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 have 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; intracellular protein transmembrane transport; and positive regulation of transport. Predicted to localize to several cellular components, including centriolar satellite; cytoplasmic vesicle membrane; and ruffle 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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-Chemical Interaction Annotations     Click to see Annotation Detail View
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
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
GRCh371222,601,511 - 22,697,452 (-)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_11222,566,544 - 22,662,523 (-)NCBICHM1_1
C2cd5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396142,956,646 - 143,045,878 (-)NCBIGRCm39mm39
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
CanFam3.1 Ensembl2724,697,016 - 24,797,543 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12724,697,036 - 24,798,138 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
C2cd5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1122,267,415 - 22,362,969 (-)Ensembl
ChlSab1.11122,267,508 - 22,362,927 (-)NCBI
C2cd5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475216,261,819 - 16,365,161 (+)NCBI

Position Markers
RH129357  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map4q44UniSTS
RH 3.4 Map41047.9UniSTS
AI716159  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map4q44UniSTS
RH 3.4 Map41048.3UniSTS
BM382971  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map4q44UniSTS
RH 3.4 Map41048.1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4136351734180689124Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4136908430182878540Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)484475257178931073Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4137171018182171018Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157423126184226339Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)4134917642179917642Rat
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)4145547014184226339Rat
6478720Alc23Alcohol consumption QTL 230.00509drinking behavior trait (VT:0001422)ethanol drink intake rate to body weight ratio (CMO:0001616)4155386197184226339Rat
6478728Anxrr36Anxiety related response QTL 360.01061locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478733Anxrr37Anxiety related response QTL 370.00095locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478737Anxrr38Anxiety related response QTL 380.00159locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
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)4145547014184226339Rat
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)4145547014184226339Rat
6478757Anxrr44Anxiety related response QTL 440.01087locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478782Anxrr52Anxiety related response QTL 520.02091locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478785Anxrr53Anxiety related response QTL 530.01397locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
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)4145547014184226339Rat
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)4145547014184226339Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4156855449184226339Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4146497452184226339Rat

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
GenBank Nucleotide AABR07062448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01033603 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01033604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231190 (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
Rnor_6.0 Ensembl4177,245,868 - 177,331,874 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091099   ⟹   ENSRNOP00000073285
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4177,245,874 - 177,331,915 (-)Ensembl
RefSeq Acc Id: NM_001134581   ⟹   NP_001128053
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_006237633   ⟹   XP_006237695
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04177,245,868 - 177,331,906 (-)NCBI
Rnor_5.04241,450,858 - 241,536,434 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237634   ⟹   XP_006237696
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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
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
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
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
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
Rnor_6.04177,245,868 - 177,331,910 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592716   ⟹   XP_017448205
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04177,245,868 - 177,331,909 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592717   ⟹   XP_017448206
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04177,245,868 - 177,331,908 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592718   ⟹   XP_017448207
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04177,245,868 - 177,331,910 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592719   ⟹   XP_017448208
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04177,245,868 - 177,331,908 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592720   ⟹   XP_017448209
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04177,245,868 - 177,321,327 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592721   ⟹   XP_017448210
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04177,245,868 - 177,331,907 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592722   ⟹   XP_017448211
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
Rnor_6.04177,245,868 - 177,331,907 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592724   ⟹   XP_017448213
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04177,245,868 - 177,305,224 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592725   ⟹   XP_017448214
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04177,245,868 - 177,308,015 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001128053   ⟸   NM_001134581
- UniProtKB: D4A5B3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237696   ⟸   XM_006237634
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_006237695   ⟸   XM_006237633
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006237699   ⟸   XM_006237637
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_006237700   ⟸   XM_006237638
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_006237698   ⟸   XM_006237636
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_006237702   ⟸   XM_006237640
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: XP_006237701   ⟸   XM_006237639
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_017448207   ⟸   XM_017592718
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017448204   ⟸   XM_017592715
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017448205   ⟸   XM_017592716
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017448206   ⟸   XM_017592717
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017448208   ⟸   XM_017592719
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017448211   ⟸   XM_017592722
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017448210   ⟸   XM_017592721
- Peptide Label: isoform X7
- UniProtKB: A0A0G2K543 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448212   ⟸   XM_017592723
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017448209   ⟸   XM_017592720
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017448214   ⟸   XM_017592725
- Peptide Label: isoform X18
- Sequence:
RefSeq Acc Id: XP_017448213   ⟸   XM_017592724
- Peptide Label: isoform X17
- Sequence:
RefSeq Acc Id: ENSRNOP00000059174   ⟸   ENSRNOT00000065387
RefSeq Acc Id: ENSRNOP00000073285   ⟸   ENSRNOT00000091099
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 (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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
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, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059174 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073285 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065387 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000091099 ENTREZGENE, 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
UniGene Rn.62095 ENTREZGENE
UniProt A0A0G2K543 ENTREZGENE, 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