Ccl25 (C-C motif chemokine ligand 25) - Rat Genome Database
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Gene: Ccl25 (C-C motif chemokine ligand 25) Rattus norvegicus
Analyze
Symbol: Ccl25
Name: C-C motif chemokine ligand 25
RGD ID: 1305530
Description: Predicted to have CCR10 chemokine receptor binding activity and chemokine activity. Predicted to be involved in several processes, including antimicrobial humoral immune response mediated by antimicrobial peptide; negative regulation of leukocyte tethering or rolling; and positive regulation of cell-matrix adhesion. Orthologous to human CCL25 (C-C motif chemokine ligand 25); PARTICIPATES IN chemokine mediated signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH 17beta-estradiol; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: C-C motif chemokine 25; chemokine (C-C motif) ligand 25; LOC360750; MGC125074
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
mRatBN7.2122,707,398 - 2,716,571 (+)NCBI
Rnor_6.0 Ensembl122,429,509 - 2,438,817 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0122,429,492 - 2,438,928 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0124,583,182 - 4,592,166 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4121,427,242 - 1,436,436 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1121,427,553 - 1,439,348 (-)NCBI
Celera124,522,920 - 4,532,044 (+)NCBICelera
Cytogenetic Map12p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10623805   PMID:10706668   PMID:12477932   PMID:12949249   PMID:15358618   PMID:18308860   PMID:19249122   PMID:21672573   PMID:23341447  


Genomics

Comparative Map Data
Ccl25
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2122,707,398 - 2,716,571 (+)NCBI
Rnor_6.0 Ensembl122,429,509 - 2,438,817 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0122,429,492 - 2,438,928 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0124,583,182 - 4,592,166 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4121,427,242 - 1,436,436 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1121,427,553 - 1,439,348 (-)NCBI
Celera124,522,920 - 4,532,044 (+)NCBICelera
Cytogenetic Map12p12NCBI
CCL25
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl198,052,767 - 8,062,650 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl198,052,318 - 8,062,660 (+)EnsemblGRCh38hg38GRCh38
GRCh38198,052,318 - 8,062,663 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37198,117,646 - 8,127,547 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36198,023,934 - 8,033,547 (+)NCBINCBI36hg18NCBI36
Build 34198,023,933 - 8,033,534NCBI
Celera197,989,167 - 7,998,769 (+)NCBI
Cytogenetic Map19p13.2NCBI
HuRef197,788,562 - 7,797,973 (+)NCBIHuRef
CHM1_1198,117,421 - 8,127,895 (+)NCBICHM1_1
Ccl25
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3984,375,207 - 4,410,020 (+)NCBIGRCm39mm39
GRCm39 Ensembl84,375,210 - 4,410,020 (+)Ensembl
GRCm3884,325,205 - 4,360,020 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl84,325,210 - 4,360,020 (+)EnsemblGRCm38mm10GRCm38
MGSCv3784,325,210 - 4,360,020 (+)NCBIGRCm37mm9NCBIm37
MGSCv3684,349,615 - 4,360,020 (+)NCBImm8
Celera84,525,811 - 4,560,621 (+)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map82.01NCBI
Ccl25
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555631,249,098 - 1,255,469 (-)NCBIChiLan1.0ChiLan1.0
CCL25
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1198,208,273 - 8,217,780 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl198,208,273 - 8,217,780 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0197,307,109 - 7,363,983 (+)NCBIMhudiblu_PPA_v0panPan3
CCL25
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2052,712,979 - 52,722,018 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12052,689,674 - 52,722,291 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ccl25
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365884,973,476 - 4,998,365 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCL25
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1271,175,066 - 71,206,950 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2271,575,448 - 71,607,365 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCL25
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.167,496,463 - 7,504,637 (+)NCBI
Ccl25
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624828975,656 - 981,610 (+)NCBI

Position Markers
BQ199385  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0122,430,121 - 2,430,336NCBIRnor6.0
Rnor_5.0124,583,811 - 4,584,026UniSTSRnor5.0
RGSC_v3.4121,427,871 - 1,428,086UniSTSRGSC3.4
Celera124,531,192 - 4,531,407UniSTS
RH 3.4 Map120.0UniSTS
Cytogenetic Map12p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300174Bw15Body weight QTL 152.93body mass (VT:0001259)body weight loss (CMO:0001399)12111765163Rat
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12122650917Rat
10450854Stl34Serum triglyceride level QTL 343.50.05blood LDL triglyceride amount (VT:0010699)blood lipoprotein triglyceride level (CMO:0002685)12122853017Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12123035872Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123758197Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12130749723Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12136919844Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12138334225Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)1215081045150810Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1215081045150810Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)1249257845492578Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)12125813910257059Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:232
Count of miRNA genes:154
Interacting mature miRNAs:180
Transcripts:ENSRNOT00000037059
Prediction methods:Microtar, 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 1 8 8
Low 2 3 2 1 2 4 1
Below cutoff 11 27 21 9 21 8 9 34 31 25 7 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000037059   ⟹   ENSRNOP00000037785
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl122,429,509 - 2,438,817 (-)Ensembl
RefSeq Acc Id: NM_001037203   ⟹   NP_001032280
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2122,707,398 - 2,716,571 (+)NCBI
Rnor_6.0122,429,492 - 2,438,817 (-)NCBI
Rnor_5.0124,583,182 - 4,592,166 (-)NCBI
RGSC_v3.4121,427,242 - 1,436,436 (-)RGD
Celera124,522,920 - 4,532,044 (+)RGD
Sequence:
RefSeq Acc Id: XM_006248766   ⟹   XP_006248828
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0122,429,784 - 2,438,928 (-)NCBI
Rnor_5.0124,583,182 - 4,592,166 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001032280 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI07946 (Get FASTA)   NCBI Sequence Viewer  
  EDL75004 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001032280   ⟸   NM_001037203
- Peptide Label: precursor
- UniProtKB: Q32PX4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248828   ⟸   XM_006248766
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000037785   ⟸   ENSRNOT00000037059
Protein Domains
SCY

Transcriptome

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

Promoters
RGD ID:13698379
Promoter ID:EPDNEW_R8903
Type:multiple initiation site
Name:Ccl25_1
Description:C-C motif chemokine ligand 25
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_6.0122,438,827 - 2,438,887EPDNEW

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)
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: 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)
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
SHRSP/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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
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)
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/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:1305530 AgrOrtholog
Ensembl Genes ENSRNOG00000028531 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000037785 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037059 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7388091 IMAGE-MGC_LOAD
InterPro Chemokine_b/g/d UniProtKB/TrEMBL
  Chemokine_IL8 UniProtKB/TrEMBL
  Interleukin_8-like_sf UniProtKB/TrEMBL
KEGG Report rno:360750 UniProtKB/TrEMBL
MGC_CLONE MGC:125074 IMAGE-MGC_LOAD
NCBI Gene 360750 ENTREZGENE
PANTHER PTHR12015 UniProtKB/TrEMBL
Pfam IL8 UniProtKB/TrEMBL
PhenoGen Ccl25 PhenoGen
SMART SCY UniProtKB/TrEMBL
Superfamily-SCOP Chemokine_IL8 UniProtKB/TrEMBL
UniProt Q32PX4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-08 Ccl25  C-C motif chemokine ligand 25  Ccl25  chemokine (C-C motif) ligand 25  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Ccl25  chemokine (C-C motif) ligand 25  Ccl25_predicted  chemokine (C-C motif) ligand 25 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Ccl25_predicted  chemokine (C-C motif) ligand 25 (predicted)      Symbol and Name status set to approved 70820 APPROVED