Lrrc20 (leucine rich repeat containing 20) - Rat Genome Database

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Gene: Lrrc20 (leucine rich repeat containing 20) Rattus norvegicus
Analyze
Symbol: Lrrc20
Name: leucine rich repeat containing 20
RGD ID: 1566140
Description: Orthologous to human LRRC20 (leucine rich repeat containing 20); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: leucine-rich repeat-containing protein 20; LOC499430; RGD1566140; similar to Leucine rich repeat containing 20
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
mRatBN7.22029,422,858 - 29,528,372 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2029,422,925 - 29,528,369 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2030,438,896 - 30,544,322 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02029,825,157 - 29,930,600 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02030,567,627 - 30,673,081 (+)NCBIRnor_WKY
Rnor_6.02031,069,406 - 31,202,502 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2031,096,214 - 31,202,514 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02032,856,913 - 32,985,241 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42028,889,911 - 28,951,225 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2030,851,720 - 30,955,474 (+)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:21873635  


Genomics

Comparative Map Data
Lrrc20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22029,422,858 - 29,528,372 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2029,422,925 - 29,528,369 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2030,438,896 - 30,544,322 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02029,825,157 - 29,930,600 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02030,567,627 - 30,673,081 (+)NCBIRnor_WKY
Rnor_6.02031,069,406 - 31,202,502 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2031,096,214 - 31,202,514 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02032,856,913 - 32,985,241 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42028,889,911 - 28,951,225 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2030,851,720 - 30,955,474 (+)NCBICelera
Cytogenetic Map20q11NCBI
LRRC20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381070,298,975 - 70,382,625 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1070,298,970 - 70,382,650 (-)EnsemblGRCh38hg38GRCh38
GRCh371072,058,731 - 72,142,381 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361071,728,735 - 71,812,388 (-)NCBINCBI36Build 36hg18NCBI36
Celera1065,338,800 - 65,422,388 (-)NCBICelera
Cytogenetic Map10q22.1NCBI
HuRef1066,052,016 - 66,136,383 (-)NCBIHuRef
CHM1_11072,341,003 - 72,424,649 (-)NCBICHM1_1
T2T-CHM13v2.01071,167,949 - 71,251,681 (-)NCBIT2T-CHM13v2.0
Lrrc20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391061,311,579 - 61,418,570 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1061,311,580 - 61,418,570 (+)EnsemblGRCm39 Ensembl
GRCm381061,475,769 - 61,582,791 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1061,475,801 - 61,582,791 (+)EnsemblGRCm38mm10GRCm38
MGSCv371060,938,581 - 61,044,990 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361060,871,190 - 60,977,599 (+)NCBIMGSCv36mm8
Celera1062,577,357 - 62,683,544 (+)NCBICelera
Cytogenetic Map10B4NCBI
Lrrc20
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543720,900,705 - 20,968,348 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543720,900,740 - 20,968,294 (+)NCBIChiLan1.0ChiLan1.0
LRRC20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11069,300,391 - 69,384,831 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1069,300,391 - 69,384,831 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01066,772,965 - 66,858,263 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LRRC20
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1421,227,105 - 21,312,072 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl421,229,479 - 21,312,203 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha421,359,561 - 21,444,527 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0421,502,603 - 21,586,853 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl421,502,607 - 21,587,081 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1421,400,001 - 21,484,877 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0421,605,317 - 21,690,265 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0421,956,623 - 22,041,576 (-)NCBIUU_Cfam_GSD_1.0
Lrrc20
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721359,743,370 - 59,813,078 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365218,236,119 - 8,305,856 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365218,236,119 - 8,305,803 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRRC20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1473,214,203 - 73,296,646 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11473,214,201 - 73,296,660 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21479,134,997 - 79,214,190 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LRRC20
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1960,915,990 - 61,015,367 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl960,922,273 - 61,015,356 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604821,663,970 - 21,754,417 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lrrc20
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247544,428,090 - 4,495,533 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247544,428,171 - 4,500,761 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lrrc20
668 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:839
Count of miRNA genes:315
Interacting mature miRNAs:424
Transcripts:ENSRNOT00000000676
Prediction methods:Microtar, Miranda, 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
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat

Markers in Region
RH131260  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22029,528,140 - 29,528,324 (+)MAPPERmRatBN7.2
Rnor_6.02031,202,271 - 31,202,454NCBIRnor6.0
Rnor_5.02032,985,010 - 32,985,193UniSTSRnor5.0
RGSC_v3.42028,950,997 - 28,951,180UniSTSRGSC3.4
Celera2030,955,246 - 30,955,429UniSTS
Cytogenetic Map20q11UniSTS


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 33 6 6 6 8 11 45 14 20 8
Low 3 10 51 35 19 35 29 21 21 11
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000676   ⟹   ENSRNOP00000000676
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,422,925 - 29,528,369 (+)Ensembl
Rnor_6.0 Ensembl2031,096,214 - 31,202,499 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078719   ⟹   ENSRNOP00000072549
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,422,925 - 29,527,401 (+)Ensembl
Rnor_6.0 Ensembl2031,102,476 - 31,202,514 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118364   ⟹   ENSRNOP00000082406
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,422,925 - 29,496,472 (+)Ensembl
RefSeq Acc Id: NM_001109171   ⟹   NP_001102641
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,422,925 - 29,528,369 (+)NCBI
Rnor_6.02031,096,214 - 31,202,499 (+)NCBI
Rnor_5.02032,856,913 - 32,985,241 (+)NCBI
RGSC_v3.42028,889,911 - 28,951,225 (+)RGD
Celera2030,851,720 - 30,955,474 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256465   ⟹   XP_006256527
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,422,858 - 29,528,372 (+)NCBI
Rnor_6.02031,096,191 - 31,202,502 (+)NCBI
Rnor_5.02032,856,913 - 32,985,241 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099014   ⟹   XP_038954942
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,429,209 - 29,528,372 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102641 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256527 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954942 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93021 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102641   ⟸   NM_001109171
- UniProtKB: F1LUD9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256527   ⟸   XM_006256465
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000000676   ⟸   ENSRNOT00000000676
RefSeq Acc Id: ENSRNOP00000072549   ⟸   ENSRNOT00000078719
RefSeq Acc Id: XP_038954942   ⟸   XM_039099014
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000082406   ⟸   ENSRNOT00000118364

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LUD9-F1-model_v2 AlphaFold F1LUD9 1-184 view protein structure

Transcriptome

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

Promoters
RGD ID:13701604
Promoter ID:EPDNEW_R12128
Type:multiple initiation site
Name:Lrrc20_1
Description:leucine rich repeat containing 20
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_6.02031,096,220 - 31,096,280EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566140 AgrOrtholog
BioCyc Gene G2FUF-3720 BioCyc
Ensembl Genes ENSRNOG00000000560 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000676 ENTREZGENE
  ENSRNOP00000000676.6 UniProtKB/TrEMBL
  ENSRNOP00000072549.1 UniProtKB/TrEMBL
  ENSRNOP00000082406.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000676 ENTREZGENE
  ENSRNOT00000000676.8 UniProtKB/TrEMBL
  ENSRNOT00000078719.2 UniProtKB/TrEMBL
  ENSRNOT00000118364.1 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  LRRC20 UniProtKB/TrEMBL
KEGG Report rno:499430 UniProtKB/TrEMBL
NCBI Gene 499430 ENTREZGENE
PANTHER PTHR16083:SF2 UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/TrEMBL
PhenoGen Lrrc20 PhenoGen
UniProt A0A0G2K395_RAT UniProtKB/TrEMBL
  A0A8I6G7D6_RAT UniProtKB/TrEMBL
  F1LUD9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Lrrc20  leucine rich repeat containing 20  RGD1566140_predicted  similar to Leucine rich repeat containing 20 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1566140_predicted  similar to Leucine rich repeat containing 20 (predicted)  LOC499430  similar to Leucine rich repeat containing 20  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499430  similar to Leucine rich repeat containing 20      Symbol and Name status set to provisional 70820 PROVISIONAL