Lrrtm4 (leucine rich repeat transmembrane neuronal 4) - Rat Genome Database

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Gene: Lrrtm4 (leucine rich repeat transmembrane neuronal 4) Rattus norvegicus
Analyze
Symbol: Lrrtm4
Name: leucine rich repeat transmembrane neuronal 4
RGD ID: 1560707
Description: Predicted to have heparan sulfate proteoglycan binding activity. Involved in synapse organization. Localizes to glutamatergic synapse and integral component of postsynaptic density membrane. Orthologous to human LRRTM4 (leucine rich repeat transmembrane neuronal 4); INTERACTS WITH (S)-nicotine; 2,3,7,8-tetrachlorodibenzodioxine; atrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: leucine-rich repeat transmembrane neuronal protein 4; LOC500219; MGC188202; RGD1560707; similar to leucine-rich repeat transmembrane neuronal 4 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24112,545,874 - 113,338,713 (+)NCBI
Rnor_6.0 Ensembl4110,699,557 - 111,497,643 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04110,699,577 - 111,497,643 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04175,389,206 - 176,188,408 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44114,142,055 - 114,940,958 (+)NCBIRGSC3.4rn4RGSC3.4
Celera4101,556,445 - 102,345,352 (+)NCBICelera
Cytogenetic Map4q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:22632720   PMID:23911104   PMID:24613359   PMID:25624497  


Genomics

Comparative Map Data
Lrrtm4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24112,545,874 - 113,338,713 (+)NCBI
Rnor_6.0 Ensembl4110,699,557 - 111,497,643 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04110,699,577 - 111,497,643 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04175,389,206 - 176,188,408 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44114,142,055 - 114,940,958 (+)NCBIRGSC3.4rn4RGSC3.4
Celera4101,556,445 - 102,345,352 (+)NCBICelera
Cytogenetic Map4q34NCBI
LRRTM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl276,747,719 - 77,593,319 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl276,747,685 - 77,593,319 (-)EnsemblGRCh38hg38GRCh38
GRCh38276,747,685 - 77,522,376 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37276,974,811 - 77,749,502 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36277,597,295 - 77,603,010 (-)NCBINCBI36hg18NCBI36
Build 34277,655,448 - 77,661,157NCBI
Celera276,805,254 - 77,579,821 (-)NCBI
Cytogenetic Map2p12NCBI
HuRef276,709,976 - 77,484,740 (-)NCBIHuRef
CHM1_1276,904,205 - 77,678,822 (-)NCBICHM1_1
Lrrtm4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39679,995,828 - 80,787,143 (+)NCBIGRCm39mm39
GRCm39 Ensembl679,995,860 - 80,787,124 (+)Ensembl
GRCm38680,018,858 - 80,810,162 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl680,018,877 - 80,810,143 (+)EnsemblGRCm38mm10GRCm38
MGSCv37679,968,871 - 79,974,926 (+)NCBIGRCm37mm9NCBIm37
MGSCv36679,948,557 - 79,955,418 (+)NCBImm8
Celera682,022,464 - 82,028,524 (+)NCBICelera
Cytogenetic Map6C3NCBI
Lrrtm4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554248,606,089 - 9,276,104 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554248,606,660 - 9,277,125 (+)NCBIChiLan1.0ChiLan1.0
LRRTM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A78,333,473 - 79,183,332 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A79,123,161 - 79,183,506 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A76,830,224 - 77,616,298 (-)NCBIMhudiblu_PPA_v0panPan3
LRRTM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11746,091,140 - 46,797,107 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1746,090,978 - 46,796,020 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1745,736,852 - 46,442,691 (+)NCBI
ROS_Cfam_1.01746,911,990 - 47,620,541 (+)NCBI
UMICH_Zoey_3.11745,978,590 - 46,683,825 (+)NCBI
UNSW_CanFamBas_1.01746,025,196 - 46,733,195 (+)NCBI
UU_Cfam_GSD_1.01746,534,851 - 47,241,087 (+)NCBI
Lrrtm4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244062927,243,844 - 7,977,608 (+)NCBI
SpeTri2.0NW_0049365562,760,294 - 3,493,517 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRRTM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl366,128,689 - 66,884,740 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1366,128,650 - 66,884,916 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2369,438,923 - 70,171,188 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LRRTM4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11429,751,187 - 30,505,542 (+)NCBI
Lrrtm4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474925,669,342 - 26,445,401 (+)NCBI

Position Markers
D4Got225  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24113,262,180 - 113,262,306 (+)MAPPER
mRatBN7.24113,262,180 - 113,262,461 (+)MAPPER
Rnor_6.04111,423,620 - 111,423,745NCBIRnor6.0
Rnor_6.04111,423,620 - 111,423,957NCBIRnor6.0
Rnor_5.04176,114,022 - 176,114,359UniSTSRnor5.0
Rnor_5.04176,114,022 - 176,114,147UniSTSRnor5.0
RGSC_v3.44114,865,107 - 114,865,232UniSTSRGSC3.4
Celera4102,270,485 - 102,270,610UniSTS
Cytogenetic Map4q34UniSTS
D4Got219  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24112,814,253 - 112,814,426 (+)MAPPER
Rnor_6.04110,970,130 - 110,970,302NCBIRnor6.0
Rnor_5.04175,659,768 - 175,659,940UniSTSRnor5.0
RGSC_v3.44114,414,132 - 114,414,304UniSTSRGSC3.4
Celera4101,823,900 - 101,824,072UniSTS
Cytogenetic Map4q34UniSTS
RH143120  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24112,794,567 - 112,794,686 (+)MAPPER
Rnor_6.04110,950,468 - 110,950,586NCBIRnor6.0
Rnor_5.04175,640,106 - 175,640,224UniSTSRnor5.0
RGSC_v3.44114,394,450 - 114,394,568UniSTSRGSC3.4
Celera4101,804,219 - 101,804,337UniSTS
RH 3.4 Map4663.3UniSTS
Cytogenetic Map4q34UniSTS
AU047169  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24113,290,786 - 113,290,988 (+)MAPPER
Rnor_6.04111,451,121 - 111,451,322NCBIRnor6.0
Rnor_5.04176,141,886 - 176,142,087UniSTSRnor5.0
RGSC_v3.44114,895,467 - 114,895,668UniSTSRGSC3.4
Celera4102,299,342 - 102,299,543UniSTS
Cytogenetic Map4q34UniSTS
AU046930  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24113,181,588 - 113,181,720 (+)MAPPER
Rnor_6.04111,342,628 - 111,342,761NCBIRnor6.0
Rnor_5.04176,032,052 - 176,032,185UniSTSRnor5.0
RGSC_v3.44114,783,181 - 114,783,314UniSTSRGSC3.4
Celera4102,189,599 - 102,189,732UniSTS
Cytogenetic Map4q34UniSTS
AU049873  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24113,238,004 - 113,238,249 (+)MAPPER
Rnor_6.04111,399,445 - 111,399,689NCBIRnor6.0
Rnor_5.04176,089,847 - 176,090,091UniSTSRnor5.0
RGSC_v3.44114,840,931 - 114,841,175UniSTSRGSC3.4
Celera4102,246,421 - 102,246,657UniSTS
Cytogenetic Map4q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)43043231145254791Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)429549895112807890Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)436615599145611886Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)437703272115372927Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)443414605155469929Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)443414792146942075Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)443414792146942075Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)446898276145611886Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)449906054145611886Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)455324953148360954Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)455375865125671711Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)458640017154427984Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)460439127113416139Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)461038901127777403Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in pulse pressure (CMO:0001882)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in systolic blood pressure (CMO:0000747)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in mean arterial blood pressure (CMO:0002035)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)461708341113100992Rat
1641919Alc22Alcohol consumption QTL 220.0005drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)462947687125671711Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)463537179157286626Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)470773471132455556Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)471476518116476518Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)471476518116476518Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)473786419132455556Rat
724522Bp146Blood pressure QTL 1462.20.0021arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)475258970120258970Rat
2302051Pia28Pristane induced arthritis QTL 285.30.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)475258970120258970Rat
738015Pia9Pristane induced arthritis QTL 94.50.048joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)476567036121567036Rat
70167Bw22Body weight QTL 223.1body mass (VT:0001259)body weight (CMO:0000012)477307388116916073Rat
1357342Bw40Body weight QTL 400.001body mass (VT:0001259)body weight (CMO:0000012)477307388116916073Rat
631662Hcar2Hepatocarcinoma resistance QTL 23.10.0003liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)479555067124555067Rat
631556Bp135Blood pressure QTL 1350.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)479557856116916073Rat
2306899Bp338Blood pressure QTL 3380.071arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)481874073119546974Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)481959983152055009Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)484475257178931073Rat
634334Xhs3X-ray hypersensitivity QTL 310intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)485794049129615056Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)486312589146942261Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)486312589147702403Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486438317168047091Rat
61476Aia3Adjuvant induced arthritis QTL 33.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)486532519131532519Rat
1578662Bss15Bone structure and strength QTL 1519.6femur width (VT:1000666)femoral neck width (CMO:0001695)487136446132136446Rat
1578670Bss14Bone structure and strength QTL 1416.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)487136446132136446Rat
631689Scl4Serum cholesterol level QTL 41.90.008blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)494414208139414208Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)494893247168046938Rat
61434Cia3Collagen induced arthritis QTL 34.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)499066823144066823Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105277348150277348Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4105682594150682594Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4105971071168047091Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106347236151347236Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4108876717169215811Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109636356154636356Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109636356154636356Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110702761155702761Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110702761155702761Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:27
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000030588
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.


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 42
Low 20 7 6 6 2 2 32 16 29 3 2
Below cutoff 3 22 29 14 13 14 5 5 4 5 5 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000030588   ⟹   ENSRNOP00000034217
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4110,699,557 - 110,704,822 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092261   ⟹   ENSRNOP00000075874
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4110,699,686 - 110,702,880 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092379   ⟹   ENSRNOP00000075837
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4110,700,403 - 111,497,643 (+)Ensembl
RefSeq Acc Id: NM_001134746   ⟹   NP_001128218
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24112,546,683 - 113,336,793 (+)NCBI
Rnor_6.04110,700,403 - 111,497,643 (+)NCBI
Rnor_5.04175,389,206 - 176,188,408 (+)NCBI
RGSC_v3.44114,142,055 - 114,940,958 (+)RGD
Celera4101,556,445 - 102,345,352 (+)RGD
Sequence:
RefSeq Acc Id: XM_008763025   ⟹   XP_008761247
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24112,545,874 - 113,338,713 (+)NCBI
Rnor_6.04110,699,578 - 111,497,643 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008763026   ⟹   XP_008761248
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24112,545,874 - 113,338,713 (+)NCBI
Rnor_6.04110,699,578 - 111,497,643 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592811   ⟹   XP_017448300
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24112,545,874 - 113,338,713 (+)NCBI
Rnor_6.04110,699,577 - 111,497,643 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592812   ⟹   XP_017448301
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04110,699,580 - 110,707,274 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039108147   ⟹   XP_038964075
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24112,545,874 - 113,335,762 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001128218   ⟸   NM_001134746
- Peptide Label: precursor
- UniProtKB: B4F7C5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008761247   ⟸   XM_008763025
- Peptide Label: isoform X2
- UniProtKB: B4F7C5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008761248   ⟸   XM_008763026
- Peptide Label: isoform X2
- UniProtKB: B4F7C5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017448300   ⟸   XM_017592811
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017448301   ⟸   XM_017592812
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000075874   ⟸   ENSRNOT00000092261
RefSeq Acc Id: ENSRNOP00000075837   ⟸   ENSRNOT00000092379
RefSeq Acc Id: ENSRNOP00000034217   ⟸   ENSRNOT00000030588
RefSeq Acc Id: XP_038964075   ⟸   XM_039108147
- Peptide Label: isoform X3
Protein Domains
LRRCT   LRRNT

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560707 AgrOrtholog
Ensembl Genes ENSRNOG00000021938 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000034217 UniProtKB/TrEMBL
  ENSRNOP00000075837 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000075874 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030588 UniProtKB/TrEMBL
  ENSRNOT00000092261 UniProtKB/TrEMBL
  ENSRNOT00000092379 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Leu-rich_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:500219 UniProtKB/Swiss-Prot
NCBI Gene 500219 ENTREZGENE
Pfam LRR_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lrrtm4 PhenoGen
PROSITE LRR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART LRR_TYP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0U1RRZ6_RAT UniProtKB/TrEMBL
  B4F7C5 ENTREZGENE
  F1LNW2_RAT UniProtKB/TrEMBL
  LRRT4_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-05 Lrrtm4  leucine rich repeat transmembrane neuronal 4   RGD1560707  similar to leucine-rich repeat transmembrane neuronal 4 protein   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1560707  similar to leucine-rich repeat transmembrane neuronal 4 protein   RGD1560707_predicted  similar to leucine-rich repeat transmembrane neuronal 4 protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1560707_predicted  similar to leucine-rich repeat transmembrane neuronal 4 protein (predicted)  LOC500219  similar to leucine-rich repeat transmembrane neuronal 4 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500219  similar to leucine-rich repeat transmembrane neuronal 4 protein      Symbol and Name status set to provisional 70820 PROVISIONAL