Lrrc58 (leucine rich repeat containing 58) - Rat Genome Database

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Gene: Lrrc58 (leucine rich repeat containing 58) Rattus norvegicus
Analyze
Symbol: Lrrc58
Name: leucine rich repeat containing 58
RGD ID: 1307440
Description: Predicted to be involved in intracellular signal transduction. Orthologous to human LRRC58 (leucine rich repeat containing 58); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: leucine-rich repeat-containing protein 58; LOC303919; RGD1307440; similar to RIKEN cDNA C330018J07 gene
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
GRCr81176,355,987 - 76,368,309 (-)NCBIGRCr8
mRatBN7.21162,850,507 - 62,862,829 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1162,847,562 - 62,862,829 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1171,662,995 - 71,675,321 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01164,325,211 - 64,337,533 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01163,375,244 - 63,387,580 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01165,747,235 - 65,759,558 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1165,747,036 - 65,759,581 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01168,841,233 - 68,853,498 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41164,635,216 - 64,646,888 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11164,703,933 - 64,704,423 (-)NCBI
Celera1162,348,644 - 62,360,967 (-)NCBICelera
Cytogenetic Map11q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548  


Genomics

Comparative Map Data
Lrrc58
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81176,355,987 - 76,368,309 (-)NCBIGRCr8
mRatBN7.21162,850,507 - 62,862,829 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1162,847,562 - 62,862,829 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1171,662,995 - 71,675,321 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01164,325,211 - 64,337,533 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01163,375,244 - 63,387,580 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01165,747,235 - 65,759,558 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1165,747,036 - 65,759,581 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01168,841,233 - 68,853,498 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41164,635,216 - 64,646,888 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11164,703,933 - 64,704,423 (-)NCBI
Celera1162,348,644 - 62,360,967 (-)NCBICelera
Cytogenetic Map11q21NCBI
LRRC58
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383120,324,509 - 120,349,354 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3120,324,509 - 120,349,354 (-)EnsemblGRCh38hg38GRCh38
GRCh373120,043,356 - 120,068,201 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363121,526,266 - 121,550,876 (-)NCBINCBI36Build 36hg18NCBI36
Celera3118,452,974 - 118,477,585 (-)NCBICelera
Cytogenetic Map3q13.33NCBI
HuRef3117,419,401 - 117,444,024 (-)NCBIHuRef
CHM1_13120,007,169 - 120,031,803 (-)NCBICHM1_1
T2T-CHM13v2.03123,044,047 - 123,068,908 (-)NCBIT2T-CHM13v2.0
Lrrc58
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391637,688,762 - 37,709,219 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1637,688,751 - 37,709,220 (+)EnsemblGRCm39 Ensembl
GRCm381637,868,400 - 37,888,857 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1637,868,389 - 37,888,858 (+)EnsemblGRCm38mm10GRCm38
MGSCv371637,868,486 - 37,888,943 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361637,787,628 - 37,801,693 (+)NCBIMGSCv36mm8
Celera1638,283,717 - 38,295,526 (+)NCBICelera
Cytogenetic Map16B3NCBI
cM Map1626.49NCBI
Lrrc58
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542719,896,034 - 19,911,233 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542719,896,034 - 19,911,233 (-)NCBIChiLan1.0ChiLan1.0
LRRC58
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22118,300,627 - 118,325,099 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13118,305,289 - 118,329,660 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03117,451,035 - 117,470,085 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13124,357,398 - 124,399,452 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3124,363,716 - 124,399,452 (-)Ensemblpanpan1.1panPan2
LRRC58
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13323,841,249 - 23,861,675 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3323,847,086 - 23,862,146 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3323,871,217 - 23,891,596 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03324,081,600 - 24,101,985 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3324,081,649 - 24,102,503 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13323,882,593 - 23,902,964 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03323,923,410 - 23,943,761 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03324,486,998 - 24,507,383 (-)NCBIUU_Cfam_GSD_1.0
Lrrc58
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602130,420,326 - 130,442,418 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365367,083,941 - 7,102,125 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365367,083,584 - 7,101,704 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRRC58
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13139,927,781 - 139,948,702 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113139,927,708 - 139,951,263 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213149,281,673 - 149,297,073 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LRRC58
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12260,462,872 - 60,481,802 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2260,463,037 - 60,480,690 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041105,822,794 - 105,847,046 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lrrc58
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473127,900,833 - 27,918,751 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lrrc58
94 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:104
Count of miRNA genes:84
Interacting mature miRNAs:94
Transcripts:ENSRNOT00000034334
Prediction methods:Microtar, Miranda, Rnahybrid
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
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111945620576331918Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat

Markers in Region
BE116020  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21162,845,118 - 62,845,304 (+)MAPPERmRatBN7.2
Rnor_6.01165,741,847 - 65,742,032NCBIRnor6.0
Rnor_5.01168,835,849 - 68,836,034UniSTSRnor5.0
RGSC_v3.41164,629,421 - 64,629,606UniSTSRGSC3.4
Celera1162,343,256 - 62,343,441UniSTS
RH 3.4 Map11495.8UniSTS
Cytogenetic Map11q21UniSTS
RH142472  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21162,856,724 - 62,856,850 (+)MAPPERmRatBN7.2
Rnor_6.01165,753,453 - 65,753,578NCBIRnor6.0
Rnor_5.01168,847,394 - 68,847,519UniSTSRnor5.0
RGSC_v3.41164,640,890 - 64,641,015UniSTSRGSC3.4
Celera1162,354,862 - 62,354,987UniSTS
RH 3.4 Map11499.1UniSTS
Cytogenetic Map11q21UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000034334   ⟹   ENSRNOP00000037105
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1162,847,562 - 62,862,829 (-)Ensembl
Rnor_6.0 Ensembl1165,747,036 - 65,759,581 (-)Ensembl
RefSeq Acc Id: NM_001195558   ⟹   NP_001182487
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81176,355,987 - 76,368,309 (-)NCBI
mRatBN7.21162,850,507 - 62,862,829 (-)NCBI
Rnor_6.01165,747,235 - 65,759,558 (-)NCBI
Rnor_5.01168,841,233 - 68,853,498 (-)NCBI
Celera1162,348,644 - 62,360,967 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001182487 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037105.5
RefSeq Acc Id: NP_001182487   ⟸   NM_001195558
- UniProtKB: D3ZWP8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000037105   ⟸   ENSRNOT00000034334

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZWP8-F1-model_v2 AlphaFold D3ZWP8 1-366 view protein structure

Transcriptome

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

Promoters
RGD ID:13698171
Promoter ID:EPDNEW_R8696
Type:initiation region
Name:Lrrc58_1
Description:leucine rich repeat containing 58
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_6.01165,759,574 - 65,759,634EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307440 AgrOrtholog
BioCyc Gene G2FUF-21261 BioCyc
Ensembl Genes ENSRNOG00000027151 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034334.6 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_4 UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  LRR-SigEffector_domain UniProtKB/TrEMBL
KEGG Report rno:303919 UniProtKB/TrEMBL
NCBI Gene 303919 ENTREZGENE
PANTHER LEUCINE-RICH REPEAT-CONTAINING UniProtKB/TrEMBL
  LEUCINE-RICH REPEAT-CONTAINING PROTEIN 58 UniProtKB/TrEMBL
Pfam LRR_1 UniProtKB/TrEMBL
  LRR_4 UniProtKB/TrEMBL
  LRR_8 UniProtKB/TrEMBL
PhenoGen Lrrc58 PhenoGen
PROSITE LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000027151 RatGTEx
SMART LRR_TYP UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
UniProt D3ZWP8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Lrrc58  leucine rich repeat containing 58   Lrrc58_predicted  leucine rich repeat containing 58 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Lrrc58_predicted  leucine rich repeat containing 58 (predicted)  RGD1307440_predicted  similar to RIKEN cDNA C330018J07 gene (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1307440_predicted  similar to RIKEN cDNA C330018J07 gene (predicted)  LOC303919_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC303919_predicted  similar to RIKEN cDNA C330018J07 gene (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL