Cxcl13 (C-X-C motif chemokine ligand 13) - Rat Genome Database
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Gene: Cxcl13 (C-X-C motif chemokine ligand 13) Rattus norvegicus
Analyze
Symbol: Cxcl13
Name: C-X-C motif chemokine ligand 13
RGD ID: 1564256
Description: Predicted to have chemokine receptor binding activity; fibroblast growth factor binding activity; and heparin binding activity. Predicted to be involved in several processes, including cell chemotaxis; regulation of chemotaxis; and response to bacterium. Predicted to localize to extracellular space. Orthologous to human CXCL13 (C-X-C motif chemokine ligand 13); PARTICIPATES IN chemokine mediated signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH 1,2-dimethylhydrazine; 1-naphthyl isothiocyanate; 2,2',4,4',5,5'-hexachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: C-X-C motif chemokine 13; chemokine (C-X-C motif) ligand 13; LOC498335; similar to Small inducible cytokine B13 precursor (CXCL13) (B lymphocyte chemoattractant) (CXC chemokine BLC)
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
Rnor_6.01415,253,146 - 15,258,221 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1415,253,125 - 15,258,207 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01415,193,472 - 15,198,546 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41415,126,332 - 15,131,368 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1413,649,303 - 13,654,347 (-)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (EXP,ISO)
1-naphthyl isothiocyanate  (EXP)
1-nitropyrene  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-chloropropane-1,2-diol  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
7,12-dimethyltetraphene  (ISO)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
andrographolide  (ISO)
antirheumatic drug  (ISO)
asperentin  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
bleomycin A2  (ISO)
bromobenzene  (EXP)
cadmium dichloride  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
choline  (ISO)
chrysene  (ISO)
ciguatoxin CTX1B  (ISO)
cyclosporin A  (EXP,ISO)
decabromodiphenyl ether  (EXP)
dextran sulfate  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
doxorubicin  (ISO)
furan  (EXP)
genistein  (ISO)
iron(2+) sulfate (anhydrous)  (ISO)
isoprenaline  (ISO)
lipopolysaccharide  (ISO)
metformin  (EXP)
methylmercury chloride  (EXP,ISO)
mifepristone  (ISO)
mycotoxin  (ISO)
N,N-diethyl-m-toluamide  (ISO)
N-nitrosodimethylamine  (EXP)
neoechinulin A  (ISO)
nickel dichloride  (ISO)
O-methyleugenol  (ISO)
paracetamol  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
rotenone  (EXP)
silicon dioxide  (EXP,ISO)
sirolimus  (EXP)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sterigmatocystin  (ISO)
succimer  (ISO)
sunitinib  (ISO)
taurocholic acid  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
tofacitinib  (ISO)
toluene 2,4-diisocyanate  (ISO)
trimellitic anhydride  (ISO)
vinclozolin  (EXP)
zinc dichloride  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9463416   PMID:10706668   PMID:11554781   PMID:11708770   PMID:12732660   PMID:12949249   PMID:15972452   PMID:17562761   PMID:17652619   PMID:19783990   PMID:23460747   PMID:27892451  
PMID:28359934  


Genomics

Comparative Map Data
Cxcl13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01415,253,146 - 15,258,221 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1415,253,125 - 15,258,207 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01415,193,472 - 15,198,546 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41415,126,332 - 15,131,368 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1413,649,303 - 13,654,347 (-)NCBICelera
Cytogenetic Map14p22NCBI
CXCL13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl477,511,753 - 77,611,834 (+)EnsemblGRCh38hg38GRCh38
GRCh38477,511,753 - 77,611,834 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37478,432,907 - 78,532,988 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36478,651,931 - 78,752,010 (+)NCBINCBI36hg18NCBI36
Build 34478,790,084 - 78,890,165NCBI
Celera475,734,287 - 75,834,362 (+)NCBI
Cytogenetic Map4q21.1NCBI
HuRef474,184,783 - 74,284,964 (+)NCBIHuRef
CHM1_1478,409,854 - 78,509,941 (+)NCBICHM1_1
Cxcl13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39596,104,798 - 96,108,927 (+)NCBIGRCm39mm39
GRCm38595,956,939 - 95,961,068 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl595,956,951 - 95,961,068 (+)EnsemblGRCm38mm10GRCm38
MGSCv37596,385,958 - 96,390,087 (+)NCBIGRCm37mm9NCBIm37
MGSCv36596,197,241 - 96,201,370 (+)NCBImm8
Celera593,306,539 - 93,310,668 (+)NCBICelera
Cytogenetic Map5E3NCBI
Cxcl13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554332,123,190 - 2,129,119 (+)NCBIChiLan1.0ChiLan1.0
CXCL13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1452,428,702 - 52,434,803 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl452,428,702 - 52,434,803 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0446,583,759 - 46,589,865 (-)NCBIMhudiblu_PPA_v0panPan3
CXCL13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl322,047,315 - 2,052,833 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1322,047,277 - 2,053,277 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cxcl13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366761,309,625 - 1,314,532 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CXCL13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1873,071,261 - 73,077,342 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2877,268,254 - 77,274,314 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CXCL13
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl726,102,714 - 26,108,690 (+)Ensembl
ChlSab1.1726,101,489 - 26,108,430 (+)NCBI
Cxcl13
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475713,488,787 - 13,494,831 (-)NCBI


