Chi3l1 (chitinase 3 like 1) - Rat Genome Database

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Gene: Chi3l1 (chitinase 3 like 1) Rattus norvegicus
Analyze
Symbol: Chi3l1
Name: chitinase 3 like 1
RGD ID: 620874
Description: Predicted to have chitin binding activity. Involved in cellular response to interleukin-1; cellular response to tumor necrosis factor; and inflammatory response. Localizes to extracellular space. Biomarker of hypertension. Human ortholog(s) of this gene implicated in asthma and schizophrenia. Orthologous to human CHI3L1 (chitinase 3 like 1); PARTICIPATES IN amino sugar metabolic pathway; nucleotide sugar metabolic pathway; INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: cartilage glycoprotein 39; CGP-39; Chil1; chitinase 3-like 1; chitinase 3-like 1 (cartilage glycoprotein-39); chitinase-3-like protein 1; GP-39; MGC109420
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
mRatBN7.21345,641,802 - 45,649,787 (+)NCBI
Rnor_6.0 Ensembl1351,022,681 - 51,030,802 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01351,022,844 - 51,030,797 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01356,074,912 - 56,086,477 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41347,139,658 - 47,147,591 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11347,155,099 - 47,161,151 (+)NCBI
Celera1345,969,872 - 45,977,855 (+)NCBICelera
Cytogenetic Map13q13NCBI
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)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (ISO)
acetamide  (EXP)
acrolein  (ISO)
aflatoxin B1  (EXP)
aldehydo-D-glucosamine  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
buta-1,3-diene  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP,ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dimethylarsinic acid  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
etoposide  (ISO)
furan  (EXP)
indometacin  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
isotretinoin  (ISO)
ketamine  (EXP)
methylmercury chloride  (EXP,ISO)
naphthalene  (ISO)
nickel dichloride  (ISO)
ozone  (ISO)
p-menthan-3-ol  (EXP)
paclitaxel  (EXP)
pentanal  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
Soman  (EXP)
testosterone  (EXP)
tetrachloromethane  (EXP)
titanium dioxide  (EXP,ISO)
triadimefon  (ISO)
tributylstannane  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
XL147  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Bergmann OJ, etal., Clin Cancer Res. 2005 Dec 15;11(24 Pt 1):8644-52.
2. Boot RG, etal., Arterioscler Thromb Vasc Biol. 1999 Mar;19(3):687-94.
3. Brasso K, etal., Prostate. 2006 Apr 1;66(5):503-13.
4. Chupp GL, etal., N Engl J Med. 2007 Nov 15;357(20):2016-27.
5. Cintin C, etal., Cancer. 2002 Jul 15;95(2):267-74.
6. Diefenbach CS, etal., Gynecol Oncol. 2007 Feb;104(2):435-42. Epub 2006 Oct 4.
7. Flister MJ, etal., Hypertension. 2013 Apr;61(4):850-6. doi: 10.1161/HYPERTENSIONAHA.111.01008. Epub 2013 Mar 4.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. GOA data from the GO Consortium
10. Hogdall EV, etal., Oncol Rep. 2003 Sep-Oct;10(5):1535-8.
11. Huang Y, etal., Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):15044-9.
12. Jin Z, etal., Acta Biochim Biophys Sin (Shanghai). 2008 Aug;40(8):740-6.
13. Johansen JS, etal., Arthritis Rheum. 1999 Dec;42(12):2624-30.
14. Johansen JS, etal., Breast Cancer Res Treat. 2003 Jul;80(1):15-21.
15. Johansen JS, etal., Lung Cancer. 2004 Dec;46(3):333-40.
16. Johansen JS, etal., Respir Med. 2005 Apr;99(4):396-402. Epub 2004 Nov 5.
17. Johansen JS, etal., Rheumatology (Oxford). 1999 Jul;38(7):618-26.
18. Korthagen NM, etal., Respir Med. 2011 Jan;105(1):106-13.
19. Kucur M, etal., Coron Artery Dis. 2007 Aug;18(5):391-6.
20. Lee CG, etal., J Exp Med. 2009 May 11;206(5):1149-66. Epub 2009 May 4.
21. Madazli R, etal., Int J Gynaecol Obstet. 2008 Mar;100(3):239-43. Epub 2007 Dec 3.
22. Markert JM, etal., Physiol Genomics. 2001 Feb 7;5(1):21-33.
23. Matsuura H, etal., Am J Respir Cell Mol Biol. 2010 Jul 23.
24. MGD data from the GO Consortium
25. Mylin AK, etal., Eur J Haematol. 2006 Nov;77(5):416-24. Epub 2006 Aug 23.
26. NCBI rat LocusLink and RefSeq merged data July 26, 2002
27. Nojgaard C, etal., Coron Artery Dis. 2008 Jun;19(4):257-63.
28. Nordenbaek C, etal., J Infect Dis. 1999 Nov;180(5):1722-6.
29. Nordenbaek C, etal., Scand J Rheumatol. 2005 Jul-Aug;34(4):293-7.
30. OMIM Disease Annotation Pipeline
31. Ostergaard C, etal., Clin Diagn Lab Immunol. 2002 May;9(3):598-604.
32. Pipeline to import KEGG annotations from KEGG into RGD
33. Rathcke CN, etal., Diabetes Care. 2009 Feb;32(2):323-8. Epub 2008 Oct 28.
34. Rathcke CN, etal., PLoS One. 2009 Jul 1;4(7):e6106.
35. Rathcke CN, etal., Scand Cardiovasc J. 2010 Apr;44(2):92-9.
36. Recklies AD, etal., J Biol Chem. 2005 Dec 16;280(50):41213-21. Epub 2005 Oct 18.
37. RGD automated data pipeline
38. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
39. RGD automated import pipeline for gene-chemical interactions
40. RGD comprehensive gene curation
41. Schmidt H, etal., Cancer. 2006 Mar 1;106(5):1130-9.
42. Sjogren H, etal., Am J Pathol. 2003 Mar;162(3):781-92.
43. Sohn MH, etal., Am J Respir Crit Care Med. 2010 Oct 1;182(7):918-28. Epub 2010 Jun 17.
44. Thom I, etal., Cancer. 2010 Sep 1;116(17):4114-21.
45. Thomsen SB, etal., Cardiovasc Diabetol. 2010 Dec 8;9:86.
46. Waki H, etal., Auton Neurosci. 2008 Nov 3;142(1-2):40-4. Epub 2008 Aug 13.
Additional References at PubMed
PMID:8245017   PMID:9492324   PMID:12477932   PMID:12775711   PMID:15489334   PMID:16502470   PMID:18403759   PMID:20650887   PMID:21385870   PMID:21478032   PMID:21546314   PMID:21987626  
PMID:23376485   PMID:23533145   PMID:23558346   PMID:24380732   PMID:25062286   PMID:26978347   PMID:31002152   PMID:31115541  


Genomics

Comparative Map Data
Chi3l1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21345,641,802 - 45,649,787 (+)NCBI
Rnor_6.0 Ensembl1351,022,681 - 51,030,802 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01351,022,844 - 51,030,797 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01356,074,912 - 56,086,477 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41347,139,658 - 47,147,591 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11347,155,099 - 47,161,151 (+)NCBI
Celera1345,969,872 - 45,977,855 (+)NCBICelera
Cytogenetic Map13q13NCBI
CHI3L1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1203,178,931 - 203,186,704 (-)EnsemblGRCh38hg38GRCh38
GRCh381203,178,931 - 203,186,704 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371203,148,059 - 203,155,832 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361201,414,682 - 201,422,545 (-)NCBINCBI36hg18NCBI36
Build 341199,879,586 - 199,887,534NCBI
Celera1176,277,300 - 176,285,163 (-)NCBI
Cytogenetic Map1q32.1NCBI
HuRef1174,313,188 - 174,321,051 (-)NCBIHuRef
CHM1_11204,570,380 - 204,578,243 (-)NCBICHM1_1
Chil1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391134,109,894 - 134,117,769 (+)NCBIGRCm39mm39
GRCm39 Ensembl1134,109,914 - 134,117,919 (+)Ensembl
GRCm381134,182,156 - 134,190,031 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1134,182,176 - 134,190,181 (+)EnsemblGRCm38mm10GRCm38
MGSCv371136,078,981 - 136,086,608 (+)NCBIGRCm37mm9NCBIm37
MGSCv361135,998,892 - 136,006,442 (+)NCBImm8
Celera1136,794,910 - 136,802,547 (+)NCBICelera
Cytogenetic Map1E4NCBI
cM Map158.15NCBI
Chi3l1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540639,191,073 - 39,202,020 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540639,195,101 - 39,201,808 (-)NCBIChiLan1.0ChiLan1.0
CHI3L1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11183,073,287 - 183,083,229 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1183,075,312 - 183,083,229 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01178,778,081 - 178,789,704 (-)NCBIMhudiblu_PPA_v0panPan3
CHI3L1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1725,620 - 32,954 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl726,316 - 33,427 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha782,048 - 88,664 (+)NCBI
ROS_Cfam_1.0736,653 - 43,433 (+)NCBI
UMICH_Zoey_3.1725,021 - 31,646 (+)NCBI
UNSW_CanFamBas_1.07134,620 - 141,244 (+)NCBI
UU_Cfam_GSD_1.07157,023 - 163,649 (+)NCBI
Chi3l1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934472,176,383 - 72,183,907 (+)NCBI
SpeTri2.0NW_0049365671,411,080 - 1,418,332 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHI3L1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9113,885,542 - 113,895,510 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19113,885,541 - 113,895,033 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29125,344,018 - 125,353,512 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CHI3L1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12526,160,993 - 26,169,005 (+)NCBI
ChlSab1.1 Ensembl2526,160,961 - 26,169,566 (+)Ensembl
Chi3l1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248077,655,777 - 7,664,484 (+)NCBI

Position Markers
RH142356  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21345,649,558 - 45,649,709 (+)MAPPER
Rnor_6.01351,030,569 - 51,030,719NCBIRnor6.0
Rnor_5.01356,086,249 - 56,086,399UniSTSRnor5.0
RGSC_v3.41347,147,363 - 47,147,513UniSTSRGSC3.4
Celera1345,977,627 - 45,977,777UniSTS
RH 3.4 Map13172.0UniSTS
Cytogenetic Map13q13UniSTS
BE106626  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21345,643,942 - 45,644,132 (+)MAPPER
Rnor_6.01351,024,983 - 51,025,172NCBIRnor6.0
Rnor_5.01356,080,630 - 56,080,819UniSTSRnor5.0
Rnor_5.01356,077,085 - 56,077,274UniSTSRnor5.0
RGSC_v3.41347,141,744 - 47,141,933UniSTSRGSC3.4
Celera1345,972,083 - 45,972,272UniSTS
RH 3.4 Map13178.0UniSTS
Cytogenetic Map13q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)131409633059096330Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)131409633059096330Rat
2302275Gluco37Glucose level QTL 373.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)131444158251577031Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131981081464810814Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)132005247765052477Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)132148248158537177Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132800833873008338Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132858445273584452Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132907693474076934Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132907693474076934Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133614753364868393Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133734634882346348Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133937292784372927Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133950130093652524Rat
4889861Pur29Proteinuria QTL 2913.80.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)134231074486833540Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)134231074487310744Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)134357571788575717Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134567662990676629Rat
4145117Mcs27Mammary carcinoma susceptibility QTL 270.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)134877665553264877Rat
6893344Cm79Cardiac mass QTL 791.50.04heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)134905850767207219Rat
12879436Bp395Blood pressure QTL 395arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134999470851081193Rat
12879472Bp399Blood pressure QTL 399arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135060922853264877Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:344
Count of miRNA genes:124
Interacting mature miRNAs:143
Transcripts:ENSRNOT00000060710, ENSRNOT00000071475
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 2 1 8 2 17 2 22 1 11
Low 1 34 45 35 2 35 8 11 11 29 21 8
Below cutoff 8 4 4 4 39 6 17

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000078599   ⟹   ENSRNOP00000074871
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1351,022,681 - 51,030,802 (+)Ensembl
RefSeq Acc Id: NM_001309820   ⟹   NP_001296749
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21345,642,097 - 45,649,787 (+)NCBI
Rnor_6.01351,023,137 - 51,030,797 (+)NCBI
Celera1345,970,164 - 45,977,855 (+)NCBI
Sequence:
RefSeq Acc Id: NM_053560   ⟹   NP_446012
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21345,641,802 - 45,649,787 (+)NCBI
Rnor_6.01351,022,844 - 51,030,797 (+)NCBI
Rnor_5.01356,074,912 - 56,086,477 (+)NCBI
RGSC_v3.41347,139,658 - 47,147,591 (+)RGD
Celera1345,969,872 - 45,977,855 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_446012   ⟸   NM_053560
- Peptide Label: isoform 2 precursor
- UniProtKB: Q9WTV1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001296749   ⟸   NM_001309820
- Peptide Label: isoform 1 precursor
- UniProtKB: Q9WTV1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074871   ⟸   ENSRNOT00000078599
Protein Domains
GH18   Glyco_18

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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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)
ACI/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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/NRrrc (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
FHH/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)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620874 AgrOrtholog
Ensembl Genes ENSRNOG00000053272 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000074871 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000078599 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.10.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7319171 IMAGE-MGC_LOAD
InterPro CHI3L1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chitinase_II UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chitinase_insertion_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glyco_hydro18_cat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glycoside_hydrolase_SF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:89824 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109420 IMAGE-MGC_LOAD
NCBI Gene 89824 ENTREZGENE
PANTHER PTHR11177:SF202 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Glyco_hydro_18 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Chi3l1 PhenoGen
PROSITE GH18_2 UniProtKB/Swiss-Prot
SMART Glyco_18 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF51445 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54556 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A4LA56_RAT UniProtKB/TrEMBL
  CH3L1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q5BJR6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-09 Chi3l1  chitinase 3 like 1  Chi3l1  chitinase 3-like 1 (cartilage glycoprotein-39)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-09 Chi3l1  chitinase 3-like 1 (cartilage glycoprotein-39)  Chi3l1  chitinase 3-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Chi3l1  chitinase 3-like 1    chitinase 3-like 1 (cartilage glycoprotein-39)  Name updated 1299863 APPROVED
2002-08-07 Chi3l1  chitinase 3-like 1 (cartilage glycoprotein-39)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease human homolog is expressed in atherosclerotic plaques 634758