Ush1c (USH1 protein network component harmonin) - Rat Genome Database

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Gene: Ush1c (USH1 protein network component harmonin) Mus musculus
Analyze
Symbol: Ush1c
Name: USH1 protein network component harmonin
RGD ID: 1553848
MGI Page MGI
Description: Predicted to enable myosin tail binding activity and spectrin binding activity. Involved in brush border assembly; protein localization to microvillus; and regulation of microvillus length. Acts upstream of or within several processes, including inner ear development; parallel actin filament bundle assembly; and sensory perception of sound. Located in several cellular components, including brush border; photoreceptor inner segment; and upper tip-link density. Is active in stereocilium. Is expressed in several structures, including alimentary system; cochlea; genitourinary system; heart; and lung epithelium. Used to study Usher syndrome type 1C and autosomal recessive nonsyndromic deafness 18A. Human ortholog(s) of this gene implicated in Usher syndrome; Usher syndrome type 1; Usher syndrome type 1C; and autosomal recessive nonsyndromic deafness 18A. Orthologous to human USH1C (USH1 protein network component harmonin).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 2010016F01Rik; ha; harmonin; PDZ domain-containing protein; Usher syndrome 1C; Usher syndrome 1C homolog; usher syndrome type-1C protein homolog
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39745,844,774 - 45,887,984 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl745,844,774 - 45,887,927 (-)EnsemblGRCm39 Ensembl
GRCm38746,195,350 - 46,238,490 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl746,195,350 - 46,238,503 (-)EnsemblGRCm38mm10GRCm38
MGSCv37753,450,721 - 53,493,860 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36746,063,399 - 46,106,532 (-)NCBIMGSCv36mm8
Celera741,668,925 - 41,712,073 (-)NCBICelera
Cytogenetic Map7B3NCBI
cM Map729.66NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal cochlear hair bundle tip links morphology  (IAGP)
abnormal cochlear hair cell inter-stereocilial links morphology  (IAGP)
abnormal cochlear hair cell morphology  (IAGP)
abnormal cochlear hair cell stereociliary bundle morphology  (IAGP)
abnormal cochlear outer hair cell morphology  (IAGP)
abnormal colon morphology  (IAGP)
abnormal electroretinogram waveform feature  (IAGP)
abnormal enterocyte morphology  (IAGP)
abnormal hair cell mechanoelectric transduction  (IAGP)
abnormal inner hair cell stereociliary bundle morphology  (IAGP)
abnormal intestinal epithelium morphology  (IAGP)
abnormal orientation of cochlear hair cell stereociliary bundles  (IAGP)
abnormal orientation of inner hair cell stereociliary bundles  (IAGP)
abnormal orientation of outer hair cell stereociliary bundles  (IAGP)
abnormal outer hair cell stereociliary bundle morphology  (IAGP)
abnormal small intestine morphology  (IAGP)
absent pinna reflex  (IAGP)
circling  (IAGP)
cochlear ganglion degeneration  (IAGP)
cochlear inner hair cell degeneration  (IAGP)
cochlear outer hair cell degeneration  (IAGP)
deafness  (IAGP)
decreased circulating amylase level  (IEA)
decreased circulating glucose level  (IEA)
decreased grip strength  (IEA)
decreased small intestinal microvillus size  (IAGP)
decreased total body fat amount  (IEA)
head bobbing  (IEA)
head tossing  (IAGP)
hyperactivity  (IAGP)
impaired balance  (IAGP)
impaired righting response  (IEA)
impaired swimming  (IAGP)
improved glucose tolerance  (IEA)
increased bone mineral content  (IEA)
increased circulating chloride level  (IEA)
increased circulating sodium level  (IEA)
increased food intake  (IEA)
increased lean body mass  (IEA)
increased or absent threshold for auditory brainstem response  (IAGP)
increased red blood cell distribution width  (IEA)
limb grasping  (IEA)
organ of Corti degeneration  (IAGP)
retina degeneration  (IAGP)
stereotypic behavior  (IEA)
trunk curl  (IEA)
vestibular hair cell degeneration  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. Myosin VIIa, harmonin and cadherin 23, three Usher I gene products that cooperate to shape the sensory hair cell bundle. Boeda B, etal., EMBO J 2002 Dec 16;21(24):6689-99.
2. Deafblindness in French Canadians from Quebec: a predominant founder mutation in the USH1C gene provides the first genetic link with the Acadian population. Ebermann I, etal., Genome Biol. 2007;8(4):R47.
3. Mechanotransduction by hair cells: models, molecules, and mechanisms. Gillespie PG and Muller U, Cell. 2009 Oct 2;139(1):33-44. doi: 10.1016/j.cell.2009.09.010.
4. Mouse models of USH1C and DFNB18: phenotypic and molecular analyses of two new spontaneous mutations of the Ush1c gene. Johnson KR, etal., Hum Mol Genet. 2003 Dec 1;12(23):3075-86. Epub 2003 Sep 30.
5. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
6. Sensing sound: molecules that orchestrate mechanotransduction by hair cells. Kazmierczak P and Muller U, Trends Neurosci. 2012 Apr;35(4):220-9. doi: 10.1016/j.tins.2011.10.007. Epub 2011 Dec 15.
7. Exome sequencing identifies a founder frameshift mutation in an alternative exon of USH1C as the cause of autosomal recessive retinitis pigmentosa with late-onset hearing loss. Khateb S, etal., PLoS One. 2012;7(12):e51566. doi: 10.1371/journal.pone.0051566. Epub 2012 Dec 12.
8. Deafness and retinal degeneration in a novel USH1C knock-in mouse model. Lentz JJ, etal., Dev Neurobiol. 2010 Mar;70(4):253-67. doi: 10.1002/dneu.20771.
9. Rescue of hearing and vestibular function by antisense oligonucleotides in a mouse model of human deafness. Lentz JJ, etal., Nat Med. 2013 Mar;19(3):345-50. doi: 10.1038/nm.3106. Epub 2013 Feb 4.
10. MGDs mouse GO annotations MGD data from the GO Consortium
11. MGD IEA MGD IEA
12. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
13. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
14. Mutations in the alternatively spliced exons of USH1C cause non-syndromic recessive deafness. Ouyang XM, etal., Hum Genet. 2002 Jul;111(1):26-30. Epub 2002 Jun 18.
15. Differential distribution of harmonin isoforms and their possible role in Usher-1 protein complexes in mammalian photoreceptor cells. Reiners J, etal., Invest Ophthalmol Vis Sci 2003 Nov;44(11):5006-15.
16. Mouse MP Annotation Import Pipeline RGD automated import pipeline
17. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
19. Mutations in the USH1C gene associated with sector retinitis pigmentosa and hearing loss. Saihan Z, etal., Retina. 2011 Sep;31(8):1708-16. doi: 10.1097/IAE.0b013e31820d3fd1.
20. Ush1c gene expression levels in the ear and eye suggest different roles for Ush1c in neurosensory organs in a new Ush1c knockout mouse. Tian C, etal., Brain Res. 2010 Apr 30;1328:57-70. doi: 10.1016/j.brainres.2010.02.079. Epub 2010 Mar 6.
21. A defect in harmonin, a PDZ domain-containing protein expressed in the inner ear sensory hair cells, underlies Usher syndrome type 1C. Verpy E, etal., Nat Genet. 2000 Sep;26(1):51-5.
22. Photoreceptor degeneration: genetic and mechanistic dissection of a complex trait. Wright AF, etal., Nat Rev Genet. 2010 Apr;11(4):273-84. doi: 10.1038/nrg2717.
23. Identification of three novel mutations in the USH1C gene and detection of thirty-one polymorphisms used for haplotype analysis. Zwaenepoel I, etal., Hum Mutat. 2001;17(1):34-41.
