Ush2a (usherin) - Rat Genome Database
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Gene: Ush2a (usherin) Rattus norvegicus
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Symbol: Ush2a
Name: usherin
RGD ID: 628777
Description: Predicted to have collagen binding activity; identical protein binding activity; and myosin binding activity. Involved in retina development in camera-type eye. Localizes to stereocilium and synapse. Colocalizes with several cellular components, including neuronal cell body; photoreceptor connecting cilium; and photoreceptor inner segment. Human ortholog(s) of this gene implicated in Usher syndrome (multiple); nonsyndromic deafness; and retinitis pigmentosa (multiple). Orthologous to human USH2A (usherin); PARTICIPATES IN auditory mechanotransduction pathway; retinitis pigmentosa pathway; INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC289369; RGD1560269; similar to usherin isoform B; Usher syndrome 2A; Usher syndrome 2A (autosomal recessive, mild); Usher syndrome 2A (autosomal recessive, mild) homolog; Usher syndrome 2A (autosomal recessive, mild) homolog (human); Usher syndrome 2A homolog; Usher syndrome 2A homolog (human); usher syndrome type IIa protein homolog; usher syndrome type-2A protein homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21399,837,445 - 100,503,935 (+)NCBI
Rnor_6.0 Ensembl13106,751,625 - 107,427,329 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.013106,750,738 - 107,434,195 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013111,395,505 - 112,057,548 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413104,481,807 - 104,606,485 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.113104,670,849 - 104,795,529 (+)NCBI
Celera1399,331,812 - 99,994,577 (+)NCBICelera
Cytogenetic Map13q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Auslender N, etal., Genet Test. 2008 Jun;12(2):289-94. doi: 10.1089/gte.2007.0107.
2. Baux D, etal., Hum Mutat. 2007 Aug;28(8):781-9.
3. Daiger SP, etal., Clin Genet. 2013 Aug;84(2):132-41. doi: 10.1111/cge.12203. Epub 2013 Jun 19.
4. Ebermann I, etal., Eur J Hum Genet. 2009 Jan;17(1):80-4. doi: 10.1038/ejhg.2008.143. Epub 2008 Jul 30.
5. Eudy JD, etal., Science. 1998 Jun 12;280(5370):1753-7.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Huang D, etal., Genomics 2002 Aug;80(2):195-203.
8. Liu X, etal., Mol Vis. 2010 Mar 17;16:454-61.
9. Liu X, etal., Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4413-8. Epub 2007 Mar 5.
10. McGee TL, etal., J Med Genet. 2010 Jul;47(7):499-506. doi: 10.1136/jmg.2009.075143. Epub 2010 May 27.
11. MGD data from the GO Consortium
12. Najera C, etal., Hum Mutat. 2002 Jul;20(1):76-7.
13. OMIM Disease Annotation Pipeline
14. Ouyang XM, etal., Clin Genet. 2004 Apr;65(4):288-93.
15. Reiners J, etal., Hum Mol Genet. 2005 Dec 15;14(24):3933-43. Epub 2005 Nov 21.
16. RGD automated data pipeline
17. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. RGD automated import pipeline for gene-chemical interactions
19. Rivolta C, etal., Am J Hum Genet. 2000 Jun;66(6):1975-8. Epub 2000 Apr 20.
20. Schwander M, etal., J Cell Biol. 2010 Jul 12;190(1):9-20. doi: 10.1083/jcb.201001138.
21. Vache C, etal., Hum Mutat. 2012 Jan;33(1):104-8. doi: 10.1002/humu.21634. Epub 2011 Nov 16.
22. van Wijk E, etal., Hum Mol Genet. 2006 Mar 1;15(5):751-65. Epub 2006 Jan 24.
23. Weston MD, etal., Am J Hum Genet. 2000 Apr;66(4):1199-210. Epub 2000 Mar 22.
24. Yang T, etal., Orphanet J Rare Dis. 2013 Jun 14;8:85. doi: 10.1186/1750-1172-8-85.
Additional References at PubMed
PMID:10090909   PMID:12433396   PMID:14676276   PMID:15671307   PMID:16301217   PMID:17567809   PMID:17906286   PMID:20502675   PMID:21212183   PMID:24334608   PMID:25406310  


Genomics

Comparative Map Data
Ush2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21399,837,445 - 100,503,935 (+)NCBI
Rnor_6.0 Ensembl13106,751,625 - 107,427,329 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.013106,750,738 - 107,434,195 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013111,395,505 - 112,057,548 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413104,481,807 - 104,606,485 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.113104,670,849 - 104,795,529 (+)NCBI
Celera1399,331,812 - 99,994,577 (+)NCBICelera
Cytogenetic Map13q26NCBI
USH2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1215,622,891 - 216,423,448 (-)EnsemblGRCh38hg38GRCh38
GRCh381215,622,891 - 216,423,448 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371215,796,233 - 216,596,790 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361213,862,859 - 214,663,361 (-)NCBINCBI36hg18NCBI36
Build 341212,735,682 - 212,985,133NCBI
Celera1189,020,056 - 189,820,422 (-)NCBI
Cytogenetic Map1q41NCBI
HuRef1186,470,498 - 187,272,188 (-)NCBIHuRef
CHM1_11217,068,567 - 217,869,890 (-)NCBICHM1_1
Ush2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391187,995,035 - 188,697,694 (+)NCBIGRCm39mm39
GRCm39 Ensembl1187,994,220 - 188,697,238 (+)Ensembl
GRCm381188,262,838 - 188,965,497 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1188,262,023 - 188,965,041 (+)EnsemblGRCm38mm10GRCm38
MGSCv371190,086,717 - 190,788,920 (+)NCBIGRCm37mm9NCBIm37
MGSCv361189,963,822 - 190,665,716 (+)NCBImm8
Celera1195,189,439 - 195,876,703 (+)NCBICelera
Cytogenetic Map1H6NCBI
cM Map192.29NCBI
Ush2a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554061,838,885 - 2,496,980 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554061,837,831 - 2,499,664 (+)NCBIChiLan1.0ChiLan1.0
USH2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11196,048,086 - 196,850,216 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1196,048,086 - 196,850,216 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01191,193,130 - 191,994,664 (-)NCBIMhudiblu_PPA_v0panPan3
USH2A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3811,063,817 - 11,750,444 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13811,063,221 - 11,750,444 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ush2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366282,123,917 - 2,859,958 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USH2A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1105,825,591 - 6,662,733 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2107,790,789 - 8,411,655 (-)NCBISscrofa10.2Sscrofa10.2susScr3
USH2A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12513,171,499 - 13,950,553 (+)NCBI
ChlSab1.1 Ensembl2513,173,576 - 13,947,724 (+)Ensembl
Ush2a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462483548,213 - 758,640 (-)NCBI

Position Markers
D13Got96  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.013106,835,467 - 106,835,739NCBIRnor6.0
Rnor_5.013111,474,382 - 111,474,654UniSTSRnor5.0
RGSC_v3.413104,507,256 - 104,507,528UniSTSRGSC3.4
RGSC_v3.413104,507,255 - 104,507,528RGDRGSC3.4
RGSC_v3.113104,696,299 - 104,696,571RGD
Celera1399,410,109 - 99,410,381UniSTS
RH 3.4 Map13663.2RGD
RH 3.4 Map13663.2UniSTS
RH 2.0 Map13731.9RGD
Cytogenetic Map13q26UniSTS
D13Got101  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.413104,872,569 - 104,872,815RGDRGSC3.4
RGSC_v3.413104,872,568 - 104,872,815UniSTSRGSC3.4
RGSC_v3.113105,061,612 - 105,061,858RGD
RH 3.4 Map13687.7UniSTS
RH 3.4 Map13687.7RGD
RH 2.0 Map13734.2RGD
Cytogenetic Map13q26UniSTS
RH137407  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1399,466,887 - 99,467,074UniSTS
RH 3.4 Map13682.2UniSTS
Cytogenetic Map13q26UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1362975663107975663Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:128
Count of miRNA genes:103
Interacting mature miRNAs:114
Transcripts:ENSRNOT00000004992
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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 3 3 3 20 15
Below cutoff 14 23 13 9 13 2 2 54 22 18 11 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004992   ⟹   ENSRNOP00000004992
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl13106,751,625 - 107,427,329 (+)Ensembl
RefSeq Acc Id: NM_001302219   ⟹   NP_001289148
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21399,837,445 - 100,503,935 (+)NCBI
Rnor_6.013106,751,625 - 107,427,328 (+)NCBI
Celera1399,331,812 - 99,994,577 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598744   ⟹   XP_017454233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,429,258 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598745   ⟹   XP_017454234
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,790 - 107,429,258 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598746   ⟹   XP_017454235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,429,258 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598747   ⟹   XP_017454236
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,429,258 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598748   ⟹   XP_017454237
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,434,195 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598749   ⟹   XP_017454238
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,429,258 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598750   ⟹   XP_017454239
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,429,258 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598751   ⟹   XP_017454240
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,429,258 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598752   ⟹   XP_017454241
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,429,258 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598753   ⟹   XP_017454242
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,429,258 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598754   ⟹   XP_017454243
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,429,258 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598755   ⟹   XP_017454244
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,429,258 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598756   ⟹   XP_017454245
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,429,258 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598757   ⟹   XP_017454246
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013106,750,738 - 107,429,258 (+)NCBI
Sequence: