Sdccag8 (SHH signaling and ciliogenesis regulator SDCCAG8) - Rat Genome Database
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Gene: Sdccag8 (SHH signaling and ciliogenesis regulator SDCCAG8) Rattus norvegicus
Analyze
Symbol: Sdccag8
Name: SHH signaling and ciliogenesis regulator SDCCAG8
RGD ID: 727781
Description: Predicted to be involved in several processes, including microtubule organizing center organization; neuron migration; and regulation of cilium assembly. Predicted to localize to several cellular components, including cell-cell junction; microtubule organizing center; and photoreceptor cell cilium. Human ortholog(s) of this gene implicated in Bardet-Biedl syndrome 16 and Senior-Loken syndrome. Orthologous to human SDCCAG8 (SHH signaling and ciliogenesis regulator SDCCAG8); INTERACTS WITH ammonium chloride; bisphenol A; fenvalerate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC305002; MGC93052; serologically defined colon cancer antigen 8; serologically defined colon cancer antigen 8 homolog; slinky
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21388,754,521 - 88,979,363 (+)NCBI
Rnor_6.0 Ensembl1394,888,078 - 95,112,033 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01394,888,046 - 95,100,833 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01399,341,101 - 99,552,432 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41392,612,281 - 92,802,650 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11392,801,164 - 92,991,534 (+)NCBI
Celera1388,335,057 - 88,523,670 (+)NCBICelera
Cytogenetic Map13q25NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:20622438   PMID:20835237   PMID:21399614   PMID:25088364   PMID:27224062   PMID:29899041  


Genomics

Comparative Map Data
Sdccag8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21388,754,521 - 88,979,363 (+)NCBI
Rnor_6.0 Ensembl1394,888,078 - 95,112,033 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01394,888,046 - 95,100,833 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01399,341,101 - 99,552,432 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41392,612,281 - 92,802,650 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11392,801,164 - 92,991,534 (+)NCBI
Celera1388,335,057 - 88,523,670 (+)NCBICelera
Cytogenetic Map13q25NCBI
SDCCAG8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1243,256,034 - 243,500,091 (+)EnsemblGRCh38hg38GRCh38
GRCh381243,255,418 - 243,503,683 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371243,419,343 - 243,663,393 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361241,485,943 - 241,730,016 (+)NCBINCBI36hg18NCBI36
Build 341239,745,516 - 239,989,128NCBI
Celera1216,706,118 - 216,951,200 (+)NCBI
Cytogenetic Map1q43-q44NCBI
HuRef1213,799,209 - 214,043,437 (+)NCBIHuRef
CHM1_11244,692,001 - 244,936,037 (+)NCBICHM1_1
Sdccag8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391176,642,226 - 176,848,004 (+)NCBIGRCm39mm39
GRCm39 Ensembl1176,642,226 - 176,848,003 (+)Ensembl
GRCm381176,814,660 - 177,020,438 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1176,814,660 - 177,020,437 (+)EnsemblGRCm38mm10GRCm38
MGSCv371178,744,943 - 178,950,563 (+)NCBIGRCm37mm9NCBIm37
MGSCv361178,651,335 - 178,857,110 (+)NCBImm8
Celera1183,882,813 - 184,082,148 (+)NCBICelera
Cytogenetic Map1H4NCBI
Sdccag8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554066,695,051 - 6,909,555 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554066,694,687 - 6,909,555 (+)NCBIChiLan1.0ChiLan1.0
SDCCAG8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11224,238,840 - 224,481,133 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1224,239,009 - 224,481,132 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01218,856,571 - 219,107,855 (+)NCBIMhudiblu_PPA_v0panPan3
SDCCAG8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl734,396,345 - 34,631,462 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1734,395,977 - 34,631,479 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sdccag8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365267,202,147 - 7,431,455 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDCCAG8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1016,191,156 - 16,441,819 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11016,191,178 - 16,441,828 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21018,268,467 - 18,473,941 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SDCCAG8
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12580,263,691 - 80,510,069 (+)NCBI
ChlSab1.1 Ensembl2580,264,274 - 80,509,765 (+)Ensembl
Sdccag8
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477115,898,172 - 16,116,013 (-)NCBI

