Plant Circular RNA Database

Detail information of Solyc10g074940.1_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc10g074940.1_circ_g.2
					
						ID in PlantcircBase
						sly_circ_003153
					
						Alias
						10:57982114|57984198
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr10: 58657582-58659666  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc10g074940.1						
					
						Parent gene annotation
						
							Phospholipid-transporting ATPase
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc10g074940.1_circ_g.1 Solyc10g074940.1_circ_g.3 						
					
						Support reads
						11
					
						Tissues
						fruit
					
						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
						Solyc10g074940.1.1:4

General Information
CircRNA Name	Solyc10g074940.1_circ_g.2
ID in PlantcircBase	sly_circ_003153
Alias	10:57982114\|57984198
Organism	Solanum lycopersicum
Position	chr10: 58657582-58659666 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc10g074940.1
Parent gene annotation	Phospholipid-transporting ATPase
Parent gene strand	+
Alternative splicing	Solyc10g074940.1_circ_g.1 Solyc10g074940.1_circ_g.3
Support reads	11
Tissues	fruit
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	Solyc10g074940.1.1:4

			
						 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  
						
							GATTGCTCCTTGTGCATGGACATTGGAATTACCAGCGAGTTGGTTATTTGGTTCTTTACAACTT
CTACAGAAATGCTGTTTTCGTTTTCATGCTTTTCTGaatcgacagctgtgccttcaaatcaagg
aaaattgaggcttaacgcagaaattccaaccgattctgaacttatggaattgttacatattgag
ctagccgg

									
								

					

						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: 1474
Transcript exons: 58657582-58657921,58658191-58658980,58659096-58659219,58
659447-58659666
AATCGACAGCTGTGCCTTCAAATCAAGGAAAATTGAGGCTTAACGCAGAAATTCCAACCGATTC
TGAACTTATGGAATTGTTACATATTGAGCTAGCCGGGGAAGAGAGGATTGCTGCACATGAGTTC
TTTATGACATTGGCAGCATGTAATACCGTGATTCCTATTCTTACCCACAGTTCATCTTCGGATG
AAGTGCATGACACTGTTGGCACCATTGAGTATCAAGGTGAATCTCCTGATGAACAAGCACTAGT
TGCTGCTGCTTCTGCATATGGATATACACTTTGTGAGCGGACATCTGGTCATATTGTGATTGAT
GTCAATGGTGAGAAACTAAGGTTGGATGTCTTGGGACTGCATGAGTTTGATAGTGTACGCAAAA
GAATGTCTGTGGTCATCAGATTCCCAAGTGGTGCTGTGAAAGTTTTGGTTAAAGGGGCTGATAC
TACGATGTTTAGCATTTTAAGGAAAGACCACAAAAGCCACCACGACATACAAAATGTCACTCTT
AGCCATTTGAATGAGTACTCATCTGAAGGTTTGCGGACCCTGGTTGTTGGTGCAAGGGATCTTA
CGGGAGAAGAACTGGAGGAGTGGCAATTCATGTATGAGGATGCTAGCACCTCTTTGACCGACAG
ATCAGCAAAATTGCGCCAAACAGCATCTCTTATAGAATGCAACTTAACTCTACTAGGGGCCAGT
GCAATTGAGGACAAACTACAAGAGGGCGTACCGGAAGCTATTGAGTCTCTGCGTCAAGCAGGAA
TGAAGGTTTGGGTTCTTACTGGAGATAAGCAAGAAACTGCAATTTCAATTGGTATGTCTTGCAA
ACTCTTGACCTCAGACATGCAGCGGATCATCATTAATGGCACTTCAGAAAACGAATGCAAGAGG
TTATTGTTTGATGCTAAAATCAAATATGGTATAAACTCTGCAAGTTGTTGTAATCAAATCTCAA
CATGCCAGAGTGATGCAGAAAATAGTTATCTCGAAGCTTCTGCTAGTATGCAGACAAGTAATTT
GCCAGAGCCGCATGCAGGAGAGGAAGGAGTTTCTGATGGACCTTTGGCACTCATAATTGATGGG
AATAGTCTGGTATACATCTTAGAGAAAGATCTCGAGACCGAGCTATTCGACCTTGCAACCTCAT
GTAGGGCTGTGATTTGTTGTCGTGTTGCTCCCTTGCAGAAGGCTGGAATTGTTGACCTAATAAA
GAGCCGCACAGATGATATGACACTAGCCATAGGTGATGGGGCTAATGACGTTTCAATGATCCAA
ATGGCGGATGTTGGTGTTGGATTATGTGGTCAAGAAGGGCGGCAAGCAGTGATGGCATCAGATT
TTGCTATGGGACAGTTTCGCTTCCTGAAAAGATTGCTCCTTGTGCATGGACATTGGAATTACCA
GCGAGTTGGTTATTTGGTTCTTTACAACTTCTACAGAAATGCTGTTTTCGTTTTCATGCTTTTC
TG
						
