Lrrn4 (leucine rich repeat neuronal 4) - Rat Genome Database

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Gene: Lrrn4 (leucine rich repeat neuronal 4) Rattus norvegicus
Analyze
Symbol: Lrrn4
Name: leucine rich repeat neuronal 4
RGD ID: 1305256
Description: Predicted to be involved in long-term memory. Predicted to act upstream of or within visual learning. Predicted to be active in plasma membrane. Orthologous to human LRRN4 (leucine rich repeat neuronal 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; aconitine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: leucine-rich repeat neuronal protein 4; LOC311443; RGD1305256; similar to chromosome 20 open reading frame 75
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
GRCr83140,592,303 - 140,603,986 (-)NCBIGRCr8
mRatBN7.23120,138,093 - 120,150,877 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3120,139,410 - 120,150,831 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.03125,521,879 - 125,547,685 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3125,523,781 - 125,533,600 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03132,005,657 - 132,017,224 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43120,667,859 - 120,678,960 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13120,573,457 - 120,582,891 (-)NCBI
Celera3118,924,058 - 118,938,227 (-)NCBICelera
Cytogenetic Map3q36NCBI
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

Biological Process

Cellular Component
plasma membrane  (IBA,ISO)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15870286   PMID:23533145  


Genomics

Comparative Map Data
Lrrn4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83140,592,303 - 140,603,986 (-)NCBIGRCr8
mRatBN7.23120,138,093 - 120,150,877 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3120,139,410 - 120,150,831 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.03125,521,879 - 125,547,685 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3125,523,781 - 125,533,600 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03132,005,657 - 132,017,224 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43120,667,859 - 120,678,960 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13120,573,457 - 120,582,891 (-)NCBI
Celera3118,924,058 - 118,938,227 (-)NCBICelera
Cytogenetic Map3q36NCBI
LRRN4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38206,040,546 - 6,054,060 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl206,040,546 - 6,054,060 (-)EnsemblGRCh38hg38GRCh38
GRCh37206,021,192 - 6,034,706 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36205,969,426 - 5,982,676 (-)NCBINCBI36Build 36hg18NCBI36
Build 34205,969,423 - 5,982,676NCBI
Celera206,092,695 - 6,105,965 (-)NCBICelera
Cytogenetic Map20p12.3NCBI
HuRef205,977,570 - 5,991,103 (-)NCBIHuRef
CHM1_1206,021,215 - 6,034,747 (-)NCBICHM1_1
T2T-CHM13v2.0206,080,866 - 6,094,379 (-)NCBIT2T-CHM13v2.0
Lrrn4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392132,710,436 - 132,735,930 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2132,710,225 - 132,722,811 (-)EnsemblGRCm39 Ensembl
GRCm382132,866,686 - 132,894,010 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2132,868,305 - 132,880,891 (-)EnsemblGRCm38mm10GRCm38
MGSCv372132,694,252 - 132,706,598 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362132,559,957 - 132,572,303 (-)NCBIMGSCv36mm8
Celera2134,096,013 - 134,108,361 (-)NCBICelera
Cytogenetic Map2F2NCBI
cM Map264.78NCBI
Lrrn4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541516,411,369 - 16,423,814 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541516,413,666 - 16,423,605 (-)NCBIChiLan1.0ChiLan1.0
LRRN4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2216,964,414 - 6,978,584 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1206,960,874 - 6,978,842 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0206,037,097 - 6,052,341 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1205,820,854 - 5,834,178 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl205,820,854 - 5,834,178 (-)Ensemblpanpan1.1panPan2
LRRN4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12415,801,220 - 15,810,954 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2415,803,125 - 15,810,930 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2415,623,936 - 15,633,180 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02416,204,375 - 16,213,624 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12415,811,132 - 15,820,384 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02415,918,191 - 15,928,529 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02416,250,952 - 16,260,205 (+)NCBIUU_Cfam_GSD_1.0
Lrrn4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640164,606,938 - 164,618,047 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648513,039,430 - 13,047,375 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648513,039,430 - 13,049,359 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRRN4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11714,895,954 - 14,908,112 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21716,009,862 - 16,022,226 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LRRN4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1232,078,993 - 32,092,725 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl232,083,313 - 32,091,660 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607112,448,425 - 12,460,382 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lrrn4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247416,857,658 - 6,864,825 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247416,855,911 - 6,865,972 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lrrn4
132 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:70
Count of miRNA genes:63
Interacting mature miRNAs:63
Transcripts:ENSRNOT00000040802
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
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)384091273129091273Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3115638168135181505Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3112287552135181505Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat


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
8 9 49 93 90 89 58 25 58 6 213 95 73 44 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000040802   ⟹   ENSRNOP00000048191
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3120,139,410 - 120,150,831 (-)Ensembl
Rnor_6.0 Ensembl3125,523,781 - 125,533,600 (-)Ensembl
RefSeq Acc Id: XM_230550   ⟹   XP_230550
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83140,592,303 - 140,603,986 (-)NCBI
mRatBN7.23120,138,093 - 120,150,877 (-)NCBI
Rnor_6.03125,521,879 - 125,547,685 (-)NCBI
Rnor_5.03132,005,657 - 132,017,224 (-)NCBI
RGSC_v3.43120,667,859 - 120,678,960 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001417380 (Get FASTA)   NCBI Sequence Viewer  
  XP_230550 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL80277 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000048191.4
RefSeq Acc Id: XP_230550   ⟸   XM_230550
- Sequence:
Ensembl Acc Id: ENSRNOP00000048191   ⟸   ENSRNOT00000040802
Protein Domains
Fibronectin type-III

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LTX4-F1-model_v2 AlphaFold F1LTX4 1-735 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:1305256 AgrOrtholog
BioCyc Gene G2FUF-47759 BioCyc
Ensembl Genes ENSRNOG00000032989 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000040802.6 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/TrEMBL
InterPro FN3_sf UniProtKB/TrEMBL
  FN_III UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  LRR_TM_domain-containing UniProtKB/TrEMBL
KEGG Report rno:311443 UniProtKB/TrEMBL
NCBI Gene 311443 ENTREZGENE
PANTHER ANTIGEN BSP, PUTATIVE-RELATED UniProtKB/TrEMBL
  CHAOPTIN-RELATED UniProtKB/TrEMBL
Pfam fn3 UniProtKB/TrEMBL
  LRR_8 UniProtKB/TrEMBL
PhenoGen Lrrn4 PhenoGen
PROSITE FN3 UniProtKB/TrEMBL
  LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000032989 RatGTEx
SMART FN3 UniProtKB/TrEMBL
  LRR_TYP UniProtKB/TrEMBL
Superfamily-SCOP FN_III-like UniProtKB/TrEMBL
  L domain-like UniProtKB/TrEMBL
UniProt F1LTX4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Lrrn4  leucine rich repeat neuronal 4  RGD1305256  similar to chromosome 20 open reading frame 75   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1305256  similar to chromosome 20 open reading frame 75   RGD1305256_predicted  similar to chromosome 20 open reading frame 75 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1305256_predicted  similar to chromosome 20 open reading frame 75 (predicted)  LOC311443_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC311443_predicted  similar to chromosome 20 open reading frame 75 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL