Plant Circular RNA Database

Detail information of orai.006G070000_circ_g.2

			
						 General Information
					
						CircRNA Name
						orai.006G070000_circ_g.2
					
						ID in PlantcircBase
						gra_circ_000580
					
						Alias
						Chr06:28293799|28294840
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr06: 28293799-28294840  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.006G070000						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							orai.006G070000_circ_g.1 						
					
						Support reads
						15
					
						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.006G070000.5:4
Gorai.006G070000.2:4
Gorai.006G070000.6:4
Gorai.006G070000.3:4
Gorai.006G070000.1:4
Gorai.006G070000.4:4

General Information
CircRNA Name	orai.006G070000_circ_g.2
ID in PlantcircBase	gra_circ_000580
Alias	Chr06:28293799\|28294840
Organism	Gossypium raimondii
Position	chrChr06: 28293799-28294840 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.006G070000
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	orai.006G070000_circ_g.1
Support reads	15
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.006G070000.5:4 Gorai.006G070000.2:4 Gorai.006G070000.6:4 Gorai.006G070000.3:4 Gorai.006G070000.1:4 Gorai.006G070000.4:4

			
						 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  
						
							TATGGTGGTTTCTTTTCAGGCAGTTGTTTGTGGTCTTTATCGGAATGGTAGGATATACTTCCAC
CCTGGAGATGATGAAGTTCTTCAGGAAATGGACAAAgtatggagttgatacagatgcgtttctc
tccgtactagcacttcaacctattcccaagatggaatccattcccacgattgtcgaggtctgca
catttgca

						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
						
							GTATGGAGTTGATACAGATGCGTTTCTCTCCGTACTAGCACTTCAACCTATTCCCAAGATGGAA
TCCATTCCCACGATTGTCGAGGTCTGCACATTTGCATCACCATAGGATCAAAATATTATTCTAC
TAAGATAAATCGAGTTTAATTTGGCATTTTTTTCCCCTGATGCAGGTTTCAAATTCCAATACAT
GTGAGCTCTTGAAGTCAATCTCCGGACTGAAAGTAGAGCCAGTGGAAAATGTTTCTTCTAAACT
ATTTGCTCAATGTTCTCGGCAAAAGGGGCTCATAAAGATCTACAGGCACTTGCTTAATTACCAA
AGTATGATATGAGTTCTTGTTGAGAACTTCTATTTTCCTGATGTCCGAAAGACAATTAAAGTGT
AAATATTAAAATTCCCTGTTTATTGCTGCTTTTAAATAATCTGGGATGGTTGTAAATCTAGATA
CCTTTTAAAACTAGGTAGTTCTTATTCTTGGTCAATAAAACTGTATGAGTGTTGGGTTTGAGTG
TTGGATAGATAATGTGACCAAGATGGGGTATGTGCAATATTTAAGTCTTTCCATGTCTCTGGAG
GGTCATATCTATGTGCCCATGTTTAAAAATGTATCAGACAATGTGTCAAATACGGATACTTAAA
AAACAATAGAGTCGGAAGAACATAGGCTTGACCTACAAAATGTTGTCATTTCTAATAGTTTCTT
CTCTTAGGGTCTTTTCTATCGGTAAATGAAACTCTATGGGTCCATTTCTTGTTCTTGTCATAGA
TTTCTACTCGAAAACTAATTATATCATGATATTGCAGAAAATGTATTCAGTCTTCACCATTTTC
CGAGTCTAACCGGGTTGACATATAGACAAATACGACAAGGGTTTCAAGAGGTAATGCTTTATGC
TAAAACTCAGTATTTGTTGGTATGAAGAACTTCCATGCTATTGTCTTATGGTGGTTTCTTTTCA
GGCAGTTGTTTGTGGTCTTTATCGGAATGGTAGGATATACTTCCACCCTGGAGATGATGAAGTT
CTTCAGGAAATGGACAAA

Sequences
Splice junction sequence	TATGGTGGTTTCTTTTCAGGCAGTTGTTTGTGGTCTTTATCGGAATGGTAGGATATACTTCCAC CCTGGAGATGATGAAGTTCTTCAGGAAATGGACAAAgtatggagttgatacagatgcgtttctc tccgtactagcacttcaacctattcccaagatggaatccattcccacgattgtcgaggtctgca catttgca
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	GTATGGAGTTGATACAGATGCGTTTCTCTCCGTACTAGCACTTCAACCTATTCCCAAGATGGAA TCCATTCCCACGATTGTCGAGGTCTGCACATTTGCATCACCATAGGATCAAAATATTATTCTAC TAAGATAAATCGAGTTTAATTTGGCATTTTTTTCCCCTGATGCAGGTTTCAAATTCCAATACAT GTGAGCTCTTGAAGTCAATCTCCGGACTGAAAGTAGAGCCAGTGGAAAATGTTTCTTCTAAACT ATTTGCTCAATGTTCTCGGCAAAAGGGGCTCATAAAGATCTACAGGCACTTGCTTAATTACCAA AGTATGATATGAGTTCTTGTTGAGAACTTCTATTTTCCTGATGTCCGAAAGACAATTAAAGTGT AAATATTAAAATTCCCTGTTTATTGCTGCTTTTAAATAATCTGGGATGGTTGTAAATCTAGATA CCTTTTAAAACTAGGTAGTTCTTATTCTTGGTCAATAAAACTGTATGAGTGTTGGGTTTGAGTG TTGGATAGATAATGTGACCAAGATGGGGTATGTGCAATATTTAAGTCTTTCCATGTCTCTGGAG GGTCATATCTATGTGCCCATGTTTAAAAATGTATCAGACAATGTGTCAAATACGGATACTTAAA AAACAATAGAGTCGGAAGAACATAGGCTTGACCTACAAAATGTTGTCATTTCTAATAGTTTCTT CTCTTAGGGTCTTTTCTATCGGTAAATGAAACTCTATGGGTCCATTTCTTGTTCTTGTCATAGA TTTCTACTCGAAAACTAATTATATCATGATATTGCAGAAAATGTATTCAGTCTTCACCATTTTC CGAGTCTAACCGGGTTGACATATAGACAAATACGACAAGGGTTTCAAGAGGTAATGCTTTATGC TAAAACTCAGTATTTGTTGGTATGAAGAACTTCCATGCTATTGTCTTATGGTGGTTTCTTTTCA GGCAGTTGTTTGTGGTCTTTATCGGAATGGTAGGATATACTTCCACCCTGGAGATGATGAAGTT CTTCAGGAAATGGACAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							ghi_circ_000350* gar_circ_000193* 						
					
						PMCS
						0.12220092

Conservation Information
Conserved circRNAs	ghi_circ_000350* gar_circ_000193*
PMCS	0.12220092

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28293857-28293807(+)
28294785-28293807(+)
						
						Potential amino acid sequence
						
							MESIPTIVEVSNSNTCELLKSISGLKVEPVENVSSKLFAQCSRQKGLIKIYRHLLNYQKNVFSL
HHFPSLTGLTYRQIRQGFQEAVVCGLYRNGRIYFHPGDDEVLQEMDKVWS*(+)
MVGYTSTLEMMKFFRKWTKYGVDTDAFLSVLALQPIPKMESIPTIVEVSNSNTCELLKSISGLK
VEPVENVSSKLFAQCSRQKGLIKIYRHLLNYQKNVFSLHHFPSLTGLTYRQIRQGFQEAVVCGL
YRNGRIYFHPGDDEVLQEMDKVWS*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28293857-28293807(+) 28294785-28293807(+)
Potential amino acid sequence	MESIPTIVEVSNSNTCELLKSISGLKVEPVENVSSKLFAQCSRQKGLIKIYRHLLNYQKNVFSL HHFPSLTGLTYRQIRQGFQEAVVCGLYRNGRIYFHPGDDEVLQEMDKVWS(+) MVGYTSTLEMMKFFRKWTKYGVDTDAFLSVLALQPIPKMESIPTIVEVSNSNTCELLKSISGLK VEPVENVSSKLFAQCSRQKGLIKIYRHLLNYQKNVFSLHHFPSLTGLTYRQIRQGFQEAVVCGL YRNGRIYFHPGDDEVLQEMDKVWS(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.006G070000_circ_g.2

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