Plant Circular RNA Database

Detail information of orai.013G178800_circ_g.2

			
						 General Information
					
						CircRNA Name
						orai.013G178800_circ_g.2
					
						ID in PlantcircBase
						gra_circ_001427
					
						Alias
						Chr13:47228145|47230020
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr13: 47228145-47230020  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.013G178800						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							orai.013G178800_circ_g.1 						
					
						Support reads
						3
					
						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
						Gorai.013G178800.8:4
Gorai.013G178800.6:4
Gorai.013G178800.4:4
Gorai.013G178800.5:4
Gorai.013G178800.1:4
Gorai.013G178800.7:4
Gorai.013G178800.2:4
Gorai.013G178800.3:4

General Information
CircRNA Name	orai.013G178800_circ_g.2
ID in PlantcircBase	gra_circ_001427
Alias	Chr13:47228145\|47230020
Organism	Gossypium raimondii
Position	chrChr13: 47228145-47230020 JBrowse»
Reference genome	Graimondii_221
Type	ue-circRNA
Identification method	CIRI
Parent gene	Gorai.013G178800
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	orai.013G178800_circ_g.1
Support reads	3
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	Gorai.013G178800.8:4 Gorai.013G178800.6:4 Gorai.013G178800.4:4 Gorai.013G178800.5:4 Gorai.013G178800.1:4 Gorai.013G178800.7:4 Gorai.013G178800.2:4 Gorai.013G178800.3:4

			
						 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  
						
							TTGCTCTGAAGAATCAAGGCGTATACAGTGCACTAAGTGTGGTAATTCACATATATGGGTATGC
ACAAATAGGAACAAGGCCAAGGCTAGATGGTGCCAGgttatatgttctccttaagccatgcacg
gttgatagtcttgatagcaactacatactctatttactttgtcaaagatcgagttggttggctt
ggtgtttt

									
								

					

						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
						
							GTTATATGTTCTCCTTAAGCCATGCACGGTTGATAGTCTTGATAGCAACTACATACTCTATTTA
CTTTGTCAAAGATCGAGTTGGTTGGCTTGGTGTTTTCCTATCAATAAACCTTGCATTTCTCTCG
AACGATGTATTGAATTATTTGGTCCAACGTTTTGATAATGTGAGTGAAACCGCACATTATGAAG
AGCCAAAGGAATCCAAACCAGTTATGGAAGATGATTTGTCTGGGGAATGTGAATACTCAAATCC
TAGTATTGACTCTGAGAAGGTGCAGCCATGCAAGTCATCTAGCAAGTCTGCTACTACATCTGTT
ATTAACCAAAAAGAGGTTTCTGCAAAAAGAGTGGTCAAGGAAGAAACGAGTTCAGCTGATGAAA
TGACAAGAATATTGAATTGCACTGATCATTATCAAGCACTGGGGATTCCTCGTCATACAAAAAT
TGACACTGCAGTCTTGAAAAAGGAATATAAAAAGAAGGTAGATTCTGTCCTGGCAAAAAGGCAT
AGATATTTCAATTATCTAAATATCTAGTCTATGCACCCGGTACTTAATTCAACAAAAAGTTAGA
CTTGAGATAGGTTTCTCCTTTTCTATGCTAGTGATATCGGGCCATGTTTAGCCTTTGTTTCTTA
TAGGTTATTTCCTAATTTGTTGTTAAGAAAACGGAAAGGATTTTAGGATTTGCATAAAGGAACT
TGATGGGTTGGAATCTAGGAGAAACATGGTTAGGAGGGAATGCTTGTGGATGAGACGGAAGATA
TCCTTCTTTGTTTTGCTTCTTCTTAGGTTCCTTTAAAGCCTTCTTATATTTTCCATTGATTTTT
GGGTATACCTACTTGTTTTATTGATTTATTTTCTCTCAATTCTACTTACAACAGGCAATGCTTG
TACATCCTGATAAAAATATGGGGAGTCCTTTAGCTAGTGAATCATTTAAGAAACTTCAATGTGC
TTACGAGGTGAGCAACTATGTTCTTCTTGTTATATTTTAGTCTTAATTTAATTTCTTATTTTGA
GTTCCTGTTTTGTGTACATATAAAATGAAAGCTGAAGAATGTCATCAGCTCTGTAAGTGTCGGC
TCTGGCCTTAAGCAGATTTGGCGTGTATTTTGTAGGTTCTTTCTGATTCCGTGAAAAAGAGGGA
CTATGATGAGCAATTAAGAAAGGAGGAATCCAGGACTCGGAGTGTCTGTCAAGAGTCCCATAGC
TCTTCACGGCAGGTAGTTTTGATTTCTATTGCGCCTTTTCATTTTTGTTGCTTCGTTTTATTTT
CTTGCAGTTCTTTTTTCAATGGAATTTATAGCCAAGAGGAATGAAAATGCAAAAATGCTTGGCA
CAATGGAGATAATATGTAACTTCTTAGAATTCAAAAATCTAGCTTCGGGGTTCTTTTCACTTGG
TTTTGCTCTGTCCAGGAGTTTCTTTATATTGATATATTGCTATAGATTTTTTGGAAAATGGAAA
AAAAAATGTCATTCTATAGTAACTTTGTCCTCTTGAGCAAAAACCAATTTATGAGTCACGGTGA
CAGAGGTTACCTGGTCTGACAATCGACTAATTAAGGGTTGTTCAACATGATGGCAGTGTTTACC
TCTGGCAGTCACTATCGAGTGTTTTATGTTGTTATGGTTAGTGCCTGCTGGCTGCATGCGAAAG
CTTGTTTTGCATTGCTGATTCATGTGATTCTGAGTTAGTCATTCATGTTGTATGATAATGTAAA
ATTAATACCTTTCAACCATTATTTATTTCAGCAGCCCAGTCCAGACTATTGCTCTGAAGAATCA
AGGCGTATACAGTGCACTAAGTGTGGTAATTCACATATATGGGTATGCACAAATAGGAACAAGG
CCAAGGCTAGATGGTGCCAG
						
