Plant Circular RNA Database

Detail information of orai.011G242300_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.011G242300_circ_g.1
					
						ID in PlantcircBase
						gra_circ_001257
					
						Alias
						Chr11:56922411|56923642
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr11: 56922411-56923642  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.011G242300						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							orai.011G242300_circ_g.2 orai.011G242300_circ_g.3 orai.011G242300_circ_g.4 						
					
						Support reads
						36
					
						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
						Gorai.011G242300.2:2
Gorai.011G242300.1:2

General Information
CircRNA Name	orai.011G242300_circ_g.1
ID in PlantcircBase	gra_circ_001257
Alias	Chr11:56922411\|56923642
Organism	Gossypium raimondii
Position	chrChr11: 56922411-56923642 JBrowse»
Reference genome	Graimondii_221
Type	ue-circRNA
Identification method	CIRI
Parent gene	Gorai.011G242300
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	orai.011G242300_circ_g.2 orai.011G242300_circ_g.3 orai.011G242300_circ_g.4
Support reads	36
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	Gorai.011G242300.2:2 Gorai.011G242300.1:2

			
						 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  
						
							AGCCATTGCTTCCTCACGAGAGCAAGAAAATCCTCCTCAGTTGCCAAAAATGCTTTGTTGATTA
CATCTGCTGACATTCCACCATTCTCAGTTGTAAACTatttcgtggacaggtgttgacgatatcg
actgcctcttgactgctaaggtgttcccatagaccatctgatgcaaatataagaaactgatctt
cagggtca

									
								

					

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 605
Transcript exons: 56922411-56922647,56923275-56923642
ATTTCGTGGACAGGTGTTGACGATATCGACTGCCTCTTGACTGCTAAGGTGTTCCCATAGACCA
TCTGATGCAAATATAAGAAACTGATCTTCAGGGTCAAGTTTCTGTACTAATGTTTCTGGCTCGG
CACTAAGGATTGGCTTATCGAATGGTTCGGGAACTCTAAACTTCGGCAATAGAGGATCTCTGTT
GAACTCCGCGCTCTTTAGATAAGCATCACCAATGGATCTCGAAATCTGTATAATACCCTTCACA
CGCCATACTGTGTGCTTGAGGACCACAATTTGTGGATCAGTGGGATGTAATGATCGTAACTCTT
CCCGTACAGATTCAACACTTGCATTGTGCTCTGATGATAATGGAACTGCCTTGACCTCTTTATA
CGTTTTATCCAATCTTCCTAAGACCACTCGAGAATCTCCTGCATTTGCAATATATAGCATTCCG
CTACAAACTATTCCTACCAAACAACACGAACCGACAGAAGCCATATGCGGGTCATTTAGCCATT
GCTTCCTCACGAGAGCAAGAAAATCCTCCTCAGTTGCCAAAAATGCTTTGTTGATTACATCTGC
TGACATTCCACCATTCTCAGTTGTAAACT
						
					

