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KNCN Gene

protein-coding   GIFtS: 37
GCID: GC01M047011

Kinocilin

  Search for KNCN
at  

(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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
kinocilin1 2
L52 5
Kino2
KINO5

External Ids:    HGNC: 264881   Entrez Gene: 1489302   Ensembl: ENSG000001624567   OMIM: 6114555   UniProtKB: A6PVL33   
ORGUL members:         

Export aliases for KNCN gene to outside databases

Previous GC identifers: GC01M046783 GC01M045127


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for KNCN Gene:
KNCN (kinocilin) is a protein-coding gene.

UniProtKB/Swiss-Prot: KNCN_HUMAN, A6PVL3
Function: May play a role in stabilizing dense microtubular networks or in vesicular trafficking (By similarity)




(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_000001.10  NC_018912.2  NT_032977.10  
Regulatory elements:
   Regulatory transcription factor binding sites in the KNCN gene promoter:
         AP-4   Nkx2-5   CBF-C   S8   CBF-A   CBF-B   CP1A   CP1C   NF-Y   CBF(2)   
         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 KNCN


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

Entrez Gene cytogenetic band: 1p33   Ensembl cytogenetic band:  1p33   HGNC cytogenetic band: 1p33

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

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M047011:  view genomic region     (about GC identifiers)

Start:
47,011,316 bp from pter      End:
47,017,199 bp from pter
Size:
5,884 bases      Orientation:
minus 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: KNCN_HUMAN, A6PVL3 (See protein sequence)
Recommended Name: Kinocilin  
Size: 124 amino acids; 12832 Da
Secondary accessions: A8MXE3
Alternative splicing: 2 isoforms:  A6PVL3-1   A6PVL3-2   

Explore the universe of human proteins at neXtProt for KNCN: NX_A6PVL3

Explore proteomics data for KNCN at MOPED


See KNCN Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001091080.1  
ENSEMBL proteins: 
 ENSP00000419705   ENSP00000379607  

KNCN Human Recombinant Protein Products:

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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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1 InterPro protein domain:
 IPR027837 Kinocilin

Graphical View of Domain Structure for InterPro Entry A6PVL3

ProtoNet protein and cluster: A6PVL3


Find genes that share domains with KNCN           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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: KNCN_HUMAN, A6PVL3
Function: May play a role in stabilizing dense microtubular networks or in vesicular trafficking (By similarity)

Animal Models:

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miRNA
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miRTarBase miRNAs that target KNCN:
hsa-mir-1 (MIRT023518)

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Selected qRT-PCR Assays for microRNAs that regulate KNCN (see all 11):
hsa-miR-550a hsa-miR-198 hsa-miR-1260b hsa-miR-1260 hsa-miR-520a-5p hsa-miR-3160-3p hsa-miR-525-5p hsa-miR-3202
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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
KNCN_HUMAN, A6PVL3: Membrane; Multi-pass membrane protein (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular3
plasma membrane3
cytoskeleton2

Gene Ontology (GO): Selected cellular component terms (see all 8):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005737cytoplasm ----
GO:0005874microtubule IEA--
GO:0016021integral component of membrane IEA--
GO:0016324apical plasma membrane IEA--
GO:0032437cuticular plate IEA--

Find genes that share ontologies with KNCN           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 KNCN
Interactions:

    Search GeneGlobe Interaction Network for KNCN

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for KNCN (ENSP000003796074) via UniProtKB, MINT, STRING, and/or I2D (see all 836)
InteractantInteraction Details
GeneCardExternal ID(s)
RPL5ENSP000003593454STRING: ENSP00000359345
UBCENSP000003448184STRING: ENSP00000344818
ENSG00000224774ENSP000004156154STRING: ENSP00000415615
PCNAENSP000003684384STRING: ENSP00000368438
CASTENSP000003791584STRING: ENSP00000379158
About this table

(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 Tocris compounds for KNCN



(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 KNCN gene (2 alternative transcripts): 
NM_001097611.1  NM_182516.1  

Unigene Cluster for KNCN:

Kinocilin
Hs.350764  [show with all ESTs]
Unigene Representative Sequence: NM_001097611
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000294445(uc001cpy.2 uc009vyh.1) ENST00000524908 ENST00000481882
ENST00000396314
miRNA
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hsa-miR-550a hsa-miR-198 hsa-miR-1260b hsa-miR-1260 hsa-miR-520a-5p hsa-miR-3160-3p hsa-miR-525-5p hsa-miR-3202
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Primer
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  QuantiFast Probe-based Assays in human, mouse, rat KNCN

Additional mRNA sequence: 

AK056573.1 BC101295.1 BC101296.1 BC101297.2 BC101298.2 

1 DOTS entry:

DT.95144764 

2 AceView cDNA sequences:

NM_182516 AK056573 

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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KNCN expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CTCTCCCCAG
KNCN Expression
About this image

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

KNCN Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.350764
    Custom PCR Arrays for KNCN
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KNCN

(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 KNCN gene from Selected species (see all 6)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Kncn1 , 5 kinocilin1, 5 83.33(n)1
82(a)1
  4 (53.06 cM)5
6544621  NM_001039124.31  NP_001034213.11 
 1158844005 
zebrafish
(Danio rerio)
Actinopterygii KNCN6
kinocilin
10(a)
1 ↔ 1
2(19323999-19332537) ENSDARG00000095506


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

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(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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Structural Variations
     Database of Genomic Variants (DGV) 1 variation for KNCN:    About this table    
Variant IDTypeSubtypePubMed ID
nsv755CNV Insertion18451855

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing KNCN
DNA2.0 Custom Variant and Variant Library Synthesis for KNCN

(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: 611455    OMIM disorders: --


Find genes that share disorders with KNCN           About GenesLikeMe


Export disorders for KNCN 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 KNCN gene integrated from 10 sources:
(articles sorted by number of sources associating them with KNCN)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Initial characterization of kinocilin, a protein of the hair cell kinocilium. (PubMed id 15855039)1, 3 Leibovici M....Petit C. (Hear. Res. 2005)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  4. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)
  5. 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)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
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: 148930 HGNC: 26488 AceView: FLJ32011 Ensembl:ENSG00000162456 euGenes: HUgn148930
ECgene: KNCN H-InvDB: KNCN

(According to HUGE)
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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 KNCN 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 KNCN gene:
Search GeneIP for patents involving KNCN

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, LSBio, eBioscience, 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
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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