Lama4 (laminin subunit alpha 4) - Rat Genome Database
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Gene: Lama4 (laminin subunit alpha 4) Rattus norvegicus
Analyze
Symbol: Lama4
Name: laminin subunit alpha 4
RGD ID: 1560062
Description: Predicted to have signaling receptor binding activity. Predicted to be involved in blood vessel development; brown fat cell differentiation; and negative regulation of cold-induced thermogenesis. Predicted to localize to basement membrane; neuromuscular junction; and synaptic cleft. Human ortholog(s) of this gene implicated in dilated cardiomyopathy 1JJ. Orthologous to human LAMA4 (laminin subunit alpha 4); INTERACTS WITH 2-amino-2-deoxy-D-glucopyranose; acrylamide; aldehydo-D-glucosamine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: laminin subunit alpha-4; laminin, alpha 4; LOC309816; RGD1560062; similar to Laminin alpha-4 chain precursor
Orthologs:
Homo sapiens (human) : LAMA4 (laminin subunit alpha 4)  HGNC  Alliance
Mus musculus (house mouse) : Lama4 (laminin, alpha 4)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Lama4 (laminin subunit alpha 4)
Pan paniscus (bonobo/pygmy chimpanzee) : LAMA4 (laminin subunit alpha 4)
Canis lupus familiaris (dog) : LAMA4 (laminin subunit alpha 4)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Lama4 (laminin subunit alpha 4)
Sus scrofa (pig) : LAMA4 (laminin subunit alpha 4)
Chlorocebus sabaeus (African green monkey) : LAMA4 (laminin subunit alpha 4)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.02044,060,715 - 44,201,966 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2044,060,731 - 44,209,614 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02045,786,892 - 45,926,468 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42043,077,612 - 43,203,519 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2043,109,537 - 43,249,577 (+)NCBICelera
Cytogenetic Map20q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
1,2-dichloroethane  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
atrazine  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
beta-D-glucosamine  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
busulfan  (ISO)
carbon nanotube  (ISO)
cobalt dichloride  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dibenz[a,h]anthracene  (ISO)
diethyl malate  (ISO)
diethylstilbestrol  (EXP)
disodium selenite  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (ISO)
fenofibrate  (ISO)
formaldehyde  (ISO)
geldanamycin  (ISO)
GW 4064  (ISO)
hydroquinone  (ISO)
medroxyprogesterone acetate  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
N-acetyl-1,4-benzoquinone imine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel sulfate  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
perfluorononanoic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
propanal  (ISO)
Ptaquiloside  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
testosterone enanthate  (ISO)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc atom  (ISO)
zinc sulfate  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:9346933   PMID:9396756   PMID:9614228   PMID:11809810   PMID:12787401   PMID:14557481   PMID:15895400   PMID:18492766   PMID:18757743   PMID:19199708   PMID:21362503   PMID:24006456  
PMID:27068509   PMID:27559042   PMID:30874465  


Genomics

Comparative Map Data
Lama4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.02044,060,715 - 44,201,966 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2044,060,731 - 44,209,614 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02045,786,892 - 45,926,468 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42043,077,612 - 43,203,519 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2043,109,537 - 43,249,577 (+)NCBICelera
Cytogenetic Map20q12NCBI
LAMA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6112,107,931 - 112,254,939 (-)EnsemblGRCh38hg38GRCh38
GRCh386112,107,931 - 112,254,722 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh376112,429,134 - 112,575,924 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366112,535,827 - 112,682,521 (-)NCBINCBI36hg18NCBI36
Build 346112,536,769 - 112,682,495NCBI
Celera6113,170,441 - 113,317,106 (-)NCBI
Cytogenetic Map6q21NCBI
HuRef6110,003,995 - 110,150,732 (-)NCBIHuRef
CHM1_16112,691,472 - 112,838,207 (-)NCBICHM1_1
Lama4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391038,841,511 - 38,986,184 (+)NCBI
GRCm381038,965,515 - 39,110,188 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1038,965,515 - 39,110,188 (+)EnsemblGRCm38mm10GRCm38
MGSCv371038,685,647 - 38,829,937 (+)NCBIGRCm37mm9NCBIm37
MGSCv361038,642,372 - 38,799,589 (+)NCBImm8
Celera1039,849,529 - 39,994,348 (+)NCBICelera
Cytogenetic Map10B1NCBI
cM Map1020.02NCBI
Lama4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555264,330,388 - 4,465,528 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555264,330,388 - 4,465,810 (+)NCBIChiLan1.0ChiLan1.0
LAMA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16113,995,888 - 114,141,276 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6113,995,888 - 114,141,273 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06109,920,329 - 110,066,076 (-)NCBIMhudiblu_PPA_v0panPan3
LAMA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1268,535,860 - 68,678,762 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11268,535,614 - 68,639,115 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Lama4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936679803,131 - 938,022 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LAMA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl178,071,446 - 78,224,365 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1178,071,990 - 78,224,564 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2187,740,885 - 87,892,989 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LAMA4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1361,596,905 - 61,748,022 (+)Ensembl
ChlSab1.11361,596,940 - 61,748,359 (+)NCBI

