C2cd5 (C2 calcium-dependent domain containing 5) - Rat Genome Database

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Gene: C2cd5 (C2 calcium-dependent domain containing 5) Rattus norvegicus
Analyze
Symbol: C2cd5
Name: C2 calcium-dependent domain containing 5
RGD ID: 1304592
Description: Predicted to enable calcium ion binding activity and calcium-dependent phospholipid binding activity. Predicted to be involved in several processes, including insulin receptor signaling pathway via phosphatidylinositol 3-kinase; positive regulation of transport; and protein localization to plasma membrane. Predicted to act upstream of or within positive regulation of glucose import and vesicle fusion. Predicted to be located in several cellular components, including centriolar satellite; cytoplasmic vesicle membrane; and ruffle membrane. Predicted to be active in plasma membrane. Orthologous to human C2CD5 (C2 calcium dependent domain containing 5); INTERACTS WITH acetamide; atrazine; benzo[a]pyrene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: C2 domain-containing protein 5; hypothetical protein LOC362461; LOC362461; RGD1304592; similar to KIAA0528 protein; uncharacterized protein LOC362461
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24175,969,544 - 176,055,597 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4175,969,545 - 176,055,558 (-)Ensembl
Rnor_6.04177,245,868 - 177,331,910 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4177,245,868 - 177,331,915 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04241,450,858 - 241,536,434 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44180,903,353 - 180,989,193 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14181,149,267 - 181,234,270 (-)NCBI
Celera4164,500,350 - 164,586,357 (-)NCBICelera
Cytogenetic Map4q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:21907143   PMID:25931508  


Genomics

Comparative Map Data
C2cd5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24175,969,544 - 176,055,597 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4175,969,545 - 176,055,558 (-)Ensembl
Rnor_6.04177,245,868 - 177,331,910 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4177,245,868 - 177,331,915 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04241,450,858 - 241,536,434 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44180,903,353 - 180,989,193 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14181,149,267 - 181,234,270 (-)NCBI
Celera4164,500,350 - 164,586,357 (-)NCBICelera
Cytogenetic Map4q44NCBI
C2CD5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1222,448,583 - 22,544,546 (-)EnsemblGRCh38hg38GRCh38
GRCh381222,448,577 - 22,544,542 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371222,601,517 - 22,697,476 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361222,492,784 - 22,588,719 (-)NCBINCBI36hg18NCBI36
Build 341222,492,786 - 22,588,719NCBI
Celera1227,749,342 - 27,845,274 (-)NCBI
Cytogenetic Map12p12.1NCBI
HuRef1222,367,856 - 22,463,789 (-)NCBIHuRef
CHM1_11222,566,581 - 22,662,495 (-)NCBICHM1_1
C2cd5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396142,956,646 - 143,045,878 (-)NCBIGRCm39mm39
GRCm39 Ensembl6142,956,646 - 143,045,867 (-)Ensembl
GRCm386143,010,920 - 143,100,155 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6143,010,920 - 143,100,141 (-)EnsemblGRCm38mm10GRCm38
MGSCv376142,959,440 - 143,048,627 (-)NCBIGRCm37mm9NCBIm37
MGSCv366142,968,151 - 143,069,912 (-)NCBImm8
Celera6146,066,244 - 146,155,543 (-)NCBICelera
Cytogenetic Map6G3NCBI
C2cd5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541317,884,556 - 17,972,851 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541317,883,411 - 17,972,865 (-)NCBIChiLan1.0ChiLan1.0
C2CD5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11266,377,634 - 66,472,883 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1266,377,634 - 66,472,877 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01263,769,552 - 63,865,681 (+)NCBIMhudiblu_PPA_v0panPan3
C2CD5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12724,697,036 - 24,798,138 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2724,697,016 - 24,797,543 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2721,564,193 - 21,665,404 (-)NCBI
ROS_Cfam_1.02724,907,508 - 25,008,844 (+)NCBI
UMICH_Zoey_3.12724,712,280 - 24,813,433 (+)NCBI
UNSW_CanFamBas_1.02724,736,875 - 24,838,054 (+)NCBI
UU_Cfam_GSD_1.02721,733,960 - 21,835,265 (-)NCBI
C2cd5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494586,554,495 - 86,649,759 (+)NCBI
SpeTri2.0NW_0049365484,477,336 - 4,572,645 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
C2CD5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl551,040,514 - 51,132,288 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1551,040,519 - 51,132,287 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
C2CD5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11122,267,508 - 22,362,927 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1122,267,415 - 22,362,969 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606912,781,268 - 12,876,482 (+)NCBIVero_WHO_p1.0
C2cd5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475216,261,819 - 16,365,161 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH129357  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,014,084 - 176,014,278 (+)MAPPERmRatBN7.2
Rnor_6.04177,290,405 - 177,290,598NCBIRnor6.0
