Plant Circular RNA Database

Detail information of Zm00001d031422_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d031422_circ_g.1
					
						ID in PlantcircBase
						zma_circ_006708
					
						Alias
						zma_circ_0000338
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 189585184-189587643  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d031422						
					
						Parent gene annotation
						
							RNA binding (RRM/RBD/RNP motifs) family protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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
						Zm00001d031422_T009:4
Zm00001d031422_T004:3
Zm00001d031422_T002:3
Zm00001d031422_T003:3
Zm00001d031422_T008:4
Zm00001d031422_T011:4
Zm00001d031422_T005:2
Zm00001d031422_T012:5
Zm00001d031422_T007:4
Zm00001d031422_T006:4
Zm00001d031422_T010:4
Zm00001d031422_T001:2

General Information
CircRNA Name	Zm00001d031422_circ_g.1
ID in PlantcircBase	zma_circ_006708
Alias	zma_circ_0000338
Organism	Zea mays
Position	chr1: 189585184-189587643 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d031422
Parent gene annotation	RNA binding (RRM/RBD/RNP motifs) family protein
Parent gene strand	+
Alternative splicing	NA
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	Zm00001d031422_T009:4 Zm00001d031422_T004:3 Zm00001d031422_T002:3 Zm00001d031422_T003:3 Zm00001d031422_T008:4 Zm00001d031422_T011:4 Zm00001d031422_T005:2 Zm00001d031422_T012:5 Zm00001d031422_T007:4 Zm00001d031422_T006:4 Zm00001d031422_T010:4 Zm00001d031422_T001:2

			
						 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  
						
							TTGCTGCCACCAAGGACTCATTATCTCGCCATTTCAACAAGTTTGGTGCAGTACTGAAAGTAGT
CATTGTCACTAATGCTGCAACGGGTCAGCCAACAGGagagacacctcatcacgccccatgcttg
gtggtggtgcttcccgtcgtcttctacagtttgctgttcgagatgcagtaaaagctgtacagcc
agccagca

									
								

					

