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

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Gene: Ccr9 (C-C motif chemokine receptor 9) Rattus norvegicus
Analyze
Symbol: Ccr9
Name: C-C motif chemokine receptor 9
RGD ID: 628750
Description: Predicted to enable C-C chemokine binding activity and C-C chemokine receptor activity. Predicted to be involved in several processes, including calcium-mediated signaling; cell chemotaxis; and positive regulation of cytosolic calcium ion concentration. Predicted to act upstream of or within several processes, including CD8-positive, gamma-delta intraepithelial T cell differentiation; G protein-coupled receptor signaling pathway; and chemokine-mediated signaling pathway. Predicted to be located in cell surface. Predicted to be active in external side of plasma membrane. Orthologous to human CCR9 (C-C motif chemokine receptor 9); PARTICIPATES IN chemokine mediated signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: C-C chemokine receptor type 9; chemokine (C-C motif) receptor 9
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
mRatBN7.28123,396,157 - 123,410,199 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,395,813 - 123,413,969 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8128,987,818 - 129,001,896 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.08127,186,795 - 127,200,873 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.08125,016,140 - 125,030,112 (+)NCBIRnor_WKY
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18128,547,679 - 128,561,719 (+)NCBI
Celera8122,504,371 - 122,518,410 (+)NCBICelera
Cytogenetic Map8q32NCBI
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 MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. V alpha 24-invariant NKT cells from patients with allergic asthma express CCR9 at high frequency and induce Th2 bias of CD3+ T cells upon CD226 engagement. Sen Y, etal., J Immunol. 2005 Oct 15;175(8):4914-26.
7. Characterization of CCR9 expression and CCL25/thymus-expressed chemokine responsiveness during T cell development: CD3(high)CD69+ thymocytes and gammadeltaTCR+ thymocytes preferentially respond to CCL25. Uehara S, etal., J Immunol 2002 Jan 1;168(1):134-42.
Additional References at PubMed
PMID:10623805   PMID:12477932   PMID:18308860   PMID:21672573   PMID:25348153   PMID:27146447   PMID:29269409  


Genomics

Comparative Map Data
Ccr9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28123,396,157 - 123,410,199 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,395,813 - 123,413,969 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8128,987,818 - 129,001,896 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.08127,186,795 - 127,200,873 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.08125,016,140 - 125,030,112 (+)NCBIRnor_WKY
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18128,547,679 - 128,561,719 (+)NCBI
Celera8122,504,371 - 122,518,410 (+)NCBICelera
Cytogenetic Map8q32NCBI
CCR9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38345,886,064 - 45,903,174 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl345,886,509 - 45,903,174 (+)EnsemblGRCh38hg38GRCh38
GRCh37345,927,556 - 45,944,666 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36345,903,023 - 45,919,671 (+)NCBINCBI36Build 36hg18NCBI36
Build 34345,903,022 - 45,919,671NCBI
Celera345,865,603 - 45,882,297 (+)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef345,971,916 - 45,988,702 (+)NCBIHuRef
CHM1_1345,877,982 - 45,894,642 (+)NCBICHM1_1
T2T-CHM13v2.0345,901,704 - 45,919,057 (+)NCBIT2T-CHM13v2.0
Ccr9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399123,596,276 - 123,612,522 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9123,507,504 - 123,613,395 (+)EnsemblGRCm39 Ensembl
GRCm389123,767,211 - 123,783,457 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,678,439 - 123,784,330 (+)EnsemblGRCm38mm10GRCm38
MGSCv379123,676,329 - 123,692,575 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369123,527,137 - 123,630,663 (+)NCBIMGSCv36mm8
Celera9124,227,741 - 124,231,922 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map974.33NCBI
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_v0Mhudiblu_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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02043,089,954 - 43,100,368 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2043,089,954 - 43,100,368 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12042,330,862 - 42,340,690 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02042,738,503 - 42,748,344 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02043,013,377 - 43,023,212 (-)NCBIUU_Cfam_GSD_1.0
Ccr9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118197,703,423 - 197,704,532 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493669555,788 - 59,251 (-)EnsemblSpeTri2.0
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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl227,354,489 - 7,377,676 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041159,791,948 - 159,811,865 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccr9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473074,990,318 - 74,996,239 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473074,989,725 - 74,991,400 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccr9
73 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:363
Count of miRNA genes:206
Interacting mature miRNAs:251
Transcripts:ENSRNOT00000008269
Prediction methods:Microtar, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat


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 8 10
Low 3 5 17 10 9 10 6 6 7 8 8 11 6
Below cutoff 12 18 17 17 2 4 14 23 19 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008269   ⟹   ENSRNOP00000008269
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,396,143 - 123,410,199 (+)Ensembl
Rnor_6.0 Ensembl8132,828,091 - 132,842,130 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000103816   ⟹   ENSRNOP00000082554
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,395,813 - 123,413,969 (+)Ensembl
RefSeq Acc Id: NM_172329   ⟹   NP_758832
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28123,396,157 - 123,410,199 (+)NCBI
Rnor_6.08132,828,091 - 132,842,130 (+)NCBI
Rnor_5.08131,978,885 - 131,993,230 (+)NCBI
RGSC_v3.48128,527,943 - 128,541,982 (+)RGD
Celera8122,504,371 - 122,518,410 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_758832 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91115 (Get FASTA)   NCBI Sequence Viewer  
  AAN76989 (Get FASTA)   NCBI Sequence Viewer  
  EDL76752 (Get FASTA)   NCBI Sequence Viewer  
  EDL76753 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_758832   ⟸   NM_172329
- UniProtKB: Q8CH33 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008269   ⟸   ENSRNOT00000008269
RefSeq Acc Id: ENSRNOP00000082554   ⟸   ENSRNOT00000103816
Protein Domains
G_PROTEIN_RECEP_F1_2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8CH33-F1-model_v2 AlphaFold Q8CH33 1-369 view protein structure

Transcriptome

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

Promoters
RGD ID:13696412
Promoter ID:EPDNEW_R6937
Type:initiation region
Name:Ccr9_1
Description:C-C motif chemokine receptor 9
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_6.08132,828,098 - 132,828,158EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628750 AgrOrtholog
BioCyc Gene G2FUF-28607 BioCyc
Ensembl Genes ENSRNOG00000006311 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008269 ENTREZGENE
  ENSRNOP00000008269.4 UniProtKB/TrEMBL
  ENSRNOP00000082554.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008269 ENTREZGENE
  ENSRNOT00000008269.8 UniProtKB/TrEMBL
  ENSRNOT00000103816.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7381553 IMAGE-MGC_LOAD
InterPro 7TM_GPCR_Rhodpsn UniProtKB/TrEMBL
  CC_9_rcpt UniProtKB/TrEMBL
  Chmkine_rcpt UniProtKB/TrEMBL
  GPCR_Rhodpsn_supfam UniProtKB/TrEMBL
KEGG Report rno:282832 UniProtKB/TrEMBL
MGC_CLONE MGC:108562 IMAGE-MGC_LOAD
NCBI Gene 282832 ENTREZGENE
Pfam 7tm_1 UniProtKB/TrEMBL
PhenoGen Ccr9 PhenoGen
PRINTS CCCHEMOKINER UniProtKB/TrEMBL
  CHEMOKINER9 UniProtKB/TrEMBL
  GPCRRHODOPSN UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/TrEMBL
  G_PROTEIN_RECEP_F1_2 UniProtKB/TrEMBL
UniProt A0A8I5ZU62_RAT UniProtKB/TrEMBL
  Q8CH33 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-22 Ccr9  C-C motif chemokine receptor 9  Ccr9  chemokine (C-C motif) receptor 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Ccr9  chemokine (C-C motif) receptor 9      Symbol and Name status set to approved 1299863 APPROVED
2003-02-27 Ccr9  chemokine (C-C motif) receptor 9      Symbol and Name status set to provisional 70820 PROVISIONAL