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Aliases & Descriptions for DFNB31
(According to
1 HGNC ,
2 Entrez Gene ,
3 UniProtKB/Swiss-Prot ,
4 UniProtKB/TrEMBL , 5 OMIM , 6 GeneLoc
, and/or 7 Ensembl ,
8 miRBase )About This Section
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Aliases CIP98 1 , 2 , 5 DKFZp434N014 2 KIAA1526 2 , 3 , 5 OTTHUMP00000021976 2 OTTHUMP00000021978 2 RP11-9M16.1 2 USH2D 1 , 2 , 5 WHRN 1 , 2 , 5 WI 2 whirlin 2
Descriptions Autosomal recessive deafness type 31 protein 3 CASK-interacting protein CIP98 2 deafness, autosomal recessive 31 2
Search outside databases for aliases for DFNB31 genePrevious GC identifers: GC09U990192 GC09M112541 GC09M114243
Summaries for DFNB31 (According to Entrez Gene ,
Wikipedia's
Gene Wiki ,
UniProtKB/Swiss-Prot ,
and/or
UniProtKB/TrEMBL )
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EntrezGene summary for DFNB31 : In rat brain, Cip98 interacts with a calmodulin-dependent serine kinase, CASK (MIM 300172), and maybe involved in the formation of scaffolding protein complexes that facilitate synaptictransmission in the central nervous system (CNS) (Yap et al., 2003 [PubMed 12641734]). Mutationsin this gene, also known as WHRN, cause DFNB31 (MIM 607084).[supplied by OMIM] UniProtKB/Swiss-Prot: WHRN_HUMAN, Q9P202 Function : Necessary for elongation and maintenance of inner and outer hair cell stereocilia in theorgan of Corti in the inner ear (By similarity)
Gene Wiki entry for DFNB31
Genomic Location for DFNB31
(According to
GeneLoc and/or
HGNC , and/or
Entrez Gene (NCBI build 36) ,
and/or miRBase ,
Genomic Views according to
UCSC and
Ensembl ,
Transcription factor binding sites according to
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Genomic View : UCSC Golden Path with GeneCards custom track Transcription factor binding sites upstream to the DFNB31 gene Entrez Gene cytogenetic band: 9q32-q34 Ensembl cytogenetic band: 9q32 HGNC cytogenetic band: 9q32-q34 DFNB31 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 9 GeneLoc Exon Structure
GeneLoc location for GC09M116204:
(about GC identifiers )
Start:
116,204,181 bp from pter
End:
116,307,557 bp from pter
Size:
103,377 bases
Orientation:
minus strand
RefSeq DNA sequence: NC_000009.10 NT_008470.18 Proteins for DFNB31
(According to
1 UniProtKB ,
and/or Ensembl ,
Phosphorylation sites according to 2 Phosphosite ,
RefSeq according to NCBI ,
PDB rendering according to OCA and/or Proteopedia ,
Recombinant Proteins
from Invitrogen ,
Millipore ,
Sigma-Aldrich ,
R&D Systems ,
Enzo Life Sciences ,
Abnova ,
OriGene and/or,
Abcam ,
Biochemical Assays by
Invitrogen ,
Millipore ,
R&D Systems ,
Cell Signaling Technology , and/or
Enzo Life Sciences ,
Ontologies according to Gene
Ontology Consortium 01 Apr 2009 and
Entrez Gene ,
Antibodies by Invitrogen ,
Millipore ,
Sigma-Aldrich ,
R&D Systems ,
Cell Signaling Technology ,
Abcam ,
Abnova , and/or
Novus Biologicals )
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UniProtKB/Swiss-Prot: WHRN_HUMAN, Q9P202 (See
protein sequence )Recommended Name: Whirlin Size : 907 amino acids; 96558 Da
Subunit : Forms homooligomers. Binds CASK, MPP1/p55 and MYO15A via the C-terminal PDZ domain.Binding to MYO15A is necessary for localization of WHRN to stereocilia tips. Interacts with USH2A,GPR98/MASS1 and LRRC4C/NGL1
Subcellular location : Cytoplasm (By similarity). Cell projection, stereocilium (By similarity).Cell projection, growth cone (By similarity). Note=Detected at the level of stereocilia in innerouter hair cells of the cochlea and vestibule. Co-localizes with the growing ends of actinfilaments (By similarity)
PDB structures from and Proteopedia : 1UEZ (3D)
 1UF1 (3D)
 1UFX (3D)
 
Secondary accessions : A5PKU1 A5PKZ9 Q5TAU9 Q5TAV0 Q96MZ9 Q9H9F4 Q9UFZ3Alternative splicing : 4 isoforms : Q9P202-1 Q9P202-2 Q9P202-3 Q9P202-4
Post-translational modifications:
View phosphorylation sites using PhosphoSite 2
REFSEQ proteins (2 alternative transcripts):
NP_001077354.1 NP_056219.2 ENSEMBL proteins: ENSP00000354623 ENSP00000363172 ENSP00000363170 ENSP00000265134 Human Recombinant Proteins Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 3 Gene Ontology (GO) cellular component terms (links to tree view) :
About this table Antibodies for DFNB31: Assays for DFNB31:
Protein
Domains/ Families for DFNB31(According to InterPro , ProtoNet ,
UniProtKB , and/or BLOCKS ,
Sets of similar genes according to GeneDecks )
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Graphical View of Domain Structure for InterPro Entry Q9P202 ProtoNet protein and cluster: Q9P202
UniProtKB/Swiss-Prot: WHRN_HUMAN, Q9P202 Similarity : Contains 3 PDZ (DHR) domains
Gene Function for DFNB31
(According to MGI Jun 06 2009, UniProtKB ,
IUBMB ,and/or Genatlas ,
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Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene .)
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               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 3 ): XM_027012 Applied Biosystems Silencer ® siRNAs for DFNB31 Sigma-Aldrich siRNA for DFNB31 Sigma-Aldrich shRNA for DFNB31 Explore Sigma-Aldrich super-pooled esiRNAs                OriGene GFP tagged cDNA clones in CMV expression vector (see all 2 ): NM_001083885                                  Myc/DDK tagged cDNA clones in CMV expression vector (see all 2 ): NM_001083885                                  untagged cDNA clones in CMV expression vector (see all 2 ): NM_001083885  Primers: Browse
Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers               OriGene genome-wide validated SYBR primer pairs: NM_015404 UniProtKB/Swiss-Prot: WHRN_HUMAN, Q9P202 Function : Necessary for elongation and maintenance of inner and outer hair cell stereocilia in theorgan of Corti in the inner ear (By similarity)
13 MGI mutant phenotypes (inferred from 1 allele ) (MGI details for Whrn) :1 Gene Ontology (GO) molecular function term (links to tree view) :
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Pathways & Interactions for DFNB31
(Pathways according to Invitrogen
(maps by GeneGo ),
Millipore ,
Cell Signaling Technology ,
Sigma-Aldrich ,
KEGG
and/or UniProtKB ,
Sets of similar genes according to GeneDecks ,
Proteins Network according to
SABiosciences ,
Interactions according to 1 UniProtKB ,
2 MINT , and/or
3 STRING ,
with links to IntAct and
Ensembl ,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene .)
