Ccr9 (chemokine (C-C motif) receptor 9) - Rat Genome Database

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Gene: Ccr9 (chemokine (C-C motif) receptor 9) Mus musculus
Analyze
Symbol: Ccr9
Name: chemokine (C-C motif) receptor 9
RGD ID: 1550219
MGI Page MGI
Description: Enables C-C chemokine receptor activity. Acts upstream of or within CD8-positive, gamma-delta intraepithelial T cell differentiation and chemotaxis. Predicted to be located in cell surface. Predicted to be active in external side of plasma membrane. Is expressed in central nervous system; immune system; and retina. Orthologous to human CCR9 (C-C motif chemokine receptor 9); INTERACTS WITH (+)-pilocarpine; 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: A130091K22Rik; C-C chemokine receptor type 9; C-C CKR-9; CC-CKR-9; CCR-9; chemokine C-C receptor 10; Cmkbr1; Cmkbr10; GPR-9; GPR-9-6; RIKEN cDNA A130091K22 gene
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399123,596,276 - 123,612,522 (+)NCBIGRCm39mm39
GRCm39 Ensembl9123,507,504 - 123,613,395 (+)Ensembl
GRCm389123,767,211 - 123,783,457 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,678,439 - 123,784,330 (+)EnsemblGRCm38mm10GRCm38
MGSCv379123,676,329 - 123,692,575 (+)NCBIGRCm37mm9NCBIm37
MGSCv369123,527,137 - 123,630,663 (+)NCBImm8
Celera9124,227,741 - 124,231,922 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map974.33NCBI
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

References

Additional References at PubMed
PMID:10229797   PMID:10349636   PMID:10602049   PMID:10623805   PMID:11042159   PMID:11076861   PMID:11675330   PMID:11751956   PMID:11884450   PMID:12080938   PMID:12393847   PMID:12461651  
PMID:12477932   PMID:12840763   PMID:12963696   PMID:14512296   PMID:14744993   PMID:15368288   PMID:15484191   PMID:15983065   PMID:16129397   PMID:16141072   PMID:16141073   PMID:16216890  
PMID:16342233   PMID:16391017   PMID:16582913   PMID:16602821   PMID:16809609   PMID:17277104   PMID:17404233   PMID:17548595   PMID:17911179   PMID:18287559   PMID:18439426   PMID:18458114  
PMID:19604301   PMID:19965655   PMID:20040757   PMID:20400707   PMID:20870939   PMID:21267068   PMID:21283540   PMID:21300065   PMID:21421850   PMID:21469133   PMID:21502490   PMID:21511186  
PMID:21565611   PMID:21659540   PMID:21873635   PMID:21925467   PMID:22079594   PMID:22196895   PMID:22444632   PMID:22626536   PMID:22633147   PMID:22771342   PMID:23063333   PMID:23152541  
PMID:23456208   PMID:23460364   PMID:24876562   PMID:25248373   PMID:25348153   PMID:25710912   PMID:26141583   PMID:26230654   PMID:26348893   PMID:26644347   PMID:27146447   PMID:27585634  
PMID:27795621   PMID:28951425   PMID:29154408   PMID:30662436   PMID:30700910   PMID:31065973   PMID:31129099   PMID:31964813   PMID:33310185  


Genomics

Comparative Map Data
Ccr9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399123,596,276 - 123,612,522 (+)NCBIGRCm39mm39
GRCm39 Ensembl9123,507,504 - 123,613,395 (+)Ensembl
GRCm389123,767,211 - 123,783,457 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,678,439 - 123,784,330 (+)EnsemblGRCm38mm10GRCm38
MGSCv379123,676,329 - 123,692,575 (+)NCBIGRCm37mm9NCBIm37
MGSCv369123,527,137 - 123,630,663 (+)NCBImm8
Celera9124,227,741 - 124,231,922 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map974.33NCBI
CCR9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl345,886,509 - 45,903,174 (+)EnsemblGRCh38hg38GRCh38
GRCh38345,886,064 - 45,903,174 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37345,927,556 - 45,944,666 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36345,903,023 - 45,919,671 (+)NCBINCBI36hg18NCBI36
Build 34345,903,022 - 45,919,671NCBI
Celera345,865,603 - 45,882,297 (+)NCBI
Cytogenetic Map3p21.31NCBI
HuRef345,971,916 - 45,988,702 (+)NCBIHuRef
CHM1_1345,877,982 - 45,894,642 (+)NCBICHM1_1
Ccr9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28123,396,157 - 123,410,199 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl8123,395,813 - 123,413,969 (+)Ensembl
Rnor_6.08132,827,325 - 132,842,130 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,828,091 - 132,842,130 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08131,978,885 - 131,993,230 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,527,943 - 128,541,982 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18128,547,679 - 128,561,719 (+)NCBI
Celera8122,504,371 - 122,518,410 (+)NCBICelera
Cytogenetic Map8q32NCBI
Ccr9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542026,083,040 - 26,093,775 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542026,083,445 - 26,093,740 (-)NCBIChiLan1.0ChiLan1.0
CCR9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1346,900,845 - 46,917,443 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl346,900,845 - 46,917,443 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0345,719,655 - 45,810,964 (+)NCBIMhudiblu_PPA_v0panPan3
CCR9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12042,607,024 - 42,616,823 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2042,607,024 - 42,616,823 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2042,522,841 - 42,532,627 (-)NCBI
ROS_Cfam_1.02043,089,954 - 43,100,368 (-)NCBI
UMICH_Zoey_3.12042,330,862 - 42,340,690 (-)NCBI
UNSW_CanFamBas_1.02042,738,503 - 42,748,344 (-)NCBI
UU_Cfam_GSD_1.02043,013,377 - 43,023,212 (-)NCBI
Ccr9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118197,703,423 - 197,704,532 (-)NCBI
SpeTri2.0NW_00493669555,788 - 59,251 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCR9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1329,033,570 - 29,054,598 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11329,033,609 - 29,051,227 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21332,130,027 - 32,147,645 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCR9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1227,354,139 - 7,375,280 (+)NCBI
ChlSab1.1 Ensembl227,354,489 - 7,377,676 (+)Ensembl
Vero_WHO_p1.0NW_023666041159,791,948 - 159,811,865 (-)NCBI
Ccr9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473074,989,725 - 74,991,400 (-)NCBI

Position Markers
Ccr9  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm389123,780,327 - 123,780,688UniSTSGRCm38
MGSCv379123,689,445 - 123,689,806UniSTSGRCm37
Celera9124,228,792 - 124,229,153UniSTS
Cytogenetic Map9FUniSTS
cM Map971.2UniSTS
AJ132336  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm389123,780,448 - 123,780,564UniSTSGRCm38
MGSCv379123,689,566 - 123,689,682UniSTSGRCm37
Celera9124,228,913 - 124,229,029UniSTS
Cytogenetic Map9FUniSTS
cM Map971.2UniSTS
Whitehead/MRC_RH91211.96UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12910770Splic1_mspleen iron content 1 (mouse)991413879124595110Mouse
12910772Lvic6_mliver iron content 6 (mouse)991413879124595110Mouse
12910773Splic3_mspleen iron content 3 (mouse)991413879124595110Mouse
1558767Skmw11_mskeletal muscle weight 11 (mouse)Not determined991641084124595110Mouse
13463474Hbbcq5_mhemoglobin concentration QTL 5 (mouse)991641084124595110Mouse
13463475Hctq7_mhematocrit QTL 7 (mouse)991641084124595110Mouse
13463477Rbc9_mred blood cell count 9 (mouse)991641084124595110Mouse
13463478Mchq18_mmean corpuscular hemoglobin QTL 18 (mouse)991641084124595110Mouse
13463480Mchcq2_mmean corpuscular hemoglobin concentration QTL 2 (mouse)991641084124595110Mouse
12904937Edlmmq9_mextensor digitorum longus muscle mass QTL 9 (mouse)991683173124595110Mouse
12904947Tammq7_mtibialis anterior muscle mass QTL 7 (mouse)991683173124595110Mouse
12904961Gmmq7_mgastrocnemius muscle mass QTL 7 (mouse)991683173124595110Mouse
1302001Bdln5_mbody length 5 (mouse)Not determined993762590124595110Mouse
1301484Bwq6_mbody weight (mouse)Not determined993762590124595110Mouse
14746992Manh67_mmandible shape 67 (mouse)994036768124595110Mouse
11537364Cnes5_mC. neoformans susceptibility locus 5 (mouse)996917590124595110Mouse
1301297Lcho1_mliver cholesterol 1 (mouse)Not determined9101060861124595110Mouse
1357627Tgq2_mtriglyceride QTL 2 (mouse)Not determined9102000187124595110Mouse
1357648Obq18_mobesity QTL 18 (mouse)Not determined9102000187124595110Mouse
1301789Pbwg4_mpostnatal body weight growth 4 (mouse)Not determined9103289445124595110Mouse
10412290Pvacm1l_mplasma vascular cell adhesion molecule 1 levels (mouse)Not determined9103289445124595110Mouse
12879896Berr3_mberghei resistance locus 3 (mouse)9103289445124595110Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:3174
Count of miRNA genes:572
Interacting mature miRNAs:722
Transcripts:ENSMUST00000111454, ENSMUST00000163559, ENSMUST00000166236, ENSMUST00000168910, ENSMUST00000180093
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


