Lrrc3b (leucine rich repeat containing 3B) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Lrrc3b (leucine rich repeat containing 3B) Rattus norvegicus
Analyze
Symbol: Lrrc3b
Name: leucine rich repeat containing 3B
RGD ID: 1311897
Description: Predicted to be located in membrane. Predicted to be active in extracellular matrix and extracellular space. Orthologous to human LRRC3B (leucine rich repeat containing 3B); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: leucine-rich repeat-containing protein 3B; LOC305705; RGD1311897; similar to CDNA sequence BC019794
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
GRCr81512,404,309 - 12,481,618 (+)NCBIGRCr8
mRatBN7.2159,973,580 - 10,050,891 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl159,969,983 - 10,051,066 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1512,107,545 - 12,184,909 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01513,024,702 - 13,102,448 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01511,320,812 - 11,398,172 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01511,221,161 - 11,299,563 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1511,298,478 - 11,299,257 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01515,263,496 - 15,339,800 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41511,523,924 - 11,525,146 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11511,446,989 - 11,525,148 (+)NCBI
Celera159,982,189 - 10,061,691 (+)NCBICelera
Cytogenetic Map15p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. 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:20080187  


Genomics

Comparative Map Data
Lrrc3b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81512,404,309 - 12,481,618 (+)NCBIGRCr8
mRatBN7.2159,973,580 - 10,050,891 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl159,969,983 - 10,051,066 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1512,107,545 - 12,184,909 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01513,024,702 - 13,102,448 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01511,320,812 - 11,398,172 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01511,221,161 - 11,299,563 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1511,298,478 - 11,299,257 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01515,263,496 - 15,339,800 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41511,523,924 - 11,525,146 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11511,446,989 - 11,525,148 (+)NCBI
Celera159,982,189 - 10,061,691 (+)NCBICelera
Cytogenetic Map15p16NCBI
LRRC3B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38326,622,772 - 26,710,776 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl326,622,772 - 26,717,537 (+)EnsemblGRCh38hg38GRCh38
GRCh37326,664,263 - 26,752,267 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36326,639,304 - 26,727,271 (+)NCBINCBI36Build 36hg18NCBI36
Build 34326,639,303 - 26,727,267NCBI
Celera326,600,894 - 26,688,865 (+)NCBICelera
Cytogenetic Map3p24.1NCBI
HuRef326,607,531 - 26,695,409 (+)NCBIHuRef
CHM1_1326,614,322 - 26,702,255 (+)NCBICHM1_1
T2T-CHM13v2.0326,625,372 - 26,713,383 (+)NCBIT2T-CHM13v2.0
Lrrc3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39147,030,776 - 7,112,248 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl147,030,776 - 7,112,248 (+)EnsemblGRCm39 Ensembl
GRCm381415,357,515 - 15,438,987 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1415,357,515 - 15,438,987 (-)EnsemblGRCm38mm10GRCm38
MGSCv371416,190,029 - 16,271,501 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361414,150,787 - 14,232,140 (-)NCBIMGSCv36mm8
Celera1411,035,950 - 11,116,191 (-)NCBICelera
Cytogenetic Map14A1NCBI
cM Map147.08NCBI
Lrrc3b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543018,351,763 - 18,440,120 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543018,351,763 - 18,440,120 (+)NCBIChiLan1.0ChiLan1.0
LRRC3B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2226,577,882 - 26,665,060 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1326,582,643 - 26,676,611 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0326,518,378 - 26,609,907 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1326,847,229 - 26,940,500 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl326,932,929 - 26,933,708 (+)Ensemblpanpan1.1panPan2
LRRC3B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12317,300,448 - 17,386,203 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2317,300,769 - 17,301,548 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2317,298,781 - 17,384,342 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02317,601,654 - 17,687,281 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2317,601,975 - 17,602,754 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12317,426,475 - 17,512,018 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02317,538,885 - 17,624,504 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02317,602,411 - 17,687,615 (-)NCBIUU_Cfam_GSD_1.0
Lrrc3b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118184,814,191 - 184,899,046 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647317,952,887 - 18,037,619 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647317,952,525 - 18,038,537 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRRC3B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1313,327,220 - 13,420,223 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11313,327,030 - 13,420,216 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21314,844,985 - 14,937,138 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LRRC3B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11571,260,811 - 71,349,584 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1571,348,482 - 71,349,258 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604144,415,643 - 44,520,224 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lrrc3b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247884,556,975 - 4,559,059 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247884,470,143 - 4,559,059 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lrrc3b
477 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:116
Count of miRNA genes:92
Interacting mature miRNAs:104
Transcripts:ENSRNOT00000007672
Prediction methods:Microtar, 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
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15105825014481294Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15226636822711984Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15226636822711984Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat

Markers in Region
RH137538  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21510,050,674 - 10,050,796 (+)MAPPERmRatBN7.2
Rnor_6.01511,299,352 - 11,299,473NCBIRnor6.0
Rnor_5.01515,339,589 - 15,339,710UniSTSRnor5.0
RGSC_v3.41511,524,930 - 11,525,051UniSTSRGSC3.4
Celera1510,061,480 - 10,061,601UniSTS
Cytogenetic Map15p16UniSTS


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 9 1 46
Low 2 24 16 2 17 2 8 10 26 22 35 10 8
Below cutoff 1 10 21 19 2 19 2 10 6 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007672   ⟹   ENSRNOP00000007672
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl159,975,106 - 10,051,066 (+)Ensembl
Rnor_6.0 Ensembl1511,298,478 - 11,299,257 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094588   ⟹   ENSRNOP00000085779
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1510,036,615 - 10,051,066 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106822   ⟹   ENSRNOP00000089225
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl159,969,983 - 10,051,066 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117616   ⟹   ENSRNOP00000081685
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl159,975,275 - 10,050,887 (+)Ensembl
RefSeq Acc Id: NM_001399495   ⟹   NP_001386424
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81512,404,309 - 12,481,618 (+)NCBI
mRatBN7.2159,973,580 - 10,050,891 (+)NCBI
RefSeq Acc Id: XM_006251719   ⟹   XP_006251781
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81512,404,434 - 12,481,618 (+)NCBI
mRatBN7.2159,975,028 - 10,050,891 (+)NCBI
Rnor_6.01511,221,161 - 11,299,563 (+)NCBI
Rnor_5.01515,263,496 - 15,339,800 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599839   ⟹   XP_017455328
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81512,404,434 - 12,481,618 (+)NCBI
mRatBN7.2159,975,213 - 10,050,891 (+)NCBI
Rnor_6.01511,221,161 - 11,299,563 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_006251781   ⟸   XM_006251719
- Peptide Label: isoform X1
- UniProtKB: D4A9I7 (UniProtKB/TrEMBL),   A6K053 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455328   ⟸   XM_017599839
- Peptide Label: isoform X1
- UniProtKB: D4A9I7 (UniProtKB/TrEMBL),   A6K053 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007672   ⟸   ENSRNOT00000007672
RefSeq Acc Id: ENSRNOP00000085779   ⟸   ENSRNOT00000094588
RefSeq Acc Id: ENSRNOP00000081685   ⟸   ENSRNOT00000117616
RefSeq Acc Id: ENSRNOP00000089225   ⟸   ENSRNOT00000106822
RefSeq Acc Id: NP_001386424   ⟸   NM_001399495
- Peptide Label: precursor
- UniProtKB: D4A9I7 (UniProtKB/TrEMBL),   A6K053 (UniProtKB/TrEMBL)
Protein Domains
LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A9I7-F1-model_v2 AlphaFold D4A9I7 1-259 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:1311897 AgrOrtholog
BioCyc Gene G2FUF-14408 BioCyc
Ensembl Genes ENSRNOG00000005857 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007672.6 UniProtKB/TrEMBL
  ENSRNOT00000094588.1 UniProtKB/TrEMBL
  ENSRNOT00000106822 ENTREZGENE
  ENSRNOT00000106822.1 UniProtKB/TrEMBL
  ENSRNOT00000117616.1 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  LRR-contain_N UniProtKB/TrEMBL
KEGG Report rno:305705 UniProtKB/TrEMBL
NCBI Gene 305705 ENTREZGENE
PANTHER ANTIGEN BSP, PUTATIVE-RELATED UniProtKB/TrEMBL
  LEUCINE-RICH REPEAT-CONTAINING PROTEIN 3B-LIKE UniProtKB/TrEMBL
Pfam LRR_1 UniProtKB/TrEMBL
  LRR_8 UniProtKB/TrEMBL
  LRRNT UniProtKB/TrEMBL
PhenoGen Lrrc3b PhenoGen
PROSITE LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000005857 RatGTEx
SMART LRR_TYP UniProtKB/TrEMBL
  LRRNT UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
UniProt A6K053 ENTREZGENE, UniProtKB/TrEMBL
  D4A9I7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Lrrc3b  leucine rich repeat containing 3B   Lrrc3b_predicted  leucine rich repeat containing 3B (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Lrrc3b_predicted  leucine rich repeat containing 3B (predicted)  RGD1311897_predicted  similar to CDNA sequence BC019794 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1311897_predicted  similar to CDNA sequence BC019794 (predicted)  LOC305705_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC305705_predicted  similar to CDNA sequence BC019794 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL