Plant Circular RNA Database

Detail information of Solyc05g017890.2_circ_g.4

			
						 General Information
					
						CircRNA Name
						Solyc05g017890.2_circ_g.4
					
						ID in PlantcircBase
						sly_circ_001723
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr5: 19101465-19105008  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc05g017890.2						
					
						Parent gene annotation
						
							THO complex subunit 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc05g017890.2_circ_g.3 						
					
						Support reads
						NA
					
						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
						Solyc05g017890.2.1:7

General Information
CircRNA Name	Solyc05g017890.2_circ_g.4
ID in PlantcircBase	sly_circ_001723
Alias	NA
Organism	Solanum lycopersicum
Position	chr5: 19101465-19105008 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc05g017890.2
Parent gene annotation	THO complex subunit 2
Parent gene strand	-
Alternative splicing	Solyc05g017890.2_circ_g.3
Support reads	NA
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	Solyc05g017890.2.1:7

			
						 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  
						
							TACTAGAGTGCTTTAATTGAAATAAAACCTTGATTATGCCAACAGTAGCAGCTGAAGCATTTTG
GCTAGAATCCTCTGGAATTTGACAAAGGAGAGTCACctgaataatccatcacatatttgtacat
gttctgctggattgagatgtgagagacggccaaacaacacatgagcatgatacctggaagttat
aaatgtta

									
								

					

