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    BCL11B BCL11 transcription factor B [ Homo sapiens (human) ]

    Gene ID: 64919, updated on 28-Oct-2024

    Summary

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    Official Symbol
    BCL11Bprovided by HGNC
    Official Full Name
    BCL11 transcription factor Bprovided by HGNC
    Primary source
    HGNC:HGNC:13222
    See related
    Ensembl:ENSG00000127152 MIM:606558; AllianceGenome:HGNC:13222
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ATL1; RIT1; CTIP2; IMD49; CTIP-2; IDDFSTA; SMARCM2; ZNF856B; ATL1-beta; ATL1-alpha; ATL1-delta; ATL1-gamma; hRIT1-alpha
    Summary
    This gene encodes a C2H2-type zinc finger protein and is closely related to BCL11A, a gene whose translocation may be associated with B-cell malignancies. Although the specific function of this gene has not been determined, the encoded protein is known to be a transcriptional repressor, and is regulated by the NURD nucleosome remodeling and histone deacetylase complex. Four alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Aug 2013]
    Expression
    Biased expression in skin (RPKM 7.8), lymph node (RPKM 5.6) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See BCL11B in Genome Data Viewer
    Location:
    14q32.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (99169287..99272197, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (93400844..93503767, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (99635624..99738534, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs622 Neighboring gene uncharacterized LOC107984696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99496427-99496927 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:99504757-99505257 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99559873-99560872 Neighboring gene uncharacterized LOC105370659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99600505-99601228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99608696-99609604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99640571-99641086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99658267-99658828 Neighboring gene uncharacterized LOC124903412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99677677-99678177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99695676-99696574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99703507-99704031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99713148-99714044 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:99723824-99724098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99734631-99735236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99735237-99735841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6061 Neighboring gene uncharacterized LOC105370660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99750257-99750979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99784572-99785298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99786594-99787222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99787223-99787850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99788913-99789673 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99798343-99799050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99799051-99799757 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99814550-99815224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99815225-99815898 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:99827260-99827481 Neighboring gene Sharpr-MPRA regulatory region 7827 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99849405-99850263 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99860795-99861575 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99874757-99875323 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:99878378-99879044 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99879711-99880376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99890523-99891386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99891387-99892249 Neighboring gene SET domain containing 3, actin N3(tau)-histidine methyltransferase Neighboring gene RNA, U6 small nuclear 91, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Integrated genome-wide genotyping and gene expression profiling reveals BCL11B as a putative oncogene in acute myeloid leukemia with 14q32 aberrations. Abbas S, et al. Haematologica, 2014 May. PMID 24441149, Free PMC Article
    2. Genes regulated by BCL11B during T-cell development are enriched for de novo mutations found in schizophrenia patients. Fahey L, et al. Am J Med Genet B Neuropsychiatr Genet, 2020 Sep. PMID 32729240
    3. Increased expression of BCL11B and its recruited chromatin remodeling factors during highly active antiretroviral therapy synergistically represses the transcription of human immunodeficiency virus type 1 and is associated with residual immune activation. Wang J, et al. Arch Virol, 2020 Feb. PMID 31828511
    4. CTIP2-Regulated Reduction in PKA-Dependent DARPP32 Phosphorylation in Human Medium Spiny Neurons: Implications for Huntington Disease. Fjodorova M, et al. Stem Cell Reports, 2019 Sep 10. PMID 31447328, Free PMC Article
    5. A De Novo heterozygous frameshift mutation identified in BCL11B causes neurodevelopmental disorder by whole exome sequencing. Qiao F, et al. Mol Genet Genomic Med, 2019 Sep. PMID 31347296, Free PMC Article

