Lama1 (laminin subunit alpha 1) - Rat Genome Database

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Gene: Lama1 (laminin subunit alpha 1) Rattus norvegicus
Analyze
Symbol: Lama1
Name: laminin subunit alpha 1
RGD ID: 1307207
Description: Predicted to have glycosphingolipid binding activity and protein C-terminus binding activity. Predicted to be an extracellular matrix structural constituent. Predicted to be involved in several processes, including axon guidance; morphogenesis of an epithelium; and retinal blood vessel morphogenesis. Predicted to localize to several cellular components, including cell-cell junction; extracellular space; and laminin complex. Orthologous to human LAMA1 (laminin subunit alpha 1); PARTICIPATES IN glypican signaling pathway; syndecan signaling pathway; cell-extracellular matrix signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-Tetrachlorodibenzofuran; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: laminin subunit alpha-1; laminin, alpha 1; laminin-1; LOC316758
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
mRatBN7.29107,692,770 - 107,816,847 (+)NCBI
Rnor_6.0 Ensembl9115,916,907 - 116,042,123 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09115,916,907 - 116,042,123 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09115,406,905 - 115,531,632 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49106,855,708 - 106,980,651 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.19107,065,234 - 107,189,814 (+)NCBI
Celera9104,852,718 - 104,977,464 (+)NCBICelera
Cytogenetic Map9q38NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetic acid  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aflatoxin M1  (ISO)
all-trans-retinoic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
Azaspiracid  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromochloroacetic acid  (ISO)
busulfan  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chromium(6+)  (ISO)
chrysene  (ISO)
ciglitazone  (EXP)
clobetasol  (ISO)
clofibrate  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP)
diethyl malate  (ISO)
diethyl maleate  (ISO)
dimethyl sulfoxide  (EXP)
dinophysistoxin 1  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
genistein  (ISO)
indometacin  (ISO)
lead diacetate  (ISO)
MeIQx  (ISO)
Nor-9-carboxy-delta9-THC  (ISO)
paracetamol  (ISO)
pentanal  (ISO)
potassium dichromate  (ISO)
propanal  (ISO)
quercetin  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
thapsigargin  (ISO)
triclosan  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (EXP)
zoledronic acid  (ISO)

References

Additional References at PubMed
PMID:1292752   PMID:1907584   PMID:2099832   PMID:7589890   PMID:8034675   PMID:8601594   PMID:8889548   PMID:9264260   PMID:9299121   PMID:10639489   PMID:10964500   PMID:11511678  
PMID:11798066   PMID:11827968   PMID:11984530   PMID:12051813   PMID:12631063   PMID:12670870   PMID:12885773   PMID:14697343   PMID:15065125   PMID:15102706   PMID:15668394   PMID:15895400  
PMID:15923608   PMID:16467571   PMID:16554364   PMID:16631359   PMID:16677310   PMID:17517882   PMID:17653607   PMID:18757743   PMID:19118221   PMID:19319192   PMID:19451651   PMID:19531352  
PMID:19651211   PMID:20123909   PMID:21052544   PMID:21131290   PMID:21146513   PMID:21519634   PMID:23658023   PMID:24006456  


Genomics

Comparative Map Data
Lama1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.29107,692,770 - 107,816,847 (+)NCBI
Rnor_6.0 Ensembl9115,916,907 - 116,042,123 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09115,916,907 - 116,042,123 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09115,406,905 - 115,531,632 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49106,855,708 - 106,980,651 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.19107,065,234 - 107,189,814 (+)NCBI
Celera9104,852,718 - 104,977,464 (+)NCBICelera
Cytogenetic Map9q38NCBI
LAMA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl186,941,742 - 7,117,797 (-)EnsemblGRCh38hg38GRCh38
GRCh38186,941,742 - 7,117,797 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37186,941,741 - 7,117,796 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36186,931,885 - 7,107,813 (-)NCBINCBI36hg18NCBI36
Build 34186,931,887 - 7,107,813NCBI
Celera186,802,111 - 7,003,045 (-)NCBI
Cytogenetic Map18p11.31NCBI
HuRef186,905,118 - 7,080,842 (-)NCBIHuRef
CHM1_1186,941,780 - 7,117,762 (-)NCBICHM1_1
Lama1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391768,004,129 - 68,129,640 (+)NCBIGRCm39mm39
GRCm39 Ensembl1768,004,254 - 68,129,642 (+)Ensembl
GRCm381767,697,127 - 67,822,645 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1767,697,259 - 67,822,647 (+)EnsemblGRCm38mm10GRCm38
MGSCv371768,046,605 - 68,171,985 (+)NCBIGRCm37mm9NCBIm37
MGSCv361767,602,232 - 67,727,594 (+)NCBImm8
Celera1771,993,823 - 72,120,045 (+)NCBICelera
Cytogenetic Map17E1.1NCBI
cM Map1738.8NCBI
Lama1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554024,285,492 - 4,400,348 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554024,281,415 - 4,397,158 (+)NCBIChiLan1.0ChiLan1.0
LAMA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1189,482,878 - 9,656,942 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl189,482,895 - 9,656,800 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0187,159,568 - 7,335,363 (+)NCBIMhudiblu_PPA_v0panPan3
LAMA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1773,309,383 - 73,438,543 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl773,309,388 - 73,448,151 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha772,704,162 - 72,859,440 (-)NCBI
ROS_Cfam_1.0773,362,093 - 73,517,591 (-)NCBI
UMICH_Zoey_3.1773,065,788 - 73,221,046 (-)NCBI
UNSW_CanFamBas_1.0773,094,647 - 73,250,187 (-)NCBI
UU_Cfam_GSD_1.0773,389,565 - 73,544,837 (-)NCBI
Lama1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494469,843,440 - 69,995,263 (-)NCBI
SpeTri2.0NW_004936670359,343 - 511,126 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LAMA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6100,332,873 - 100,468,454 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16100,332,843 - 100,468,457 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LAMA1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11865,996,233 - 66,162,510 (-)NCBI
Lama1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477016,358,952 - 16,490,986 (-)NCBI

Position Markers
D9Got221  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.09116,018,884 - 116,019,093NCBIRnor6.0
Rnor_5.09115,508,524 - 115,508,733UniSTSRnor5.0
RGSC_v3.49106,957,739 - 106,957,948UniSTSRGSC3.4
Celera9104,954,088 - 104,954,297UniSTS
Cytogenetic Map9q37UniSTS
RH128223  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.09116,041,316 - 116,041,503NCBIRnor6.0
Rnor_5.09115,530,825 - 115,531,012UniSTSRnor5.0
RGSC_v3.49106,980,345 - 106,980,532UniSTSRGSC3.4
Celera9104,976,657 - 104,976,844UniSTS
Cytogenetic Map9q37UniSTS
BF401259  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.09115,941,759 - 115,941,853NCBIRnor6.0
Rnor_5.09115,431,350 - 115,431,444UniSTSRnor5.0
RGSC_v3.49106,880,906 - 106,881,000UniSTSRGSC3.4
Celera9104,877,662 - 104,877,756UniSTS
Cytogenetic Map9q37UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)990024661119983851Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:72
Count of miRNA genes:60
Interacting mature miRNAs:69
Transcripts:ENSRNOT00000023226
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 2 18 22 30
Low 3 18 26 11 18 11 1 1 56 13 11 10 1
Below cutoff 17 23 22 1 22 7 9 1 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000023226   ⟹   ENSRNOP00000023224
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9115,916,907 - 116,042,123 (+)Ensembl
RefSeq Acc Id: NM_001108237   ⟹   NP_001101707
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29107,692,770 - 107,816,847 (+)NCBI
Rnor_6.09115,916,907 - 116,042,123 (+)NCBI
Rnor_5.09115,406,905 - 115,531,632 (+)NCBI
RGSC_v3.49106,855,708 - 106,980,651 (+)RGD
Celera9104,852,718 - 104,977,464 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039083800   ⟹   XP_038939728
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29107,693,175 - 107,774,271 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001101707 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939728 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAJ33456 (Get FASTA)   NCBI Sequence Viewer  
  BAJ33457 (Get FASTA)   NCBI Sequence Viewer  
  EDL90914 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101707   ⟸   NM_001108237
- Peptide Label: precursor
- UniProtKB: D4A409 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000023224   ⟸   ENSRNOT00000023226
RefSeq Acc Id: XP_038939728   ⟸   XM_039083800
- 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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 115449442 115449443 A T snv LE/Stm (Illumina) (KNAW), LE/Stm (KyushuU), GH/OmrMcwi (MCW), HTX/Kyo (KyushuU), LE/Stm (SOLiD) (KNAW), RCS/Kyo (KyushuU)
9 115481171 115481172 A G snv SDLEF7/Barth (UDEL), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), LE/Stm (KyushuU), M520/N (KNAW), LE/Stm (SOLiD) (KNAW), LE/Stm (Illumina) (KNAW), GK/Ox (KNAW), BUF/N (KNAW), WAG/Rij (KNAW), GH/OmrMcwi (MCW), RCS/Kyo (KyushuU), HTX/Kyo (KyushuU)
9 115488017 115488018 G C snv NIG-III/Hok (KyushuU)
9 115498423 115498424 C T snv NIG-III/Hok (KyushuU)
9 115518000 115518001 C T snv DOB/Oda (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 115960092 115960093 A T snv LE/Stm (RGD)
9 115991531 115991532 A G snv M520/N (MCW), WAG/Rij (RGD), LE/Stm (RGD), Buf/N (MCW), GK/Ox (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307207 AgrOrtholog
Ensembl Genes ENSRNOG00000017237 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000023224 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023226 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.1490 UniProtKB/TrEMBL
InterPro ConA-like_subgrp UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/TrEMBL
  EGF_laminin UniProtKB/TrEMBL
  Laminin_B_type_IV UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
  Laminin_I UniProtKB/TrEMBL
  Laminin_II UniProtKB/TrEMBL
  Laminin_N UniProtKB/TrEMBL
  Laminin_N_sf UniProtKB/TrEMBL
KEGG Report rno:316758 UniProtKB/TrEMBL
NCBI Gene 316758 ENTREZGENE
Pfam Laminin_B UniProtKB/TrEMBL
  Laminin_EGF UniProtKB/TrEMBL
  Laminin_G_1 UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/TrEMBL
  Laminin_I UniProtKB/TrEMBL
  Laminin_II UniProtKB/TrEMBL
  Laminin_N UniProtKB/TrEMBL
PhenoGen Lama1 PhenoGen
PROSITE EGF_1 UniProtKB/TrEMBL
  EGF_LAM_1 UniProtKB/TrEMBL
  EGF_LAM_2 UniProtKB/TrEMBL
  LAM_G_DOMAIN UniProtKB/TrEMBL
  LAMININ_IVA UniProtKB/TrEMBL
  LAMININ_NTER UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_Lam UniProtKB/TrEMBL
  LamB UniProtKB/TrEMBL
  LamG UniProtKB/TrEMBL
  LamNT UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
UniProt D4A409 ENTREZGENE, UniProtKB/TrEMBL
  E3W9F8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-02 Lama1  laminin subunit alpha 1  Lama1  laminin, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-12-18 Lama1  laminin, alpha 1  Lama1_predicted  laminin, alpha 1 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Lama1_predicted  laminin, alpha 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED