Rubcnl (rubicon like autophagy enhancer) - Rat Genome Database

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Gene: Rubcnl (rubicon like autophagy enhancer) Rattus norvegicus
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Symbol: Rubcnl
Name: rubicon like autophagy enhancer
RGD ID: 1304929
Description: Predicted to enable phosphatidylinositol-3-phosphate binding activity; phosphatidylinositol-4-phosphate binding activity; and phosphatidylinositol-5-phosphate binding activity. Predicted to be involved in macroautophagy; regulation of glycogen metabolic process; and regulation of lipid metabolic process. Predicted to be active in autophagosome membrane. Orthologous to human RUBCNL (rubicon like autophagy enhancer); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC290403; RGD1304929; rubicon like autophagy regulator; RUN and cysteine rich domain containing beclin 1 interacting protein like; similar to chromosome 13 open reading frame 18; uncharacterized protein KIAA0226-like homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81556,741,897 - 56,807,086 (+)NCBIGRCr8
mRatBN7.21550,332,458 - 50,377,494 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1550,332,418 - 50,400,849 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01557,065,512 - 57,109,197 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1557,065,428 - 57,102,599 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01560,777,541 - 60,821,362 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41555,894,968 - 55,913,448 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11555,815,486 - 55,929,226 (+)NCBI
Celera1549,964,999 - 50,008,655 (+)NCBICelera
Cytogenetic Map15q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:28306502   PMID:30704899  


Genomics

Comparative Map Data
Rubcnl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81556,741,897 - 56,807,086 (+)NCBIGRCr8
mRatBN7.21550,332,458 - 50,377,494 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1550,332,418 - 50,400,849 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01557,065,512 - 57,109,197 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1557,065,428 - 57,102,599 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01560,777,541 - 60,821,362 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41555,894,968 - 55,913,448 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11555,815,486 - 55,929,226 (+)NCBI
Celera1549,964,999 - 50,008,655 (+)NCBICelera
Cytogenetic Map15q11NCBI
RUBCNL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381346,334,681 - 46,390,042 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1346,334,681 - 46,438,190 (-)EnsemblGRCh38hg38GRCh38
GRCh371346,908,816 - 46,964,177 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361345,814,137 - 45,859,636 (-)NCBINCBI36Build 36hg18NCBI36
Build 341345,815,100 - 45,859,385NCBI
Celera1327,971,122 - 28,016,591 (-)NCBICelera
Cytogenetic Map13q14.13NCBI
HuRef1327,713,683 - 27,759,154 (-)NCBIHuRef
CHM1_11346,884,932 - 46,930,398 (-)NCBICHM1_1
T2T-CHM13v2.01345,555,685 - 45,611,047 (-)NCBIT2T-CHM13v2.0
Rubcnl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391475,253,467 - 75,289,977 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1475,253,467 - 75,289,972 (+)EnsemblGRCm39 Ensembl
GRCm381475,015,987 - 75,052,537 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1475,016,027 - 75,052,532 (+)EnsemblGRCm38mm10GRCm38
MGSCv371475,415,834 - 75,452,339 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361473,736,988 - 73,786,572 (+)NCBIMGSCv36mm8
Celera1472,515,864 - 72,552,426 (+)NCBICelera
Cytogenetic Map14D3NCBI
cM Map1439.53NCBI
Rubcnl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955431140,922 - 206,951 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955431140,999 - 206,570 (-)NCBIChiLan1.0ChiLan1.0
RUBCNL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21444,953,710 - 45,049,079 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11336,007,854 - 36,111,800 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01326,594,545 - 26,600,412 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RUBCNL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1224,874,384 - 4,903,044 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl224,874,575 - 4,903,033 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha224,916,030 - 4,953,319 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0224,980,314 - 5,017,734 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl224,976,624 - 5,016,959 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1224,762,415 - 4,800,374 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0224,825,919 - 4,863,052 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0224,830,727 - 4,868,748 (+)NCBIUU_Cfam_GSD_1.0
Rubcnl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945156,428,120 - 156,521,426 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004936857839,418 - 870,961 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RUBCNL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1120,995,688 - 21,036,014 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11120,995,439 - 21,036,429 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21121,427,767 - 21,445,259 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RUBCNL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1324,400,507 - 24,445,514 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl324,399,500 - 24,430,601 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605719,554,526 - 19,600,019 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rubcnl
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247488,605,272 - 8,652,785 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rubcnl
383 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:22
Count of miRNA genes:21
Interacting mature miRNAs:22
Transcripts:ENSRNOT00000039518
Prediction methods: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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat


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 2 11 1
Low 1 21 54 38 8 38 7 9 25 30 36 11 7
Below cutoff 22 3 3 3 1 2 49 5 4 1

Sequence


RefSeq Acc Id: ENSRNOT00000039518   ⟹   ENSRNOP00000035595
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1550,332,418 - 50,400,849 (+)Ensembl
Rnor_6.0 Ensembl1557,065,428 - 57,102,599 (+)Ensembl
RefSeq Acc Id: XM_008770905   ⟹   XP_008769127
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81556,741,897 - 56,781,917 (+)NCBI
mRatBN7.21550,332,458 - 50,370,226 (+)NCBI
Rnor_6.01557,065,512 - 57,103,301 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039093952   ⟹   XP_038949880
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81556,742,289 - 56,781,917 (+)NCBI
mRatBN7.21550,332,858 - 50,370,226 (+)NCBI
RefSeq Acc Id: XM_039093953   ⟹   XP_038949881
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81556,742,289 - 56,807,086 (+)NCBI
mRatBN7.21550,332,858 - 50,377,494 (+)NCBI
Protein Sequences
Protein RefSeqs XP_008769127 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949880 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949881 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02285 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000035595
  ENSRNOP00000035595.6
RefSeq Acc Id: XP_008769127   ⟸   XM_008770905
- Peptide Label: isoform X1
- UniProtKB: D4A680 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000035595   ⟸   ENSRNOT00000039518
RefSeq Acc Id: XP_038949881   ⟸   XM_039093953
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038949880   ⟸   XM_039093952
- Peptide Label: isoform X1
- UniProtKB: D4A680 (UniProtKB/TrEMBL)
Protein Domains
Rubicon Homology

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A680-F1-model_v2 AlphaFold D4A680 1-681 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304929 AgrOrtholog
BioCyc Gene G2FUF-13139 BioCyc
Ensembl Genes ENSRNOG00000022760 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039518.7 UniProtKB/TrEMBL
InterPro DUF4206 UniProtKB/TrEMBL
  RUBC_PIKBD UniProtKB/TrEMBL
KEGG Report rno:290403 UniProtKB/TrEMBL
NCBI Gene 290403 ENTREZGENE
PANTHER PHOX (PX) DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
  PROTEIN ASSOCIATED WITH UVRAG AS AUTOPHAGY ENHANCER UniProtKB/TrEMBL
Pfam DUF4206 UniProtKB/TrEMBL
  RUBC_PIKBD UniProtKB/TrEMBL
PhenoGen Rubcnl PhenoGen
RatGTEx ENSRNOG00000022760 RatGTEx
SMART DUF4206 UniProtKB/TrEMBL
UniProt D4A680 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-02 Rubcnl  rubicon like autophagy enhancer  Rubcnl  rubicon like autophagy regulator  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2018-12-10 Rubcnl  rubicon like autophagy regulator  Rubcnl  RUN and cysteine rich domain containing beclin 1 interacting protein like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-08-24 Rubcnl  RUN and cysteine rich domain containing beclin 1 interacting protein like  RGD1304929  similar to chromosome 13 open reading frame 18  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1304929  similar to chromosome 13 open reading frame 18   RGD1304929_predicted  similar to chromosome 13 open reading frame 18 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1304929_predicted  similar to chromosome 13 open reading frame 18 (predicted)  LOC290403_predicted  similar to chromosome 13 open reading frame 18 (predicted)  Symbol and Name status set to approved 1331353 APPROVED