Cdkl4 (cyclin-dependent kinase-like 4) - Rat Genome Database

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Gene: Cdkl4 (cyclin-dependent kinase-like 4) Rattus norvegicus
Analyze
Symbol: Cdkl4
Name: cyclin-dependent kinase-like 4
RGD ID: 1583704
Description: Predicted to enable ATP binding activity and protein serine/threonine kinase activity. Orthologous to human CDKL4 (cyclin dependent kinase like 4); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC503009; similar to Cyclin-dependent kinase-like 4
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
mRatBN7.2614,449,822 - 14,492,568 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl614,450,681 - 14,492,046 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.063,232,278 - 3,272,454 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl63,234,090 - 3,254,779 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.063,201,459 - 3,242,903 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.463,426,817 - 3,469,408 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera614,127,256 - 14,169,222 (+)NCBICelera
Cytogenetic Map6q12NCBI
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
nucleus  (IBA,IEA)

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Cdkl4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2614,449,822 - 14,492,568 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl614,450,681 - 14,492,046 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.063,232,278 - 3,272,454 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl63,234,090 - 3,254,779 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.063,201,459 - 3,242,903 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.463,426,817 - 3,469,408 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera614,127,256 - 14,169,222 (+)NCBICelera
Cytogenetic Map6q12NCBI
CDKL4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38239,168,045 - 39,247,120 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl239,168,045 - 39,243,983 (-)EnsemblGRCh38hg38GRCh38
GRCh37239,395,186 - 39,471,124 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36239,259,192 - 39,310,177 (-)NCBINCBI36Build 36hg18NCBI36
Celera239,246,740 - 39,297,635 (-)NCBICelera
Cytogenetic Map2p22.1NCBI
HuRef239,144,443 - 39,195,833 (-)NCBIHuRef
CHM1_1239,336,239 - 39,387,164 (-)NCBICHM1_1
T2T-CHM13v2.0239,176,994 - 39,255,940 (-)NCBIT2T-CHM13v2.0
Cdkl4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391780,830,979 - 80,885,242 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1780,830,979 - 80,885,242 (-)EnsemblGRCm39 Ensembl
GRCm381780,523,550 - 80,577,813 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1780,523,550 - 80,577,813 (-)EnsemblGRCm38mm10GRCm38
MGSCv371780,922,890 - 80,963,174 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361780,432,482 - 80,472,160 (-)NCBIMGSCv36mm8
Celera1784,840,840 - 84,881,149 (-)NCBICelera
Cytogenetic Map17E3NCBI
cM Map1750.9NCBI
Cdkl4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554416,802,669 - 6,841,896 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554416,802,669 - 6,842,378 (-)NCBIChiLan1.0ChiLan1.0
CDKL4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan12A87,225,335 - 87,294,337 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A39,216,483 - 39,267,026 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A39,970,427 - 40,020,694 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A39,970,427 - 40,020,694 (-)Ensemblpanpan1.1panPan2
CDKL4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11731,189,107 - 31,255,268 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1731,200,156 - 31,250,300 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1730,953,582 - 30,987,983 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01731,829,840 - 31,892,165 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1731,856,455 - 31,907,159 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11731,078,778 - 31,113,149 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01731,148,730 - 31,183,247 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01731,362,358 - 31,396,961 (-)NCBIUU_Cfam_GSD_1.0
Cdkl4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629240,638,254 - 40,685,505 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493650812,066,877 - 12,110,693 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493650812,066,880 - 12,112,764 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDKL4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3101,089,243 - 101,151,518 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13101,087,156 - 101,138,839 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23107,234,753 - 107,251,395 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CDKL4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11468,123,349 - 68,196,182 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604543,785,341 - 43,860,379 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cdkl4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473820,637,362 - 20,712,894 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473820,639,229 - 20,712,582 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cdkl4
325 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:34
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000061975
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6127574569Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6127574569Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6127574569Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6127574569Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6127574569Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6507449719988050Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6984331220338915Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6984331220338915Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat


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 16 1
Low 3 32 55 41 13 41 3 4 58 35 41 10 3
Below cutoff 10 2 6 5 7 5

Sequence


RefSeq Acc Id: ENSRNOT00000061975   ⟹   ENSRNOP00000058687
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl614,450,681 - 14,492,046 (+)Ensembl
Rnor_6.0 Ensembl63,234,090 - 3,254,779 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103530   ⟹   ENSRNOP00000083479
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl614,450,681 - 14,492,046 (+)Ensembl
RefSeq Acc Id: XM_039113062   ⟹   XP_038968990
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2614,449,827 - 14,492,568 (+)NCBI
RefSeq Acc Id: XM_039113063   ⟹   XP_038968991
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2614,450,570 - 14,492,568 (+)NCBI
RefSeq Acc Id: XM_039113064   ⟹   XP_038968992
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2614,465,315 - 14,492,568 (+)NCBI
RefSeq Acc Id: XM_039113065   ⟹   XP_038968993
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2614,449,826 - 14,492,568 (+)NCBI
RefSeq Acc Id: XM_039113066   ⟹   XP_038968994
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2614,450,570 - 14,492,568 (+)NCBI
RefSeq Acc Id: XM_039113068   ⟹   XP_038968996
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2614,449,822 - 14,492,568 (+)NCBI
RefSeq Acc Id: ENSRNOP00000058687   ⟸   ENSRNOT00000061975
RefSeq Acc Id: XP_038968996   ⟸   XM_039113068
- Peptide Label: isoform X2
- UniProtKB: F1LYD6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038968993   ⟸   XM_039113065
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZVG4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038968990   ⟸   XM_039113062
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZVG4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038968991   ⟸   XM_039113063
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZVG4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038968994   ⟸   XM_039113066
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZVG4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038968992   ⟸   XM_039113064
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZVG4 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000083479   ⟸   ENSRNOT00000103530
Protein Domains
Protein kinase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LYD6-F1-model_v2 AlphaFold F1LYD6 1-289 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1583704 AgrOrtholog
BioCyc Gene G2FUF-38529 BioCyc
Ensembl Genes ENSRNOG00000040266 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061975 ENTREZGENE
  ENSRNOT00000061975.2 UniProtKB/TrEMBL
  ENSRNOT00000103530 ENTREZGENE
  ENSRNOT00000103530.1 UniProtKB/TrEMBL
Gene3D-CATH Transferase(Phosphotransferase) domain 1 UniProtKB/TrEMBL
InterPro Kinase-like_dom_sf UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/TrEMBL
  Ser/Thr_kinase_AS UniProtKB/TrEMBL
NCBI Gene 503009 ENTREZGENE
PANTHER CELL DIVISION PROTEIN KINASE UniProtKB/TrEMBL
  CYCLIN-DEPENDENT KINASE-LIKE 4 UniProtKB/TrEMBL
Pfam Haspin_kinase UniProtKB/TrEMBL
  Pkinase UniProtKB/TrEMBL
PhenoGen Cdkl4 PhenoGen
PROSITE PROTEIN_KINASE_ATP UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/TrEMBL
RatGTEx ENSRNOG00000040266 RatGTEx
SMART S_TKc UniProtKB/TrEMBL
Superfamily-SCOP SSF56112 UniProtKB/TrEMBL
UniProt A0A8I5ZVG4 ENTREZGENE, UniProtKB/TrEMBL
  F1LYD6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Cdkl4  cyclin-dependent kinase-like 4  LOC503009  similar to Cyclin-dependent kinase-like 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC503009  similar to Cyclin-dependent kinase-like 4      Symbol and Name status set to provisional 70820 PROVISIONAL