Rnor_5.04241,494,950 - 241,495,143UniSTSRnor5.0
RGSC_v3.44180,947,724 - 180,947,917UniSTSRGSC3.4
Celera4164,544,888 - 164,545,081UniSTS
RH 3.4 Map41047.9UniSTS
Cytogenetic Map4q44UniSTS
AI716159  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24175,969,731 - 175,969,971 (+)MAPPERmRatBN7.2
Rnor_6.04177,246,056 - 177,246,295NCBIRnor6.0
Rnor_5.04241,451,046 - 241,451,285UniSTSRnor5.0
RGSC_v3.44180,903,541 - 180,903,780UniSTSRGSC3.4
Celera4164,500,538 - 164,500,777UniSTS
RH 3.4 Map41048.3UniSTS
Cytogenetic Map4q44UniSTS
BM382971  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map41048.1UniSTS
Cytogenetic Map4q44UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:153
Count of miRNA genes:102
Interacting mature miRNAs:127
Transcripts:ENSRNOT00000065387
Prediction methods:Miranda, 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 30 30 22 19 22 74 34 30 9
Low 13 27 19 19 8 11 1 11 2 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001134581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237634 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237636 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237638 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592716 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592720 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592721 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107923 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107925 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107926 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107927 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107932 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107938 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107939 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107940 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107941 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107942 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107943 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000065387   ⟹   ENSRNOP00000059174
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4175,969,545 - 176,055,558 (-)Ensembl
Rnor_6.0 Ensembl4177,245,868 - 177,331,874 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091099   ⟹   ENSRNOP00000073285
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4175,969,545 - 176,055,558 (-)Ensembl
Rnor_6.0 Ensembl4177,245,874 - 177,331,915 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099143   ⟹   ENSRNOP00000083139
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4175,969,545 - 176,055,558 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105102   ⟹   ENSRNOP00000079948
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4175,969,545 - 176,055,558 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111414   ⟹   ENSRNOP00000087996
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4175,969,545 - 176,055,558 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114647   ⟹   ENSRNOP00000088901
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4175,969,545 - 176,055,558 (-)Ensembl
RefSeq Acc Id: NM_001134581   ⟹   NP_001128053
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,558 (-)NCBI
Rnor_6.04177,245,868 - 177,331,874 (-)NCBI
Rnor_5.04241,450,858 - 241,536,434 (-)NCBI
RGSC_v3.44180,903,353 - 180,989,193 (-)RGD
Celera4164,500,350 - 164,586,357 (-)RGD
Sequence:
RefSeq Acc Id: XM_006237634   ⟹   XP_006237696
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,587 (-)NCBI
Rnor_6.04177,245,868 - 177,331,907 (-)NCBI
Rnor_5.04241,450,858 - 241,536,434 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237636   ⟹   XP_006237698
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,585 (-)NCBI
Rnor_6.04177,245,868 - 177,331,904 (-)NCBI
Rnor_5.04241,450,858 - 241,536,434 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237637   ⟹   XP_006237699
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,586 (-)NCBI
Rnor_6.04177,245,868 - 177,331,905 (-)NCBI
Rnor_5.04241,450,858 - 241,536,434 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237638   ⟹   XP_006237700
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,585 (-)NCBI
Rnor_6.04177,245,868 - 177,331,904 (-)NCBI
Rnor_5.04241,450,858 - 241,536,434 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237639   ⟹   XP_006237701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,584 (-)NCBI
Rnor_6.04177,245,868 - 177,331,902 (-)NCBI
Rnor_5.04241,450,858 - 241,536,434 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237640   ⟹   XP_006237702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,585 (-)NCBI
Rnor_6.04177,245,868 - 177,331,903 (-)NCBI
Rnor_5.04241,450,858 - 241,536,434 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592715   ⟹   XP_017448204
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,589 (-)NCBI
Rnor_6.04177,245,868 - 177,331,910 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592722   ⟹   XP_017448211
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,588 (-)NCBI
Rnor_6.04177,245,868 - 177,331,908 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592723   ⟹   XP_017448212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,586 (-)NCBI
Rnor_6.04177,245,868 - 177,331,907 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592725   ⟹   XP_017448214
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,031,746 (-)NCBI
