Bcl11b BCL11 transcription factor B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Bcl11bprovided by RGD
Official Full Name: BCL11 transcription factor Bprovided by RGD
Primary source: RGD:1311128
See related: EnsemblRapid:ENSRNOG00000005776 AllianceGenome:RGD:1311128
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Ctip2
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in hematopoietic stem cell migration; lymphoid lineage cell migration into thymus; and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including animal organ development; cell morphogenesis involved in differentiation; and regulation of keratinocyte proliferation. Predicted to be located in neuron projection. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in immunodeficiency 49. Orthologous to human BCL11B (BAF chromatin remodeling complex subunit BCL11B). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 403.6), Brain (RPKM 64.9) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 6q32

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (132598968..132692123, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (126834531..126927720, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (131834097..131927251, complement)

Chromosome 6 - NC_086024.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

An increase in fetal cortical thickness was noted in the LPS-treated group. In the enlarged fetal cortex, laminar positioning of the early born cortical cells expressing Tbr1 and Ctip2 was disrupted, with a scattered distribution
Title: N-acetylcysteine attenuates lipopolysaccharide-induced impairment in lamination of Ctip2-and Tbr1- expressing cortical neurons in the developing rat fetal brain.
this is the first study to show that the inhibition of Bcl11b suppresses glioma cell growth by regulating the expression of the cell cycle regulator p21 and stemness-associated genes (Sox-2/Bmi-1).
Title: Depletion of B cell CLL/Lymphoma 11B Gene Expression Represses Glioma Cell Growth.
The present study suggested that Bcl11b serves a potentially important role in the regulation of ameloblast differentiation and enamel matrix protein expression. In addition, a complex feedback regulatory network may exist between Bcl11b and Msx2.
Title: Bcl11b regulates enamel matrix protein expression and dental epithelial cell differentiation during rat tooth development.
Ctip2 regulates Sp6 gene expression through direct binding to the Sp6 second promoter region in rat dental epithelium-derived cells.
Title: Ctip2-mediated Sp6 transcriptional regulation in dental epithelium-derived cells.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

REN47699 (e-PCR)
- UniSTS:372499

REN47704 (e-PCR)
- UniSTS:372504

stSG632080 (e-PCR)
- UniSTS:459546

REN47709 (e-PCR)
- UniSTS:372509

REN47976 (e-PCR)
- UniSTS:372776

stSG632129 (e-PCR)
- UniSTS:459592

ECD17061 (e-PCR)
- UniSTS:298074

Bcl11b (e-PCR), detects polymorphism
- UniSTS:258469

REN47882 (e-PCR)
- UniSTS:372682

REN47927 (e-PCR)
- UniSTS:372727

Bcl11b (e-PCR), detects polymorphism
- UniSTS:530680

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor 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 sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of T cell apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within T cell differentiation in thymus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within T cell receptor V(D)J recombination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within alpha-beta T cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within axonogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within central nervous system neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within commitment of neuronal cell to specific neuron type in forebrain	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within epithelial cell morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in hematopoietic stem cell migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within keratinocyte development	ISO Inferred from Sequence Orthology more info
involved_in lymphoid lineage cell migration into thymus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of T cell apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of thymocyte apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within odontogenesis of dentin-containing tooth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within olfactory bulb axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive T cell selection	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within post-embryonic camera-type eye development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within post-embryonic development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of keratinocyte proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of lipid metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skin development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within striatal medium spiny neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of thymocyte apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within thymus development	ISO Inferred from Sequence Orthology more info
acts_upstream_of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of SWI/SNF complex	ISO Inferred from Sequence Orthology more info
located_in neuron projection	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

General protein information

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Preferred Names: B-cell lymphoma/leukemia 11B

Names: B-cell CLL/lymphoma 11B (zinc finger protein); B-cell leukemia/lymphoma 11B; BAF chromatin remodeling complex subunit BCL11B; BCL11B, BAF complex component; COUP-TF-interacting protein 2 long form

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_001277287.1 → NP_001264216.1 B-cell lymphoma/leukemia 11B isoform 1

See identical proteins and their annotated locations for NP_001264216.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

JAXUCZ010000006, JF520429

UniProtKB/TrEMBL

A6KBF0, H9N1L4

Related

ENSRNOP00000091986.1, ENSRNOT00000098362.2

Conserved Domains (3) summary

sd00017
Location:784 → 804

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:783 → 804

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:796 → 821

zf-H2C2_2; Zinc-finger double domain
NM_001277288.1 → NP_001264217.1 B-cell lymphoma/leukemia 11B isoform 2

See identical proteins and their annotated locations for NP_001264217.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

JAXUCZ010000006, JF520428

UniProtKB/TrEMBL

A0A0G2JVA1, H9N1L3

Related

ENSRNOP00000078832.1, ENSRNOT00000111465.2

Conserved Domains (3) summary

sd00017
Location:716 → 736

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:715 → 736

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:728 → 753

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_086024.1 Reference GRCr8

Range

132598968..132692123 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063262010.1 → XP_063118080.1 B-cell lymphoma/leukemia 11B isoform X3

UniProtKB/TrEMBL

A6KBF0
XM_039112400.2 → XP_038968328.1 B-cell lymphoma/leukemia 11B isoform X2

UniProtKB/TrEMBL

A6KBF0

Conserved Domains (4) summary

sd00017
Location:787 → 807

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:427 → 447

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:786 → 807

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:799 → 824

zf-H2C2_2; Zinc-finger double domain
XM_039112399.2 → XP_038968327.1 B-cell lymphoma/leukemia 11B isoform X1

UniProtKB/TrEMBL

A6KBF0

Conserved Domains (4) summary

sd00017
Location:788 → 808

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:428 → 448

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:787 → 808

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:800 → 825

zf-H2C2_2; Zinc-finger double domain
XM_006240540.5 → XP_006240602.1 B-cell lymphoma/leukemia 11B isoform X4

UniProtKB/TrEMBL

A0A0G2JVA1

Conserved Domains (3) summary

sd00017
Location:715 → 735

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:714 → 735

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:727 → 752

zf-H2C2_2; Zinc-finger double domain

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001108057.1: Suppressed sequence

Description

NM_001108057.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.