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 enable CCR10 chemokine receptor binding activity and chemokine activity. Predicted to be involved in several processes, including cellular response to cytokine stimulus; leukocyte chemotaxis; and negative regulation of leukocyte tethering or rolling. Predicted to act upstream of or within chemotaxis; leukocyte migration; and lymphoid lineage cell migration. Predicted to be active in extracellular space. Orthologous to human CCL25 (C-C motif chemokine ligand 25); PARTICIPATES IN chemokine mediated signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH 17beta-estradiol; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8127,505,231 - 7,514,402 (+)NCBIGRCr8
mRatBN7.2122,707,398 - 2,716,571 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl122,707,398 - 2,716,554 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx123,355,480 - 3,364,652 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0123,979,068 - 3,988,240 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0122,742,050 - 2,751,328 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0122,429,492 - 2,438,928 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,429,509 - 2,438,817 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0124,583,182 - 4,592,166 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4121,427,242 - 1,436,436 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Decreased expression of intestinal chemokine TECK/CCL25 in experimental obstructive jaundice and its reversal following internal biliary drainage. Matsumoto T, etal., J Gastroenterol. 2008;43(5):390-6. Epub 2008 Jul 1.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Involvement of CC chemokines in gammadelta T lymphocyte trafficking during allergic inflammation: the role of CCL2/CCR2 pathway. Penido C, etal., Int Immunol. 2008 Jan;20(1):129-39. Epub 2007 Dec 4.
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
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
GRCr8127,505,231 - 7,514,402 (+)NCBIGRCr8
mRatBN7.2122,707,398 - 2,716,571 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl122,707,398 - 2,716,554 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx123,355,480 - 3,364,652 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0123,979,068 - 3,988,240 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0122,742,050 - 2,751,328 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0122,429,492 - 2,438,928 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,429,509 - 2,438,817 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0124,583,182 - 4,592,166 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4121,427,242 - 1,436,436 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38198,052,341 - 8,062,650 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl198,052,318 - 8,062,660 (+)EnsemblGRCh38hg38GRCh38
GRCh37198,117,225 - 8,127,534 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36198,023,934 - 8,033,547 (+)NCBINCBI36Build 36hg18NCBI36
Build 34198,023,933 - 8,033,534NCBI
Celera197,989,167 - 7,998,769 (+)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef197,788,562 - 7,797,973 (+)NCBIHuRef
CHM1_1198,117,421 - 8,127,895 (+)NCBICHM1_1
T2T-CHM13v2.0198,053,362 - 8,063,660 (+)NCBIT2T-CHM13v2.0
Ccl25
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3984,375,207 - 4,410,020 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl84,375,210 - 4,410,020 (+)EnsemblGRCm39 Ensembl
GRCm3884,325,205 - 4,360,020 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl84,325,210 - 4,360,020 (+)EnsemblGRCm38mm10GRCm38
MGSCv3784,325,210 - 4,360,020 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3684,349,615 - 4,360,020 (+)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v22012,734,718 - 12,745,594 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11911,851,953 - 11,862,815 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0197,307,109 - 7,363,983 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1198,208,273 - 8,217,780 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl198,208,273 - 8,217,780 (+)Ensemblpanpan1.1panPan2
CCL25
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12052,689,674 - 52,722,291 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2052,712,979 - 52,722,018 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2052,520,955 - 52,523,887 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02053,217,788 - 53,250,217 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2053,217,446 - 53,250,227 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12052,450,071 - 52,453,004 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02052,894,798 - 52,897,724 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02053,126,468 - 53,129,402 (+)NCBIUU_Cfam_GSD_1.0
Ccl25
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118212,836,389 - 212,861,308 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365884,973,476 - 4,998,365 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCL25
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl271,175,075 - 71,206,950 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1271,175,066 - 71,206,950 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2271,575,448 - 71,607,365 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCL25
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.167,496,463 - 7,504,637 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666081306,230 - 353,525 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccl25
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624828975,656 - 981,610 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccl25
74 total Variants
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.


QTLs in Region (mRatBN7.2)
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)1219318387Rat
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12119611090Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)127977298525593Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat

Markers in Region
BQ199385  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2122,715,726 - 2,715,942 (-)MAPPERmRatBN7.2
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


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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl122,707,398 - 2,716,554 (+)Ensembl
Rnor_6.0 Ensembl122,429,509 - 2,438,817 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093774   ⟹   ENSRNOP00000097134
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl122,707,398 - 2,713,749 (+)Ensembl
RefSeq Acc Id: NM_001037203   ⟹   NP_001032280
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8127,505,235 - 7,514,402 (+)NCBI
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_063271424   ⟹   XP_063127494
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8127,505,231 - 7,514,110 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001032280 (Get FASTA)   NCBI Sequence Viewer  
  XP_063127494 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI07946 (Get FASTA)   NCBI Sequence Viewer  
  EDL75004 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037785
  ENSRNOP00000037785.4
  ENSRNOP00000097134.1
Reference Protein Sequences
RefSeq Acc Id: NP_001032280   ⟸   NM_001037203
- Peptide Label: precursor
- UniProtKB: Q32PX4 (UniProtKB/TrEMBL),   A6KQ79 (UniProtKB/TrEMBL),   A0A8I6AS46 (UniProtKB/TrEMBL),   F7F2H8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000037785   ⟸   ENSRNOT00000037059
RefSeq Acc Id: ENSRNOP00000097134   ⟸   ENSRNOT00000093774
RefSeq Acc Id: XP_063127494   ⟸   XM_063271424
- Peptide Label: isoform X1
- UniProtKB: A6KQ79 (UniProtKB/TrEMBL),   F7F2H8 (UniProtKB/TrEMBL),   Q32PX4 (UniProtKB/TrEMBL)
Protein Domains
Chemokine interleukin-8-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q32PX4-F1-model_v2 AlphaFold Q32PX4 1-147 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305530 AgrOrtholog
BioCyc Gene G2FUF-20339 BioCyc
Ensembl Genes ENSRNOG00000028531 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037059 ENTREZGENE
  ENSRNOT00000037059.5 UniProtKB/TrEMBL
  ENSRNOT00000093774.1 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.40 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 C-C MOTIF CHEMOKINE 25 UniProtKB/TrEMBL
  PTHR12015 UniProtKB/TrEMBL
Pfam IL8 UniProtKB/TrEMBL
PhenoGen Ccl25 PhenoGen
RatGTEx ENSRNOG00000028531 RatGTEx
SMART SCY UniProtKB/TrEMBL
Superfamily-SCOP Chemokine_IL8 UniProtKB/TrEMBL
UniProt A0A8I6AS46 ENTREZGENE, UniProtKB/TrEMBL
  A6KQ79 ENTREZGENE, UniProtKB/TrEMBL
  F7F2H8 ENTREZGENE, UniProtKB/TrEMBL
  Q32PX4 ENTREZGENE
UniProt Secondary Q32PX4 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