Plant Circular RNA Database

Detail information of Cotton_A_04542_circ_g.2

			
						 General Information
					
						CircRNA Name
						Cotton_A_04542_circ_g.2
					
						ID in PlantcircBase
						gar_circ_000768
					
						Alias
						CA_chr6_BGI-A2_v1.0:104749731|104751984
					
						Organism
						
							Gossypium arboreum						
					
						Position
						
							chrCA_chr6_BGI-A2_v1.0: 104749731-104751984  JBrowse»						
					
						Reference genome
						
							BGI-A2_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Cotton_A_04542						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Cotton_A_04542_circ_g.1 Cotton_A_04542_circ_g.3 						
					
						Support reads
						13
					
						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  
						
							CT-AC							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_04542:4

General Information
CircRNA Name	Cotton_A_04542_circ_g.2
ID in PlantcircBase	gar_circ_000768
Alias	CA_chr6_BGI-A2_v1.0:104749731\|104751984
Organism	Gossypium arboreum
Position	chrCA_chr6_BGI-A2_v1.0: 104749731-104751984 JBrowse»
Reference genome	BGI-A2_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	Cotton_A_04542
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Cotton_A_04542_circ_g.1 Cotton_A_04542_circ_g.3
Support reads	13
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	CT-AC 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_04542:4

			
						 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  
						
							TCAAATTTGTCATGCTACTACCAAGGGTGTCCAAAACTTCCACAGCCTTTCCAAGCCCAGCAGT
ACCAGCTCTACCTAAAAGAGAGCCAACCTCAGAAACctctttgaacagcagttgaattatcctc
ttcctgaagcttccgtcgataatcttgttcaaatctgtccaaggcatgcaactcatgatataat
tcctgcaa

									
								

					

						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
						
							CTCTTTGAACAGCAGTTGAATTATCCTCTTCCTGAAGCTTCCGTCGATAATCTTGTTCAAATCT
GTCCAAGGCATGCAACTCATGATATAATTCCTGCAAAGAGAACAGTTCTCTCCTTAAATGATTA
GATCAGTTATAAATTACCAATGAATTGTACCATTATTCATATGCCTTCTATCATAAGAAATGCA
TCAGAACAGCAAATTCGAAAGCAAGAAAATTTTCAGCACTCTCAGCTAATCTAAAACTCTGTAC
CATCAGCCGCTATAAATAGAATTTATATCCTCTTTTGTTCCTAGAGCCAATCAGCTTAAACTAA
CAATTCTCTAAGATGTCCTTAGAAAGTAACTATTCTCATAAAATATGCCTACATAGCAAATTAT
TCCCATTAGTGAATCATCAACGAAAGAAGATAATTGGTTTTTCAACTTAAAAGTGCAGGGAGGC
TAGAGATCTACGTCATACTTGACTTATGCATTAAAACTGGGGGAAAAAAGTGTTAGTATTAAGA
GATGATACAGATTTCTTTCATACTTCAAAAAAATAAAGCACTATACCATTGTCACAGTAAACTT
TAAAGAGGAAAAACTGCCCTATGAGACAAAGAACTGCATTAAAGTGCAAAAATAAAGAAGCAAT
TTGTCCTTAAAAGTTCCAAGGTAAAAAATGTAGGTCGATCATTCCTTTCTAAAAGCTTGAGAAT
CAAGCCTTACTGGATTTGGATTGAACACTATTCTACCATCCTTGAATAAACCACCAACGTTTGA
GGTCAAAATTTCTCTCACCCACTATGAATTATCCAATATAGGTAATAATAAGAAAAGCAGCAAA
AACAGAATTTCAGAAGTGGGTGCAAAATATGGGAGCAACAAAAGTGTTATATAAGGAGAAGAGA
GGATGATATCAAGCCAATGGAAATTAGTGTCATTGGCAAATCACTCTTACAAAGTTCCGTAACA
AAGCCATGAATCAACAAATAATTGGAATAGGTAGCAAGTTTTATGAATGTTGCAACAGTAGGAA
TGCCCACGACTTATTCTAGAGCCTCAACAGTGTTAAACATATTGCAAGATTGATTCACATGCTA
AAATGCAATAGAACAAAACAGCATCATCATTACTTAAAATATTGTAATAGATAATTTAAGAAAG
AAATTACCGAAGCCTTACAAAAGAAAAAACCAACAGAGAGAATATTTAAAAAAAAAAAAAACTT
TGCCGCATGGATTTGTAGTTCAGACAAAGTCTCCAAATATAAAGGGAAAAAAAATAATGCAATA
GATAATTTAAGAAGAAAATTTCTGAAGCCTTGCAGGATAAAGAATAAACAGAAATAAAATATTT
GCCATATGGATTTATGGTTCATACAACGTCTCCAAACATAAAGGGAAAAAAGAAATATTTTCTC
TACTGCTTAGGAAAAAATGGAATGTAAATTTCGGTTTTAAACAATTTAATCTTACACTGCAACT
TCTAAGAGCAGCTTTCTCAGAATAATCGTAGGAACTGATACTTACAGCTGTATACTGAACATAA
GACATCAATTGTTGCATTATTGCCTCTGCTTCGTCCTTCAATTGCTTCTCAGGTGTAAGCTCAG
AACCCAACCTAAATATTACAAAAGACGCAGCATGAAAGATTTTAGAATCTTGCACTAATGTCAT
AAATAACACTTAAAAAAGTGCAACAAGCTGGAAAATTACTTTTCAAAATAACGATCCAAATTAT
GCCACTGAGGATCTTTACAACGGTTGCCAAAACGTACCACCTCTCCAGAAAAAACTTTTAACTC
TTCCCTGTTGGAAATGGATAACAAAAAATGTTCAAAACTTTCACATTCTTTGAAATTTAACCAC
CATTAGAGAGGATCTTAACAAACTGTATAACAACAAAATCATTTTCAAAGCAACATGGCATTTA
TTATCCACCTCTTATCAGCAGCTGCAATTCTCAGGAGTTCATCCATATCTCTTGATATCAAATT
TTGCACTCCTTCTGATGAAAGGACCACCTCTTTTAAATGTCTGATGTTCTCCTTAGAAAGTGAT
TGCATCAGATTGGCACCTTTAACGATCGTATTTGCAACTTCAAAAGCTAGAATTGCTATTTTAT
TCCCTTTTGTTGTTACCCCTGAGGTAAAGCCACTGCTGAGGTTCAAATTTGTCATGCTACTACC
AAGGGTGTCCAAAACTTCCACAGCCTTTCCAAGCCCAGCAGTACCAGCTCTACCTAAAAGAGAG
CCAACCTCAGAAAC
						
					

			
		

Sequences
Splice junction sequence	TCAAATTTGTCATGCTACTACCAAGGGTGTCCAAAACTTCCACAGCCTTTCCAAGCCCAGCAGT ACCAGCTCTACCTAAAAGAGAGCCAACCTCAGAAACctctttgaacagcagttgaattatcctc ttcctgaagcttccgtcgataatcttgttcaaatctgtccaaggcatgcaactcatgatataat tcctgcaa
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	CTCTTTGAACAGCAGTTGAATTATCCTCTTCCTGAAGCTTCCGTCGATAATCTTGTTCAAATCT GTCCAAGGCATGCAACTCATGATATAATTCCTGCAAAGAGAACAGTTCTCTCCTTAAATGATTA GATCAGTTATAAATTACCAATGAATTGTACCATTATTCATATGCCTTCTATCATAAGAAATGCA TCAGAACAGCAAATTCGAAAGCAAGAAAATTTTCAGCACTCTCAGCTAATCTAAAACTCTGTAC CATCAGCCGCTATAAATAGAATTTATATCCTCTTTTGTTCCTAGAGCCAATCAGCTTAAACTAA CAATTCTCTAAGATGTCCTTAGAAAGTAACTATTCTCATAAAATATGCCTACATAGCAAATTAT TCCCATTAGTGAATCATCAACGAAAGAAGATAATTGGTTTTTCAACTTAAAAGTGCAGGGAGGC TAGAGATCTACGTCATACTTGACTTATGCATTAAAACTGGGGGAAAAAAGTGTTAGTATTAAGA GATGATACAGATTTCTTTCATACTTCAAAAAAATAAAGCACTATACCATTGTCACAGTAAACTT TAAAGAGGAAAAACTGCCCTATGAGACAAAGAACTGCATTAAAGTGCAAAAATAAAGAAGCAAT TTGTCCTTAAAAGTTCCAAGGTAAAAAATGTAGGTCGATCATTCCTTTCTAAAAGCTTGAGAAT CAAGCCTTACTGGATTTGGATTGAACACTATTCTACCATCCTTGAATAAACCACCAACGTTTGA GGTCAAAATTTCTCTCACCCACTATGAATTATCCAATATAGGTAATAATAAGAAAAGCAGCAAA AACAGAATTTCAGAAGTGGGTGCAAAATATGGGAGCAACAAAAGTGTTATATAAGGAGAAGAGA GGATGATATCAAGCCAATGGAAATTAGTGTCATTGGCAAATCACTCTTACAAAGTTCCGTAACA AAGCCATGAATCAACAAATAATTGGAATAGGTAGCAAGTTTTATGAATGTTGCAACAGTAGGAA TGCCCACGACTTATTCTAGAGCCTCAACAGTGTTAAACATATTGCAAGATTGATTCACATGCTA AAATGCAATAGAACAAAACAGCATCATCATTACTTAAAATATTGTAATAGATAATTTAAGAAAG AAATTACCGAAGCCTTACAAAAGAAAAAACCAACAGAGAGAATATTTAAAAAAAAAAAAAACTT TGCCGCATGGATTTGTAGTTCAGACAAAGTCTCCAAATATAAAGGGAAAAAAAATAATGCAATA GATAATTTAAGAAGAAAATTTCTGAAGCCTTGCAGGATAAAGAATAAACAGAAATAAAATATTT GCCATATGGATTTATGGTTCATACAACGTCTCCAAACATAAAGGGAAAAAAGAAATATTTTCTC TACTGCTTAGGAAAAAATGGAATGTAAATTTCGGTTTTAAACAATTTAATCTTACACTGCAACT TCTAAGAGCAGCTTTCTCAGAATAATCGTAGGAACTGATACTTACAGCTGTATACTGAACATAA GACATCAATTGTTGCATTATTGCCTCTGCTTCGTCCTTCAATTGCTTCTCAGGTGTAAGCTCAG AACCCAACCTAAATATTACAAAAGACGCAGCATGAAAGATTTTAGAATCTTGCACTAATGTCAT AAATAACACTTAAAAAAGTGCAACAAGCTGGAAAATTACTTTTCAAAATAACGATCCAAATTAT GCCACTGAGGATCTTTACAACGGTTGCCAAAACGTACCACCTCTCCAGAAAAAACTTTTAACTC TTCCCTGTTGGAAATGGATAACAAAAAATGTTCAAAACTTTCACATTCTTTGAAATTTAACCAC CATTAGAGAGGATCTTAACAAACTGTATAACAACAAAATCATTTTCAAAGCAACATGGCATTTA TTATCCACCTCTTATCAGCAGCTGCAATTCTCAGGAGTTCATCCATATCTCTTGATATCAAATT TTGCACTCCTTCTGATGAAAGGACCACCTCTTTTAAATGTCTGATGTTCTCCTTAGAAAGTGAT TGCATCAGATTGGCACCTTTAACGATCGTATTTGCAACTTCAAAAGCTAGAATTGCTATTTTAT TCCCTTTTGTTGTTACCCCTGAGGTAAAGCCACTGCTGAGGTTCAAATTTGTCATGCTACTACC AAGGGTGTCCAAAACTTCCACAGCCTTTCCAAGCCCAGCAGTACCAGCTCTACCTAAAAGAGAG CCAACCTCAGAAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							gra_circ_000458* 						
					
						PMCS

Conservation Information
Conserved circRNAs	gra_circ_000458*
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							104751898-104751979(-)
104749815-104751979(-)
104751758-104749746(+)
						
						Potential amino acid sequence
						
							MTNLNLSSGFTSGVTTKGNKIAILAFEVANTIVKGANLMQSLSKENIRHLKEVVLSSEGVQNLI
SRDMDELLRIAAADKREELKVFSGEVVRFGNRCKDPQWHNLDRYFEKLGSELTPEKQLKDEAEA
IMQQLMSYVQYTAVSISSYDYSEKAALRSCSELYHELHALDRFEQDYRRKLQEEDNSTAVQRGF
*(-)
MSCMPWTDLNKIIDGSFRKRIIQLLFKEVSEVGSLLGRAGTAGLGKAVEVLDTLGSSMTNLNLS
SGFTSGVTTKGNKIAILAFEVANTIVKGANLMQSLSKENIRHLKEVVLSSEGVQNLISRDMDEL
LRIAAADKREELKVFSGEVVRFGNRCKDPQWHNLDRYFEKLGSELTPEKQLKDEAEAIMQQLMS
YVQYTAVSISSYDYSEKAALRSCSELYHELHALDRFEQDYRRKLQEEDNSTAVQRGF*(-)
MFSLESDCIRLAPLTIVFATSKARIAILFPFVVTPEVKPLLRFKFVMLLPRVSKTSTAFPSPAV
PALPKREPTSETSLNSS*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	104751898-104751979(-) 104749815-104751979(-) 104751758-104749746(+)
Potential amino acid sequence	MTNLNLSSGFTSGVTTKGNKIAILAFEVANTIVKGANLMQSLSKENIRHLKEVVLSSEGVQNLI SRDMDELLRIAAADKREELKVFSGEVVRFGNRCKDPQWHNLDRYFEKLGSELTPEKQLKDEAEA IMQQLMSYVQYTAVSISSYDYSEKAALRSCSELYHELHALDRFEQDYRRKLQEEDNSTAVQRGF (-) MSCMPWTDLNKIIDGSFRKRIIQLLFKEVSEVGSLLGRAGTAGLGKAVEVLDTLGSSMTNLNLS SGFTSGVTTKGNKIAILAFEVANTIVKGANLMQSLSKENIRHLKEVVLSSEGVQNLISRDMDEL LRIAAADKREELKVFSGEVVRFGNRCKDPQWHNLDRYFEKLGSELTPEKQLKDEAEAIMQQLMS YVQYTAVSISSYDYSEKAALRSCSELYHELHALDRFEQDYRRKLQEEDNSTAVQRGF(-) MFSLESDCIRLAPLTIVFATSKARIAILFPFVVTPEVKPLLRFKFVMLLPRVSKTSTAFPSPAV PALPKREPTSETSLNSS*(+)
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_04542_circ_g.2

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