Plant Circular RNA Database

Detail information of Solyc01g099100.2_circ_g.4

			
						 General Information
					
						CircRNA Name
						Solyc01g099100.2_circ_g.4
					
						ID in PlantcircBase
						sly_circ_000372
					
						Alias
						1:81186696|81189884, Slcirc024
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 89425896-89429084  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc01g099100.2						
					
						Parent gene annotation
						
							Long chain acyl-CoA synthetase 7, peroxisomal
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc01g099100.2_circ_g.1 Solyc01g099100.2_circ_g.2 Solyc01g099100.2_circ_g.3 						
					
						Support reads
						96/31
					
						Tissues
						fruit/leaf
					
						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
						Solyc01g099100.2.1:7

General Information
CircRNA Name	Solyc01g099100.2_circ_g.4
ID in PlantcircBase	sly_circ_000372
Alias	1:81186696\|81189884, Slcirc024
Organism	Solanum lycopersicum
Position	chr1: 89425896-89429084 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc01g099100.2
Parent gene annotation	Long chain acyl-CoA synthetase 7, peroxisomal
Parent gene strand	+
Alternative splicing	Solyc01g099100.2_circ_g.1 Solyc01g099100.2_circ_g.2 Solyc01g099100.2_circ_g.3
Support reads	96/31
Tissues	fruit/leaf
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	Solyc01g099100.2.1:7

			
						 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  
						
							TGCAACATTCACAGGTGATAGCTTTAATTCCTCTTTAGTAGCAATAGTTTGTGTAGAGCCAGAT
GTCTTGAAGGAATGGGCATCATCTGAGGGAATCAAGgatcacaaatgccgtacaaacttctggt
gtactgaagcagagactatttaatgctgcctacaactccaagaagcaagctgtgatgaacggtg
agttattt

									
								

					

						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: 739
Transcript exons: 89425896-89425984,89427327-89427456,89427578-89427696,89
428228-89428351,89428442-89428528,89428803-89428906,8942
8999-89429084
GATCACAAATGCCGTACAAACTTCTGGTGTACTGAAGCAGAGACTATTTAATGCTGCCTACAAC
TCCAAGAAGCAAGCTGTGATGAACGGTAGAAAGCCATCACCAATGTGGGATAGGTTGGTGTTCA
ACAAAATAAAGGACAAACTGGGCGGACGAGTTCGTCTTATGACCTCAGGTGCCTCACCATTGTC
CCCTGATGTGTTGGAGTTCTTGAGAGTATGTTTTGGCTGTCAAGTAATGGAAGGGTATGGCATG
ACTGAGACTTCATGTGTCATAAGCTCAATGGACGAGACTGATAACTTAATTGGTCATGTTGGTT
CTCCAAATACAGCATGTGAGATAAAGCTTGTGGATGTCCCCGAAATGAGTTACACATCAGAGGA
TCAGCCTCATCCTCGTGGAGAGATTTGTGTTAGAGGTCCTATTGTTTTTCAAGGCTATTACAAA
GATGAAGTGCAGACGAAGGAGGTAGTTGATGATGACGGTTGGCTGCATACTGGTGATATTGGAT
TATGGTTACCTGGAGGCCGCTTGAAGATTATTGACAGGAAGAAGAATATCTTCAAGTTGGCACA
GGGTGAATACATAGCTCCTGAGAAAATTGAGAATGTTTATGCTAAATGCAAATTTATTGCACAA
TGCTTCGTCTATGGTGATAGCTTTAATTCCTCTTTAGTAGCAATAGTTTGTGTAGAGCCAGATG
TCTTGAAGGAATGGGCATCATCTGAGGGAATCAAG
						
					

						Genomic sequence
						
							GATCACAAATGCCGTACAAACTTCTGGTGTACTGAAGCAGAGACTATTTAATGCTGCCTACAAC
TCCAAGAAGCAAGCTGTGATGAACGGTGAGTTATTTCAATTTTATTTGTGATTCTCCTCTGGTT
GCTTTAGATGATTGCAACATACACTCATCTAGAAAAAGATGATCCCTCAATATCATGATGTTAT
GCAACACATTGGCTCCTGTCTATCACTGCTAGGACTCTGTTTCTCCTTGCTTAACAACTTATTT
CCTGCCTCACAAATTATTCGAGGGAACTTTTGGTGGCTCAATTCTCAAATTGAGAATGCACACT
TCATGATTCTAGAACACTTCTCAAATAATGAAGAGAGAAATTGACACGAGTTTCCATCTCATCT
TCCTTATTTAGCACATTGTTTGGAAACCTGTCTCATTCATATAATATTGCGAGCCAATTAACAT
TTTAGAAGTGTTTAATGGTTTGACTGCTGTAAGTTTTTTTAATTCCTAATATAAAACTAGAACT
CGTTAGAAAAGTTAAAGCATATAAGAGAAGAACAAAGGCTTTCTTACCTATTTCAATCTTTTCT
TTTGCGACACGGATGAGGGTTGTAGGGGTTGAGCTGTTATAGAGCATTTAATTAAATGATTATT
TATAGTGTTTTTCCATTTGAGAATTTTTCCTTTTTCAATTCACGTGACTACCTATAACCGGAAA
AATATCCGATCCAATTTTTTTATTTAAACAACGGTTGAAAATGTTTTAAAAGTTAAGGGCATAA
AAGATGTGATGTACTGGCATTTTATTCAGTGGGCATTGATTATGAGCTCTTACATTTTCCTTCT
TTTCTTTGAGGAAGAGTGGCAGTTTCTGAGCTGTTATAACAGAAATTAAATCAGATTTTATCTT
ATTGTATTTTTTCTTTTAAAAGGACTATGTTTTTCGAGTGGTCAGACTAAGACTCATTTACCCC
CTGTAGAAGTATAATTTACTGTTCATGCCACAAAGCTGAGTTCTCCAATTCTGTTCTGTTGTGC
TGGAAAGAGGTTTCAAGAGTCAAGTCTGCTTAAGATTTTAAATGAAAAGTGAATTACTTACTAT
CAGCTAGTAAGTGTAGTATGTACAACCTGGAAAGAGTAACGCATGCAAATTAAAATTATAATAT
TACTCTTGAAGAGATTCCTTTAGTTATCTCAAATCACTTGAGAGTAAGGGTCTTGGATTAATCC
ATTTATCAAGCAGTAGGTCACCTTAGGTGTCCCGCCTAGGCAATATAGAATTCGTGCTAGAAAA
CTATTTGGCCATGCATTGGTTTATAAGTGTTATTGGCTTGGACGAAATCTGATGTTATCACGGA
TTATCGATTGCATATCAGCAGTAAATACTTTTGCTGCATATCTTTATGAGTTTTTATCTCTCTT
TTAACAGAATCTCATATTTTCAGGTAGAAAGCCATCACCAATGTGGGATAGGTTGGTGTTCAAC
AAAATAAAGGACAAACTGGGCGGACGAGTTCGTCTTATGACCTCAGGTGCCTCACCATTGTCCC
CTGATGTGTTGGAGTTCTTGAGAGTGTAAGTTGACCATTATTGCTGTTCTAAAGTACTGGGAGA
TTTTGTTCATCAAATTCTGGCTCTTGTTAGTGCTGAGGACTTCCAGTAGTTGGCTTTGCTCTGA
ATAAATTCCTTCCTGCAGATGTTTTGGCTGTCAAGTAATGGAAGGGTATGGCATGACTGAGACT
TCATGTGTCATAAGCTCAATGGACGAGACTGATAACTTAATTGGTCATGTTGGTTCTCCAAATA
CAGCATGTGGTGAGGTTTTAACTAATTATGGCATATAAACTTCATTGATATCACTAGTTTCGGT
TCTTGATTTGCTTTCCCTTCGATATTATTCCCCTTGTTGAGCTGAATTAAAGGCTGTTTGAGGC
ATATCGAAGGTTTTCATGACCACTGGAAGGTTAATAATTTGTTTATAGAAGCTTAACAACATGA
GAGAAATTCATGAAAAAGTTCCTAATTGTGTTGCAGTCTCGGAGGGCCAAGATTTCCACTAAAA
AGTTTGTGGCTGATAAGTTGATCCGCGAAATTAGAAGCTTGCAAGAGAAAGTTAAGGCTTAAAA
CTTTAAATGCCAACAAGGTTAATATGCAAAATTACCTTGCACAAAATGTCGTAGTACTATAAGT
GAACTGCACATTTCCATGCTGAATTTGCTAAAGAGTGTGTCAACTTTCTTTTGTGGTTCCTGTT
CTTCTACTTTTTGCGGCGCTATAGTTAACTTAATGATTGCTAAAGAAAAGCTGTAAAGGAGTTT
AAATTGTCTACGATTCTGCTATTTTCAGAGATAAAGCTTGTGGATGTCCCCGAAATGAGTTACA
CATCAGAGGATCAGCCTCATCCTCGTGGAGAGATTTGTGTTAGAGGTCCTATTGTTTTTCAAGG
CTATTACAAAGATGAAGTGCAGACGTACATACCTTACTCATTGATATTTCATTTCTTGTTTTGT
CATTGCCATGAGCTTCTCCAAGATAATTTGCCTGACCTAGTAGTTAACAGGAAGGAGGTAGTTG
ATGATGACGGTTGGCTGCATACTGGTGATATTGGATTATGGTTACCTGGAGGCCGCTTGAAGAT
TATTGACAGGTAGAATCTATTCGGCTTGATCAGGAGAGATAACCTTAGATATTTTTAATTTGAG
ATACAAAACAACTTTTACCCACCCCACCCATTTATTTGTGGCACCTAGTGGTTGGCAAGGATTT
CTATCAACCCTACCATTTCCATCAAATATTTTATTATGATGTAGTTACATCGTTCTCAACGTTA
ATTTTACCCCCTTTTGATATTAGAACATCTATCTTTCTGTGTTTGCTTGTCTTCCATGGTAGAA
TGATCTCTGAATTGTCATTGTGGACAGGAAGAAGAATATCTTCAAGTTGGCACAGGGTGAATAC
ATAGCTCCTGAGAAAATTGAGAATGTTTATGCTAAATGCAAATTTATTGCACAATGCTTCGTCT
ATGGTAAGCAGATAATGGAATTCTCTCTTATGGATTAAACCATGTCCTTTGCTCACTATATAAA
TGTCCTTTGCTCACTGTTGCAACATTCACAGGTGATAGCTTTAATTCCTCTTTAGTAGCAATAG
TTTGTGTAGAGCCAGATGTCTTGAAGGAATGGGCATCATCTGAGGGAATCAAG
						
					

			
		

Sequences
Splice junction sequence	TGCAACATTCACAGGTGATAGCTTTAATTCCTCTTTAGTAGCAATAGTTTGTGTAGAGCCAGAT GTCTTGAAGGAATGGGCATCATCTGAGGGAATCAAGgatcacaaatgccgtacaaacttctggt gtactgaagcagagactatttaatgctgcctacaactccaagaagcaagctgtgatgaacggtg agttattt
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: 739 Transcript exons: 89425896-89425984,89427327-89427456,89427578-89427696,89 428228-89428351,89428442-89428528,89428803-89428906,8942 8999-89429084 GATCACAAATGCCGTACAAACTTCTGGTGTACTGAAGCAGAGACTATTTAATGCTGCCTACAAC TCCAAGAAGCAAGCTGTGATGAACGGTAGAAAGCCATCACCAATGTGGGATAGGTTGGTGTTCA ACAAAATAAAGGACAAACTGGGCGGACGAGTTCGTCTTATGACCTCAGGTGCCTCACCATTGTC CCCTGATGTGTTGGAGTTCTTGAGAGTATGTTTTGGCTGTCAAGTAATGGAAGGGTATGGCATG ACTGAGACTTCATGTGTCATAAGCTCAATGGACGAGACTGATAACTTAATTGGTCATGTTGGTT CTCCAAATACAGCATGTGAGATAAAGCTTGTGGATGTCCCCGAAATGAGTTACACATCAGAGGA TCAGCCTCATCCTCGTGGAGAGATTTGTGTTAGAGGTCCTATTGTTTTTCAAGGCTATTACAAA GATGAAGTGCAGACGAAGGAGGTAGTTGATGATGACGGTTGGCTGCATACTGGTGATATTGGAT TATGGTTACCTGGAGGCCGCTTGAAGATTATTGACAGGAAGAAGAATATCTTCAAGTTGGCACA GGGTGAATACATAGCTCCTGAGAAAATTGAGAATGTTTATGCTAAATGCAAATTTATTGCACAA TGCTTCGTCTATGGTGATAGCTTTAATTCCTCTTTAGTAGCAATAGTTTGTGTAGAGCCAGATG TCTTGAAGGAATGGGCATCATCTGAGGGAATCAAG
Genomic sequence	GATCACAAATGCCGTACAAACTTCTGGTGTACTGAAGCAGAGACTATTTAATGCTGCCTACAAC TCCAAGAAGCAAGCTGTGATGAACGGTGAGTTATTTCAATTTTATTTGTGATTCTCCTCTGGTT GCTTTAGATGATTGCAACATACACTCATCTAGAAAAAGATGATCCCTCAATATCATGATGTTAT GCAACACATTGGCTCCTGTCTATCACTGCTAGGACTCTGTTTCTCCTTGCTTAACAACTTATTT CCTGCCTCACAAATTATTCGAGGGAACTTTTGGTGGCTCAATTCTCAAATTGAGAATGCACACT TCATGATTCTAGAACACTTCTCAAATAATGAAGAGAGAAATTGACACGAGTTTCCATCTCATCT TCCTTATTTAGCACATTGTTTGGAAACCTGTCTCATTCATATAATATTGCGAGCCAATTAACAT TTTAGAAGTGTTTAATGGTTTGACTGCTGTAAGTTTTTTTAATTCCTAATATAAAACTAGAACT CGTTAGAAAAGTTAAAGCATATAAGAGAAGAACAAAGGCTTTCTTACCTATTTCAATCTTTTCT TTTGCGACACGGATGAGGGTTGTAGGGGTTGAGCTGTTATAGAGCATTTAATTAAATGATTATT TATAGTGTTTTTCCATTTGAGAATTTTTCCTTTTTCAATTCACGTGACTACCTATAACCGGAAA AATATCCGATCCAATTTTTTTATTTAAACAACGGTTGAAAATGTTTTAAAAGTTAAGGGCATAA AAGATGTGATGTACTGGCATTTTATTCAGTGGGCATTGATTATGAGCTCTTACATTTTCCTTCT TTTCTTTGAGGAAGAGTGGCAGTTTCTGAGCTGTTATAACAGAAATTAAATCAGATTTTATCTT ATTGTATTTTTTCTTTTAAAAGGACTATGTTTTTCGAGTGGTCAGACTAAGACTCATTTACCCC CTGTAGAAGTATAATTTACTGTTCATGCCACAAAGCTGAGTTCTCCAATTCTGTTCTGTTGTGC