Plant Circular RNA Database

Detail information of orai.006G135500_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.006G135500_circ_g.1
					
						ID in PlantcircBase
						gra_circ_000624
					
						Alias
						Chr06:39141258|39141910
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr06: 39141258-39141910  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.006G135500						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2
					
						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.006G135500.5:2
Gorai.006G135500.1:2
Gorai.006G135500.4:1
Gorai.006G135500.3:2
Gorai.006G135500.2:2

General Information
CircRNA Name	orai.006G135500_circ_g.1
ID in PlantcircBase	gra_circ_000624
Alias	Chr06:39141258\|39141910
Organism	Gossypium raimondii
Position	chrChr06: 39141258-39141910 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.006G135500
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	NA
Support reads	2
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.006G135500.5:2 Gorai.006G135500.1:2 Gorai.006G135500.4:1 Gorai.006G135500.3:2 Gorai.006G135500.2:2

			
						 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  
						
							AGCGAGCAGGGTTTTATGATATGGAGACCACATCTGAATGGATGAATGATGTTAGTTCTCAGAG
GTTTGCAAACTATCATGAAGCAGATCTTGTGCCCAAcctttgatgaacttcaaagttccacaac
ctgatgatgattttgattattatgggaatagtagtcaggacgagagcagaggtagccaaggtag
tttttttt

						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: 470
Transcript exons: 39141258-39141345,39141529-39141910
CCTTTGATGAACTTCAAAGTTCCACAACCTGATGATGATTTTGATTATTATGGGAATAGTAGTC
AGGACGAGAGCAGAGGTAGCCAAGGTGGAGCAATGTCGCACCATGGTAATGGAACTATGTCTGA
GAGGGAATTGAGTTTGGCGAAGCGAAAGTGGAGGGGGGCATTAAATAGTGACGAGGAGGACGAC
GATTATCAAGGCACCCATATCACAGAGGAGCGGTATCGGTCAATGCTTGGAGAACACGTACAAA
AGTACAAAAGGAGGTTCAAGGATACCTCTGCGAGTCCTGCTCCTTCACGAATGGGTATTCCAGC
TCCAAAGAGCAATTTGGGTAGTTCCAAAAATAGGAAATTGTTGAATGAGCAGCGAGCAGGGTTT
TATGATATGGAGACCACATCTGAATGGATGAATGATGTTAGTTCTCAGAGGTTTGCAAACTATC
ATGAAGCAGATCTTGTGCCCAA
						
						Genomic sequence
						
							CCTTTGATGAACTTCAAAGTTCCACAACCTGATGATGATTTTGATTATTATGGGAATAGTAGTC
AGGACGAGAGCAGAGGTAGCCAAGGTAGTTTTTTTTTTTTTTTTACAACTCGGAATTAAGGGCT
CCTTTGGATTCTATCCTTGTAAATGCACCTTTTTTTCATTGGTTTTTTATACGTCTAGAGAATT
TTGGTGGTTAAAACAGTTCGATTTAAAAAAAAAAATTGACCTAGTGAATGTGCATTGTTCTTTA
ATGGGATTTCAATAGGTGGAGCAATGTCGCACCATGGTAATGGAACTATGTCTGAGAGGGAATT
GAGTTTGGCGAAGCGAAAGTGGAGGGGGGCATTAAATAGTGACGAGGAGGACGACGATTATCAA
GGCACCCATATCACAGAGGAGCGGTATCGGTCAATGCTTGGAGAACACGTACAAAAGTACAAAA
GGAGGTTCAAGGATACCTCTGCGAGTCCTGCTCCTTCACGAATGGGTATTCCAGCTCCAAAGAG
CAATTTGGGTAGTTCCAAAAATAGGAAATTGTTGAATGAGCAGCGAGCAGGGTTTTATGATATG
GAGACCACATCTGAATGGATGAATGATGTTAGTTCTCAGAGGTTTGCAAACTATCATGAAGCAG
ATCTTGTGCCCAA

Sequences
Splice junction sequence	AGCGAGCAGGGTTTTATGATATGGAGACCACATCTGAATGGATGAATGATGTTAGTTCTCAGAG GTTTGCAAACTATCATGAAGCAGATCTTGTGCCCAAcctttgatgaacttcaaagttccacaac ctgatgatgattttgattattatgggaatagtagtcaggacgagagcagaggtagccaaggtag tttttttt
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: 470 Transcript exons: 39141258-39141345,39141529-39141910 CCTTTGATGAACTTCAAAGTTCCACAACCTGATGATGATTTTGATTATTATGGGAATAGTAGTC AGGACGAGAGCAGAGGTAGCCAAGGTGGAGCAATGTCGCACCATGGTAATGGAACTATGTCTGA GAGGGAATTGAGTTTGGCGAAGCGAAAGTGGAGGGGGGCATTAAATAGTGACGAGGAGGACGAC GATTATCAAGGCACCCATATCACAGAGGAGCGGTATCGGTCAATGCTTGGAGAACACGTACAAA AGTACAAAAGGAGGTTCAAGGATACCTCTGCGAGTCCTGCTCCTTCACGAATGGGTATTCCAGC TCCAAAGAGCAATTTGGGTAGTTCCAAAAATAGGAAATTGTTGAATGAGCAGCGAGCAGGGTTT TATGATATGGAGACCACATCTGAATGGATGAATGATGTTAGTTCTCAGAGGTTTGCAAACTATC ATGAAGCAGATCTTGTGCCCAA
Genomic sequence	CCTTTGATGAACTTCAAAGTTCCACAACCTGATGATGATTTTGATTATTATGGGAATAGTAGTC AGGACGAGAGCAGAGGTAGCCAAGGTAGTTTTTTTTTTTTTTTTACAACTCGGAATTAAGGGCT CCTTTGGATTCTATCCTTGTAAATGCACCTTTTTTTCATTGGTTTTTTATACGTCTAGAGAATT TTGGTGGTTAAAACAGTTCGATTTAAAAAAAAAAATTGACCTAGTGAATGTGCATTGTTCTTTA ATGGGATTTCAATAGGTGGAGCAATGTCGCACCATGGTAATGGAACTATGTCTGAGAGGGAATT GAGTTTGGCGAAGCGAAAGTGGAGGGGGGCATTAAATAGTGACGAGGAGGACGACGATTATCAA GGCACCCATATCACAGAGGAGCGGTATCGGTCAATGCTTGGAGAACACGTACAAAAGTACAAAA GGAGGTTCAAGGATACCTCTGCGAGTCCTGCTCCTTCACGAATGGGTATTCCAGCTCCAAAGAG CAATTTGGGTAGTTCCAAAAATAGGAAATTGTTGAATGAGCAGCGAGCAGGGTTTTATGATATG GAGACCACATCTGAATGGATGAATGATGTTAGTTCTCAGAGGTTTGCAAACTATCATGAAGCAG ATCTTGTGCCCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.565094755

Conservation Information
Conserved circRNAs	NA
PMCS	0.565094755

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							39141264-39141261(+)
39141856-39141286(+)
39141549-39141889(-)
						
						Potential amino acid sequence
						
							MNFKVPQPDDDFDYYGNSSQDESRGSQGGAMSHHGNGTMSERELSLAKRKWRGALNSDEEDDDY
QGTHITEERYRSMLGEHVQKYKRRFKDTSASPAPSRMGIPAPKSNLGSSKNRKLLNEQRAGFYD
METTSEWMNDVSSQRFANYHEADLVPNL*(+)
MMLVLRGLQTIMKQILCPTFDELQSSTT*(+)
MVRHCSTLATSALVLTTIPIIIKIIIRLWNFEVHQRLGTRSAS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	39141264-39141261(+) 39141856-39141286(+) 39141549-39141889(-)
Potential amino acid sequence	MNFKVPQPDDDFDYYGNSSQDESRGSQGGAMSHHGNGTMSERELSLAKRKWRGALNSDEEDDDY QGTHITEERYRSMLGEHVQKYKRRFKDTSASPAPSRMGIPAPKSNLGSSKNRKLLNEQRAGFYD METTSEWMNDVSSQRFANYHEADLVPNL(+) MMLVLRGLQTIMKQILCPTFDELQSSTT(+) MVRHCSTLATSALVLTTIPIIIKIIIRLWNFEVHQRLGTRSAS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.006G135500_circ_g.1

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