Rubcn (rubicon autophagy regulator) - Rat Genome Database

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Gene: Rubcn (rubicon autophagy regulator) Rattus norvegicus
Analyze
Symbol: Rubcn
Name: rubicon autophagy regulator
RGD ID: 1305422
Description: Predicted to be involved in negative regulation of autophagosome maturation; negative regulation of endocytosis; and negative regulation of phosphatidylinositol 3-kinase activity. Predicted to localize to cytosol; endosome; and nucleoplasm. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 15. Orthologous to human RUBCN (rubicon autophagy regulator); PARTICIPATES IN autophagy pathway; INTERACTS WITH 3,3',4,4',5-pentachlorobiphenyl; bisphenol A; 17beta-estradiol (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC303885; RGD1305422; RUN and cysteine rich domain containing beclin 1 interacting protein; RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein; similar to mKIAA0226 protein
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
mRatBN7.21167,907,534 - 67,964,347 (+)NCBI
Rnor_6.0 Ensembl1171,151,132 - 71,197,035 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01171,150,506 - 71,199,254 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01174,228,171 - 74,284,327 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41169,735,303 - 69,784,725 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11169,791,474 - 69,840,095 (+)NCBI
Celera1167,351,336 - 67,408,299 (+)NCBICelera
Cytogenetic Map11q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:19270696   PMID:21062745  


Genomics

Comparative Map Data
Rubcn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21167,907,534 - 67,964,347 (+)NCBI
Rnor_6.0 Ensembl1171,151,132 - 71,197,035 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01171,150,506 - 71,199,254 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01174,228,171 - 74,284,327 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41169,735,303 - 69,784,725 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11169,791,474 - 69,840,095 (+)NCBI
Celera1167,351,336 - 67,408,299 (+)NCBICelera
Cytogenetic Map11q22NCBI
RUBCN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3197,668,867 - 197,749,727 (-)EnsemblGRCh38hg38GRCh38
GRCh383197,668,867 - 197,749,820 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh373197,395,738 - 197,476,570 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363198,882,656 - 198,948,170 (-)NCBINCBI36hg18NCBI36
Celera3196,014,953 - 196,093,675 (-)NCBI
Cytogenetic Map3q29NCBI
HuRef3194,700,863 - 194,779,394 (-)NCBIHuRef
CHM1_13197,369,087 - 197,447,452 (-)NCBICHM1_1
Rubcn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391632,642,072 - 32,698,121 (-)NCBIGRCm39mm39
GRCm39 Ensembl1632,642,073 - 32,698,136 (-)Ensembl
GRCm381632,821,702 - 32,877,729 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1632,821,703 - 32,877,766 (-)EnsemblGRCm38mm10GRCm38
MGSCv371632,790,776 - 32,868,452 (-)NCBIGRCm37mm9NCBIm37
MGSCv361632,821,822 - 32,868,425 (-)NCBImm8
Celera1633,300,516 - 33,347,564 (-)NCBICelera
Cytogenetic Map16B3NCBI
Rubcn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542012,123,450 - 12,187,154 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542012,124,193 - 12,187,154 (+)NCBIChiLan1.0ChiLan1.0
RUBCN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13204,974,746 - 205,049,871 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3204,973,968 - 205,034,011 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03195,088,936 - 195,166,771 (-)NCBIMhudiblu_PPA_v0panPan3
RUBCN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13328,947,439 - 29,011,737 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3328,946,944 - 29,009,346 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3328,968,568 - 29,032,995 (+)NCBI
ROS_Cfam_1.03329,178,166 - 29,242,864 (+)NCBI
UMICH_Zoey_3.13328,974,845 - 29,039,065 (+)NCBI
UNSW_CanFamBas_1.03329,021,133 - 29,085,572 (+)NCBI
UU_Cfam_GSD_1.03329,641,226 - 29,705,388 (+)NCBI
Rubcn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602125,447,313 - 125,515,113 (-)NCBI
SpeTri2.0NW_004936784370,173 - 438,263 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RUBCN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13134,254,969 - 134,363,265 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113134,299,971 - 134,363,620 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213143,893,948 - 143,947,349 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RUBCN
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11591,401,565 - 91,468,837 (-)NCBI
ChlSab1.1 Ensembl1591,400,031 - 91,457,933 (-)Ensembl
Rubcn
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473061,040,848 - 61,111,998 (+)NCBI

