Col18a1 (collagen type XVIII alpha 1 chain) - Rat Genome Database
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Gene: Col18a1 (collagen type XVIII alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col18a1
Name: collagen type XVIII alpha 1 chain
RGD ID: 70936
Description: Predicted to have extracellular matrix structural constituent and identical protein binding activity. Involved in response to drug and response to hydrostatic pressure. Localizes to extracellular space. Used to study hepatocellular carcinoma. Biomarker of gastric ulcer and ulcerative colitis. Human ortholog(s) of this gene implicated in primary angle-closure glaucoma. Orthologous to human COL18A1 (collagen type XVIII alpha 1 chain); PARTICIPATES IN forkhead class A signaling pathway; INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 2,2',5,5'-tetrachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: collagen alpha-1(XVIII) chain; collagen type XVIII alpha 1; collagen, type XVIII, alpha 1; procollagen, type XVIII, alpha 1
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
mRatBN7.22011,474,104 - 11,582,593 (+)NCBI
Rnor_6.0 Ensembl2012,225,202 - 12,332,858 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02012,225,202 - 12,332,858 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02014,388,743 - 14,495,241 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42011,920,816 - 11,982,468 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12011,979,239 - 11,981,856 (+)NCBI
Celera2012,974,396 - 13,081,322 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2,6-dinitrotoluene  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arachidonic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
cadmium dichloride  (EXP)
calcium atom  (ISO)
calcium(0)  (ISO)
capsaicin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chlorpromazine  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (EXP,ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dieldrin  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
fenhexamid  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fumonisin B1  (ISO)
furosemide  (EXP)
genistein  (ISO)
glafenine  (EXP)
heparin  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
lead diacetate  (EXP)
manganese(II) chloride  (ISO)
methapyrilene  (ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
naphthalene  (ISO)
nefazodone  (EXP)
nickel dichloride  (EXP)
nimesulide  (EXP)
O-methyleugenol  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
pentane-2,3-dione  (EXP)
perfluorooctanoic acid  (ISO)
phenethyl caffeate  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
phosphorus atom  (ISO)
phosphorus(.)  (ISO)
pirinixic acid  (EXP,ISO)
propiconazole  (ISO)
quercetin  (ISO)
reactive oxygen species  (ISO)
resveratrol  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
succimer  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
ticlopidine  (EXP)
titanium dioxide  (ISO)
triacsin C  (ISO)
Tributyltin oxide  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
wortmannin  (ISO)
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:7568013   PMID:8889548   PMID:11927538   PMID:12588956   PMID:15188432   PMID:15254016   PMID:15326124   PMID:15464359   PMID:16269408   PMID:17688061   PMID:17942095   PMID:18757743  
PMID:19056867   PMID:19199708   PMID:19651211   PMID:19966499   PMID:20551380   PMID:23376485   PMID:23533145   PMID:23658023   PMID:23788612   PMID:23979707   PMID:24006456   PMID:25024173  
PMID:27068509   PMID:27559042   PMID:30361391  


Genomics

Comparative Map Data
Col18a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22011,474,104 - 11,582,593 (+)NCBI
Rnor_6.0 Ensembl2012,225,202 - 12,332,858 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02012,225,202 - 12,332,858 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02014,388,743 - 14,495,241 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42011,920,816 - 11,982,468 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12011,979,239 - 11,981,856 (+)NCBI
Celera2012,974,396 - 13,081,322 (+)NCBICelera
Cytogenetic Map20p12NCBI
COL18A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2145,405,165 - 45,513,720 (+)EnsemblGRCh38hg38GRCh38
GRCh382145,405,165 - 45,513,720 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372146,825,080 - 46,933,634 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh372146,825,058 - 46,933,634 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362145,649,525 - 45,758,062 (+)NCBINCBI36hg18NCBI36
Build 342145,649,524 - 45,758,061NCBI
Celera2131,935,820 - 32,044,503 (+)NCBI
Cytogenetic Map21q22.3NCBI
HuRef2132,201,756 - 32,310,095 (+)NCBIHuRef
CHM1_12146,385,890 - 46,494,464 (+)NCBICHM1_1
Col18a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391076,888,013 - 77,002,391 (-)NCBIGRCm39mm39
GRCm381077,052,178 - 77,166,530 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1077,052,178 - 77,166,548 (-)EnsemblGRCm38mm10GRCm38
MGSCv371076,514,924 - 76,629,275 (-)NCBIGRCm37mm9NCBIm37
MGSCv361076,495,895 - 76,610,217 (-)NCBImm8
Celera1078,096,179 - 78,210,613 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Col18a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540742,091,211 - 42,131,343 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540742,091,211 - 42,131,343 (+)NCBIChiLan1.0ChiLan1.0
COL18A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12145,046,791 - 45,106,225 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02131,720,358 - 31,834,470 (+)NCBIMhudiblu_PPA_v0panPan3
COL18A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13138,915,872 - 38,957,484 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Col18a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936778847,473 - 943,038 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL18A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13207,907,857 - 207,985,181 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113207,907,835 - 207,984,082 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213218,076,734 - 218,090,016 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL18A1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1289,129,674 - 89,186,490 (+)NCBI
Col18a1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474530,754,654 - 30,792,352 (+)NCBI

