Lama5 (laminin subunit alpha 5) - Rat Genome Database
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Gene: Lama5 (laminin subunit alpha 5) Rattus norvegicus
Analyze
Symbol: Lama5
Name: laminin subunit alpha 5
RGD ID: 621023
Description: Predicted to have extracellular matrix structural constituent and integrin binding activity. Predicted to be involved in several processes, including animal organ development; cell morphogenesis involved in differentiation; and morphogenesis of an epithelium. Localizes to laminin-5 complex. Orthologous to human LAMA5 (laminin subunit alpha 5); PARTICIPATES IN syndecan signaling pathway; cell-extracellular matrix signaling pathway; Entamoebiasis pathway; INTERACTS WITH 1,2-dimethylhydrazine; 1-naphthyl isothiocyanate; 2,2',5,5'-tetrachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: laminin subunit alpha-5; laminin, alpha 5
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
mRatBN7.23167,270,296 - 167,318,370 (-)NCBI
Rnor_6.0 Ensembl3175,553,045 - 175,601,127 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03175,553,042 - 175,601,112 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03181,517,512 - 181,565,641 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43169,233,897 - 169,282,410 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13169,144,153 - 169,145,258 (-)NCBI
Celera3165,261,840 - 165,309,879 (+)NCBICelera
Cytogenetic Map3q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (EXP,ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-methylcholine  (ISO)
2-nitrofluorene  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acetamide  (EXP)
aflatoxin B1  (EXP,ISO)
aldrin  (ISO)
all-trans-retinoic acid  (EXP,ISO)
anthracen-2-amine  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
boric acid  (ISO)
butanal  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
chlordecone  (ISO)
chloropicrin  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
dicrotophos  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
fenvalerate  (EXP)
fipronil  (EXP)
folic acid  (ISO)
gossypol  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
menadione  (ISO)
mifepristone  (EXP)
N-nitrosodiethylamine  (EXP)
paracetamol  (ISO)
PCB138  (EXP)
perfluorooctanoic acid  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
retinyl acetate  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
T-2 toxin  (EXP)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
triclosan  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zalcitabine  (EXP)
zinc atom  (ISO)
zinc(0)  (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:8707838   PMID:9299121   PMID:9396756   PMID:9735344   PMID:10964500   PMID:11507772   PMID:11741585   PMID:11821406   PMID:12051813   PMID:12379663   PMID:12743034   PMID:12921739  
PMID:14557481   PMID:14568553   PMID:15024036   PMID:15895400   PMID:16236823   PMID:16316641   PMID:16365040   PMID:16554364   PMID:16884540   PMID:16886065   PMID:18676816   PMID:18757743  
PMID:19056867   PMID:19199708   PMID:19651211   PMID:20551380   PMID:21099277   PMID:21630459   PMID:22665518   PMID:23376485   PMID:23533145   PMID:23658023   PMID:27068509   PMID:27559042  


Genomics

Comparative Map Data
Lama5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23167,270,296 - 167,318,370 (-)NCBI
Rnor_6.0 Ensembl3175,553,045 - 175,601,127 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03175,553,042 - 175,601,112 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03181,517,512 - 181,565,641 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43169,233,897 - 169,282,410 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13169,144,153 - 169,145,258 (-)NCBI
Celera3165,261,840 - 165,309,879 (+)NCBICelera
Cytogenetic Map3q43NCBI
LAMA5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2062,307,955 - 62,367,312 (-)EnsemblGRCh38hg38GRCh38
GRCh382062,309,060 - 62,367,318 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372060,884,121 - 60,942,368 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh372060,884,116 - 60,942,368 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362060,317,516 - 60,375,763 (-)NCBINCBI36hg18NCBI36
Build 342060,317,515 - 60,375,763NCBI
Celera2057,619,270 - 57,677,579 (-)NCBI
Cytogenetic Map20q13.33NCBI
HuRef2057,659,916 - 57,715,071 (-)NCBIHuRef
CHM1_12060,784,876 - 60,843,394 (-)NCBICHM1_1
Lama5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392179,818,166 - 179,868,092 (-)NCBIGRCm39mm39
GRCm382180,176,373 - 180,225,904 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2180,176,373 - 180,225,859 (-)EnsemblGRCm38mm10GRCm38
MGSCv372179,911,078 - 179,960,564 (-)NCBIGRCm37mm9NCBIm37
MGSCv362180,105,781 - 180,155,267 (-)NCBImm8
Celera2184,258,583 - 184,308,017 (-)NCBICelera
Cytogenetic Map2H4NCBI
cM Map2102.7NCBI
Lama5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555281,713,125 - 1,753,116 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555281,713,110 - 1,753,374 (+)NCBIChiLan1.0ChiLan1.0
LAMA5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12059,991,859 - 60,052,486 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2059,992,130 - 60,055,765 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02058,673,850 - 58,677,760 (-)NCBIMhudiblu_PPA_v0panPan3
LAMA5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12446,315,008 - 46,351,279 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Lama5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365149,928,234 - 9,973,425 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LAMA5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11761,698,370 - 61,747,795 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LAMA5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121,872,740 - 1,930,037 (+)NCBI
ChlSab1.1 Ensembl21,872,832 - 1,929,854 (+)Ensembl
Lama5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474128,156,956 - 28,217,133 (-)NCBI

Position Markers
RH144643  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03175,580,803 - 175,580,952NCBIRnor6.0
Rnor_5.03181,537,731 - 181,537,880UniSTSRnor5.0
RGSC_v3.43169,261,658 - 169,261,807UniSTSRGSC3.4
Celera3165,281,997 - 165,282,146UniSTS
RH 3.4 Map31526.8UniSTS
Cytogenetic Map3q43UniSTS
RH128438  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03175,553,185 - 175,553,382NCBIRnor6.0
Rnor_5.03181,565,301 - 181,565,498UniSTSRnor5.0
RGSC_v3.43169,234,040 - 169,234,237UniSTSRGSC3.4
Celera3165,309,539 - 165,309,736UniSTS
RH 3.4 Map31525.3UniSTS
Cytogenetic Map3q43UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3150368003177699992Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3153918022177699992Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3146232777177699992Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3156381661176418101Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3170428815177699992Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3132875075176418101Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3153412455177699992Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3148034701177699992Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:165
Count of miRNA genes:127
Interacting mature miRNAs:140
Transcripts:ENSRNOT00000008981
Prediction methods:Microtar, 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 31 6 4 4 1 1 4 34 29 11 1
Low 3 12 49 35 19 35 7 10 70 1 12 7
Below cutoff 2 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000081226   ⟹   ENSRNOP00000074084
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3175,553,045 - 175,601,127 (-)Ensembl
RefSeq Acc Id: NM_001191609   ⟹   NP_001178538
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23167,270,296 - 167,318,370 (-)NCBI
Rnor_6.03175,553,042 - 175,601,112 (-)NCBI
Rnor_5.03181,517,512 - 181,565,641 (+)NCBI
Celera3165,261,840 - 165,309,879 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178538 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA70093 (Get FASTA)   NCBI Sequence Viewer  
  EDL88819 (Get FASTA)   NCBI Sequence Viewer  
  EDL88820 (Get FASTA)   NCBI Sequence Viewer  
  EDL88821 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001178538   ⟸   NM_001191609
- Peptide Label: precursor
- UniProtKB: F1MAN8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074084   ⟸   ENSRNOT00000081226
Transcriptome

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

Promoters
RGD ID:13692732
Promoter ID:EPDNEW_R3257
Type:initiation region
Name:Lama5_1
Description:laminin subunit alpha 5
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03175,601,171 - 175,601,231EPDNEW

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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 181562510 181562511 C T snv KFRS3B/Kyo (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 175600931 175600932 C T snv MR/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621023 AgrOrtholog
Ensembl Genes ENSRNOG00000053691 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000074084 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000081226 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:140433 UniProtKB/TrEMBL
NCBI Gene 140433 ENTREZGENE
Pfam Laminin_B UniProtKB/TrEMBL
  Laminin_EGF UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/TrEMBL
  Laminin_I UniProtKB/TrEMBL
  Laminin_II UniProtKB/TrEMBL
  Laminin_N UniProtKB/TrEMBL
PhenoGen Lama5 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 F1MAN8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-02 Lama5  laminin subunit alpha 5  Lama5  laminin, alpha 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Lama5  laminin, alpha 5      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Lama5  laminin, alpha 5      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression highly expressed in both normal and the malignant liver epithelial cells 633095
gene_process may have a specific role in development and malignancy 633095