Cxcl6 (C-X-C motif chemokine ligand 6) - Rat Genome Database

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Gene: Cxcl6 (C-X-C motif chemokine ligand 6) Rattus norvegicus
Analyze
Symbol: Cxcl6
Name: C-X-C motif chemokine ligand 6
RGD ID: 708540
Description: Enables chemokine activity. Involved in several processes, including cellular response to lipopolysaccharide; positive regulation of receptor signaling pathway via JAK-STAT; and response to gamma radiation. Located in extracellular space. Used to study colon carcinoma. Biomarker of prostatitis and severe acute respiratory syndrome. Human ortholog(s) of this gene implicated in idiopathic pulmonary fibrosis. Orthologous to several human genes including CXCL6 (C-X-C motif chemokine ligand 6); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: C-X-C motif chemokine 5; chemokine (C-X-C motif) ligand 5; chemokine (C-X-C motif) ligand 6; chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2); CXC chemokine LIX; Cxcl5; cytokine LIX; LOC60665; small-inducible cytokine B5
RGD Orthologs
Human
Mouse
Bonobo
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21417,310,089 - 17,312,303 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl1418,860,264 - 18,862,407 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01418,860,201 - 18,920,839 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01418,770,999 - 18,771,910 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41418,825,357 - 18,826,269 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11418,825,357 - 18,826,269 (-)NCBI
Celera1416,687,262 - 16,688,187 (-)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
extracellular space  (IBA,IDA,IEA)

Molecular Function

References

References - curated
1. Alzoghaibi MA and Bahammam AS, Sleep Breath. 2005 Sep;9(3):119-26.
2. Cai S, etal., J Immunol. 2009 Nov 15;183(10):6629-38. Epub 2009 Oct 21.
3. Chandrasekar B, etal., Circulation. 2001 May 8;103(18):2296-302.
4. Chandrasekar B, etal., J Biol Chem 2003 Feb 14;278(7):4675-86.
5. Chen HW, etal., FASEB J. 2006 Nov;20(13):2393-5. Epub 2006 Oct 5.
6. Colletti LM and Green M, Shock. 2001 Oct;16(4):312-9.
7. Colletti LM, etal., Hepatology. 2000 Feb;31(2):435-45.
8. Colletti LM, etal., J Clin Invest. 1995 Jan;95(1):134-41.
9. Colletti LM, etal., Shock. 1998 Oct;10(4):248-57.
10. Donninger H, etal., J Infect Dis. 2003 Jun 1;187(11):1809-17.
11. Edman LC, etal., Stem Cells. 2008 Jul;26(7):1891-900. Epub 2008 Apr 24.
12. Esposito R, etal., Front Cell Infect Microbiol. 2017 Oct 9;7:434. doi: 10.3389/fcimb.2017.00434. eCollection 2017.
13. Funk CJ, etal., J Gen Virol. 2009 Dec;90(Pt 12):2956-64. Epub 2009 Sep 9.
14. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
15. GOA data from the GO Consortium
16. Goodman RB, etal., Am J Respir Crit Care Med. 1996 Sep;154(3 Pt 1):602-11.
17. Halloran MM, etal., J Immunol. 1999 Jun 15;162(12):7492-500.
18. Holven KB, etal., Arterioscler Thromb Vasc Biol. 2002 Apr 1;22(4):699-703.
19. Huvenne W, etal., Respir Res. 2010 Jul 23;11:100.
20. Jeyaseelan S, etal., Am J Respir Cell Mol Biol. 2005 Jun;32(6):531-9. Epub 2005 Mar 18.
21. Jeyaseelan S, etal., Infect Immun. 2004 Dec;72(12):7247-56.
22. Keane MP, etal., Am J Respir Crit Care Med. 2001 Dec 15;164(12):2239-42.
23. Keller C, etal., Infect Immun. 2006 Jul;74(7):4295-309.
24. Liu L, etal., Zhonghua Yi Xue Za Zhi. 2009 Oct 20;89(38):2690-4.
25. Lukacs NW, etal., J Leukoc Biol. 1998 Jun;63(6):746-51.
26. Malik IA, etal., Am J Pathol. 2010 Apr;176(4):1801-15. Epub 2010 Feb 25.
27. MGD data from the GO Consortium
28. Nakayama S, etal., Respir Med. 2005 Sep;99(9):1145-51. Epub 2005 Mar 25.
29. Nanji AA, etal., Hepatology. 1999 Oct;30(4):934-43.
30. Nomura S, etal., Platelets. 2008 May;19(3):192-8.
31. Qiu Y, etal., Am J Respir Crit Care Med. 2003 Oct 15;168(8):968-75. Epub 2003 Jul 11.
32. Qiu Y, etal., Thorax. 2007 Jun;62(6):475-82. Epub 2007 Jan 18.
33. RGD automated data pipeline
34. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
35. RGD automated import pipeline for gene-chemical interactions
36. RGD comprehensive gene curation
37. Rovai LE, etal., J Leukoc Biol. 1998 Oct;64(4):494-502.
38. Sachidanandan C, etal., J Cell Sci 2002 Jul 1;115(Pt 13):2701-12.
39. Smith JB, etal., Immunogenetics 2002 Nov;54(8):599-603. Epub 2002 Oct 1.
40. Speetjens FM, etal., Clin Cancer Res. 2008 Apr 15;14(8):2276-84.
41. Sugimoto M, etal., Prostate. 2011 Mar 1;71(4):438-44. doi: 10.1002/pros.21299. Epub 2010 Oct 28.
42. Sugiyama K, etal., Respirology. 2006 Nov;11(6):708-14.
43. Tateda K, etal., Infect Immun. 2001 Apr;69(4):2017-24.
44. Tsushima K, etal., Respirology. 2008 Jun;13(4):546-52. Epub 2008 Apr 10.
45. Wakefield TW, etal., Arterioscler Thromb Vasc Biol. 1995 Feb;15(2):258-68.
46. Walley KR, etal., Infect Immun. 1997 Sep;65(9):3847-51.
47. Wang H, etal., Allergy. 2011 Jan;66(1):132-40. doi: 10.1111/j.1398-9995.2010.02444.x.
48. Williams AS, etal., Eur Respir J. 2008 Sep;32(3):571-8. Epub 2008 Apr 16.
49. Wu X, etal., Arch Otolaryngol Head Neck Surg. 2009 Jan;135(1):65-72.
50. Zhang H, etal., J Sex Med. 2011 Feb;8(2):437-46. doi: 10.1111/j.1743-6109.2010.02128.x. Epub 2010 Nov 29.
Additional References at PubMed
PMID:8399143   PMID:20643340   PMID:21734176   PMID:22034072   PMID:27717828   PMID:29126185   PMID:33741291  


Genomics

Comparative Map Data
Cxcl6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21417,310,089 - 17,312,303 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl1418,860,264 - 18,862,407 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01418,860,201 - 18,920,839 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01418,770,999 - 18,771,910 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41418,825,357 - 18,826,269 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11418,825,357 - 18,826,269 (-)NCBI
Celera1416,687,262 - 16,688,187 (-)NCBICelera
Cytogenetic Map14p22NCBI
CXCL6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl473,836,640 - 73,849,064 (+)EnsemblGRCh38hg38GRCh38
GRCh38473,836,678 - 73,838,760 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37474,702,395 - 74,704,477 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36474,921,277 - 74,923,341 (+)NCBINCBI36hg18NCBI36
Build 34475,067,447 - 75,069,511NCBI
Celera472,062,419 - 72,064,623 (+)NCBI
Cytogenetic Map4q13.3NCBI
HuRef470,513,410 - 70,515,614 (+)NCBIHuRef
CHM1_1474,738,258 - 74,740,462 (+)NCBICHM1_1
Cxcl5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39590,907,157 - 90,909,484 (+)NCBIGRCm39mm39
GRCm39 Ensembl590,907,219 - 90,909,483 (+)Ensembl
GRCm38590,759,298 - 90,761,625 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl590,759,360 - 90,761,624 (+)EnsemblGRCm38mm10GRCm38
MGSCv37591,188,325 - 91,190,651 (+)NCBIGRCm37mm9NCBIm37
MGSCv36591,834,578 - 91,836,824 (+)NCBImm8
Celera588,910,984 - 88,913,251 (+)NCBICelera
Cytogenetic Map5E1NCBI
cM Map544.78NCBI
CXCL6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1456,190,130 - 56,192,402 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl456,189,961 - 56,192,402 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0450,357,643 - 50,359,822 (-)NCBIMhudiblu_PPA_v0panPan3
AMCF-II
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl870,008,162 - 70,010,358 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1870,008,225 - 70,010,360 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2874,160,033 - 74,162,170 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CXCL6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1722,291,949 - 22,294,191 (+)NCBI
ChlSab1.1 Ensembl722,292,045 - 22,294,207 (+)Ensembl
Vero_WHO_p1.0NW_023666084497,366 - 499,651 (-)NCBI

