Plant Circular RNA Database

Detail information of orai.004G261400_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.004G261400_circ_g.1
					
						ID in PlantcircBase
						gra_circ_000403
					
						Alias
						Chr04:59679549|59680639
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr04: 59679549-59680639  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.004G261400						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2/19
					
						Tissues
						leaf/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.004G261400.2:4
Gorai.004G261400.1:4

General Information
CircRNA Name	orai.004G261400_circ_g.1
ID in PlantcircBase	gra_circ_000403
Alias	Chr04:59679549\|59680639
Organism	Gossypium raimondii
Position	chrChr04: 59679549-59680639 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.004G261400
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	NA
Support reads	2/19
Tissues	leaf/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.004G261400.2:4 Gorai.004G261400.1:4

			
						 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  
						
							ATCTTTACGTAATAGGTTATTGTTTCTTCATGAGGGGAAGGTTGTTTGGCAAGGAATGACCGAA
GAATTTACAACGTCGACAAATCCAATTGTTAGACAGatacgaaaattcatgcatgtctgatgaa
caaatttcacagctcgtgacggagaccttggctgctgttggtttaaaggtatgcttgtgattcc
acttcctt

									
								

					

						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: 445
Transcript exons: 59679549-59679624,59679943-59680050,59680292-59680467,59
680555-59680639
ATACGAAAATTCATGCATGTCTGATGAACAAATTTCACAGCTCGTGACGGAGACCTTGGCTGCT
GTTGGTTTAAAGGGAGTTGAAGAAAGATTACCTTCTGAGTTGTCCGGAGGAATGAAGAAAAGAG
TTGCTTTAGCTCGTTCTATAATTTGTGACATCTCCAAAGAATCAATTGAGCCGGAGGTGCTTTT
ATATGACGAACCAACAGCTGGGCTCGATCCAATTGCATCGACCGTTGTTGAAGATCTCATCCGC
TCTGTCCATACAAAGGGTGAAGATGCATCGGGGAAACAAGGGAAGATTGCATCTTATGTGGTTG
TTACTCATCAACATAGTACCATTCTAAGAGCTGTTGACAGGTTATTGTTTCTTCATGAGGGGAA
GGTTGTTTGGCAAGGAATGACCGAAGAATTTACAACGTCGACAAATCCAATTGTTAGACAG
						
					

						Genomic sequence
						
							ATACGAAAATTCATGCATGTCTGATGAACAAATTTCACAGCTCGTGACGGAGACCTTGGCTGCT
GTTGGTTTAAAGGTATGCTTGTGATTCCACTTCCTTTTCTTGGATAGCATAGAATGTTAATTAT
CTGTCCTGGCTCGGAACTTTTTGGCTTGATTCAGAGTTAACCTGTAACAAATAAGTAAGATCTT
AGCAAGATGTTGGGTCGGGCTTAAGTGAAAATCAGCATAATGAACAGTTGGAACTTGTTTTCCG
TAGTTAATTGTGGAATCTCAATTCTCATAGAACGTAACAAGTGTATGCCTTTACTTCTGTCACC
TCTTTCTGCACTGTAGGTGCCTTAGTATTTAAGTTTCCGGCTGATTAAAAATTCTGACGCAATG
TTCTCTTCAGGGAGTTGAAGAAAGATTACCTTCTGAGTTGTCCGGAGGAATGAAGAAAAGAGTT
GCTTTAGCTCGTTCTATAATTTGTGACATCTCCAAAGAATCAATTGAGCCGGAGGTACAGTAAA
TTTCTCTTTGAAATTAATGGATGTGGATCGGAAGTTGTAATGACGTATAACTGCCTCGGTTTTG
TATCTTAAGATAAACATTCAATTGGTCTTCCTTTCAAGTTTCTACTAGTATCCAGCCGATCCTA
TTTTCTTTCAGAGTTTAATCCCTAACTGTAGGACCATAAAATTTAGTCCACATTCCCACTGGAG
TATATATTCCGGCTTGGTCACCTCCTTTTATTTCTTCAGGTGCTTTTATATGACGAACCAACAG
CTGGGCTCGATCCAATTGCATCGACCGTTGTTGAAGATCTCATCCGCTCTGTCCATACAAAGGG
TGAAGATGCATCGGGGAAACAAGGGAAGATTGCATCTTATGTGGTTGTTACTCATCAACATAGT
ACCATTCTAAGAGCTGTTGACAGGTTTACCCCGAAATCATGATGTTTTTAATTGGTTTTTTGCT
ATGATGTTGGATGCCATACTTAATGAACTTCATCTTTACGTAATAGGTTATTGTTTCTTCATGA
GGGGAAGGTTGTTTGGCAAGGAATGACCGAAGAATTTACAACGTCGACAAATCCAATTGTTAGA
CAG
						
					

			
		

