CCL13 (chemokine (C-C motif) ligand 13) - Rat Genome Database

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Pathways
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Gene: CCL13 (chemokine (C-C motif) ligand 13) Canis lupus familiaris
Analyze
Symbol: CCL13
Name: chemokine (C-C motif) ligand 13
RGD ID: 12121376
Description: ENCODES a protein that exhibits CCR2 chemokine receptor binding (ortholog); INVOLVED IN angiogenesis (ortholog); cytoskeleton organization (ortholog); monocyte chemotaxis (ortholog); ASSOCIATED WITH allergic disease (ortholog); brain ischemia (ortholog); Bronchial Hyperreactivity (ortholog); FOUND IN extracellular region (inferred); extracellular space (inferred)
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: C-C motif chemokine 13; MCP-4; monocyte chemoattractant protein 4; monocyte chemotactic protein-4; small-inducible cytokine A13
RGD Orthologs
Human
Mouse
Rat
Bonobo
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1938,938,944 - 38,940,231 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl938,938,135 - 38,940,231 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha938,162,012 - 38,163,300 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0939,752,155 - 39,753,443 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl939,728,462 - 39,769,550 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1938,539,350 - 38,540,637 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0938,818,831 - 38,820,119 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0938,907,308 - 38,908,596 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:16341006   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
CCL13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1938,938,944 - 38,940,231 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl938,938,135 - 38,940,231 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha938,162,012 - 38,163,300 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0939,752,155 - 39,753,443 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl939,728,462 - 39,769,550 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1938,539,350 - 38,540,637 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0938,818,831 - 38,820,119 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0938,907,308 - 38,908,596 (-)NCBIUU_Cfam_GSD_1.0
CCL13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381734,356,480 - 34,358,610 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1734,356,480 - 34,358,610 (+)EnsemblGRCh38hg38GRCh38
GRCh371732,683,499 - 32,685,629 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361729,707,584 - 29,709,742 (+)NCBINCBI36Build 36hg18NCBI36
Build 341729,707,583 - 29,709,741NCBI
Celera1729,593,701 - 29,595,859 (+)NCBICelera
Cytogenetic Map17q12NCBI
HuRef1728,869,568 - 28,871,726 (+)NCBIHuRef
CHM1_11732,747,735 - 32,749,893 (+)NCBICHM1_1
T2T-CHM13v2.01735,303,463 - 35,305,593 (+)NCBIT2T-CHM13v2.0
Ccl12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391181,992,671 - 81,994,225 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1181,992,671 - 81,994,226 (+)EnsemblGRCm39 Ensembl
GRCm381182,101,845 - 82,103,399 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1182,101,845 - 82,103,400 (+)EnsemblGRCm38mm10GRCm38
MGSCv371181,915,347 - 81,916,901 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361181,918,073 - 81,919,486 (+)NCBIMGSCv36mm8
Celera1186,814,429 - 86,815,983 (+)NCBICelera
Cytogenetic Map11CNCBI
cM Map1149.9NCBI
Ccl12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81067,567,876 - 67,569,426 (+)NCBIGRCr8
mRatBN7.21067,070,230 - 67,071,780 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1067,070,230 - 67,071,780 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1071,691,474 - 71,693,024 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01071,196,825 - 71,198,375 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01066,657,944 - 66,659,494 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01069,476,866 - 69,478,416 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1069,476,775 - 69,478,462 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01069,111,876 - 69,113,426 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41070,321,036 - 70,322,586NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1066,017,637 - 66,019,187 (+)NCBICelera
Cytogenetic Map10q26NCBI
CCL13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21930,110,619 - 30,120,918 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11731,991,689 - 32,002,241 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01722,430,633 - 22,432,893 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11722,724,145 - 22,726,306 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1722,723,888 - 22,726,381 (-)Ensemblpanpan1.1panPan2
CCL13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11627,864,260 - 27,867,457 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1627,865,318 - 27,867,415 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660752,152,140 - 2,154,842 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in CCL13
30 total Variants

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 hemolymphoid system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium 2 3 6 1 8 3
Low 2 5 12 5 4 10 5 2 3
Below cutoff 1 1 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000037424   ⟹   ENSCAFP00000032928
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl938,938,135 - 38,940,231 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845019799   ⟹   ENSCAFP00845015499
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl939,728,462 - 39,769,550 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845019830   ⟹   ENSCAFP00845015525
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl939,751,675 - 39,753,541 (-)Ensembl
RefSeq Acc Id: NM_001003966   ⟹   NP_001003966
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1938,938,944 - 38,940,231 (-)NCBI
Dog10K_Boxer_Tasha938,162,012 - 38,163,300 (-)NCBI
ROS_Cfam_1.0939,752,155 - 39,753,443 (-)NCBI
UMICH_Zoey_3.1938,539,350 - 38,540,637 (-)NCBI
UNSW_CanFamBas_1.0938,818,831 - 38,820,119 (-)NCBI
UU_Cfam_GSD_1.0938,907,308 - 38,908,596 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001003966 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAD36827 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCAFP00000032928.3
  ENSCAFP00000072478.1
  ENSCAFP00030027590.1
  ENSCAFP00030027680.1
  ENSCAFP00805007012
  ENSCAFP00845015499.1
  ENSCAFP00845015525
  ENSCAFP00845015525.1
GenBank Protein Q68Y88 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001003966   ⟸   NM_001003966
- Peptide Label: precursor
- UniProtKB: Q68Y88 (UniProtKB/Swiss-Prot),   A0A8C0KN11 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000032928   ⟸   ENSCAFT00000037424
RefSeq Acc Id: ENSCAFP00845015525   ⟸   ENSCAFT00845019830
RefSeq Acc Id: ENSCAFP00845015499   ⟸   ENSCAFT00845019799
Protein Domains
Chemokine interleukin-8-like


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000024205 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSCAFG00030017108 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSCAFG00805004793 UniProtKB/Swiss-Prot
  ENSCAFG00845011162 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000037424.3 UniProtKB/Swiss-Prot
  ENSCAFT00000108943.1 UniProtKB/TrEMBL
  ENSCAFT00030031636.1 UniProtKB/TrEMBL
  ENSCAFT00030031740.1 UniProtKB/Swiss-Prot
  ENSCAFT00805008958 UniProtKB/Swiss-Prot
  ENSCAFT00845019799.1 UniProtKB/TrEMBL
  ENSCAFT00845019830 ENTREZGENE
  ENSCAFT00845019830.1 UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.50.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Chemokine_b/g/d UniProtKB/Swiss-Prot
  Chemokine_CC_CS UniProtKB/Swiss-Prot
  Chemokine_IL8-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Interleukin_8-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report cfa:445451 UniProtKB/Swiss-Prot
NCBI Gene CCL13 ENTREZGENE
PANTHER C-C MOTIF CHEMOKINE 7 UniProtKB/Swiss-Prot
  PTHR12015 UniProtKB/Swiss-Prot
Pfam IL8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS FRACTALKINE UniProtKB/Swiss-Prot
PROSITE SMALL_CYTOKINES_CC UniProtKB/Swiss-Prot
SMART SCY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54117 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8C0KN11 ENTREZGENE
  A0A8C0RM81_CANLF UniProtKB/TrEMBL
  A0A8I3NTR7_CANLF UniProtKB/TrEMBL
  CCL13_CANLF UniProtKB/Swiss-Prot, ENTREZGENE