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

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Pathways
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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 enable protein kinase binding activity and protein-membrane adaptor activity. Predicted to be involved in several processes, including macroautophagy; positive regulation of autophagy; and regulation of protein modification process. Predicted to act upstream of or within several processes, including defense response to symbiont; positive regulation of cell size; and regulation of signal transduction. Predicted to be located in cytosol; nuclear membrane; and vacuole. Predicted to be part of Atg1/ULK1 kinase complex. Predicted to be active in phagophore assembly site membrane. 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 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC312927; RB1-inducible coiled-coil protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8517,948,522 - 18,012,434 (-)NCBIGRCr8
mRatBN7.2513,161,648 - 13,225,560 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl513,161,648 - 13,225,560 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx515,333,280 - 15,397,217 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0516,965,204 - 17,029,035 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0516,667,973 - 16,731,910 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0513,033,918 - 13,097,369 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl513,033,918 - 13,097,341 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0517,805,493 - 17,868,916 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4513,301,486 - 13,365,398 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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

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

References - curated
# Reference Title Reference Citation
1. Truncating mutations of RB1CC1 in human breast cancer. Chano T, etal., Nat Genet. 2002 Jul;31(3):285-8. Epub 2002 Jun 17.
2. 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.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. Mammalian autophagy: core molecular machinery and signaling regulation. Yang Z and Klionsky DJ, Curr Opin Cell Biol. 2010 Apr;22(2):124-31. Epub 2009 Dec 23.
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
GRCr8517,948,522 - 18,012,434 (-)NCBIGRCr8
mRatBN7.2513,161,648 - 13,225,560 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl513,161,648 - 13,225,560 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx515,333,280 - 15,397,217 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0516,965,204 - 17,029,035 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0516,667,973 - 16,731,910 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0513,033,918 - 13,097,369 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl513,033,918 - 13,097,341 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0517,805,493 - 17,868,916 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4513,301,486 - 13,365,398 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38852,622,458 - 52,714,435 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl852,622,458 - 52,745,843 (-)EnsemblGRCh38hg38GRCh38
GRCh37853,535,018 - 53,626,995 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36853,697,571 - 53,789,579 (-)NCBINCBI36Build 36hg18NCBI36
Build 34853,697,571 - 53,789,545NCBI
Celera849,525,378 - 49,617,590 (-)NCBICelera
Cytogenetic Map8q11.23NCBI
HuRef849,002,571 - 49,094,645 (-)NCBIHuRef
CHM1_1853,587,331 - 53,679,316 (-)NCBICHM1_1
T2T-CHM13v2.0852,998,490 - 53,090,429 (-)NCBIT2T-CHM13v2.0
Rb1cc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3916,284,858 - 6,346,599 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl16,276,421 - 6,346,872 (+)EnsemblGRCm39 Ensembl
GRCm3816,214,634 - 6,276,375 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl16,206,197 - 6,276,648 (+)EnsemblGRCm38mm10GRCm38
MGSCv3716,204,743 - 6,266,185 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3616,204,743 - 6,265,656 (+)NCBIMGSCv36mm8
Celera16,202,698 - 6,263,115 (+)NCBICelera
Cytogenetic Map1A1NCBI
cM Map11.89NCBI
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
NHGRI_mPanPan1-v2768,258,420 - 68,352,784 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1843,983,056 - 44,077,344 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0849,046,830 - 49,138,795 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1846,430,131 - 46,521,722 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl846,430,131 - 46,521,722 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0294,511,613 - 4,608,379 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl294,511,616 - 4,608,599 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1294,442,480 - 4,540,952 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0294,668,260 - 4,766,907 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0294,742,370 - 4,841,030 (-)NCBIUU_Cfam_GSD_1.0
Rb1cc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530375,070,885 - 75,145,333 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936590260,685 - 334,721 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936590260,685 - 335,143 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RB1CC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl477,594,324 - 77,649,548 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1477,593,204 - 77,649,551 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
RB1CC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1848,726,551 - 48,818,027 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl848,724,393 - 48,817,928 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603993,172,844 - 93,267,874 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rb1cc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247352,778,191 - 2,860,762 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rb1cc1
252 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
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)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat

Markers in Region
RH127582  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2513,162,882 - 13,163,074 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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


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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl513,161,648 - 13,225,560 (-)Ensembl
Rnor_6.0 Ensembl513,033,918 - 13,097,341 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097670   ⟹   ENSRNOP00000093616
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl513,161,648 - 13,225,560 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118113   ⟹   ENSRNOP00000093981
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl513,163,441 - 13,225,560 (-)Ensembl
RefSeq Acc Id: NM_001107901   ⟹   NP_001101371
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8517,948,522 - 18,012,434 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8517,949,239 - 18,012,269 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8517,949,239 - 17,981,730 (-)NCBI
mRatBN7.2513,162,362 - 13,194,853 (-)NCBI
RefSeq Acc Id: XM_063287519   ⟹   XP_063143589
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8517,957,067 - 18,012,269 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001101371   ⟸   NM_001107901
- UniProtKB: D3ZHK4 (UniProtKB/TrEMBL),   A6JFI0 (UniProtKB/TrEMBL),   A0A8I6AJ48 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237856   ⟸   XM_006237794
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AJ48 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000060201   ⟸   ENSRNOT00000061884
RefSeq Acc Id: XP_038965677   ⟸   XM_039109749
- Peptide Label: isoform X3
- UniProtKB: A0A8I6AJ48 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000093616   ⟸   ENSRNOT00000097670
RefSeq Acc Id: ENSRNOP00000093981   ⟸   ENSRNOT00000118113
RefSeq Acc Id: XP_063143589   ⟸   XM_063287519
- Peptide Label: isoform X2
- UniProtKB: A0A8I6AIK3 (UniProtKB/TrEMBL)
Protein Domains
Autophagy-related protein 11 C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZHK4-F1-model_v2 AlphaFold D3ZHK4 1-1588 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309346 AgrOrtholog
BioCyc Gene G2FUF-42174 BioCyc
Ensembl Genes ENSRNOG00000006833 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061884 ENTREZGENE
  ENSRNOT00000061884.3 UniProtKB/TrEMBL
  ENSRNOT00000097670.1 UniProtKB/TrEMBL
  ENSRNOT00000118113.1 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
  RB1-INDUCIBLE COILED-COIL PROTEIN 1 UniProtKB/TrEMBL
Pfam ATG11 UniProtKB/TrEMBL
PhenoGen Rb1cc1 PhenoGen
RatGTEx ENSRNOG00000006833 RatGTEx
Superfamily-SCOP SSF54236 UniProtKB/TrEMBL
UniProt A0A8I6AIK3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AJ48 ENTREZGENE, UniProtKB/TrEMBL
  A6JFI0 ENTREZGENE, UniProtKB/TrEMBL
  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