Plant Circular RNA Database

Detail information of Cotton_A_12712_circ_g.1

			
						 General Information
					
						CircRNA Name
						Cotton_A_12712_circ_g.1
					
						ID in PlantcircBase
						gar_circ_000841
					
						Alias
						CA_chr7_BGI-A2_v1.0:89054785|89057173
					
						Organism
						
							Gossypium arboreum						
					
						Position
						
							chrCA_chr7_BGI-A2_v1.0: 89054785-89057173  JBrowse»						
					
						Reference genome
						
							BGI-A2_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Cotton_A_12712						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2
					
						Tissues
						ovule
					
						Exon boundary  
						
							Yes-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-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_12712:6

General Information
CircRNA Name	Cotton_A_12712_circ_g.1
ID in PlantcircBase	gar_circ_000841
Alias	CA_chr7_BGI-A2_v1.0:89054785\|89057173
Organism	Gossypium arboreum
Position	chrCA_chr7_BGI-A2_v1.0: 89054785-89057173 JBrowse»
Reference genome	BGI-A2_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	Cotton_A_12712
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	NA
Support reads	2
Tissues	ovule
Exon boundary	Yes-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-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_12712:6

			
						 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  
						
							GATTCTTTTATTTTTAGTGGATTTCTTATGATCTTTTAGCTTTGGATTTTTCTTTTCTTTTTCA
CAGGTTGAGACATTCATTCAAGATGCGATGTCAAAGggtgttataaatgtggttatggggaatg
ctactaaaattggtgatgctttacttgcaagtacacaggtcttctacccttaacttgaaactga
ttcctttc

									
								

					

						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
						
							GGTGTTATAAATGTGGTTATGGGGAATGCTACTAAAATTGGTGATGCTTTACTTGCAAGTACAC
AGGTCTTCTACCCTTAACTTGAAACTGATTCCTTTCTAGAAATTAATGGATGTATAAATTAAAG
AACGTTAAATATTCCTGCTTCTTATTACTTATCCAGGTAAGAAAAATCACATTTACAGGCTCAA
CTGCAGTCGGGAAGAAGTTAATGGCTGGTGCCGCGGAGACTGTCAAAAGGGTATGGTTATCCTA
TGAAATGGATATGTACACCAAATCAGTGTAGTTTTGAAAATTATCCTGCAGTTGACTGTCTATA
TTCTGAACTTTTCTAGGTATCACTTGAACTCGGTGGTAATGCCCCCTGCATTGTATTTGATGAT
GCAGACCTGGATGTGGCAGTTAAAGGAACAGTAAGTTTACTCAATAGAATAGCTTTGATATATA
TTGACATCAATAGCATTCTCATCCTAGATATTCCTGAGTTCCACTTGTAATTGGTTGTGTGGCT
GCTGCCATTCTGGATAGCGATAGTAGTAACATGATTTTGTACCATCACTTTATGTCAAGTTTCA
AGCATATGATTTTGTTTCTCATTGTACTTAAAAAAGTTCCTTGACATCTATTTGTTTCCTTTTT
ACTTTTCCAACTTCCTCTCCGTATCGATTGTCTTGTGTTTCATAGCTTACACCTTTTCTTCTTC
CTCCTCTTCCAGCCTGAGCAAGAGGAATTTGGTTAGCTATAGGATCATATTTTTAGTTTCCTAA
TTCTCAGGGTTGTTCTTGAATCTGTCATTGCAGTATTGGTCCATGTAGTGGTGGAAAAAACCGC
ACCTGAATCCAAAAACCACTTGAATTCAGCCTGGTTCAAGTTGGATTGACCAAAAGATCTATGA
ATTAATATGAAAAATTATAAGAGCTAAAAGTGCCCAAGCCCGATAAGGGTTCAAAGCTTAAATG
ATTCGAAGCTGAAATGACATGAGCTGAAACAATCTGAAACAGAAACCCGAAATCAACCTGGAAT
CTAAAGCTGACCTGACCAGGATCCTTTATTTCCCAAAGTCATAATCTGAGAAGATTGCAACTGA
AAGAAACACTGACACTCAGGCTGGTTAAAAGCTAACAAGACTTGTTCAGTTTTCATGATGCATG
AAAATTAACTGTAAATATGCATTCTACTATCCTGTCCAGTAGTACCTTTCATTTGATTCTTAAC
TTGAGTATGCACTCTTATCTTTGTTGCCTCATTTACAATACCATGCAATTTGCAGCTTGCAGCA
AAATTTCGTAACAGTGGACAGACTTGTGTCTGTGCGAACAGAGTAATTGTGCAAGAAGGTATGG
ATGTAAATGTATTCTGATGGAAATCTGTAAGCAATTTCCTTTTTTTTTTTATGTTTCCCCATAT
TGAGAGACTTTGGGTGCATTTGGATCTAGAAAATATTTGCTGTTGTCATGTCTGAGGATTTTTT
TTCTAATTTCTATTTATTAGCCAAATGAAAATTTAGTAATTTTTTTTTCTACAGAATAAAAATG
ATAAAAGTACATTTAGTATCAAGAATTTATATTTTAAAAAAATGACTAATAAATATAGCTTCTG
TTAACATTTCAATTAAAATATATATAGTGGAATACTTATTATTATACTTATTATTTCCTTTTGA
AAACAAACAAATAACATTGTTTCCTTTTGTACTTCTGATATGTGAGCAGTTGAGTTGTAAACCC
ACAGGCCAGTATTTTCCTTAATTATACAAGGATATTCTAAAACAAGAAGATATAGTTGCTTTAA
TTTTTATTTACCTTTTGTTTCAGGTATTTATGAGAAGTTTGCAGAGGCTTTTTCAAAAGCTGTC
CAGAAGCTGCAAGTTGGAGATGGCTTCACTGAAGGGGTGGTCCAGGTAGTTAGCCTAAGCCATG
CATTTGTGGTTCATATATTAATTGTTGTTGCCAAATTGGTCTTTACATTTATACGTGGTGAGCC
TATGCATTTTATGTTTCTCAGTCTTTAGTTTATAAGGATAATATTTTATGGAAAATTGTATTGA
ACTTTTTTCTCGAGGTATTGTAAACAAATCATAAGATTTGTAAAGATATGCAGTTATGTTGGTA
ATAATGCTAAGTTGCTCGGAGCTTTTTCTTTTAATTAAGTCTAACAAGTGAATTTAGCTTAAAG
ATAATAATTTTGTTTTACTATACTTACCTATGTAGGGTCCACTAATTAATGAAGCTGCAGTGCA
AAAGGTTACTTTGCTTCCTTTTCCAGTTTTTATCAATTAACTTATCTATGATTCTTTTATTTTT
AGTGGATTTCTTATGATCTTTTAGCTTTGGATTTTTCTTTTCTTTTTCACAGGTTGAGACATTC
ATTCAAGATGCGATGTCAAAG
						
					

			
		

Sequences
Splice junction sequence	GATTCTTTTATTTTTAGTGGATTTCTTATGATCTTTTAGCTTTGGATTTTTCTTTTCTTTTTCA CAGGTTGAGACATTCATTCAAGATGCGATGTCAAAGggtgttataaatgtggttatggggaatg ctactaaaattggtgatgctttacttgcaagtacacaggtcttctacccttaacttgaaactga ttcctttc
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	GGTGTTATAAATGTGGTTATGGGGAATGCTACTAAAATTGGTGATGCTTTACTTGCAAGTACAC AGGTCTTCTACCCTTAACTTGAAACTGATTCCTTTCTAGAAATTAATGGATGTATAAATTAAAG AACGTTAAATATTCCTGCTTCTTATTACTTATCCAGGTAAGAAAAATCACATTTACAGGCTCAA CTGCAGTCGGGAAGAAGTTAATGGCTGGTGCCGCGGAGACTGTCAAAAGGGTATGGTTATCCTA TGAAATGGATATGTACACCAAATCAGTGTAGTTTTGAAAATTATCCTGCAGTTGACTGTCTATA TTCTGAACTTTTCTAGGTATCACTTGAACTCGGTGGTAATGCCCCCTGCATTGTATTTGATGAT GCAGACCTGGATGTGGCAGTTAAAGGAACAGTAAGTTTACTCAATAGAATAGCTTTGATATATA TTGACATCAATAGCATTCTCATCCTAGATATTCCTGAGTTCCACTTGTAATTGGTTGTGTGGCT GCTGCCATTCTGGATAGCGATAGTAGTAACATGATTTTGTACCATCACTTTATGTCAAGTTTCA AGCATATGATTTTGTTTCTCATTGTACTTAAAAAAGTTCCTTGACATCTATTTGTTTCCTTTTT ACTTTTCCAACTTCCTCTCCGTATCGATTGTCTTGTGTTTCATAGCTTACACCTTTTCTTCTTC CTCCTCTTCCAGCCTGAGCAAGAGGAATTTGGTTAGCTATAGGATCATATTTTTAGTTTCCTAA TTCTCAGGGTTGTTCTTGAATCTGTCATTGCAGTATTGGTCCATGTAGTGGTGGAAAAAACCGC ACCTGAATCCAAAAACCACTTGAATTCAGCCTGGTTCAAGTTGGATTGACCAAAAGATCTATGA ATTAATATGAAAAATTATAAGAGCTAAAAGTGCCCAAGCCCGATAAGGGTTCAAAGCTTAAATG ATTCGAAGCTGAAATGACATGAGCTGAAACAATCTGAAACAGAAACCCGAAATCAACCTGGAAT CTAAAGCTGACCTGACCAGGATCCTTTATTTCCCAAAGTCATAATCTGAGAAGATTGCAACTGA AAGAAACACTGACACTCAGGCTGGTTAAAAGCTAACAAGACTTGTTCAGTTTTCATGATGCATG AAAATTAACTGTAAATATGCATTCTACTATCCTGTCCAGTAGTACCTTTCATTTGATTCTTAAC TTGAGTATGCACTCTTATCTTTGTTGCCTCATTTACAATACCATGCAATTTGCAGCTTGCAGCA AAATTTCGTAACAGTGGACAGACTTGTGTCTGTGCGAACAGAGTAATTGTGCAAGAAGGTATGG ATGTAAATGTATTCTGATGGAAATCTGTAAGCAATTTCCTTTTTTTTTTTATGTTTCCCCATAT TGAGAGACTTTGGGTGCATTTGGATCTAGAAAATATTTGCTGTTGTCATGTCTGAGGATTTTTT TTCTAATTTCTATTTATTAGCCAAATGAAAATTTAGTAATTTTTTTTTCTACAGAATAAAAATG ATAAAAGTACATTTAGTATCAAGAATTTATATTTTAAAAAAATGACTAATAAATATAGCTTCTG TTAACATTTCAATTAAAATATATATAGTGGAATACTTATTATTATACTTATTATTTCCTTTTGA AAACAAACAAATAACATTGTTTCCTTTTGTACTTCTGATATGTGAGCAGTTGAGTTGTAAACCC ACAGGCCAGTATTTTCCTTAATTATACAAGGATATTCTAAAACAAGAAGATATAGTTGCTTTAA TTTTTATTTACCTTTTGTTTCAGGTATTTATGAGAAGTTTGCAGAGGCTTTTTCAAAAGCTGTC CAGAAGCTGCAAGTTGGAGATGGCTTCACTGAAGGGGTGGTCCAGGTAGTTAGCCTAAGCCATG CATTTGTGGTTCATATATTAATTGTTGTTGCCAAATTGGTCTTTACATTTATACGTGGTGAGCC TATGCATTTTATGTTTCTCAGTCTTTAGTTTATAAGGATAATATTTTATGGAAAATTGTATTGA ACTTTTTTCTCGAGGTATTGTAAACAAATCATAAGATTTGTAAAGATATGCAGTTATGTTGGTA ATAATGCTAAGTTGCTCGGAGCTTTTTCTTTTAATTAAGTCTAACAAGTGAATTTAGCTTAAAG ATAATAATTTTGTTTTACTATACTTACCTATGTAGGGTCCACTAATTAATGAAGCTGCAGTGCA AAAGGTTACTTTGCTTCCTTTTCCAGTTTTTATCAATTAACTTATCTATGATTCTTTTATTTTT AGTGGATTTCTTATGATCTTTTAGCTTTGGATTTTTCTTTTCTTTTTCACAGGTTGAGACATTC ATTCAAGATGCGATGTCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							gra_circ_000143 						
					
						PMCS

Conservation Information
Conserved circRNAs	gra_circ_000143
PMCS

			
						 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
						Zhao et al., 2017b

circRNA

Detail information of Cotton_A_12712_circ_g.1

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