						Genomic sequence
						
							ATTTCGTGGACAGGTGTTGACGATATCGACTGCCTCTTGACTGCTAAGGTGTTCCCATAGACCA
TCTGATGCAAATATAAGAAACTGATCTTCAGGGTCAAGTTTCTGTACTAATGTTTCTGGCTCGG
CACTAAGGATTGGCTTATCGAATGGTTCGGGAACTCTAAACTTCGGCAATAGAGGATCTCTGTT
GAACTCCGCGCTCTTTAGATAAGCATCACCAATGGATCTCGAAATCTGTCACATAGCGAACCTT
GGTTAACAGACTATAAGTTTGCACGTGCCTGTTGTGTAGATTGTGCTAATTCGCTTTGTCGGAT
TGATAGTAACTCAAACGGCAATTACCCTTAAAAGTTCCTAAAGCTGGTTCTCCAGGTGGAACTA
TTCAACGCATAAAATAAGCATGGGGACAATTCGGGCTTCTATGATGGTTTTTTATTTTATTTTA
TGAAAATAAGCATACAAATGGATAACAACTTGGGTACTAATGCTCCTATGGAAACTTCCAAATT
CTGGAACCTAGAAATGAAAATGACTTAGCACTTGTATTGTTATTCTTCGAAACTTCATATTCAA
AAGTCATAAGATTTGGAACGAGAAGGCAATCGACCAATTTTCATCAATTTTAAGTAGTTACTTC
AACTCAAGAAAACAATTGTTTATAGAAGTAAACCTATGTTACTCAAACTTGGATGTGACTGTTG
GACACAGGTATGTTCAAATTCTTTTCTAAGTTTTTCCACGTATTTGGTGAGTCCTAGGAGGGTC
ATATCCAGATAACCTTGTCCAAATATATGTCGGACACGGATACTTCAAGTAGAATGATGAGTTG
GAGCAACATAAATGAAAATGACAAAAAACTACCTGTATAATACCCTTCACACGCCATACTGTGT
GCTTGAGGACCACAATTTGTGGATCAGTGGGATGTAATGATCGTAACTCTTCCCGTACAGATTC
AACACTTGCATTGTGCTCTGATGATAATGGAACTGCCTTGACCTCTTTATACGTTTTATCCAAT
CTTCCTAAGACCACTCGAGAATCTCCTGCATTTGCAATATATAGCATTCCGCTACAAACTATTC
CTACCAAACAACACGAACCGACAGAAGCCATATGCGGGTCATTTAGCCATTGCTTCCTCACGAG
AGCAAGAAAATCCTCCTCAGTTGCCAAAAATGCTTTGTTGATTACATCTGCTGACATTCCACCA
TTCTCAGTTGTAAACT
						
					

			
		

Sequences
Splice junction sequence	AGCCATTGCTTCCTCACGAGAGCAAGAAAATCCTCCTCAGTTGCCAAAAATGCTTTGTTGATTA CATCTGCTGACATTCCACCATTCTCAGTTGTAAACTatttcgtggacaggtgttgacgatatcg actgcctcttgactgctaaggtgttcccatagaccatctgatgcaaatataagaaactgatctt cagggtca
Assembled circRNA sequence	Yes 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	Transcript length: 605 Transcript exons: 56922411-56922647,56923275-56923642 ATTTCGTGGACAGGTGTTGACGATATCGACTGCCTCTTGACTGCTAAGGTGTTCCCATAGACCA TCTGATGCAAATATAAGAAACTGATCTTCAGGGTCAAGTTTCTGTACTAATGTTTCTGGCTCGG CACTAAGGATTGGCTTATCGAATGGTTCGGGAACTCTAAACTTCGGCAATAGAGGATCTCTGTT GAACTCCGCGCTCTTTAGATAAGCATCACCAATGGATCTCGAAATCTGTATAATACCCTTCACA CGCCATACTGTGTGCTTGAGGACCACAATTTGTGGATCAGTGGGATGTAATGATCGTAACTCTT CCCGTACAGATTCAACACTTGCATTGTGCTCTGATGATAATGGAACTGCCTTGACCTCTTTATA CGTTTTATCCAATCTTCCTAAGACCACTCGAGAATCTCCTGCATTTGCAATATATAGCATTCCG CTACAAACTATTCCTACCAAACAACACGAACCGACAGAAGCCATATGCGGGTCATTTAGCCATT GCTTCCTCACGAGAGCAAGAAAATCCTCCTCAGTTGCCAAAAATGCTTTGTTGATTACATCTGC TGACATTCCACCATTCTCAGTTGTAAACT
Genomic sequence	ATTTCGTGGACAGGTGTTGACGATATCGACTGCCTCTTGACTGCTAAGGTGTTCCCATAGACCA TCTGATGCAAATATAAGAAACTGATCTTCAGGGTCAAGTTTCTGTACTAATGTTTCTGGCTCGG CACTAAGGATTGGCTTATCGAATGGTTCGGGAACTCTAAACTTCGGCAATAGAGGATCTCTGTT GAACTCCGCGCTCTTTAGATAAGCATCACCAATGGATCTCGAAATCTGTCACATAGCGAACCTT GGTTAACAGACTATAAGTTTGCACGTGCCTGTTGTGTAGATTGTGCTAATTCGCTTTGTCGGAT TGATAGTAACTCAAACGGCAATTACCCTTAAAAGTTCCTAAAGCTGGTTCTCCAGGTGGAACTA TTCAACGCATAAAATAAGCATGGGGACAATTCGGGCTTCTATGATGGTTTTTTATTTTATTTTA TGAAAATAAGCATACAAATGGATAACAACTTGGGTACTAATGCTCCTATGGAAACTTCCAAATT CTGGAACCTAGAAATGAAAATGACTTAGCACTTGTATTGTTATTCTTCGAAACTTCATATTCAA AAGTCATAAGATTTGGAACGAGAAGGCAATCGACCAATTTTCATCAATTTTAAGTAGTTACTTC AACTCAAGAAAACAATTGTTTATAGAAGTAAACCTATGTTACTCAAACTTGGATGTGACTGTTG GACACAGGTATGTTCAAATTCTTTTCTAAGTTTTTCCACGTATTTGGTGAGTCCTAGGAGGGTC ATATCCAGATAACCTTGTCCAAATATATGTCGGACACGGATACTTCAAGTAGAATGATGAGTTG GAGCAACATAAATGAAAATGACAAAAAACTACCTGTATAATACCCTTCACACGCCATACTGTGT GCTTGAGGACCACAATTTGTGGATCAGTGGGATGTAATGATCGTAACTCTTCCCGTACAGATTC AACACTTGCATTGTGCTCTGATGATAATGGAACTGCCTTGACCTCTTTATACGTTTTATCCAAT CTTCCTAAGACCACTCGAGAATCTCCTGCATTTGCAATATATAGCATTCCGCTACAAACTATTC CTACCAAACAACACGAACCGACAGAAGCCATATGCGGGTCATTTAGCCATTGCTTCCTCACGAG AGCAAGAAAATCCTCCTCAGTTGCCAAAAATGCTTTGTTGATTACATCTGCTGACATTCCACCA TTCTCAGTTGTAAACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							gar_circ_000849 ghi_circ_000160* ghi_circ_000375* gar_circ_000847 
ghi_circ_000376* 						
					
