Plant Circular RNA Database

Detail information of Solyc01g056690.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc01g056690.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_000119
					
						Alias
						1:48828543|48829750
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 55928143-55929350  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc01g056690.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc01g056690.2_circ_g.1 Solyc01g056690.2_circ_g.2 Solyc01g056690.2_circ_g.4 						
					
						Support reads
						8
					
						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  
						
							CT-AC							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
						Solyc01g056690.2.1:4

General Information
CircRNA Name	Solyc01g056690.2_circ_g.3
ID in PlantcircBase	sly_circ_000119
Alias	1:48828543\|48829750
Organism	Solanum lycopersicum
Position	chr1: 55928143-55929350 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc01g056690.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc01g056690.2_circ_g.1 Solyc01g056690.2_circ_g.2 Solyc01g056690.2_circ_g.4
Support reads	8
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	CT-AC 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	Solyc01g056690.2.1:4

			
						 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  
						
							CGCTGGATTGAATGTCAGCTAGAACGGGTCGTAAGCCTTCAGATACAACGGCTGCAGTAAGTTG
CTGCTCAGTGTAGTTCATTTCAAGCACCGTATGGGCctggagagccgcatcacccaccctccat
gtatccacttgccatttgacaaggccacctgcacggataatacgttcccgctcctcaagacaac
ttgcaaca

									
								

					

						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: 927
Transcript exons: 55928143-55928247,55928329-55928548,55928647-55928716,55
928819-55929350
CTGGAGAGCCGCATCACCCACCCTCCATGTATCCACTTGCCATTTGACAAGGCCACCTGCACGG
ATAATACGTTCCCGCTCCTCAAGACAACTTGCAACATGATCCCTACTTAGAGCATATGGAATCC
CAGATCGACACAGAATTGTTCTGCAATCACCAGCATTAGCAACAATAAGTTTGTTTCTGACGAT
AAGAGCAGCTATTGCAGTACAACCAGGGTGCCAATCTTTCTGAACTGCTCCCTTGCGTTTGCGA
GAAGAATCAAGTTGTGTCCTGAATGCAACATCTGTCTTTATGAATGCTTCAAAAAGCGCATCAG
AGGGACTGCAAACTGAACCAAGATTCTGCAAAAATCCTGGTAAAGCTCCAGAGGAAAACTCAGC
AGCTGCTGAACCTCGATGACCATCAAAGATTGCAAAGATGTGAATATCCTTTTCATCACACAAC
TGAGGCATAAGGAAGTGTCTATCTTCCATTGTTTCCCTTCTCCCACATGATGCAAAGGAACCCC
AAGACAGAACTGGACTATAGATATGATCATCTGAAGAATCCAGCCATGTGCTAGCAGCAAGGGC
AGTAGGAACTCTTTTCATAAAGTCTTTACCTTGACTGAACCAGCTAATATTCTCCTGATAGGTT
TGGAAATTTGCAGCATAGACGCCATTTGAAGAAATAAAAGCTTCCCCTGAGGCCTTCTCCATAC
AGCCCCTTCCAACATCATGTTCCAGAATGAAATCAAGTTCCACGACAATATCATCAAAAGAAGG
CCTATTTTGTGGATCTTTATCCCAACATCTTTCTATCAAAGAGACTAAACTTGCTGGAGCGCTG
GATTGAATGTCAGCTAGAACGGGTCGTAAGCCTTCAGATACAACGGCTGCAGTAAGTTGCTGCT
CAGTGTAGTTCATTTCAAGCACCGTATGGGC
						
					

