Plant Circular RNA Database

Detail information of Zm00001d015400_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d015400_circ_g.2
					
						ID in PlantcircBase
						zma_circ_008612
					
						Alias
						zma_circ_0002245, GRMZM2G082683_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 88445424-88446948  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d015400						
					
						Parent gene annotation
						
							S-adenosyl-L-methionine-dependent methyltransferases superfamily
 protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d015400_circ_g.1 						
					
						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
						Zm00001d015400_T005:2
Zm00001d015400_T001:1
Zm00001d015400_T003:1
Zm00001d015400_T002:3
Zm00001d015400_T004:3

General Information
CircRNA Name	Zm00001d015400_circ_g.2
ID in PlantcircBase	zma_circ_008612
Alias	zma_circ_0002245, GRMZM2G082683_C1
Organism	Zea mays
Position	chr5: 88445424-88446948 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d015400
Parent gene annotation	S-adenosyl-L-methionine-dependent methyltransferases superfamily protein
Parent gene strand	+
Alternative splicing	Zm00001d015400_circ_g.1
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	Zm00001d015400_T005:2 Zm00001d015400_T001:1 Zm00001d015400_T003:1 Zm00001d015400_T002:3 Zm00001d015400_T004:3

			
						 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  
						
							AAAAGGAGATGCAACTACATTCATGAAAGGAGCTATCTCAGAAAATGAGCTATGGGACTTGGTA
ATCCTTGACCCTCCAAAGTTGGCGCCACGAAAGAAGattgtctggtctaatagtggacatcttt
gctgatgttgctgtcattgcttcatctgctgcttgggttgagaaatataggcaagaaatacaat
ttcttgtt

									
								

					

						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: 589
Transcript exons: 88445424-88445640,88446390-88446576,88446764-88446948
ATTGTCTGGTCTAATAGTGGACATCTTTGCTGATGTTGCTGTCATTGCTTCATCTGCTGCTTGG
GTTGAGAAATATAGGCAAGAAATACAATTTCTTGTTAGCAAAGTTAATGGCGTCAGCCATATAA
AGTGGAGGCCATCGACAGATATTTTGAAAGAAGAAGGATTGGATATATCAGAGCATAAGGAGCC
TGCTTCAACATGCTCAACTGTCAAGGTCATGGAGAATGGCATTGTCTACTTAGTCTCATTAGAG
GGTCAGAAGACAGGGTTTTATGCAGATCAACGGGAAAACCGCTATATCATATCATTACTTTCAA
AGGATCAAAGAGTCCTTGACCTTTGCTGCTACAGTGGCGGCTTTGCTCTTAACGCAGCTAAGGG
TGGCGCTGATAATGTCATTGGCATTGATTCATCAGGATCAGCACTAGACCTTGCCAATGAGAAT
ATTGTTCTCAATGAGCTAAACCAAGGAAAAGTCTCATTTGTAAAAGGAGATGCAACTACATTCA
TGAAAGGAGCTATCTCAGAAAATGAGCTATGGGACTTGGTAATCCTTGACCCTCCAAAGTTGGC
GCCACGAAAGAAG
						
					

						Genomic sequence
						
							ATTGTCTGGTCTAATAGTGGACATCTTTGCTGATGTTGCTGTCATTGCTTCATCTGCTGCTTGG
GTTGAGAAATATAGGCAAGAAATACAATTTCTTGTTAGCAAAGTTAATGGCGTCAGCCATATAA
AGTGGAGGCCATCGACAGATATTTTGAAAGAAGAAGGATTGGATATATCAGAGCATAAGGAGCC
TGCTTCAACATGCTCAACTGTCAAGGTGGACCTGTTGACTTAGACAAGTTTATGATTCAGTATA
AATTGGTCTTGATAGTTCATGTTATAGGTTTAGTTCTCTCATAGTTGTACCTTACCGTACTCAT
TGAGTTGGCAAGATGGTAATTAGATTGACGCGAAACATAGGAACCAATGTGTCTCTTACGGCTT
TGCTGCCAATATGGCTGCTGCTTGCTGAGGAGGAGGGCCAGCTTTGGGCAATGGCTGGAGCGCG
AGGATCTCCTTCTTGTTGGCCCTTGTTCCTAGTGGCTAGGTCGTTGGTATATGTAAGAAAAGGT
GTGTATGTCATTTTGTGATCCAATGGTTGTGTGGGGTGTACCTAGGGTTCTTTACTATCTTCCT
TTTTTTTAATATAGTGATACACAACTCTATGAGTCAGACGTGTTTGGGGGGGGGGATGCAAGTG
TGTGCGATGTTGTATCATCCATGGTATTGTTTTGTGTTAGAGTGGACATACTAACCAATTCAAC
CCAAAAGCTTAATCTGACGAGAGAAGGTAATCAATTCACTTATACACTTCAACATCCCCACTCA
CGTGCAGTTAGAGAGAAAGATGTAAACATGGAAATAAATGAGTGGAGACACGAATAAAGCCTCT
GTCAGGATTCAAATTCGAGACCTCTGACTTTGATACAATGTTAGAGTGGACACACTAACCAGTT
CAGTCCAAAAGCTTAAGCTGATAGGAGAAGGTAGCTAATCCACTTATACACTTCAACATTTTAT
TTTCAGGTCATGGAGAATGGCATTGTCTACTTAGTCTCATTAGAGGGTCAGAAGACAGGGTTTT
ATGCAGATCAACGGGAAAACCGCTATATCATATCATTACTTTCAAAGGATCAAAGAGTCCTTGA
CCTTTGCTGCTACAGTGGCGGCTTTGCTCTTAACGCAGCTAAGGGTGGCGCTGATAATGTCATT
GGTGAGATACTTTAAGCTGATAAACATCTTTCAAGTGCTTTTCAAGTTATTTACAATTGAGTTT
GGTGGGATAGCATCGTCAGTTTGAAAGTTTGACACCGAGATATATATTTTTTGGTAGCCTCCTT
CCTATAATACTCTGCTGGATTTCCAGTACAAAATATTTCAATCAATGTAATCATTTTCAGGCAT
TGATTCATCAGGATCAGCACTAGACCTTGCCAATGAGAATATTGTTCTCAATGAGCTAAACCAA
GGAAAAGTCTCATTTGTAAAAGGAGATGCAACTACATTCATGAAAGGAGCTATCTCAGAAAATG
AGCTATGGGACTTGGTAATCCTTGACCCTCCAAAGTTGGCGCCACGAAAGAAG
						
					

			
		