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11138009   PMID:12407180   PMID:12477932   PMID:12588794   PMID:15177554   PMID:15461667   PMID:15489334   PMID:15590703   PMID:15747579  
PMID:15928608   PMID:16141072   PMID:16141073   PMID:16219682   PMID:16301216   PMID:16301217   PMID:16464467   PMID:16481439   PMID:16545802   PMID:17174357   PMID:17906286   PMID:18339676  
PMID:18554416   PMID:18849963   PMID:19028668   PMID:19324851   PMID:19447093   PMID:19756723   PMID:20016102   PMID:20058854   PMID:20111592   PMID:20332152   PMID:20505086   PMID:20639393  
PMID:20671281   PMID:21156003   PMID:21165971   PMID:21267068   PMID:21436032   PMID:21677750   PMID:21822269   PMID:21873635   PMID:22114352   PMID:22381527   PMID:22808246   PMID:23217710  
PMID:23613530   PMID:23704327   PMID:24239741   PMID:24721909   PMID:24725409   PMID:26620972   PMID:26754646   PMID:28031293   PMID:28633508   PMID:29037661   PMID:29386551   PMID:30275467  
PMID:30973865   PMID:31448880   PMID:31776257   PMID:32249312   PMID:32290105   PMID:38355793  


Genomics

Comparative Map Data
Ush1c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39745,844,774 - 45,887,984 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl745,844,774 - 45,887,927 (-)EnsemblGRCm39 Ensembl
GRCm38746,195,350 - 46,238,490 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl746,195,350 - 46,238,503 (-)EnsemblGRCm38mm10GRCm38
MGSCv37753,450,721 - 53,493,860 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36746,063,399 - 46,106,532 (-)NCBIMGSCv36mm8
Celera741,668,925 - 41,712,073 (-)NCBICelera
Cytogenetic Map7B3NCBI
cM Map729.66NCBI
USH1C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381117,493,900 - 17,544,416 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1117,493,895 - 17,544,416 (-)EnsemblGRCh38hg38GRCh38
GRCh371117,515,447 - 17,565,963 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361117,472,018 - 17,522,539 (-)NCBINCBI36Build 36hg18NCBI36
Celera1117,645,289 - 17,695,946 (-)NCBICelera
Cytogenetic Map11p15.1NCBI
HuRef1117,199,243 - 17,249,828 (-)NCBIHuRef
CHM1_11117,515,265 - 17,565,784 (-)NCBICHM1_1
T2T-CHM13v2.01117,591,495 - 17,642,149 (-)NCBIT2T-CHM13v2.0
Ush1c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81105,831,719 - 105,880,082 (-)NCBIGRCr8
GRCr8 Ensembl1105,831,723 - 105,880,082 (-)EnsemblGRCr8 Ensembl
mRatBN7.2196,695,303 - 96,743,671 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl196,695,307 - 96,743,671 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1102,081,448 - 102,129,809 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01110,553,421 - 110,601,783 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01103,843,796 - 103,892,162 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01102,207,096 - 102,256,779 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1102,207,096 - 102,255,459 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01103,291,318 - 103,340,928 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4196,720,185 - 96,768,550 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera190,943,948 - 90,992,307 (-)NCBICelera
RGSC_v3.1196,798,295 - 96,846,661 (-)NCBI
Cytogenetic Map1q22NCBI
Ush1c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541432,298,759 - 32,351,505 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541432,303,045 - 32,351,401 (-)NCBIChiLan1.0ChiLan1.0
