Bcl11a BCL11 transcription factor A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Bcl11aprovided by RGD
Official Full Name: BCL11 transcription factor Aprovided by RGD
Primary source: RGD:1309923
See related: Ensembl:ENSRNOG00000007049 AllianceGenome:RGD:1309923
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables protein kinase binding activity. Involved in several processes, including cellular response to L-glutamate; negative regulation of branching morphogenesis of a nerve; and negative regulation of dendrite development. Located in cytoplasm; nucleus; and postsynaptic density. 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 Spleen (RPKM 70.7), Brain (RPKM 24.9) and 5 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 14q22

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (102230147..102325289)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (98029018..98124181)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (108826717..108921197)

Chromosome 14 - NC_086032.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Transcription Factor BCL11A Regulates Schwann Cell Behavior During Peripheral Nerve Regeneration.
Title: Transcription Factor BCL11A Regulates Schwann Cell Behavior During Peripheral Nerve Regeneration.
Over-expression of Bcl11A or deleted in colorectal cancer (DCC) counters the effect of N-methylaspartate (NMDA) or glutamate on axon branching and dendrite outgrowth, indicating that Bcl11A/DCC is a novel pathway regulating axon and dendrite arborization.
Title: Bcl11A/CTIP1 mediates the effect of the glutamate receptor on axon branching and dendrite outgrowth.
regional and subcellular distributions of Bcl11A/Evi9/CTIP1 in rat brain were investigated by immunostaining and biochemical fractionation
Title: Expression of zinc finger transcription factor Bcl11A/Evi9/CTIP1 in rat brain.

Submit: New GeneRIF Correction

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

AU049785 (e-PCR)
- UniSTS:146231

RH138170 (e-PCR)
- UniSTS:220257

D14Rat32 (e-PCR)
- UniSTS:118373

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

RH140039 (e-PCR)
- UniSTS:222121

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

RH140926 (e-PCR)
- UniSTS:222938

RH139319 (e-PCR)
- UniSTS:221405

Gene Ontology Provided by RGD

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 heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coregulator activity	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in cellular response to L-glutamate	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of branching morphogenesis of a nerve	IMP Inferred from Mutant Phenotype more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of dendrite development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of dendrite extension	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron remodeling	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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in protein sumoylation	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
located_in paraspeckles	ISO Inferred from Sequence Orthology more info
is_active_in postsynapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: B-cell lymphoma/leukemia 11A

Names: B-cell CLL/lymphoma 11A (zinc finger protein); BAF chromatin remodeling complex subunit BCL11A; BCL11A, BAF complex component

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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.

mRNA and Protein(s)

NM_001191683.1 → NP_001178612.1 B-cell lymphoma/leukemia 11A

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000014

UniProtKB/TrEMBL

A0A8I6ATN1, A0A8I6AXE0

Related

ENSRNOP00000093688.1, ENSRNOT00000106316.1

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086032.1 Reference GRCr8

Range

102230147..102325289

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039092105.2 → XP_038948033.1 B-cell lymphoma/leukemia 11A isoform X8

UniProtKB/TrEMBL

A0A8I6ATN1

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_039092106.2 → XP_038948034.1 B-cell lymphoma/leukemia 11A isoform X10

UniProtKB/TrEMBL

A0A8I6ATN1

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_063273278.1 → XP_063129348.1 B-cell lymphoma/leukemia 11A isoform X13
XM_063273276.1 → XP_063129346.1 B-cell lymphoma/leukemia 11A isoform X7
XM_006251588.5 → XP_006251650.2 B-cell lymphoma/leukemia 11A isoform X11

UniProtKB/TrEMBL

A0A8I6ATN1, A6JQ83, D3ZSY3

Related

ENSRNOP00000009421.5

Conserved Domains (3) summary

sd00019
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_063273280.1 → XP_063129350.1 B-cell lymphoma/leukemia 11A isoform X17

UniProtKB/TrEMBL

A0A0G2K4M7
XM_006251594.5 → XP_006251656.2 B-cell lymphoma/leukemia 11A isoform X16

UniProtKB/TrEMBL

B0BN54, Q5RJJ9

Related

ENSRNOP00000073102.2
XM_063273277.1 → XP_063129347.1 B-cell lymphoma/leukemia 11A isoform X9
XM_063273275.1 → XP_063129345.1 B-cell lymphoma/leukemia 11A isoform X3
XM_039092107.2 → XP_038948035.2 B-cell lymphoma/leukemia 11A isoform X4
XM_063273274.1 → XP_063129344.1 B-cell lymphoma/leukemia 11A isoform X2
XM_017599256.2 → XP_017454745.2 B-cell lymphoma/leukemia 11A isoform X5

UniProtKB/TrEMBL

A0A8I6ATN1

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_063273273.1 → XP_063129343.1 B-cell lymphoma/leukemia 11A isoform X1
XM_063273272.1 → XP_063129342.1 B-cell lymphoma/leukemia 11A isoform X1
XM_063273279.1 → XP_063129349.1 B-cell lymphoma/leukemia 11A isoform X15
XM_017599258.2 → XP_017454747.2 B-cell lymphoma/leukemia 11A isoform X14

UniProtKB/TrEMBL

A6JQ84
XM_039092109.2 → XP_038948037.2 B-cell lymphoma/leukemia 11A isoform X1
XM_039092108.2 → XP_038948036.2 B-cell lymphoma/leukemia 11A isoform X6
XM_039092110.2 → XP_038948038.2 B-cell lymphoma/leukemia 11A isoform X12

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001013129.1: Suppressed sequence

Description

NM_001013129.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.