    See all (112) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association between BCL11B gene polymorphisms and age-related hearing loss in the elderly: A case-control study in Qingdao, China.
      Title: Association between BCL11B gene polymorphisms and age-related hearing loss in the elderly: A case-control study in Qingdao, China.
    2. A Bcl11b[N797K] variant isolated from an immunodeficient patient inhibits early thymocyte development in mice.
      Title: A Bcl11b(N797K) variant isolated from an immunodeficient patient inhibits early thymocyte development in mice.
    3. The function of BCL11B in base excision repair contributes to its dual role as an oncogene and a haplo-insufficient tumor suppressor gene.
      Title: The function of BCL11B in base excision repair contributes to its dual role as an oncogene and a haplo-insufficient tumor suppressor gene.
    4. Differential expression of BCL11b and CDKN2A in CD30-positive peripheral T cell lymphoma: Retrospective study.
      Title: Differential expression of BCL11b and CDKN2A in CD30-positive peripheral T cell lymphoma: Retrospective study.
    5. BCL11B and the NuRD complex cooperatively guard T-cell fate and inhibit OPA1-mediated mitochondrial fusion in T cells.
      Title: BCL11B and the NuRD complex cooperatively guard T-cell fate and inhibit OPA1-mediated mitochondrial fusion in T cells.
    6. BCL11B Upregulates the Expression of RelA in T Cells Stimulated with Staphylococcal Enterotoxin A.
      Title: BCL11B Upregulates the Expression of RelA in T Cells Stimulated with Staphylococcal Enterotoxin A.
    7. Expression pattern and diagnostic utility of BCL11B in mature T- and NK-cell neoplasms.
      Title: Expression pattern and diagnostic utility of BCL11B in mature T- and NK-cell neoplasms.
    8. Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker.
      Title: Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker.
    9. A de novo BCL11B variant case manifesting with dystonic movement disorder regarding the article ""BCL11B-related disorder in two canadian children: Expanding the clinical phenotype (Prasad et al., 2020).""
      Title: A de novo BCL11B variant case manifesting with dystonic movement disorder regarding the article "BCL11B-related disorder in two canadian children: Expanding the clinical phenotype (Prasad et al., 2020).".
    10. Decreased TCF1 and BCL11B expression predicts poor prognosis for patients with chronic lymphocytic leukemia.
      Title: Decreased TCF1 and BCL11B expression predicts poor prognosis for patients with chronic lymphocytic leukemia.
    Submit: New GeneRIF Correction See all GeneRIFs (74)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Immunodeficiency 49
    MedGen: C4310656 OMIM: 617237 GeneReviews: Not available
    		Compare labs
    Intellectual developmental disorder with speech delay, dysmorphic facies, and t-cell abnormalities
    MedGen: C4748152 OMIM: 618092 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Common genetic variation in the 3'-BCL11B gene desert is associated with carotid-femoral pulse wave velocity and excess cardiovascular disease risk: the AortaGen Consortium.
    EBI GWAS Catalog
    Genetic variants near PDGFRA are associated with corneal curvature in Australians.
    EBI GWAS Catalog
    Genome wide association study of SNP-, gene-, and pathway-based approaches to identify genes influencing susceptibility to Staphylococcus aureus infections.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat LSD1 interacts with CTIP2 and co-localizes with HIV-1 Tat. LSD1 is required for CTIP2 recruitment at the HIV-1 proximal promoter to repress HIV-1 replication and transcription PubMed
    tat BCL11B and metastasis associated 1 protein (MTA1) inhibits HIV-1 Tat-mediated LTR transactivation by association with the integrated HIV-LTR PubMed
    tat CTIP2 forms a complex with HIV-1 Tat and HP1alpha resulting in relocalization of Tat and inactivation of Tat-mediated transactivation of the HIV-1 LTR promoter PubMed
    tat CTIP2 harbors two HIV-1 Tat interaction interfaces (amino acids 145-434 and 717-813) and binds to the N-terminus (amino acids 1-48) of Tat PubMed
    Vpr vpr COUP-TF-interacting protein 2 (CTIP2) abolishes Vpr-mediated stimulation of p21 by cooperating with SUV39H1 and HDAC1/HDAC2 to silence the p21 gene transcription PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in T cell differentiation in thymus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in T cell receptor V(D)J recombination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in alpha-beta T cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in commitment of neuronal cell to specific neuron type in forebrain IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in epithelial cell morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in hematopoietic stem cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in keratinocyte development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lymphoid lineage cell migration into thymus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of thymocyte apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in odontogenesis of dentin-containing tooth IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in olfactory bulb axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive T cell selection IEA
    Inferred from Electronic Annotation
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in post-embryonic camera-type eye development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of keratinocyte proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in striatal medium spiny neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in thymocyte apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in thymus development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of SWI/SNF complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in neuron projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    B-cell lymphoma/leukemia 11B
    Names
    B cell CLL/lymphoma 11B
    B-cell CLL/lymphoma 11B (zinc finger protein)
    B-cell CLL/lymphoma 11B/T-cell receptor delta constant region fusion protein
    B-cell lymphoma/leukaemia 11B
    BAF chromatin remodeling complex subunit BCL11B
    BCL-11B
    BCL11B, BAF complex component
    BCL11B/TRDC fusion
    COUP-TF-interacting protein 2
    hRit1
    radiation-induced tumor suppressor gene 1 protein
    zinc finger protein hRit1 alpha

    NCBI Reference Sequences (RefSeq)

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    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.

    Genomic

    1. NG_027894.1 RefSeqGene

      Range
      4289..107199
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001282237.2 → NP_001269166.1  B-cell lymphoma/leukemia 11B isoform 3

      See identical proteins and their annotated locations for NP_001269166.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.
      Source sequence(s)
      AB057668, AJ404614, AL109767
      UniProtKB/TrEMBL
      L8B8F6
      Conserved Domains (4) summary
      sd00017
      Location:797 → 817
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:428 → 448
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:796 → 817
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:809 → 834
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001282238.2 → NP_001269167.1  B-cell lymphoma/leukemia 11B isoform 4

      See identical proteins and their annotated locations for NP_001269167.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice junction at the 5' end of an exon and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AB057670, AJ404614, AL109767
      UniProtKB/TrEMBL
      D3YTK1, L8B862
      Conserved Domains (4) summary
      sd00017
      Location:726 → 746
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:357 → 377
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:725 → 746
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:738 → 763
      zf-H2C2_2; Zinc-finger double domain

    3. NM_022898.3 → NP_075049.1  B-cell lymphoma/leukemia 11B isoform 2

      See identical proteins and their annotated locations for NP_075049.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AB057669, AJ404614, AL109767
      Consensus CDS
      CCDS9949.1
      UniProtKB/TrEMBL
      D3YTK1, L8B567
      Related
      ENSP00000280435.6, ENST00000345514.2
      Conserved Domains (4) summary
      sd00017
      Location:727 → 747
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:358 → 378
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:726 → 747
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:739 → 764
      zf-H2C2_2; Zinc-finger double domain

    4. NM_138576.4 → NP_612808.1  B-cell lymphoma/leukemia 11B isoform 1

      See identical proteins and their annotated locations for NP_612808.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AB041218, AB043584, AJ404614, AL109767
      Consensus CDS
      CCDS9950.1
      UniProtKB/Swiss-Prot
      Q9C0K0, Q9H162
      UniProtKB/TrEMBL
      L8B7P7
      Related
      ENSP00000349723.3, ENST00000357195.8
      Conserved Domains (4) summary
      sd00017
      Location:798 → 818
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:429 → 449
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:797 → 818
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:810 → 835
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      99169287..99272197 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431708.1 → XP_047287664.1  B-cell lymphoma/leukemia 11B isoform X2

    2. XM_047431707.1 → XP_047287663.1  B-cell lymphoma/leukemia 11B isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      93400844..93503767 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376624.1 → XP_054232599.1  B-cell lymphoma/leukemia 11B isoform X2

    2. XM_054376623.1 → XP_054232598.1  B-cell lymphoma/leukemia 11B isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9C0K0.1 GenPept UniProtKB/Swiss-Prot:Q9C0K0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools