L1cam (L1 cell adhesion molecule) - Rat Genome Database

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Gene: L1cam (L1 cell adhesion molecule) Rattus norvegicus
Analyze
Symbol: L1cam
Name: L1 cell adhesion molecule
RGD ID: 619777
Description: Exhibits PDZ domain binding activity. Involved in several processes, including cellular response to growth factor stimulus; cellular response to hormone stimulus; and generation of neurons. Localizes to several cellular components, including Schaffer collateral - CA1 synapse; growth cone; and membrane raft. Used to study hydrocephalus. Biomarker of anxiety disorder; hypothyroidism; and mental depression. Human ortholog(s) of this gene implicated in MASA syndrome; hydrocephalus; ovarian carcinoma; pancreatic cancer; and schizophrenia. Orthologous to human L1CAM (L1 cell adhesion molecule); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-Tetrachlorodibenzofuran; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Hsas; Hyd; L1; L1 cell adhesion molecule (mapped); L1cam_mapped; N-CAM L1; N-CAM-L1; NCAM-L1; NCAML1; nerve-growth factor-inducible large external glycoprotein; neural cell adhesion molecule L1; neuron-glia cell adhesion molecule; NgCAM; NILE
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: L1cam_v1   L1cam_v2   L1camem2Jgn   L1camem1Jgn  
Genetic Models: SD-L1camem2Jgn SD-L1camem1Jgn
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X151,597,270 - 151,623,776 (-)NCBI
Rnor_6.0 EnsemblX156,909,913 - 156,928,057 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X156,901,244 - 156,928,064 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01152,649,353 - 152,676,124 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,784,792 - 159,801,553 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1136,279,868 - 136,293,057 (+)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (EXP)
amphetamine  (EXP)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
Butylbenzyl phthalate  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
captan  (ISO)
carbamazepine  (ISO)
chlorpyrifos  (EXP)
choline  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
dextran sulfate  (ISO)
diallyl trisulfide  (ISO)
dibutyl phthalate  (EXP)
diethyl phthalate  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
entinostat  (ISO)
ethanol  (ISO)
fluoxetine  (EXP)
folic acid  (ISO)
genistein  (ISO)
L-methionine  (ISO)
methanol  (ISO)
methylmercury chloride  (ISO)
mitomycin C  (ISO)
Ondansetron  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
pentanal  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
propanal  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
Triptolide  (EXP)
triptonide  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Alvarez-Dolado M, etal., Mol Cell Neurosci. 2000 Oct;16(4):499-514.
2. Arlt MJ, etal., Cancer Res. 2006 Jan 15;66(2):936-43.
3. Ben QW, etal., Ann Surg Oncol. 2010 Aug;17(8):2213-21. Epub 2010 Feb 17.
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6. Du YZ, etal., J Med Genet. 1998 Jun;35(6):456-62.
7. Duan P, etal., PLoS One. 2014 May 19;9(5):e97684. doi: 10.1371/journal.pone.0097684. eCollection 2014.
8. Emmert AS, etal., J Neurosurg. 2019 Feb 8:1-14. doi: 10.3171/2018.10.JNS181015.
9. Fogel M, etal., Lancet. 2003 Sep 13;362(9387):869-75.
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12. Guseva D, etal., Exp Neurol. 2011 Jun;229(2):339-52. Epub 2011 Mar 2.
13. Haas MA, etal., Eur J Neurosci. 2004 Sep;20(6):1436-44.
14. Hai J, etal., Clin Cancer Res. 2012 Apr 1;18(7):1914-24. doi: 10.1158/1078-0432.CCR-11-2893. Epub 2012 Feb 3.
15. Hoffman EJ, etal., Neuroscience. 2008 Dec 2;157(3):556-65. doi: 10.1016/j.neuroscience.2008.08.071. Epub 2008 Sep 25.
16. Hu Y, etal., Neurochem Int. 2010 Feb;56(3):461-5. Epub 2009 Dec 14.
17. Jouet M, etal., Nat Genet. 1994 Jul;7(3):402-7.
18. Kaifi JT, etal., Mod Pathol. 2007 Nov;20(11):1183-90. Epub 2007 Sep 14.
19. Koroll M, etal., J Biol Chem 2001 Apr 6;276(14):10646-54.
20. Kurumaji A, etal., Am J Med Genet. 2001 Jan 8;105(1):99-104.
21. Lin B, etal., PLoS One. 2010 Apr 19;5(4):e10210.
22. L├╝thl A, etal., Nature. 1994 Dec 22-29;372(6508):777-9. doi: 10.1038/372777a0.
23. Macias M, etal., Neuroreport. 2002 Dec 20;13(18):2527-30.
24. MGD data from the GO Consortium
25. Miller MW, etal., J Neurochem. 2006 May;97(4):1182-90.
26. Miura M, etal., FEBS Lett 1991 Sep 2;289(1):91-5.
27. Molatore S, etal., Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18493-8. doi: 10.1073/pnas.1003956107. Epub 2010 Oct 11.
28. Montgomery AM, etal., J Cell Biol. 1996 Feb;132(3):475-85.
29. Morales DM, etal., Mol Cell Proteomics. 2011 Dec 20.
30. NCBI rat LocusLink and RefSeq merged data July 26, 2002
31. OMIM Disease Annotation Pipeline
32. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
33. RGD automated import pipeline for gene-chemical interactions
34. Sauce B, etal., Behav Brain Res. 2015 Oct 1;292:432-42. doi: 10.1016/j.bbr.2015.05.040. Epub 2015 Jun 14.
35. Schafer H, etal., Carcinogenesis. 2012 Jan;33(1):84-93. doi: 10.1093/carcin/bgr262. Epub 2011 Nov 17.
36. Schafer H, etal., Oncogene. 2012 Feb 20. doi: 10.1038/onc.2012.44.
37. Shimada T, etal., J Cell Biol. 2008 Jun 2;181(5):817-29. doi: 10.1083/jcb.200712138.
38. Shults CW, etal., Exp Neurol. 1992 Jun;116(3):275-85.
39. Stallcup WB and Beasley L, Proc Natl Acad Sci U S A. 1985 Feb;82(4):1276-80.
40. Strekalova H, etal., Neurobiol Aging. 2006 Jan;27(1):1-9.
41. Takechi T, etal., Hum Genet. 1996 Mar;97(3):353-6.
42. Tang N, etal., J Neurochem. 2006 Mar;96(5):1480-90.
43. Tang N, etal., J Neurochem. 2011 Nov;119(4):859-67. doi: 10.1111/j.1471-4159.2011.07467.x. Epub 2011 Oct 11.
44. Tapanes-Castillo A, etal., Neurogenetics. 2010 Feb;11(1):53-71. Epub 2009 Jun 30.
45. Thornton MR, etal., Biotechnol Appl Biochem. 2008 Feb;49(Pt 2):165-74.
46. Tocco MD, etal., J Neurosci Res. 1992 Jan;31(1):28-32.
47. Tsoory MM, etal., J Neurosci Res. 2010 Feb 1;88(2):369-80.
48. Vits L, etal., Nat Genet. 1994 Jul;7(3):408-13.
49. Wakabayashi Y, etal., Prog Neuropsychopharmacol Biol Psychiatry. 2008 Jul 1;32(5):1199-205. Epub 2008 Mar 15.
50. Wallace AS, etal., Neurogastroenterol Motil. 2011 Nov;23(11):e510-22. doi: 10.1111/j.1365-2982.2011.01692.x. Epub 2011 Mar 14.
51. Xu JC, etal., J Neurotrauma. 2011 Sep;28(9):1921-37. Epub 2011 Aug 31.
52. Yap CC, etal., J Cell Biol. 2008 Feb 25;180(4):827-42. doi: 10.1083/jcb.200707143.
Additional References at PubMed
PMID:2466966   PMID:2723751   PMID:7613634   PMID:7669058   PMID:8117278   PMID:8125140   PMID:8557754   PMID:9048906   PMID:11283023   PMID:11948808   PMID:12070130   PMID:12453492  
PMID:12514225   PMID:12533613   PMID:12900915   PMID:14608600   PMID:14705138   PMID:15803510   PMID:15880726   PMID:15905095   PMID:15911348   PMID:16022864   PMID:16537644   PMID:16554297  
PMID:17151951   PMID:17234591   PMID:18321067   PMID:18464795   PMID:18478542   PMID:18550718   PMID:18650339   PMID:19185025   PMID:19458237   PMID:19581412   PMID:20124415   PMID:20463227  
PMID:20621658   PMID:20964729   PMID:21423176   PMID:22815787   PMID:22973895   PMID:23050935   PMID:24155914   PMID:24223996   PMID:27027721   PMID:27559042   PMID:31426714  


Genomics

Comparative Map Data
L1cam
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X151,597,270 - 151,623,776 (-)NCBI
Rnor_6.0 EnsemblX156,909,913 - 156,928,057 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X156,901,244 - 156,928,064 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01152,649,353 - 152,676,124 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,784,792 - 159,801,553 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1136,279,868 - 136,293,057 (+)NCBICelera
Cytogenetic MapXq37NCBI
L1CAM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX153,861,514 - 153,886,173 (-)EnsemblGRCh38hg38GRCh38
GRCh38X153,861,514 - 153,886,173 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X153,126,969 - 153,151,627 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X152,780,581 - 152,794,505 (-)NCBINCBI36hg18NCBI36
Build 34X152,648,233 - 152,662,158NCBI
CeleraX153,360,655 - 153,375,083 (-)NCBI
Cytogenetic MapXq28NCBI
HuRefX141,783,485 - 141,798,078 (-)NCBIHuRef
CHM1_1X153,001,369 - 153,026,043 (-)NCBICHM1_1
L1cam
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X72,897,384 - 72,924,843 (-)NCBIGRCm39mm39
GRCm39 EnsemblX72,897,384 - 72,939,711 (-)Ensembl
GRCm38X73,853,778 - 73,880,838 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX73,853,778 - 73,896,105 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X71,099,119 - 71,126,173 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X70,107,755 - 70,122,524 (-)NCBImm8
CeleraX65,106,167 - 65,133,066 (-)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX37.43NCBI
L1cam
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955580549,368 - 561,486 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955580548,442 - 561,580 (-)NCBIChiLan1.0ChiLan1.0
L1CAM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X153,298,690 - 153,324,228 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX153,298,690 - 153,324,228 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X143,412,303 - 143,437,090 (-)NCBIMhudiblu_PPA_v0panPan3
L1CAM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X121,708,695 - 121,722,819 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX121,708,894 - 121,733,365 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX107,037,463 - 107,051,578 (-)NCBI
ROS_Cfam_1.0X124,849,997 - 124,864,112 (-)NCBI
UMICH_Zoey_3.1X120,619,271 - 120,633,384 (-)NCBI
UNSW_CanFamBas_1.0X123,134,526 - 123,148,641 (-)NCBI
UU_Cfam_GSD_1.0X122,895,999 - 122,910,117 (-)NCBI
L1cam
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X118,998,614 - 119,024,196 (-)NCBI
SpeTri2.0NW_004936809736,385 - 768,822 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
L1CAM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX124,595,651 - 124,618,307 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X124,595,649 - 124,618,292 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X142,160,416 - 142,182,924 (-)NCBISscrofa10.2Sscrofa10.2susScr3
L1CAM
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X128,285,128 - 128,309,173 (-)NCBI
ChlSab1.1 EnsemblX128,285,130 - 128,299,570 (-)Ensembl
Vero_WHO_p1.0NW_02366606566,154,181 - 66,179,381 (-)NCBI
L1cam
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624946512,413 - 533,669 (-)NCBI

Position Markers
REN87933  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,600,403 - 151,600,681 (-)MAPPER
Rnor_6.0X156,924,648 - 156,924,925NCBIRnor6.0
Rnor_5.01152,672,716 - 152,672,993UniSTSRnor5.0
RGSC_v3.4X159,787,923 - 159,788,200UniSTSRGSC3.4
Celera1136,289,649 - 136,289,926UniSTS
Cytogenetic MapXq37UniSTS
REN87932  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,600,155 - 151,600,415 (-)MAPPER
Rnor_6.0X156,924,914 - 156,925,173NCBIRnor6.0
Rnor_5.01152,672,982 - 152,673,241UniSTSRnor5.0
Celera1136,289,915 - 136,290,174UniSTS
Cytogenetic MapXq37UniSTS
Ncam  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,598,493 - 151,599,274 (-)MAPPER
Rnor_6.0X156,926,055 - 156,926,835NCBIRnor6.0
Rnor_5.01152,674,123 - 152,674,903UniSTSRnor5.0
RGSC_v3.4X159,786,013 - 159,786,793UniSTSRGSC3.4
Celera1136,291,056 - 136,291,836UniSTS
Cytogenetic MapXq37UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X134627816159970021Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118715462159970021Rat


Genetic Models
This gene L1cam is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:134
Count of miRNA genes:110
Interacting mature miRNAs:115
Transcripts:ENSRNOT00000056354
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 68 28 4
Low 3 43 18 2 19 2 5 5 6 7 29 11 5
Below cutoff 29 29 29 3 6 8 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000080945   ⟹   ENSRNOP00000075170
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX156,911,345 - 156,928,033 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084390   ⟹   ENSRNOP00000075314
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX156,909,913 - 156,928,057 (+)Ensembl
RefSeq Acc Id: NM_017345   ⟹   NP_059041
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,597,273 - 151,613,659 (-)NCBI
Rnor_6.0X156,911,345 - 156,928,056 (+)NCBI
Rnor_5.01152,649,353 - 152,676,124 (+)NCBI
RGSC_v3.4X159,784,792 - 159,801,553 (-)RGD
Celera1136,279,868 - 136,293,057 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773635   ⟹   XP_008771857
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,597,270 - 151,623,775 (-)NCBI
Rnor_6.0X156,901,244 - 156,928,064 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773636   ⟹   XP_008771858
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X156,901,244 - 156,928,064 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017602140   ⟹   XP_017457629
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,597,270 - 151,623,775 (-)NCBI
Rnor_6.0X156,901,244 - 156,928,056 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017602141   ⟹   XP_017457630
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,597,270 - 151,623,775 (-)NCBI
Rnor_6.0X156,901,244 - 156,928,064 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099993   ⟹   XP_038955921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,597,270 - 151,623,776 (-)NCBI
RefSeq Acc Id: XM_039099994   ⟹   XP_038955922
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,597,270 - 151,623,776 (-)NCBI
RefSeq Acc Id: XM_039099995   ⟹   XP_038955923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,597,270 - 151,623,776 (-)NCBI
RefSeq Acc Id: XM_039099996   ⟹   XP_038955924
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,597,270 - 151,623,776 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_059041   ⟸   NM_017345
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_008771857   ⟸   XM_008773635
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008771858   ⟸   XM_008773636
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017457630   ⟸   XM_017602141
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017457629   ⟸   XM_017602140
- Peptide Label: isoform X5
- UniProtKB: D3ZPC4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075170   ⟸   ENSRNOT00000080945
RefSeq Acc Id: ENSRNOP00000075314   ⟸   ENSRNOT00000084390
RefSeq Acc Id: XP_038955922   ⟸   XM_039099994
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955924   ⟸   XM_039099996
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955923   ⟸   XM_039099995
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955921   ⟸   XM_039099993
- Peptide Label: isoform X1
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:619777 AgrOrtholog
Ensembl Genes ENSRNOG00000061230 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000075170 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075314 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000080945 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000084390 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neurofascin/L1/NrCAM_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:50687 UniProtKB/Swiss-Prot
NCBI Gene 50687 ENTREZGENE
Pfam Bravo_FIGEY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  fn3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen L1cam PhenoGen
PROSITE FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2KA95_RAT UniProtKB/TrEMBL
  D3ZPC4 ENTREZGENE, UniProtKB/TrEMBL
  L1CAM_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-10-17 L1cam  L1 cell adhesion molecule  L1cam_mapped  L1 cell adhesion molecule (mapped)  Data Merged 737654 APPROVED
2005-11-18 L1cam  L1 cell adhesion molecule  NCAML1  neural cell adhesion molecule L1  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2005-11-17 L1cam_mapped  L1 cell adhesion molecule (mapped)  L1cam  L1 cell adhesion molecule  Symbol and Name updated 1556543 APPROVED
2002-08-07 NCAML1  neural cell adhesion molecule L1      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 L1cam  L1 cell adhesion molecule (Hydrocephalus, stenosis of aqueduct of Sylvius 1)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_homology has high homology to the mouse L1 homolog 633424
gene_process may have a role in anxiety-like responses 1300205
gene_regulation mRNA expression increased by stress 1300206