Rb1cc1 (RB1-inducible coiled-coil 1) - Rat Genome Database

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Gene: Rb1cc1 (RB1-inducible coiled-coil 1) Rattus norvegicus
Analyze
Symbol: Rb1cc1
Name: RB1-inducible coiled-coil 1
RGD ID: 1309346
Description: Predicted to have molecular adaptor activity and protein kinase binding activity. Predicted to be involved in several processes, including macroautophagy; piecemeal microautophagy of the nucleus; and regulation of signal transduction. Predicted to localize to several cellular components, including Atg1/ULK1 kinase complex; nuclear membrane; and vacuole. Human ortholog(s) of this gene implicated in breast cancer. Orthologous to human RB1CC1 (RB1 inducible coiled-coil 1); PARTICIPATES IN autophagy pathway; mTOR signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; chloroprene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC312927; RB1-inducible coiled-coil protein 1
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
mRatBN7.2513,161,648 - 13,225,560 (-)NCBI
Rnor_6.0 Ensembl513,033,918 - 13,097,341 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0513,033,918 - 13,097,369 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0517,805,493 - 17,868,916 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4513,301,486 - 13,365,398 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1513,302,204 - 13,344,260 (-)NCBI
Celera512,575,595 - 12,639,516 (-)NCBICelera
Cytogenetic Map5q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12095676   PMID:12477932   PMID:17015619   PMID:18443221   PMID:19211835   PMID:19258318   PMID:28561066   PMID:31006538  


Genomics

Comparative Map Data
Rb1cc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2513,161,648 - 13,225,560 (-)NCBI
Rnor_6.0 Ensembl513,033,918 - 13,097,341 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0513,033,918 - 13,097,369 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0517,805,493 - 17,868,916 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4513,301,486 - 13,365,398 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1513,302,204 - 13,344,260 (-)NCBI
Celera512,575,595 - 12,639,516 (-)NCBICelera
Cytogenetic Map5q12NCBI
RB1CC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl852,622,458 - 52,745,843 (-)EnsemblGRCh38hg38GRCh38
GRCh38852,622,458 - 52,714,466 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37853,535,018 - 53,626,995 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36853,697,571 - 53,789,579 (-)NCBINCBI36hg18NCBI36
Build 34853,697,571 - 53,789,545NCBI
Celera849,525,378 - 49,617,590 (-)NCBI
Cytogenetic Map8q11.23NCBI
HuRef849,002,571 - 49,094,645 (-)NCBIHuRef
CHM1_1853,587,331 - 53,679,316 (-)NCBICHM1_1
Rb1cc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3916,284,858 - 6,346,599 (+)NCBIGRCm39mm39
GRCm39 Ensembl16,276,421 - 6,346,872 (+)Ensembl
GRCm3816,214,634 - 6,276,375 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl16,206,197 - 6,276,648 (+)EnsemblGRCm38mm10GRCm38
MGSCv3716,204,743 - 6,266,185 (+)NCBIGRCm37mm9NCBIm37
MGSCv3616,204,743 - 6,265,656 (+)NCBImm8
Celera16,202,698 - 6,263,115 (+)NCBICelera
Cytogenetic Map1A1NCBI
Rb1cc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545412,200,750 - 12,257,389 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545412,201,566 - 12,257,383 (-)NCBIChiLan1.0ChiLan1.0
RB1CC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1846,430,131 - 46,521,722 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl846,430,131 - 46,521,722 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0849,046,830 - 49,138,795 (-)NCBIMhudiblu_PPA_v0panPan3
RB1CC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1294,445,668 - 4,544,223 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl294,375,785 - 4,517,168 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha294,885,675 - 4,984,178 (-)NCBI
ROS_Cfam_1.0294,511,613 - 4,608,379 (-)NCBI
UMICH_Zoey_3.1294,442,480 - 4,540,952 (-)NCBI
UNSW_CanFamBas_1.0294,668,260 - 4,766,907 (-)NCBI
UU_Cfam_GSD_1.0294,742,370 - 4,841,030 (-)NCBI
Rb1cc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530375,070,885 - 75,145,333 (+)NCBI
SpeTri2.0NW_004936590260,685 - 335,143 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RB1CC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl477,594,338 - 77,649,550 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1477,593,204 - 77,649,551 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
RB1CC1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1848,726,551 - 48,818,027 (-)NCBI
ChlSab1.1 Ensembl848,724,393 - 48,817,928 (-)Ensembl
Rb1cc1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247352,778,191 - 2,860,762 (+)NCBI

Position Markers
RH127582  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2513,162,882 - 13,163,074 (+)MAPPER
Rnor_6.0513,035,153 - 13,035,344NCBIRnor6.0
Rnor_5.0517,806,728 - 17,806,919UniSTSRnor5.0
RGSC_v3.4513,302,721 - 13,302,912UniSTSRGSC3.4
Celera512,576,830 - 12,577,021UniSTS
Cytogenetic Map5q12UniSTS
BF390556  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2513,174,485 - 13,174,643 (+)MAPPER
Rnor_6.0513,046,756 - 13,046,913NCBIRnor6.0
Rnor_5.0517,818,331 - 17,818,488UniSTSRnor5.0
RGSC_v3.4513,314,324 - 13,314,481UniSTSRGSC3.4
Celera512,588,433 - 12,588,590UniSTS
Cytogenetic Map5q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5452573847978104Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5325132948722188Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5863228553632285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5787561118592319Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5152509833001026Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5325132926252076Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5166658771552720Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:318
Count of miRNA genes:186
Interacting mature miRNAs:231
Transcripts:ENSRNOT00000061884
Prediction methods:Microtar, 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 40 51 35 19 35 8 10 74 34 41 11 8
Low 3 6 6 6 1 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000061884   ⟹   ENSRNOP00000060201
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl513,033,918 - 13,097,341 (-)Ensembl
RefSeq Acc Id: NM_001107901   ⟹   NP_001101371
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2513,161,648 - 13,225,560 (-)NCBI
Rnor_6.0513,033,918 - 13,097,341 (-)NCBI
Rnor_5.0517,805,493 - 17,868,916 (-)NCBI
RGSC_v3.4513,301,486 - 13,365,398 (-)RGD
Celera512,575,595 - 12,639,516 (-)RGD
Sequence:
RefSeq Acc Id: XM_006237794   ⟹   XP_006237856
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2513,162,776 - 13,225,392 (-)NCBI
Rnor_6.0513,034,632 - 13,097,369 (-)NCBI
Rnor_5.0517,805,493 - 17,868,916 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109749   ⟹   XP_038965677
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2513,162,362 - 13,194,853 (-)NCBI
RefSeq Acc Id: XR_001837839
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2513,162,776 - 13,225,392 (-)NCBI
Rnor_6.0513,034,632 - 13,097,369 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101371 (Get FASTA)   NCBI Sequence Viewer  
  XP_006237856 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965677 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM11576 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101371   ⟸   NM_001107901
- UniProtKB: D3ZHK4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237856   ⟸   XM_006237794
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000060201   ⟸   ENSRNOT00000061884
RefSeq Acc Id: XP_038965677   ⟸   XM_039109749
- Peptide Label: isoform X2
Protein Domains
ATG11

Transcriptome

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

Promoters
RGD ID:13693541
Promoter ID:EPDNEW_R4065
Type:initiation region
Name:Rb1cc1_1
Description:RB1-inducible coiled-coil 1
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_6.0513,097,339 - 13,097,399EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
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)
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
SS/Jr (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
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)
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
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)
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
WKY/NHsd (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
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
5 17828179 17828180 T A snv NIG-III/Hok (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309346 AgrOrtholog
Ensembl Genes ENSRNOG00000006833 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060201 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061884 ENTREZGENE, UniProtKB/TrEMBL
InterPro ATG11 UniProtKB/TrEMBL
  Autophagy-rel_prot_11 UniProtKB/TrEMBL
  Ubiquitin-rel_dom UniProtKB/TrEMBL
KEGG Report rno:312927 UniProtKB/TrEMBL
NCBI Gene 312927 ENTREZGENE
PANTHER PTHR13222 UniProtKB/TrEMBL
Pfam ATG11 UniProtKB/TrEMBL
PhenoGen Rb1cc1 PhenoGen
Superfamily-SCOP SSF54236 UniProtKB/TrEMBL
UniProt D3ZHK4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Rb1cc1  RB1-inducible coiled-coil 1   Rb1cc1_predicted  RB1-inducible coiled-coil 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Rb1cc1_predicted  RB1-inducible coiled-coil 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED