Ccl17 (C-C motif chemokine ligand 17) - Rat Genome Database

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Gene: Ccl17 (C-C motif chemokine ligand 17) Rattus norvegicus
Analyze
Symbol: Ccl17
Name: C-C motif chemokine ligand 17
RGD ID: 619924
Description: Exhibits CCR4 chemokine receptor binding activity. Predicted to be involved in several processes, including cellular response to cytokine stimulus; leukocyte chemotaxis; and positive regulation of ERK1 and ERK2 cascade. Predicted to localize to extracellular space. Biomarker of anti-basement membrane glomerulonephritis; asthma; pneumonia; and pulmonary fibrosis. Orthologous to human CCL17 (C-C motif chemokine ligand 17); PARTICIPATES IN interleukin-4 signaling pathway; chemokine mediated signaling pathway; INTERACTS WITH 6-propyl-2-thiouracil; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: C-C motif chemokine 17; chemokine (C-C motif) ligand 17; Scya17; small inducible cytokine subfamily A (Cys-Cys), member 17; Tarc
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
mRatBN7.21910,202,317 - 10,203,768 (-)NCBI
Rnor_6.0 Ensembl1910,619,220 - 10,620,671 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01910,619,220 - 10,620,671 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01910,614,027 - 10,615,478 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41910,641,376 - 10,642,827 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11910,646,201 - 10,647,653 (-)NCBI
Celera1910,088,700 - 10,090,151 (-)NCBICelera
Cytogenetic Map19p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-nitropyrene  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-di-tert-butyl-4-methylphenol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
allopurinol  (ISO)
alloxanthine  (ISO)
ammonium chloride  (EXP)
Bandrowski's base  (ISO)
benomyl  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP)
bleomycin A2  (ISO)
budesonide  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (ISO)
carbon nanotube  (EXP,ISO)
cefaloridine  (EXP)
ceric oxide  (EXP,ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt atom  (ISO)
crocidolite asbestos  (ISO)
decabromodiphenyl ether  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
dichloroacetic acid  (ISO)
diflorasone  (ISO)
diisononyl phthalate  (ISO)
dioxygen  (ISO)
enzacamene  (ISO)
Fexofenadine hydrochloride  (ISO)
fragrance  (ISO)
furan  (EXP)
graphene oxide  (ISO)
iron(2+) sulfate (anhydrous)  (ISO)
isoprenaline  (ISO)
linuron  (ISO)
manganese(II) chloride  (EXP)
methylmercury chloride  (ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
naphthalene  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
nifuroxazide  (ISO)
ozone  (ISO)
pevonedistat  (ISO)
pirinixic acid  (ISO)
platycodin D  (ISO)
prostaglandin E2  (ISO)
quartz  (EXP)
silicon dioxide  (EXP,ISO)
sodium arsenite  (ISO)
tacrolimus hydrate  (ISO)
titanium dioxide  (EXP,ISO)
toluene 2,4-diisocyanate  (ISO)
tremolite asbestos  (ISO)
trimellitic anhydride  (ISO)
undecane  (EXP)
valproic acid  (ISO)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc(0)  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Adib-Conquy M, etal., Mol Med. 2008 Jan-Feb;14(1-2):36-44.
2. Aki K, etal., Am J Physiol Renal Physiol. 2010 Apr;298(4):F870-82. Epub 2010 Jan 13.
3. Baumer W, etal., Br J Dermatol. 2004 Oct;151(4):823-30.
4. Chae JI, etal., Mol Biol (Mosk). 2008 Jul-Aug;42(4):639-44.
5. Chiba Y, etal., Int J Immunopathol Pharmacol. 2009 Oct-Dec;22(4):929-35.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Hartl D, etal., J Allergy Clin Immunol. 2006 Jan;117(1):204-11. Epub 2005 Nov 28.
9. Inoue T, etal., Eur Respir J. 2004 Jul;24(1):49-56.
10. Jakubzick C, etal., Am J Pathol. 2004 Oct;165(4):1211-21.
11. Kawasaki S, etal., J Immunol. 2001 Feb 1;166(3):2055-62.
12. Kishi M, etal., Thorax. 2008 Sep;63(9):810-6. Epub 2008 Feb 14.
13. Kurokawa M, etal., Int Arch Allergy Immunol. 2005;137 Suppl 1:60-8. Epub 2005 Jun 2.
14. Latzin P, etal., Eur Respir J. 2008 Jan;31(1):36-42. Epub 2007 Sep 26.
15. MGD data from the GO Consortium
16. Miyazaki E, etal., Am J Respir Crit Care Med. 2002 Apr 15;165(8):1125-31.
17. Monick MM, etal., J Immunol. 2007 Aug 1;179(3):1648-58.
18. NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Nureki S, etal., Respir Med. 2008 Feb;102(2):239-47. Epub 2007 Oct 18.
20. Paantjens AW, etal., Clin Exp Immunol. 2008 Nov;154(2):202-8. Epub 2008 Sep 8.
21. Pipeline to import KEGG annotations from KEGG into RGD
22. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
23. RGD automated data pipeline
24. RGD automated import pipeline for gene-chemical interactions
25. RGD comprehensive gene curation
26. RGD, Sept. 2003
27. Ritter M, etal., Biochem Biophys Res Commun. 2005 Aug 19;334(1):254-62.
28. Sun J, etal., Clin Exp Allergy. 2007 Jun;37(6):901-8.
29. Thielen C, etal., Leuk Res. 2008 Sep;32(9):1431-8. doi: 10.1016/j.leukres.2008.02.016. Epub 2008 Apr 18.
30. Vijayanand P, etal., J Immunol. 2010 Apr 15;184(8):4568-74. Epub 2010 Mar 17.
31. Ying S, etal., J Immunol. 2008 Aug 15;181(4):2790-8.
32. Yogo Y, etal., Respir Res. 2009 Aug 29;10:80.
Additional References at PubMed
PMID:12949249   PMID:23844157  


Genomics

Comparative Map Data
Ccl17
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21910,202,317 - 10,203,768 (-)NCBI
Rnor_6.0 Ensembl1910,619,220 - 10,620,671 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01910,619,220 - 10,620,671 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01910,614,027 - 10,615,478 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41910,641,376 - 10,642,827 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11910,646,201 - 10,647,653 (-)NCBI
Celera1910,088,700 - 10,090,151 (-)NCBICelera
Cytogenetic Map19p13NCBI
CCL17
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1657,404,767 - 57,416,063 (+)EnsemblGRCh38hg38GRCh38
GRCh381657,396,076 - 57,416,063 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371657,438,679 - 57,449,975 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361655,996,180 - 56,007,475 (+)NCBINCBI36hg18NCBI36
Build 341655,996,179 - 56,007,475NCBI
Celera1641,938,673 - 41,949,969 (+)NCBI
Cytogenetic Map16q21NCBI
HuRef1643,306,559 - 43,317,854 (+)NCBIHuRef
CHM1_11658,846,760 - 58,858,057 (+)NCBICHM1_1
Ccl17
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39895,535,996 - 95,538,666 (+)NCBIGRCm39mm39
GRCm39 Ensembl895,537,081 - 95,538,664 (+)Ensembl
GRCm38894,809,380 - 94,812,038 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl894,810,453 - 94,812,036 (+)EnsemblGRCm38mm10GRCm38
MGSCv37897,334,353 - 97,335,936 (+)NCBIGRCm37mm9NCBIm37
MGSCv36897,699,598 - 97,701,165 (+)NCBImm8
Celera899,134,583 - 99,136,166 (+)NCBICelera
Cytogenetic Map8C5NCBI
cM Map846.85NCBI
Ccl17
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543315,053,061 - 15,054,572 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543315,052,616 - 15,054,732 (+)NCBIChiLan1.0ChiLan1.0
CCL17
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11656,810,923 - 56,822,131 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1656,819,949 - 56,822,131 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01637,678,518 - 37,689,350 (+)NCBIMhudiblu_PPA_v0panPan3
CCL17
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1259,001,463 - 59,014,347 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl259,001,464 - 59,005,230 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha255,630,918 - 55,633,430 (-)NCBI
ROS_Cfam_1.0259,539,866 - 59,550,154 (-)NCBI
UMICH_Zoey_3.1256,371,394 - 56,373,906 (-)NCBI
UNSW_CanFamBas_1.0257,379,129 - 57,381,635 (-)NCBI
UU_Cfam_GSD_1.0258,272,358 - 58,274,870 (-)NCBI
Ccl17
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934950,112,663 - 50,114,927 (-)NCBI
SpeTri2.0NW_0049364759,475,013 - 9,476,326 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCL17
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl619,345,941 - 19,348,926 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1619,345,929 - 19,372,972 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2617,342,591 - 17,345,444 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCL17
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1543,343,525 - 43,350,096 (+)NCBI
ChlSab1.1 Ensembl543,346,329 - 43,348,599 (+)Ensembl
Ccl17
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474628,655,288 - 28,657,563 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124933090Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127635288Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19129558305Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19129558305Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19132379055Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19138221845Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19138221845Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19138221845Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19138221845Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:117
Count of miRNA genes:93
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000021842
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 6 9 1
Low 1 3 3 10 1 30 15 20 9
Below cutoff 9 16 12 12 3 3 16 8 9 1 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021842   ⟹   ENSRNOP00000021842
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1910,619,220 - 10,620,671 (-)Ensembl
RefSeq Acc Id: NM_057151   ⟹   NP_476492
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21910,202,317 - 10,203,768 (-)NCBI
Rnor_6.01910,619,220 - 10,620,671 (-)NCBI
Rnor_5.01910,614,027 - 10,615,478 (-)NCBI
RGSC_v3.41910,641,376 - 10,642,827 (-)RGD
Celera1910,088,700 - 10,090,151 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_476492 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAG31159 (Get FASTA)   NCBI Sequence Viewer  
  EDL87324 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_476492   ⟸   NM_057151
- Peptide Label: precursor
- UniProtKB: Q9ERE0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000021842   ⟸   ENSRNOT00000021842
Protein Domains
SCY

Transcriptome

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

Promoters
RGD ID:13700941
Promoter ID:EPDNEW_R11465
Type:single initiation site
Name:Ccl17_1
Description:C-C motif chemokine ligand 17
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_6.01910,620,720 - 10,620,780EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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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)
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
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)
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
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:619924 AgrOrtholog
Ensembl Genes ENSRNOG00000016278 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021842 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021842 ENTREZGENE, UniProtKB/TrEMBL
InterPro Chemokine_b/g/d UniProtKB/TrEMBL
  Chemokine_CC_CS UniProtKB/TrEMBL
  Chemokine_IL8-like_dom UniProtKB/TrEMBL
  Interleukin_8-like_sf UniProtKB/TrEMBL
KEGG Report rno:117518 UniProtKB/TrEMBL
NCBI Gene 117518 ENTREZGENE
PANTHER PTHR12015 UniProtKB/TrEMBL
Pfam IL8 UniProtKB/TrEMBL
PhenoGen Ccl17 PhenoGen
PROSITE SMALL_CYTOKINES_CC UniProtKB/TrEMBL
SMART SCY UniProtKB/TrEMBL
Superfamily-SCOP Chemokine_IL8 UniProtKB/TrEMBL
UniProt E9PTY9_RAT UniProtKB/TrEMBL
  Q9ERE0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-08 Ccl17  C-C motif chemokine ligand 17  Ccl17  chemokine (C-C motif) ligand 17  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Ccl17  chemokine (C-C motif) ligand 17    small inducible cytokine subfamily A (Cys-Cys), member 17  Name updated 1299863 APPROVED
2004-09-10 Ccl17  small inducible cytokine subfamily A (Cys-Cys), member 17  Scya17    Symbol and Name updated 1299863 APPROVED
2002-08-07 Scya17  small inducible cytokine subfamily A (Cys-Cys), member 17      Symbol and Name status set to provisional 70820 PROVISIONAL