						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
						
							AGAGACACCTCATCACGCCCCATGCTTGGTGGTGGTGCTTCCCGTCGTCTTCTACAGTTTGCTG
TTCGAGATGCAGTAAAAGCTGTACAGCCAGCCAGCACCTCTGCTGAACCAGCATCCAAGCGTCT
GCGCTCTGTGGTTGCCACTACTTCTGCAGAGAACATGCGTGATAGGAGATCAGAAAAATCTCAG
GACTACCTGAACGATAGAAGATCAGAAAGATCTCAAGATAACTCGAGTGACAGAAGATCAGAAA
GAACTAGACCAATGCTACAGGTACAAGGAGCTGCTTTAGCTCTTAGAGCTGCAGCGGAAGCTGC
TGCAGATTCTACAAAGGCTAGATCTACTGGAAGTGTTTTCAAGCGATTGGGTCAAGGGAATGTT
GTGAAACAACCATCTCGTTCTCGTGAAGAGAAGAGAGATTATGCTGATTTTGAGCCAGTTACGA
CCGCAAATGAACATGGTTCTGATCGATATGTTAATAATGAGGAATCTGAAGAGGAATATAGAGA
GCTAACCATGGCTGATAGGGTAGCAGGAATGAATGTTGATTCGGGCTCTGAAGATGATGTGGAC
CGAGATGAGGGGGTTACAAGATACCAAACTTCTATTTCACATGAAGATACTTTCTCATCATTTG
CAGAGAAGAAAACTGTATCGGCACAATGCAGTGTTGAACTAGAGACCGATGCAATAAGGCCTTC
AAGTGTGAATCACGAGGAGCAACCTGTCCCTTCATTAACAAATACAACAAGTAAAGCTGTGTCT
ATTTCTGTTGATGTAAATATGGTGGAACCTCCCAGTTATGAAACACCAAAAGATGTTCATGTTG
TGGAGAAGCCTTATGTTGCACCCATGAATTCAAATGCCACAAGTGTGGCTACCAATACCAAAGT
AAGCAGCCATGTATGTTGAAAAAACAAGTTTGGTACTTAAATTTCTTCCTACATATTGAGTCAC
CCATTCTTTTGCATTTTGGTTAGGTTTGTATTATATATGGTTAAGGTTTCTACCAGATGTCCTT
TTGATTTGTGACTAGATTTTTACAGTTCATAATCAAGTCCTAAGGCAATATTGTAGTCTTTCCT
TGATAAATAATAGTTACACTTATATGCTACTTGAATAAATGGCAGAGCAGTTGGGGCATGGATC
TTTCTATTCTGCCTTCTCTTGATGATAACTGCCTGTGAATGCTTATTTGCATTTGCTTCCAGTA
AAAAAAAGGATGAAAAAAAACAGTTGTTGGCATCTCCTATTACTGCTGTATATGCTCTCAGCCA
TTAACAAAATGGCACATCATGTCTTCTTCCACACATCTTGTTGATTATGATGCTCATTGGTTTT
CTTGTCTATTTCCTATGATCATTTGTCTTGTCTCGTGGGTGTATGCCCTAACTATGGGATAATC
CTTGAGTAAATTTGCTTCTGACTGGTGTCAACTTTCATTCAGGAATTAGGCCATGCAGAAGTTC
AAAAGGATTCTCAGCGGTCTGCACCATCTGGTATGTCACATATCTACCGATATAAGATTCACTT
AAGGGTGGTAATGGATCGTGATCCAAATGGTTTCTTTACAATTTGTTTGAGCCCTTAATTAATT
TTAGTTCAAAATTGAATAGAAATAGAGCCCGATCCTAATCCAATCCGATCCTTGAATTTTATAG
TGTAAAGTTTAGAGCCCATTACCACCCCTAAATCCACTTATGTTATTACCTTTCATCTGCTGAT
CTGTTCATATTGACACATGCCAATCTTCTGTCCGGTTGACTATATCTGATCGTTCCTGTTGGTT
TTGTGTCCTTCCTTTTCTTCAATAATTGTTAAAACATTGATACATGCAGTAATACACTAGTCAG
CCCACCATATTTATTTTACCATATCCCAACTTGCATGGGATTAGAAGGGCAGGCCTGGTACAGT
GGTGAGAGCTGTCTCAATGAATCACCAGGTTGTGCGTTCGAAGCGGCCTCTTCGCATTTGTGGG
AGAAAGACTTAGCCTCGGTTTATCCCTTACCTAAGAAAAAAAATGTGCAGTTACTACTTACTAG
TACAGCAAAATTTGTAAGGATCTGTTGCCTTTGTGATATATTGAGATATGTTGATGCACTGCGC
AAGTCATTATTACAATCAATCATAAATAGGAATGGGTTAATCTTGAAGACTGTCATTGATCGCT
TGGTATAATATATCTTGTCTTTGTAGTTCCGGTTTCATATAGCACATCACATCCGACAGTGGAT
GCAGATTCGAGAACACTTTATGTTAGCAATGTGGGTATTTATATACTCTCATCACCTTTATATT
ATTTTGTGCCAAATAATTATTTTATTCACCTCTGTCAAATTATTTGAAGGTTCACTTTGCTGCC
ACCAAGGACTCATTATCTCGCCATTTCAACAAGTTTGGTGCAGTACTGAAAGTAGTCATTGTCA
CTAATGCTGCAACGGGTCAGCCAACAGG
						
					

			
		