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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:91
Count of miRNA genes:71
Interacting mature miRNAs:83
Transcripts:ENSRNOT00000039383
Prediction methods:Miranda, 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 3 12 4 19 4 6 22 3
Low 30 43 35 35 3 3 25 29 17 8 3
Below cutoff 7 2 2 2 5 8 43 2 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039383   ⟹   ENSRNOP00000034304
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1415,253,125 - 15,258,207 (-)Ensembl
RefSeq Acc Id: NM_001017496   ⟹   NP_001017496
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01415,253,149 - 15,258,185 (-)NCBI
Rnor_5.01415,193,472 - 15,198,546 (-)NCBI
RGSC_v3.41415,126,332 - 15,131,368 (-)RGD
Celera1413,649,303 - 13,654,347 (-)RGD
Sequence:
RefSeq Acc Id: XM_006250710   ⟹   XP_006250772
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01415,253,146 - 15,258,221 (-)NCBI
Rnor_5.01415,193,472 - 15,198,546 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001017496 (Get FASTA)   NCBI Sequence Viewer  
  XP_006250772 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88260 (Get FASTA)   NCBI Sequence Viewer  
  EDL99643 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001017496   ⟸   NM_001017496
- Peptide Label: precursor
- UniProtKB: Q5I0J6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006250772   ⟸   XM_006250710
- Peptide Label: isoform X1
- UniProtKB: F7F7W7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000034304   ⟸   ENSRNOT00000039383
Protein Domains
SCY

Transcriptome

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

Promoters
RGD ID:13699204
Promoter ID:EPDNEW_R9729
Type:single initiation site
Name:Cxcl13_1
Description:C-X-C motif chemokine ligand 13
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_6.01415,258,208 - 15,258,268EPDNEW

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)
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
LN/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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: 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)
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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:1564256 AgrOrtholog
Ensembl Genes ENSRNOG00000024899 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000034304 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039383 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7375992 IMAGE-MGC_LOAD
InterPro Chemokine_IL8 UniProtKB/TrEMBL
  CXC_Chemokine_domain UniProtKB/TrEMBL
  CXC_chmkine_smll UniProtKB/TrEMBL
  Interleukin_8-like_sf UniProtKB/TrEMBL
KEGG Report rno:498335 UniProtKB/TrEMBL
MGC_CLONE MGC:109086 IMAGE-MGC_LOAD
NCBI Gene 498335 ENTREZGENE
PANTHER PTHR10179 UniProtKB/TrEMBL
Pfam IL8 UniProtKB/TrEMBL
PhenoGen Cxcl13 PhenoGen
PRINTS SMALLCYTKCXC UniProtKB/TrEMBL
SMART SCY UniProtKB/TrEMBL
Superfamily-SCOP Chemokine_IL8 UniProtKB/TrEMBL
UniGene Rn.6917 ENTREZGENE
UniProt F7F7W7 ENTREZGENE, UniProtKB/TrEMBL
  Q5I0J6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-08 Cxcl13  C-X-C motif chemokine ligand 13  Cxcl13  chemokine (C-X-C motif) ligand 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Cxcl13  chemokine (C-X-C motif) ligand 13  LOC498335  similar to Small inducible cytokine B13 precursor (CXCL13) (B lymphocyte chemoattractant) (CXC chemokine BLC)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC498335  similar to Small inducible cytokine B13 precursor (CXCL13) (B lymphocyte chemoattractant) (CXC chemokine BLC)      Symbol and Name status set to provisional 70820 PROVISIONAL