						PMCS
						0.660388799

Conservation Information
Conserved circRNAs	gar_circ_000849 ghi_circ_000160* ghi_circ_000375* gar_circ_000847 ghi_circ_000376*
PMCS	0.660388799

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							56922476-56923632(-)
56923620-56923606(-)
56922634-56922427(+)
						
						Potential amino acid sequence
						
							MVYGNTLAVKRQSISSTPVHEIVYN*(-)
MSADVINKAFLATEEDFLALVRKQWLNDPHMASVGSCCLVGIVCSGMLYIANAGDSRVVLGRLD
KTYKEVKAVPLSSEHNASVESVREELRSLHPTDPQIVVLKHTVWRVKGIIQISRSIGDAYLKSA
EFNRDPLLPKFRVPEPFDKPILSAEPETLVQKLDPEDQFLIFASDGLWEHLSSQEAVDIVNTCP
RNSLQLRMVECQQM*(-)
MDLEICIIPFTRHTVCLRTTICGSVGCNDRNSSRTDSTLALCSDDNGTALTSLYVLSNLPKTTR
ESPAFAIYSIPLQTIPTKQHEPTEAICGSFSHCFLTRARKSSSVAKNALLITSADIPPFSVVNY
FVDRC*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	56922476-56923632(-) 56923620-56923606(-) 56922634-56922427(+)
Potential amino acid sequence	MVYGNTLAVKRQSISSTPVHEIVYN(-) MSADVINKAFLATEEDFLALVRKQWLNDPHMASVGSCCLVGIVCSGMLYIANAGDSRVVLGRLD KTYKEVKAVPLSSEHNASVESVREELRSLHPTDPQIVVLKHTVWRVKGIIQISRSIGDAYLKSA EFNRDPLLPKFRVPEPFDKPILSAEPETLVQKLDPEDQFLIFASDGLWEHLSSQEAVDIVNTCP RNSLQLRMVECQQM(-) MDLEICIIPFTRHTVCLRTTICGSVGCNDRNSSRTDSTLALCSDDNGTALTSLYVLSNLPKTTR ESPAFAIYSIPLQTIPTKQHEPTEAICGSFSHCFLTRARKSSSVAKNALLITSADIPPFSVVNY FVDRC*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.011G242300_circ_g.1

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