						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
						
							CTGAATAATCCATCACATATTTGTACATGTTCTGCTGGATTGAGATGTGAGAGACGGCCAAACA
ACACATGAGCATGATACCTGGAAGTTATAAATGTTATATGTAAAGGTATCCATATGTCTAAATT
ATAAAAGAAGACAGAAGAGCAAAAGATCAAGATACCACAAACGAGTCAACAAACATGGAACTCA
AATGACTCTACCTACAGATGATGAGAGAAATTTTTTTACCTGCTGAACAAGAAAAAAGGGATAT
CTAGGGAAACAGCATAGAGAAAGACAACACTGACAAAAATCAAAGTATATAACCCTACTTTAAA
ATGGATTCTTCCAACAGAGAATACTCCAAAGAATGTATTCTACTTCTTAAAAGCAAAAACAAAG
TGGGTTTCTGAAAAAAATCACGAGTAAAAATACTTGGCAATTATACAAAGACAAATTAGAAAAA
CACTGATTAAGGCCTAACAAGTATGTGAAAAACTCTTCATAGTTTTAGGCAGTTAGCTAGACTG
TACTGCAAATAATCCACGAAATTAGTACTGTGATAAAGTAAAACATTGAAATTGGTACAGTACC
TCCAAATAATGGGATAAGAAACCAATAAAACTTATTTAGCATACATGTCGGTCGTTAAAATAGC
ACTCTCAGAGAAAAAGTAAAAATACTCATTCTACGAGTTCTTATAAGTAAGATAAAGTTGGCCA
TTTAACCTCACCAGTTTCAAAACAAAAAAAGATTAAGTTGGCCATCATTAGTTGATTAGTCATT
CTGATTAGCATACTATAAAACAAATTCACTAATTAAAATCAAGCACATGAGTATTCTTGACTTT
TGAGATATAGACATTTGTGATTACTAAAATTAAATTAAAAACAATAGCAAGAGACAAATATATG
ACCAAAGAAATTGAAAAAAGATTATGATCAAGTGAAATATCAATTATTTAGTTTCACTTCTTCA
TACGAGCTCATTGGCAAGGAAACTTTTGCCTTAGAACCTTGATGACGACACTGAAGCGCACGTA
AAGTGAGGCAAAGCGCTCAACACATTTTGAGCCTCGCTTCAGGGCTTAAGCGCGCTTTGATAAC
ACTAGGTATAAACCAAGAAACATTAGCATATTTCCCATCAGAGGATCAATATCGACCAATAAGG
AATAAGGATTAACATGCAGCTAAAAACTAAGACATAGCAGTCTAATCCCACTAGTGGGGTTTGA
GGATGGTAGGACGTACGCAAAACCTTACCCCTAACTTAGTGGGGTAGAAAGGTTGTTTGCGAAA
GATCCTCGGAACAGGCAGACAAAAGAATGGATATTATATGCCTAAATGTCTGACACAAACAAAA
GTAAGTTGCTATATCACTAGACAAAAGAACTGATATTTACTTTCTAGAAGAAAAGGAGAGACCC
AAAAGTTATAGTCAAAATATAACCCTGAGAAAAGATAGTCAATTATTACATGCATAAAATCAAT
CGGAGCAAAGTAAAGGTGAACAGATGGCCAGAACACGCACACTGGCAAATGCAAAGGTTAGCTC
ATAATCATGGAACTTCGAAATCAAACTTACCAGTCATTCACTTCAAGAAATCCCATAAGCAATC
CCAGGGGTTGACTATTTTCCAGCTCGGAGGAACGCTCAGCAACTGCCTCTGTTTCCATGTCCAA
TGCAGCATACAGATCCACTGTCACATCTCCTTGTTTCTCTTCATCCATGAGATCCTTCCCAGTA
GCAGCAAGATTTATTCTCCCTATTTTGTTGGCCTACATAAATCCAAGAGGAAAACTAAAATAAC
CCCCTAACCAAAAAAGCACGCAGAATTTCAAGCTAAAATACCCGCATTGAACAGAAGTATTCAC
ACTAGAAAATGTTGGAACCTCATCAAGTCTCTTAGCTGAAAAGGCATTGTAATGGTCAAAAGCA
TCCTCCTCCTTGGGAAGTAAATGTGCATAACTGAAACAAAAACCAGGTTGTCAGTAGCAATAAG
TTAATTAAATCCAATAGTCTAGGTTACCCACCAAAAGGCAACTAGAAAGCCCAATTATGCTTTG
GGCCTTTGGCAACTCAAATTAATTAGTAGATGCTTAATGCTCTAGCTTAGAATAAGCAACTCCT
TATATCTATAACATGAGGATGTAAAGATCCTACTTATTATCTCAACAAGAGAAGAAACATAAGT
AGCATATGTTTTCCCTGTACTCATTTTATCAAGCTTAGAATTCTCTGCCTTCAATGGCCTACCT
AGTGCCCTTTGACAATAATCTCAGGGAAATATCATTTTTATCATCATCATCAAACGATCTTTTA
GATGATAACATTCATATCATCCTTTTACAAGCAGTATGTTGTACACAAAAGAAGCCACGAGAAA
ACCACACGAGATACTCTAAACTCTTTAAAATACTTTTATTTGGTCCAACAAATAACAGTGCCTT
TGATTATCTATTTTGTTCCCCTAACATAATTCACATTAGTCGCCAGCATCAAAAGGCATTTGTA
TCCTATATACTCTTAGTGATGTCAATGTGCATGAGATAATAACCAAAATCATCGAGTCAAACTC
TTAGTTTTTGATAAGATACACAACTTTTTACATTTTTTTACAAGGTAAATTTCTCAATATGTGT
GTGTCATCCAAACTTGTATCTATACATAAGAATGTGTCTGATAATATACACAGTTTAATTACAA
TCTATGGTTTGTGAAATAGATAATAAATAACAAAATCCATTTTTGCAAGAGCAAAATAAAGAGA
GAGAAAAACTACTCAAGCACAAAGAAAGACATAATACTAGCTAGCAACTCAGAACTTATTTAAA
GCCTAATGTTCACTATAAAAGTTATCTTTTTTGGCACTCAAATACTAAAAAGAAATTGTGAAGG
GAAGGAGGAAAAGGTGGGATGAGGTAACCAAGCATAGAGATATACTCACATGCTGTCGACATCA
ATGAAGTCTCTTTTCACCAGCAAGGCCGTCAGCTGATAAAGTTCACTTGGAACAGGATCATTAA
CTTCCAGGCGTTGGTAGTATTGAAACTTAAACCCCAGAATCTGGGAGGCATGGGACTACAAATA
GTAGAGAAAAAATGGAAAACAAATGCACTTTCAAGACTGCGAGAGCTCCACAAAACGAGAAAAC
AACAACTCAACCACAACTATACCTTGGGAAATATGGGAATCAAGTCCAAAAATATACTATTACC
AGGCTGACGTTCAAAACACTCCAAAACCTGGAAAATCATAGCCAAAGATAGACGTGAACACTAA
AATTTCAAAAGTTTAAAAGGATGGAACTAAAAAAAAGCATAGAACGGAGTAGAAATGCACGATA
TCATTATGGATAAAAACGTACAATATCAAATACTCGGTTTGGATCCAAATCAAAGTGCCCAATC
AACGACTGCATATAGTCCAAGAATTAGAAATACATAAAAATAAAATCTCAGCTACTAGAGTGCT
TTAATTGAAATAAAACCTTGATTATGCCAACAGTAGCAGCTGAAGCATTTTGGCTAGAATCCTC
TGGAATTTGACAAAGGAGAGTCAC
						
					

			
		

Sequences
Splice junction sequence	TACTAGAGTGCTTTAATTGAAATAAAACCTTGATTATGCCAACAGTAGCAGCTGAAGCATTTTG GCTAGAATCCTCTGGAATTTGACAAAGGAGAGTCACctgaataatccatcacatatttgtacat gttctgctggattgagatgtgagagacggccaaacaacacatgagcatgatacctggaagttat aaatgtta
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	CTGAATAATCCATCACATATTTGTACATGTTCTGCTGGATTGAGATGTGAGAGACGGCCAAACA ACACATGAGCATGATACCTGGAAGTTATAAATGTTATATGTAAAGGTATCCATATGTCTAAATT ATAAAAGAAGACAGAAGAGCAAAAGATCAAGATACCACAAACGAGTCAACAAACATGGAACTCA AATGACTCTACCTACAGATGATGAGAGAAATTTTTTTACCTGCTGAACAAGAAAAAAGGGATAT CTAGGGAAACAGCATAGAGAAAGACAACACTGACAAAAATCAAAGTATATAACCCTACTTTAAA ATGGATTCTTCCAACAGAGAATACTCCAAAGAATGTATTCTACTTCTTAAAAGCAAAAACAAAG TGGGTTTCTGAAAAAAATCACGAGTAAAAATACTTGGCAATTATACAAAGACAAATTAGAAAAA CACTGATTAAGGCCTAACAAGTATGTGAAAAACTCTTCATAGTTTTAGGCAGTTAGCTAGACTG TACTGCAAATAATCCACGAAATTAGTACTGTGATAAAGTAAAACATTGAAATTGGTACAGTACC TCCAAATAATGGGATAAGAAACCAATAAAACTTATTTAGCATACATGTCGGTCGTTAAAATAGC ACTCTCAGAGAAAAAGTAAAAATACTCATTCTACGAGTTCTTATAAGTAAGATAAAGTTGGCCA TTTAACCTCACCAGTTTCAAAACAAAAAAAGATTAAGTTGGCCATCATTAGTTGATTAGTCATT CTGATTAGCATACTATAAAACAAATTCACTAATTAAAATCAAGCACATGAGTATTCTTGACTTT TGAGATATAGACATTTGTGATTACTAAAATTAAATTAAAAACAATAGCAAGAGACAAATATATG ACCAAAGAAATTGAAAAAAGATTATGATCAAGTGAAATATCAATTATTTAGTTTCACTTCTTCA TACGAGCTCATTGGCAAGGAAACTTTTGCCTTAGAACCTTGATGACGACACTGAAGCGCACGTA AAGTGAGGCAAAGCGCTCAACACATTTTGAGCCTCGCTTCAGGGCTTAAGCGCGCTTTGATAAC ACTAGGTATAAACCAAGAAACATTAGCATATTTCCCATCAGAGGATCAATATCGACCAATAAGG AATAAGGATTAACATGCAGCTAAAAACTAAGACATAGCAGTCTAATCCCACTAGTGGGGTTTGA GGATGGTAGGACGTACGCAAAACCTTACCCCTAACTTAGTGGGGTAGAAAGGTTGTTTGCGAAA GATCCTCGGAACAGGCAGACAAAAGAATGGATATTATATGCCTAAATGTCTGACACAAACAAAA GTAAGTTGCTATATCACTAGACAAAAGAACTGATATTTACTTTCTAGAAGAAAAGGAGAGACCC AAAAGTTATAGTCAAAATATAACCCTGAGAAAAGATAGTCAATTATTACATGCATAAAATCAAT CGGAGCAAAGTAAAGGTGAACAGATGGCCAGAACACGCACACTGGCAAATGCAAAGGTTAGCTC ATAATCATGGAACTTCGAAATCAAACTTACCAGTCATTCACTTCAAGAAATCCCATAAGCAATC CCAGGGGTTGACTATTTTCCAGCTCGGAGGAACGCTCAGCAACTGCCTCTGTTTCCATGTCCAA TGCAGCATACAGATCCACTGTCACATCTCCTTGTTTCTCTTCATCCATGAGATCCTTCCCAGTA GCAGCAAGATTTATTCTCCCTATTTTGTTGGCCTACATAAATCCAAGAGGAAAACTAAAATAAC CCCCTAACCAAAAAAGCACGCAGAATTTCAAGCTAAAATACCCGCATTGAACAGAAGTATTCAC ACTAGAAAATGTTGGAACCTCATCAAGTCTCTTAGCTGAAAAGGCATTGTAATGGTCAAAAGCA TCCTCCTCCTTGGGAAGTAAATGTGCATAACTGAAACAAAAACCAGGTTGTCAGTAGCAATAAG TTAATTAAATCCAATAGTCTAGGTTACCCACCAAAAGGCAACTAGAAAGCCCAATTATGCTTTG GGCCTTTGGCAACTCAAATTAATTAGTAGATGCTTAATGCTCTAGCTTAGAATAAGCAACTCCT TATATCTATAACATGAGGATGTAAAGATCCTACTTATTATCTCAACAAGAGAAGAAACATAAGT AGCATATGTTTTCCCTGTACTCATTTTATCAAGCTTAGAATTCTCTGCCTTCAATGGCCTACCT AGTGCCCTTTGACAATAATCTCAGGGAAATATCATTTTTATCATCATCATCAAACGATCTTTTA GATGATAACATTCATATCATCCTTTTACAAGCAGTATGTTGTACACAAAAGAAGCCACGAGAAA ACCACACGAGATACTCTAAACTCTTTAAAATACTTTTATTTGGTCCAACAAATAACAGTGCCTT TGATTATCTATTTTGTTCCCCTAACATAATTCACATTAGTCGCCAGCATCAAAAGGCATTTGTA TCCTATATACTCTTAGTGATGTCAATGTGCATGAGATAATAACCAAAATCATCGAGTCAAACTC TTAGTTTTTGATAAGATACACAACTTTTTACATTTTTTTACAAGGTAAATTTCTCAATATGTGT GTGTCATCCAAACTTGTATCTATACATAAGAATGTGTCTGATAATATACACAGTTTAATTACAA TCTATGGTTTGTGAAATAGATAATAAATAACAAAATCCATTTTTGCAAGAGCAAAATAAAGAGA GAGAAAAACTACTCAAGCACAAAGAAAGACATAATACTAGCTAGCAACTCAGAACTTATTTAAA GCCTAATGTTCACTATAAAAGTTATCTTTTTTGGCACTCAAATACTAAAAAGAAATTGTGAAGG GAAGGAGGAAAAGGTGGGATGAGGTAACCAAGCATAGAGATATACTCACATGCTGTCGACATCA ATGAAGTCTCTTTTCACCAGCAAGGCCGTCAGCTGATAAAGTTCACTTGGAACAGGATCATTAA CTTCCAGGCGTTGGTAGTATTGAAACTTAAACCCCAGAATCTGGGAGGCATGGGACTACAAATA GTAGAGAAAAAATGGAAAACAAATGCACTTTCAAGACTGCGAGAGCTCCACAAAACGAGAAAAC AACAACTCAACCACAACTATACCTTGGGAAATATGGGAATCAAGTCCAAAAATATACTATTACC AGGCTGACGTTCAAAACACTCCAAAACCTGGAAAATCATAGCCAAAGATAGACGTGAACACTAA AATTTCAAAAGTTTAAAAGGATGGAACTAAAAAAAAGCATAGAACGGAGTAGAAATGCACGATA TCATTATGGATAAAAACGTACAATATCAAATACTCGGTTTGGATCCAAATCAAAGTGCCCAATC AACGACTGCATATAGTCCAAGAATTAGAAATACATAAAAATAAAATCTCAGCTACTAGAGTGCT TTAATTGAAATAAAACCTTGATTATGCCAACAGTAGCAGCTGAAGCATTTTGGCTAGAATCCTC TGGAATTTGACAAAGGAGAGTCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.157444422

Conservation Information
Conserved circRNAs	NA
PMCS	0.157444422

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							19103178-19105007(-)
19103039-19104976(-)
						
						Potential amino acid sequence
						
							MDEEKQGDVTVDLYAALDMETEAVAERSSELENSQPLGLLMGFLEVNDWYHAHVLFGRLSHLNP
AEHVQICDGLFR*(-)
MTGIMLMCCLAVSHISIQQNMYKYVMDYSGDSPLSNSRGF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	19103178-19105007(-) 19103039-19104976(-)
Potential amino acid sequence	MDEEKQGDVTVDLYAALDMETEAVAERSSELENSQPLGLLMGFLEVNDWYHAHVLFGRLSHLNP AEHVQICDGLFR(-) MTGIMLMCCLAVSHISIQQNMYKYVMDYSGDSPLSNSRGF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017

circRNA

Detail information of Solyc05g017890.2_circ_g.4

Address

Any questions?

Supported by