Cklf (chemokine-like factor) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Cklf (chemokine-like factor) Rattus norvegicus
Analyze
Symbol: Cklf
Name: chemokine-like factor
RGD ID: 620708
Description: Predicted to enable chemokine activity. Involved in neutrophil chemotaxis. Predicted to be located in extracellular region. Predicted to be active in membrane. Orthologous to human CKLF (chemokine like factor); INTERACTS WITH 1,3-dinitrobenzene; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: chemokine-like factor 1; Cklf1
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr819704,528 - 712,998 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl19697,451 - 712,998 (-)EnsemblGRCr8
mRatBN7.219698,097 - 706,570 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl19698,033 - 706,570 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx19693,813 - 702,288 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0191,460,613 - 1,469,088 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.019735,831 - 744,306 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.019903,609 - 914,880 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl19906,411 - 914,880 (-)Ensemblrn6Rnor6.0
Rnor_5.019907,066 - 915,792 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.419655,880 - 665,215 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera19693,868 - 702,193 (-)NCBICelera
RGSC_v3.119655,880 - 665,215 (-)NCBI
Cytogenetic Map19p14NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,4'-trichlorobiphenyl  (ISO)
2,4-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
AM-251  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
beta-lapachone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
C60 fullerene  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dimethyl sulfoxide  (ISO)
Enterolactone  (ISO)
epoxiconazole  (ISO)
folic acid  (ISO)
indometacin  (ISO)
isobutanol  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
methimazole  (EXP)
mitoxantrone  (ISO)
nickel atom  (ISO)
paracetamol  (EXP,ISO)
PCB138  (ISO)
pirinixic acid  (ISO)
propiconazole  (EXP)
quercetin  (ISO)
sarin  (ISO)
silicon dioxide  (ISO)
sunitinib  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
triptonide  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
extracellular region  (IEA,ISO)
extracellular space  (IEA)
membrane  (IBA,IEA,ISO)

Molecular Function

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. Molecular cloning and characterization of rat chemokine-like factor 1 and 2. Lou Y, etal., Gene 2003 Mar 27;307:125-32.
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11415443   PMID:19946888   PMID:21964493   PMID:23203409   PMID:25042180   PMID:25144394   PMID:27283776   PMID:31387172   PMID:32446198   PMID:33578361   PMID:34385606  


Genomics

Comparative Map Data
Cklf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr819704,528 - 712,998 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl19697,451 - 712,998 (-)EnsemblGRCr8
mRatBN7.219698,097 - 706,570 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl19698,033 - 706,570 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx19693,813 - 702,288 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0191,460,613 - 1,469,088 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.019735,831 - 744,306 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.019903,609 - 914,880 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl19906,411 - 914,880 (-)Ensemblrn6Rnor6.0
Rnor_5.019907,066 - 915,792 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.419655,880 - 665,215 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera19693,868 - 702,193 (-)NCBICelera
RGSC_v3.119655,880 - 665,215 (-)NCBI
Cytogenetic Map19p14NCBI
CKLF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381666,552,563 - 66,566,287 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1666,552,563 - 66,566,251 (+)Ensemblhg38GRCh38
GRCh371666,586,466 - 66,600,190 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361665,143,967 - 65,157,655 (+)NCBIBuild 36Build 36hg18NCBI36
Celera1651,093,039 - 51,106,728 (+)NCBICelera
Cytogenetic Map16q21NCBI
HuRef1652,462,390 - 52,476,113 (+)NCBIHuRef
CHM1_11667,993,645 - 68,007,368 (+)NCBICHM1_1
T2T-CHM13v2.01672,346,858 - 72,360,582 (+)NCBIT2T-CHM13v2.0
Cklf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398104,977,493 - 104,992,642 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8104,977,493 - 104,991,570 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm388104,250,861 - 104,266,010 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8104,250,861 - 104,264,938 (+)Ensemblmm10GRCm38
MGSCv378106,774,803 - 106,788,836 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv368107,140,032 - 107,154,039 (+)NCBIMGSCv36mm8
Celera8108,482,363 - 108,496,392 (+)NCBICelera
Cytogenetic Map8D3NCBI
CKLF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21876,054,760 - 76,068,676 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11681,967,198 - 81,981,105 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01646,870,637 - 46,884,165 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11665,972,218 - 65,985,745 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1665,972,218 - 65,998,677 (+)EnsemblpanPan2panpan1.1
CKLF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1582,709,791 - 82,726,866 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl582,709,851 - 82,726,778 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha582,698,347 - 82,715,262 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0583,146,575 - 83,163,652 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl583,146,331 - 83,164,277 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1582,969,678 - 82,986,594 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0582,663,054 - 82,679,940 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0583,295,194 - 83,312,111 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
CKLF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl627,258,551 - 27,267,753 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1627,258,392 - 27,267,701 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CKLF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1552,244,853 - 52,272,231 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl552,244,909 - 52,258,567 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604723,656,490 - 23,670,984 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Cklf
72 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:157
Count of miRNA genes:103
Interacting mature miRNAs:111
Transcripts:ENSRNOT00000017127, ENSRNOT00000017129
Prediction methods:Microtar, Miranda, Rnahybrid
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131969901Rat
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124694445Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127361636Rat

