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PCDHB11 Gene

protein-coding   GIFtS: 51
GCID: GC05P140579

Protocadherin Beta 11

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Protocadherin Beta 111 2
Cadherin ME21 2
PCDH-beta-112 3
ME22
PCDH-BETA112
Protocadherin Beta-112

External Ids:    HGNC: 86821   Entrez Gene: 561252   Ensembl: ENSG000001974797   OMIM: 6063375   UniProtKB: Q9Y5F23   

Export aliases for PCDHB11 gene to outside databases

Previous GC identifers: GC05P140395 GC05P141162 GC05P140562 GC05P140607 GC05P140559 GC05P135724


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PCDHB11 Gene:
This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked
on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and
T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6
extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The
extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the
alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common
3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins.
Their specific functions are unknown but they most likely play a critical role in the establishment and function
of specific cell-cell neural connections. (provided by RefSeq, Jul 2008)

GeneCards Summary for PCDHB11 Gene:
PCDHB11 (protocadherin beta 11) is a protein-coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB16.

UniProtKB/Swiss-Prot: PCDBB_HUMAN, Q9Y5F2
Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
of specific neuronal connections in the brain

Gene Wiki entry for PCDHB11 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000005.9  NC_018916.2  NT_029289.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the PCDHB11 gene promoter:
         FOXD1   Pax-2   Pax-2a   LCR-F1   NF-AT   PPAR-alpha   NF-AT4   NF-AT2   NF-AT3   NF-AT1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDHB11


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q31   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31

PCDHB11 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHB11 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140579:  view genomic region     (about GC identifiers)

Start:
140,579,183 bp from pter      End:
140,582,618 bp from pter
Size:
3,436 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: PCDBB_HUMAN, Q9Y5F2 (See protein sequence)
Recommended Name: Protocadherin beta-11 precursor  
Size: 797 amino acids; 87088 Da
Secondary accessions: Q2M223

Explore the universe of human proteins at neXtProt for PCDHB11: NX_Q9Y5F2

Explore proteomics data for PCDHB11 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn418, Asn436, Asn487, Asn567
  • Modification sites at PhosphoSitePlus

  • See PCDHB11 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_061754.1  
    ENSEMBL proteins: 
     ENSP00000346802   ENSP00000440344  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    PCDHC: Cadherins / Protocadherins : Clustered

    4 InterPro protein domains:
     IPR015919 Cadherin-like
     IPR013164 Cadherin_N
     IPR020894 Cadherin_CS
     IPR002126 Cadherin

    Graphical View of Domain Structure for InterPro Entry Q9Y5F2

    ProtoNet protein and cluster: Q9Y5F2

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDBB_HUMAN, Q9Y5F2
    Similarity: Contains 6 cadherin domains


    Find genes that share domains with PCDHB11           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PCDBB_HUMAN, Q9Y5F2
    Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
    of specific neuronal connections in the brain

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    Find genes that share ontologies with PCDHB11           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for PCDHB11

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    hsa-mir-92a-3p (MIRT049487)

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PCDBB_HUMAN, Q9Y5F2: Cell membrane; Single-pass type I membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    extracellular2
    peroxisome1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane ----
    GO:0005887integral component of plasma membrane TAS10380929
    GO:0016020membrane ----
    GO:0016021integral component of membrane NAS11322959

    Find genes that share ontologies with PCDHB11           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PCDHB11
    Interactions:

        Search GeneGlobe Interaction Network for PCDHB11

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155cell adhesion TAS10380929
    GO:0007156homophilic cell adhesion IEA--
    GO:0007268synaptic transmission TAS12231349
    GO:0007399nervous system development TAS10380929
    GO:0007416synapse assembly TAS12231349

    Find genes that share ontologies with PCDHB11           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PCDHB11 (PCDBB)

    1 HMDB Compound for PCDHB11    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PCDHB11 gene: 
    NM_018931.2  

    Unigene Cluster for PCDHB11:

    Protocadherin beta 11
    Hs.283084  [show with all ESTs]
    Unigene Representative Sequence: AF217747
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000354757(uc003liy.3) ENST00000536699
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat PCDHB11

    Additional mRNA sequence: 

    AB209225.1 AF152490.1 AF217747.1 AK299719.1 AK313428.1 BC112132.1 BC113611.1 D88795.1 

    1 DOTS entry:

    DT.100000940 

    11 AceView cDNA sequences:

    NM_018931 AF152490 AF217747 BQ876879 BQ778156 D88795 CB410788 BQ776974 
    CB410697 CB410640 BF949614 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PCDHB11 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCCGGCTACT
    PCDHB11 Expression
    About this image