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5/8 Interacting proteins for DFNB31 (ENSP00000354623 3 ) via UniProtKB, MINT, and/or STRING (see all 8
)About this table 5 Gene Ontology (GO) biological process terms (links to tree view) :
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Drugs & Compounds for DFNB31 (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 )
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Browse Tocris compounds for DFNB31 1 Novoseek chemical compound relationship for DFNB31 gene
Compound
Score
Articles
PubMed IDs for Articles with Shared Sentences (# sentences)
guanylate
49.20
2
12641734 (1), 16829577 (1)
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Transcripts for DFNB31(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 219 Homo sapiens; Jun 2 2009) or GenBank , RefSeq according to Entrez Gene ,
DOTS (version 10), and/or
AceView ,
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 Invitrogen ,
Millipore , and/or
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               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 3 ): XM_027012 Sigma-Aldrich siRNA for DFNB31 Sigma-Aldrich shRNA for DFNB31 Explore Sigma-Aldrich super-pooled esiRNAs
Applied Biosystems Silencer ® siRNAs: NM_001083885 NM_015404
REFSEQ mRNAs for DFNB31 gene (2 alternative transcripts): NM_001083885.1 NM_015404.2
Applied Biosystems TaqMan ® Gene Expression Assays: NM_001083885 NM_015404
               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2 ): NM_001083885                                  Myc/DDK tagged cDNA clones in CMV expression vector (see all 2 ): NM_001083885                                  untagged cDNA clones in CMV expression vector (see all 2 ): NM_001083885  
Additional cDNA sequence: AB040959.1 AK022854.1 AK056190.1 AL110228.1 BC011918.2 BC014524.1 BC136416.1 BC142614.1 BC142684.1
12 DOTS entries : DT.444082 DT.91744357 DT.121168256 DT.100744759 DT.91741714 DT.100744760 DT.121168276 DT.121168280 DT.121168282 DT.91741712 DT.91741713 DT.95232238
24/96 AceView cDNA sequences (see all 96
):AI669619 CA428581 AW246635 BG983396 AK056190 AL557526 BQ636975 AA746058 BM725795 NM_015404 AA938876 AI627755 BQ772091 AA317697 BM677917 BE890168 BQ773251 AI122701 AA378757 BM714728 BX329269 BQ668361 BI767551 BC011918
highest scoring ESTs for DFNB31 :AA813332 AB040959 AK056190 AL555201 BC014524 BE890168 BF969269 BM737698 BM738414 BM743995
Unigene Cluster for DFNB31: Deafness, autosomal recessive 31 Hs.93836 [show with all ESTs ] Unigene Representative Sequence: BC014524 GeneLoc Exon Structure 5/11 Alternative Splicing Database (ASD) splice patterns (SP) for DFNB31 (see all 11
) ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c · 13d ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b ^ 18a · SP1 :             -   -   -     -   -   -     -           -         -       SP2 :                                               -       SP3 :                 -     -   -   -     -                         SP4 :                     -   -   -     -                         SP5 :                             -   -   -   -   -   -              
ExUns: 18b ^ 19 ^ 20 ^ 21 SP1 :         SP2 :         SP3 :         SP4 :         SP5 :        
About this scheme ECgene alternative splicing isoforms for DFNB31 4 Ensembl transcripts including schematic representations : ENST00000362057
ENST00000374059
ENST00000374057
ENST00000265134
Expression for DFNB31
(Experimental results according to
1 GeneNote
and GNF BioGPS ,
probe sets-to-genes annotations according to
2 GeneAnnot ,
3 GeneTide ,
Sets of similar genes according to GeneDecks ,
Electronic Northern calculations according to data from
UniGene (Build 219 Homo sapiens),
SAGE tags according to
CGAP ,
plus additional links to
SOURCE , and/or
GNF
BioGPS , and/or
EXPOLDB , and/or
UniProtKB ,
Expression Assays from
Applied Biosystems
)
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DFNB31 expression in normal and diseased human tissues Applied Biosystems TaqMan ® Gene Expression Assays for DFNB31 1 / 2 / 3
5 probe-sets matching DFNB31 gene Data from
(Publications) and GNF BioGPS About these images About these images CGAP SAGE TAG: CCCCTGGGGASOURCE GeneReport for Unigene cluster: Hs.93836
Orthologs for DFNB31
(Orthologs according to
1,2 HomoloGene (2 older version, for species not in 1 newer version),
3 euGenes ,
4 SGD
and/or
5 MGI Jun 06 2009,
with possible further links to
Flybase
and/or
WormBase ,
Gene Trees according to Ensembl )
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Orthologs for DFNB31 gene from 5/7 species (see all 7
)
About this table Species with no ortholog for DFNB31 ENSEMBL Gene Tree for DFNB31 Paralogs for DFNB31 (Paralogs according to 1 HomoloGene and 2 Ensembl , Pseudogenes according to 3 Pseudogene.org )About This Section
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Paralogs for DFNB31 gene PDZD7 2 USH1C 2
SNPs/Variants for DFNB31 (According to the
1 NCBI SNP Database ,
2 Ensembl ,
3 PupaSUITE , and
UniProtKB ,
Linkage Disequilibrium by HapMap ,
Genotyping Reagents from
Applied Biosystems )
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HapMap Linkage Disequilibrium images for DFNB31 (up to first 250kb)
Disorders & Mutations for DFNB31
(in which this Gene is Involved, According to
OMIM, UniProtKB ,
PharmGKB ,
Genatlas , GeneTests ,
Blood group antigen gene mutations by BGMUT ,
HGMD, GAD ,
HuGE Navigator ,
BCGD ,
and/or TGDB .)
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OMIM: 607928 disorders : 607084 611383 UniProtKB/Swiss-Prot: WHRN_HUMAN, Q9P202
Defects in WHRN are the cause of non-syndromic sensorineural deafness autosomal recessivetype 31 (DFNB31) [MIM:607084]. DFNB31 is a form of sensorineural hearing loss. Sensorineuraldeafness results from damage to the neural receptors of the inner ear, the nerve pathways to thebrain, or the area of the brain that receives sound information Defects in WHRN are the cause of Usher syndrome type 2D (USH2D) [MIM:611383]. USH is agenetically heterogeneous condition characterized by the association of retinitis pigmentosa andsensorineural deafness. Age at onset and differences in auditory and vestibular functiondistinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3(USH3). USH2 is characterized by congenital mild hearing impairment with normal vestibularresponses
GeneTests: DFNB31 Usher Syndrome Type 2 Human Gene Mutation Database : DFNB31 Human Genome Epidemiology Navigator: DFNB31 (1 document)
Medical News for DFNB31 (Possibly Related Articles in
Doctor's Guide )
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--
Publications for DFNB31 (in
PubMed .
Associations of this gene to articles via
1 Novoseek ,
2 HGNC ,
3 Entrez Gene ,
4 UniProtKB/Swiss-Prot ,
5 UniProtKB/TrEMBL ,
6 GAD , and/or
7 PharmGKB )
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10/22 PubMed articles for DFNB31 gene (see all 22
): A novel gene for Usher syndrome type 2: mutations in the long isoform of whirlin are associated with retinitis pigmentosa and sensorineural hearing loss. (PubMed id 17171570) 1, 2, 3, 4 Ebermann I....Bolz H. (2007) Defects in whirlin, a PDZ domain molecule involved in stereocilia elongation, cause deafness in the whirler mouse and families with DFNB31. (PubMed id 12833159) 1, 2, 3, 4 Mburu P.... Brown S.D. (2003) The DFNB31 gene product whirlin connects to the Usher protein network in the cochlea and retina by direct association with USH2A and VLGR1. (PubMed id 16434480) 1, 3, 4 van Wijk E....Kremer H. (2006) Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039) 3, 4 Ota T....Sugano S. (2004) DFNB31, a recessive form of sensorineural hearing loss, maps to chromosome 9q32-34. (PubMed id 11973626) 3, 4 Mustapha M....Petit C. (2002) Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10819331) 3, 4 Nagase T....Ohara O. (2000) CIP98, a novel PDZ domain protein, is expressed in the central nervous system and interacts with calmodulin-dependent serine kinase. (PubMed id 12641734) 1, 3 Yap C.C....Yano R. (2003) Identification of a novel frameshift mutation in the DFNB31/WHRN gene in a Tunisian consanguineous family with hereditary non-syndromic recessive hearing loss. (PubMed id 15841483) 1, 4 Tlili A.... Ayadi H. (2005) Findings from bipolar disorder genome-wide association studies replicate in a Finnish bipolar family-cohort. (PubMed id 19308021) 3 Ollila H.M....Paunio T. (2009) Automated phosphoproteome analysis for cultured cancer cells by two- dimensional nanoLC-MS using a calcined titania/C18 biphasic column. (PubMed id 18187866) 4 Imami K.... Ishihama Y. (2008)
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Genome Databases showing DFNB31
(According to
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Ensembl ,
miRBase ,
ECgene ,
and/or
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Other Databases showing DFNB31
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Specialized Databases showing DFNB31 (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
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Name Description
Hereditary hearing loss homepage http://webhost.ua.ac.be/hhh/
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-- Services for DFNB31 (Reagents available from Applied Biosystems , Antibodies and assays by Cell
Signaling Technology , Abcam , Novus Biologicals ,Sigma-Aldrich , R&D Systems , Millipore , Abnova , and/or Invitrogen , Clones available from OriGene ,and/or Invitrogen , Drugs and/or compounds by Sigma-Aldrich , Enzo Life Sciences , and/or Tocris Bioscience )About This Section
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