USH1C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2919,827,448 - 19,877,874 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11119,787,920 - 19,838,443 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01117,548,501 - 17,598,923 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11117,233,854 - 17,284,256 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1117,233,854 - 17,284,256 (-)Ensemblpanpan1.1panPan2
USH1C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12140,055,786 - 40,100,685 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2140,055,730 - 40,101,430 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2139,555,651 - 39,600,543 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02141,161,015 - 41,205,900 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2141,160,539 - 41,205,845 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12140,173,714 - 40,218,550 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02140,380,893 - 40,425,786 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02140,719,734 - 40,764,634 (-)NCBIUU_Cfam_GSD_1.0
Ush1c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494745,513,303 - 45,560,765 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365281,552,289 - 1,594,801 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365281,552,175 - 1,594,740 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USH1C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl241,593,802 - 41,647,247 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1241,593,793 - 41,646,777 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2244,613,841 - 44,706,204 (+)NCBISscrofa10.2Sscrofa10.2susScr3
USH1C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1147,428,181 - 47,477,578 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl147,437,596 - 47,477,834 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666038144,848,688 - 144,898,245 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ush1c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247669,105,990 - 9,153,663 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247669,097,466 - 9,153,602 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ush1c
2941 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:2414
Count of miRNA genes:576
Interacting mature miRNAs:672
Transcripts:ENSMUST00000009667, ENSMUST00000078680, ENSMUST00000129266, ENSMUST00000143155, ENSMUST00000148527, ENSMUST00000154292, ENSMUST00000176371, ENSMUST00000177212
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
25314307Mlh1fc2_mMLH1 foci count 2 (mouse)76502999133501729Mouse
4141566Femwf8_mfemur work to failure 8 (mouse)Not determined1303248547032621Mouse
1301969Lbw5_mlupus NZB x NZW 5 (mouse)Not determined72684761560851775Mouse
38501071Stsl6_mSalmonella typhimurium susceptibility locus 6 (mouse)73419942551149748Mouse
1357586Mdmsc3_mmodifier of muscularity 3 (mouse)Not determined73444786968448018Mouse
38501068Tip1_mtuberculosis immunophenotype 1, spleen CFU (mouse)7360299972549748Mouse
39128210Lwq19_mliver weight QTL 19 (mouse)73349772758148965Mouse
11252140Fdr1_mfat response to dietary restriction 1 (mouse)74114882075148965Mouse
25314314Sccor1_msynaptonemal complex length to mean MLH1 count ratio 1 (mouse)71333392547349748Mouse
1357469Kidq5_mkidney weight QTL 5 (mouse)Not determined73349772758148965Mouse
1301082Bbaa16_mB.burgdorferi-associated arthritis 16 (mouse)Not determined736280015116416877Mouse
4142003W3q10_mweight 3 weeks QTL 10 (mouse)Not determined3349772758148965Mouse
