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

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Gene: Ush1c (USH1 protein network component harmonin) Rattus norvegicus
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Symbol: Ush1c
Name: USH1 protein network component harmonin
RGD ID: 1303329
Description: Enables myosin tail binding activity. Predicted to be involved in several processes, including G2/M transition of mitotic cell cycle; neuron development; and photoreceptor cell maintenance. Predicted to act upstream of or within inner ear development; neuromuscular process controlling balance; and parallel actin filament bundle assembly. Located in photoreceptor inner segment; photoreceptor outer segment; and stereocilium. 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); PARTICIPATES IN auditory mechanotransduction pathway; retinitis pigmentosa pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: harmonin; harmonin a1; MGC112571; Usher syndrome 1C; Usher syndrome 1C homolog; Usher syndrome 1C homolog (human)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81105,831,719 - 105,880,082 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1105,831,723 - 105,880,082 (-)EnsemblGRCr8
mRatBN7.2196,695,303 - 96,743,671 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl196,695,307 - 96,743,671 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1102,081,448 - 102,129,809 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01110,553,421 - 110,601,783 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01103,843,796 - 103,892,162 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01102,207,096 - 102,256,779 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1102,207,096 - 102,255,459 (-)Ensemblrn6Rnor6.0
Rnor_5.01103,291,318 - 103,340,928 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4196,720,185 - 96,768,550 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera190,943,948 - 90,992,307 (-)NCBICelera
RGSC_v3.1196,798,295 - 96,846,661 (-)NCBI
Cytogenetic Map1q22NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
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. 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.
6. 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.
7. 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.
8. 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.
9. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
10. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
11. 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.
12. The giant spectrin betaV couples the molecular motors to phototransduction and Usher syndrome type I proteins along their trafficking route. Papal S, etal., Hum Mol Genet. 2013 Sep 15;22(18):3773-88. doi: 10.1093/hmg/ddt228. Epub 2013 May 23.
13. Scaffold protein harmonin (USH1C) provides molecular links between Usher syndrome type 1 and type 2. Reiners J, etal., Hum Mol Genet. 2005 Dec 15;14(24):3933-43. Epub 2005 Nov 21.
14. 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.
15. GOA pipeline RGD automated data pipeline
16. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
18. 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.
19. 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.
20. 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.
21. 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.
22. 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:10209257   PMID:11398101   PMID:12477932   PMID:12485990   PMID:14962669   PMID:15219944   PMID:15461667   PMID:17906286   PMID:18339676   PMID:20016102   PMID:21330445   PMID:22114352  
PMID:24725409   PMID:26754646   PMID:26812018  


Genomics

Comparative Map Data
Ush1c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81105,831,719 - 105,880,082 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1105,831,723 - 105,880,082 (-)EnsemblGRCr8
mRatBN7.2196,695,303 - 96,743,671 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl196,695,307 - 96,743,671 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1102,081,448 - 102,129,809 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01110,553,421 - 110,601,783 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01103,843,796 - 103,892,162 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01102,207,096 - 102,256,779 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1102,207,096 - 102,255,459 (-)Ensemblrn6Rnor6.0
Rnor_5.01103,291,318 - 103,340,928 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4196,720,185 - 96,768,550 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera190,943,948 - 90,992,307 (-)NCBICelera
RGSC_v3.1196,798,295 - 96,846,661 (-)NCBI
Cytogenetic Map1q22NCBI
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 (-)Ensemblhg38GRCh38
GRCh371117,515,447 - 17,565,963 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361117,472,018 - 17,522,539 (-)NCBIBuild 36Build 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
(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 EnsemblGRCm39
GRCm38746,195,350 - 46,238,490 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl746,195,350 - 46,238,503 (-)Ensemblmm10GRCm38
MGSCv37753,450,721 - 53,493,860 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36746,063,399 - 46,106,532 (-)NCBIMGSCv36mm8
Celera741,668,925 - 41,712,073 (-)NCBICelera
Cytogenetic Map7B3NCBI
cM Map729.66NCBI
Ush1c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541432,298,759 - 32,351,505 (-)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2139,555,651 - 39,600,543 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02141,161,015 - 41,205,900 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (+)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247669,097,466 - 9,153,602 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ush1c
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12153,261,489 - 153,309,693 (+)NCBIRrattus_CSIRO_v1

Variants

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

Predicted Target Of
Summary Value
Count of predictions:159
Count of miRNA genes:115
Interacting mature miRNAs:123
Transcripts:ENSRNOT00000067392
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)187889942132889942Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)139728272132889942Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1102780511182384005Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)151940904168768703Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)192963855109494029Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1101228864146228864Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)187785026142582336Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183019780128019780Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)166404680111404680Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)166009857160501508Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)193903998191260518Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)166400974132889942Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)184107164115183752Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)191302413136302413Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)151511344153680016Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)1102359314153680016Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)199645382182701046Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)199645382221502378Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)186622262131622262Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)166077886111077886Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1103779152223964440Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)198879955208479939Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of, or within a discrete space in an open field apparatus (CMO:0001514)192683681137683681Rat
152025249Scl82Serum cholesterol level QTL 824.77blood cholesterol amount (VT:0000180)152891222109116986Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)186993904131993904Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)187558587132558587Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)192683681137683681Rat
737977Bp160Blood pressure QTL 1600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)197582336142582336Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1101594089146594089Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1100345976145345976Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)196717367160111531Rat