    PCDHB11 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PCDHB11 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.283084
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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for PCDHB11 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhb195
    Pcdhb211
    protocadherin beta 195
    protocadherin beta 211
    72.18(n)1
    65.62(a)1
      18 (19.51 cM)5
    938921  NM_053146.21  NP_444376.11 
     374969985 
    chicken
    (Gallus gallus)
    Aves LOC1008576451 protocadherin beta-4-like 57.56(n)
    50.53(a)
      100857645  XM_004944734.1  XP_004944791.1 


    ENSEMBL Gene Tree for PCDHB11 (if available)
    TreeFam Gene Tree for PCDHB11 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PCDHB11 gene
    PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  PCDHGA102  PCDHGA122  PCDHGB22  
    PCDHGA92  PCDHGA82  PCDHGB32  PCDHGB62  PCDHGA52  PCDHB52  PCDHB132  PCDHGA42  
    PCDHGA72  PCDHB42  ENSG000002556222  PCDHB142  PCDHB122  PCDHB82  PCDHGB12  PCDHGB42  
    PCDHGA22  PCDHGA62  PCDHB32  PCDHGA112  PCDHB62  PCDHGC42  PCDHGC52  PCDHGA12  
    PCDHB102  PCDHB12  PCDHGB72  PCDHGA32  
    Selected SIMAP similar genes for PCDHB11 using alignment to 2 protein entries:     PCDBB_HUMAN (see all proteins) (see all similar genes):
    PCDHB12    PCDHB16    PCDHB14    DKFZp586I1919    PCDHB4    PCDHB5
    PCDHB8    PCDHB15    PCDHB18    PCDHB3    PCDHB2    PCDHB10
    PCDHB13    PCDHB6    PCDHB7    PCDHB9    PCDHB17    ME2

    Find genes that share paralogs with PCDHB11           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PCDHB11 (see all 248)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1920662631,2
    --140577350(+) TCAGGC/TATATA 1 -- us2k10--------
    rs1495972871,2
    C--140577426(+) CCTAAA/TCTCCC 1 -- us2k10--------
    rs1445426001,2
    --140577533(+) CCAGAA/GTATAA 1 -- us2k10--------
    rs732736501,2
    C,F--140577647(+) TTTTTT/CAAGCC 1 -- us2k14Minor allele frequency- C:0.10NA WA 242
    rs795556071,2
    C,F--140577745(+) TTTAGT/GATCTC 1 -- us2k11Minor allele frequency- G:0.03WA 118
    rs1833832061,2
    --140577905(+) GAGGGG/TTTAAG 1 -- us2k10--------
    rs1885076041,2
    --140577985(+) TTCAAC/TCATGT 1 -- us2k10--------
    rs6682071,2
    H--140577995(-) TGAACT/CAGATA 1 -- us2k15Minor allele frequency- C:0.00NS EA NA 422
    rs746216041,2
    F--140578100(+) GATACC/TATTGG 1 -- us2k11Minor allele frequency- T:0.01EA 120
    rs1902659651,2
    --140578236(+) CTTTAG/TATTCT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for PCDHB11 (140579183 - 140582618 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for PCDHB11 (see all 13):    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv1005e201CNV Deletion23290073
    esv2664767CNV Deletion23128226
    esv2730846CNV Deletion23290073
    nsv5031CNV Insertion18451855
    dgv6349n71CNV Loss21882294
    dgv6348n71CNV Loss21882294
    dgv6350n71CNV Loss21882294
    nsv428127CNV Loss18775914
    nsv882981CNV Gain21882294
    nsv823266CNV Gain20364138

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 606337    OMIM disorders: --


    Find genes that share disorders with PCDHB11           About GenesLikeMe

    Genetic Association Database (GAD): PCDHB11
    Human Genome Epidemiology (HuGE) Navigator: PCDHB11 (1 document)

    Export disorders for PCDHB11 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PCDHB11 gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with PCDHB11)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PubMed id 10380929)1, 2, 3 Wu Q. and Maniatis T. (Cell 1999)
    2. Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence. (PubMed id 19054571)1, 4 GregA^rio S.P....Dias-Neto E. (Psychiatry Res 2009)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. (PubMed id 11322959)1, 2 Vanhalst K.... van Roy F. (FEBS Lett. 2001)
    5. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    6. Protocadherins. (PubMed id 12231349)1 Frank M. and Kemler R. (Curr. Opin. Cell Biol. 2002)
    7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    8. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (Genome Res. 2001)
    9. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (PubMed id 10835267)1 Nollet F....van Roy F. (J. Mol. Biol. 2000)
    10. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (Proc. Natl. Acad. Sci. U.S.A. 2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 56125 HGNC: 8682 AceView: PCDHB11 Ensembl:ENSG00000197479 euGenes: HUgn56125
    ECgene: PCDHB11 H-InvDB: PCDHB11

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PCDHB11 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PCDHB11 gene:
    Search GeneIP for patents involving PCDHB11

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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