12790989Tgl6_mtriglyceride 6 (mouse)72754054961540549Mouse
1559000Ossc1_mosteosarcoma susceptibility 1 (mouse)Not determined73405302568053223Mouse
10043926Bw1n_mbody weight 1 in NSY (mouse)Not determined745161966118693530Mouse
11522751Cocia17_mcocaine-induced activity, QTL 17 (mouse)71313520447135204Mouse
12792978Fbmd3_mfemoral bone mineral density 3, females only (mouse)77050288142367832Mouse
4141805Sle19_msystematic lupus erythematosus susceptibility 19 (mouse)Not determined3003248581135653Mouse
1357634Splq7_mspleen weight QTL 7 (mouse)Not determined73349772758148965Mouse
4141929Chlq18_mcirculating hormone level QTL 18 (mouse)Not determined74114882075148965Mouse
1300996Aorls2_maortic lesion size 2 (mouse)Not determined73239453266394681Mouse
10449158Eosn3_meosinophil differential 3 (mouse)71248087746480877Mouse
1301514Rigs1_mradiation induced gastroschisis 1 (mouse)Not determined73628001592394346Mouse
1300878Skts1_mskin tumor susceptibility 1 (mouse)Not determined73789138671891582Mouse
1301709Bdt4_mbone density traits 4 (mouse)Not determined72288857256888716Mouse
1300722Sle3_msystemic lupus erythmatosus susceptibility 3 (mouse)Not determined7351172887142720Mouse
12904742Litsq2_mlitter size QTL 2 (mouse)72267388756674033Mouse
1301175Ap7q_malcohol preference 7 QTL (mouse)Not determined73171484565715077Mouse
1300791Abbp3_mA/J and C57BL/6 blood pressure 3 (mouse)Not determined739673887103510010Mouse
1301622Eae12_msusceptibility to experimental allergic encephalomyelitis 12 (mouse)Not determined71928001553280104Mouse
11354952Pdcc1_mplasmacytoid dentritic cell compartment 1 (mouse)72306653157066531Mouse
12880417V125Dq5_mvitamin D active form serum level QTL 5 (mouse)74524974879249748Mouse
10402488Dipa2_mdrug induced psychomotor activation 2 (mouse)Not determined73842154872421684Mouse
4142102Tailq5_mtail length QTL 5 (mouse)Not determined3349772758148965Mouse
4141909W10q18_mweight 10 weeks QTL 18 (mouse)Not determined3349772758148965Mouse
10449139Eosn1_meosinophil differential 1 (mouse)71248087746480877Mouse
26884404Huml1_mhumerus length 1, 5 week (mouse)730199425108999207Mouse
1301052Bhr6_mbronchial hyperresponsiveness 6 (mouse)Not determined71984225053842367Mouse
1357883Epfq5_mepididymal fat pad weight QTL 5 (mouse)Not determined73349772758148965Mouse
10045622Heal20_mwound healing/regeneration 20 (mouse)Not determined73431688768317043Mouse
1301158Eae4_msusceptibility to experimental allergic encephalomyelitis 4 (mouse)Not determined719147398141919804Mouse
4142218W6q17_mweight 6 weeks QTL 17 (mouse)Not determined3349772758148965Mouse
10412199Sst2_msusceptibility to tuberculosis 2 (mouse)Not determined718728794119485380Mouse
25314303Vmm4_mvariable multisystem mineralization 4, kidney (mouse)73729942587049208Mouse
1559016Drsi_mDCC-related Spp1 induction (mouse)Not determined71663729349159331Mouse
25314301Vmm3_mvariable multisystem mineralization 3, lung (mouse)73729942572049748Mouse

Markers in Region
Ush1c  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map7B4UniSTS
cM Map729.66UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000009667   ⟹   ENSMUSP00000009667
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl745,844,781 - 45,887,927 (-)Ensembl
GRCm38.p6 Ensembl746,195,357 - 46,238,503 (-)Ensembl
Ensembl Acc Id: ENSMUST00000078680   ⟹   ENSMUSP00000077747
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl745,844,774 - 45,887,916 (-)Ensembl
GRCm38.p6 Ensembl746,195,350 - 46,238,492 (-)Ensembl
Ensembl Acc Id: ENSMUST00000129266
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl745,845,094 - 45,851,194 (-)Ensembl
GRCm38.p6 Ensembl746,195,670 - 46,201,770 (-)Ensembl
Ensembl Acc Id: ENSMUST00000143155   ⟹   ENSMUSP00000119676
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl745,844,781 - 45,887,914 (-)Ensembl
GRCm38.p6 Ensembl746,195,357 - 46,238,490 (-)Ensembl
Ensembl Acc Id: ENSMUST00000148527
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl745,850,450 - 45,869,191 (-)Ensembl
GRCm38.p6 Ensembl746,201,026 - 46,219,767 (-)Ensembl
Ensembl Acc Id: ENSMUST00000154292   ⟹   ENSMUSP00000114494
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl745,845,055 - 45,887,888 (-)Ensembl
GRCm38.p6 Ensembl746,195,631 - 46,238,464 (-)Ensembl
Ensembl Acc Id: ENSMUST00000176371   ⟹   ENSMUSP00000134783
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl745,845,075 - 45,879,738 (-)Ensembl
GRCm38.p6 Ensembl746,195,651 - 46,230,314 (-)Ensembl
Ensembl Acc Id: ENSMUST00000177212   ⟹   ENSMUSP00000135734
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl745,845,074 - 45,887,922 (-)Ensembl
GRCm38.p6 Ensembl746,195,650 - 46,238,498 (-)Ensembl
Ensembl Acc Id: ENSMUST00000238793   ⟹   ENSMUSP00000158923
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl745,872,243 - 45,880,007 (-)Ensembl
GRCm38.p6 Ensembl746,222,819 - 46,230,583 (-)Ensembl
RefSeq Acc Id: NM_001163733   ⟹   NP_001157205
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39745,844,775 - 45,887,914 (-)NCBI
GRCm38746,195,351 - 46,238,490 (-)NCBI
MGSCv37753,450,721 - 53,493,860 (-)RGD
Celera741,668,925 - 41,712,073 (-)RGD
cM Map7 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_001291182   ⟹   NP_001278111
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39745,844,775 - 45,887,914 (-)NCBI
GRCm38746,195,351 - 46,238,490 (-)NCBI
Celera741,668,925 - 41,712,073 (-)NCBI
Sequence:
RefSeq Acc Id: NM_023649   ⟹   NP_076138
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39745,844,775 - 45,887,914 (-)NCBI
GRCm38746,195,351 - 46,238,490 (-)NCBI
MGSCv37753,450,721 - 53,493,860 (-)RGD
Celera741,668,925 - 41,712,073 (-)RGD
cM Map7 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_153677   ⟹   NP_710143
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39745,844,775 - 45,887,914 (-)NCBI
GRCm38746,195,351 - 46,238,490 (-)NCBI
MGSCv37753,450,721 - 53,493,860 (-)RGD
Celera741,668,925 - 41,712,073 (-)RGD
cM Map7 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006541212   ⟹   XP_006541275
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39745,844,774 - 45,886,757 (-)NCBI
GRCm38746,195,350 - 46,237,334 (-)NCBI
Sequence:
RefSeq Acc Id: XM_036153453   ⟹   XP_036009346
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39745,859,875 - 45,887,984 (-)NCBI
Sequence:
RefSeq Acc Id: NP_710143   ⟸   NM_153677
- Peptide Label: isoform b3
- UniProtKB: Q9ES65 (UniProtKB/Swiss-Prot),   Q9CVG7 (UniProtKB/Swiss-Prot),   Q91XD1 (UniProtKB/Swiss-Prot),   Q9ES64 (UniProtKB/Swiss-Prot),   E9QMN1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_076138   ⟸   NM_023649
- Peptide Label: isoform a1
- UniProtKB: A0A0R4J0Z8 (UniProtKB/TrEMBL),   H3BLC4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001157205   ⟸   NM_001163733
- Peptide Label: isoform b4
- UniProtKB: E9PYX1 (UniProtKB/TrEMBL),   Q6XA19 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006541275   ⟸   XM_006541212