Sequences
Splice junction sequence	AAAAGGAGATGCAACTACATTCATGAAAGGAGCTATCTCAGAAAATGAGCTATGGGACTTGGTA ATCCTTGACCCTCCAAAGTTGGCGCCACGAAAGAAGattgtctggtctaatagtggacatcttt gctgatgttgctgtcattgcttcatctgctgcttgggttgagaaatataggcaagaaatacaat ttcttgtt
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: 589 Transcript exons: 88445424-88445640,88446390-88446576,88446764-88446948 ATTGTCTGGTCTAATAGTGGACATCTTTGCTGATGTTGCTGTCATTGCTTCATCTGCTGCTTGG GTTGAGAAATATAGGCAAGAAATACAATTTCTTGTTAGCAAAGTTAATGGCGTCAGCCATATAA AGTGGAGGCCATCGACAGATATTTTGAAAGAAGAAGGATTGGATATATCAGAGCATAAGGAGCC TGCTTCAACATGCTCAACTGTCAAGGTCATGGAGAATGGCATTGTCTACTTAGTCTCATTAGAG GGTCAGAAGACAGGGTTTTATGCAGATCAACGGGAAAACCGCTATATCATATCATTACTTTCAA AGGATCAAAGAGTCCTTGACCTTTGCTGCTACAGTGGCGGCTTTGCTCTTAACGCAGCTAAGGG TGGCGCTGATAATGTCATTGGCATTGATTCATCAGGATCAGCACTAGACCTTGCCAATGAGAAT ATTGTTCTCAATGAGCTAAACCAAGGAAAAGTCTCATTTGTAAAAGGAGATGCAACTACATTCA TGAAAGGAGCTATCTCAGAAAATGAGCTATGGGACTTGGTAATCCTTGACCCTCCAAAGTTGGC GCCACGAAAGAAG
Genomic sequence	ATTGTCTGGTCTAATAGTGGACATCTTTGCTGATGTTGCTGTCATTGCTTCATCTGCTGCTTGG GTTGAGAAATATAGGCAAGAAATACAATTTCTTGTTAGCAAAGTTAATGGCGTCAGCCATATAA AGTGGAGGCCATCGACAGATATTTTGAAAGAAGAAGGATTGGATATATCAGAGCATAAGGAGCC TGCTTCAACATGCTCAACTGTCAAGGTGGACCTGTTGACTTAGACAAGTTTATGATTCAGTATA AATTGGTCTTGATAGTTCATGTTATAGGTTTAGTTCTCTCATAGTTGTACCTTACCGTACTCAT TGAGTTGGCAAGATGGTAATTAGATTGACGCGAAACATAGGAACCAATGTGTCTCTTACGGCTT TGCTGCCAATATGGCTGCTGCTTGCTGAGGAGGAGGGCCAGCTTTGGGCAATGGCTGGAGCGCG AGGATCTCCTTCTTGTTGGCCCTTGTTCCTAGTGGCTAGGTCGTTGGTATATGTAAGAAAAGGT GTGTATGTCATTTTGTGATCCAATGGTTGTGTGGGGTGTACCTAGGGTTCTTTACTATCTTCCT TTTTTTTAATATAGTGATACACAACTCTATGAGTCAGACGTGTTTGGGGGGGGGGATGCAAGTG TGTGCGATGTTGTATCATCCATGGTATTGTTTTGTGTTAGAGTGGACATACTAACCAATTCAAC CCAAAAGCTTAATCTGACGAGAGAAGGTAATCAATTCACTTATACACTTCAACATCCCCACTCA CGTGCAGTTAGAGAGAAAGATGTAAACATGGAAATAAATGAGTGGAGACACGAATAAAGCCTCT GTCAGGATTCAAATTCGAGACCTCTGACTTTGATACAATGTTAGAGTGGACACACTAACCAGTT CAGTCCAAAAGCTTAAGCTGATAGGAGAAGGTAGCTAATCCACTTATACACTTCAACATTTTAT TTTCAGGTCATGGAGAATGGCATTGTCTACTTAGTCTCATTAGAGGGTCAGAAGACAGGGTTTT ATGCAGATCAACGGGAAAACCGCTATATCATATCATTACTTTCAAAGGATCAAAGAGTCCTTGA CCTTTGCTGCTACAGTGGCGGCTTTGCTCTTAACGCAGCTAAGGGTGGCGCTGATAATGTCATT GGTGAGATACTTTAAGCTGATAAACATCTTTCAAGTGCTTTTCAAGTTATTTACAATTGAGTTT GGTGGGATAGCATCGTCAGTTTGAAAGTTTGACACCGAGATATATATTTTTTGGTAGCCTCCTT CCTATAATACTCTGCTGGATTTCCAGTACAAAATATTTCAATCAATGTAATCATTTTCAGGCAT TGATTCATCAGGATCAGCACTAGACCTTGCCAATGAGAATATTGTTCTCAATGAGCTAAACCAA GGAAAAGTCTCATTTGTAAAAGGAGATGCAACTACATTCATGAAAGGAGCTATCTCAGAAAATG AGCTATGGGACTTGGTAATCCTTGACCCTCCAAAGTTGGCGCCACGAAAGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.091036803

Conservation Information
Conserved circRNAs	NA
PMCS	0.091036803

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							88446394-88445453(+)
88446408-88446900(-)
						
						Potential amino acid sequence
						
							MENGIVYLVSLEGQKTGFYADQRENRYIISLLSKDQRVLDLCCYSGGFALNAAKGGADNVIGID
SSGSALDLANENIVLNELNQGKVSFVKGDATTFMKGAISENELWDLVILDPPKLAPRKKIVWSN
SGHLC*(+)
MPFSMTLTVEHVEAGSLCSDISNPSSFKISVDGLHFIWLTPLTLLTRNCISCLYFSTQAADEAM
TATSAKMSTIRPDNLLSWRQLWRVKDYQVP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	88446394-88445453(+) 88446408-88446900(-)
Potential amino acid sequence	MENGIVYLVSLEGQKTGFYADQRENRYIISLLSKDQRVLDLCCYSGGFALNAAKGGADNVIGID SSGSALDLANENIVLNELNQGKVSFVKGDATTFMKGAISENELWDLVILDPPKLAPRKKIVWSN SGHLC(+) MPFSMTLTVEHVEAGSLCSDISNPSSFKISVDGLHFIWLTPLTLLTRNCISCLYFSTQAADEAM TATSAKMSTIRPDNLLSWRQLWRVKDYQVP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d015400_circ_g.2

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