Lama3 (laminin subunit alpha 3) - Rat Genome Database

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Gene: Lama3 (laminin subunit alpha 3) Rattus norvegicus
Analyze
Symbol: Lama3
Name: laminin subunit alpha 3
RGD ID: 628776
Description: Predicted to have signaling receptor binding activity. Involved in cell-cell adhesion and hemidesmosome assembly. Localizes to adherens junction; hemidesmosome; and laminin-3 complex. Human ortholog(s) of this gene implicated in junctional epidermolysis bullosa; junctional epidermolysis bullosa Herlitz type; junctional epidermolysis bullosa non-Herlitz type; and lung small cell carcinoma. Orthologous to human LAMA3 (laminin subunit alpha 3); PARTICIPATES IN syndecan signaling pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: laminin 5 alpha 3; laminin subunit alpha-3; laminin, alpha 3; LOC307582; LOW QUALITY PROTEIN: laminin subunit alpha-3; similar to Laminin alpha-3 chain precursor (Nicein alpha subunit)
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
mRatBN7.2183,523,168 - 3,751,722 (+)NCBI
Rnor_6.0 Ensembl183,705,916 - 3,940,838 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0183,704,866 - 3,941,215 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0183,712,673 - 3,939,550 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4184,030,463 - 4,121,355 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1184,030,462 - 4,121,355 (+)NCBI
Celera183,569,544 - 3,806,888 (+)NCBICelera
Cytogenetic Map18p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-octadec-9-enoylglycero-3-phosphate  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4,6-trinitrotoluene  (EXP)
2,4-dinitrotoluene  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
8-Br-cAMP  (ISO)
9-cis-retinoic acid  (ISO)
acrolein  (ISO)
adefovir pivoxil  (ISO)
aflatoxin B1  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butan-1-ol  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloroacetaldehyde  (ISO)
chloropicrin  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dichloroacetic acid  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP,ISO)
ethanol  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
ibuprofen  (ISO)
ifosfamide  (ISO)
indole-3-methanol  (EXP)
isotretinoin  (ISO)
lead diacetate  (EXP,ISO)
leflunomide  (EXP)
lysophosphatidylcholine  (ISO)
mercury dichloride  (EXP)
methapyrilene  (ISO)
methylphenidate  (ISO)
mifepristone  (ISO)
ML-7  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
nefazodone  (EXP)
ochratoxin A  (EXP)
ozone  (ISO)
palbociclib  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sphingosine 1-phosphate  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
testosterone  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (ISO)
trichloroethene  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
troglitazone  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
Y-27632  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9264260   PMID:12051813   PMID:15895400   PMID:18757743   PMID:20039268   PMID:20301201   PMID:23154389   PMID:23533145   PMID:27068509  


Genomics

Comparative Map Data
Lama3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2183,523,168 - 3,751,722 (+)NCBI
Rnor_6.0 Ensembl183,705,916 - 3,940,838 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0183,704,866 - 3,941,215 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0183,712,673 - 3,939,550 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4184,030,463 - 4,121,355 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1184,030,462 - 4,121,355 (+)NCBI
Celera183,569,544 - 3,806,888 (+)NCBICelera
Cytogenetic Map18p13NCBI
LAMA3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1823,689,453 - 23,956,222 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1823,689,443 - 23,956,222 (+)EnsemblGRCh38hg38GRCh38
GRCh381823,689,443 - 23,955,066 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371821,269,417 - 21,535,030 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361819,523,560 - 19,789,028 (+)NCBINCBI36hg18NCBI36
Build 341819,707,003 - 19,789,025NCBI
Celera1818,085,885 - 18,351,313 (+)NCBI
Cytogenetic Map18q11.2NCBI
HuRef1818,125,049 - 18,390,663 (+)NCBIHuRef
CHM1_11821,196,719 - 21,462,312 (+)NCBICHM1_1
Lama3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391812,466,806 - 12,716,070 (+)NCBIGRCm39mm39
GRCm39 Ensembl1812,466,876 - 12,716,070 (+)Ensembl
GRCm381812,333,417 - 12,583,013 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1812,333,819 - 12,583,013 (+)EnsemblGRCm38mm10GRCm38
MGSCv371812,492,533 - 12,741,522 (+)NCBIGRCm37mm9NCBIm37
MGSCv361812,477,560 - 12,726,182 (+)NCBImm8
Celera1812,567,449 - 12,814,993 (+)NCBICelera
Cytogenetic Map18A1NCBI
cM Map186.2NCBI
Lama3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540211,980,980 - 12,362,143 (+)NCBIChiLan1.0ChiLan1.0
LAMA3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11820,750,271 - 20,832,028 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1820,565,649 - 20,831,957 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01816,941,316 - 17,208,363 (+)NCBIMhudiblu_PPA_v0panPan3
LAMA3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1764,405,719 - 64,654,910 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl764,406,082 - 64,655,268 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha763,854,180 - 64,103,577 (-)NCBI
ROS_Cfam_1.0764,463,775 - 64,714,403 (-)NCBI
UMICH_Zoey_3.1764,132,606 - 64,382,587 (-)NCBI
UNSW_CanFamBas_1.0764,147,994 - 64,397,958 (-)NCBI
UU_Cfam_GSD_1.0764,453,184 - 64,703,083 (-)NCBI
LOC101971816
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494460,496,309 - 60,694,484 (-)NCBI
SpeTri2.0NW_0049365503,121,163 - 3,357,517 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LAMA3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6108,548,837 - 108,805,693 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16108,548,818 - 108,805,700 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26101,146,225 - 101,337,451 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LAMA3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11856,580,245 - 56,851,381 (-)NCBI
ChlSab1.1 Ensembl1856,580,700 - 56,850,451 (-)Ensembl
Lama3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247708,237,085 - 8,482,770 (-)NCBI

Position Markers
BF406322  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2183,643,357 - 3,643,522 (+)MAPPER
Rnor_6.0183,826,815 - 3,826,979NCBIRnor6.0
Rnor_5.0183,832,653 - 3,832,817UniSTSRnor5.0
RGSC_v3.4183,995,549 - 3,995,713UniSTSRGSC3.4
Celera183,699,431 - 3,699,595UniSTS
RH 3.4 Map1881.41UniSTS
Cytogenetic Map18p13UniSTS
PMC113197P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2183,677,970 - 3,678,151 (+)MAPPER
Rnor_6.0183,861,420 - 3,861,600NCBIRnor6.0
Rnor_5.0183,867,258 - 3,867,438UniSTSRnor5.0
RGSC_v3.4184,030,403 - 4,030,583UniSTSRGSC3.4
Celera183,733,932 - 3,734,112UniSTS
Cytogenetic Map18p13UniSTS
ECD14724  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0183,787,813 - 3,789,309NCBIRnor6.0
Rnor_5.0183,793,999 - 3,795,495UniSTSRnor5.0
Cytogenetic Map18p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590248Scort10Serum corticosterone level QTL 1019.710.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)18125999214Rat
8552968Pigfal19Plasma insulin-like growth factor 1 level QTL 1911.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)18125999214Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135097280Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18138195967Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18138195967Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18138753381Rat
1641910Colcr3Colorectal carcinoma resistance QTL 35.020.000007intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor surface area measurement (CMO:0002078)18247709623184414Rat
1641910Colcr3Colorectal carcinoma resistance QTL 35.020.000007intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)18247709623184414Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18371954732487870Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:30
Interacting mature miRNAs:32
Transcripts:ENSRNOT00000015363
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 1 7 7 2 5 11
Low 2 18 36 27 12 27 8 11 60 31 24 8
Below cutoff 23 14 14 14 12 4 11

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015363   ⟹   ENSRNOP00000015363
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl183,861,539 - 3,940,823 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092814   ⟹   ENSRNOP00000075975
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl183,900,714 - 3,940,838 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092846   ⟹   ENSRNOP00000075948
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl183,705,916 - 3,887,148 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093089   ⟹   ENSRNOP00000076030
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl183,887,419 - 3,893,314 (+)Ensembl
RefSeq Acc Id: NM_173306   ⟹   NP_775428
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,678,031 - 3,751,353 (+)NCBI
RefSeq Acc Id: XM_003753026   ⟹   XP_003753074
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera183,569,544 - 3,806,888 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008774089   ⟹   XP_008772311
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera183,733,956 - 3,806,888 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601153   ⟹   XP_017456642
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0183,704,866 - 3,941,215 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039096922   ⟹   XP_038952850
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,523,265 - 3,751,722 (+)NCBI
RefSeq Acc Id: XM_039096923   ⟹   XP_038952851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,523,172 - 3,751,722 (+)NCBI
RefSeq Acc Id: XM_039096924   ⟹   XP_038952852
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,567,893 - 3,751,326 (+)NCBI
RefSeq Acc Id: XM_039096925   ⟹   XP_038952853
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,597,529 - 3,751,326 (+)NCBI
RefSeq Acc Id: XM_039096926   ⟹   XP_038952854
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,634,707 - 3,751,722 (+)NCBI
RefSeq Acc Id: XM_039096927   ⟹   XP_038952855
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,658,410 - 3,751,722 (+)NCBI
RefSeq Acc Id: XR_005496046
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,523,168 - 3,705,490 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_003753074   ⟸   XM_003753026
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008772311   ⟸   XM_008774089
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017456642   ⟸   XM_017601153
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000075948   ⟸   ENSRNOT00000092846
RefSeq Acc Id: ENSRNOP00000075975   ⟸   ENSRNOT00000092814
RefSeq Acc Id: ENSRNOP00000076030   ⟸   ENSRNOT00000093089
RefSeq Acc Id: ENSRNOP00000015363   ⟸   ENSRNOT00000015363
RefSeq Acc Id: XP_038952851   ⟸   XM_039096923
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038952850   ⟸   XM_039096922
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038952852   ⟸   XM_039096924
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038952853   ⟸   XM_039096925
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038952854   ⟸   XM_039096926
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038952855   ⟸   XM_039096927
- Peptide Label: isoform X6
RefSeq Acc Id: NP_775428   ⟸   NM_173306
- Peptide Label: precursor
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)
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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:628776 AgrOrtholog
Ensembl Genes ENSRNOG00000011300 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000015363 UniProtKB/TrEMBL
  ENSRNOP00000075948 UniProtKB/TrEMBL
  ENSRNOP00000075975 UniProtKB/TrEMBL
  ENSRNOP00000076030 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015363 UniProtKB/TrEMBL
  ENSRNOT00000092814 UniProtKB/TrEMBL
  ENSRNOT00000092846 UniProtKB/TrEMBL
  ENSRNOT00000093089 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.1490 UniProtKB/TrEMBL
InterPro ConA-like_dom_sf UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/TrEMBL
  Laminin_aI UniProtKB/TrEMBL
  Laminin_dom_II UniProtKB/TrEMBL
  Laminin_EGF UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
  Laminin_IV UniProtKB/TrEMBL
  Laminin_N UniProtKB/TrEMBL
  Laminin_N_sf UniProtKB/TrEMBL
NCBI Gene 307582 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 Lama3 PhenoGen
PROSITE 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 SSF49899 UniProtKB/TrEMBL
UniProt A0A1B0GWM3_RAT UniProtKB/TrEMBL
  A0A1B0GWP7_RAT UniProtKB/TrEMBL
  A0A1B0GWV1_RAT UniProtKB/TrEMBL
  D3ZN05_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-02 Lama3  laminin subunit alpha 3  Lama3  laminin, alpha 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-09-11 Lama3  laminin, alpha 3  LOC307582  similar to Laminin alpha-3 chain precursor (Nicein alpha subunit)  Data Merged 737654 APPROVED
2006-11-19 LOC307582  similar to Laminin alpha-3 chain precursor (Nicein alpha subunit)      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-09-10 Lama3  laminin, alpha 3    laminin 5 alpha 3  Name updated 1299863 APPROVED
2003-02-27 Lama3  laminin 5 alpha 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_protein 150 kDa in size 633107