Position Markers
U27267  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21417,310,695 - 17,310,820 (+)MAPPERmRatBN7.2
Rnor_6.01418,860,803 - 18,860,927NCBIRnor6.0
Rnor_5.01418,770,445 - 18,770,569UniSTSRnor5.0
RGSC_v3.41418,824,804 - 18,824,928UniSTSRGSC3.4
Celera1416,686,708 - 16,686,832UniSTS
Cytogenetic Map14p22UniSTS
U27267  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21417,311,119 - 17,311,242 (+)MAPPERmRatBN7.2
Rnor_6.01418,861,227 - 18,861,349NCBIRnor6.0
Rnor_5.01418,770,869 - 18,770,991UniSTSRnor5.0
RGSC_v3.41418,825,228 - 18,825,350UniSTSRGSC3.4
Celera1416,687,132 - 16,687,254UniSTS
Cytogenetic Map14p22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14134403399Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14141333960Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14141333960Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14142766285Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14222782519230541Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14483323319909932Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14483323319909932Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14483323323004027Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14483323326466248Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14483323333040042Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin141053997755539977Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)141053997755539977Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141268042430155192Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141268061332593926Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141633698833163485Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:47
Count of miRNA genes:42
Interacting mature miRNAs:45
Transcripts:ENSRNOT00000003823
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 2
Low 3 5 40 24 18 24 1 1 38 9 21 11 1
Below cutoff 30 17 17 17 7 10 32 14 15 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003823   ⟹   ENSRNOP00000003823
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1418,860,264 - 18,862,407 (-)Ensembl
RefSeq Acc Id: NM_022214   ⟹   NP_071550
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21417,311,250 - 17,312,163 (-)NCBI
Rnor_6.01418,861,357 - 18,862,268 (-)NCBI
Rnor_5.01418,770,999 - 18,771,910 (-)NCBI
RGSC_v3.41418,825,357 - 18,826,269 (-)RGD
Celera1416,687,262 - 16,688,187 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039092389   ⟹   XP_038948317
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21417,310,089 - 17,312,303 (-)NCBI
Protein Sequences
Protein RefSeqs NP_071550 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948317 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB61460 (Get FASTA)   NCBI Sequence Viewer  
  EDL88563 (Get FASTA)   NCBI Sequence Viewer  
  P97885 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_071550   ⟸   NM_022214
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000003823   ⟸   ENSRNOT00000003823
RefSeq Acc Id: XP_038948317   ⟸   XM_039092389
- Peptide Label: isoform X1
Protein Domains
SCY

Transcriptome

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

Promoters
RGD ID:13699230
Promoter ID:EPDNEW_R9754
Type:single initiation site
Name:Cxcl6_1
Description:C-X-C motif chemokine ligand 6
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_6.01418,862,352 - 18,862,412EPDNEW

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)
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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)
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
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)
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
WKY/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
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:708540 AgrOrtholog
Ensembl Genes ENSRNOG00000002843 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003823 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003823 ENTREZGENE, UniProtKB/TrEMBL
InterPro Chemokine_CXC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_CXC_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_IL8-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CXC_Chemokine_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Interleukin_8-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:60665 UniProtKB/Swiss-Prot
NCBI Gene 60665 ENTREZGENE
PANTHER PTHR10179 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam IL8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cxcl6 PhenoGen
PRINTS SMALLCYTKCXC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SMALL_CYTOKINES_CXC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SCY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54117 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CXCL5_RAT UniProtKB/Swiss-Prot
  G3V6C8_RAT UniProtKB/TrEMBL
  P97885 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-08 Cxcl6  C-X-C motif chemokine ligand 6  Cxcl6  chemokine (C-X-C motif) ligand 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-04-29 Cxcl6  chemokine (C-X-C motif) ligand 6  Cxcl5  chemokine (C-X-C motif) ligand 5  Name and Symbol changed 629549 APPROVED
2011-07-14 Cxcl5  chemokine (C-X-C motif) ligand 5  Cxcl6  chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-26 Cxcl6  chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2)  Cxcl5  chemokine (C-X-C motif) ligand 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Cxcl5  chemokine (C-X-C motif) ligand 5  LOC60665  CXC chemokine LIX  Symbol and Name updated 1299863 APPROVED