Plant Circular RNA Database

Detail information of Zm00001d042777_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d042777_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007731
					
						Alias
						zma_circ_0001244
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 179390515-179391264  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d042777						
					
						Parent gene annotation
						
							Basic leucine zipper protein; Liguleless2  
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d042777_circ_g.1 Zm00001d042777_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf, root
					
						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-AG							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
						Zm00001d042777_T006:2
Zm00001d042777_T013:1
Zm00001d042777_T004:2
Zm00001d042777_T012:2
Zm00001d042777_T011:2
Zm00001d042777_T008:2
Zm00001d042777_T014:1
Zm00001d042777_T007:2
Zm00001d042777_T001:1
Zm00001d042777_T010:2
Zm00001d042777_T009:2
Zm00001d042777_T005:2
Zm00001d042777_T003:2
Zm00001d042777_T002:2
Zm00001d042777_T015:1

General Information
CircRNA Name	Zm00001d042777_circ_g.3
ID in PlantcircBase	zma_circ_007731
Alias	zma_circ_0001244
Organism	Zea mays
Position	chr3: 179390515-179391264 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d042777
Parent gene annotation	Basic leucine zipper protein; Liguleless2
Parent gene strand	+
Alternative splicing	Zm00001d042777_circ_g.1 Zm00001d042777_circ_g.2
Support reads	NA
Tissues	leaf, root
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-AG 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	Zm00001d042777_T006:2 Zm00001d042777_T013:1 Zm00001d042777_T004:2 Zm00001d042777_T012:2 Zm00001d042777_T011:2 Zm00001d042777_T008:2 Zm00001d042777_T014:1 Zm00001d042777_T007:2 Zm00001d042777_T001:1 Zm00001d042777_T010:2 Zm00001d042777_T009:2 Zm00001d042777_T005:2 Zm00001d042777_T003:2 Zm00001d042777_T002:2 Zm00001d042777_T015:1

			
						 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  
						
							CGCCGCTGCGCCCGCTGCTGCCGCCCCGCCGAGCTTTCAGCAGCACCACCCGCTCCCGCTGCAG
CTGCACGGAGGAGAGGGAGGGGGAGACCATGACAAGcagcggcaggatatctcgcgggcgctgg
caccggcaggccccccacgctggagatcttcccttcgtggccaatgaggcaccaacagcagctg
cacagtgt

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 350
Transcript exons: 179390515-179390612,179391013-179391264
CAGCGGCAGGATATCTCGCGGGCGCTGGCACCGGCAGGCCCCCCACGCTGGAGATCTTCCCTTC
GTGGCCAATGAGGCACCAACAGCAGCTGCACAGTGGGAATTCGCAGTCAGTAGGGAGCACCGGC
ACTGACTCGAGCTCAGCTCAGAACACAATGTCTCAGATGGAGTTGGTGTCCCCAGCCTCCTCTG
CGCCGCGGCAGGAGGTCATGATGGTGACCACTGATGATTACAGCTACAAGCCAGGCCTCGCCGC
TGCGCCCGCTGCTGCCGCCCCGCCGAGCTTTCAGCAGCACCACCCGCTCCCGCTGCAGCTGCAC
GGAGGAGAGGGAGGGGGAGACCATGACAAG
						
						Genomic sequence
						
							CAGCGGCAGGATATCTCGCGGGCGCTGGCACCGGCAGGCCCCCCACGCTGGAGATCTTCCCTTC
GTGGCCAATGAGGCACCAACAGCAGCTGCACAGTGTAAAGGCCCCGCCACCTCCCGATGTCCCA
TGATCACTGATTCATGCATGCACGCATTCATTCATTCATTCATTCATCGCCTCGCCGCGCGCCC
GTCTCTCGTCGTCTCCTCCGCTGGCTCGTCATCGTCGCTGAACCCAAGAAAAGATGTGGCTGTT
TTTCTTGGTGATTCGCTCTCTGCATGTGGTCTGCACTCTGCATCTGCACCTGCAGGCTGCAGCC
AGCCACGACGAGGCGAGCTAAAGAGGATGAAGACGAGAGAGGGAGATCGAGAGCTAGCGACGGT
CGTTGTCGATCGGTTCCCTTTTTTGTTACCGCACTTGGATTTACCGCAGCAGCAGACATGGCAT
AATAAATCCTTTTACCCGCCGCTCACTGTTGCTGTGTAATTGCTGAACAGGGGAATTCGCAGTC
AGTAGGGAGCACCGGCACTGACTCGAGCTCAGCTCAGAACACAATGTCTCAGATGGAGTTGGTG
TCCCCAGCCTCCTCTGCGCCGCGGCAGGAGGTCATGATGGTGACCACTGATGATTACAGCTACA
AGCCAGGCCTCGCCGCTGCGCCCGCTGCTGCCGCCCCGCCGAGCTTTCAGCAGCACCACCCGCT
CCCGCTGCAGCTGCACGGAGGAGAGGGAGGGGGAGACCATGACAAG

Sequences
Splice junction sequence	CGCCGCTGCGCCCGCTGCTGCCGCCCCGCCGAGCTTTCAGCAGCACCACCCGCTCCCGCTGCAG CTGCACGGAGGAGAGGGAGGGGGAGACCATGACAAGcagcggcaggatatctcgcgggcgctgg caccggcaggccccccacgctggagatcttcccttcgtggccaatgaggcaccaacagcagctg cacagtgt
Assembled circRNA sequence	Yes 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	Transcript length: 350 Transcript exons: 179390515-179390612,179391013-179391264 CAGCGGCAGGATATCTCGCGGGCGCTGGCACCGGCAGGCCCCCCACGCTGGAGATCTTCCCTTC GTGGCCAATGAGGCACCAACAGCAGCTGCACAGTGGGAATTCGCAGTCAGTAGGGAGCACCGGC ACTGACTCGAGCTCAGCTCAGAACACAATGTCTCAGATGGAGTTGGTGTCCCCAGCCTCCTCTG CGCCGCGGCAGGAGGTCATGATGGTGACCACTGATGATTACAGCTACAAGCCAGGCCTCGCCGC TGCGCCCGCTGCTGCCGCCCCGCCGAGCTTTCAGCAGCACCACCCGCTCCCGCTGCAGCTGCAC GGAGGAGAGGGAGGGGGAGACCATGACAAG
Genomic sequence	CAGCGGCAGGATATCTCGCGGGCGCTGGCACCGGCAGGCCCCCCACGCTGGAGATCTTCCCTTC GTGGCCAATGAGGCACCAACAGCAGCTGCACAGTGTAAAGGCCCCGCCACCTCCCGATGTCCCA TGATCACTGATTCATGCATGCACGCATTCATTCATTCATTCATTCATCGCCTCGCCGCGCGCCC GTCTCTCGTCGTCTCCTCCGCTGGCTCGTCATCGTCGCTGAACCCAAGAAAAGATGTGGCTGTT TTTCTTGGTGATTCGCTCTCTGCATGTGGTCTGCACTCTGCATCTGCACCTGCAGGCTGCAGCC AGCCACGACGAGGCGAGCTAAAGAGGATGAAGACGAGAGAGGGAGATCGAGAGCTAGCGACGGT CGTTGTCGATCGGTTCCCTTTTTTGTTACCGCACTTGGATTTACCGCAGCAGCAGACATGGCAT AATAAATCCTTTTACCCGCCGCTCACTGTTGCTGTGTAATTGCTGAACAGGGGAATTCGCAGTC AGTAGGGAGCACCGGCACTGACTCGAGCTCAGCTCAGAACACAATGTCTCAGATGGAGTTGGTG TCCCCAGCCTCCTCTGCGCCGCGGCAGGAGGTCATGATGGTGACCACTGATGATTACAGCTACA AGCCAGGCCTCGCCGCTGCGCCCGCTGCTGCCGCCCCGCCGAGCTTTCAGCAGCACCACCCGCT CCCGCTGCAGCTGCACGGAGGAGAGGGAGGGGGAGACCATGACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002548 osa_circ_004897 osi_circ_010951 						
					
						PMCS
						0.226806033

Conservation Information
Conserved circRNAs	osi_circ_002548 osa_circ_004897 osi_circ_010951
PMCS	0.226806033

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							179391141-179391044(+)
179390587-179390586(+)
						
						Potential amino acid sequence
						
							MITATSQASPLRPLLPPRRAFSSTTRSRCSCTEEREGETMTSSGRISRGRWHRQAPHAGDLPFV
ANEAPTAAAQWEFAVSREHRH*(+)
MRHQQQLHSGNSQSVGSTGTDSSSAQNTMSQMELVSPASSAPRQEVMMVTTDDYSYKPGLAAAP
AAAAPPSFQQHHPLPLQLHGGEGGGDHDKQRQDISRALAPAGPPRWRSSLRGQ*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	179391141-179391044(+) 179390587-179390586(+)
Potential amino acid sequence	MITATSQASPLRPLLPPRRAFSSTTRSRCSCTEEREGETMTSSGRISRGRWHRQAPHAGDLPFV ANEAPTAAAQWEFAVSREHRH(+) MRHQQQLHSGNSQSVGSTGTDSSSAQNTMSQMELVSPASSAPRQEVMMVTTDDYSYKPGLAAAP AAAAPPSFQQHHPLPLQLHGGEGGGDHDKQRQDISRALAPAGPPRWRSSLRGQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d042777_circ_g.3

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