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000111454   ⟹   ENSMUSP00000107081
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl9123,596,292 - 123,610,837 (+)Ensembl
GRCm38.p6 Ensembl9123,767,227 - 123,781,772 (+)Ensembl
RefSeq Acc Id: ENSMUST00000163559   ⟹   ENSMUSP00000131782
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl9123,507,504 - 123,611,030 (+)Ensembl
GRCm38.p6 Ensembl9123,678,439 - 123,781,965 (+)Ensembl
RefSeq Acc Id: ENSMUST00000166236   ⟹   ENSMUSP00000127024
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl9123,596,276 - 123,613,395 (+)Ensembl
GRCm38.p6 Ensembl9123,767,211 - 123,784,330 (+)Ensembl
RefSeq Acc Id: ENSMUST00000168910   ⟹   ENSMUSP00000126758
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl9123,596,294 - 123,611,036 (+)Ensembl
GRCm38.p6 Ensembl9123,767,229 - 123,781,971 (+)Ensembl
RefSeq Acc Id: ENSMUST00000180093   ⟹   ENSMUSP00000137144
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl9123,603,605 - 123,612,522 (+)Ensembl
GRCm38.p6 Ensembl9123,774,540 - 123,783,457 (+)Ensembl
RefSeq Acc Id: ENSMUST00000215921
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl9123,596,234 - 123,601,044 (+)Ensembl
GRCm38.p6 Ensembl9123,767,169 - 123,771,979 (+)Ensembl
RefSeq Acc Id: NM_001166625   ⟹   NP_001160097
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm399123,596,276 - 123,612,522 (+)NCBI
GRCm389123,767,211 - 123,783,457 (+)ENTREZGENE
MGSCv379123,676,329 - 123,692,575 (+)RGD
Celera9124,227,741 - 124,231,922 (+)RGD
cM Map9 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_009913   ⟹   NP_034043
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm399123,596,276 - 123,612,522 (+)NCBI
GRCm389123,767,211 - 123,783,457 (+)ENTREZGENE
MGSCv379123,676,329 - 123,692,575 (+)RGD
Celera9124,227,741 - 124,231,922 (+)RGD
cM Map9 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_034043   ⟸   NM_009913
- UniProtKB: Q9WUT7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001160097   ⟸   NM_001166625
- UniProtKB: Q9WUT7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000107081   ⟸   ENSMUST00000111454
RefSeq Acc Id: ENSMUSP00000131782   ⟸   ENSMUST00000163559
RefSeq Acc Id: ENSMUSP00000127024   ⟸   ENSMUST00000166236
RefSeq Acc Id: ENSMUSP00000126758   ⟸   ENSMUST00000168910
RefSeq Acc Id: ENSMUSP00000137144   ⟸   ENSMUST00000180093
Protein Domains
G_PROTEIN_RECEP_F1_2

Promoters
RGD ID:6844305
Promoter ID:MM_KWN:59281
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   Kidney
Transcripts:NM_001166625,   NM_009913,   UC009SGO.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv369123,675,921 - 123,678,722 (+)MPROMDB
RGD ID:8671350
Promoter ID:EPDNEW_M13705
Type:initiation region
Name:Ccr9_1
Description:Mus musculus chemokine (C-C motif) receptor 9 , transcript variant2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M13706  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm389123,767,234 - 123,767,294EPDNEW
RGD ID:8671406
Promoter ID:EPDNEW_M13706
Type:single initiation site
Name:Ccr9_2
Description:Mus musculus chemokine (C-C motif) receptor 9 , transcript variant2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M13705  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm389123,773,437 - 123,773,497EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1341902 AgrOrtholog
Ensembl Genes ENSMUSG00000029530 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000107081 UniProtKB/TrEMBL
  ENSMUSP00000126758 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000127024 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000131782 UniProtKB/Swiss-Prot
  ENSMUSP00000137144 UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000111454 UniProtKB/TrEMBL
  ENSMUST00000163559 UniProtKB/Swiss-Prot
  ENSMUST00000166236 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000168910 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000180093 UniProtKB/Swiss-Prot
InterPro Chemokine_CCR9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCR_Rhodpsn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:12769 UniProtKB/Swiss-Prot
MGD MGI:1341902 ENTREZGENE
NCBI Gene 12769 ENTREZGENE
Pfam 7tm_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ccr9 PhenoGen
PRINTS CCCHEMOKINER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CHEMOKINER9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCRRHODOPSN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CCR9_MOUSE UniProtKB/Swiss-Prot
  F8WIS0_MOUSE UniProtKB/TrEMBL
  Q9WUT7 ENTREZGENE
UniProt Secondary A2RSM5 UniProtKB/Swiss-Prot
  Q543I4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-24 Ccr9  chemokine (C-C motif) receptor 9  A130091K22Rik  RIKEN cDNA A130091K22 gene  Data Merged 737654 PROVISIONAL