Rnor_6.04177,245,868 - 177,308,015 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039107916   ⟹   XP_038963844
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,590 (-)NCBI
RefSeq Acc Id: XM_039107917   ⟹   XP_038963845
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,592 (-)NCBI
RefSeq Acc Id: XM_039107918   ⟹   XP_038963846
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,590 (-)NCBI
RefSeq Acc Id: XM_039107919   ⟹   XP_038963847
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,591 (-)NCBI
RefSeq Acc Id: XM_039107920   ⟹   XP_038963848
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,589 (-)NCBI
RefSeq Acc Id: XM_039107921   ⟹   XP_038963849
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,588 (-)NCBI
RefSeq Acc Id: XM_039107922   ⟹   XP_038963850
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,591 (-)NCBI
RefSeq Acc Id: XM_039107923   ⟹   XP_038963851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,586 (-)NCBI
RefSeq Acc Id: XM_039107924   ⟹   XP_038963852
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,589 (-)NCBI
RefSeq Acc Id: XM_039107925   ⟹   XP_038963853
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,588 (-)NCBI
RefSeq Acc Id: XM_039107926   ⟹   XP_038963854
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,590 (-)NCBI
RefSeq Acc Id: XM_039107927   ⟹   XP_038963855
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,587 (-)NCBI
RefSeq Acc Id: XM_039107928   ⟹   XP_038963856
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,589 (-)NCBI
RefSeq Acc Id: XM_039107929   ⟹   XP_038963857
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,586 (-)NCBI
RefSeq Acc Id: XM_039107932   ⟹   XP_038963860
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,588 (-)NCBI
RefSeq Acc Id: XM_039107933   ⟹   XP_038963861
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,587 (-)NCBI
RefSeq Acc Id: XM_039107934   ⟹   XP_038963862
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,586 (-)NCBI
RefSeq Acc Id: XM_039107935   ⟹   XP_038963863
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,586 (-)NCBI
RefSeq Acc Id: XM_039107936   ⟹   XP_038963864
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,586 (-)NCBI
RefSeq Acc Id: XM_039107937   ⟹   XP_038963865
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,586 (-)NCBI
RefSeq Acc Id: XM_039107938   ⟹   XP_038963866
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,055,585 (-)NCBI
RefSeq Acc Id: XM_039107939   ⟹   XP_038963867
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,976,910 - 176,055,597 (-)NCBI
RefSeq Acc Id: XM_039107940   ⟹   XP_038963868
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,031,746 (-)NCBI
RefSeq Acc Id: XM_039107941   ⟹   XP_038963869
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,031,746 (-)NCBI
RefSeq Acc Id: XM_039107942   ⟹   XP_038963870
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,031,710 (-)NCBI
RefSeq Acc Id: XM_039107943   ⟹   XP_038963871
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,969,544 - 176,031,710 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001128053 (Get FASTA)   NCBI Sequence Viewer  
  XP_006237696 (Get FASTA)   NCBI Sequence Viewer  
  XP_006237698 (Get FASTA)   NCBI Sequence Viewer  
  XP_006237699 (Get FASTA)   NCBI Sequence Viewer  
  XP_006237700 (Get FASTA)   NCBI Sequence Viewer  
  XP_006237701 (Get FASTA)   NCBI Sequence Viewer  
  XP_006237702 (Get FASTA)   NCBI Sequence Viewer  
  XP_017448204 (Get FASTA)   NCBI Sequence Viewer  
  XP_017448211 (Get FASTA)   NCBI Sequence Viewer  
  XP_017448212 (Get FASTA)   NCBI Sequence Viewer  
  XP_017448214 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963844 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963845 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963846 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963847 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963848 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963849 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963850 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963851 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963852 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963853 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963854 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963855 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963856 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963857 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963860 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963861 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963862 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963863 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963864 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963865 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963866 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963867 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963868 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963869 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963870 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963871 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM01471 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001128053   ⟸   NM_001134581
- UniProtKB: D4A5B3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237696   ⟸   XM_006237634
