Strc (stereocilin) - Rat Genome Database

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Gene: Strc (stereocilin) Rattus norvegicus
Analyze
Symbol: Strc
Name: stereocilin
RGD ID: 1593345
Description: Predicted to be involved in cell-matrix adhesion. Predicted to act upstream of or within auditory receptor cell stereocilium organization and detection of mechanical stimulus involved in sensory perception of sound. Predicted to be active in cell surface; kinocilium; and stereocilium tip. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness 16 and sensorineural hearing loss. Orthologous to several human genes including STRC (stereocilin); INTERACTS WITH 6-propyl-2-thiouracil; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC691937; otoancorin-like; similar to stereocilin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83128,785,817 - 128,811,773 (-)NCBIGRCr8
mRatBN7.23108,335,920 - 108,355,114 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3108,335,747 - 108,354,134 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.03113,324,403 - 113,343,513 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3113,324,698 - 113,342,675 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03119,863,952 - 119,882,260 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43108,164,129 - 108,182,106 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3107,237,716 - 107,256,326 (-)NCBICelera
Cytogenetic Map3q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cell surface  (IBA)
kinocilium  (IBA,ISO)
stereocilium tip  (IBA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
6. Mutations in a new gene encoding a protein of the hair bundle cause non-syndromic deafness at the DFNB16 locus. Verpy E, etal., Nat Genet. 2001 Nov;29(3):345-9.
Additional References at PubMed
PMID:18849963   PMID:21165971   PMID:24920589  


Genomics

Comparative Map Data
Strc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83128,785,817 - 128,811,773 (-)NCBIGRCr8
mRatBN7.23108,335,920 - 108,355,114 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3108,335,747 - 108,354,134 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.03113,324,403 - 113,343,513 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3113,324,698 - 113,342,675 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03119,863,952 - 119,882,260 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43108,164,129 - 108,182,106 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3107,237,716 - 107,256,326 (-)NCBICelera
Cytogenetic Map3q35NCBI
STRC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381543,599,563 - 43,618,800 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1543,599,563 - 43,618,800 (-)EnsemblGRCh38hg38GRCh38
GRCh371543,891,761 - 43,910,998 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361541,679,053 - 41,698,290 (-)NCBINCBI36Build 36hg18NCBI36
Build 341541,679,052 - 41,698,290NCBI
Celera1520,720,867 - 20,723,140 (+)NCBICelera
Celera1520,841,352 - 20,846,505 (-)NCBICelera
Cytogenetic Map15q15.3NCBI
HuRef1520,721,598 - 20,740,111 (-)NCBIHuRef
CHM1_11544,009,808 - 44,029,087 (-)NCBICHM1_1
T2T-CHM13v2.01541,406,922 - 41,426,159 (-)NCBIT2T-CHM13v2.0
Strc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392121,193,729 - 121,211,851 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2121,194,209 - 121,217,649 (-)EnsemblGRCm39 Ensembl
GRCm382121,363,248 - 121,381,370 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2121,363,728 - 121,387,168 (-)EnsemblGRCm38mm10GRCm38
MGSCv372121,189,463 - 121,206,676 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362121,055,168 - 121,072,381 (-)NCBIMGSCv36mm8
Celera2122,514,641 - 122,531,929 (-)NCBICelera
Cytogenetic Map2E5NCBI
cM Map260.37NCBI
Strc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541610,139,420 - 10,141,906 (-)NCBIChiLan1.0ChiLan1.0
LOC103785466
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21632,952,613 - 32,977,519 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11537,114,439 - 37,139,237 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01522,660,952 - 22,706,416 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11540,740,196 - 40,771,092 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1540,740,387 - 40,757,999 (-)Ensemblpanpan1.1panPan2
STRC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13010,444,726 - 10,459,058 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3010,444,793 - 10,460,785 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3010,503,116 - 10,517,450 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03010,581,219 - 10,595,553 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3010,581,288 - 10,597,280 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13010,490,359 - 10,505,838 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03010,612,124 - 10,626,458 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03010,732,015 - 10,746,349 (-)NCBIUU_Cfam_GSD_1.0
Strc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864088,912,019 - 88,929,362 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364716,760,294 - 6,777,425 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364716,760,289 - 6,777,425 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
STRC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1127,835,622 - 127,852,339 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11127,830,759 - 127,852,392 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21142,660,378 - 142,682,006 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103245735
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12639,376,441 - 39,397,613 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2639,378,318 - 39,401,072 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366618275,632 - 121,228 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Strc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248382,896,147 - 2,910,268 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248382,894,945 - 2,913,030 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Strc
107 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:25
Count of miRNA genes:22
Interacting mature miRNAs:25
Transcripts:ENSRNOT00000020130
Prediction methods: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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)364655305115665732Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)364655305115665732Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)373376539118376539Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)380800231114297550Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
1582219Bw63Body weight QTL 633.80.001body mass (VT:0001259)body weight (CMO:0000012)396127817115665732Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
1582216Bw65Body weight QTL 656.3body mass (VT:0001259)body weight (CMO:0000012)3102200529115665732Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat

Markers in Region
ECD01483  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23108,336,874 - 108,337,903 (+)MAPPERmRatBN7.2
Rnor_6.03113,325,574 - 113,326,602NCBIRnor6.0
Rnor_5.03119,865,121 - 119,866,149UniSTSRnor5.0
RGSC_v3.43108,165,005 - 108,166,033UniSTSRGSC3.4
Celera3107,238,886 - 107,239,914UniSTS
Cytogenetic Map3q35UniSTS


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

alimentary part of gastrointestinal system nervous system renal system reproductive system respiratory system
High
Medium
Low 2 9
Below cutoff 3 13 9 9 6

Sequence


RefSeq Acc Id: ENSRNOT00000020130   ⟹   ENSRNOP00000020130
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3108,335,747 - 108,354,134 (-)Ensembl
Rnor_6.0 Ensembl3113,324,698 - 113,342,675 (-)Ensembl
RefSeq Acc Id: XM_001080205   ⟹   XP_001080205
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83128,785,817 - 128,811,773 (-)NCBI
mRatBN7.23108,335,920 - 108,355,114 (-)NCBI
Rnor_6.03113,324,403 - 113,343,513 (-)NCBI
Rnor_5.03119,863,952 - 119,882,260 (-)NCBI
RGSC_v3.43108,164,129 - 108,182,106 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_001080205 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000020130
  ENSRNOP00000020130.4
RefSeq Acc Id: XP_001080205   ⟸   XM_001080205
- UniProtKB: D3ZUE8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000020130   ⟸   ENSRNOT00000020130
Protein Domains
Stereocilin LRR

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZUE8-F1-model_v2 AlphaFold D3ZUE8 1-1809 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1593345 AgrOrtholog
BioCyc Gene G2FUF-48136 BioCyc
Ensembl Genes ENSRNOG00000014845 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020130.5 UniProtKB/TrEMBL
InterPro Stereocilin_LRR UniProtKB/TrEMBL
  Stereocilin_related UniProtKB/TrEMBL
NCBI Gene 691937 ENTREZGENE
PANTHER PTHR23412 UniProtKB/TrEMBL
  PTHR23412:SF14 UniProtKB/TrEMBL
Pfam Stereocilin UniProtKB/TrEMBL
PhenoGen Strc PhenoGen
RatGTEx ENSRNOG00000014845 RatGTEx
UniProt D3ZUE8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Strc  stereocilin  LOC100363936  otoancorin-like  Data merged from RGD:2322020 1643240 APPROVED
2010-05-06 LOC100363936  otoancorin-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-06 Strc  stereocilin  LOC691937  similar to stereocilin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC691937  similar to stereocilin  LOC688039  similar to stereocilin  Data merged from RGD:1593623 1643240 APPROVED
2006-11-20 LOC691937  similar to stereocilin      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC688039  similar to stereocilin      Symbol and Name status set to provisional 70820 PROVISIONAL