Position Markers
RH127712  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21167,963,974 - 67,964,162 (+)MAPPER
Rnor_6.01171,198,882 - 71,199,069NCBIRnor6.0
Rnor_5.01174,283,955 - 74,284,142UniSTSRnor5.0
RGSC_v3.41169,784,353 - 69,784,540UniSTSRGSC3.4
Celera1167,407,927 - 67,408,114UniSTS
RH 3.4 Map11380.8UniSTS
Cytogenetic Map11q22UniSTS
RH128519  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21167,928,333 - 67,928,518 (+)MAPPER
Rnor_6.01171,163,352 - 71,163,536NCBIRnor6.0
Rnor_5.01174,248,283 - 74,248,467UniSTSRnor5.0
RGSC_v3.41169,748,437 - 69,748,621UniSTSRGSC3.4
Celera1167,372,026 - 67,372,210UniSTS
RH 3.4 Map11390.4UniSTS
Cytogenetic Map11q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113215552082443118Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113590063480900634Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114309033886714631Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114658320986714631Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
4889859Pur28Proteinuria QTL 2819.50.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114790104978471527Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115785881090463843Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115994302390463843Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)116010984287141948Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)116265336586714475Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116265336586714483Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116449467190463843Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116934231986312439Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116964970890463843Rat


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 37 14 4 13 4 1 1 74 35 41 11 1
Low 6 43 37 6 37 7 10 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000082435   ⟹   ENSRNOP00000075115
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1171,151,132 - 71,197,035 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082594   ⟹   ENSRNOP00000073717
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1171,151,132 - 71,197,035 (+)Ensembl
RefSeq Acc Id: XM_001065343   ⟹   XP_001065343
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1167,358,576 - 67,408,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006221165   ⟹   XP_006221227
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1167,358,575 - 67,408,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006221166   ⟹   XP_006221228
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1167,351,336 - 67,408,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008776733   ⟹   XP_008774955
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1167,358,574 - 67,408,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598222   ⟹   XP_017453711
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01171,150,506 - 71,199,254 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039088921   ⟹   XP_038944849
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21167,915,184 - 67,964,347 (+)NCBI
RefSeq Acc Id: XM_039088922   ⟹   XP_038944850
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21167,915,185 - 67,964,347 (+)NCBI
RefSeq Acc Id: XM_039088923   ⟹   XP_038944851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21167,907,534 - 67,964,346 (+)NCBI
RefSeq Acc Id: XM_039088924   ⟹   XP_038944852
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21167,938,336 - 67,964,347 (+)NCBI
RefSeq Acc Id: XM_039088925   ⟹   XP_038944853
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21167,915,184 - 67,964,347 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_001065343   ⟸   XM_001065343
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006221228   ⟸   XM_006221166
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006221227   ⟸   XM_006221165
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008774955   ⟸   XM_008776733
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017453711   ⟸   XM_017598222
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000075115   ⟸   ENSRNOT00000082435
RefSeq Acc Id: ENSRNOP00000073717   ⟸   ENSRNOT00000082594
RefSeq Acc Id: XP_038944851   ⟸   XM_039088923
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944853   ⟸   XM_039088925
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038944849   ⟸   XM_039088921
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944850   ⟸   XM_039088922
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944852   ⟸   XM_039088924
- Peptide Label: isoform X4
Protein Domains
RUN

Transcriptome

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


Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305422 AgrOrtholog
Ensembl Genes ENSRNOG00000059880 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000073717 UniProtKB/TrEMBL
  ENSRNOP00000075115 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000082435 UniProtKB/TrEMBL
  ENSRNOT00000082594 UniProtKB/TrEMBL
Gene3D-CATH 1.20.58.900 UniProtKB/TrEMBL
InterPro Run_dom UniProtKB/TrEMBL
  Run_dom_sf UniProtKB/TrEMBL
  Zf-RING_9 UniProtKB/TrEMBL
NCBI Gene 303885 ENTREZGENE
Pfam RUN UniProtKB/TrEMBL
  zf-RING_9 UniProtKB/TrEMBL
PhenoGen Rubcn PhenoGen
PROSITE RUN UniProtKB/TrEMBL
SMART DUF4206 UniProtKB/TrEMBL
  RUN UniProtKB/TrEMBL
Superfamily-SCOP SSF140741 UniProtKB/TrEMBL
UniProt A0A0G2K687_RAT UniProtKB/TrEMBL
  A0A0G2K9T0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-12-10 Rubcn  rubicon autophagy regulator  Rubcn  RUN and cysteine rich domain containing beclin 1 interacting protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-03 Rubcn  RUN and cysteine rich domain containing beclin 1 interacting protein  Rubcn  RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-10-26 Rubcn  RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein  RGD1305422  similar to mKIAA0226 protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1305422  similar to mKIAA0226 protein   RGD1305422_predicted  similar to mKIAA0226 protein (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1305422_predicted  similar to mKIAA0226 protein (predicted)  LOC303885_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC303885_predicted  similar to mKIAA0226 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL