaminergic neurons.
Ctip1 regulates epidermal differentiation and expression of Elvol4 and Fosl2 during skin development.
Title: Transcription Factor CTIP1/ BCL11A Regulates Epidermal Differentiation and Lipid Metabolism During Skin Development.
Our studies define a mechanism for BCL11A in regulation of hematopoietic stem cell function
Title: Bcl11a Deficiency Leads to Hematopoietic Stem Cell Defects with an Aging-like Phenotype.
Bcl11a enhancer-deleted mice, Bcl11a(Deltaenh), phenocopy the BCL11A-null state with respect to alterations of globin expression.
Title: Strict in vivo specificity of the Bcl11a erythroid enhancer.
data identify Ctip1 as a critical control over sensory cortex development
Title: Ctip1 Controls Acquisition of Sensory Area Identity and Establishment of Sensory Input Fields in the Developing Neocortex.
Bcl11a haploinsufficiency in mice causes impaired cognition, abnormal social behavior, and microcephaly in accordance with the human phenotype
Title: BCL11A Haploinsufficiency Causes an Intellectual Disability Syndrome and Dysregulates Transcription.
deletion of Bcl11a alters the regulation of hematopoietic stem cell quiescence, self-renewal, and fate choice
Title: Single-cell analysis reveals key roles for Bcl11a in regulating stem cell fate decisions.
This study showed that the expression of Sema3c is increased in migrating Bcl11a-deficient neurons and that Bcl11a is a direct negative regulator of Sema3c transcription
Title: Bcl11a (Ctip1) Controls Migration of Cortical Projection Neurons through Regulation of Sema3c.

Submit: New GeneRIF Correction See all GeneRIFs (24)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (6) 1 citation
Targeted (13) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BE447163 (e-PCR)
- UniSTS:208646

Bcl11a (e-PCR), detects polymorphism
- UniSTS:258468

Bcl11a (e-PCR), detects polymorphism
- UniSTS:258253

Bcl11a (e-PCR), detects polymorphism
- UniSTS:530679

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology 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 protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables transcription coregulator activity	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription regulatory region nucleic acid binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within B cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within T cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of branching morphogenesis of a nerve	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of collateral sprouting	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of dendrite development	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of dendrite development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of dendrite extension	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron remodeling	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of collateral sprouting	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in protein sumoylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of dendrite development	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of SWI/SNF complex	IDA Inferred from Direct Assay more info	PubMed
part_of SWI/SNF complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nuclear body	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in paraspeckles	ISO Inferred from Sequence Orthology more info
is_active_in postsynapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: B-cell lymphoma/leukemia 11A

Names: B cell CLL/lymphoma 11A (zinc finger protein); B-cell CLL/lymphoma 11A; COUP-TF interacting protein 1; EVI-9; ecotropic viral integration site 9 protein; myeloid leukemia

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

NM_001159289.1 → NP_001152761.1 B-cell lymphoma/leukemia 11A isoform 2

See identical proteins and their annotated locations for NP_001152761.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses a different splice site in the 3' coding region, compared to variant 4. The resulting protein (isoform 2) has a shorter C-terminus when it is compared to isoform 4.

Source sequence(s)

AA008362, AK004395, AK045556, BB853515, BY735002

Consensus CDS

CCDS48758.1

UniProtKB/Swiss-Prot

Q9QYE3

Related

ENSMUSP00000105142.2, ENSMUST00000109516.8
NM_001159290.1 → NP_001152762.1 B-cell lymphoma/leukemia 11A isoform 3

See identical proteins and their annotated locations for NP_001152762.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) has multiple differences, one of which results in the use of a downstream start codon, compared to variant 4. The resulting protein (isoform 3) is shorter when it is compared to isoform 4.

Source sequence(s)

AK045556

Consensus CDS

CCDS48759.1

UniProtKB/Swiss-Prot

Q9QYE3

Related

ENSMUSP00000112948.2, ENSMUST00000118955.2
NM_001242934.1 → NP_001229863.1 B-cell lymphoma/leukemia 11A isoform 4

See identical proteins and their annotated locations for NP_001229863.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) represents the longest transcript and encodes the longest protein (isoform 4).

Source sequence(s)

AK045556, AK140949, AK164574, BB649527, BB662872, BF731393, BY735002, CB524780, CD355476

Consensus CDS

CCDS56764.1

UniProtKB/TrEMBL

Q3US10, Q5STS9

Related

ENSMUSP00000105140.2, ENSMUST00000109514.8

Conserved Domains (3) summary

sd00017
Location:744 → 764

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:743 → 764

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:391 → 416

zf-H2C2_2; Zinc-finger double domain
NM_016707.3 → NP_057916.1 B-cell lymphoma/leukemia 11A isoform 1

See identical proteins and their annotated locations for NP_057916.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) uses a different splice site in the 3' coding region, compared to variant 4. The resulting protein (isoform 1) has a shorter C-terminus when it is compared to isoform 4.

