Lingo3 (leucine rich repeat and Ig domain containing 3) - Rat Genome Database

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Gene: Lingo3 (leucine rich repeat and Ig domain containing 3) Rattus norvegicus
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Symbol: Lingo3
Name: leucine rich repeat and Ig domain containing 3
RGD ID: 1592209
Description: Predicted to enable signaling receptor activity. Predicted to be involved in regulation of nervous system development. Predicted to be located in membrane. Predicted to be active in plasma membrane. Orthologous to human LINGO3 (leucine rich repeat and Ig domain containing 3); INTERACTS WITH 6-propyl-2-thiouracil; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 3; LOC686868; LOC690755; similar to leucine rich repeat neuronal 6C
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
GRCr879,519,252 - 9,530,675 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl79,513,743 - 9,531,155 (+)EnsemblGRCr8
mRatBN7.278,869,025 - 8,878,431 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl78,869,025 - 8,878,431 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx711,753,044 - 11,762,461 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0713,628,548 - 13,637,965 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0711,495,081 - 11,504,496 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,737,293 - 11,746,703 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,737,293 - 11,746,703 (+)Ensemblrn6Rnor6.0
Rnor_5.0711,905,008 - 11,914,418 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4710,379,660 - 10,389,070 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera77,053,134 - 7,062,544 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse:




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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Lingo3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr879,519,252 - 9,530,675 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl79,513,743 - 9,531,155 (+)EnsemblGRCr8
mRatBN7.278,869,025 - 8,878,431 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl78,869,025 - 8,878,431 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx711,753,044 - 11,762,461 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0713,628,548 - 13,637,965 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0711,495,081 - 11,504,496 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,737,293 - 11,746,703 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,737,293 - 11,746,703 (+)Ensemblrn6Rnor6.0
Rnor_5.0711,905,008 - 11,914,418 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4710,379,660 - 10,389,070 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera77,053,134 - 7,062,544 (+)NCBICelera
Cytogenetic Map7q11NCBI
LINGO3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38192,287,164 - 2,308,154 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl192,287,164 - 2,308,174 (-)Ensemblhg38GRCh38
GRCh37192,287,163 - 2,308,153 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36192,240,774 - 2,259,156 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34192,240,998 - 2,243,023NCBI
Celera192,223,699 - 2,242,250 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef192,061,655 - 2,063,324 (-)NCBIHuRef
CHM1_1192,289,362 - 2,307,712 (-)NCBICHM1_1
T2T-CHM13v2.0192,260,807 - 2,281,793 (-)NCBIT2T-CHM13v2.0
Lingo3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391080,668,635 - 80,679,873 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1080,668,635 - 80,679,873 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381080,832,801 - 80,844,039 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1080,832,801 - 80,844,039 (-)Ensemblmm10GRCm38
MGSCv371080,295,546 - 80,306,784 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361080,235,930 - 80,247,159 (-)NCBIMGSCv36mm8
Celera1081,851,599 - 81,862,837 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Lingo3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554955,860,126 - 5,861,939 (+)Ensembl
ChiLan1.0NW_0049554955,850,956 - 5,862,249 (+)NCBIChiLan1.0ChiLan1.0
LINGO3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2206,672,881 - 6,691,244 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1195,902,227 - 5,920,590 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0191,299,345 - 1,317,706 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LINGO3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12056,755,986 - 56,757,919 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2056,551,520 - 56,555,841 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02057,489,312 - 57,493,633 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2057,479,171 - 57,493,653 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12056,541,372 - 56,545,693 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02057,026,564 - 57,030,880 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02057,226,955 - 57,231,276 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Lingo3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118216,461,823 - 216,466,729 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365881,369,707 - 1,371,485 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365881,368,048 - 1,372,364 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LINGO3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl276,264,071 - 76,280,623 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1276,264,077 - 76,280,627 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2276,825,890 - 76,843,050 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LINGO3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.162,081,234 - 2,103,094 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl62,082,224 - 2,084,002 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660816,609,756 - 6,628,671 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lingo3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248286,592,957 - 6,609,665 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248286,592,941 - 6,609,698 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Lingo3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11154,040,481 - 154,051,642 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Lingo3
73 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:46
Interacting mature miRNAs:51
Transcripts:ENSRNOT00000046059
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7166965846669658Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7123748937Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7721609752216097Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)7131777942Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7170952746709527Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7132612984Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7946087754460877Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7129716167Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134650782Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7132612984Rat


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
15 11 26 158 59 58 27 85 27 6 246 143 9 134 53 90 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000046059   ⟹   ENSRNOP00000051446
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl79,527,138 - 9,529,118 (+)Ensembl
mRatBN7.2 Ensembl78,869,025 - 8,878,431 (+)Ensembl
Rnor_6.0 Ensembl711,737,293 - 11,746,703 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000121498   ⟹   ENSRNOP00000109029
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl79,526,205 - 9,530,118 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000145182   ⟹   ENSRNOP00000100230
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl79,519,402 - 9,530,107 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000159580   ⟹   ENSRNOP00000110002
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl79,523,682 - 9,531,155 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000167882   ⟹   ENSRNOP00000103480
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl79,513,743 - 9,530,107 (+)Ensembl
RefSeq Acc Id: NM_001109609   ⟹   NP_001103079
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,519,698 - 9,529,106 (+)NCBI
mRatBN7.278,869,025 - 8,878,431 (+)NCBI
Rnor_6.0711,737,293 - 11,746,703 (+)NCBI
Rnor_5.0711,905,008 - 11,914,418 (+)NCBI
RGSC_v3.4710,379,660 - 10,389,070 (+)RGD
Celera77,053,134 - 7,062,544 (+)RGD
Sequence:
RefSeq Acc Id: XM_063264283   ⟹   XP_063120353
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,519,252 - 9,530,675 (+)NCBI
RefSeq Acc Id: NP_001103079   ⟸   NM_001109609
- Peptide Label: precursor
- UniProtKB: D3ZW19 (UniProtKB/TrEMBL),   A6K8F1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000051446   ⟸   ENSRNOT00000046059
RefSeq Acc Id: XP_063120353   ⟸   XM_063264283
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000109029   ⟸   ENSRNOT00000121498
Ensembl Acc Id: ENSRNOP00000100230   ⟸   ENSRNOT00000145182
Ensembl Acc Id: ENSRNOP00000103480   ⟸   ENSRNOT00000167882
Ensembl Acc Id: ENSRNOP00000110002   ⟸   ENSRNOT00000159580
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZW19-F1-model_v2 AlphaFold D3ZW19 1-589 view protein structure

Transcriptome

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

Promoters
RGD ID:13695001
Promoter ID:EPDNEW_R5525
Type:single initiation site
Name:Lingo3_1
Description:leucine rich repeat and Ig domain containing 3
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_6.0711,737,320 - 11,737,380EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1592209 AgrOrtholog
BioCyc Gene G2FUF-34972 BioCyc
Ensembl Genes ENSRNOG00000032569 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000046059 ENTREZGENE
  ENSRNOT00000046059.5 UniProtKB/TrEMBL
  ENSRNOT00000121498.1 UniProtKB/TrEMBL
  ENSRNOT00000145182.1 UniProtKB/TrEMBL
  ENSRNOT00000159580 ENTREZGENE
  ENSRNOT00000159580.1 UniProtKB/TrEMBL
  ENSRNOT00000167882.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/TrEMBL
InterPro Cys-rich_flank_reg_C UniProtKB/TrEMBL
  Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_I-set UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/TrEMBL
  L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  LRFN UniProtKB/TrEMBL
  LRR-contain_N UniProtKB/TrEMBL
KEGG Report rno:690755 UniProtKB/TrEMBL
NCBI Gene 690755 ENTREZGENE
PANTHER CARBOXYPEPTIDASE N SUBUNIT 2-LIKE UniProtKB/TrEMBL
  SYNAPTIC ADHESION-LIKE MOLECULE SALM UniProtKB/TrEMBL
Pfam I-set UniProtKB/TrEMBL
  LRR_1 UniProtKB/TrEMBL
  LRR_8 UniProtKB/TrEMBL
PhenoGen Lingo3 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
  LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000032569 RatGTEx
SMART IGc2 UniProtKB/TrEMBL
  LRR_TYP UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
  LRRNT UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0ABK0LAU1_RAT UniProtKB/TrEMBL
  A0ABK0LDF3_RAT UniProtKB/TrEMBL
  A0ABK0M4X1_RAT UniProtKB/TrEMBL
  A6K8F1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZW19 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-09 LOC690755  similar to leucine rich repeat neuronal 6C  LOC686868  similar to leucine rich repeat neuronal 6C  Data merged from RGD:1592486 737654 APPROVED
2008-10-09 Lingo3  leucine rich repeat and Ig domain containing 3  LOC690755  similar to leucine rich repeat neuronal 6C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC686868  similar to leucine rich repeat neuronal 6C      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC690755  similar to leucine rich repeat neuronal 6C      Symbol and Name status set to provisional 70820 PROVISIONAL