					

			
		

Sequences
Splice junction sequence	TTGCTCTGAAGAATCAAGGCGTATACAGTGCACTAAGTGTGGTAATTCACATATATGGGTATGC ACAAATAGGAACAAGGCCAAGGCTAGATGGTGCCAGgttatatgttctccttaagccatgcacg gttgatagtcttgatagcaactacatactctatttactttgtcaaagatcgagttggttggctt ggtgtttt
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	GTTATATGTTCTCCTTAAGCCATGCACGGTTGATAGTCTTGATAGCAACTACATACTCTATTTA CTTTGTCAAAGATCGAGTTGGTTGGCTTGGTGTTTTCCTATCAATAAACCTTGCATTTCTCTCG AACGATGTATTGAATTATTTGGTCCAACGTTTTGATAATGTGAGTGAAACCGCACATTATGAAG AGCCAAAGGAATCCAAACCAGTTATGGAAGATGATTTGTCTGGGGAATGTGAATACTCAAATCC TAGTATTGACTCTGAGAAGGTGCAGCCATGCAAGTCATCTAGCAAGTCTGCTACTACATCTGTT ATTAACCAAAAAGAGGTTTCTGCAAAAAGAGTGGTCAAGGAAGAAACGAGTTCAGCTGATGAAA TGACAAGAATATTGAATTGCACTGATCATTATCAAGCACTGGGGATTCCTCGTCATACAAAAAT TGACACTGCAGTCTTGAAAAAGGAATATAAAAAGAAGGTAGATTCTGTCCTGGCAAAAAGGCAT AGATATTTCAATTATCTAAATATCTAGTCTATGCACCCGGTACTTAATTCAACAAAAAGTTAGA CTTGAGATAGGTTTCTCCTTTTCTATGCTAGTGATATCGGGCCATGTTTAGCCTTTGTTTCTTA TAGGTTATTTCCTAATTTGTTGTTAAGAAAACGGAAAGGATTTTAGGATTTGCATAAAGGAACT TGATGGGTTGGAATCTAGGAGAAACATGGTTAGGAGGGAATGCTTGTGGATGAGACGGAAGATA TCCTTCTTTGTTTTGCTTCTTCTTAGGTTCCTTTAAAGCCTTCTTATATTTTCCATTGATTTTT GGGTATACCTACTTGTTTTATTGATTTATTTTCTCTCAATTCTACTTACAACAGGCAATGCTTG TACATCCTGATAAAAATATGGGGAGTCCTTTAGCTAGTGAATCATTTAAGAAACTTCAATGTGC TTACGAGGTGAGCAACTATGTTCTTCTTGTTATATTTTAGTCTTAATTTAATTTCTTATTTTGA GTTCCTGTTTTGTGTACATATAAAATGAAAGCTGAAGAATGTCATCAGCTCTGTAAGTGTCGGC TCTGGCCTTAAGCAGATTTGGCGTGTATTTTGTAGGTTCTTTCTGATTCCGTGAAAAAGAGGGA CTATGATGAGCAATTAAGAAAGGAGGAATCCAGGACTCGGAGTGTCTGTCAAGAGTCCCATAGC TCTTCACGGCAGGTAGTTTTGATTTCTATTGCGCCTTTTCATTTTTGTTGCTTCGTTTTATTTT CTTGCAGTTCTTTTTTCAATGGAATTTATAGCCAAGAGGAATGAAAATGCAAAAATGCTTGGCA CAATGGAGATAATATGTAACTTCTTAGAATTCAAAAATCTAGCTTCGGGGTTCTTTTCACTTGG TTTTGCTCTGTCCAGGAGTTTCTTTATATTGATATATTGCTATAGATTTTTTGGAAAATGGAAA AAAAAATGTCATTCTATAGTAACTTTGTCCTCTTGAGCAAAAACCAATTTATGAGTCACGGTGA CAGAGGTTACCTGGTCTGACAATCGACTAATTAAGGGTTGTTCAACATGATGGCAGTGTTTACC TCTGGCAGTCACTATCGAGTGTTTTATGTTGTTATGGTTAGTGCCTGCTGGCTGCATGCGAAAG CTTGTTTTGCATTGCTGATTCATGTGATTCTGAGTTAGTCATTCATGTTGTATGATAATGTAAA ATTAATACCTTTCAACCATTATTTATTTCAGCAGCCCAGTCCAGACTATTGCTCTGAAGAATCA AGGCGTATACAGTGCACTAAGTGTGGTAATTCACATATATGGGTATGCACAAATAGGAACAAGG CCAAGGCTAGATGGTGCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							gar_circ_000408* 						
					
						PMCS
						0.127626297

Conservation Information
Conserved circRNAs	gar_circ_000408*
PMCS	0.127626297

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							47230011-47228159(+)
47228150-47228159(+)
						
						Potential amino acid sequence
						
							MVPGYMFSLSHARLIVLIATTYSIYFVKDRVGWLGVFLSINLAFLSNDVLNYLVQRFDNVSETA
HYEEPKESKPVMEDDLSGECEYSNPSIDSEKVQPCKSSSKSATTSVINQKEVSAKRVVKEETSS
ADEMTRILNCTDHYQALGIPRHTKIDTAVLKKEYKKKAMLVHPDKNMGSPLASESFKKLQCAYE
VLSDSVKKRDYDEQLRKEESRTRSVCQESHSSSRQQPSPDYCSEESRRIQCTKCGNSHIWVCTN
RNKAKARWCQVICSP*(+)
MFSLSHARLIVLIATTYSIYFVKDRVGWLGVFLSINLAFLSNDVLNYLVQRFDNVSETAHYEEP
KESKPVMEDDLSGECEYSNPSIDSEKVQPCKSSSKSATTSVINQKEVSAKRVVKEETSSADEMT
RILNCTDHYQALGIPRHTKIDTAVLKKEYKKKAMLVHPDKNMGSPLASESFKKLQCAYEVLSDS
VKKRDYDEQLRKEESRTRSVCQESHSSSRQQPSPDYCSEESRRIQCTKCGNSHIWVCTNRNKAK
ARWCQVICSP*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	47230011-47228159(+) 47228150-47228159(+)
Potential amino acid sequence	MVPGYMFSLSHARLIVLIATTYSIYFVKDRVGWLGVFLSINLAFLSNDVLNYLVQRFDNVSETA HYEEPKESKPVMEDDLSGECEYSNPSIDSEKVQPCKSSSKSATTSVINQKEVSAKRVVKEETSS ADEMTRILNCTDHYQALGIPRHTKIDTAVLKKEYKKKAMLVHPDKNMGSPLASESFKKLQCAYE VLSDSVKKRDYDEQLRKEESRTRSVCQESHSSSRQQPSPDYCSEESRRIQCTKCGNSHIWVCTN RNKAKARWCQVICSP(+) MFSLSHARLIVLIATTYSIYFVKDRVGWLGVFLSINLAFLSNDVLNYLVQRFDNVSETAHYEEP KESKPVMEDDLSGECEYSNPSIDSEKVQPCKSSSKSATTSVINQKEVSAKRVVKEETSSADEMT RILNCTDHYQALGIPRHTKIDTAVLKKEYKKKAMLVHPDKNMGSPLASESFKKLQCAYEVLSDS VKKRDYDEQLRKEESRTRSVCQESHSSSRQQPSPDYCSEESRRIQCTKCGNSHIWVCTNRNKAK ARWCQVICSP(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.013G178800_circ_g.2

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