- Peptide Label: isoform X1
- UniProtKB: H3BIZ2 (UniProtKB/TrEMBL),   H3BLC4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001278111   ⟸   NM_001291182
- Peptide Label: isoform b2
- UniProtKB: D6RIM8 (UniProtKB/TrEMBL),   Q6XA19 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000119676   ⟸   ENSMUST00000143155
Ensembl Acc Id: ENSMUSP00000135734   ⟸   ENSMUST00000177212
Ensembl Acc Id: ENSMUSP00000009667   ⟸   ENSMUST00000009667
Ensembl Acc Id: ENSMUSP00000158923   ⟸   ENSMUST00000238793
Ensembl Acc Id: ENSMUSP00000114494   ⟸   ENSMUST00000154292
Ensembl Acc Id: ENSMUSP00000077747   ⟸   ENSMUST00000078680
Ensembl Acc Id: ENSMUSP00000134783   ⟸   ENSMUST00000176371
RefSeq Acc Id: XP_036009346   ⟸   XM_036153453
- Peptide Label: isoform X2
Protein Domains
PDZ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9ES64-F1-model_v2 AlphaFold Q9ES64 1-910 view protein structure

Promoters
RGD ID:8664117
Promoter ID:EPDNEW_M10089
Type:initiation region
Name:Ush1c_1
Description:Mus musculus USH1 protein network component harmonin , transcriptvariant a1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38746,238,526 - 46,238,586EPDNEW
RGD ID:6842311
Promoter ID:MM_KWN:50486
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:ES_Cell,   Kidney
Transcripts:OTTMUST00000064140
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36753,457,059 - 53,457,559 (-)MPROMDB
RGD ID:6842310
Promoter ID:MM_KWN:50489
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney
Transcripts:ENSMUST00000107685,   NM_001163733,   OTTMUST00000064135,   OTTMUST00000064136,   OTTMUST00000064138
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36753,493,616 - 53,494,116 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1919338 AgrOrtholog
Ensembl Genes ENSMUSG00000030838 Ensembl, ENTREZGENE
Ensembl Transcript ENSMUST00000009667 ENTREZGENE
  ENSMUST00000078680 ENTREZGENE
  ENSMUST00000143155 ENTREZGENE
  ENSMUST00000154292 ENTREZGENE
  ENSMUST00000176371 ENTREZGENE
Gene3D-CATH 1.20.1160.20 UniProtKB/Swiss-Prot
  2.30.42.10 UniProtKB/Swiss-Prot
InterPro Harmonin UniProtKB/Swiss-Prot
  PDZ/DHR/GLGF UniProtKB/Swiss-Prot
  PDZ_sf UniProtKB/Swiss-Prot
  USH2_Complex_Protein UniProtKB/Swiss-Prot
KEGG Report mmu:72088 UniProtKB/Swiss-Prot
MGD MGI:1919338 ENTREZGENE
NCBI Gene 72088 ENTREZGENE
PANTHER PDZ DOMAIN CONTAINING WHIRLIN AND HARMONIN-RELATED UniProtKB/Swiss-Prot
  PTHR23116:SF36 UniProtKB/Swiss-Prot
Pfam PDZ UniProtKB/Swiss-Prot
  USH1C_N UniProtKB/Swiss-Prot
PhenoGen Ush1c PhenoGen
PROSITE PDZ UniProtKB/Swiss-Prot
SMART PDZ UniProtKB/Swiss-Prot
Superfamily-SCOP PDZ UniProtKB/Swiss-Prot
UniProt A0A0R4J0Z8 ENTREZGENE, UniProtKB/TrEMBL
  A0A5F8MPR9_MOUSE UniProtKB/TrEMBL
  D6RIM8 ENTREZGENE, UniProtKB/TrEMBL
  E9PYX1 ENTREZGENE, UniProtKB/TrEMBL
  E9QMN1 ENTREZGENE, UniProtKB/TrEMBL
  H3BIZ2 ENTREZGENE, UniProtKB/TrEMBL
  H3BLC4 ENTREZGENE, UniProtKB/TrEMBL
  Q6XA19 ENTREZGENE, UniProtKB/TrEMBL
  Q91XD1 ENTREZGENE
  Q9CVG7 ENTREZGENE
  Q9ES64 ENTREZGENE
  Q9ES65 ENTREZGENE
  USH1C_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q91XD1 UniProtKB/Swiss-Prot
  Q9CVG7 UniProtKB/Swiss-Prot
  Q9ES65 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-21 Ush1c  USH1 protein network component harmonin    Usher syndrome 1C  Symbol and/or name change 5135510 APPROVED
2012-07-05 Ush1c  Usher syndrome 1C  Ush1c  Usher syndrome 1C homolog (human)  Symbol and/or name change 5135510 APPROVED