Plant Circular RNA Database

Detail information of Zm00001d014640_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d014640_circ_g.1
					
						ID in PlantcircBase
						zma_circ_001976
					
						Alias
						circ2108
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 56927373-56927765  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d014640						
					
						Parent gene annotation
						
							E3 ubiquitin-protein ligase BRE1-like 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d014640_circ_g.2 						
					
						Support reads
						3
					
						Tissues
						seedling leaves
					
						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  
						
							GT-CA							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
						Zm00001d014640_T009:2
Zm00001d014640_T019:2
Zm00001d014640_T013:1
Zm00001d014640_T010:2
Zm00001d014640_T014:1
Zm00001d014640_T004:2
Zm00001d014640_T006:2
Zm00001d014640_T012:2
Zm00001d014640_T008:2
Zm00001d014640_T002:2
Zm00001d014640_T034:1
Zm00001d014640_T020:2
Zm00001d014640_T030:2
Zm00001d014640_T011:2
Zm00001d014640_T029:2
Zm00001d014640_T035:1
Zm00001d014640_T036:1
Zm00001d014640_T018:2
Zm00001d014640_T027:2
Zm00001d014640_T033:1
Zm00001d014640_T007:2
Zm00001d014640_T003:2
Zm00001d014640_T005:2

General Information
CircRNA Name	Zm00001d014640_circ_g.1
ID in PlantcircBase	zma_circ_001976
Alias	circ2108
Organism	Zea mays
Position	chr5: 56927373-56927765 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d014640
Parent gene annotation	E3 ubiquitin-protein ligase BRE1-like 1
Parent gene strand	+
Alternative splicing	Zm00001d014640_circ_g.2
Support reads	3
Tissues	seedling leaves
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	GT-CA 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	Zm00001d014640_T009:2 Zm00001d014640_T019:2 Zm00001d014640_T013:1 Zm00001d014640_T010:2 Zm00001d014640_T014:1 Zm00001d014640_T004:2 Zm00001d014640_T006:2 Zm00001d014640_T012:2 Zm00001d014640_T008:2 Zm00001d014640_T002:2 Zm00001d014640_T034:1 Zm00001d014640_T020:2 Zm00001d014640_T030:2 Zm00001d014640_T011:2 Zm00001d014640_T029:2 Zm00001d014640_T035:1 Zm00001d014640_T036:1 Zm00001d014640_T018:2 Zm00001d014640_T027:2 Zm00001d014640_T033:1 Zm00001d014640_T007:2 Zm00001d014640_T003:2 Zm00001d014640_T005:2

			
						 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  
						
							CCTTTCTCAAATCATAACAAATCTTAGGCAGTTCAAGCTTAGCTGAATGTCAACTTGCCTCCAC
GTGCAAGATCCCAGAAACATTGCTATGTCTCGTCCGgatcaaactctagatattgccactctac
gtcccagcatcctatgaccacatggtttagacagtgctgtccaggtggatgatgaattgtggtg
cccaaacg

						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
						
							GATCAAACTCTAGATATTGCCACTCTACGTCCCAGCATCCTATGACCACATGGTTTAGACAGTG
CTGTCCAGGTGGATGATGAATTGTGGTGCCCAAACGGAGGCACGTGGCACGCCTCTTGAAGATA
GGTAAATTATGTGCATCTTGTCAGTTCCTTGAACATACTATAAGATCATGTACCTCTCTAAGGT
CTAAGACAAATAAGTGCTCTTAACACTCTACATCACCATGCACAGGCACTGGTTGGAAACAGAT
TTTGTTGGCGCTCCAAGAGTTCATACTTATGTACTTTCCTTTCTCAAATCATAACAAATCTTAG
GCAGTTCAAGCTTAGCTGAATGTCAACTTGCCTCCACGTGCAAGATCCCAGAAACATTGCTATG
TCTCGTCCG

Sequences
Splice junction sequence	CCTTTCTCAAATCATAACAAATCTTAGGCAGTTCAAGCTTAGCTGAATGTCAACTTGCCTCCAC GTGCAAGATCCCAGAAACATTGCTATGTCTCGTCCGgatcaaactctagatattgccactctac gtcccagcatcctatgaccacatggtttagacagtgctgtccaggtggatgatgaattgtggtg cccaaacg
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	GATCAAACTCTAGATATTGCCACTCTACGTCCCAGCATCCTATGACCACATGGTTTAGACAGTG CTGTCCAGGTGGATGATGAATTGTGGTGCCCAAACGGAGGCACGTGGCACGCCTCTTGAAGATA GGTAAATTATGTGCATCTTGTCAGTTCCTTGAACATACTATAAGATCATGTACCTCTCTAAGGT CTAAGACAAATAAGTGCTCTTAACACTCTACATCACCATGCACAGGCACTGGTTGGAAACAGAT TTTGTTGGCGCTCCAAGAGTTCATACTTATGTACTTTCCTTTCTCAAATCATAACAAATCTTAG GCAGTTCAAGCTTAGCTGAATGTCAACTTGCCTCCACGTGCAAGATCCCAGAAACATTGCTATG TCTCGTCCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.24602852

Conservation Information
Conserved circRNAs	NA
PMCS	0.24602852

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							56927713-56927414(+)
56927415-56927382(+)
						
						Potential amino acid sequence
						
							MSTCLHVQDPRNIAMSRPDQTLDIATLRPSIL*(+)
MTTWFRQCCPGSSSLAECQLASTCKIPETLLCLVRIKL*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	56927713-56927414(+) 56927415-56927382(+)
Potential amino acid sequence	MSTCLHVQDPRNIAMSRPDQTLDIATLRPSIL(+) MTTWFRQCCPGSSSLAECQLASTCKIPETLLCLVRIKL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d014640_circ_g.1

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