Plant Circular RNA Database

Detail information of Cotton_A_10339_circ_g.1

			
						 General Information
					
						CircRNA Name
						Cotton_A_10339_circ_g.1
					
						ID in PlantcircBase
						gar_circ_000002
					
						Alias
						CA_chr1_BGI-A2_v1.0:891797|894412
					
						Organism
						
							Gossypium arboreum						
					
						Position
						
							chrCA_chr1_BGI-A2_v1.0: 891797-894412  JBrowse»						
					
						Reference genome
						
							BGI-A2_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Cotton_A_10339						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						4/7
					
						Tissues
						leaf/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_10339:8

General Information
CircRNA Name	Cotton_A_10339_circ_g.1
ID in PlantcircBase	gar_circ_000002
Alias	CA_chr1_BGI-A2_v1.0:891797\|894412
Organism	Gossypium arboreum
Position	chrCA_chr1_BGI-A2_v1.0: 891797-894412 JBrowse»
Reference genome	BGI-A2_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	Cotton_A_10339
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	NA
Support reads	4/7
Tissues	leaf/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_10339:8

			
						 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  
						
							AGAAGTTATCTAGTGAGAGAACATTTACAATTTGTGGGATGGCAGACTCTTTAGCACCAGAGGT
AATTCAGGGAAAGGGCCATGGTCTTCCTGCTGACTGgaagataaaaatggagcagtgccaaggg
ttctgcaacggtatacagctgataagttgtcatcgtttggggagctggcactgatgtatgtttt
cttctctt

									
								

					

						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
						
							GAAGATAAAAATGGAGCAGTGCCAAGGGTTCTGCAACGGTATACAGCTGATAAGTTGTCATCGT
TTGGGGAGCTGGCACTGATGTATGTTTTCTTCTCTTTTCCTTTCTCACCTCATAGTAAATGAAG
AGCTCTCTAATATATTTTTTGAAGTTGACATTGTTTTGCTTATTAGAAATTGAAGCGCACATTT
ATTTTTATTTTTTAAAAAAGAAATGCACATTTGGAAAGCTTATTGAGAATTTATACGGAGTAGC
AAACCAAAATTAGGTTAACATGTTACCACCATTTATTTGGAGTAGTAACAAAGCAAAAATCCAC
CTAATTTTCTTAACACCTACGACCTATCAGTCACTATTTTGGTGCATTTTTAGTTTTCACATGT
GGTGTGTGTGTGAAACCTGCTGGTTTCTTGAATTGGGGTTATTTTACTTCTCTTTCTGGCTAAT
TGTGTTGTACAACTTACCTTGATAATTTGTTTTATTGGTATACAGGTACAATAAGCCTCTCCAA
GCTTCTGTGCTCGCTGTGACAAGTGGAACTCTCTGGGCTTTGAAACGAGAAGATTTTCGTGGAA
TTCTGATGTCTGAGTTTTCTAATTTATCATCCTTGAAGTTGCTCCGCTCTGTCGATCTTCTATC
AAGGTTAACAATTTTACAGCTGAGTCATGTTGCAGATTCTCTTTTCGAAGTTTCTTTCTCTAAT
GGGCAGACCATATTTAATAAGGTAGAAGTTTTCCTTCCAATGTTATATTTCATTTTCTGTGTAT
TATTTATGGTTCATATTCTTATTTTGTATATTTCTCTTGCATATCTGCAGAATGAAGGCCTCTC
AGCATTGCACATTATCCAGAAGGGCCAAGTGAGGATTACTTTTGACAGGGATTTGTTAAGCAGC
CCAAATGTCTGCAGTCTCAAGTCTGATAACTCCAACGAGGATGATGATCAGCAGACTGCGAAAG
AGCTGTCTGTTGAAAAGACAGAAGGAAGCTATTTTGGGGAATGGACACTTCTTGGTGAGCAGAT
GGATTCTTTAAGTGCAGTTGCAGTGGGTGATGTCATGTGTGCTGTTTTGACGAAGGAGAAGTTT
GATTCAGTTGTGGGTCCTTTGACAAAGCTTTCCCAGGATGATCAGAAGTATGTCTTAGTCTAAT
GCACTGAATGCTGCATCTTTGTTTTCCTCCTTTTTTCTGTTAGAATGCGTTTCATTTTATATTT
CACATAAACCTTCCATTTTAGAATCTGTAAGCTTTTAGAATTCTCTAACTGAACAACAATGAAC
TTTTTATTCCTTCTCTTCTCATTTGAATGTTTAATACTTTGTTTGAGAATGATATTGTTGTCTT
CATTGCCATTTAGGATTAGAGACTATCCTCTAGACGTGACCAAGGATTCTTCCAAAGAAATTGA
TATTTCAAGTCTTGCTAAAGTTAGCTTCACTCAGTTGGTAAGAAGTGCTTAGTTCTACCTCTGC
CTTGTGGCTAATGTAGCAAAATGTGATCATCAAGAGAACAATTCCTAAACTCAGCTAATGGCAT
ATGCAGGAGTGGAGAACAAGTTTATATTCCACTGACTGTAGTGAGATTGGGCTTGTACTTGTAA
GAGACTCAGGTTGGTTATATCTGTGTATTTACTTTTCCTCTCATTTTAAATTAAAAAAAGAAGC
TTTTTCTTGCGTAACAAGTTTAGGCACAACAGTTAACTGACATGCGATATATAGACTGATTATG
CATGCTTATATTAACTGACCAAGGCATGTCAGTTGCATTATGGGAGTATAGGAAAATAAGCATG
TTAGGTGCTATCTGCTATGTTGTGTTTTTAAGGAACTTGTTATGGAACGACTGATAAATATTTT
TTTTGTGCTAAATGGATTGATTACTAGAAAAAATCCTTAGTTTGAAGAGGTTTTCAAAGCAGAA
GGTAAAAAAACTAGGAAAAGAAGCCCAAGTTTTAAAGGAGAAGGGTCTGATGAAGAGCATGAGC
TCTGCAGCTTGCATGCCGGAGATTTTGTGCACTTGTGCTGATCAAATGCATGCTGGAATTTTAT
TGAATACCTACCTTGTCTGCCCTTTGGCTTCTATACTTCACACTCCTCTAGATGAACAATCAGC
ACGGTTCTGTGCTGCATCTGTTGTTACTGCTTTAGAAGATCTACATGAGGCGAGTTTCTAGCAG
TAGTTTTCTTCCACTTCATTTCCTTAATTCCTTGTGTAGCTGTAATTTATTTTAGTTTGTCATT
AACACCCACATTTCATTTGAATTTCAGAATGGTGTCCTTTACAGAGGAGTCTCTCCGGATGTTT
TAATGTTGAACAAAACTGGCCATTTACAGGTTGGTACTATTGTATGCTGTGTTATAGTTTGTGC
TGACTTTTATATTTAAATTACTATTAAGTTTACACATAATCAAAGGTCTCCCTTCTCTTTTACA
TATGAAGGATGGCAAATCACGAGCTAAGCTTAGTTATTTTATTTTGTTATGTTGCATTGCAGCT
TGTCGATTTCAGATTTGGGAAGAAGTTATCTAGTGAGAGAACATTTACAATTTGTGGGATGGCA
GACTCTTTAGCACCAGAGGTAATTCAGGGAAAGGGCCATGGTCTTCCTGCTGACTG
						
					

			
		

Sequences
Splice junction sequence	AGAAGTTATCTAGTGAGAGAACATTTACAATTTGTGGGATGGCAGACTCTTTAGCACCAGAGGT AATTCAGGGAAAGGGCCATGGTCTTCCTGCTGACTGgaagataaaaatggagcagtgccaaggg ttctgcaacggtatacagctgataagttgtcatcgtttggggagctggcactgatgtatgtttt cttctctt
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	GAAGATAAAAATGGAGCAGTGCCAAGGGTTCTGCAACGGTATACAGCTGATAAGTTGTCATCGT TTGGGGAGCTGGCACTGATGTATGTTTTCTTCTCTTTTCCTTTCTCACCTCATAGTAAATGAAG AGCTCTCTAATATATTTTTTGAAGTTGACATTGTTTTGCTTATTAGAAATTGAAGCGCACATTT ATTTTTATTTTTTAAAAAAGAAATGCACATTTGGAAAGCTTATTGAGAATTTATACGGAGTAGC AAACCAAAATTAGGTTAACATGTTACCACCATTTATTTGGAGTAGTAACAAAGCAAAAATCCAC CTAATTTTCTTAACACCTACGACCTATCAGTCACTATTTTGGTGCATTTTTAGTTTTCACATGT GGTGTGTGTGTGAAACCTGCTGGTTTCTTGAATTGGGGTTATTTTACTTCTCTTTCTGGCTAAT TGTGTTGTACAACTTACCTTGATAATTTGTTTTATTGGTATACAGGTACAATAAGCCTCTCCAA GCTTCTGTGCTCGCTGTGACAAGTGGAACTCTCTGGGCTTTGAAACGAGAAGATTTTCGTGGAA TTCTGATGTCTGAGTTTTCTAATTTATCATCCTTGAAGTTGCTCCGCTCTGTCGATCTTCTATC AAGGTTAACAATTTTACAGCTGAGTCATGTTGCAGATTCTCTTTTCGAAGTTTCTTTCTCTAAT GGGCAGACCATATTTAATAAGGTAGAAGTTTTCCTTCCAATGTTATATTTCATTTTCTGTGTAT TATTTATGGTTCATATTCTTATTTTGTATATTTCTCTTGCATATCTGCAGAATGAAGGCCTCTC AGCATTGCACATTATCCAGAAGGGCCAAGTGAGGATTACTTTTGACAGGGATTTGTTAAGCAGC CCAAATGTCTGCAGTCTCAAGTCTGATAACTCCAACGAGGATGATGATCAGCAGACTGCGAAAG AGCTGTCTGTTGAAAAGACAGAAGGAAGCTATTTTGGGGAATGGACACTTCTTGGTGAGCAGAT GGATTCTTTAAGTGCAGTTGCAGTGGGTGATGTCATGTGTGCTGTTTTGACGAAGGAGAAGTTT GATTCAGTTGTGGGTCCTTTGACAAAGCTTTCCCAGGATGATCAGAAGTATGTCTTAGTCTAAT GCACTGAATGCTGCATCTTTGTTTTCCTCCTTTTTTCTGTTAGAATGCGTTTCATTTTATATTT CACATAAACCTTCCATTTTAGAATCTGTAAGCTTTTAGAATTCTCTAACTGAACAACAATGAAC TTTTTATTCCTTCTCTTCTCATTTGAATGTTTAATACTTTGTTTGAGAATGATATTGTTGTCTT CATTGCCATTTAGGATTAGAGACTATCCTCTAGACGTGACCAAGGATTCTTCCAAAGAAATTGA TATTTCAAGTCTTGCTAAAGTTAGCTTCACTCAGTTGGTAAGAAGTGCTTAGTTCTACCTCTGC CTTGTGGCTAATGTAGCAAAATGTGATCATCAAGAGAACAATTCCTAAACTCAGCTAATGGCAT ATGCAGGAGTGGAGAACAAGTTTATATTCCACTGACTGTAGTGAGATTGGGCTTGTACTTGTAA GAGACTCAGGTTGGTTATATCTGTGTATTTACTTTTCCTCTCATTTTAAATTAAAAAAAGAAGC TTTTTCTTGCGTAACAAGTTTAGGCACAACAGTTAACTGACATGCGATATATAGACTGATTATG CATGCTTATATTAACTGACCAAGGCATGTCAGTTGCATTATGGGAGTATAGGAAAATAAGCATG TTAGGTGCTATCTGCTATGTTGTGTTTTTAAGGAACTTGTTATGGAACGACTGATAAATATTTT TTTTGTGCTAAATGGATTGATTACTAGAAAAAATCCTTAGTTTGAAGAGGTTTTCAAAGCAGAA GGTAAAAAAACTAGGAAAAGAAGCCCAAGTTTTAAAGGAGAAGGGTCTGATGAAGAGCATGAGC TCTGCAGCTTGCATGCCGGAGATTTTGTGCACTTGTGCTGATCAAATGCATGCTGGAATTTTAT TGAATACCTACCTTGTCTGCCCTTTGGCTTCTATACTTCACACTCCTCTAGATGAACAATCAGC ACGGTTCTGTGCTGCATCTGTTGTTACTGCTTTAGAAGATCTACATGAGGCGAGTTTCTAGCAG TAGTTTTCTTCCACTTCATTTCCTTAATTCCTTGTGTAGCTGTAATTTATTTTAGTTTGTCATT AACACCCACATTTCATTTGAATTTCAGAATGGTGTCCTTTACAGAGGAGTCTCTCCGGATGTTT TAATGTTGAACAAAACTGGCCATTTACAGGTTGGTACTATTGTATGCTGTGTTATAGTTTGTGC TGACTTTTATATTTAAATTACTATTAAGTTTACACATAATCAAAGGTCTCCCTTCTCTTTTACA TATGAAGGATGGCAAATCACGAGCTAAGCTTAGTTATTTTATTTTGTTATGTTGCATTGCAGCT TGTCGATTTCAGATTTGGGAAGAAGTTATCTAGTGAGAGAACATTTACAATTTGTGGGATGGCA GACTCTTTAGCACCAGAGGTAATTCAGGGAAAGGGCCATGGTCTTCCTGCTGACTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							gra_circ_000005* 						
					