						Genomic sequence
						
							CTGGAGAGCCGCATCACCCACCCTCCATGTATCCACTTGCCATTTGACAAGGCCACCTGCACGG
ATAATACGTTCCCGCTCCTCAAGACAACTTGCAACATGATCCTATGACAGTACCATATATCAGT
GAAAATGCATAGCCTTGTAATTCATCAGAAAGCTAGCTAAGAAAATGAATCATCTTACCCTACT
TAGAGCATATGGAATCCCAGATCGACACAGAATTGTTCTGCAATCACCAGCATTAGCAACAATA
AGTTTGTTTCTGACGATAAGAGCAGCTATTGCAGTACAACCAGGGTGCCAATCTTTCTGAACTG
CTCCCTTGCGTTTGCGAGAAGAATCAAGTTGTGTCCTGAATGCAACATCTGTCTTTATGAATGC
TTCAAAAAGCGCATCAGAGGGACTGCAAAGTCATAAACATCCAAGAGTTGAGTGCCTTGACTCT
TTGAAAACTTCTTGGTCATTCACAAACAAAAAAATCACAAGTTAAGCATGTAAAACCTGCAAAC
TGAACCAAGATTCTGCAAAAATCCTGGTAAAGCTCCAGAGGAAAACTCAGCAGCTGCTGAACCT
GTAGGCACACTAGTTAAGACGGCCATATTCGAGTGAAAAATGTTTATAATAAGTTTCACTTACG
AGAAATAAAATGGCTTCATAGTGACTGGTATACTACCTCGATGACCATCAAAGATTGCAAAGAT
GTGAATATCCTTTTCATCACACAACTGAGGCATAAGGAAGTGTCTATCTTCCATTGTTTCCCTT
CTCCCACATGATGCAAAGGAACCCCAAGACAGAACTGGACTATAGATATGATCATCTGAAGAAT
CCAGCCATGTGCTAGCAGCAAGGGCAGTAGGAACTCTTTTCATAAAGTCTTTACCTTGACTGAA
CCAGCTAATATTCTCCTGATAGGTTTGGAAATTTGCAGCATAGACGCCATTTGAAGAAATAAAA
GCTTCCCCTGAGGCCTTCTCCATACAGCCCCTTCCAACATCATGTTCCAGAATGAAATCAAGTT
CCACGACAATATCATCAAAAGAAGGCCTATTTTGTGGATCTTTATCCCAACATCTTTCTATCAA
AGAGACTAAACTTGCTGGAGCGCTGGATTGAATGTCAGCTAGAACGGGTCGTAAGCCTTCAGAT
ACAACGGCTGCAGTAAGTTGCTGCTCAGTGTAGTTCATTTCAAGCACCGTATGGGC
						
					

			
		

Sequences
Splice junction sequence	CGCTGGATTGAATGTCAGCTAGAACGGGTCGTAAGCCTTCAGATACAACGGCTGCAGTAAGTTG CTGCTCAGTGTAGTTCATTTCAAGCACCGTATGGGCctggagagccgcatcacccaccctccat gtatccacttgccatttgacaaggccacctgcacggataatacgttcccgctcctcaagacaac ttgcaaca
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: 927 Transcript exons: 55928143-55928247,55928329-55928548,55928647-55928716,55 928819-55929350 CTGGAGAGCCGCATCACCCACCCTCCATGTATCCACTTGCCATTTGACAAGGCCACCTGCACGG ATAATACGTTCCCGCTCCTCAAGACAACTTGCAACATGATCCCTACTTAGAGCATATGGAATCC CAGATCGACACAGAATTGTTCTGCAATCACCAGCATTAGCAACAATAAGTTTGTTTCTGACGAT AAGAGCAGCTATTGCAGTACAACCAGGGTGCCAATCTTTCTGAACTGCTCCCTTGCGTTTGCGA GAAGAATCAAGTTGTGTCCTGAATGCAACATCTGTCTTTATGAATGCTTCAAAAAGCGCATCAG AGGGACTGCAAACTGAACCAAGATTCTGCAAAAATCCTGGTAAAGCTCCAGAGGAAAACTCAGC AGCTGCTGAACCTCGATGACCATCAAAGATTGCAAAGATGTGAATATCCTTTTCATCACACAAC TGAGGCATAAGGAAGTGTCTATCTTCCATTGTTTCCCTTCTCCCACATGATGCAAAGGAACCCC AAGACAGAACTGGACTATAGATATGATCATCTGAAGAATCCAGCCATGTGCTAGCAGCAAGGGC AGTAGGAACTCTTTTCATAAAGTCTTTACCTTGACTGAACCAGCTAATATTCTCCTGATAGGTT TGGAAATTTGCAGCATAGACGCCATTTGAAGAAATAAAAGCTTCCCCTGAGGCCTTCTCCATAC AGCCCCTTCCAACATCATGTTCCAGAATGAAATCAAGTTCCACGACAATATCATCAAAAGAAGG CCTATTTTGTGGATCTTTATCCCAACATCTTTCTATCAAAGAGACTAAACTTGCTGGAGCGCTG GATTGAATGTCAGCTAGAACGGGTCGTAAGCCTTCAGATACAACGGCTGCAGTAAGTTGCTGCT CAGTGTAGTTCATTTCAAGCACCGTATGGGC
Genomic sequence	CTGGAGAGCCGCATCACCCACCCTCCATGTATCCACTTGCCATTTGACAAGGCCACCTGCACGG ATAATACGTTCCCGCTCCTCAAGACAACTTGCAACATGATCCTATGACAGTACCATATATCAGT GAAAATGCATAGCCTTGTAATTCATCAGAAAGCTAGCTAAGAAAATGAATCATCTTACCCTACT TAGAGCATATGGAATCCCAGATCGACACAGAATTGTTCTGCAATCACCAGCATTAGCAACAATA AGTTTGTTTCTGACGATAAGAGCAGCTATTGCAGTACAACCAGGGTGCCAATCTTTCTGAACTG CTCCCTTGCGTTTGCGAGAAGAATCAAGTTGTGTCCTGAATGCAACATCTGTCTTTATGAATGC TTCAAAAAGCGCATCAGAGGGACTGCAAAGTCATAAACATCCAAGAGTTGAGTGCCTTGACTCT TTGAAAACTTCTTGGTCATTCACAAACAAAAAAATCACAAGTTAAGCATGTAAAACCTGCAAAC TGAACCAAGATTCTGCAAAAATCCTGGTAAAGCTCCAGAGGAAAACTCAGCAGCTGCTGAACCT GTAGGCACACTAGTTAAGACGGCCATATTCGAGTGAAAAATGTTTATAATAAGTTTCACTTACG AGAAATAAAATGGCTTCATAGTGACTGGTATACTACCTCGATGACCATCAAAGATTGCAAAGAT GTGAATATCCTTTTCATCACACAACTGAGGCATAAGGAAGTGTCTATCTTCCATTGTTTCCCTT CTCCCACATGATGCAAAGGAACCCCAAGACAGAACTGGACTATAGATATGATCATCTGAAGAAT CCAGCCATGTGCTAGCAGCAAGGGCAGTAGGAACTCTTTTCATAAAGTCTTTACCTTGACTGAA CCAGCTAATATTCTCCTGATAGGTTTGGAAATTTGCAGCATAGACGCCATTTGAAGAAATAAAA GCTTCCCCTGAGGCCTTCTCCATACAGCCCCTTCCAACATCATGTTCCAGAATGAAATCAAGTT CCACGACAATATCATCAAAAGAAGGCCTATTTTGTGGATCTTTATCCCAACATCTTTCTATCAA AGAGACTAAACTTGCTGGAGCGCTGGATTGAATGTCAGCTAGAACGGGTCGTAAGCCTTCAGAT ACAACGGCTGCAGTAAGTTGCTGCTCAGTGTAGTTCATTTCAAGCACCGTATGGGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.726850486

Conservation Information
Conserved circRNAs	NA
PMCS	0.726850486

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							55929346-55928334(+)
55929334-55928145(-)
55928245-55929331(-)
						
					

						Potential amino acid sequence
						
							MGLESRITHPPCIHLPFDKATCTDNTFPLLKTTCNMIPT*(+)
MNYTEQQLTAAVVSEGLRPVLADIQSSAPASLVSLIERCWDKDPQNRPSFDDIVVELDFILEHD
VGRGCMEKASGEAFISSNGVYAANFQTYQENISWFSQGKDFMKRVPTALAASTWLDSSDDHIYS
PVLSWGSFASCGRRETMEDRHFLMPQLCDEKDIHIFAIFDGHRGSAAAEFSSGALPGFLQNLGS
VCSPSDALFEAFIKTDVAFRTQLDSSRKRKGAVQKDWHPGCTAIAALIVRNKLIVANAGDCRTI
LCRSGIPYALSRDHVASCLEERERIIRAGGLVKWQVDTWRVGDAALQAHTVLEMNYTEQQLTAA
VVSEGLRPVLADIQSSAPASLVSLIERCWDKDPQNRPSFDDIVVELDFILEHDVGRGCMEKASG
EAFISSNGVYAANFQTYQENISWFSQGKDFMKRVPTALAASTWLDSSDDHIYSPVLSWGSFASC
GRRETMEDRHFLMPQLCDEKDIHIFAIFDGHRGSAAAEFSSGALPGFLQNLGSVCSPSDALFEA
FIKTDVAFRTQLDSSRKRKGAVQKDWHPGCTAIAALIVRNKLIVANAGDCRTILCRSGIPYALS
RDHVASCLEERERIIRAGGLVKWQVDTWRVGDAALQAHTVLEMNYTEQQLTAAVVSEGLRPVLA
DIQSSAPASLVSLIERCWDKDPQNRPSFDDIVVELDFILEHDVGRGCMEKASGEAFISSNGVYA
ANFQTYQENISWFSQGKDFMKRVPTALAASTWLDSSDDHIYSPVLSWGSFASCGRRETMEDRHF
LMPQLCDEKDIHIFAIFDGHRGSAAAEFSSGALPGFLQNLGSVCSPSDALFEAFIKTDVAFRTQ
LDSSRKRKGAVQKDWHPGCTAIAALIVRNKLIVANAGDCRTILCRSGIPYALSRDHVASCLEER
ERIIRAGGLVKWQVDTWRVGDAALQAHTVLEMNYTEQQLTAAVVSEGLRPVLADIQSSAPASLV
SLIERCWDKDPQNRPSFDDIVVELDFILEHDVGRGCMEKASGEAFISSNGVYAANFQTYQENIS
WFSQGKDFMKRVPTALAASTWLDSSDDHIYSPVLSWGSFASCGRRETMEDRHFLMPQLCDEKDI
HIFAIFDGHRGSAAAEFSSGALPGFLQNLGSVCSPSDALFEAFIKTDVAFRTQLDSSRKRKGAV
QKDWHPGCTAIAALIVRNKLIVANAGDCRTILCRSGIPYALSRDHVASCLEERERIIRAGGLVK
WQVDTWRVGDAALQ(-)
MLQVVLRSGNVLSVQVALSNGKWIHGGWVMRLSRPIRCLK*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	55929346-55928334(+) 55929334-55928145(-) 55928245-55929331(-)
Potential amino acid sequence	MGLESRITHPPCIHLPFDKATCTDNTFPLLKTTCNMIPT(+) MNYTEQQLTAAVVSEGLRPVLADIQSSAPASLVSLIERCWDKDPQNRPSFDDIVVELDFILEHD VGRGCMEKASGEAFISSNGVYAANFQTYQENISWFSQGKDFMKRVPTALAASTWLDSSDDHIYS PVLSWGSFASCGRRETMEDRHFLMPQLCDEKDIHIFAIFDGHRGSAAAEFSSGALPGFLQNLGS VCSPSDALFEAFIKTDVAFRTQLDSSRKRKGAVQKDWHPGCTAIAALIVRNKLIVANAGDCRTI LCRSGIPYALSRDHVASCLEERERIIRAGGLVKWQVDTWRVGDAALQAHTVLEMNYTEQQLTAA VVSEGLRPVLADIQSSAPASLVSLIERCWDKDPQNRPSFDDIVVELDFILEHDVGRGCMEKASG EAFISSNGVYAANFQTYQENISWFSQGKDFMKRVPTALAASTWLDSSDDHIYSPVLSWGSFASC GRRETMEDRHFLMPQLCDEKDIHIFAIFDGHRGSAAAEFSSGALPGFLQNLGSVCSPSDALFEA FIKTDVAFRTQLDSSRKRKGAVQKDWHPGCTAIAALIVRNKLIVANAGDCRTILCRSGIPYALS RDHVASCLEERERIIRAGGLVKWQVDTWRVGDAALQAHTVLEMNYTEQQLTAAVVSEGLRPVLA DIQSSAPASLVSLIERCWDKDPQNRPSFDDIVVELDFILEHDVGRGCMEKASGEAFISSNGVYA ANFQTYQENISWFSQGKDFMKRVPTALAASTWLDSSDDHIYSPVLSWGSFASCGRRETMEDRHF LMPQLCDEKDIHIFAIFDGHRGSAAAEFSSGALPGFLQNLGSVCSPSDALFEAFIKTDVAFRTQ LDSSRKRKGAVQKDWHPGCTAIAALIVRNKLIVANAGDCRTILCRSGIPYALSRDHVASCLEER ERIIRAGGLVKWQVDTWRVGDAALQAHTVLEMNYTEQQLTAAVVSEGLRPVLADIQSSAPASLV SLIERCWDKDPQNRPSFDDIVVELDFILEHDVGRGCMEKASGEAFISSNGVYAANFQTYQENIS WFSQGKDFMKRVPTALAASTWLDSSDDHIYSPVLSWGSFASCGRRETMEDRHFLMPQLCDEKDI HIFAIFDGHRGSAAAEFSSGALPGFLQNLGSVCSPSDALFEAFIKTDVAFRTQLDSSRKRKGAV QKDWHPGCTAIAALIVRNKLIVANAGDCRTILCRSGIPYALSRDHVASCLEERERIIRAGGLVK WQVDTWRVGDAALQ(-) MLQVVLRSGNVLSVQVALSNGKWIHGGWVMRLSRPIRCLK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc01g056690.2_circ_g.3

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