Plant Circular RNA Database

Detail information of Zm00001d023640_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d023640_circ_g.4
					
						ID in PlantcircBase
						zma_circ_010166
					
						Alias
						Zm10circ00012, GRMZM2G303655_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 13323882-13324639  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d023640						
					
						Parent gene annotation
						
							Ubiquitin carboxyl-terminal hydrolase 13
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d023640_circ_g.1 Zm00001d023640_circ_g.2 Zm00001d023640_circ_g.3 Zm00001d023640_circ_g.5 Zm00001d023640_circ_g.6 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							CT-AC							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						Zm00001d023640_T015:4
Zm00001d023640_T004:4
Zm00001d023640_T023:3
Zm00001d023640_T032:4
Zm00001d023640_T033:4
Zm00001d023640_T022:4
Zm00001d023640_T005:4
Zm00001d023640_T008:4
Zm00001d023640_T001:4
Zm00001d023640_T034:4
Zm00001d023640_T018:4
Zm00001d023640_T012:4
Zm00001d023640_T024:4
Zm00001d023640_T011:4
Zm00001d023640_T028:4
Zm00001d023640_T020:4
Zm00001d023640_T003:4
Zm00001d023640_T006:4
Zm00001d023640_T021:4
Zm00001d023640_T013:4
Zm00001d023640_T009:4
Zm00001d023640_T043:4
Zm00001d023640_T042:4
Zm00001d023640_T044:4
Zm00001d023640_T014:4
Zm00001d023640_T007:4
Zm00001d023640_T019:4
Zm00001d023640_T016:4
Zm00001d023640_T017:4
Zm00001d023640_T002:4
Zm00001d023640_T010:4

General Information
CircRNA Name	Zm00001d023640_circ_g.4
ID in PlantcircBase	zma_circ_010166
Alias	Zm10circ00012, GRMZM2G303655_C2
Organism	Zea mays
Position	chr10: 13323882-13324639 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d023640
Parent gene annotation	Ubiquitin carboxyl-terminal hydrolase 13
Parent gene strand	-
Alternative splicing	Zm00001d023640_circ_g.1 Zm00001d023640_circ_g.2 Zm00001d023640_circ_g.3 Zm00001d023640_circ_g.5 Zm00001d023640_circ_g.6
Support reads	NA
Tissues	leaf, endosperm
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	CT-AC The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Zm00001d023640_T015:4 Zm00001d023640_T004:4 Zm00001d023640_T023:3 Zm00001d023640_T032:4 Zm00001d023640_T033:4 Zm00001d023640_T022:4 Zm00001d023640_T005:4 Zm00001d023640_T008:4 Zm00001d023640_T001:4 Zm00001d023640_T034:4 Zm00001d023640_T018:4 Zm00001d023640_T012:4 Zm00001d023640_T024:4 Zm00001d023640_T011:4 Zm00001d023640_T028:4 Zm00001d023640_T020:4 Zm00001d023640_T003:4 Zm00001d023640_T006:4 Zm00001d023640_T021:4 Zm00001d023640_T013:4 Zm00001d023640_T009:4 Zm00001d023640_T043:4 Zm00001d023640_T042:4 Zm00001d023640_T044:4 Zm00001d023640_T014:4 Zm00001d023640_T007:4 Zm00001d023640_T019:4 Zm00001d023640_T016:4 Zm00001d023640_T017:4 Zm00001d023640_T002:4 Zm00001d023640_T010:4

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
						 Sequences
					
						Splice junction sequence  
						
							ACAAATAAAAATAACATTTTACCGGTCCAAGTTCAACTTCCAGAAACAGCTTCAGCTCAGCATT
GTGTGCCTTATTTGAGACTTCCCTAAGCTGCCCGACctgactagagcggaaagtaagtttcttg
tcaatatgttcgcacatcacatttggctcaaacttaatttcctgcagaataagaatgtcaaaag
catcagaa

						Assembled circRNA sequence  
						
							NA
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

						Full-length trsnacripts
						
							NA						
					
						Genomic sequence
						
							CTGACTAGAGCGGAAAGTAAGTTTCTTGTCAATATGTTCGCACATCACATTTGGCTCAAACTTA
ATTTCCTGCAGAATAAGAATGTCAAAAGCATCAGAATATTCAACTTGGGAAGATCATCACGACA
TCGTTAAGTGCACAACATTTTACTACATTAAATTAATTATTGAGCAGGATACACTCGAACAATC
AAGGACTTTAACAGATTTTATGAGCACAAGGAGCACATAGGCAGAAAACATGCATACAGCAAGT
TAGAATGTGTACTCTAGAGAAATAAATACAGAATTGTGAAGCACCTCGTACAGCTCAATTTCTT
CATTTGGAGAAAATCCAGCCATTGCATTCAGTTTTGTCAATATTTCAGATGGCTTTCCCAGAGC
CTTCACAAAAAGCCTACCAACAAAACTGTAACAGCAGAGGATGTCGACATGTGTGTCATCTCTA
ATAGAAGTTCAACAGAATGATTGACAAATAGATTAACATGAAACATACTGAAGCTCTTCCTTCT
CAGCATTATAAAGCTTGAAGAAAAGAAGTATGTCTTCTTTGCTCTTCTCAGGTGGACGAATTGG
ACATAACTCCTATATAATTAATAATTAGAAACAACCAAGCATCTCAAAATCTAGAAGGCATAAA
CAAGAGGGAAAATAAAAGACAAATAAAAATAACATTTTACCGGTCCAAGTTCAACTTCCAGAAA
CAGCTTCAGCTCAGCATTGTGTGCCTTATTTGAGACTTCCCTAAGCTGCCCGAC

Sequences
Splice junction sequence	ACAAATAAAAATAACATTTTACCGGTCCAAGTTCAACTTCCAGAAACAGCTTCAGCTCAGCATT GTGTGCCTTATTTGAGACTTCCCTAAGCTGCCCGACctgactagagcggaaagtaagtttcttg tcaatatgttcgcacatcacatttggctcaaacttaatttcctgcagaataagaatgtcaaaag catcagaa
Assembled circRNA sequence	NA The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	NA
Genomic sequence	CTGACTAGAGCGGAAAGTAAGTTTCTTGTCAATATGTTCGCACATCACATTTGGCTCAAACTTA ATTTCCTGCAGAATAAGAATGTCAAAAGCATCAGAATATTCAACTTGGGAAGATCATCACGACA TCGTTAAGTGCACAACATTTTACTACATTAAATTAATTATTGAGCAGGATACACTCGAACAATC AAGGACTTTAACAGATTTTATGAGCACAAGGAGCACATAGGCAGAAAACATGCATACAGCAAGT TAGAATGTGTACTCTAGAGAAATAAATACAGAATTGTGAAGCACCTCGTACAGCTCAATTTCTT CATTTGGAGAAAATCCAGCCATTGCATTCAGTTTTGTCAATATTTCAGATGGCTTTCCCAGAGC CTTCACAAAAAGCCTACCAACAAAACTGTAACAGCAGAGGATGTCGACATGTGTGTCATCTCTA ATAGAAGTTCAACAGAATGATTGACAAATAGATTAACATGAAACATACTGAAGCTCTTCCTTCT CAGCATTATAAAGCTTGAAGAAAAGAAGTATGTCTTCTTTGCTCTTCTCAGGTGGACGAATTGG ACATAACTCCTATATAATTAATAATTAGAAACAACCAAGCATCTCAAAATCTAGAAGGCATAAA CAAGAGGGAAAATAAAAGACAAATAAAAATAACATTTTACCGGTCCAAGTTCAACTTCCAGAAA CAGCTTCAGCTCAGCATTGTGTGCCTTATTTGAGACTTCCCTAAGCTGCCCGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.184222845

Conservation Information
Conserved circRNAs	NA
PMCS	0.184222845

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13324424-13323882(+)
13324225-13323884(-)
						
						Potential amino acid sequence
						
							MSSLLFSGGRIGHNSGPSSTSRNSFSSALCALFETSLSCPT*(+)
MAGFSPNEEIELYEEIKFEPNVMCEHIDKKLTFRSSQVGQLREVSNKAHNAELKLFLEVELGPE
LCPIRPPEKSKEDILLFFKLYNAEKEELHFVGRLFVKALGKPSEILTKLNAMAGFSPNEEIELY
EEIKFEPNVMCEHIDKKLTFRSSQVGQLREVSNKAHNAELKLFLEVELGPELCPIRPPEKSKED
ILLFFKLYNAEKEELHFVGRLFVKALGKPSEILTKLNAMAGFSPNEEIELYEEIKFEPNVMCEH
IDKKLTFRSSQVGQLREVSNKAHNAELKLFLEVELGPELCPIRPPEKSKEDILLFFKLYNAEKE
ELHFVGRLFVKALGKPSEILTKLNAMAGFSPNEEIELYEEIKFEPNVMCEHIDKKLTFRSSQ(-
)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13324424-13323882(+) 13324225-13323884(-)
Potential amino acid sequence	MSSLLFSGGRIGHNSGPSSTSRNSFSSALCALFETSLSCPT*(+) MAGFSPNEEIELYEEIKFEPNVMCEHIDKKLTFRSSQVGQLREVSNKAHNAELKLFLEVELGPE LCPIRPPEKSKEDILLFFKLYNAEKEELHFVGRLFVKALGKPSEILTKLNAMAGFSPNEEIELY EEIKFEPNVMCEHIDKKLTFRSSQVGQLREVSNKAHNAELKLFLEVELGPELCPIRPPEKSKED ILLFFKLYNAEKEELHFVGRLFVKALGKPSEILTKLNAMAGFSPNEEIELYEEIKFEPNVMCEH IDKKLTFRSSQVGQLREVSNKAHNAELKLFLEVELGPELCPIRPPEKSKEDILLFFKLYNAEKE ELHFVGRLFVKALGKPSEILTKLNAMAGFSPNEEIELYEEIKFEPNVMCEHIDKKLTFRSSQ(- )
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020;Zhang et al., 2019

circRNA

Detail information of Zm00001d023640_circ_g.4

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