COCH Gene
protein-coding GIFtS: 60
GC14P011460
|
|
coagulation factor C homolog, cochlin (Limulus polyphemus)
(Previous name: coagulation factor C (Limulus polyphemus homolog); cochlin )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbols: DFNA31, DFNA9)
|
Aliases &
Descriptions
for COCH gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase)
About This Section
|
| Aliases & Descriptions |
|---|
| coagulation factor C homolog, cochlin (Limulus polyphemus)1 2 | | COCH-5B21 2 3 | | COCH5B22 3 | | DFNA92 5 | | coagulation factor C (Limulus polyphemus homolog); cochlin1 | | cochlin2 |
Export aliases for COCH gene to outside databasesPrevious GC identifers: GC14P028719 GC14P025131 GC14P029333 GC14P030413 GC14P031343 |
Summaries
for COCH gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for COCH:
The protein encoded by this gene is highly conserved in human, mouse, and chicken, showing 94% and 79% amino acididentity of human to mouse and chicken sequences, respectively. Hybridization to this gene was detected inspindle-shaped cells located along nerve fibers between the auditory ganglion and sensory epithelium. These cellsaccompany neurites at the habenula perforata, the opening through which neurites extend to innervate hair cells. Thisand the pattern of expression of this gene in chicken inner ear paralleled the histologic findings of acidophilicdeposits, consistent with mucopolysaccharide ground substance, in temporal bones from DFNA9 (autosomal dominantnonsyndromic sensorineural deafness 9) patients. Mutations that cause DFNA9 have been reported in this gene.Alternative splicing results in multiple transcript variants encoding the same protein. Additional splice variantsencoding distinct isoforms have been described but their biological validities have not been demonstrated. (providedby RefSeq)
Gene Wiki entry for COCH |
Genomic Views
for COCH 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 60),
Regulatory elements and Epigenetics data according to
Qiagen and/or
SABiosciences)
About This Section
|
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the COCH gene promoter:
MEF-2A FOXO3a FOXO3b FOXD1 FOXO4 SRY FOXF2 RORalpha2 FOXO1a FOXC1
Other transcription factors
Search SABiosciences Chromatin IP Primers for COCH
Epigenetics:
|  | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for COCH  |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 14q12-q13 Ensembl cytogenetic band: 14q12 HGNC cytogenetic band: 14q11.2-q13COCH Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc gene densities for chromosome 14 GeneLoc Exon Structure GeneLoc location for GC14P011460: view genomic region
(about GC identifiers)
Start:
|
11,460,861 bp from pter |
End:
|
11,476,943 bp from pter |
Size:
|
16,083 bases |
Orientation:
|
plus strand |
1 alternative location:
| Chr14+ 31,343,741-31,364,271 |
RefSeq DNA sequence:- NC_000014.8 NT_026437.12
|
Proteins
for COCH gene
(According to
1UniProtKB,
neXtProt,
and/or Ensembl,
Phosphorylation sites according to 2Phosphosite,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological, and/or
ProSpec,
Biochemical Assays by
Millipore,
Sigma-Aldrich,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Dec 2010 and
Entrez Gene,
Antibodies by
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals, and/or
Epitomics)
About This Section
|
UniProtKB/Swiss-Prot: COCH_HUMAN, O43405 (See
protein sequence)Recommended Name: Cochlin precursor Size: 550 amino acids; 59483 Da
Subunit: Interacts with SLC44A2
Subcellular location: Secreted, extracellular space, extracellular matrix
PDB structures from  and Proteopedia  :1JBI (3D)
Secondary accessions: A8K9K9Explore the universe of human proteins at neXtProt for COCH: NX_O43405
Post-translational modifications:
N-glycosylated1
A 50 kDa form is created by proteolytic cleavage1
REFSEQ proteins (2 alternative transcripts):
NP_001128530.1 NP_004077.1
ENSEMBL proteins: ENSP00000216361 ENSP00000379862 ENSP00000371933
Human Recombinant Proteins
2 Gene Ontology (GO) cellular component terms (GO ID links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005576 | extracellular region |
IEA | -- | | GO:0005578 | proteinaceous extracellular matrix |
IEA | -- |
About this table
COCH for ontologies About GeneDecksing
Antibodies for COCH:
Assays for COCH: |
Protein
Domains/
Families
for COCH gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
COCH for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry O43405ProtoNet protein and cluster: O43405 2 Blocks protein families: IPB002035 Von Willebrand factor type A domain signature IPB004043 LCCL domain
UniProtKB/Swiss-Prot: COCH_HUMAN, O43405Similarity: Contains 1 LCCL domainSimilarity: Contains 2 VWFA domains |
Gene Function
for COCH gene
(According to UniProtKB,
IUBMB,and/or
Genatlas, Animal models from MGI Dec 24 2010,
shRNA from
OriGene,
Sigma-Aldrich,
RNAi from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Clones from Millipore,
Sigma-Aldrich,
OriGene,
GenScript,
Sino Biological,
Cell Lines from GenScript,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene.)
About This Section
|
1 Gene Ontology (GO) molecular function term (GO ID links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005515 | protein binding |
IEA | -- |
About this table
COCH for ontologies About GeneDecksing
Animal Models: 2 MGI mutant phenotypes (inferred from 3 alleles ) (MGI details for Coch):
COCH for phenotypes About GeneDecksing
|
Pathways & Interactions
for COCH gene
(Pathways according to
Millipore,
Cell Signaling Technology,
Sigma-Aldrich,
KEGG
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
PCR Arrays from
SABiosciences,
Proteins Network according to
SABiosciences,
Sigma-Aldrich,
Interactions according to 1UniProtKB,
2MINT, and/or
3STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene).
About This Section
|
SABiosciences Custom Pathway-Focused PCR Arrays for COCH
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for COCH
3 Interacting proteins for COCH (O434052) via UniProtKB, MINT, and/or STRINGAbout this table
1 Gene Ontology (GO) biological process term (GO ID links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0007605 | sensory perception of sound |
IEA | -- |
About this table
COCH for ontologies About GeneDecksing
|
Drugs & Compounds
for COCH gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
Sigma-Aldrich, Tocris Bioscience, and/or
Novoseek and Drugs according to
Enzo Life Sciences and/or
PharmGKB)
About This Section
|
COCH for compounds About GeneDecksing
 Browse Tocris compounds for COCH
1  Novoseek chemical compound relationship for COCH gene
| Compound |
-log (P-Val) |
Hits |
PubMed IDs for Articles with Shared Sentences (# sentences) |
| cysteine |
0 |
2 |
16261627 (2) |
About this table
|
Transcripts
for COCH gene(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
non coding RNAs according to
RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from
Sigma-Aldrich,
OriGene,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Tagged/untagged cDNA clones from
OriGene,
Sigma-Aldrich,
GenScript,
Primers from
OriGene and/or
SABiosciences)
About This Section
|
REFSEQ mRNAs for COCH gene (2 alternative transcripts): NM_001135058.1 NM_004086.2 Additional cDNA sequence: AF006740.1 AK123362.1 AK130273.1 AK292724.1 AY358900.1 BC000640.2 BC007230.1 BC018827.2 CR611655.1 CR614743.1 U09203.1 20 DOTS entries: DT.91810438 DT.215769 DT.91736056 DT.99937247 DT.100732556 DT.100708572 DT.95276067 DT.92424962 DT.100661620 DT.120794834 DT.75131276 DT.100650407 DT.100699817 DT.100775399 DT.312608 DT.95359658 DT.100692422 DT.100719117 DT.92425860 DT.99970948 24/154 AceView cDNA sequences (see all 154): BC007230 AY358900 U09203 BU165034 BX375927 AK130273 BM763613 Z42204 AA411944 AV709175 BE259324 AA311438 AW198224 AA663103 BQ887456 CR611655 NM_004086 CD679268 CR614743 CD676547 BQ002467 AV717153 BU159461 H47370
 highest scoring ESTs for COCH:AF006740 AA016308 AA199816 AA203418 AA311438 AA411944 AA480780 AA626668 AA669336 AI669544 Unigene Cluster for COCH: Coagulation factor C homolog, cochlin (Limulus polyphemus) Hs.21016 [show with all ESTs]Unigene Representative Sequence: NM_001135058
GeneLoc Exon Structure
5/11 Alternative Splicing Database (ASD) splice patterns (SP) for COCH (see all 11)
| ExUns: | 1a | · | 1b | · | 1c | ^ | 2a | · | 2b | · | 2c | · | 2d | · | 2e | · | 2f | ^ | 3 | ^ | 4a | · | 4b | ^ | 5 | ^ | 6 | ^ | 7 | ^ | 8 | ^ | 9a | · | 9b | ^ | 10 | ^ | 11a | · | 11b | ^ | 12 | ^ | 13a | · | 13b |
|---|
|
| SP1: | | | | | | | - | | - | | | | - | | | | - | | - | | - | | | | | | | | | | | | | | | | - | | | | | | | | | | | | |
| SP2: | | | | | | | | | | | | | - | | | | - | | - | | - | | | | | | | | | | | | | | | | - | | | | | | | | | | | | |
| SP3: | | | | | | | | | | | | | | | - | | - | | - | | - | | | | | | | | | | | | | | | | - | | | | | | | | | | | | |
| SP4: | | | | | | | - | | - | | | | - | | | | - | | - | | - | | | | - | | - | | | | | | | | | | | | | | | | | | | | | | |
| SP5: | | | | | | | | | | | | | - | | | | - | | - | | - | | - | | - | | - | | | | | | | | | | - | | | | | | | | | | | |
About this scheme
ECgene alternative splicing isoforms for COCH
7 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000216361(uc001wqr.2 uc001wqp.2) ENST00000468826 ENST00000396618
ENST00000468444 ENST00000460581 ENST00000382493(uc001wqt.1) ENST00000475087(uc001wqq.3)
|
Expression
for COCH gene
(Experimental results according to
1GeneNote
and GNF BioGPS,
probe sets-to-genes annotations according to
2GeneAnnot ,
3GeneTide ,
Sets of similar genes according to GeneDecks,
Electronic Northern calculations according to data from
UniGene (Build 228 Homo sapiens),
SAGE tags according to
CGAP,
plus additional links to
SOURCE, and/or
GNF
BioGPS, and/or
EXPOLDB, and/or
UniProtKB,
Primers from
OriGene and/or
SABiosciences
)
About This Section
| COCH expression in normal and diseased human tissues
1 / 2 / 3 5 probe-sets matching COCH gene
Affymetrix
probe-set |
Array |
GeneAnnot data |
GeneNote data |
GeneTide data |
| # genes |
Sensitivity |
Specificity |
Correlation |
Length |
Gb_Accession |
Consensus |
Uniqueness |
Score |
Rank |
| 34190_at2, 3
|
U95-A |
1 |
1.00 |
1.00 |
1.00 |
1.00 |
AF006740 |
1.00 |
1.00 |
1.00 |
1 |
| 205229_s_at2, 3
|
U133-A |
1 |
1.00 |
1.00 |
-- |
-- |
AA669336 |
0.80 |
1.00 |
0.91 |
1 |
| 205229_s_at2
|
U133Plus2 |
1 |
1.00 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 1554242_a_at2
|
U133Plus2 |
1 |
1.00 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 1554241_at2
|
U133Plus2 |
1 |
0.36 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
About this table
COCH for expression About GeneDecksing
Data from
Genenote
(Publications) and GNF BioGPS
About these images
About these images
CGAP SAGE TAG: CCTACTAAAT
SOURCE GeneReport for Unigene cluster: Hs.21016
Expression variation in blood from EXPOLDB for COCH UniProtKB/Swiss-Prot: COCH_HUMAN, O43405Tissue specificity: Expressed in inner ear structures; the cochlea and the vestibule
SABiosciences Custom PCR Arrays for COCH
|
Orthologs
for COCH gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
and/or
5MGI Dec 24 2010,
with possible further links to
Flybase
and/or
WormBase,
Gene Trees according to Ensembl)
About This Section
|
Orthologs for COCH gene from 5/7 species (see all 7)
About this table Species with no ortholog for COCH
ENSEMBL Gene Tree for COCH (if available) |
Paralogs
for COCH gene(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section
| Paralogs for COCH gene
- MATN22 VIT2 MATN42 VWA22 MATN32 MATN12
COCH for paralogs About GeneDecksing
|
Genomic Variants
for COCH gene(SNPs according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Chr 14 pos | Sequence | Recs | AA
Chg | Type | More | Recs | Allele
freq | Pop | Total
sample | More |
|---|
About this tableHapMap Linkage Disequilibrium images for COCH (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for COCH
1 CNV: 7031 | | QIAGEN SeqTarget long-range PCR primers for resequencing COCH |
|
Disorders & Mutations
for COCH gene
(in which this Gene is Involved, According to
OMIM, UniProtKB,
Novoseek, PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
LSDB, HGMD, GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
COCH for disorders About GeneDecksing
OMIM: 603196 disorders: 601369 UniProtKB/Swiss-Prot: COCH_HUMAN, O43405
Defects in COCH are the cause of deafness autosomal dominant type 9 (DFNA9) [MIM:601369]. DFNA9 is a form ofsensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, thenerve pathways to the brain, or the area of the brain that receives sound information. DFNA9 is characterized by onsetin the fourth or fifth decade of life and initially involves the high frequencies. Deafness is progressive and usuallycomplete by the sixth decade. In addition to cochlear involvement, DFNA9 patients also exhibit a spectrum ofvestibular dysfunctions. Penetrance of the vestibular symptoms is often incomplete, and some patients are minimallyaffected, whereas others suffer from severe balance disturbances and episodes of vertigo. Affected individuals havemucopolysaccharide depositions in the channels of the cochlear and vestibular nerves. These depositions apparentlycause strangulation and degeneration of dendritic fibers