Markers in Region
AI449770  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.219703,982 - 704,129 (+)MAPPERmRatBN7.2
Rnor_6.019912,294 - 912,440NCBIRnor6.0
Rnor_5.019913,178 - 913,324UniSTSRnor5.0
RGSC_v3.419661,764 - 661,910UniSTSRGSC3.4
Celera19699,752 - 699,898UniSTS
Cytogenetic Map19p14UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 66 161 91 90 59 92 59 6 352 191 11 140 78 92 31 13 13

Sequence


Ensembl Acc Id: ENSRNOT00000017127   ⟹   ENSRNOP00000017127
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl19697,451 - 712,998 (-)Ensembl
mRatBN7.2 Ensembl19698,102 - 706,570 (-)Ensembl
Rnor_6.0 Ensembl19906,411 - 914,880 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000096547   ⟹   ENSRNOP00000088472
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl19704,574 - 712,998 (-)Ensembl
mRatBN7.2 Ensembl19698,145 - 706,570 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000097455   ⟹   ENSRNOP00000085411
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl19704,462 - 712,998 (-)Ensembl
mRatBN7.2 Ensembl19698,033 - 706,570 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000106021   ⟹   ENSRNOP00000085854
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl19704,531 - 712,998 (-)Ensembl
mRatBN7.2 Ensembl19698,102 - 706,570 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000115456   ⟹   ENSRNOP00000087290
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl19709,952 - 712,998 (-)Ensembl
mRatBN7.2 Ensembl19703,523 - 706,570 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000121142   ⟹   ENSRNOP00000101131
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl19698,550 - 712,998 (-)Ensembl
RefSeq Acc Id: NM_139111   ⟹   NP_620811
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819704,528 - 712,998 (-)NCBI
mRatBN7.219698,099 - 706,570 (-)NCBI
Rnor_6.019906,410 - 914,880 (-)NCBI
Rnor_5.019907,066 - 915,792 (-)NCBI
RGSC_v3.419655,880 - 665,215 (-)RGD
Celera19693,868 - 702,193 (-)RGD
Sequence:
RefSeq Acc Id: XM_039097473   ⟹   XP_038953401
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819704,528 - 712,993 (-)NCBI
mRatBN7.219698,097 - 706,565 (-)NCBI
RefSeq Acc Id: NP_620811   ⟸   NM_139111
- UniProtKB: Q9JK80 (UniProtKB/Swiss-Prot),   Q9JK79 (UniProtKB/Swiss-Prot),   A6JXW7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000017127   ⟸   ENSRNOT00000017127
RefSeq Acc Id: XP_038953401   ⟸   XM_039097473
- Peptide Label: isoform X1
- UniProtKB: A6JXW6 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000085854   ⟸   ENSRNOT00000106021
Ensembl Acc Id: ENSRNOP00000088472   ⟸   ENSRNOT00000096547
Ensembl Acc Id: ENSRNOP00000085411   ⟸   ENSRNOT00000097455
Ensembl Acc Id: ENSRNOP00000087290   ⟸   ENSRNOT00000115456
Ensembl Acc Id: ENSRNOP00000101131   ⟸   ENSRNOT00000121142
Protein Domains
MARVEL

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JK79-F1-model_v2 AlphaFold Q9JK79 1-151 view protein structure

Transcriptome

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

Promoters
RGD ID:13700913
Promoter ID:EPDNEW_R11437
Type:initiation region
Name:Cklf_1
Description:chemokine-like factor
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_6.019914,834 - 914,894EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620708 AgrOrtholog
BioCyc Gene G2FUF-6636 BioCyc
Ensembl Genes ENSRNOG00000012752 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000017127 ENTREZGENE
  ENSRNOT00000017127.7 UniProtKB/Swiss-Prot
  ENSRNOT00000106021 ENTREZGENE
  ENSRNOT00000106021.1 UniProtKB/Swiss-Prot
InterPro Marvel UniProtKB/Swiss-Prot
  MARVEL-CKLF_proteins UniProtKB/Swiss-Prot
KEGG Report rno:245978 UniProtKB/Swiss-Prot
NCBI Gene 245978 ENTREZGENE
PANTHER CHEMOKINE-LIKE FACTOR UniProtKB/Swiss-Prot
  MARVEL-CONTAINING POTENTIAL LIPID RAFT-ASSOCIATED PROTEIN UniProtKB/Swiss-Prot
Pfam MARVEL UniProtKB/Swiss-Prot
PhenoGen Cklf PhenoGen
PROSITE MARVEL UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000012752 RatGTEx
UniProt A0A8I6A1B3_RAT UniProtKB/TrEMBL
  A0A8I6A428_RAT UniProtKB/TrEMBL
  A0A8I6A9V2_RAT UniProtKB/TrEMBL
  A0ABK0L984_RAT UniProtKB/TrEMBL
  A6JXW6 ENTREZGENE, UniProtKB/TrEMBL
  A6JXW7 ENTREZGENE, UniProtKB/TrEMBL
  A6JXW8_RAT UniProtKB/TrEMBL
  A6JXW9_RAT UniProtKB/TrEMBL
  CKLF_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q9JK80 ENTREZGENE
UniProt Secondary Q9JK80 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Cklf  chemokine-like factor  Cklf1  chemokine-like factor 1  Symbol and Name updated 1299863 APPROVED
2005-01-20 Cklf1  chemokine-like factor 1      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Cklf1  chemokine-like factor 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression displays high level of expression in testis 632447
gene_process protein is a potent chemoattractant for neutrophils, monocytes and lymphocytes 632447
gene_protein predicted protein contains 98 aa residues 632447