Sequences
Splice junction sequence	TTGCTGCCACCAAGGACTCATTATCTCGCCATTTCAACAAGTTTGGTGCAGTACTGAAAGTAGT CATTGTCACTAATGCTGCAACGGGTCAGCCAACAGGagagacacctcatcacgccccatgcttg gtggtggtgcttcccgtcgtcttctacagtttgctgttcgagatgcagtaaaagctgtacagcc agccagca
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	AGAGACACCTCATCACGCCCCATGCTTGGTGGTGGTGCTTCCCGTCGTCTTCTACAGTTTGCTG TTCGAGATGCAGTAAAAGCTGTACAGCCAGCCAGCACCTCTGCTGAACCAGCATCCAAGCGTCT GCGCTCTGTGGTTGCCACTACTTCTGCAGAGAACATGCGTGATAGGAGATCAGAAAAATCTCAG GACTACCTGAACGATAGAAGATCAGAAAGATCTCAAGATAACTCGAGTGACAGAAGATCAGAAA GAACTAGACCAATGCTACAGGTACAAGGAGCTGCTTTAGCTCTTAGAGCTGCAGCGGAAGCTGC TGCAGATTCTACAAAGGCTAGATCTACTGGAAGTGTTTTCAAGCGATTGGGTCAAGGGAATGTT GTGAAACAACCATCTCGTTCTCGTGAAGAGAAGAGAGATTATGCTGATTTTGAGCCAGTTACGA CCGCAAATGAACATGGTTCTGATCGATATGTTAATAATGAGGAATCTGAAGAGGAATATAGAGA GCTAACCATGGCTGATAGGGTAGCAGGAATGAATGTTGATTCGGGCTCTGAAGATGATGTGGAC CGAGATGAGGGGGTTACAAGATACCAAACTTCTATTTCACATGAAGATACTTTCTCATCATTTG CAGAGAAGAAAACTGTATCGGCACAATGCAGTGTTGAACTAGAGACCGATGCAATAAGGCCTTC AAGTGTGAATCACGAGGAGCAACCTGTCCCTTCATTAACAAATACAACAAGTAAAGCTGTGTCT ATTTCTGTTGATGTAAATATGGTGGAACCTCCCAGTTATGAAACACCAAAAGATGTTCATGTTG TGGAGAAGCCTTATGTTGCACCCATGAATTCAAATGCCACAAGTGTGGCTACCAATACCAAAGT AAGCAGCCATGTATGTTGAAAAAACAAGTTTGGTACTTAAATTTCTTCCTACATATTGAGTCAC CCATTCTTTTGCATTTTGGTTAGGTTTGTATTATATATGGTTAAGGTTTCTACCAGATGTCCTT TTGATTTGTGACTAGATTTTTACAGTTCATAATCAAGTCCTAAGGCAATATTGTAGTCTTTCCT TGATAAATAATAGTTACACTTATATGCTACTTGAATAAATGGCAGAGCAGTTGGGGCATGGATC TTTCTATTCTGCCTTCTCTTGATGATAACTGCCTGTGAATGCTTATTTGCATTTGCTTCCAGTA AAAAAAAGGATGAAAAAAAACAGTTGTTGGCATCTCCTATTACTGCTGTATATGCTCTCAGCCA TTAACAAAATGGCACATCATGTCTTCTTCCACACATCTTGTTGATTATGATGCTCATTGGTTTT CTTGTCTATTTCCTATGATCATTTGTCTTGTCTCGTGGGTGTATGCCCTAACTATGGGATAATC CTTGAGTAAATTTGCTTCTGACTGGTGTCAACTTTCATTCAGGAATTAGGCCATGCAGAAGTTC AAAAGGATTCTCAGCGGTCTGCACCATCTGGTATGTCACATATCTACCGATATAAGATTCACTT AAGGGTGGTAATGGATCGTGATCCAAATGGTTTCTTTACAATTTGTTTGAGCCCTTAATTAATT TTAGTTCAAAATTGAATAGAAATAGAGCCCGATCCTAATCCAATCCGATCCTTGAATTTTATAG TGTAAAGTTTAGAGCCCATTACCACCCCTAAATCCACTTATGTTATTACCTTTCATCTGCTGAT CTGTTCATATTGACACATGCCAATCTTCTGTCCGGTTGACTATATCTGATCGTTCCTGTTGGTT TTGTGTCCTTCCTTTTCTTCAATAATTGTTAAAACATTGATACATGCAGTAATACACTAGTCAG CCCACCATATTTATTTTACCATATCCCAACTTGCATGGGATTAGAAGGGCAGGCCTGGTACAGT GGTGAGAGCTGTCTCAATGAATCACCAGGTTGTGCGTTCGAAGCGGCCTCTTCGCATTTGTGGG AGAAAGACTTAGCCTCGGTTTATCCCTTACCTAAGAAAAAAAATGTGCAGTTACTACTTACTAG TACAGCAAAATTTGTAAGGATCTGTTGCCTTTGTGATATATTGAGATATGTTGATGCACTGCGC AAGTCATTATTACAATCAATCATAAATAGGAATGGGTTAATCTTGAAGACTGTCATTGATCGCT TGGTATAATATATCTTGTCTTTGTAGTTCCGGTTTCATATAGCACATCACATCCGACAGTGGAT GCAGATTCGAGAACACTTTATGTTAGCAATGTGGGTATTTATATACTCTCATCACCTTTATATT ATTTTGTGCCAAATAATTATTTTATTCACCTCTGTCAAATTATTTGAAGGTTCACTTTGCTGCC ACCAAGGACTCATTATCTCGCCATTTCAACAAGTTTGGTGCAGTACTGAAAGTAGTCATTGTCA CTAATGCTGCAACGGGTCAGCCAACAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.043020783

Conservation Information
Conserved circRNAs	NA
PMCS	0.043020783

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							189585206-189585259(+)
189587620-189585290(+)
189585349-189587618(-)
189585303-189587566(-)
						
						Potential amino acid sequence
						
							MLGGGASRRLLQFAVRDAVKAVQPASTSAEPASKRLRSVVATTSAENMRDRRSEKSQDYLNDRR
SERSQDNSSDRRSERTRPMLQVQGAALALRAAAEAAADSTKARSTGSVFKRLGQGNVVKQPSRS
REEKRDYADFEPVTTANEHGSDRYVNNEESEEEYRELTMADRVAGMNVDSGSEDDVDRDEGVTR
YQTSISHEDTFSSFAEKKTVSAQCSVELETDAIRPSSVNHEEQPVPSLTNTTSKAVSISVDVNM
VEPPSYETPKDVHVVEKPYVAPMNSNATSVATNTKFRFHIAHHIRQWMQIREHFMLAMWVHFAA
TKDSLSRHFNKFGAVLKVVIVTNAATGQPTGETPHHAPCLVVVLPVVFYSLLFEMQ*(+)
MLQRVSQQERHLITPHAWWWCFPSSSTVCCSRCSKSCTASQHLC*(+)
MFSAEVVATTERRRLDAGSAEVLAGCTAFTASRTANCRRRREAPPPSMGRDEVSLLLADPLQH*
(-)
MLVQQRCWLAVQLLLHLEQQTVEDDGKHHHQAWGVMRCLSCWLTRCSISDNDYFQYCTKLVEMA
R*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	189585206-189585259(+) 189587620-189585290(+) 189585349-189587618(-) 189585303-189587566(-)
Potential amino acid sequence	MLGGGASRRLLQFAVRDAVKAVQPASTSAEPASKRLRSVVATTSAENMRDRRSEKSQDYLNDRR SERSQDNSSDRRSERTRPMLQVQGAALALRAAAEAAADSTKARSTGSVFKRLGQGNVVKQPSRS REEKRDYADFEPVTTANEHGSDRYVNNEESEEEYRELTMADRVAGMNVDSGSEDDVDRDEGVTR YQTSISHEDTFSSFAEKKTVSAQCSVELETDAIRPSSVNHEEQPVPSLTNTTSKAVSISVDVNM VEPPSYETPKDVHVVEKPYVAPMNSNATSVATNTKFRFHIAHHIRQWMQIREHFMLAMWVHFAA TKDSLSRHFNKFGAVLKVVIVTNAATGQPTGETPHHAPCLVVVLPVVFYSLLFEMQ(+) MLQRVSQQERHLITPHAWWWCFPSSSTVCCSRCSKSCTASQHLC(+) MFSAEVVATTERRRLDAGSAEVLAGCTAFTASRTANCRRRREAPPPSMGRDEVSLLLADPLQH* (-) MLVQQRCWLAVQLLLHLEQQTVEDDGKHHHQAWGVMRCLSCWLTRCSISDNDYFQYCTKLVEMA R*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d031422_circ_g.1

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