TGGAAAGAGGTTTCAAGAGTCAAGTCTGCTTAAGATTTTAAATGAAAAGTGAATTACTTACTAT CAGCTAGTAAGTGTAGTATGTACAACCTGGAAAGAGTAACGCATGCAAATTAAAATTATAATAT TACTCTTGAAGAGATTCCTTTAGTTATCTCAAATCACTTGAGAGTAAGGGTCTTGGATTAATCC ATTTATCAAGCAGTAGGTCACCTTAGGTGTCCCGCCTAGGCAATATAGAATTCGTGCTAGAAAA CTATTTGGCCATGCATTGGTTTATAAGTGTTATTGGCTTGGACGAAATCTGATGTTATCACGGA TTATCGATTGCATATCAGCAGTAAATACTTTTGCTGCATATCTTTATGAGTTTTTATCTCTCTT TTAACAGAATCTCATATTTTCAGGTAGAAAGCCATCACCAATGTGGGATAGGTTGGTGTTCAAC AAAATAAAGGACAAACTGGGCGGACGAGTTCGTCTTATGACCTCAGGTGCCTCACCATTGTCCC CTGATGTGTTGGAGTTCTTGAGAGTGTAAGTTGACCATTATTGCTGTTCTAAAGTACTGGGAGA TTTTGTTCATCAAATTCTGGCTCTTGTTAGTGCTGAGGACTTCCAGTAGTTGGCTTTGCTCTGA ATAAATTCCTTCCTGCAGATGTTTTGGCTGTCAAGTAATGGAAGGGTATGGCATGACTGAGACT TCATGTGTCATAAGCTCAATGGACGAGACTGATAACTTAATTGGTCATGTTGGTTCTCCAAATA CAGCATGTGGTGAGGTTTTAACTAATTATGGCATATAAACTTCATTGATATCACTAGTTTCGGT TCTTGATTTGCTTTCCCTTCGATATTATTCCCCTTGTTGAGCTGAATTAAAGGCTGTTTGAGGC ATATCGAAGGTTTTCATGACCACTGGAAGGTTAATAATTTGTTTATAGAAGCTTAACAACATGA GAGAAATTCATGAAAAAGTTCCTAATTGTGTTGCAGTCTCGGAGGGCCAAGATTTCCACTAAAA AGTTTGTGGCTGATAAGTTGATCCGCGAAATTAGAAGCTTGCAAGAGAAAGTTAAGGCTTAAAA CTTTAAATGCCAACAAGGTTAATATGCAAAATTACCTTGCACAAAATGTCGTAGTACTATAAGT GAACTGCACATTTCCATGCTGAATTTGCTAAAGAGTGTGTCAACTTTCTTTTGTGGTTCCTGTT CTTCTACTTTTTGCGGCGCTATAGTTAACTTAATGATTGCTAAAGAAAAGCTGTAAAGGAGTTT AAATTGTCTACGATTCTGCTATTTTCAGAGATAAAGCTTGTGGATGTCCCCGAAATGAGTTACA CATCAGAGGATCAGCCTCATCCTCGTGGAGAGATTTGTGTTAGAGGTCCTATTGTTTTTCAAGG CTATTACAAAGATGAAGTGCAGACGTACATACCTTACTCATTGATATTTCATTTCTTGTTTTGT CATTGCCATGAGCTTCTCCAAGATAATTTGCCTGACCTAGTAGTTAACAGGAAGGAGGTAGTTG ATGATGACGGTTGGCTGCATACTGGTGATATTGGATTATGGTTACCTGGAGGCCGCTTGAAGAT TATTGACAGGTAGAATCTATTCGGCTTGATCAGGAGAGATAACCTTAGATATTTTTAATTTGAG ATACAAAACAACTTTTACCCACCCCACCCATTTATTTGTGGCACCTAGTGGTTGGCAAGGATTT CTATCAACCCTACCATTTCCATCAAATATTTTATTATGATGTAGTTACATCGTTCTCAACGTTA ATTTTACCCCCTTTTGATATTAGAACATCTATCTTTCTGTGTTTGCTTGTCTTCCATGGTAGAA TGATCTCTGAATTGTCATTGTGGACAGGAAGAAGAATATCTTCAAGTTGGCACAGGGTGAATAC ATAGCTCCTGAGAAAATTGAGAATGTTTATGCTAAATGCAAATTTATTGCACAATGCTTCGTCT ATGGTAAGCAGATAATGGAATTCTCTCTTATGGATTAAACCATGTCCTTTGCTCACTATATAAA TGTCCTTTGCTCACTGTTGCAACATTCACAGGTGATAGCTTTAATTCCTCTTTAGTAGCAATAG TTTGTGTAGAGCCAGATGTCTTGAAGGAATGGGCATCATCTGAGGGAATCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.731260212

Conservation Information
Conserved circRNAs	NA
PMCS	0.731260212

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							89425979-89425943(+)
						
						Potential amino acid sequence
						
							MNGRKPSPMWDRLVFNKIKDKLGGRVRLMTSGASPLSPDVLEFLRVCFGCQVMEGYGMTETSCV
ISSMDETDNLIGHVGSPNTACEIKLVDVPEMSYTSEDQPHPRGEICVRGPIVFQGYYKDEVQTK
EVVDDDGWLHTGDIGLWLPGGRLKIIDRKKNIFKLAQGEYIAPEKIENVYAKCKFIAQCFVYGD
SFNSSLVAIVCVEPDVLKEWASSEGIKDHKCRTNFWCTEAETI*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	89425979-89425943(+)
Potential amino acid sequence	MNGRKPSPMWDRLVFNKIKDKLGGRVRLMTSGASPLSPDVLEFLRVCFGCQVMEGYGMTETSCV ISSMDETDNLIGHVGSPNTACEIKLVDVPEMSYTSEDQPHPRGEICVRGPIVFQGYYKDEVQTK EVVDDDGWLHTGDIGLWLPGGRLKIIDRKKNIFKLAQGEYIAPEKIENVYAKCKFIAQCFVYGD SFNSSLVAIVCVEPDVLKEWASSEGIKDHKCRTNFWCTEAETI*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016; Yin et al., 2018; Wang et al., 2018b

circRNA

Detail information of Solyc01g099100.2_circ_g.4

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