Lrrc63 (leucine rich repeat containing 63) - Rat Genome Database

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Gene: Lrrc63 (leucine rich repeat containing 63) Rattus norvegicus
Analyze
Symbol: Lrrc63
Name: leucine rich repeat containing 63
RGD ID: 1559507
Description: Predicted to be involved in signal transduction. Orthologous to human LRRC63 (leucine rich repeat containing 63); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; atrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: leucine-rich repeat-containing protein 63; LOC364427; similar to CG5407-PA, isoform A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81556,809,629 - 56,846,831 (-)NCBIGRCr8
mRatBN7.21550,400,199 - 50,437,321 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1550,400,200 - 50,437,321 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1554,541,718 - 54,578,922 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01555,660,024 - 55,697,228 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01552,492,968 - 52,530,092 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01557,132,507 - 57,170,467 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1557,133,192 - 57,170,443 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01560,845,439 - 60,881,819 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41555,944,203 - 55,981,232 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1550,032,736 - 50,069,818 (-)NCBICelera
Cytogenetic Map15q11NCBI
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

Biological Process

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. GOA pipeline RGD automated data 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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Genomics

Comparative Map Data
Lrrc63
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81556,809,629 - 56,846,831 (-)NCBIGRCr8
mRatBN7.21550,400,199 - 50,437,321 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1550,400,200 - 50,437,321 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1554,541,718 - 54,578,922 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01555,660,024 - 55,697,228 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01552,492,968 - 52,530,092 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01557,132,507 - 57,170,467 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1557,133,192 - 57,170,443 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01560,845,439 - 60,881,819 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41555,944,203 - 55,981,232 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1550,032,736 - 50,069,818 (-)NCBICelera
Cytogenetic Map15q11NCBI
LRRC63
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381346,211,928 - 46,277,115 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1346,211,928 - 46,277,115 (+)EnsemblGRCh38hg38GRCh38
GRCh371346,786,063 - 46,851,250 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361345,684,084 - 45,739,112 (+)NCBINCBI36Build 36hg18NCBI36
Celera1327,841,088 - 27,905,853 (+)NCBICelera
Cytogenetic Map13q14.13NCBI
HuRef1327,583,775 - 27,648,525 (+)NCBIHuRef
CHM1_11346,754,895 - 46,819,759 (+)NCBICHM1_1
T2T-CHM13v2.01345,432,940 - 45,498,131 (+)NCBIT2T-CHM13v2.0
Lrrc63
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391475,321,743 - 75,368,402 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1475,321,743 - 75,368,321 (-)EnsemblGRCm39 Ensembl
GRCm381475,084,303 - 75,130,962 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1475,084,303 - 75,130,881 (-)EnsemblGRCm38mm10GRCm38
MGSCv371475,484,110 - 75,530,690 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361473,818,458 - 73,865,038 (-)NCBIMGSCv36mm8
Celera1472,584,216 - 72,630,816 (-)NCBICelera
Cytogenetic Map14D3NCBI
cM Map1439.59NCBI
Lrrc63
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555183,891,327 - 3,940,895 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555183,891,612 - 3,940,698 (+)NCBIChiLan1.0ChiLan1.0
LRRC63
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21445,114,289 - 45,180,200 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11336,168,504 - 36,234,404 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01326,754,849 - 26,820,720 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LRRC63
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1224,940,884 - 4,978,619 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl224,941,452 - 4,978,526 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha224,954,695 - 4,964,365 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0225,055,806 - 5,093,311 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl225,056,374 - 5,093,214 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1224,838,173 - 4,875,890 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0224,901,463 - 4,938,960 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0224,906,546 - 4,944,285 (-)NCBIUU_Cfam_GSD_1.0
Lrrc63
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945156,304,090 - 156,333,389 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936857727,530 - 760,626 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRRC63
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1121,080,028 - 21,125,646 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11121,079,430 - 21,125,611 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21121,488,417 - 21,534,898 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LRRC63
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1324,267,654 - 24,332,931 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl324,268,773 - 24,325,625 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605719,683,042 - 19,748,916 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lrrc63
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247488,705,041 - 8,740,064 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lrrc63
223 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:73
Count of miRNA genes:58
Interacting mature miRNAs:70
Transcripts:ENSRNOT00000058294
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
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat


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 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 7
Low 12 3 53 4 14 2
Below cutoff 2 24 15 5 16 5 4 4 21 12 18 9 4

