Ckap5 (cytoskeleton associated protein 5) - Rat Genome Database

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Gene: Ckap5 (cytoskeleton associated protein 5) Rattus norvegicus
Analyze
Symbol: Ckap5
Name: cytoskeleton associated protein 5
RGD ID: 1563596
Description: Predicted to have microtubule binding activity; microtubule plus end polymerase; and ribonucleoprotein complex binding activity. Predicted to be involved in several processes, including learning; microtubule cytoskeleton organization; and positive regulation of cellular component organization. Predicted to colocalize with gamma-tubulin complex and microtubule plus-end. Orthologous to human CKAP5 (cytoskeleton associated protein 5); INTERACTS WITH 2,6-dinitrotoluene; bisphenol A; methapyrilene.
Type: protein-coding
RefSeq Status: MODEL
Also known as: cytoskeleton-associated protein 5; LOC311191; similar to colonic and hepatic tumor over-expressed protein isoform a
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
mRatBN7.2377,491,195 - 77,593,300 (+)NCBI
Rnor_6.0 Ensembl380,468,154 - 80,526,593 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0380,424,320 - 80,526,583 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0387,124,448 - 87,225,813 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4375,903,605 - 76,002,422 (+)NCBIRGSC3.4rn4RGSC3.4
Celera376,696,182 - 76,798,097 (+)NCBICelera
Cytogenetic Map3q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:10770946   PMID:14718566   PMID:15703215   PMID:17634360   PMID:18468998   PMID:19946888   PMID:21399614   PMID:21646404   PMID:25468996   PMID:25596274   PMID:26414402   PMID:28063167  


Genomics

Comparative Map Data
Ckap5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2377,491,195 - 77,593,300 (+)NCBI
Rnor_6.0 Ensembl380,468,154 - 80,526,593 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0380,424,320 - 80,526,583 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0387,124,448 - 87,225,813 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4375,903,605 - 76,002,422 (+)NCBIRGSC3.4rn4RGSC3.4
Celera376,696,182 - 76,798,097 (+)NCBICelera
Cytogenetic Map3q24NCBI
CKAP5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1146,743,048 - 46,846,308 (-)EnsemblGRCh38hg38GRCh38
GRCh381146,743,048 - 46,846,280 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371146,764,598 - 46,867,831 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361146,721,660 - 46,824,419 (-)NCBINCBI36hg18NCBI36
Celera1146,913,051 - 47,013,611 (-)NCBI
Cytogenetic Map11p11.2NCBI
HuRef1146,470,971 - 46,573,773 (-)NCBIHuRef
CHM1_11146,763,483 - 46,866,270 (-)NCBICHM1_1
Ckap5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39291,357,092 - 91,451,024 (+)NCBIGRCm39mm39
GRCm39 Ensembl291,357,107 - 91,451,009 (+)Ensembl
GRCm38291,526,747 - 91,620,679 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl291,526,762 - 91,620,664 (+)EnsemblGRCm38mm10GRCm38
MGSCv37291,386,479 - 91,460,822 (+)NCBIGRCm37mm9NCBIm37
MGSCv36291,347,180 - 91,421,504 (+)NCBImm8
Celera292,935,690 - 93,010,177 (+)NCBICelera
Cytogenetic Map2E1NCBI
Ckap5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554221,279,158 - 1,353,894 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554221,266,686 - 1,354,323 (+)NCBIChiLan1.0ChiLan1.0
CKAP5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11147,252,269 - 47,353,770 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1147,252,752 - 47,329,274 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01146,694,967 - 46,797,500 (-)NCBIMhudiblu_PPA_v0panPan3
CKAP5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11842,673,432 - 42,780,320 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1842,711,471 - 42,780,090 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1841,403,038 - 41,509,238 (+)NCBI
ROS_Cfam_1.01843,329,658 - 43,436,336 (+)NCBI
UMICH_Zoey_3.11842,815,144 - 42,921,639 (+)NCBI
UNSW_CanFamBas_1.01842,370,301 - 42,476,795 (+)NCBI
UU_Cfam_GSD_1.01843,100,004 - 43,206,556 (+)NCBI
Ckap5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494720,157,680 - 20,257,456 (+)NCBI
SpeTri2.0NW_0049365622,269,341 - 2,369,098 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CKAP5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl215,680,787 - 15,792,633 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1215,680,723 - 15,790,580 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2217,094,654 - 17,142,320 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CKAP5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1118,504,588 - 18,584,635 (+)NCBI
ChlSab1.1 Ensembl118,484,372 - 18,586,623 (+)Ensembl
Ckap5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247671,761,983 - 1,874,534 (+)NCBI

