Cdkal1 (CDK5 regulatory subunit associated protein 1-like 1) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References FTP Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner
Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Cdkal1 (CDK5 regulatory subunit associated protein 1-like 1) Rattus norvegicus
Analyze
Symbol: Cdkal1
Name: CDK5 regulatory subunit associated protein 1-like 1
RGD ID: 1310246
Description: Predicted to have N6-threonylcarbomyladenosine methylthiotransferase activity. Predicted to be involved in maintenance of translational fidelity and tRNA methylthiolation. Predicted to localize to rough endoplasmic reticulum. Human ortholog(s) of this gene implicated in diabetes mellitus; gestational diabetes; and type 2 diabetes mellitus. Orthologous to human CDKAL1 (CDK5 regulatory subunit associated protein 1 like 1); INTERACTS WITH cadmium dichloride; diallyl disulfide; oxaliplatin.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CDK5 regulatory subunit-associated protein 1-like 1; LOC361243; threonylcarbamoyladenosine tRNA methylthiotransferase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21734,718,680 - 34,769,614 (+)NCBI
Rnor_6.0 Ensembl1736,451,058 - 37,295,069 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01736,451,031 - 37,157,882 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01737,759,260 - 37,935,320 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01738,780,937 - 39,026,953 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41741,208,037 - 41,259,863 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11741,211,591 - 42,031,602 (+)NCBI
Celera1734,245,172 - 34,795,596 (+)NCBICelera
Cytogenetic Map17p12NCBI
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

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:19946888   PMID:20584901   PMID:21151568   PMID:21841312   PMID:23048041  


Genomics

Comparative Map Data
Cdkal1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21734,718,680 - 34,769,614 (+)NCBI
Rnor_6.0 Ensembl1736,451,058 - 37,295,069 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01736,451,031 - 37,157,882 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01737,759,260 - 37,935,320 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01738,780,937 - 39,026,953 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41741,208,037 - 41,259,863 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11741,211,591 - 42,031,602 (+)NCBI
Celera1734,245,172 - 34,795,596 (+)NCBICelera
Cytogenetic Map17p12NCBI
CDKAL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl620,534,457 - 21,232,404 (+)EnsemblGRCh38hg38GRCh38
GRCh38620,534,457 - 21,232,404 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37620,534,688 - 21,232,635 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36620,642,667 - 21,339,743 (+)NCBINCBI36hg18NCBI36
Build 34620,642,735 - 21,340,611NCBI
Celera621,767,810 - 22,465,949 (+)NCBI
Cytogenetic Map6p22.3NCBI
HuRef620,478,924 - 21,176,389 (+)NCBIHuRef
CHM1_1620,536,980 - 21,234,732 (+)NCBICHM1_1
Cdkal1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391329,375,729 - 30,039,665 (-)NCBIGRCm39mm39
GRCm381329,191,746 - 29,855,683 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1329,191,746 - 29,855,674 (-)EnsemblGRCm38mm10GRCm38
MGSCv371329,417,175 - 29,947,457 (-)NCBIGRCm37mm9NCBIm37
MGSCv361329,332,771 - 29,863,053 (-)NCBImm8
Celera1329,544,145 - 30,074,351 (-)NCBICelera
Cytogenetic Map13A3.1- A3.2NCBI
Cdkal1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554835,398,687 - 5,993,079 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554835,398,748 - 5,993,071 (-)NCBIChiLan1.0ChiLan1.0
CDKAL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1620,705,442 - 21,406,933 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl620,717,011 - 21,405,566 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0620,357,897 - 21,064,873 (+)NCBIMhudiblu_PPA_v0panPan3
CDKAL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3519,138,918 - 19,929,429 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13519,138,904 - 19,802,545 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cdkal1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365525,903,042 - 6,347,498 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDKAL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl715,910,666 - 16,685,053 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1715,910,645 - 16,569,643 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2716,819,882 - 17,480,999 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CDKAL1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11750,970,764 - 51,673,551 (-)NCBI
ChlSab1.1 Ensembl1750,970,678 - 51,673,579 (-)Ensembl
Cdkal1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247565,498,557 - 6,143,184 (-)NCBI

Position Markers
D17Got48  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01737,027,460 - 37,027,744NCBIRnor6.0
Rnor_5.01738,895,524 - 38,895,808UniSTSRnor5.0
RGSC_v3.41741,636,531 - 41,636,816RGDRGSC3.4
RGSC_v3.41741,636,532 - 41,636,816UniSTSRGSC3.4
RGSC_v3.11741,639,373 - 41,639,657RGD
Celera1734,663,702 - 34,663,986UniSTS
RH 3.4 Map17389.7RGD
RH 3.4 Map17389.7UniSTS
RH 2.0 Map17290.7RGD
Cytogenetic Map17p12UniSTS
RH131644  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01737,004,240 - 37,004,435NCBIRnor6.0
Rnor_5.01738,872,304 - 38,872,499UniSTSRnor5.0
RGSC_v3.41741,613,312 - 41,613,507UniSTSRGSC3.4
Celera1734,640,482 - 34,640,677UniSTS
RH 3.4 Map17393.5UniSTS
Cytogenetic Map17p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17138243814Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17163676140Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17173413148Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17173413148Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17333697237790462Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17333697263676140Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17333697273413148Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17333697273413148Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17333697273413148Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17519104750191047Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17519104750191047Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17982730454827304Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)171052970942542027Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171574375561036897Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171867614063676140Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171867614063676140Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172149095062195822Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172149095066490950Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172149095066490950Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172149095066490950Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172149095066490950Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172149095066490950Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172149095074823273Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172213681453475276Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172277506564946194Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172403061863676140Rat
4889891Eae32Experimental allergic encephalomyelitis QTL 324.80.0002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)172769095938110914Rat
1581512Cm55Cardiac mass QTL 552.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172769095961794615Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172769095963994435Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)172807358956207236Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172841314873413148Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)173097522875975228Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)173097522875975228Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)173205588258468016Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173205588277922655Rat
2313854Bp343Blood pressure QTL 3433.9life span trait (VT:0005372)age at time of death (CMO:0001193)173330362753475276Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173330362778303627Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173330362785321557Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173628324577922655Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:36
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000024854
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


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 10 22 6 16 6 8 11 56 27 38 10 8
Low 3 33 35 35 3 35 18 8 3 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024854   ⟹   ENSRNOP00000024854
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1736,956,385 - 37,295,069 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000071408   ⟹   ENSRNOP00000065627
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1736,451,058 - 36,627,167 (+)Ensembl
RefSeq Acc Id: NM_001108413   ⟹   NP_001101883
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21734,718,680 - 34,769,614 (+)NCBI
RefSeq Acc Id: XM_006222382   ⟹   XP_006222444
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1734,245,172 - 34,795,596 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771610   ⟹   XP_008769832
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01736,451,031 - 37,157,882 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773955   ⟹   XP_008772177
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1734,246,543 - 34,795,596 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017587765   ⟹   XP_017443254
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1734,245,172 - 34,795,596 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101883 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AFY09824 (Get FASTA)   NCBI Sequence Viewer  
  EDL98384 (Get FASTA)   NCBI Sequence Viewer  
  EDL98385 (Get FASTA)   NCBI Sequence Viewer  
  EDL98386 (Get FASTA)   NCBI Sequence Viewer  
  EDL98387 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006222444   ⟸   XM_006222382
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008772177   ⟸   XM_008773955
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008769832   ⟸   XM_008771610
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017443254   ⟸   XM_017587765
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000065627   ⟸   ENSRNOT00000071408
RefSeq Acc Id: ENSRNOP00000024854   ⟸   ENSRNOT00000024854
RefSeq Acc Id: NP_001101883   ⟸   NM_001108413
Protein Domains
MTTase N-terminal   TRAM

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310246 AgrOrtholog
Ensembl Genes ENSRNOG00000018381 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024854 UniProtKB/TrEMBL
  ENSRNOP00000065627 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024854 UniProtKB/TrEMBL
  ENSRNOT00000071408 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.12160 UniProtKB/TrEMBL
  3.80.30.20 UniProtKB/TrEMBL
InterPro Elp3/MiaB/NifB UniProtKB/TrEMBL
  Methylthiotransferase UniProtKB/TrEMBL
  Methylthiotransferase_CS UniProtKB/TrEMBL
  Methylthiotransferase_N UniProtKB/TrEMBL
  Methylthiotransferase_N_sf UniProtKB/TrEMBL
  MiaB-like_B UniProtKB/TrEMBL
  rSAM UniProtKB/TrEMBL
  rSAM_horseshoe UniProtKB/TrEMBL
  TRAM_dom UniProtKB/TrEMBL
NCBI Gene 361243 ENTREZGENE
Pfam Radical_SAM UniProtKB/TrEMBL
  TRAM UniProtKB/TrEMBL
  UPF0004 UniProtKB/TrEMBL
PhenoGen Cdkal1 PhenoGen
PROSITE MTTASE_N UniProtKB/TrEMBL
  MTTASE_RADICAL UniProtKB/TrEMBL
  TRAM UniProtKB/TrEMBL
SMART Elp3 UniProtKB/TrEMBL
TIGRFAMs MiaB-like-B UniProtKB/TrEMBL
  TIGR00089 UniProtKB/TrEMBL
UniProt F1LV76_RAT UniProtKB/TrEMBL
  K9N0M9_RAT UniProtKB/TrEMBL
  M0R837_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Cdkal1  CDK5 regulatory subunit associated protein 1-like 1   Cdkal1_predicted  CDK5 regulatory subunit associated protein 1-like 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Cdkal1_predicted  CDK5 regulatory subunit associated protein 1-like 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED