Cdk5rap2 (CDK5 regulatory subunit associated protein 2) - Rat Genome Database

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Gene: Cdk5rap2 (CDK5 regulatory subunit associated protein 2) Rattus norvegicus
Analyze
Symbol: Cdk5rap2
Name: CDK5 regulatory subunit associated protein 2
RGD ID: 708451
Description: Predicted to have several functions, including calmodulin binding activity; protein kinase binding activity; and tubulin binding activity. Involved in negative regulation of cyclin-dependent protein serine/threonine kinase activity. Predicted to colocalize with gamma-tubulin ring complex. Human ortholog(s) of this gene implicated in Seckel syndrome; microcephaly; and primary autosomal recessive microcephaly 3. Orthologous to human CDK5RAP2 (CDK5 regulatory subunit associated protein 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; aconitine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CDK5 activator-binding protein C48; CDK5 regulatory subunit-associated protein 2; LOC286919
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
mRatBN7.2583,792,282 - 83,961,129 (-)NCBI
Rnor_6.0 Ensembl586,387,078 - 86,554,102 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0586,387,238 - 86,554,108 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0590,474,206 - 90,641,334 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4587,564,010 - 87,738,257 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1587,569,157 - 87,585,659 (-)NCBI
Celera582,598,401 - 82,765,611 (-)NCBICelera
Cytogenetic Map5q31NCBI
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
cell junction  (IEA,ISO)
centrosome  (ISO,ISS)
cytoplasm  (IEA,ISO,ISS)
cytosol  (IEA,ISO)
gamma-tubulin large complex  (IEA,ISO)
Golgi apparatus  (IEA,ISO,ISS)
microtubule  (ISO,ISS)
microtubule organizing center  (IEA)
microtubule plus-end  (IEA,ISO,ISS)
mitotic spindle pole  (IEA,ISO)
pericentriolar material  (IEA,ISO,ISS)
perinuclear region of cytoplasm  (IEA,ISO,ISS)
spindle pole  (ISO,ISS)

Molecular Function

References

Additional References at PubMed
PMID:14654843   PMID:17920017   PMID:17959831   PMID:18042621   PMID:19056867   PMID:19282672   PMID:19543530   PMID:19553473   PMID:20460369   PMID:20466722   PMID:20471352   PMID:20627074  
PMID:21399614   PMID:22179047   PMID:23376485   PMID:25220058   PMID:25657325   PMID:26297806   PMID:26485573   PMID:26550838   PMID:28057765   PMID:29162697  


Genomics

Comparative Map Data
Cdk5rap2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2583,792,282 - 83,961,129 (-)NCBI
Rnor_6.0 Ensembl586,387,078 - 86,554,102 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0586,387,238 - 86,554,108 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0590,474,206 - 90,641,334 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4587,564,010 - 87,738,257 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1587,569,157 - 87,585,659 (-)NCBI
Celera582,598,401 - 82,765,611 (-)NCBICelera
Cytogenetic Map5q31NCBI
CDK5RAP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9120,388,869 - 120,580,170 (-)EnsemblGRCh38hg38GRCh38
GRCh389120,388,875 - 120,580,167 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh379123,151,153 - 123,342,445 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369122,190,968 - 122,382,258 (-)NCBINCBI36hg18NCBI36
Build 349120,230,701 - 120,421,991NCBI
Celera993,799,407 - 93,990,706 (-)NCBI
Cytogenetic Map9q33.2NCBI
HuRef992,769,151 - 92,960,484 (-)NCBIHuRef
CHM1_19123,298,715 - 123,489,623 (-)NCBICHM1_1
Cdk5rap2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39470,135,092 - 70,328,672 (-)NCBIGRCm39mm39
GRCm39 Ensembl470,135,093 - 70,328,680 (-)Ensembl
GRCm38470,216,855 - 70,410,435 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl470,216,856 - 70,410,443 (-)EnsemblGRCm38mm10GRCm38
MGSCv37469,884,058 - 70,071,401 (-)NCBIGRCm37mm9NCBIm37
MGSCv36469,709,385 - 69,896,728 (-)NCBImm8
Celera468,823,988 - 69,004,683 (-)NCBICelera
Cytogenetic Map4C2NCBI
Cdk5rap2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554197,412,331 - 7,610,353 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554197,412,177 - 7,606,883 (+)NCBIChiLan1.0ChiLan1.0
CDK5RAP2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19119,867,654 - 120,055,608 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9119,868,015 - 120,055,608 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0991,519,179 - 91,707,469 (-)NCBIMhudiblu_PPA_v0panPan3
CDK5RAP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11173,548,003 - 73,693,044 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1173,548,038 - 73,690,199 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1171,961,518 - 72,114,600 (-)NCBI
ROS_Cfam_1.01174,680,442 - 74,834,175 (-)NCBI
UMICH_Zoey_3.11173,193,623 - 73,346,570 (-)NCBI
UNSW_CanFamBas_1.01173,225,707 - 73,378,608 (-)NCBI
UU_Cfam_GSD_1.01173,962,635 - 74,115,691 (-)NCBI
Cdk5rap2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947189,132,141 - 189,313,032 (-)NCBI
SpeTri2.0NW_0049364878,900,375 - 9,081,547 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDK5RAP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1260,467,159 - 260,635,443 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11260,465,809 - 260,648,070 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21292,619,819 - 292,719,239 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CDK5RAP2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11218,999,203 - 19,186,801 (+)NCBI
ChlSab1.1 Ensembl1218,999,213 - 19,186,785 (+)Ensembl
Cdk5rap2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476014,736,273 - 14,930,168 (+)NCBI

Position Markers
RH104241  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2583,912,064 - 83,912,200 (+)MAPPER
Rnor_6.0586,505,863 - 86,505,998NCBIRnor6.0
Rnor_5.0590,593,083 - 90,593,218UniSTSRnor5.0
RGSC_v3.4587,684,740 - 87,684,875UniSTSRGSC3.4
Celera582,718,075 - 82,718,210UniSTS
Cytogenetic Map5q31UniSTS
RH130294  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2583,959,417 - 83,959,598 (+)MAPPER
Rnor_6.0586,552,738 - 86,552,918NCBIRnor6.0
Rnor_5.0590,639,958 - 90,640,138UniSTSRnor5.0
RGSC_v3.4587,736,977 - 87,737,157UniSTSRGSC3.4
Celera582,764,247 - 82,764,427UniSTS
RH 3.4 Map5656.1UniSTS
Cytogenetic Map5q31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531926122136640934Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)535225432108092802Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)535661945117554267Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535788756147487820Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540777918154732375Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54440427689432042Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)544404276134502294Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)547745646167946134Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54872203893587756Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)551418671147487820Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)55180442696804426Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)55180442696804426Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55330956898309568Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)555903593100903593Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)556902367101902367Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)556991667137729065Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)560072951133313852Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)561086525149030144Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)56108665393273130Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)561086653117554114Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)561612600102331727Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)565696672129038896Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)568838385113838385Rat
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)571154828108092802Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)571154828108092802Rat
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)571154828108092802Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)571154828108092802Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)571154828108092802Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)571552569157225114Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)583424556128424556Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)583424556128424556Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)583424556128424556Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
1331782Rf36Renal function QTL 363.296kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)585800910100745614Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:215
Count of miRNA genes:169
Interacting mature miRNAs:189
Transcripts:ENSRNOT00000007710
Prediction methods:Microtar, 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 1 18 25 16 18 16 57 23 41 10
Low 2 25 32 25 1 25 8 11 17 12 1 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_173134 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238280 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109346 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF177478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB806103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JX524852 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MF541099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000007710   ⟹   ENSRNOP00000007710
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl586,387,240 - 86,554,102 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083340   ⟹   ENSRNOP00000073851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl586,387,078 - 86,554,102 (-)Ensembl
RefSeq Acc Id: NM_173134   ⟹   NP_775157
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2583,792,284 - 83,960,782 (-)NCBI
Rnor_6.0586,387,240 - 86,554,102 (-)NCBI
Rnor_5.0590,474,206 - 90,641,334 (-)NCBI
Celera582,598,401 - 82,765,611 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238273   ⟹   XP_006238335
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2583,792,282 - 83,961,125 (-)NCBI
Rnor_6.0586,387,238 - 86,554,108 (-)NCBI
Rnor_5.0590,474,206 - 90,641,334 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238274   ⟹   XP_006238336
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2583,792,282 - 83,961,120 (-)NCBI
Rnor_6.0586,387,238 - 86,554,108 (-)NCBI
Rnor_5.0590,474,206 - 90,641,334 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238276   ⟹   XP_006238338
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2583,792,282 - 83,961,118 (-)NCBI
Rnor_6.0586,387,238 - 86,554,108 (-)NCBI
Rnor_5.0590,474,206 - 90,641,334 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238277   ⟹   XP_006238339
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2583,792,282 - 83,961,116 (-)NCBI
Rnor_6.0586,387,238 - 86,554,107 (-)NCBI
Rnor_5.0590,474,206 - 90,641,334 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238278   ⟹   XP_006238340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2583,792,282 - 83,961,117 (-)NCBI
Rnor_6.0586,387,238 - 86,554,107 (-)NCBI
Rnor_5.0590,474,206 - 90,641,334 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238279   ⟹   XP_006238341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2583,792,282 - 83,961,032 (-)NCBI
Rnor_6.0586,387,238 - 86,554,107 (-)NCBI
Rnor_5.0590,474,206 - 90,641,334 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238280   ⟹   XP_006238342
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2583,792,282 - 83,961,120 (-)NCBI
Rnor_6.0586,387,238 - 86,554,108 (-)NCBI
Rnor_5.0590,474,206 - 90,641,334 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763760   ⟹   XP_008761982
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2583,792,282 - 83,961,127 (-)NCBI
Rnor_6.0586,387,238 - 86,554,108 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763761   ⟹   XP_008761983
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0586,387,238 - 86,554,108 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593184   ⟹   XP_017448673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2583,792,282 - 83,961,129 (-)NCBI
Rnor_6.0586,387,238 - 86,554,108 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109346   ⟹   XP_038965274
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2583,792,282 - 83,954,045 (-)NCBI
RefSeq Acc Id: XM_039109347   ⟹   XP_038965275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2583,792,282 - 83,961,117 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_775157   ⟸   NM_173134
- UniProtKB: F1M4B7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238336   ⟸   XM_006238274
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K6K7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238342   ⟸   XM_006238280
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_006238335   ⟸   XM_006238273
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006238339   ⟸   XM_006238277
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006238338   ⟸   XM_006238276
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006238341   ⟸   XM_006238279
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_006238340   ⟸   XM_006238278
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_008761983   ⟸   XM_008763761
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008761982   ⟸   XM_008763760
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017448673   ⟸   XM_017593184
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000007710   ⟸   ENSRNOT00000007710
RefSeq Acc Id: ENSRNOP00000073851   ⟸   ENSRNOT00000083340
RefSeq Acc Id: XP_038965275   ⟸   XM_039109347
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038965274   ⟸   XM_039109346
- Peptide Label: isoform X7
Protein Domains
Cnn_1N

Transcriptome

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

Promoters
RGD ID:13693809
Promoter ID:EPDNEW_R4334
Type:multiple initiation site
Name:Cdk5rap2_1
Description:CDK5 regulatory subunit associated protein 2
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_6.0586,554,106 - 86,554,166EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 90524189 90524190 G A snv GH/OmrMcwi (MCW), ZFDM (KyushuU), SBH/Ygl (MCW), ZF (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), BDIX/NemOda (KyushuU), F344/Jcl (KyushuU), F344/Stm (KyushuU), F344/NSlc (KyushuU), F344/DuCrlCrlj (KyushuU), NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), LE/OrlBarth (UDEL), WN/N (KNAW), MNS/Gib (KNAW), M520/N (KNAW), LEW/NCrl (KNAW), LEW/Crl (KNAW), F344/NHsd (KNAW), F344/NCrl (KNAW), F344/NRrrc (SOLiD) (KNAW), BUF/N (KNAW), F344/NRrrc (Illumina) (KNAW), SBN/Ygl (KNAW), SBH/Ygl (KNAW), BBDP/WorN (KNAW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), LL/MavRrrc (KNAW), MHS/Gib (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW)
5 90529142 90529143 G A snv WKY/N (KNAW), FHH/EurMcwi (MCW), SDLEF7/Barth (UDEL), SHRSP/Gcrc (KNAW), SHR/OlaIpcvPrin (KNAW), SHR/OlaIpcv (KNAW), SHR/NHsd (KNAW), SHR/NCrlPrin (KNAW), LE/Stm (SOLiD) (KNAW), LE/Stm (Illumina) (KNAW), FHL/EurMcwi (KNAW), FHH/EurMcwi (KNAW), HTX/Kyo (KyushuU), LE/Stm (KyushuU), SR/JrHsd (KNAW), Crl:SD (UDEL), LN/MavRrrc (KNAW), LEC/Tj (KyushuU), LH/MavRrrc (KNAW), WKY/NHsd (KNAW), SR/JrHsd (MCW), WKY/NCrl (KNAW), FHL/EurMcwi (MCW), WKY/Gcrc (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 86436921 86436922 G A snv SBN/Ygl (MCW), CDR, WAG/Rij (RGD), SS/JrHsdMcwi (RGD), SS/Jr (RGD), SBH/Ygl (MCW), M520/N (MCW), F344/NRrrc (MCW), SBN/Ygl (RGD), SBH/Ygl (RGD), MNS/Gib (RGD), MHS/Gib (RGD), LL/MavRrrc (RGD), Buf/N (MCW), BBDP/Wor (RGD), F344/NCrl (RGD), GH/OmrMcwi (MCW), SS/JrHsdMcwi (MCW), LEW/Crl (RGD), LEW/NCrlBR (RGD), WN/N (MCW)
5 86441793 86441794 G A snv WKY/Gcrc (RGD), WKY/NCrl (RGD), SR/JrHsd (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD), LN/MavRrrc (RGD), LH/MavRrrc (RGD), WKY/NHsd (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), WKY/N (MCW), SR/JrHsd (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), LE/Stm (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:708451 AgrOrtholog
Ensembl Genes ENSRNOG00000005788 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007710 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073851 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007710 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000083340 UniProtKB/TrEMBL
InterPro CDK5RAP2 UniProtKB/TrEMBL
  Cnn_1N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:286919 UniProtKB/TrEMBL
NCBI Gene 286919 ENTREZGENE
PANTHER PTHR46930 UniProtKB/TrEMBL
Pfam Cnn_1N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cdk5rap2 PhenoGen
UniProt A0A0G2K6K7 ENTREZGENE, UniProtKB/TrEMBL
  A0A3G1T2C5_RAT UniProtKB/TrEMBL
  CK5P2_RAT UniProtKB/Swiss-Prot
  F1M4B7 ENTREZGENE, UniProtKB/TrEMBL
  Q9JLH5 ENTREZGENE
UniProt Secondary K7QQW0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Cdk5rap2  CDK5 regulatory subunit associated protein 2    CDK5 activator-binding protein  Name updated 1299863 APPROVED
2004-09-10 Cdk5rap2  CDK5 activator-binding protein  LOC286919    Symbol and Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction interacts with p35nck5a complexed with Cdk5 632478