						PMCS

Conservation Information
Conserved circRNAs	gra_circ_000005*
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							891878-891875(+)
891858-894365(-)
						
						Potential amino acid sequence
						
							MYNKPLQASVLAVTSGTLWALKREDFRGILMSEFSNLSSLKLLRSVDLLSRLTILQLSHVADSL
FEVSFSNGQTIFNKNEGLSALHIIQKGQVRITFDRDLLSSPNVCSLKSDNSNEDDDQQTAKELS
VEKTEGSYFGEWTLLGEQMDSLSAVAVGDVMCAVLTKEKFDSVVGPLTKLSQDDQKIRDYPLDV
TKDSSKEIDISSLAKVSFTQLEWRTSLYSTDCSEIGLVLVRDSEKILSLKRFSKQKVKKLGKEA
QVLKEKGLMKSMSSAACMPEILCTCADQMHAGILLNTYLVCPLASILHTPLDEQSARFCAASVN
GVLYRGVSPDVLMLNKTGHLQLVDFRFGKKLSSERTFTICGMADSLAPEVIQGKGHGLPADWKI
KMEQCQGFCNGIQLISCHRLGSWH*(+)
MTTYQLYTVAEPLALLHFYLPVSRKTMALSLNYLWC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	891878-891875(+) 891858-894365(-)
Potential amino acid sequence	MYNKPLQASVLAVTSGTLWALKREDFRGILMSEFSNLSSLKLLRSVDLLSRLTILQLSHVADSL FEVSFSNGQTIFNKNEGLSALHIIQKGQVRITFDRDLLSSPNVCSLKSDNSNEDDDQQTAKELS VEKTEGSYFGEWTLLGEQMDSLSAVAVGDVMCAVLTKEKFDSVVGPLTKLSQDDQKIRDYPLDV TKDSSKEIDISSLAKVSFTQLEWRTSLYSTDCSEIGLVLVRDSEKILSLKRFSKQKVKKLGKEA QVLKEKGLMKSMSSAACMPEILCTCADQMHAGILLNTYLVCPLASILHTPLDEQSARFCAASVN GVLYRGVSPDVLMLNKTGHLQLVDFRFGKKLSSERTFTICGMADSLAPEVIQGKGHGLPADWKI KMEQCQGFCNGIQLISCHRLGSWH(+) MTTYQLYTVAEPLALLHFYLPVSRKTMALSLNYLWC(-)
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_10339_circ_g.1

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