Position Markers
D20Rat3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02012,317,154 - 12,317,307NCBIRnor6.0
Rnor_5.02014,479,656 - 14,479,835UniSTSRnor5.0
RH 3.4 Map20165.8RGD
RH 3.4 Map20165.8UniSTS
RH 2.0 Map20166.7RGD
SHRSP x BN Map2011.54RGD
FHH x ACI Map204.6798RGD
Cytogenetic Map20p12UniSTS
RH129672  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02012,332,642 - 12,332,840NCBIRnor6.0
Rnor_5.02014,495,025 - 14,495,223UniSTSRnor5.0
RGSC_v3.42011,982,250 - 11,982,448UniSTSRGSC3.4
Celera2013,081,106 - 13,081,304UniSTS
RH 3.4 Map20157.7UniSTS
Cytogenetic Map20p12UniSTS
RH135187  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02012,325,503 - 12,325,697NCBIRnor6.0
Rnor_5.02014,487,886 - 14,488,080UniSTSRnor5.0
RGSC_v3.42011,975,111 - 11,975,305UniSTSRGSC3.4
RH 3.4 Map20155.6UniSTS
Cytogenetic Map20p12UniSTS
RH137498  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02012,324,354 - 12,324,567NCBIRnor6.0
Rnor_5.02014,486,737 - 14,486,950UniSTSRnor5.0
RGSC_v3.42011,973,962 - 11,974,175UniSTSRGSC3.4
Cytogenetic Map20p12UniSTS
RH80498  
Rat AssemblyChrPosition (strand)SourceJBrowse
CeleraX67,592,383 - 67,592,505UniSTS
Celera2013,001,028 - 13,001,145UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
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
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
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
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20587544818739210Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20865434118872273Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20965564214411641Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:373
Count of miRNA genes:207
Interacting mature miRNAs:246
Transcripts:ENSRNOT00000045315
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 3 34 51 41 13 41 2 3 56 35 39 11 2
Low 9 6 6 6 8 18 2 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000045315   ⟹   ENSRNOP00000047962
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2012,225,202 - 12,332,858 (+)Ensembl
RefSeq Acc Id: NM_053489   ⟹   NP_445941
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22011,474,104 - 11,582,593 (+)NCBI
Rnor_6.02012,225,202 - 12,332,858 (+)NCBI
Rnor_5.02014,388,743 - 14,495,241 (+)NCBI
Celera2012,974,396 - 13,081,322 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_445941 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF00975 (Get FASTA)   NCBI Sequence Viewer  
  CAB44263 (Get FASTA)   NCBI Sequence Viewer  
  EDL97114 (Get FASTA)   NCBI Sequence Viewer  
  EDL97116 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_445941   ⟸   NM_053489
- Peptide Label: precursor
- UniProtKB: F1LR02 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000047962   ⟸   ENSRNOT00000045315
Protein Domains
Endostatin   LAM_G_DOMAIN

Transcriptome

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

Promoters
RGD ID:13701509
Promoter ID:EPDNEW_R12033
Type:initiation region
Name:Col18a1_1
Description:collagen type XVIII alpha 1 chain
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_6.02012,225,220 - 12,225,280EPDNEW

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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 14474716 14474717 G A snv ACI/EurMcwi (MCW), ACI/EurMcwi (KNAW), ACI/N (KNAW), COP/CrCrl (MCW & UW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 12312214 12312215 G A snv ACI/EurMcwi (MCW), ACI/EurMcwi (RGD), ACI/N (MCW), COP/CrCrl (MCW & UW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70936 AgrOrtholog
Ensembl Genes ENSRNOG00000001229 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000047962 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000045315 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
  Collagenase_NC10/endostatin UniProtKB/TrEMBL
  ConA-like_subgrp UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
KEGG Report rno:85251 UniProtKB/TrEMBL
NCBI Gene 85251 ENTREZGENE
Pfam Collagen UniProtKB/TrEMBL
  Endostatin UniProtKB/TrEMBL
PhenoGen Col18a1 PhenoGen
SMART TSPN UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
  ConA_like_lec_gl UniProtKB/TrEMBL
UniProt F1LR02 ENTREZGENE, UniProtKB/TrEMBL
  Q9WUW5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Col18a1  collagen type XVIII alpha 1 chain  Col18a1  collagen, type XVIII, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-25 Col18a1  collagen, type XVIII, alpha 1  Col18a1  procollagen, type XVIII, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Col18a1  procollagen, type XVIII, alpha 1    collagen, type XVIII, alpha 1  Name updated 1299863 APPROVED
2002-07-09 Col18a1  collagen, type XVIII, alpha 1      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_protein protein fragment of Mr 20,000 forms endostatin 70690
gene_regulation expression remains constant in acute fibrogenesis and is upregulated in biliary fibrosis 632362