Plant Circular RNA Database

Detail information of Cotton_A_32453_circ_g.1

			
						 General Information
					
						CircRNA Name
						Cotton_A_32453_circ_g.1
					
						ID in PlantcircBase
						gar_circ_000784
					
						Alias
						CA_chr7_BGI-A2_v1.0:6304098|6306300
					
						Organism
						
							Gossypium arboreum						
					
						Position
						
							chrCA_chr7_BGI-A2_v1.0: 6304098-6306300  JBrowse»						
					
						Reference genome
						
							BGI-A2_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Cotton_A_32453						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Cotton_A_32453_circ_g.3 Cotton_A_32453_circ_g.2 						
					
						Support reads
						6
					
						Tissues
						ovule
					
						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
						Cotton_A_32453:5

General Information
CircRNA Name	Cotton_A_32453_circ_g.1
ID in PlantcircBase	gar_circ_000784
Alias	CA_chr7_BGI-A2_v1.0:6304098\|6306300
Organism	Gossypium arboreum
Position	chrCA_chr7_BGI-A2_v1.0: 6304098-6306300 JBrowse»
Reference genome	BGI-A2_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	Cotton_A_32453
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Cotton_A_32453_circ_g.3 Cotton_A_32453_circ_g.2
Support reads	6
Tissues	ovule
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	Cotton_A_32453:5

			
						 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  
						
							ATTGTCGGTTGCCTTCGACCAGCCTTTGCTGATGAAGAATCATATCTAAGAAGGCTATTCCATT
TTGACTATGATGAAGGATACACCTCAGATTGGAAAGgcaaacagcagcgctttgctagtctttc
ctgggacagtacattctgaacctcatgaacagatttcatgggctgagtttcgatatgttgttga
tgattatg

									
								

					

						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
						
							GCAAACAGCAGCGCTTTGCTAGTCTTTCCTGGGACAGTACATTCTGAACCTCATGAACAGATTT
CATGGGCTGAGTTTCGATATGTTGTTGATGATTATGGAGGTAAGTTTATGGGAGACCACCATTG
AGCTCTATTAGGCTTTTATTCCCGTCAAGGCTTTAGGATTTGTCTCCAGTTTCCTTGTATATGT
ATACAAATGAGCACACACCTACATATGCATATATATATATATTAAACCATTAGTTCTCTTTCTG
TGTTAACCTAATTTATGTGTTATCTTTTGTTTCAAATTTAGATATCTTTTTTGAAATTTTGGAT
GATGAGAACATCTTAAAAGATCGCGGAGCGAGTAACCTTGTGGTGAGGATATCATTTCTACTCA
AATGTTTTTTTGATTTTCTAGCTCAAGTTTGGTGCCACTCGTTACTTCAAAATTACGTGTCATT
TGGCTAATCATTTAGAAGCCACTAGTGTAACAGTTTCATGCGTTGCAACGTTGTTTTGACTCTT
CATCTTTTTTTAAGTTTACGTGTGTGACACATATTTGGACATGGGTATTGGAATATGATTCTCA
AAAGATCCTTCAAATACATGGAAAAAGCTTCTAAAAATTGAATATACTCGTGTTAAATACATAC
TTGTATCCTATGCTCTCATATGAGTATGAGAATCCAACGGAATGGTAAATTAGTTAAGCTTGTT
GAGATATCATAGCAAAATCTATGTTACTTAGGCTCAAGTGTGAGTGTTTAATAAGGGTGTGTCC
AACATAGGTATATTTAAGTTTGTTCCGTGTATCTGGAGGGTTCTTAGAGGGTTATACTCTTGCC
GAAATATATGTTGGACATGGTTATTTCAAGAAAAGTGAAGAGAGCCAGAACACCATAGACTACA
ACAAATGTTAAAAATGGAAATGCTAACAGTTGATTGACGGAATTATGTTTTCTAAGTAGCTCTA
CATTTTCACTTGGCTTTAATTCCTATTCAATGAGTGCCATATTCTAAAATTTGTAATGATTTCT
TTTCTTTCAGAATGTTCTGATTGGGATGGACATTCCTGTACGAGAGAATAACCAGGCAGTCGGT
GACTTCAACTATTCAGACATCGGGATTGATGACGAAGTTCCTTTTGATGATGAATATTTTGAGG
TTAGAAACCACTGATTATTGACTTCTGAAGTGAAATCTGTGATATTCTCTTTTGTTAATTTTGG
CTACTCAAGTCCCATTCACGTAAATAGGTTATGGATTCTGAAATATACGAGGCTCCGGTTCGTT
GGGGGATGCCAGATTCGGCTGATAGCAGCTGGGTTCATCCTATTTATTTTGCCAAGTGCTTGAT
GAAGGTGATTGTGCCTGGGTTTCCCTTAAGTACAAGTCATATTATAAGTTTTAATTGTACTCAA
TGACTATGTTACTCGGACTCTAGACTGATGGGTTATGCATCTGACACGGGTATGCTCAAGTTTT
CTTAGTTTGTCTATATATATGGTGGATTATACCTTATACCCATGCTGAGTATGTGTCAAACACA
AGTCTTGGACACTGATACTTAAAGAAAAATAGAGTTCCAAGTAACATGGTTCAATGATATCAAG
GATGAAGCAAGGCCGGTATGCCCCCCGGCTAAACAGGATAATTACAGTTATAGCCCCTCGTAAT
AATCAATTAGTTAATTTAAGCATTTTTGAACCTTTGATTCATGGAAAAATTGCATTTTTCCCTC
TGAAAAAGTAGTAATTCTATTTTTTTTTTTGGCCTAACCAAAAAAAAAAAAAAAAAGTAATTCA
ATTTAAACCCTTTTAACAAAATTTGTTAGCTTTGGCCCTCCTAAGATTTTATAATTTTATATCG
GTTGCTGAATGATATTATGAGTTTTTATCCTTTTCTCTCTCCAATATGCTGCTAAGACAGTTTT
TATCATGAGTTTGATAAGGCAGAAGTCTTAATTGGATCAAAGAGAATTCATGAGATGATGAGTA
GATGCGTATTTGCATTTTGAATTTATAGGTAACTCTGTTTACACTTAGTTTCTGCATTCATGCA
GGCTGTTCATGTAGAACATGACAGGAAAATGGACCATCCCTCTAATGGTGTTTCGATTGTCGGT
TGCCTTCGACCAGCCTTTGCTGATGAAGAATCATATCTAAGAAGGCTATTCCATTTTGACTATG
ATGAAGGATACACCTCAGATTGGAAAG
						
					

			
		

Sequences
Splice junction sequence	ATTGTCGGTTGCCTTCGACCAGCCTTTGCTGATGAAGAATCATATCTAAGAAGGCTATTCCATT TTGACTATGATGAAGGATACACCTCAGATTGGAAAGgcaaacagcagcgctttgctagtctttc ctgggacagtacattctgaacctcatgaacagatttcatgggctgagtttcgatatgttgttga tgattatg
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	GCAAACAGCAGCGCTTTGCTAGTCTTTCCTGGGACAGTACATTCTGAACCTCATGAACAGATTT CATGGGCTGAGTTTCGATATGTTGTTGATGATTATGGAGGTAAGTTTATGGGAGACCACCATTG AGCTCTATTAGGCTTTTATTCCCGTCAAGGCTTTAGGATTTGTCTCCAGTTTCCTTGTATATGT ATACAAATGAGCACACACCTACATATGCATATATATATATATTAAACCATTAGTTCTCTTTCTG TGTTAACCTAATTTATGTGTTATCTTTTGTTTCAAATTTAGATATCTTTTTTGAAATTTTGGAT GATGAGAACATCTTAAAAGATCGCGGAGCGAGTAACCTTGTGGTGAGGATATCATTTCTACTCA AATGTTTTTTTGATTTTCTAGCTCAAGTTTGGTGCCACTCGTTACTTCAAAATTACGTGTCATT TGGCTAATCATTTAGAAGCCACTAGTGTAACAGTTTCATGCGTTGCAACGTTGTTTTGACTCTT CATCTTTTTTTAAGTTTACGTGTGTGACACATATTTGGACATGGGTATTGGAATATGATTCTCA AAAGATCCTTCAAATACATGGAAAAAGCTTCTAAAAATTGAATATACTCGTGTTAAATACATAC TTGTATCCTATGCTCTCATATGAGTATGAGAATCCAACGGAATGGTAAATTAGTTAAGCTTGTT GAGATATCATAGCAAAATCTATGTTACTTAGGCTCAAGTGTGAGTGTTTAATAAGGGTGTGTCC AACATAGGTATATTTAAGTTTGTTCCGTGTATCTGGAGGGTTCTTAGAGGGTTATACTCTTGCC GAAATATATGTTGGACATGGTTATTTCAAGAAAAGTGAAGAGAGCCAGAACACCATAGACTACA ACAAATGTTAAAAATGGAAATGCTAACAGTTGATTGACGGAATTATGTTTTCTAAGTAGCTCTA CATTTTCACTTGGCTTTAATTCCTATTCAATGAGTGCCATATTCTAAAATTTGTAATGATTTCT TTTCTTTCAGAATGTTCTGATTGGGATGGACATTCCTGTACGAGAGAATAACCAGGCAGTCGGT GACTTCAACTATTCAGACATCGGGATTGATGACGAAGTTCCTTTTGATGATGAATATTTTGAGG TTAGAAACCACTGATTATTGACTTCTGAAGTGAAATCTGTGATATTCTCTTTTGTTAATTTTGG CTACTCAAGTCCCATTCACGTAAATAGGTTATGGATTCTGAAATATACGAGGCTCCGGTTCGTT GGGGGATGCCAGATTCGGCTGATAGCAGCTGGGTTCATCCTATTTATTTTGCCAAGTGCTTGAT GAAGGTGATTGTGCCTGGGTTTCCCTTAAGTACAAGTCATATTATAAGTTTTAATTGTACTCAA TGACTATGTTACTCGGACTCTAGACTGATGGGTTATGCATCTGACACGGGTATGCTCAAGTTTT CTTAGTTTGTCTATATATATGGTGGATTATACCTTATACCCATGCTGAGTATGTGTCAAACACA AGTCTTGGACACTGATACTTAAAGAAAAATAGAGTTCCAAGTAACATGGTTCAATGATATCAAG GATGAAGCAAGGCCGGTATGCCCCCCGGCTAAACAGGATAATTACAGTTATAGCCCCTCGTAAT AATCAATTAGTTAATTTAAGCATTTTTGAACCTTTGATTCATGGAAAAATTGCATTTTTCCCTC TGAAAAAGTAGTAATTCTATTTTTTTTTTTGGCCTAACCAAAAAAAAAAAAAAAAAGTAATTCA ATTTAAACCCTTTTAACAAAATTTGTTAGCTTTGGCCCTCCTAAGATTTTATAATTTTATATCG GTTGCTGAATGATATTATGAGTTTTTATCCTTTTCTCTCTCCAATATGCTGCTAAGACAGTTTT TATCATGAGTTTGATAAGGCAGAAGTCTTAATTGGATCAAAGAGAATTCATGAGATGATGAGTA GATGCGTATTTGCATTTTGAATTTATAGGTAACTCTGTTTACACTTAGTTTCTGCATTCATGCA GGCTGTTCATGTAGAACATGACAGGAAAATGGACCATCCCTCTAATGGTGTTTCGATTGTCGGT TGCCTTCGACCAGCCTTTGCTGATGAAGAATCATATCTAAGAAGGCTATTCCATTTTGACTATG ATGAAGGATACACCTCAGATTGGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							gra_circ_001019* 						
					
						PMCS

Conservation Information
Conserved circRNAs	gra_circ_001019*
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6305147-6304141(+)
6306271-6304141(+)
6304165-6306271(-)
						
						Potential amino acid sequence
						
							MDIPVRENNQAVGDFNYSDIGIDDEVPFDDEYFEVMDSEIYEAPVRWGMPDSADSSWVHPIYFA
KCLMKAVHVEHDRKMDHPSNGVSIVGCLRPAFADEESYLRRLFHFDYDEGYTSDWKGKQQRFAS
LSWDSTF*(+)
MMKDTPQIGKANSSALLVFPGTVHSEPHEQISWAEFRYVVDDYGDIFFEILDDENILKDRGASN
LVNVLIGMDIPVRENNQAVGDFNYSDIGIDDEVPFDDEYFEVMDSEIYEAPVRWGMPDSADSSW
VHPIYFAKCLMKAVHVEHDRKMDHPSNGVSIVGCLRPAFADEESYLRRLFHFDYDEGYTSDWKG
KQQRFASLSWDSTF*(+)
MKSVHEVQNVLSQERLAKRCCLPFQSEVYPSS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6305147-6304141(+) 6306271-6304141(+) 6304165-6306271(-)
Potential amino acid sequence	MDIPVRENNQAVGDFNYSDIGIDDEVPFDDEYFEVMDSEIYEAPVRWGMPDSADSSWVHPIYFA KCLMKAVHVEHDRKMDHPSNGVSIVGCLRPAFADEESYLRRLFHFDYDEGYTSDWKGKQQRFAS LSWDSTF(+) MMKDTPQIGKANSSALLVFPGTVHSEPHEQISWAEFRYVVDDYGDIFFEILDDENILKDRGASN LVNVLIGMDIPVRENNQAVGDFNYSDIGIDDEVPFDDEYFEVMDSEIYEAPVRWGMPDSADSSW VHPIYFAKCLMKAVHVEHDRKMDHPSNGVSIVGCLRPAFADEESYLRRLFHFDYDEGYTSDWKG KQQRFASLSWDSTF(+) MKSVHEVQNVLSQERLAKRCCLPFQSEVYPSS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of Cotton_A_32453_circ_g.1

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