Source sequence(s)

AF169037, AL672018, BB649527, BY735002

Consensus CDS

CCDS24483.1

UniProtKB/Swiss-Prot

Q80T89, Q8BLC7, Q8BLR4, Q8BWX3, Q921V4, Q9D0V2, Q9JIT4, Q9JLK8, Q9JLK9, Q9QYE3

UniProtKB/TrEMBL

Q3US10

Related

ENSMUSP00000000881.7, ENSMUST00000000881.13

Conserved Domains (3) summary

sd00017
Location:379 → 399

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:378 → 399

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:391 → 416

zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000077.7 Reference GRCm39 C57BL/6J

Range

24026498..24123558

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036156319.1 → XP_036012212.1 B-cell lymphoma/leukemia 11A isoform X6

UniProtKB/Swiss-Prot

Q80T89, Q8BLC7, Q8BLR4, Q8BWX3, Q921V4, Q9D0V2, Q9JIT4, Q9JLK8, Q9JLK9, Q9QYE3

UniProtKB/TrEMBL

Q3US10

Conserved Domains (3) summary

sd00017
Location:379 → 399

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:378 → 399

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:391 → 416

zf-H2C2_2; Zinc-finger double domain
XM_036156320.1 → XP_036012213.1 B-cell lymphoma/leukemia 11A isoform X9
XM_036156315.1 → XP_036012208.1 B-cell lymphoma/leukemia 11A isoform X1

UniProtKB/TrEMBL

Q3US10, Q5STS9

Conserved Domains (3) summary

sd00017
Location:744 → 764

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:743 → 764

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:391 → 416

zf-H2C2_2; Zinc-finger double domain
XM_036156318.1 → XP_036012211.1 B-cell lymphoma/leukemia 11A isoform X1

UniProtKB/TrEMBL

Q3US10, Q5STS9

Conserved Domains (3) summary

sd00017
Location:744 → 764

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:743 → 764

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:391 → 416

zf-H2C2_2; Zinc-finger double domain
XM_036156314.1 → XP_036012207.1 B-cell lymphoma/leukemia 11A isoform X1

UniProtKB/TrEMBL

Q3US10, Q5STS9

Conserved Domains (3) summary

sd00017
Location:744 → 764

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:743 → 764

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:391 → 416

zf-H2C2_2; Zinc-finger double domain
XM_011243659.3 → XP_011241961.1 B-cell lymphoma/leukemia 11A isoform X2

UniProtKB/TrEMBL

Q3US10

Conserved Domains (4) summary

sd00017
Location:379 → 399

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:744 → 764

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:743 → 764

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:391 → 416

zf-H2C2_2; Zinc-finger double domain
XM_036156321.1 → XP_036012214.1 B-cell lymphoma/leukemia 11A isoform X9
XM_036156316.1 → XP_036012209.1 B-cell lymphoma/leukemia 11A isoform X1

UniProtKB/TrEMBL

Q3US10, Q5STS9

Conserved Domains (3) summary

sd00017
Location:744 → 764

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:743 → 764

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:391 → 416

zf-H2C2_2; Zinc-finger double domain
XM_006514504.4 → XP_006514567.1 B-cell lymphoma/leukemia 11A isoform X1

See identical proteins and their annotated locations for XP_006514567.1

UniProtKB/TrEMBL

Q3US10, Q5STS9

Conserved Domains (3) summary

sd00017
Location:744 → 764

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:743 → 764

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:391 → 416

zf-H2C2_2; Zinc-finger double domain
XM_030245548.2 → XP_030101408.1 B-cell lymphoma/leukemia 11A isoform X9
XM_036156322.1 → XP_036012215.1 B-cell lymphoma/leukemia 11A isoform X9
XM_030245543.2 → XP_030101403.1 B-cell lymphoma/leukemia 11A isoform X4

UniProtKB/TrEMBL

Q3US10

Conserved Domains (4) summary

sd00017
Location:345 → 365

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:710 → 730

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:709 → 730

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:357 → 382

zf-H2C2_2; Zinc-finger double domain
XM_011243660.3 → XP_011241962.1 B-cell lymphoma/leukemia 11A isoform X3

UniProtKB/TrEMBL

Q3US10

Conserved Domains (3) summary

sd00017
Location:710 → 730

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:709 → 730

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:357 → 382

zf-H2C2_2; Zinc-finger double domain
XM_036156317.1 → XP_036012210.1 B-cell lymphoma/leukemia 11A isoform X1

UniProtKB/TrEMBL

Q3US10, Q5STS9

Conserved Domains (3) summary

sd00017
Location:744 → 764

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:743 → 764

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:391 → 416

zf-H2C2_2; Zinc-finger double domain
XM_030245545.1 → XP_030101405.1 B-cell lymphoma/leukemia 11A isoform X7

UniProtKB/TrEMBL

Q3US10

Conserved Domains (3) summary

sd00017
Location:658 → 678

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:657 → 678

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:305 → 330

zf-H2C2_2; Zinc-finger double domain
XM_030245547.2 → XP_030101407.1 B-cell lymphoma/leukemia 11A isoform X8

UniProtKB/TrEMBL

Q3US10

Conserved Domains (3) summary

sd00019
Location:327 → 347

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:326 → 347

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:339 → 364

zf-H2C2_2; Zinc-finger double domain
XM_006514507.4 → XP_006514570.1 B-cell lymphoma/leukemia 11A isoform X5

UniProtKB/TrEMBL

Q3US10

Conserved Domains (3) summary

sd00017
Location:692 → 712

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:691 → 712

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:339 → 364

zf-H2C2_2; Zinc-finger double domain