Clrn2 (clarin 2) - Rat Genome Database

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Gene: Clrn2 (clarin 2) Rattus norvegicus
Analyze
Symbol: Clrn2
Name: clarin 2
RGD ID: 1591112
Description: Predicted to be involved in auditory receptor cell stereocilium organization. Predicted to act upstream of or within inner ear auditory receptor cell differentiation; sensory perception of sound; and stereocilium maintenance. Predicted to be located in stereocilium bundle. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness. Orthologous to human CLRN2 (clarin 2); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; methimazole.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: clarin-2; LOC689515; similar to Usher syndrome type III A
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
GRCr81469,868,556 - 69,878,850 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1469,868,556 - 69,878,850 (-)EnsemblGRCr8
mRatBN7.21465,656,029 - 65,666,325 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1465,656,550 - 65,666,193 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1470,049,346 - 70,058,998 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01471,336,571 - 71,346,211 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01467,759,735 - 67,769,387 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01470,150,983 - 70,160,624 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1470,150,983 - 70,160,624 (-)Ensemblrn6Rnor6.0
Rnor_5.01470,194,126 - 70,203,808 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41470,728,250 - 70,737,940 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1464,637,652 - 64,647,294 (-)NCBICelera
Cytogenetic Map14q11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IEA)
stereocilium bundle  (IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Clrn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81469,868,556 - 69,878,850 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1469,868,556 - 69,878,850 (-)EnsemblGRCr8
mRatBN7.21465,656,029 - 65,666,325 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1465,656,550 - 65,666,193 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1470,049,346 - 70,058,998 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01471,336,571 - 71,346,211 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01467,759,735 - 67,769,387 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01470,150,983 - 70,160,624 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1470,150,983 - 70,160,624 (-)Ensemblrn6Rnor6.0
Rnor_5.01470,194,126 - 70,203,808 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41470,728,250 - 70,737,940 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1464,637,652 - 64,647,294 (-)NCBICelera
Cytogenetic Map14q11NCBI
CLRN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38417,515,165 - 17,527,104 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl417,515,165 - 17,527,104 (+)Ensemblhg38GRCh38
GRCh37417,516,788 - 17,528,727 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36417,125,886 - 17,137,825 (+)NCBIBuild 36Build 36hg18NCBI36
Celera417,981,782 - 17,993,722 (+)NCBICelera
Cytogenetic Map4p15.32NCBI
HuRef416,871,458 - 16,883,399 (+)NCBIHuRef
CHM1_1417,514,705 - 17,526,632 (+)NCBICHM1_1
T2T-CHM13v2.0417,496,915 - 17,508,853 (+)NCBIT2T-CHM13v2.0
Clrn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39545,611,021 - 45,621,824 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl545,611,093 - 45,621,491 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38545,453,751 - 45,464,149 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl545,453,751 - 45,464,149 (+)Ensemblmm10GRCm38
MGSCv37545,844,990 - 45,855,388 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36545,742,059 - 45,752,212 (+)NCBIMGSCv36mm8
Celera542,879,648 - 42,890,040 (+)NCBICelera
Cytogenetic Map5B3NCBI
Clrn2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554806,631,962 - 6,645,499 (-)Ensembl
ChiLan1.0NW_0049554806,634,653 - 6,645,499 (-)NCBIChiLan1.0ChiLan1.0
CLRN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2317,774,025 - 17,792,183 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1417,972,763 - 17,988,604 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0411,933,869 - 11,948,049 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1417,228,544 - 17,240,743 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl417,228,544 - 17,240,743 (+)EnsemblpanPan2panpan1.1
CLRN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1362,958,242 - 62,967,878 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl362,959,224 - 62,967,994 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha365,475,071 - 65,483,728 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0363,434,070 - 63,442,746 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl363,434,059 - 63,442,741 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1362,925,039 - 62,933,914 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0363,129,190 - 63,137,869 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0363,488,676 - 63,497,337 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Clrn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528556,973,340 - 56,982,281 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647710,672,661 - 10,683,872 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647710,674,996 - 10,683,851 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLRN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl812,551,892 - 12,564,379 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1812,551,855 - 12,564,512 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2812,354,163 - 12,366,652 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLRN2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12732,681,525 - 32,695,858 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2732,682,435 - 32,694,564 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604779,413,391 - 79,427,231 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clrn2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475514,317,093 - 14,329,604 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475514,319,151 - 14,330,329 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Clrn2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11160,417,154 - 60,425,513 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Clrn2
95 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:45
Count of miRNA genes:41
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000022589
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143802371083023710Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1459848686104848686Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143900944484009444Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143123808072970315Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143067446985041098Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1433424686102238540Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143802371083023710Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1462398852107398852Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1460854936105854936Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1459848686104848686Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144261625899224555Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143802371083023710Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)146592028399224555Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143941117087582095Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143802371083023710Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
2 1 5 12 10 9 2 9 27 4 3 11 22 1 1 1

Sequence


Ensembl Acc Id: ENSRNOT00000022589   ⟹   ENSRNOP00000022589
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1469,868,556 - 69,878,850 (-)Ensembl
mRatBN7.2 Ensembl1465,656,550 - 65,666,193 (-)Ensembl
Rnor_6.0 Ensembl1470,150,983 - 70,160,624 (-)Ensembl
RefSeq Acc Id: NM_001191097   ⟹   NP_001178026
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81469,868,556 - 69,878,850 (-)NCBI
mRatBN7.21465,656,029 - 65,666,325 (-)NCBI
Rnor_6.01470,150,983 - 70,160,624 (-)NCBI
Rnor_5.01470,194,126 - 70,203,808 (-)NCBI
Celera1464,637,652 - 64,647,294 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178026 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000022589
  ENSRNOP00000022589.4
RefSeq Acc Id: NP_001178026   ⟸   NM_001191097
- UniProtKB: D3ZL71 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000022589   ⟸   ENSRNOT00000022589

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZL71-F1-model_v2 AlphaFold D3ZL71 1-232 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:1591112 AgrOrtholog
BioCyc Gene G2FUF-15537 BioCyc
Ensembl Genes ENSRNOG00000027195 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022589 ENTREZGENE
  ENSRNOT00000022589.6 UniProtKB/TrEMBL
Gene3D-CATH 1.20.140.150 UniProtKB/TrEMBL
InterPro Clarin UniProtKB/TrEMBL
KEGG Report rno:689515 UniProtKB/TrEMBL
NCBI Gene 689515 ENTREZGENE
PANTHER CLARIN-2 UniProtKB/TrEMBL
  PTHR31548 UniProtKB/TrEMBL
Pfam Clarin-2 UniProtKB/TrEMBL
PhenoGen Clrn2 PhenoGen
RatGTEx ENSRNOG00000027195 RatGTEx
UniProt D3ZL71 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Clrn2  clarin 2  LOC689515  similar to Usher syndrome type III A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC689515  similar to Usher syndrome type III A  LOC681950  similar to Usher syndrome type III A  Data merged from RGD:1589329 1643240 APPROVED
2006-11-20 LOC689515  similar to Usher syndrome type III A      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC681950  similar to Usher syndrome type III A      Symbol and Name status set to provisional 70820 PROVISIONAL