Position Markers
RH133674  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01395,076,007 - 95,076,197NCBIRnor6.0
Rnor_5.01399,527,652 - 99,527,842UniSTSRnor5.0
RGSC_v3.41392,802,089 - 92,802,279UniSTSRGSC3.4
Celera1388,523,109 - 88,523,299UniSTS
RH 3.4 Map13592.5UniSTS
Cytogenetic Map13q25UniSTS
Cytogenetic Map13q24-q26UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135108098996080989Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135156924896569248Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1357903612102903612Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1362975663107975663Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1379567081103613733Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:192
Count of miRNA genes:143
Interacting mature miRNAs:158
Transcripts:ENSRNOT00000005647
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 15 1 15 1 36 5 22 11
Low 3 43 42 40 4 40 8 11 38 30 19 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_177929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250322 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090807 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090808 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090809 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090810 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090811 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090812 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090813 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090814 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090816 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF352814 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC086973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000005647   ⟹   ENSRNOP00000005647
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1394,888,174 - 95,076,568 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077345   ⟹   ENSRNOP00000070918
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1394,888,277 - 95,013,016 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077995   ⟹   ENSRNOP00000069051
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1394,888,078 - 95,112,033 (+)Ensembl
RefSeq Acc Id: NM_177929   ⟹   NP_808790
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,649 - 88,944,055 (+)NCBI
Rnor_6.01394,888,174 - 95,076,568 (+)NCBI
Rnor_5.01399,341,101 - 99,552,432 (+)NCBI
RGSC_v3.41392,612,281 - 92,802,650 (+)RGD
Celera1388,335,057 - 88,523,670 (+)RGD
Sequence:
RefSeq Acc Id: XM_006250321   ⟹   XP_006250383
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,969,415 (+)NCBI
Rnor_6.01394,888,046 - 95,100,833 (+)NCBI
Rnor_5.01399,341,101 - 99,552,432 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006250322   ⟹   XP_006250384
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,956,758 (+)NCBI
Rnor_6.01394,888,046 - 95,082,416 (+)NCBI
Rnor_5.01399,341,101 - 99,552,432 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769789   ⟹   XP_008768011
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,894,604 (+)NCBI
Rnor_6.01394,888,046 - 95,029,070 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769790   ⟹   XP_008768012
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01394,888,046 - 95,029,997 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039090807   ⟹   XP_038946735
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,979,363 (+)NCBI
RefSeq Acc Id: XM_039090808   ⟹   XP_038946736
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,881,094 (+)NCBI
RefSeq Acc Id: XM_039090809   ⟹   XP_038946737
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,979,363 (+)NCBI
RefSeq Acc Id: XM_039090810   ⟹   XP_038946738
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,969,418 (+)NCBI
RefSeq Acc Id: XM_039090811   ⟹   XP_038946739
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,761,843 - 88,979,363 (+)NCBI
RefSeq Acc Id: XM_039090812   ⟹   XP_038946740
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,535 - 88,979,363 (+)NCBI
RefSeq Acc Id: XM_039090813   ⟹   XP_038946741
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,535 - 88,979,363 (+)NCBI
RefSeq Acc Id: XM_039090814   ⟹   XP_038946742
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,851,549 (+)NCBI
RefSeq Acc Id: XM_039090815   ⟹   XP_038946743
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,849,054 (+)NCBI
RefSeq Acc Id: XM_039090816   ⟹   XP_038946744
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,815,511 (+)NCBI
RefSeq Acc Id: XR_005492248
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,896,752 (+)NCBI
RefSeq Acc Id: XR_005492249
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,896,752 (+)NCBI
RefSeq Acc Id: XR_005492250
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21388,754,521 - 88,896,752 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_808790   ⟸   NM_177929
- Sequence:
RefSeq Acc Id: XP_006250383   ⟸   XM_006250321
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006250384   ⟸   XM_006250322
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008768012   ⟸   XM_008769790
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008768011   ⟸   XM_008769789
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000070918   ⟸   ENSRNOT00000077345
RefSeq Acc Id: ENSRNOP00000069051   ⟸   ENSRNOT00000077995
RefSeq Acc Id: ENSRNOP00000005647   ⟸   ENSRNOT00000005647
RefSeq Acc Id: XP_038946735   ⟸   XM_039090807
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946737   ⟸   XM_039090809
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038946738   ⟸   XM_039090810
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038946736   ⟸   XM_039090808
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038946742   ⟸   XM_039090814
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038946743   ⟸   XM_039090815
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038946744   ⟸   XM_039090816
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038946740   ⟸   XM_039090812
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038946741   ⟸   XM_039090813
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038946739   ⟸   XM_039090811
- Peptide Label: isoform X8

Transcriptome

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

Promoters
RGD ID:13699048
Promoter ID:EPDNEW_R9568
Type:initiation region
Name:Sdccag8_1
Description:serologically defined colon cancer antigen 8
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_6.01394,888,153 - 94,888,213EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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
13 99362807 99362808 G T snv SR/JrHsd (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), KFRS3B/Kyo (KyushuU), SR/JrHsd (KNAW), MNS/Gib (KNAW), WN/N (KNAW), RCS/Kyo (KyushuU), MR/N (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 94909752 94909753 G T snv SR/JrHsd (MCW), CDS, MR/N (MCW), WN/N (MCW), SR/JrHsd (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), MNS/Gib (RGD), LH/MavRrrc (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 92634825 92634826 G T snv MR/N (KNAW), WN/N (KNAW), SR/JrHsd (MCW), LH/MavRrrc (ICL), LCR/1Mco (UMich), LN/MavRrrc (ICL), MNS/Gib (ICL), SR/JrHsd (ICL), LL/MavRrrc (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727781 AgrOrtholog
Ensembl Genes ENSRNOG00000004181 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005647 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069051 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070918 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005647 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000077345 UniProtKB/TrEMBL
  ENSRNOT00000077995 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7191324 IMAGE-MGC_LOAD
InterPro SDCCAG8 UniProtKB/TrEMBL
KEGG Report rno:305002 UniProtKB/TrEMBL
MGC_CLONE MGC:93052 IMAGE-MGC_LOAD
NCBI Gene 305002 ENTREZGENE
PANTHER PTHR34343 UniProtKB/TrEMBL
Pfam CCCAP UniProtKB/TrEMBL
PhenoGen Sdccag8 PhenoGen
UniProt A0A0G2JUD0_RAT UniProtKB/TrEMBL
  A0A0G2JZ58_RAT UniProtKB/TrEMBL
  Q5PQY1_RAT UniProtKB/TrEMBL
  Q812C8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-02-13 Sdccag8  SHH signaling and ciliogenesis regulator SDCCAG8  Sdccag8  serologically defined colon cancer antigen 8  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Sdccag8  serologically defined colon cancer antigen 8    slinky  Name updated 1299863 APPROVED
2004-09-10 Sdccag8  slinky  LOC305002    Symbol and Name updated 1299863 APPROVED