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

    Gene ID: 314423, updated on 9-Dec-2024

    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 T cell differentiation; epithelial cell development; and neuron differentiation. Predicted to be located in neuron projection. Predicted to be part of SWI/SNF complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in immunodeficiency 49. Orthologous to human BCL11B (BCL11 transcription factor B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 403.6), Brain (RPKM 64.9) and 1 other tissue See more
    Orthologs
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    Genomic context

    See Bcl11b in Genome Data Viewer
    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_086024.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134479475 Neighboring gene uncharacterized LOC134479294 Neighboring gene uncharacterized LOC103692704 Neighboring gene uncharacterized LOC103692702 Neighboring gene SET domain containing 3, actin N3(tau)-histidine methyltransferase Neighboring gene cyclin K

    Genomic regions, transcripts, and products

    Expression

    • 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

    Interactions

    General gene information

    Gene Ontology Provided by RGD

    Items 1 - 25 of 31
    Process Evidence Code Pubs
    acts_upstream_of T cell apoptotic process  
    acts_upstream_of_or_within T cell differentiation in thymus  
    acts_upstream_of_or_within T cell receptor V(D)J recombination  
    acts_upstream_of_or_within alpha-beta T cell differentiation  
    acts_upstream_of apoptotic process  
    acts_upstream_of_or_within axonogenesis  
    acts_upstream_of_or_within central nervous system neuron differentiation  
    acts_upstream_of_or_within commitment of neuronal cell to specific neuron type in forebrain  
    acts_upstream_of_or_within epithelial cell morphogenesis  
    involved_in hematopoietic stem cell migration  
    acts_upstream_of_or_within keratinocyte development  
    involved_in lymphoid lineage cell migration into thymus  
    acts_upstream_of_or_within negative regulation of T cell apoptotic process  
    acts_upstream_of_or_within negative regulation of cell population proliferation  
    acts_upstream_of_or_within negative regulation of thymocyte apoptotic process  
    acts_upstream_of_or_within odontogenesis of dentin-containing tooth  
    acts_upstream_of_or_within olfactory bulb axon guidance  
    acts_upstream_of_or_within positive T cell selection  
    involved_in positive regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within post-embryonic camera-type eye development  
    acts_upstream_of_or_within post-embryonic development  
    acts_upstream_of_or_within regulation of gene expression  
    acts_upstream_of_or_within regulation of keratinocyte proliferation  
    acts_upstream_of_or_within regulation of lipid metabolic process  
    acts_upstream_of_or_within regulation of neuron differentiation  
    acts_upstream_of_or_within skin development  
    acts_upstream_of_or_within striatal medium spiny neuron differentiation  
    acts_upstream_of thymocyte apoptotic process  
    acts_upstream_of_or_within thymus development  
    acts_upstream_of transcription by RNA polymerase II  
    Items 1 - 25 of 31
    Component Evidence Code Pubs
    part_of SWI/SNF complex  
    located_in neuron projection  
    is_active_in nucleus  
    located_in nucleus  

    General protein information

    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)

    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)

    1. NM_001277287.1NP_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:784804
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:783804
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:796821
      zf-H2C2_2; Zinc-finger double domain
    2. NM_001277288.1NP_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:716736
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:715736
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:728753
      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

    1. NC_086024.1 Reference GRCr8

      Range
      132598968..132692123 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

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

      UniProtKB/TrEMBL
      A6KBF0
      Conserved Domains (4) summary
      sd00017
      Location:787807
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:427447
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:786807
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:799824
      zf-H2C2_2; Zinc-finger double domain
    3. XM_039112399.2XP_038968327.1  B-cell lymphoma/leukemia 11B isoform X1

      UniProtKB/TrEMBL
      A6KBF0
      Conserved Domains (4) summary
      sd00017
      Location:788808
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:428448
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:787808
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:800825
      zf-H2C2_2; Zinc-finger double domain
    4. XM_006240540.5XP_006240602.1  B-cell lymphoma/leukemia 11B isoform X4

      UniProtKB/TrEMBL
      A0A0G2JVA1
      Conserved Domains (3) summary
      sd00017
      Location:715735
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:714735
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:727752
      zf-H2C2_2; Zinc-finger double domain

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