Cep104 (centrosomal protein 104) - Rat Genome Database

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Gene: Cep104 (centrosomal protein 104) Rattus norvegicus
Analyze
Symbol: Cep104
Name: centrosomal protein 104
RGD ID: 708505
Description: Exhibits glutamate binding activity; glycine binding activity; and thienylcyclohexylpiperidine binding activity. Predicted to localize to centriole and cilium. Human ortholog(s) of this gene implicated in Joubert syndrome 25. Orthologous to human CEP104 (centrosomal protein 104); INTERACTS WITH bisphenol A; methamphetamine; SCH 23390.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: centrosomal protein of 104 kDa; GlyBP; glycine-, glutamate-, thienylcyclohexylpiperidine-binding protein; LOC246295
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
mRatBN7.25164,534,773 - 164,567,260 (+)NCBI
Rnor_6.0 Ensembl5171,262,278 - 171,294,559 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.05171,262,278 - 171,294,560 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05174,753,900 - 174,786,095 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45170,762,437 - 170,793,899 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15170,785,668 - 170,805,838 (+)NCBI
Celera5162,746,921 - 162,779,233 (+)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
centriole  (ISO)
cilium  (IBA)
cytoplasm  (IEA)
spindle pole  (IEA)

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:8939461   PMID:21399614  


Genomics

Comparative Map Data
Cep104
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25164,534,773 - 164,567,260 (+)NCBI
Rnor_6.0 Ensembl5171,262,278 - 171,294,559 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.05171,262,278 - 171,294,560 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05174,753,900 - 174,786,095 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45170,762,437 - 170,793,899 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15170,785,668 - 170,805,838 (+)NCBI
Celera5162,746,921 - 162,779,233 (+)NCBICelera
Cytogenetic Map5q36NCBI
CEP104
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl13,812,086 - 3,857,214 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl13,812,086 - 3,857,396 (-)EnsemblGRCh38hg38GRCh38
GRCh3813,812,086 - 3,857,233 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3713,728,650 - 3,773,775 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3613,721,204 - 3,763,657 (-)NCBINCBI36hg18NCBI36
Celera12,982,705 - 3,023,114 (-)NCBI
Cytogenetic Map1p36.32NCBI
HuRef13,024,327 - 3,069,355 (-)NCBIHuRef
CHM1_113,715,664 - 3,760,800 (-)NCBICHM1_1
Cep104
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394154,059,649 - 154,093,189 (+)NCBIGRCm39mm39
GRCm39 Ensembl4154,059,651 - 154,093,189 (+)Ensembl
GRCm384153,975,126 - 154,008,732 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4153,975,194 - 154,008,732 (+)EnsemblGRCm38mm10GRCm38
MGSCv374153,349,670 - 153,381,334 (+)NCBIGRCm37mm9NCBIm37
MGSCv364152,819,361 - 152,851,025 (+)NCBImm8
Celera4156,263,741 - 156,294,655 (+)NCBICelera
Cytogenetic Map4E2NCBI
Cep104
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554867,853,641 - 7,876,047 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554867,849,921 - 7,877,598 (+)NCBIChiLan1.0ChiLan1.0
CEP104
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113,607,940 - 3,649,450 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13,606,659 - 3,648,832 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012,485,711 - 2,529,745 (-)NCBIMhudiblu_PPA_v0panPan3
CEP104
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1558,301,767 - 58,339,920 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl558,305,589 - 58,335,438 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha558,312,060 - 58,350,211 (-)NCBI
ROS_Cfam_1.0558,509,183 - 58,547,344 (-)NCBI
UMICH_Zoey_3.1558,516,904 - 58,555,051 (-)NCBI
UNSW_CanFamBas_1.0558,385,797 - 58,423,948 (-)NCBI
UU_Cfam_GSD_1.0558,776,065 - 58,814,220 (-)NCBI
Cep104
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505829,338,027 - 29,369,250 (-)NCBI
SpeTri2.0NW_00493673798,346 - 127,932 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CEP104
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl665,274,486 - 65,310,728 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1665,274,092 - 65,310,735 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2660,132,912 - 60,157,253 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CEP104
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120127,823,789 - 127,866,172 (+)NCBI
ChlSab1.1 Ensembl20127,828,995 - 127,865,544 (+)Ensembl
Cep104
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248186,712,616 - 6,737,377 (+)NCBI

Position Markers
RH133619  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25164,566,782 - 164,566,988 (+)MAPPER
Rnor_6.05171,294,094 - 171,294,299NCBIRnor6.0
Rnor_5.05174,785,629 - 174,785,834UniSTSRnor5.0
RGSC_v3.45170,794,882 - 170,795,087UniSTSRGSC3.4
Celera5162,778,767 - 162,778,972UniSTS
RH 3.4 Map51138.3UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5128687766173687766Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5131077716173707219Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132551937173707219Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133943857173707219Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133943857173707219Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5134197905173707219Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5134712342173707219Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5134712342173707219Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5136354114173707219Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136640731173707219Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138154677172402610Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5142307322173707219Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5142309061173707219Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5149029982173687766Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5157319671173707219Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5161084664173707219Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:255
Count of miRNA genes:164
Interacting mature miRNAs:215
Transcripts:ENSRNOT00000031138
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 29 28 14 14 14 3 74 35 41 11
Low 3 14 29 27 5 27 8 8 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_145082 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005504363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005504364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA924538 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BI289406 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB544954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB792008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK843167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO390283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CV797293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DV722335 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM108776 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U53513 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000031138   ⟹   ENSRNOP00000034972
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5171,262,278 - 171,294,559 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077307   ⟹   ENSRNOP00000069101
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5171,274,544 - 171,294,555 (+)Ensembl
RefSeq Acc Id: NM_145082   ⟹   NP_659550
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25164,534,956 - 164,567,249 (+)NCBI
Rnor_6.05171,262,278 - 171,294,560 (+)NCBI
Rnor_5.05174,753,900 - 174,786,095 (+)NCBI
Celera5162,746,921 - 162,779,233 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039109276   ⟹   XP_038965204
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25164,534,773 - 164,567,260 (+)NCBI
RefSeq Acc Id: XM_039109277   ⟹   XP_038965205
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25164,535,024 - 164,567,260 (+)NCBI
RefSeq Acc Id: XM_039109278   ⟹   XP_038965206
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25164,535,024 - 164,567,260 (+)NCBI
RefSeq Acc Id: XM_039109279   ⟹   XP_038965207
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25164,534,773 - 164,567,260 (+)NCBI
RefSeq Acc Id: XR_005504363
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25164,535,024 - 164,567,252 (+)NCBI
RefSeq Acc Id: XR_005504364
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25164,535,024 - 164,567,252 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_659550   ⟸   NM_145082
- UniProtKB: D3Z8X7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000034972   ⟸   ENSRNOT00000031138
RefSeq Acc Id: ENSRNOP00000069101   ⟸   ENSRNOT00000077307
RefSeq Acc Id: XP_038965204   ⟸   XM_039109276
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038965207   ⟸   XM_039109279
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038965205   ⟸   XM_039109277
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038965206   ⟸   XM_039109278
- Peptide Label: isoform X3

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)
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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)
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:708505 AgrOrtholog
Ensembl Genes ENSRNOG00000025000 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000034972 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000069101 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000031138 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000077307 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
InterPro ARM-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Galactose-bd-like_sf UniProtKB/Swiss-Prot
  TOG UniProtKB/Swiss-Prot
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:246295 UniProtKB/Swiss-Prot
NCBI Gene 246295 ENTREZGENE
PhenoGen Cep104 PhenoGen
SMART TOG UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49785 UniProtKB/Swiss-Prot
UniProt A0A1P0QEF5_RAT UniProtKB/TrEMBL
  CE104_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A0A0G2JUH6 UniProtKB/Swiss-Prot
  Q62965 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-09-17 Cep104  centrosomal protein 104  LOC246295  glycine-, glutamate-, thienylcyclohexylpiperidine-binding protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-09-30 LOC246295        Symbol and Name status set to provisional 70820 PROVISIONAL