					

						Genomic sequence
						
							AATCGACAGCTGTGCCTTCAAATCAAGGAAAATTGAGGCTTAACGCAGAAATTCCAACCGATTC
TGAACTTATGGAATTGTTACATATTGAGCTAGCCGGGGAAGAGAGGATTGCTGCACATGAGTTC
TTTATGACATTGGCAGCATGTAATACCGTGATTCCTATTCTTACCCACAGTTCATCTTCGGATG
AAGTGCATGACACTGTTGGCACCATTGAGTATCAAGGTGAATCTCCTGATGAACAAGCACTAGT
TGCTGCTGCTTCTGCATATGGATATACACTTTGTGAGCGGACATCTGGTCATATTGTGATTGAT
GTCAATGGTGAGAAACTAAGGTAGTTGCTCTCACTCAAAATCTCTAATTTGGTGTTAGTTGCAC
ATGGACACTTGTAGAACTTAACTAAATATTGTGGATTAGTCTAGTAGGTGTGATGTACTCTATC
TATGACATAGGAATGTTTCTGAAGCATAGTTTCTTCTCTCCTTAAATTTCACTTTTCTCTTCTT
GTTTACTTTAGTCTGTTGTAAAAATATCTTTTGTTATACAATAGTCTGTTCTTCCTCCTTCAGA
ATTGGGGACTGATGTATTGGCCTGCTGCCACAGGTTGGATGTCTTGGGACTGCATGAGTTTGAT
AGTGTACGCAAAAGAATGTCTGTGGTCATCAGATTCCCAAGTGGTGCTGTGAAAGTTTTGGTTA
AAGGGGCTGATACTACGATGTTTAGCATTTTAAGGAAAGACCACAAAAGCCACCACGACATACA
AAATGTCACTCTTAGCCATTTGAATGAGTACTCATCTGAAGGTTTGCGGACCCTGGTTGTTGGT
GCAAGGGATCTTACGGGAGAAGAACTGGAGGAGTGGCAATTCATGTATGAGGATGCTAGCACCT
CTTTGACCGACAGATCAGCAAAATTGCGCCAAACAGCATCTCTTATAGAATGCAACTTAACTCT
ACTAGGGGCCAGTGCAATTGAGGACAAACTACAAGAGGGCGTACCGGAAGCTATTGAGTCTCTG
CGTCAAGCAGGAATGAAGGTTTGGGTTCTTACTGGAGATAAGCAAGAAACTGCAATTTCAATTG
GTATGTCTTGCAAACTCTTGACCTCAGACATGCAGCGGATCATCATTAATGGCACTTCAGAAAA
CGAATGCAAGAGGTTATTGTTTGATGCTAAAATCAAATATGGTATAAACTCTGCAAGTTGTTGT
AATCAAATCTCAACATGCCAGAGTGATGCAGAAAATAGTTATCTCGAAGCTTCTGCTAGTATGC
AGACAAGTAATTTGCCAGAGCCGCATGCAGGAGAGGAAGGAGTTTCTGATGGACCTTTGGCACT
CATAATTGATGGGAATAGTCTGGTATACATCTTAGAGAAAGATCTCGAGACCGAGGTATGGACC
ATATCTCCCTTCTAAGGCTTTATTGTGATAATATACATGTTGTGGTACTTTTTTTCTTCTTTTT
GTGTAGCTTGTGTCCTAATGTGTGATTCCAATCCTTCCACAGCTATTCGACCTTGCAACCTCAT
GTAGGGCTGTGATTTGTTGTCGTGTTGCTCCCTTGCAGAAGGCTGGAATTGTTGACCTAATAAA
GAGCCGCACAGATGATATGACACTAGCCATAGGTGATGGTGAGTTAGCTACATCCGATGCCTTG
TCTGTACAAGGGAAAACTTATGTCAGAACCTTCATTGGTTGTTGGAAGAATGCAGTTCTATGAT
TTGTGCATAAAGTTTTGAAGTTTTTTTTTGGAGTCATGTTTTAAGGTTTTTCATGTGCATTGCG
TTACTGCTTTTTGAGATGCATTTCATGGGACGTTTTTCTTCATTTGTTTGCCCCTAATTTAAAT
CTTGCTCAGGGGCTAATGACGTTTCAATGATCCAAATGGCGGATGTTGGTGTTGGATTATGTGG
TCAAGAAGGGCGGCAAGCAGTGATGGCATCAGATTTTGCTATGGGACAGTTTCGCTTCCTGAAA
AGATTGCTCCTTGTGCATGGACATTGGAATTACCAGCGAGTTGGTTATTTGGTTCTTTACAACT
TCTACAGAAATGCTGTTTTCGTTTTCATGCTTTTCTG
						