Markers in Region
RH132432  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2196,695,430 - 96,695,611 (+)MAPPERmRatBN7.2
Rnor_6.01102,207,224 - 102,207,404NCBIRnor6.0
Rnor_5.01103,291,446 - 103,291,626UniSTSRnor5.0
RGSC_v3.4196,720,309 - 96,720,489UniSTSRGSC3.4
Celera190,944,072 - 90,944,252UniSTS
RH 3.4 Map1907.8UniSTS
Cytogenetic Map1q22UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 11 13 105 68 63 36 25 36 6 211 70 9 77 81 84 27 15 15

Sequence


Ensembl Acc Id: ENSRNOT00000067392   ⟹   ENSRNOP00000061783
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1105,831,723 - 105,880,082 (-)Ensembl
mRatBN7.2 Ensembl196,695,307 - 96,743,671 (-)Ensembl
Rnor_6.0 Ensembl1102,207,096 - 102,255,459 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000100210   ⟹   ENSRNOP00000080627
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1105,832,035 - 105,880,082 (-)Ensembl
mRatBN7.2 Ensembl196,695,619 - 96,743,671 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000103742   ⟹   ENSRNOP00000077287
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1105,831,723 - 105,880,082 (-)Ensembl
mRatBN7.2 Ensembl196,695,307 - 96,743,671 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000120175   ⟹   ENSRNOP00000086685
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1105,831,723 - 105,867,408 (-)Ensembl
mRatBN7.2 Ensembl196,697,168 - 96,731,071 (-)Ensembl
RefSeq Acc Id: NM_212521   ⟹   NP_997686
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81105,831,723 - 105,880,082 (-)NCBI
mRatBN7.2196,695,307 - 96,743,671 (-)NCBI
Rnor_6.01102,207,100 - 102,255,459 (-)NCBI
Rnor_5.01103,291,318 - 103,340,928 (-)NCBI
RGSC_v3.4196,720,185 - 96,768,550 (-)RGD
Celera190,943,948 - 90,992,307 (-)RGD
Sequence:
RefSeq Acc Id: XM_006229222   ⟹   XP_006229284
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81105,831,719 - 105,880,072 (-)NCBI
mRatBN7.2196,695,303 - 96,743,650 (-)NCBI
Rnor_6.01102,207,096 - 102,256,779 (-)NCBI
Rnor_5.01103,291,318 - 103,340,928 (-)NCBI
Sequence:
RefSeq Acc Id: NP_997686   ⟸   NM_212521
- UniProtKB: Q4KMB9 (UniProtKB/TrEMBL),   A6JBB6 (UniProtKB/TrEMBL),   Q6PPF3 (UniProtKB/TrEMBL),   F7FHE4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229284   ⟸   XM_006229222
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZR66 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000061783   ⟸   ENSRNOT00000067392
Ensembl Acc Id: ENSRNOP00000080627   ⟸   ENSRNOT00000100210
Ensembl Acc Id: ENSRNOP00000077287   ⟸   ENSRNOT00000103742
Ensembl Acc Id: ENSRNOP00000086685   ⟸   ENSRNOT00000120175
Protein Domains
PDZ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4KMB9-F1-model_v2 AlphaFold Q4KMB9 1-548 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13690060
Promoter ID:EPDNEW_R585
Type:initiation region
Name:Ush1c_1
Description:USH1 protein network component harmonin
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01102,255,431 - 102,255,491EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303329 AgrOrtholog
BioCyc Gene G2FUF-59631 BioCyc
Ensembl Genes ENSRNOG00000021149 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067392 ENTREZGENE
  ENSRNOT00000067392.4 UniProtKB/TrEMBL
  ENSRNOT00000100210 ENTREZGENE
  ENSRNOT00000100210.2 UniProtKB/TrEMBL
  ENSRNOT00000103742.2 UniProtKB/TrEMBL
  ENSRNOT00000120175.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1160.20 UniProtKB/TrEMBL
  2.30.42.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7109129 IMAGE-MGC_LOAD
InterPro Harmonin UniProtKB/TrEMBL
  PDZ/DHR/GLGF UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
  USH2_Complex_Protein UniProtKB/TrEMBL
KEGG Report rno:308596 UniProtKB/TrEMBL
MGC_CLONE MGC:112571 IMAGE-MGC_LOAD
NCBI Gene 308596 ENTREZGENE
PANTHER PDZ DOMAIN CONTAINING WHIRLIN AND HARMONIN-RELATED UniProtKB/TrEMBL
  PTHR23116:SF36 UniProtKB/TrEMBL
Pfam PDZ UniProtKB/TrEMBL
  USH1C_N UniProtKB/TrEMBL
PhenoGen Ush1c PhenoGen
PROSITE PDZ UniProtKB/TrEMBL
RatGTEx ENSRNOG00000021149 RatGTEx
SMART PDZ UniProtKB/TrEMBL
Superfamily-SCOP PDZ UniProtKB/TrEMBL
UniProt A0A8I5Y9F7_RAT UniProtKB/TrEMBL
  A0A8I5ZR66 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A2P6_RAT UniProtKB/TrEMBL
  A6JBB6 ENTREZGENE, UniProtKB/TrEMBL
  F7FHE4 ENTREZGENE, UniProtKB/TrEMBL
  Q4KMB9 ENTREZGENE
  Q6PPF3 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q4KMB9 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-24 Ush1c  USH1 protein network component harmonin  Ush1c  Usher syndrome 1C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-03-27 Ush1c  Usher syndrome 1C  Ush1c  Usher syndrome 1C homolog (human)  Name changed 629549 APPROVED
2005-11-17 Ush1c  Usher syndrome 1C homolog (human)      Name updated 1299863 APPROVED
2005-02-14 Ush1c  harmonin a1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease mutation of the human homolog causes Usher syndrome type 1C, which is characterized by congenital deafness and prepubertal-onset retinitis pigmentosa 1303964