Position Markers
RH137917  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0380,449,989 - 80,450,147NCBIRnor6.0
Rnor_5.0387,150,549 - 87,150,707UniSTSRnor5.0
RGSC_v3.4375,909,387 - 75,909,545UniSTSRGSC3.4
Celera376,721,667 - 76,721,825UniSTS
Cytogenetic Map3q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31009408193415837Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)330114912123700444Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33347735481136227Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333477354108914061Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)334394121103141944Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)339248391140271184Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)34042292185422921Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)34052359392654473Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)34052359392654473Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)343295930108914061Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34540605894467785Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)345406058127023997Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)348562146115249962Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)348562146115249962Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)351821836124513579Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)351822008120917851Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)354630948119830094Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)354630948119830094Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)354630948119830094Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35463104693415673Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35524527695176874Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)35524527695176874Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35524527695176874Rat
1358293Bw38Body weight QTL 3860.0000031body mass (VT:0001259)body weight (CMO:0000012)356735995101735995Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)362922868127023997Rat
631200Cm25Cardiac mass QTL 254.80.0001heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)36304905092654302Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)366711607119830094Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)366711607119830094Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)372672290127023997Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)372973445127023997Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)378700444123700444Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:166
Count of miRNA genes:69
Interacting mature miRNAs:73
Transcripts:ENSRNOT00000021837, ENSRNOT00000066005
Prediction methods:Microtar, 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 3 42 48 32 19 32 8 10 74 35 41 11 8
Low 1 9 9 9 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_006224522 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592173 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592174 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592175 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602549 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602551 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602552 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106800 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106801 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106802 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106803 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106804 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC107910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000021837   ⟹   ENSRNOP00000021837
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl380,468,154 - 80,526,593 (+)Ensembl
RefSeq Acc Id: XM_006224522   ⟹   XP_006224584
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera376,696,182 - 76,798,097 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006234604   ⟹   XP_006234666
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0380,424,320 - 80,526,583 (+)NCBI
Rnor_5.0387,124,448 - 87,225,813 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592171   ⟹   XP_017447660
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0380,424,320 - 80,526,583 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592172   ⟹   XP_017447661
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0380,436,383 - 80,526,583 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592173   ⟹   XP_017447662
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0380,438,127 - 80,526,583 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592174   ⟹   XP_017447663
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0380,424,758 - 80,526,583 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592175   ⟹   XP_017447664
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,491,195 - 77,593,300 (+)NCBI
Rnor_6.0380,454,584 - 80,526,583 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017602549   ⟹   XP_017458038
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera376,696,182 - 76,798,097 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017602550   ⟹   XP_017458039
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera376,708,066 - 76,798,097 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017602551   ⟹   XP_017458040
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera376,709,808 - 76,798,097 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017602552   ⟹   XP_017458041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera376,696,617 - 76,798,097 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039106800   ⟹   XP_038962728
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,503,062 - 77,593,300 (+)NCBI
RefSeq Acc Id: XM_039106801   ⟹   XP_038962729
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,504,865 - 77,593,300 (+)NCBI
RefSeq Acc Id: XM_039106802   ⟹   XP_038962730
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,491,629 - 77,593,300 (+)NCBI
RefSeq Acc Id: XM_039106803   ⟹   XP_038962731
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,491,546 - 77,593,300 (+)NCBI
RefSeq Acc Id: XM_039106804   ⟹   XP_038962732
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,491,195 - 77,593,300 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_006224584   ⟸   XM_006224522
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006234666   ⟸   XM_006234604
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017458038   ⟸   XM_017602549
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017458041   ⟸   XM_017602552
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017458039   ⟸   XM_017602550
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017458040   ⟸   XM_017602551
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447660   ⟸   XM_017592171
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447663   ⟸   XM_017592174
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447661   ⟸   XM_017592172
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447662   ⟸   XM_017592173
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447664   ⟸   XM_017592175
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000021837   ⟸   ENSRNOT00000021837
RefSeq Acc Id: XP_038962732   ⟸   XM_039106804
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038962731   ⟸   XM_039106803
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038962730   ⟸   XM_039106802
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038962728   ⟸   XM_039106800
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038962729   ⟸   XM_039106801
- Peptide Label: isoform X1
Protein Domains
TOG

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)
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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
3 87148488 87148489 A G snv COP/CrCrl (MCW & UW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), GK/Ox (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), WKY/Gcrc (KNAW), SHR/OlaIpcv (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 80447928 80447929 A G snv COP/CrCrl (MCW & UW), GK/Ox (RGD), WKY/Gcrc (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563596 AgrOrtholog
Ensembl Genes ENSRNOG00000016067 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021837 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021837 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7453732 IMAGE-MGC_LOAD
InterPro ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  CLASP_N_dom UniProtKB/TrEMBL
  HEAT UniProtKB/TrEMBL
  HEAT_type_2 UniProtKB/TrEMBL
  TOG UniProtKB/TrEMBL
MGC_CLONE MGC:125219 IMAGE-MGC_LOAD
NCBI Gene 311191 ENTREZGENE
Pfam CLASP_N UniProtKB/TrEMBL
  HEAT UniProtKB/TrEMBL
PhenoGen Ckap5 PhenoGen
PROSITE HEAT_REPEAT UniProtKB/TrEMBL
SMART TOG UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
UniProt F1M949_RAT UniProtKB/TrEMBL
  Q32Q01_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Ckap5  cytoskeleton associated protein 5  LOC311191  similar to colonic and hepatic tumor over-expressed protein isoform a  Symbol and Name updated 1299863 APPROVED
2006-02-09 LOC311191  similar to colonic and hepatic tumor over-expressed protein isoform a      Symbol and Name status set to provisional 70820 PROVISIONAL