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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81176,355,987 - 76,368,309 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1176,344,923 - 76,368,309 (-)EnsemblGRCr8
mRatBN7.21162,850,507 - 62,862,829 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1162,847,562 - 62,862,829 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1171,662,995 - 71,675,321 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01164,325,211 - 64,337,533 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01163,375,244 - 63,387,580 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01165,747,235 - 65,759,558 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1165,747,036 - 65,759,581 (-)Ensemblrn6Rnor6.0
Rnor_5.01168,841,233 - 68,853,498 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41164,635,216 - 64,646,888 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1162,348,644 - 62,360,967 (-)NCBICelera
RGSC_v3.11164,703,933 - 64,704,423 (-)NCBI
Cytogenetic Map11q21NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. 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 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1176,344,923 - 76,368,309 (-)EnsemblGRCr8
mRatBN7.21162,850,507 - 62,862,829 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1162,847,562 - 62,862,829 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1171,662,995 - 71,675,321 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01164,325,211 - 64,337,533 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01163,375,244 - 63,387,580 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01165,747,235 - 65,759,558 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1165,747,036 - 65,759,581 (-)Ensemblrn6Rnor6.0
Rnor_5.01168,841,233 - 68,853,498 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41164,635,216 - 64,646,888 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1162,348,644 - 62,360,967 (-)NCBICelera
RGSC_v3.11164,703,933 - 64,704,423 (-)NCBI
Cytogenetic Map11q21NCBI
LRRC58
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383120,324,509 - 120,349,354 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3120,324,509 - 120,349,409 (-)Ensemblhg38GRCh38
GRCh373120,043,356 - 120,068,201 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363121,526,266 - 121,550,876 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm381637,868,400 - 37,888,857 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1637,868,389 - 37,888,858 (+)Ensemblmm10GRCm38
MGSCv371637,868,486 - 37,888,943 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (-)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3323,871,217 - 23,891,596 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03324,081,600 - 24,101,985 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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 1.0HetGla 1.0hetGla2
Lrrc58
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1422,832,806 - 22,846,229 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Lrrc58
177 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)114644316891443168Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)117330848796070872Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113330600878306008Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)115892833699753367Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113294306789836615Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)113642841681428416Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)117385089499753367Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)113461876079618760Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)115893182292356038Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)115775483796071021Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112019354996351019Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)116796218499753367Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)117330831599753367Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)113674945981749459Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)115107102196071021Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)112252474682951192Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)113330600878306008Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)113674945981749459Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113191546976915469Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)115441539196071021Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)113674945981749459Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)113674945981749459Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)116859932196497754Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)116985594399753367Rat

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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 11 67 160 91 90 59 89 59 6 352 188 9 139 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000034334   ⟹   ENSRNOP00000037105
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1176,344,923 - 76,368,309 (-)Ensembl
mRatBN7.2 Ensembl1162,847,562 - 62,862,829 (-)Ensembl
Rnor_6.0 Ensembl1165,747,036 - 65,759,581 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000128937   ⟹   ENSRNOP00000107230
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1176,354,986 - 76,368,309 (-)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 ENSRNOP00000037105.6
  ENSRNOP00000107230
  ENSRNOP00000107230.1
RefSeq Acc Id: NP_001182487   ⟸   NM_001195558
- UniProtKB: D3ZWP8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000037105   ⟸   ENSRNOT00000034334
Ensembl Acc Id: ENSRNOP00000107230   ⟸   ENSRNOT00000128937

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, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034334.7 UniProtKB/TrEMBL
  ENSRNOT00000128937 ENTREZGENE
  ENSRNOT00000128937.1 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 AND IQ DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
  LEUCINE-RICH REPEAT-CONTAINING 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 A0ABK0LTN7_RAT UniProtKB/TrEMBL
  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