Sequence


RefSeq Acc Id: ENSRNOT00000058294   ⟹   ENSRNOP00000055096
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1550,400,200 - 50,437,321 (-)Ensembl
Rnor_6.0 Ensembl1557,133,275 - 57,170,394 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079097   ⟹   ENSRNOP00000072416
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1550,400,200 - 50,437,321 (-)Ensembl
Rnor_6.0 Ensembl1557,133,192 - 57,170,443 (-)Ensembl
RefSeq Acc Id: NM_001024803   ⟹   NP_001019974
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81556,809,629 - 56,846,749 (-)NCBI
mRatBN7.21550,400,199 - 50,437,321 (-)NCBI
Rnor_6.01557,133,274 - 57,170,394 (-)NCBI
Rnor_5.01560,845,439 - 60,881,819 (-)NCBI
RGSC_v3.41555,944,203 - 55,981,232 (-)RGD
Celera1550,032,736 - 50,069,818 (-)RGD
Sequence:
RefSeq Acc Id: XM_006252325   ⟹   XP_006252387
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81556,809,629 - 56,846,475 (-)NCBI
mRatBN7.21550,400,199 - 50,437,075 (-)NCBI
Rnor_6.01557,132,507 - 57,170,193 (-)NCBI
Rnor_5.01560,845,439 - 60,881,819 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252326   ⟹   XP_006252388
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81556,809,629 - 56,846,831 (-)NCBI
mRatBN7.21550,400,199 - 50,437,316 (-)NCBI
Rnor_6.01557,132,507 - 57,170,467 (-)NCBI
Rnor_5.01560,845,439 - 60,881,819 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252327   ⟹   XP_006252389
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81556,809,629 - 56,846,339 (-)NCBI
mRatBN7.21550,400,199 - 50,436,875 (-)NCBI
Rnor_6.01557,132,507 - 57,169,968 (-)NCBI
Rnor_5.01560,845,439 - 60,881,819 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001019974   ⟸   NM_001024803
- UniProtKB: Q4V8G0 (UniProtKB/Swiss-Prot),   A0A0G2K2X5 (UniProtKB/TrEMBL),   A6HTS3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252388   ⟸   XM_006252326
- Peptide Label: isoform X1
- UniProtKB: Q4V8G0 (UniProtKB/Swiss-Prot),   A0A0G2K2X5 (UniProtKB/TrEMBL),   A6HTS3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252387   ⟸   XM_006252325
- Peptide Label: isoform X1
- UniProtKB: Q4V8G0 (UniProtKB/Swiss-Prot),   A0A0G2K2X5 (UniProtKB/TrEMBL),   A6HTS3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252389   ⟸   XM_006252327
- Peptide Label: isoform X1
- UniProtKB: Q4V8G0 (UniProtKB/Swiss-Prot),   A0A0G2K2X5 (UniProtKB/TrEMBL),   A6HTS3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072416   ⟸   ENSRNOT00000079097
RefSeq Acc Id: ENSRNOP00000055096   ⟸   ENSRNOT00000058294

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4V8G0-F1-model_v2 AlphaFold Q4V8G0 1-607 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:1559507 AgrOrtholog
BioCyc Gene G2FUF-13138 BioCyc
Ensembl Genes ENSRNOG00000038291 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00065008980 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000058294 ENTREZGENE
  ENSRNOT00000058294.3 UniProtKB/Swiss-Prot
  ENSRNOT00000079097.2 UniProtKB/TrEMBL
  ENSRNOT00065014352 UniProtKB/Swiss-Prot
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7133329 IMAGE-MGC_LOAD
  IMAGE:7453994 IMAGE-MGC_LOAD
InterPro Leu-rich_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:364427 UniProtKB/Swiss-Prot
MGC_CLONE MGC:114451 IMAGE-MGC_LOAD
  MGC:94356 IMAGE-MGC_LOAD
NCBI Gene 364427 ENTREZGENE
PANTHER LEUCINE-RICH REPEAT-CONTAINING PROTEIN 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR48051 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam LRR_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lrrc63 PhenoGen
PROSITE LRR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000038291 RatGTEx
  ENSRNOG00065008980 RatGTEx
SMART LRR_TYP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP RNI-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K2X5 ENTREZGENE, UniProtKB/TrEMBL
  A6HTS3 ENTREZGENE, UniProtKB/TrEMBL
  LRC63_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-20 Lrrc63  leucine rich repeat containing 63  LOC364427  similar to CG5407-PA, isoform A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC364427  similar to CG5407-PA, isoform A      Symbol and Name status set to provisional 70820 PROVISIONAL