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 enable identical protein binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Involved in response to hydrostatic pressure and response to xenobiotic stimulus. Located in 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
Previously 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 Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82011,473,645 - 11,582,111 (+)NCBIGRCr8
mRatBN7.22011,474,104 - 11,582,593 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2011,474,104 - 11,582,593 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2012,170,630 - 12,278,993 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02011,531,618 - 11,639,977 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02012,003,376 - 12,111,737 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02012,225,202 - 12,332,858 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2012,225,202 - 12,332,858 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02014,388,743 - 14,495,241 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42011,920,816 - 11,982,468 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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->4)-beta-D-glucan  (ISO)
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)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-Nitrobenzanthrone  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arachidonic acid  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (EXP)
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)
bleomycin A2  (ISO)
butanal  (ISO)
cadmium dichloride  (EXP)
calcium atom  (ISO)
calcium(0)  (ISO)
capsaicin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carnosic acid  (ISO)
chlordecone  (ISO)
chlorpromazine  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (EXP,ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cytarabine  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dieldrin  (EXP)
dioxygen  (EXP,ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
epoxiconazole  (ISO)
fenhexamid  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
furosemide  (EXP)
genistein  (ISO)
gentamycin  (EXP)
glafenine  (EXP)
heparin  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
lead diacetate  (EXP)
manganese(II) chloride  (ISO)
methapyrilene  (ISO)
methimazole  (EXP)
N,N-diethyl-m-toluamide  (EXP)
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)
Nor-9-carboxy-delta9-THC  (ISO)
O-methyleugenol  (ISO)
ozone  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
pentane-2,3-dione  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
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)
senecionine  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
succimer  (ISO)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
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

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Combined endostatin/sFlt-1 antiangiogenic gene therapy is highly effective in a rat model of HCC. Graepler F, etal., Hepatology. 2005 Apr;41(4):879-86.
4. Modulation of collagen XVIII/endostatin expression in lobular and biliary rat liver fibrogenesis. Jia JD, etal., J Hepatol 2001 Sep;35(3):386-91.
5. Effect of oral Lactococcus lactis containing endostatin on 1, 2-dimethylhydrazine-induced colon tumor in rats. Li W and Li CB, World J Gastroenterol. 2005 Dec 14;11(46):7242-7.
6. Platelets modulate gastric ulcer healing: role of endostatin and vascular endothelial growth factor release. Ma L, etal., Proc Natl Acad Sci U S A. 2001 May 22;98(11):6470-5. Epub 2001 May 15.
7. Gene Data Set MGD Curation, June 12, 2002
8. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
9. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
11. Antitumor activity of endostatin against carcinogen-induced rat primary mammary tumors. Perletti G, etal., Cancer Res 2000 Apr 1;60(7):1793-6.
12. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
13. Mechanical factors influence the expression of endostatin--an inhibitor of angiogenesis--in tendons. Pufe T, etal., J Orthop Res. 2003 Jul;21(4):610-6.
14. GOA pipeline RGD automated data pipeline
15. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
17. Comprehensive gene review and curation RGD comprehensive gene curation
18. Altered angiogenic balance in ulcerative colitis: a key to impaired healing? Sandor Z, etal., Biochem Biophys Res Commun. 2006 Nov 10;350(1):147-50. Epub 2006 Sep 15.
19. Molecular analysis of collagen XVIII reveals novel mutations, presence of a third isoform, and possible genetic heterogeneity in Knobloch syndrome. Suzuki OT, etal., Am J Hum Genet. 2002 Dec;71(6):1320-9. Epub 2002 Nov 1.
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   PMID:35352799  


Genomics

Comparative Map Data
Col18a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82011,473,645 - 11,582,111 (+)NCBIGRCr8
mRatBN7.22011,474,104 - 11,582,593 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2011,474,104 - 11,582,593 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2012,170,630 - 12,278,993 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02011,531,618 - 11,639,977 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02012,003,376 - 12,111,737 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02012,225,202 - 12,332,858 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2012,225,202 - 12,332,858 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02014,388,743 - 14,495,241 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42011,920,816 - 11,982,468 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh382145,405,165 - 45,513,720 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2145,405,165 - 45,513,720 (+)EnsemblGRCh38hg38GRCh38
GRCh372146,825,080 - 46,933,634 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362145,649,525 - 45,758,062 (+)NCBINCBI36Build 36hg18NCBI36
Build 342145,649,524 - 45,758,061NCBI
Celera2131,935,820 - 32,044,503 (+)NCBICelera
Cytogenetic Map21q22.3NCBI
HuRef2132,201,756 - 32,310,095 (+)NCBIHuRef
CHM1_12146,385,935 - 46,494,464 (+)NCBICHM1_1
T2T-CHM13v2.02143,770,922 - 43,881,831 (+)NCBIT2T-CHM13v2.0
Col18a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391076,888,013 - 77,002,351 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1076,888,012 - 77,002,382 (-)EnsemblGRCm39 Ensembl
GRCm381077,052,178 - 77,166,530 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1077,052,178 - 77,166,548 (-)EnsemblGRCm38mm10GRCm38
MGSCv371076,514,924 - 76,629,275 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361076,495,895 - 76,610,217 (-)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v22241,474,960 - 41,590,499 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12136,343,211 - 36,459,037 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02131,720,358 - 31,834,470 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12145,046,791 - 45,106,225 (+)NCBIpanpan1.1PanPan1.1panPan2
COL18A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13138,915,872 - 38,957,484 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3138,143,980 - 38,184,998 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03138,552,331 - 38,593,457 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3138,519,589 - 38,593,442 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13138,415,729 - 38,457,167 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03138,375,432 - 38,416,875 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03138,893,993 - 38,935,752 (+)NCBIUU_Cfam_GSD_1.0
Col18a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497138,186,994 - 38,282,739 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936778847,473 - 943,038 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL18A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13207,940,948 - 207,982,938 (+)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1289,129,674 - 89,186,490 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605417,263,431 - 17,447,521 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col18a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474530,754,820 - 30,791,426 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474530,754,654 - 30,792,352 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Col18a1
1020 total Variants
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.


QTLs in Region (mRatBN7.2)
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)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
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)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat
1581577Pur15Proteinuria QTL 154.380.0002urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804241017617956Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20903971913461775Rat

Markers in Region
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
mRatBN7.22011,582,376 - 11,582,575 (+)MAPPERmRatBN7.2
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
mRatBN7.22011,575,237 - 11,575,432 (+)MAPPERmRatBN7.2
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
mRatBN7.22011,574,088 - 11,574,302 (+)MAPPERmRatBN7.2
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


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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2011,474,104 - 11,582,593 (+)Ensembl
Rnor_6.0 Ensembl2012,225,202 - 12,332,858 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095032   ⟹   ENSRNOP00000082737
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2011,474,104 - 11,582,593 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116507   ⟹   ENSRNOP00000096747
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2011,521,290 - 11,582,593 (+)Ensembl
RefSeq Acc Id: NM_053489   ⟹   NP_445941
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82011,473,645 - 11,582,111 (+)NCBI
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  
Ensembl Protein ENSRNOP00000047962
  ENSRNOP00000047962.4
  ENSRNOP00000082737.1
  ENSRNOP00000096747.1
Reference Protein Sequences
RefSeq Acc Id: NP_445941   ⟸   NM_053489
- Peptide Label: precursor
- UniProtKB: F1LR02 (UniProtKB/TrEMBL),   A6JK98 (UniProtKB/TrEMBL),   A0A8I5ZV54 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000047962   ⟸   ENSRNOT00000045315
RefSeq Acc Id: ENSRNOP00000096747   ⟸   ENSRNOT00000116507
RefSeq Acc Id: ENSRNOP00000082737   ⟸   ENSRNOT00000095032
Protein Domains
Collagenase NC10/endostatin   FZ   Thrombospondin-like N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LR02-F1-model_v2 AlphaFold F1LR02 1-1311 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70936 AgrOrtholog
BioCyc Gene G2FUF-4216 BioCyc
Ensembl Genes ENSRNOG00000001229 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000045315 ENTREZGENE
  ENSRNOT00000045315.5 UniProtKB/TrEMBL
  ENSRNOT00000095032.1 UniProtKB/TrEMBL
  ENSRNOT00000116507.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.2000.10 UniProtKB/TrEMBL
  2.60.120.200 UniProtKB/TrEMBL
  3.10.100.10 UniProtKB/TrEMBL
  3.40.1620.70 UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
  Collagen_XVIII_Fz UniProtKB/TrEMBL
  Collagenase_NC10/endostatin UniProtKB/TrEMBL
  ConA-like_subgrp UniProtKB/TrEMBL
  DUF959_COL18_N UniProtKB/TrEMBL
  Frizzled_dom UniProtKB/TrEMBL
  Frizzled_dom_sf UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
  TSPN-like_N UniProtKB/TrEMBL
  XV/XVIII_trimerization_dom UniProtKB/TrEMBL
KEGG Report rno:85251 UniProtKB/TrEMBL
NCBI Gene 85251 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(XVIII) CHAIN UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  Collagen_trimer UniProtKB/TrEMBL
  DUF959 UniProtKB/TrEMBL
  Endostatin UniProtKB/TrEMBL
  Laminin_G_3 UniProtKB/TrEMBL
  PF01392 UniProtKB/TrEMBL
PhenoGen Col18a1 PhenoGen
PROSITE PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
  PS50038 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000001229 RatGTEx
SMART FRI UniProtKB/TrEMBL
  TSPN UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
  ConA_like_lec_gl UniProtKB/TrEMBL
  SSF63501 UniProtKB/TrEMBL
UniProt A0A8I5ZV54 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GLR1_RAT UniProtKB/TrEMBL
  A6JK98 ENTREZGENE, UniProtKB/TrEMBL
  A6JK99_RAT UniProtKB/TrEMBL
  A6JKA0_RAT UniProtKB/TrEMBL
  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