					

			
		

Sequences
Splice junction sequence	GATTGCTCCTTGTGCATGGACATTGGAATTACCAGCGAGTTGGTTATTTGGTTCTTTACAACTT CTACAGAAATGCTGTTTTCGTTTTCATGCTTTTCTGaatcgacagctgtgccttcaaatcaagg aaaattgaggcttaacgcagaaattccaaccgattctgaacttatggaattgttacatattgag ctagccgg
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: 1474 Transcript exons: 58657582-58657921,58658191-58658980,58659096-58659219,58 659447-58659666 AATCGACAGCTGTGCCTTCAAATCAAGGAAAATTGAGGCTTAACGCAGAAATTCCAACCGATTC TGAACTTATGGAATTGTTACATATTGAGCTAGCCGGGGAAGAGAGGATTGCTGCACATGAGTTC TTTATGACATTGGCAGCATGTAATACCGTGATTCCTATTCTTACCCACAGTTCATCTTCGGATG AAGTGCATGACACTGTTGGCACCATTGAGTATCAAGGTGAATCTCCTGATGAACAAGCACTAGT TGCTGCTGCTTCTGCATATGGATATACACTTTGTGAGCGGACATCTGGTCATATTGTGATTGAT GTCAATGGTGAGAAACTAAGGTTGGATGTCTTGGGACTGCATGAGTTTGATAGTGTACGCAAAA GAATGTCTGTGGTCATCAGATTCCCAAGTGGTGCTGTGAAAGTTTTGGTTAAAGGGGCTGATAC TACGATGTTTAGCATTTTAAGGAAAGACCACAAAAGCCACCACGACATACAAAATGTCACTCTT AGCCATTTGAATGAGTACTCATCTGAAGGTTTGCGGACCCTGGTTGTTGGTGCAAGGGATCTTA CGGGAGAAGAACTGGAGGAGTGGCAATTCATGTATGAGGATGCTAGCACCTCTTTGACCGACAG ATCAGCAAAATTGCGCCAAACAGCATCTCTTATAGAATGCAACTTAACTCTACTAGGGGCCAGT GCAATTGAGGACAAACTACAAGAGGGCGTACCGGAAGCTATTGAGTCTCTGCGTCAAGCAGGAA TGAAGGTTTGGGTTCTTACTGGAGATAAGCAAGAAACTGCAATTTCAATTGGTATGTCTTGCAA ACTCTTGACCTCAGACATGCAGCGGATCATCATTAATGGCACTTCAGAAAACGAATGCAAGAGG TTATTGTTTGATGCTAAAATCAAATATGGTATAAACTCTGCAAGTTGTTGTAATCAAATCTCAA CATGCCAGAGTGATGCAGAAAATAGTTATCTCGAAGCTTCTGCTAGTATGCAGACAAGTAATTT GCCAGAGCCGCATGCAGGAGAGGAAGGAGTTTCTGATGGACCTTTGGCACTCATAATTGATGGG AATAGTCTGGTATACATCTTAGAGAAAGATCTCGAGACCGAGCTATTCGACCTTGCAACCTCAT GTAGGGCTGTGATTTGTTGTCGTGTTGCTCCCTTGCAGAAGGCTGGAATTGTTGACCTAATAAA GAGCCGCACAGATGATATGACACTAGCCATAGGTGATGGGGCTAATGACGTTTCAATGATCCAA ATGGCGGATGTTGGTGTTGGATTATGTGGTCAAGAAGGGCGGCAAGCAGTGATGGCATCAGATT TTGCTATGGGACAGTTTCGCTTCCTGAAAAGATTGCTCCTTGTGCATGGACATTGGAATTACCA GCGAGTTGGTTATTTGGTTCTTTACAACTTCTACAGAAATGCTGTTTTCGTTTTCATGCTTTTC TG
Genomic sequence	AATCGACAGCTGTGCCTTCAAATCAAGGAAAATTGAGGCTTAACGCAGAAATTCCAACCGATTC TGAACTTATGGAATTGTTACATATTGAGCTAGCCGGGGAAGAGAGGATTGCTGCACATGAGTTC TTTATGACATTGGCAGCATGTAATACCGTGATTCCTATTCTTACCCACAGTTCATCTTCGGATG AAGTGCATGACACTGTTGGCACCATTGAGTATCAAGGTGAATCTCCTGATGAACAAGCACTAGT TGCTGCTGCTTCTGCATATGGATATACACTTTGTGAGCGGACATCTGGTCATATTGTGATTGAT GTCAATGGTGAGAAACTAAGGTAGTTGCTCTCACTCAAAATCTCTAATTTGGTGTTAGTTGCAC ATGGACACTTGTAGAACTTAACTAAATATTGTGGATTAGTCTAGTAGGTGTGATGTACTCTATC TATGACATAGGAATGTTTCTGAAGCATAGTTTCTTCTCTCCTTAAATTTCACTTTTCTCTTCTT GTTTACTTTAGTCTGTTGTAAAAATATCTTTTGTTATACAATAGTCTGTTCTTCCTCCTTCAGA ATTGGGGACTGATGTATTGGCCTGCTGCCACAGGTTGGATGTCTTGGGACTGCATGAGTTTGAT AGTGTACGCAAAAGAATGTCTGTGGTCATCAGATTCCCAAGTGGTGCTGTGAAAGTTTTGGTTA AAGGGGCTGATACTACGATGTTTAGCATTTTAAGGAAAGACCACAAAAGCCACCACGACATACA AAATGTCACTCTTAGCCATTTGAATGAGTACTCATCTGAAGGTTTGCGGACCCTGGTTGTTGGT GCAAGGGATCTTACGGGAGAAGAACTGGAGGAGTGGCAATTCATGTATGAGGATGCTAGCACCT CTTTGACCGACAGATCAGCAAAATTGCGCCAAACAGCATCTCTTATAGAATGCAACTTAACTCT ACTAGGGGCCAGTGCAATTGAGGACAAACTACAAGAGGGCGTACCGGAAGCTATTGAGTCTCTG CGTCAAGCAGGAATGAAGGTTTGGGTTCTTACTGGAGATAAGCAAGAAACTGCAATTTCAATTG GTATGTCTTGCAAACTCTTGACCTCAGACATGCAGCGGATCATCATTAATGGCACTTCAGAAAA CGAATGCAAGAGGTTATTGTTTGATGCTAAAATCAAATATGGTATAAACTCTGCAAGTTGTTGT AATCAAATCTCAACATGCCAGAGTGATGCAGAAAATAGTTATCTCGAAGCTTCTGCTAGTATGC AGACAAGTAATTTGCCAGAGCCGCATGCAGGAGAGGAAGGAGTTTCTGATGGACCTTTGGCACT CATAATTGATGGGAATAGTCTGGTATACATCTTAGAGAAAGATCTCGAGACCGAGGTATGGACC ATATCTCCCTTCTAAGGCTTTATTGTGATAATATACATGTTGTGGTACTTTTTTTCTTCTTTTT GTGTAGCTTGTGTCCTAATGTGTGATTCCAATCCTTCCACAGCTATTCGACCTTGCAACCTCAT GTAGGGCTGTGATTTGTTGTCGTGTTGCTCCCTTGCAGAAGGCTGGAATTGTTGACCTAATAAA GAGCCGCACAGATGATATGACACTAGCCATAGGTGATGGTGAGTTAGCTACATCCGATGCCTTG TCTGTACAAGGGAAAACTTATGTCAGAACCTTCATTGGTTGTTGGAAGAATGCAGTTCTATGAT TTGTGCATAAAGTTTTGAAGTTTTTTTTTGGAGTCATGTTTTAAGGTTTTTCATGTGCATTGCG TTACTGCTTTTTGAGATGCATTTCATGGGACGTTTTTCTTCATTTGTTTGCCCCTAATTTAAAT CTTGCTCAGGGGCTAATGACGTTTCAATGATCCAAATGGCGGATGTTGGTGTTGGATTATGTGG TCAAGAAGGGCGGCAAGCAGTGATGGCATCAGATTTTGCTATGGGACAGTTTCGCTTCCTGAAA AGATTGCTCCTTGTGCATGGACATTGGAATTACCAGCGAGTTGGTTATTTGGTTCTTTACAACT TCTACAGAAATGCTGTTTTCGTTTTCATGCTTTTCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.78315244

Conservation Information
Conserved circRNAs	NA
PMCS	0.78315244

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							58659583-58659664(+)
58659497-58657614(+)
						
						Potential amino acid sequence
						
							MDIGITSELVIWFFTTSTEMLFSFSCFSESTAVPSNQGKLRLNAEIPTDSELMELLHIELAGEE
RIAAHEFFMTLAACNTVIPILTHSSSSDEVHDTVGTIEYQGESPDEQALVAAASAYGYTLCERT
SGHIVIDVNGEKLRLDVLGLHEFDSVRKRMSVVIRFPSGAVKVLVKGADTTMFSILRKDHKSHH
DIQNVTLSHLNEYSSEGLRTLVVGARDLTGEELEEWQFMYEDASTSLTDRSAKLRQTASLIECN
LTLLGASAIEDKLQEGVPEAIESLRQAGMKVWVLTGDKQETAISIGMSCKLLTSDMQRIIINGT
SENECKRLLFDAKIKYGINSASCCNQISTCQSDAENSYLEASASMQTSNLPEPHAGEEGVSDGP
LALIIDGNSLVYILEKDLETELFDLATSCRAVICCRVAPLQKAGIVDLIKSRTDDMTLAIGDGA
NDVSMIQMADVGVGLCGQEGRQAVMASDFAMGQFRFLKRLLLVHGHWNYQRVGYLVLYNFYRNA
VFVFMLF*(+)
MWSRRAASSDGIRFCYGTVSLPEKIAPCAWTLELPASWLFGSLQLLQKCCFRFHAFLNRQLCLQ
IKEN*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	58659583-58659664(+) 58659497-58657614(+)
Potential amino acid sequence	MDIGITSELVIWFFTTSTEMLFSFSCFSESTAVPSNQGKLRLNAEIPTDSELMELLHIELAGEE RIAAHEFFMTLAACNTVIPILTHSSSSDEVHDTVGTIEYQGESPDEQALVAAASAYGYTLCERT SGHIVIDVNGEKLRLDVLGLHEFDSVRKRMSVVIRFPSGAVKVLVKGADTTMFSILRKDHKSHH DIQNVTLSHLNEYSSEGLRTLVVGARDLTGEELEEWQFMYEDASTSLTDRSAKLRQTASLIECN LTLLGASAIEDKLQEGVPEAIESLRQAGMKVWVLTGDKQETAISIGMSCKLLTSDMQRIIINGT SENECKRLLFDAKIKYGINSASCCNQISTCQSDAENSYLEASASMQTSNLPEPHAGEEGVSDGP LALIIDGNSLVYILEKDLETELFDLATSCRAVICCRVAPLQKAGIVDLIKSRTDDMTLAIGDGA NDVSMIQMADVGVGLCGQEGRQAVMASDFAMGQFRFLKRLLLVHGHWNYQRVGYLVLYNFYRNA VFVFMLF(+) MWSRRAASSDGIRFCYGTVSLPEKIAPCAWTLELPASWLFGSLQLLQKCCFRFHAFLNRQLCLQ IKEN(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc10g074940.1_circ_g.2

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