Xcl1 (X-C motif chemokine ligand 1) - Rat Genome Database
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Gene: Xcl1 (X-C motif chemokine ligand 1) Rattus norvegicus
Analyze
Symbol: Xcl1
Name: X-C motif chemokine ligand 1
RGD ID: 620452
Description: Predicted to have CCR chemokine receptor binding activity; chemokine activity; and protein homodimerization activity. Predicted to be involved in several processes, including cellular response to cytokine stimulus; positive regulation of leukocyte migration; and regulation of cytokine production. Predicted to localize to extracellular space. Biomarker of anti-basement membrane glomerulonephritis. Orthologous to several human genes including XCL1 (X-C motif chemokine ligand 1); PARTICIPATES IN chemokine mediated signaling pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 1,2-dimethylhydrazine; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: c motif chemokine 1; chemokine (C motif) ligand 1; cytokine SCM-1; Ltn; lymphotactin; Scyc1; small inducible cytokine subfamily C, member 1 (lymphotactin); small-inducible cytokine C1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
Rnor_6.01383,199,402 - 83,202,845 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1383,199,264 - 83,202,864 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01388,079,753 - 88,083,196 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41380,691,195 - 80,694,638 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11380,705,382 - 80,708,826 (-)NCBI
Celera1376,965,267 - 76,968,710 (-)NCBICelera
Cytogenetic Map13q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
antimicrobial humoral immune response mediated by antimicrobial peptide  (ISO)
cell-cell signaling  (ISO)
cellular response to interferon-gamma  (IBA)
cellular response to interleukin-1  (IBA)
cellular response to interleukin-4  (IEA,ISO)
cellular response to transforming growth factor beta stimulus  (IEA,ISO)
cellular response to tumor necrosis factor  (IBA)
chemokine-mediated signaling pathway  (IBA)
chemotaxis  (ISO)
G protein-coupled receptor signaling pathway  (IBA)
immune response  (IEA)
inflammatory response  (IBA)
killing of cells of other organism  (ISO)
lymphocyte chemotaxis  (IBA)
mature natural killer cell chemotaxis  (IEA,ISO)
monocyte chemotaxis  (IBA)
negative regulation of CD4-positive, alpha-beta T cell proliferation  (ISO)
negative regulation of DNA-binding transcription factor activity  (ISO)
negative regulation of interferon-gamma production  (ISO)
negative regulation of interleukin-2 production  (ISO)
negative regulation of T cell cytokine production  (ISO)
negative regulation of T-helper 1 cell activation  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
neutrophil chemotaxis  (IBA)
positive regulation of B cell chemotaxis  (IEA,ISO)
positive regulation of CD4-positive, alpha-beta T cell proliferation  (IEA,ISO)
positive regulation of CD8-positive, alpha-beta T cell proliferation  (ISO)
positive regulation of ERK1 and ERK2 cascade  (IBA)
positive regulation of granzyme A production  (ISO)
positive regulation of granzyme B production  (ISO)
positive regulation of GTPase activity  (IBA)
positive regulation of immunoglobulin production in mucosal tissue  (IEA,ISO)
positive regulation of interleukin-10 production  (ISO)
positive regulation of leukocyte chemotaxis  (ISO)
positive regulation of natural killer cell chemotaxis  (IEA,ISO)
positive regulation of neutrophil chemotaxis  (IEA,ISO)
positive regulation of release of sequestered calcium ion into cytosol  (ISO)
positive regulation of T cell chemotaxis  (IBA,IEA,ISO)
positive regulation of T cell cytokine production  (ISO)
positive regulation of T cell mediated cytotoxicity  (ISO)
positive regulation of T-helper 1 cell cytokine production  (IEA,ISO)
positive regulation of T-helper 2 cell cytokine production  (IEA,ISO)
positive regulation of thymocyte migration  (IEA,ISO)
positive regulation of transforming growth factor beta production  (ISO)
regulation of inflammatory response  (ISO)
release of sequestered calcium ion into cytosol  (IEA,ISO)
response to virus  (ISO)
signal transduction  (IEA)

Cellular Component
extracellular space  (IBA,IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:7602097   PMID:8757601   PMID:9013979   PMID:9029087   PMID:9632725   PMID:9973465   PMID:10518929   PMID:10887101   PMID:11181058   PMID:11889129   PMID:12949249   PMID:14734774  
PMID:18832695   PMID:24155383   PMID:29588250   PMID:31649144  