Sequences
Splice junction sequence	ATCTTTACGTAATAGGTTATTGTTTCTTCATGAGGGGAAGGTTGTTTGGCAAGGAATGACCGAA GAATTTACAACGTCGACAAATCCAATTGTTAGACAGatacgaaaattcatgcatgtctgatgaa caaatttcacagctcgtgacggagaccttggctgctgttggtttaaaggtatgcttgtgattcc acttcctt
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: 445 Transcript exons: 59679549-59679624,59679943-59680050,59680292-59680467,59 680555-59680639 ATACGAAAATTCATGCATGTCTGATGAACAAATTTCACAGCTCGTGACGGAGACCTTGGCTGCT GTTGGTTTAAAGGGAGTTGAAGAAAGATTACCTTCTGAGTTGTCCGGAGGAATGAAGAAAAGAG TTGCTTTAGCTCGTTCTATAATTTGTGACATCTCCAAAGAATCAATTGAGCCGGAGGTGCTTTT ATATGACGAACCAACAGCTGGGCTCGATCCAATTGCATCGACCGTTGTTGAAGATCTCATCCGC TCTGTCCATACAAAGGGTGAAGATGCATCGGGGAAACAAGGGAAGATTGCATCTTATGTGGTTG TTACTCATCAACATAGTACCATTCTAAGAGCTGTTGACAGGTTATTGTTTCTTCATGAGGGGAA GGTTGTTTGGCAAGGAATGACCGAAGAATTTACAACGTCGACAAATCCAATTGTTAGACAG
Genomic sequence	ATACGAAAATTCATGCATGTCTGATGAACAAATTTCACAGCTCGTGACGGAGACCTTGGCTGCT GTTGGTTTAAAGGTATGCTTGTGATTCCACTTCCTTTTCTTGGATAGCATAGAATGTTAATTAT CTGTCCTGGCTCGGAACTTTTTGGCTTGATTCAGAGTTAACCTGTAACAAATAAGTAAGATCTT AGCAAGATGTTGGGTCGGGCTTAAGTGAAAATCAGCATAATGAACAGTTGGAACTTGTTTTCCG TAGTTAATTGTGGAATCTCAATTCTCATAGAACGTAACAAGTGTATGCCTTTACTTCTGTCACC TCTTTCTGCACTGTAGGTGCCTTAGTATTTAAGTTTCCGGCTGATTAAAAATTCTGACGCAATG TTCTCTTCAGGGAGTTGAAGAAAGATTACCTTCTGAGTTGTCCGGAGGAATGAAGAAAAGAGTT GCTTTAGCTCGTTCTATAATTTGTGACATCTCCAAAGAATCAATTGAGCCGGAGGTACAGTAAA TTTCTCTTTGAAATTAATGGATGTGGATCGGAAGTTGTAATGACGTATAACTGCCTCGGTTTTG TATCTTAAGATAAACATTCAATTGGTCTTCCTTTCAAGTTTCTACTAGTATCCAGCCGATCCTA TTTTCTTTCAGAGTTTAATCCCTAACTGTAGGACCATAAAATTTAGTCCACATTCCCACTGGAG TATATATTCCGGCTTGGTCACCTCCTTTTATTTCTTCAGGTGCTTTTATATGACGAACCAACAG CTGGGCTCGATCCAATTGCATCGACCGTTGTTGAAGATCTCATCCGCTCTGTCCATACAAAGGG TGAAGATGCATCGGGGAAACAAGGGAAGATTGCATCTTATGTGGTTGTTACTCATCAACATAGT ACCATTCTAAGAGCTGTTGACAGGTTTACCCCGAAATCATGATGTTTTTAATTGGTTTTTTGCT ATGATGTTGGATGCCATACTTAATGAACTTCATCTTTACGTAATAGGTTATTGTTTCTTCATGA GGGGAAGGTTGTTTGGCAAGGAATGACCGAAGAATTTACAACGTCGACAAATCCAATTGTTAGA CAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							gar_circ_000549 						
					
						PMCS
						0.464813665

Conservation Information
Conserved circRNAs	gar_circ_000549
PMCS	0.464813665

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							59679565-59679569(+)
59680360-59680558(-)
59679563-59680569(-)
						
						Potential amino acid sequence
						
							MSDEQISQLVTETLAAVGLKGVEERLPSELSGGMKKRVALARSIICDISKESIEPEVLLYDEPT
AGLDPIASTVVEDLIRSVHTKGEDASGKQGKIASYVVVTHQHSTILRAVDRLLFLHEGKVVWQG
MTEEFTTSTNPIVRQIRKFMHV*(+)
MRSSTTVDAIGSSPAVGSSYKSTSGSIDSLEMSQIIERAKATLFFIPPDNSEGNLSSTPFKPTA
AKVSVTSCEICSSDMHEFSYLSNNWICRRCKFFGHSLPNNLPLMKKQ*(-)
MNFRICLTIGFVDVVNSSVIPCQTTFPS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	59679565-59679569(+) 59680360-59680558(-) 59679563-59680569(-)
Potential amino acid sequence	MSDEQISQLVTETLAAVGLKGVEERLPSELSGGMKKRVALARSIICDISKESIEPEVLLYDEPT AGLDPIASTVVEDLIRSVHTKGEDASGKQGKIASYVVVTHQHSTILRAVDRLLFLHEGKVVWQG MTEEFTTSTNPIVRQIRKFMHV(+) MRSSTTVDAIGSSPAVGSSYKSTSGSIDSLEMSQIIERAKATLFFIPPDNSEGNLSSTPFKPTA AKVSVTSCEICSSDMHEFSYLSNNWICRRCKFFGHSLPNNLPLMKKQ(-) MNFRICLTIGFVDVVNSSVIPCQTTFPS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.004G261400_circ_g.1

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