7 Novoseek disease relationships for COCH gene
| Disease |
-log (P-Val) |
Hits |
PubMed IDs for Articles with Shared Sentences (# sentences) |
| vestibular disorder |
78.8 |
10 |
11709536 (2), 11278165 (1), 14704763 (1), 14733925 (1) (see all 6) |
| hearing loss sensorineural |
78.2 |
12 |
16481359 (2), 10942145 (1), 10890144 (1), 14733925 (1) (see all 8) |
| menieres disease |
72 |
11 |
14704763 (2), 10400989 (2), 11278165 (1), 11698812 (1) |
| deafness sensorineural |
70.5 |
7 |
11709536 (2), 12843317 (1), 12928864 (1), 16374056 (1) |
| aqueous humor |
52.9 |
2 |
15862180 (1), 15579465 (1) |
| primary open angle glaucoma |
49.1 |
1 |
15579465 (1) |
| glaucoma |
45.7 |
9 |
16332271 (3), 15862180 (1), 16379021 (1), 17687037 (1) (see all 6) |
About this table
Locus Specific Mutation Databases (LSDB): COCH
Human Gene Mutation Database (HGMD): COCH
Human Genome Epidemiology (HuGE) Navigator: COCH (1 document)
Export disorders and mutations for COCH gene to outside databases
|
Medical News
for COCH gene(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications
for COCH gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6UniProtKB/TrEMBL, and/or
7Novoseek)
About This Section
|
10/75 PubMed articles for COCH gene, integrated from 7 sources (see all 75):
(articles sorted by number of sources associating them with COCH)- Mutations in a novel cochlear gene cause DFNA9, a human nonsyndromic deafness with vestibular dysfunction. (PubMed id 9806553)1, 2, 3 Robertson N.G.... Seidman J.G. (1998)
- Subcellular localisation, secretion, and post-translational processing of normal cochlin, and of mutants causing the sensorineural deafness and vestibular disorder, DFNA9. (PubMed id 12843317)1, 2, 7 Robertson N.G.... Morton C.C. (2003)
- Mutations in COCH that result in non-syndromic autosomal dominant deafness (DFNA9) affect matrix deposition of cochlin. (PubMed id 12928864)1, 2, 7 Grabski R....Sztul E. (2003)
- Cochlin isoforms and their interaction with CTL2 (SLC44A2) in the inner ear. (PubMed id 17926100)1, 2, 7 Kommareddi P.K.... Carey T.E. (2007)
- A Pro51Ser mutation in the COCH gene is associated with late onset autosomal dominant progressive sensorineural hearing loss with vestibular defects. (PubMed id 9931344)1, 2, 7 de Kok Y.J.M.... Cremers F.P.M. (1999)
- High prevalence of symptoms of Meniere's disease in three families with a mutation in the COCH gene. (PubMed id 10400989)1, 2, 7 Fransen E.... Van Camp G. (1999)
- Identification of a novel COCH mutation, I109N, highlights the similar clinical features observed in DFNA9 families. (PubMed id 11295836)1, 2, 7 Kamarinos M.... Dahl H.-H.M. (2001)
- NMR structure of the LCCL domain and implications for DFNA9 deafness disorder. (PubMed id 11574466)1, 2, 7 Liepinsh E.... Otting G. (2001)
- Mutations in the COCH gene are a frequent cause of autosomal dominant progressive cochleo-vestibular dysfunction, but not of Meniere's disease. (PubMed id 14512963)1, 2 Usami S.... Van Camp G. (2003)
- The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (2003)
|
External Searches for COCH gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing COCH gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing COCH gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing COCH gene(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| ATLAS Chromosomes in Cancer entry for COCH | Genetics and Cytogenetics in Oncology and Haematology | | Protein Spotlight | http://www.expasy.org/spotlight/back_issues/sptlt004.shtml | | Hereditary hearing loss homepage | http://webhost.ua.ac.be/hhh/ | | GeneReviews | http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COCH | | SeattleSNPs | http://pga.gs.washington.edu/data/coch/ |
|
| | |
About This Section
| Patent Information for COCH gene:
Search GeneIP for patents involving COCH
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for COCH gene(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or
Enzo Life Sciences)
About This Section
|
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