Plant Circular RNA Database

Detail information of Zm00001d028818_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d028818_circ_g.3
					
						ID in PlantcircBase
						zma_circ_003406
					
						Alias
						stemctrl_test_circ_003519
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 47588304-47588631  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d028818						
					
						Parent gene annotation
						
							Calpain-type cysteine protease DEK1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						stem
					
						Exon boundary  
						
							No-No							"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
						Zm00001d028818_T003:2
Zm00001d028818_T029:2
Zm00001d028818_T044:2
Zm00001d028818_T005:2
Zm00001d028818_T050:2
Zm00001d028818_T035:2
Zm00001d028818_T057:2
Zm00001d028818_T032:2
Zm00001d028818_T040:2
Zm00001d028818_T036:2
Zm00001d028818_T019:2
Zm00001d028818_T034:2
Zm00001d028818_T027:2
Zm00001d028818_T026:2
Zm00001d028818_T053:2
Zm00001d028818_T051:2
Zm00001d028818_T047:2
Zm00001d028818_T012:2
Zm00001d028818_T015:2
Zm00001d028818_T042:2
Zm00001d028818_T009:2
Zm00001d028818_T016:2
Zm00001d028818_T008:2
Zm00001d028818_T043:2
Zm00001d028818_T055:2
Zm00001d028818_T046:2
Zm00001d028818_T014:2
Zm00001d028818_T013:2
Zm00001d028818_T038:2
Zm00001d028818_T006:2
Zm00001d028818_T010:2
Zm00001d028818_T056:2
Zm00001d028818_T024:2
Zm00001d028818_T004:2
Zm00001d028818_T028:2
Zm00001d028818_T017:2
Zm00001d028818_T031:2
Zm00001d028818_T011:2
Zm00001d028818_T054:2

General Information
CircRNA Name	Zm00001d028818_circ_g.3
ID in PlantcircBase	zma_circ_003406
Alias	stemctrl_test_circ_003519
Organism	Zea mays
Position	chr1: 47588304-47588631 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d028818
Parent gene annotation	Calpain-type cysteine protease DEK1
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
Tissues	stem
Exon boundary	No-No "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	Zm00001d028818_T003:2 Zm00001d028818_T029:2 Zm00001d028818_T044:2 Zm00001d028818_T005:2 Zm00001d028818_T050:2 Zm00001d028818_T035:2 Zm00001d028818_T057:2 Zm00001d028818_T032:2 Zm00001d028818_T040:2 Zm00001d028818_T036:2 Zm00001d028818_T019:2 Zm00001d028818_T034:2 Zm00001d028818_T027:2 Zm00001d028818_T026:2 Zm00001d028818_T053:2 Zm00001d028818_T051:2 Zm00001d028818_T047:2 Zm00001d028818_T012:2 Zm00001d028818_T015:2 Zm00001d028818_T042:2 Zm00001d028818_T009:2 Zm00001d028818_T016:2 Zm00001d028818_T008:2 Zm00001d028818_T043:2 Zm00001d028818_T055:2 Zm00001d028818_T046:2 Zm00001d028818_T014:2 Zm00001d028818_T013:2 Zm00001d028818_T038:2 Zm00001d028818_T006:2 Zm00001d028818_T010:2 Zm00001d028818_T056:2 Zm00001d028818_T024:2 Zm00001d028818_T004:2 Zm00001d028818_T028:2 Zm00001d028818_T017:2 Zm00001d028818_T031:2 Zm00001d028818_T011:2 Zm00001d028818_T054:2

			
						 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  
						
							CAATCTAGCCATGATTCTTCAATGTTTTACATTGGAATGAGGATACTCAAGACACAGGGCTGCC
GTGCTGCTTACAATATCTACATGCATGAAAGCGCTGggtggttgccaagattatgactcgtggc
accaaaatccacagtatcgacttagagtaacaggacgtgatgcactataccctgttcacgtttt
tattaccc

						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
						
							GGTGGTTGCCAAGATTATGACTCGTGGCACCAAAATCCACAGTATCGACTTAGAGTAACAGGAC
GTGATGCACTATACCCTGTTCACGTTTTTATTACCCTTACTCAGGTATGTTGGAACCTACCTAT
CAACCTAACCAGGAGAAGCACAATGATGTTTTATCTGTGTAAATTTCATGCTTTTCAGGGTGTT
GGTTTCTCTAGAAAGACGAATGGTTTTCGGAACTACCAATCTAGCCATGATTCTTCAATGTTTT
ACATTGGAATGAGGATACTCAAGACACAGGGCTGCCGTGCTGCTTACAATATCTACATGCATGA
AAGCGCTG

Sequences
Splice junction sequence	CAATCTAGCCATGATTCTTCAATGTTTTACATTGGAATGAGGATACTCAAGACACAGGGCTGCC GTGCTGCTTACAATATCTACATGCATGAAAGCGCTGggtggttgccaagattatgactcgtggc accaaaatccacagtatcgacttagagtaacaggacgtgatgcactataccctgttcacgtttt tattaccc
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	GGTGGTTGCCAAGATTATGACTCGTGGCACCAAAATCCACAGTATCGACTTAGAGTAACAGGAC GTGATGCACTATACCCTGTTCACGTTTTTATTACCCTTACTCAGGTATGTTGGAACCTACCTAT CAACCTAACCAGGAGAAGCACAATGATGTTTTATCTGTGTAAATTTCATGCTTTTCAGGGTGTT GGTTTCTCTAGAAAGACGAATGGTTTTCGGAACTACCAATCTAGCCATGATTCTTCAATGTTTT ACATTGGAATGAGGATACTCAAGACACAGGGCTGCCGTGCTGCTTACAATATCTACATGCATGA AAGCGCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.359598222

Conservation Information
Conserved circRNAs	NA
PMCS	0.359598222

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tang et al., 2018

circRNA

Detail information of Zm00001d028818_circ_g.3

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