Position Markers
RH133403  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02044,136,645 - 44,136,826NCBIRnor6.0
Rnor_5.02045,861,270 - 45,861,451UniSTSRnor5.0
RGSC_v3.42043,194,173 - 43,194,354UniSTSRGSC3.4
Celera2043,183,719 - 43,183,900UniSTS
Cytogenetic Map20q12UniSTS
RH 3.4 Map20461.6UniSTS
BI274433  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02044,201,718 - 44,201,930NCBIRnor6.0
Rnor_5.02045,926,220 - 45,926,432UniSTSRnor5.0
RGSC_v3.42043,260,482 - 43,260,694UniSTSRGSC3.4
Celera2043,249,329 - 43,249,541UniSTS
Cytogenetic Map20q12UniSTS
RH 3.4 Map20462.7UniSTS
RH142948  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02044,063,626 - 44,063,789NCBIRnor6.0
Rnor_5.02045,789,957 - 45,790,120UniSTSRnor5.0
RGSC_v3.42043,080,532 - 43,080,695UniSTSRGSC3.4
Celera2043,112,525 - 43,112,688UniSTS
Cytogenetic Map20q12UniSTS
RH 3.4 Map20458.4UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201887215049108956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)203091348156205956Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203335478345719230Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:50
Count of miRNA genes:48
Interacting mature miRNAs:50
Transcripts:ENSRNOT00000000737
Prediction methods:Miranda, Rnahybrid
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 3 43 22 6 9 6 7 9 58 24 36 11 7
Low 35 35 10 35 1 2 16 11 5 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000737   ⟹   ENSRNOP00000000737
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2044,060,731 - 44,209,614 (+)Ensembl
RefSeq Acc Id: NM_001309447   ⟹   NP_001296376
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02044,060,715 - 44,201,966 (+)NCBI
Celera2043,109,537 - 43,249,577 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001296376 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87800 (Get FASTA)   NCBI Sequence Viewer  
  EDL87801 (Get FASTA)   NCBI Sequence Viewer  
  EDL87802 (Get FASTA)   NCBI Sequence Viewer  
  EDL87803 (Get FASTA)   NCBI Sequence Viewer  
  EDL87804 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001296376   ⟸   NM_001309447
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000000737   ⟸   ENSRNOT00000000737
Protein Domains
LAM_G_DOMAIN   Laminin EGF-like

Transcriptome

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

Promoters
RGD ID:13701646
Promoter ID:EPDNEW_R12170
Type:initiation region
Name:Lama4_1
Description:laminin subunit alpha 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12171  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02044,060,747 - 44,060,807EPDNEW
RGD ID:13701647
Promoter ID:EPDNEW_R12171
Type:multiple initiation site
Name:Lama4_2
Description:laminin subunit alpha 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12170  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02044,061,140 - 44,061,200EPDNEW

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)
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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_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 44061228 44061229 G A snv LE/Stm (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560062 AgrOrtholog
Ensembl Genes ENSRNOG00000000599 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000737 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000737 ENTREZGENE, UniProtKB/TrEMBL
InterPro ConA-like_subgrp UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/TrEMBL
  EGF_laminin UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
  Laminin_I UniProtKB/TrEMBL
  Laminin_II UniProtKB/TrEMBL
NCBI Gene 309816 ENTREZGENE
Pfam Laminin_EGF UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/TrEMBL
  Laminin_I UniProtKB/TrEMBL
  Laminin_II UniProtKB/TrEMBL
PhenoGen Lama4 PhenoGen
PROSITE EGF_LAM_1 UniProtKB/TrEMBL
  EGF_LAM_2 UniProtKB/TrEMBL
  LAM_G_DOMAIN UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_Lam UniProtKB/TrEMBL
  LamG UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
UniGene Rn.204816 ENTREZGENE
UniProt F1LTF8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-02 Lama4  laminin subunit alpha 4  Lama4  laminin, alpha 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Lama4  laminin, alpha 4  RGD1560062_predicted  similar to Laminin alpha-4 chain precursor (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560062_predicted  similar to Laminin alpha-4 chain precursor (predicted)  LOC309816  similar to Laminin alpha-4 chain precursor  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC309816  similar to Laminin alpha-4 chain precursor      Symbol and Name status set to provisional 70820 PROVISIONAL