Genomics

Comparative Map Data
Xcl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01383,199,402 - 83,202,845 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1383,199,264 - 83,202,864 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01388,079,753 - 88,083,196 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41380,691,195 - 80,694,638 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11380,705,382 - 80,708,826 (-)NCBI
Celera1376,965,267 - 76,968,710 (-)NCBICelera
Cytogenetic Map13q23NCBI
XCL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1168,576,605 - 168,582,069 (+)EnsemblGRCh38hg38GRCh38
GRCh381168,574,128 - 168,582,069 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371168,545,711 - 168,551,315 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361166,812,480 - 166,817,939 (+)NCBINCBI36hg18NCBI36
Build 341165,277,513 - 165,282,973NCBI
Celera1141,655,651 - 141,661,108 (+)NCBI
Cytogenetic Map1q24.2NCBI
HuRef1139,791,807 - 139,797,411 (+)NCBIHuRef
CHM1_11169,967,701 - 169,973,305 (+)NCBICHM1_1
Xcl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391164,759,213 - 164,763,091 (-)NCBIGRCm39mm39
GRCm381164,931,644 - 164,935,522 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1164,931,644 - 164,935,527 (-)EnsemblGRCm38mm10GRCm38
MGSCv371166,861,779 - 166,865,641 (-)NCBIGRCm37mm9NCBIm37
MGSCv361166,768,323 - 166,772,185 (-)NCBImm8
Celera1167,368,241 - 167,372,103 (-)NCBICelera
Cytogenetic Map1H2.2NCBI
cM Map172.26NCBI
Xcl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554628,594,416 - 8,598,101 (-)NCBIChiLan1.0ChiLan1.0
XCL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11147,563,331 - 147,790,587 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1147,785,654 - 147,790,587 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01143,837,578 - 144,068,261 (+)NCBIMhudiblu_PPA_v0panPan3
LOC490356
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1729,986,433 - 29,991,096 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
LOC101970885
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493648117,825,714 - 17,828,955 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XCL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl482,432,198 - 82,436,180 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1482,432,845 - 82,436,150 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2490,116,396 - 90,119,701 (-)NCBISscrofa10.2Sscrofa10.2susScr3
XCL1
(Chlorocebus sabaeus - African green monkey)		 No map positions available.

Position Markers
AI236158  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01383,199,341 - 83,199,461NCBIRnor6.0
Rnor_5.01388,079,692 - 88,079,812UniSTSRnor5.0
RGSC_v3.41380,691,134 - 80,691,254UniSTSRGSC3.4
Celera1376,965,206 - 76,965,326UniSTS
Cytogenetic Map13q23UniSTS
RH 3.4 Map13485.8UniSTS


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)systolic blood pressure (CMO:0000004)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)diastolic blood pressure (CMO:0000005)131107975663Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)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)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
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
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135108098996080989Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135156924896569248Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)135157782490675199Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1357903612102903612Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1362975663107975663Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)136500824591629354Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)137456837892916783Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)137456837892916783Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)137456837892916783Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
11530006Niddm72Non-insulin dependent diabetes mellitus QTL 720.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)137956708186833540Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1379567081103613733Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)138040355991629354Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:19
Count of miRNA genes:15
Interacting mature miRNAs:18
Transcripts:ENSRNOT00000003976
Prediction methods: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 1 6 14 2
Low 3 14 35 29 5 29 1 2 8 22 18 11 1
Below cutoff 18 16 12 12 7 7 33 13 18 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003976   ⟹   ENSRNOP00000003976
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1383,199,264 - 83,202,864 (-)Ensembl
RefSeq Acc Id: NM_134361   ⟹   NP_599188
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01383,199,402 - 83,202,845 (-)NCBI
Rnor_5.01388,079,753 - 88,083,196 (-)NCBI
RGSC_v3.41380,691,195 - 80,694,638 (-)RGD
Celera1376,965,267 - 76,968,710 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_599188 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA69478 (Get FASTA)   NCBI Sequence Viewer  
  EDM09342 (Get FASTA)   NCBI Sequence Viewer  
  P51672 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_599188   ⟸   NM_134361
- Peptide Label: precursor
- UniProtKB: P51672 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003976   ⟸   ENSRNOT00000003976
Protein Domains
SCY

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)
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)
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
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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620452 AgrOrtholog
Ensembl Genes ENSRNOG00000002964 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003976 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003976 ENTREZGENE, UniProtKB/TrEMBL
InterPro Chemokine_b/g/d UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_IL8-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_XCL1/XCL2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Interleukin_8-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171371 UniProtKB/Swiss-Prot
NCBI Gene 171371 ENTREZGENE
PANTHER PTHR12015 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12015:SF101 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam IL8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Xcl1 PhenoGen
PRINTS LYMPHOTACTIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SCY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54117 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.90962 ENTREZGENE
UniProt A0A4D6YKM5_RAT UniProtKB/TrEMBL
  A0A4D6YMT2_RAT UniProtKB/TrEMBL
  A0A4D6YMU3_RAT UniProtKB/TrEMBL
  A0A4D6YMV4_RAT UniProtKB/TrEMBL
  A0A4D6YNR9_RAT UniProtKB/TrEMBL
  A0A4D6YW90_RAT UniProtKB/TrEMBL
  G3V6D4_RAT UniProtKB/TrEMBL
  P51672 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-08 Xcl1  X-C motif chemokine ligand 1  Xcl1  chemokine (C motif) ligand 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Xcl1  chemokine (C motif) ligand 1    small inducible cytokine subfamily C, member 1 (lymphotactin)  Name updated 1299863 APPROVED
2004-09-10 Xcl1  small inducible cytokine subfamily C, member 1 (lymphotactin)  Scyc1    Symbol and Name updated 1299863 APPROVED
2002-08-07 Scyc1  small inducible cytokine subfamily C, member 1 (lymphotactin)      Symbol and Name status set to provisional 70820 PROVISIONAL