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: XP_006237699   ⟸   XM_006237637
- Peptide Label: isoform X20
- Sequence:
RefSeq Acc Id: XP_006237700   ⟸   XM_006237638
- Peptide Label: isoform X26
- Sequence:
RefSeq Acc Id: XP_006237698   ⟸   XM_006237636
- Peptide Label: isoform X19
- Sequence:
RefSeq Acc Id: XP_006237702   ⟸   XM_006237640
- Peptide Label: isoform X30
- Sequence:
RefSeq Acc Id: XP_006237701   ⟸   XM_006237639
- Peptide Label: isoform X29
- Sequence:
RefSeq Acc Id: XP_017448204   ⟸   XM_017592715
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017448211   ⟸   XM_017592722
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_017448212   ⟸   XM_017592723
- Peptide Label: isoform X18
- Sequence:
RefSeq Acc Id: XP_017448214   ⟸   XM_017592725
- Peptide Label: isoform X32
- Sequence:
RefSeq Acc Id: ENSRNOP00000059174   ⟸   ENSRNOT00000065387
RefSeq Acc Id: ENSRNOP00000073285   ⟸   ENSRNOT00000091099
RefSeq Acc Id: XP_038963845   ⟸   XM_039107917
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038963847   ⟸   XM_039107919
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038963850   ⟸   XM_039107922
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038963846   ⟸   XM_039107918
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038963844   ⟸   XM_039107916
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963854   ⟸   XM_039107926
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038963848   ⟸   XM_039107920
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038963852   ⟸   XM_039107924
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038963856   ⟸   XM_039107928
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038963860   ⟸   XM_039107932
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038963853   ⟸   XM_039107925
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038963849   ⟸   XM_039107921
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038963861   ⟸   XM_039107933
- Peptide Label: isoform X22
RefSeq Acc Id: XP_038963855   ⟸   XM_039107927
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038963851   ⟸   XM_039107923
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038963862   ⟸   XM_039107934
- Peptide Label: isoform X23
RefSeq Acc Id: XP_038963865   ⟸   XM_039107937
- Peptide Label: isoform X27
RefSeq Acc Id: XP_038963864   ⟸   XM_039107936
- Peptide Label: isoform X25
RefSeq Acc Id: XP_038963863   ⟸   XM_039107935
- Peptide Label: isoform X24
RefSeq Acc Id: XP_038963857   ⟸   XM_039107929
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038963866   ⟸   XM_039107938
- Peptide Label: isoform X28
RefSeq Acc Id: XP_038963869   ⟸   XM_039107941
- Peptide Label: isoform X34
RefSeq Acc Id: XP_038963868   ⟸   XM_039107940
- Peptide Label: isoform X33
RefSeq Acc Id: XP_038963871   ⟸   XM_039107943
- Peptide Label: isoform X36
RefSeq Acc Id: XP_038963870   ⟸   XM_039107942
- Peptide Label: isoform X35
RefSeq Acc Id: XP_038963867   ⟸   XM_039107939
- Peptide Label: isoform X31
RefSeq Acc Id: ENSRNOP00000087996   ⟸   ENSRNOT00000111414
RefSeq Acc Id: ENSRNOP00000079948   ⟸   ENSRNOT00000105102
RefSeq Acc Id: ENSRNOP00000088901   ⟸   ENSRNOT00000114647
RefSeq Acc Id: ENSRNOP00000083139   ⟸   ENSRNOT00000099143
Protein Domains
C2

Transcriptome

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

Promoters
RGD ID:13693493
Promoter ID:EPDNEW_R4017
Type:multiple initiation site
Name:C2cd5_1
Description:C2 calcium-dependent domain containing 5
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_6.04177,331,847 - 177,331,907EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
4 241512550 241512551 T C snv GH/OmrMcwi (MCW), Crl:SD (UDEL), ZF (KyushuU), HWY/Slc (KyushuU), HTX/Kyo (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 177307982 177307983 G C snv SR/JrHsd (RGD)
4 177307984 177307985 A C snv SR/JrHsd (RGD)
4 177308005 177308006 T C snv GH/OmrMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 180965324 180965325 T C snv GH/OmrMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304592 AgrOrtholog
Ensembl Genes ENSRNOG00000014382 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059174 UniProtKB/TrEMBL
  ENSRNOP00000073285 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065387 UniProtKB/TrEMBL
  ENSRNOT00000091099 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.150 UniProtKB/TrEMBL
InterPro C2_C2CD5 UniProtKB/TrEMBL
  C2_Ca-dep UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/TrEMBL
  C2CD5 UniProtKB/TrEMBL
KEGG Report rno:362461 UniProtKB/TrEMBL
NCBI Gene 362461 ENTREZGENE
PANTHER PTHR37412 UniProtKB/TrEMBL
Pfam PF00168 UniProtKB/TrEMBL
PhenoGen C2cd5 PhenoGen
PROSITE PS50004 UniProtKB/TrEMBL
SMART SM00239 UniProtKB/TrEMBL
Superfamily-SCOP SSF49562 UniProtKB/TrEMBL
UniProt A0A0G2K543_RAT UniProtKB/TrEMBL
  D4A5B3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-01-02 C2cd5  C2 calcium-dependent domain containing 5  RGD1304592  similar to KIAA0528 protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1304592  similar to KIAA0528 protein   RGD1304592_predicted  similar to KIAA0528 protein (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1304592_predicted  similar to KIAA0528 protein (predicted)  LOC362461_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC362461_predicted  similar to KIAA0528 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL