Plant Circular RNA Database

Detail information of Solyc09g009940.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc09g009940.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_002789
					
						Alias
						SL3.0ch09:3403942|3407015
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr9: 3403812-3406885  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRI; find_circ
					
						Parent gene
						
							Solyc09g009940.2						
					
						Parent gene annotation
						
							Signal recognition particle 54 kDa protein, chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						Exon boundary  
						
							No-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-TA							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
						Solyc09g009940.2.1:8

General Information
CircRNA Name	Solyc09g009940.2_circ_g.1
ID in PlantcircBase	sly_circ_002789
Alias	SL3.0ch09:3403942\|3407015
Organism	Solanum lycopersicum
Position	chr9: 3403812-3406885 JBrowse»
Reference genome	SL2.50.38
Type	ei-circRNA
Identification method	CIRI; find_circ
Parent gene	Solyc09g009940.2
Parent gene annotation	Signal recognition particle 54 kDa protein, chloroplastic
Parent gene strand	-
Alternative splicing	NA
Support reads	NA
Tissues	leaf
Exon boundary	No-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-TA 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	Solyc09g009940.2.1:8

			
						 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  
						
							GAGATTAGTTGTTGAAACAGTAAGCAACATACATCAGCTTCTAAAAGAGCCCTCCTGATGTCCC
TCATAGGTTCCACGATGTTTTCCTTGGTCAAAACCTcaacttcttgggctttctcaacaaacga
tagaacatctcccattcctaaaatacgtccagccatgcggtcaggatagaaaggttcaaggtcc
tccatacg

									
								

					

						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
						
							CAACTTCTTGGGCTTTCTCAACAAACGATAGAACATCTCCCATTCCTAAAATACGTCCAGCCAT
GCGGTCAGGATAGAAAGGTTCAAGGTCCTCCATACGTTCACCCCTTCCTACGAGCTTGATTGGC
TTTCCTGATACCTGTGGTAGTGAACATATAATTGTGATGCACAATCTTAGTTCATTTAACCAAA
AACCTGACCGTTAAAGAGCAATCAGTGATTTTTTTTGTCTATACATATGATTCGTGTACAATCT
CTACCCCATAAAAGGTAGGAGTAAGATCTGCTTACATCCTCCCCTCCCCATTACACACATGTCG
GACTACACTGGGTTGTTGTTCTGTTGTAACTTGTGACCCATATTGGCAACATTTGACACAACCA
CTTAAACAGATATCATCAATTGCCTATTGGCTTCAAATCTATTCCATTCAGTTTAAACCTTGAC
AAAAGTAAATTTCTTCCAAGATAATACGCAAAAGACATGTTGAACATAGAGGAAATCTGAAGTT
TGTGGTCCAATCACTCTTTACGTTTTAGTATTTGTTTCGCCGCATGATCCCTTCAAGGAAGAAA
AGCTTTTGGATATTTATAATCATCTACTTCCATCATTAACTCTCCTTCATCTTTGCTGCTCTAA
GTTCAAAAGTAGAAATGTTGACTTTGCTAATCAAGAGAAGTTGAAGCAAAGTAAACTGCAAGGT
TAAACTTAGAACAAGGAAAAAACGAATGTATGTGTCGTGTAGTAAAAAGACCCCACCTCCTTGA
CACTTAAAGCTGCTCCACCCCTAGAATCTCCATCTAGCTTCGTCAAGATGGCACCAGTAATTCC
AATTTCGAGATTGAATGTTGTGACCAAAGCTACAATTTCATCAATGTGAACGATAAGAGAGAAA
ACAAATCGGAATTTTCTGTTTTCAACATGAAATGATTGGTATAGGGCAGAAATTATGTCCTTGT
GTCAGTAATAACTCAATGAAAGTGCAGTACTATGATTTCTGTTTTGAGATGTTACAGAATTTTA
ATGCACTATCTAGTAACAAATTTCAAGAGTTCAGATTCATTTAACAACTCAGATATGGAATGCC
TCTCTCCATTAACCTCAAAAAACCAATTCCGTTTATTTTTTTCTGACTAAAAAAGTTTCAAGTA
AATGAAACTAATTCCTTAAACTCCATATCAACCAAGCATGTCGCGTGAATAGAGGGAGTATTAA
AATAGTTAAACAGCTTCAGATTATCAAAGATAACATCCATATTTATGTAATGAAGTCCCAAAAA
TAACTTATATTCGTACAAGACAAGCACAAGAAAGAAATTAACTGTCATATACAGCTGTGCTATA
AGTCTCCAAGCTTCGATGAGAAGCAATATAACGTTCTCTTGAGAAAAACGCTCGGTGGCAACAT
TACACAAACAACAGATATTTTGCTCTCTCTGTGAGAAGCAGACCTCAGATAACAGAATGGCCTG
GATTGTTAAGGAAAGTTTTTCGTATCAGACGGTTAGTTCTTGGAACATGAAAATGCAAGTGTGG
TAAGTCAAAAGTATGCATGGCAAGATACACTTCTTTGGCAATATGTGAATGTCCATGGTTAAGA
AAAAAAAGATGTTCCTCAACGATCAACCACAGAGCATAAATATTAGTGCGACCTTGCTGTAGAT
CAAAGCATGTGAAAAGTGATATGACCATGCTAGTCAAAAGCCATATTTCACAAGAAGCGAACTG
TCTGTGGCATGTAATAGATCATTTGCATGTTTTATGAGTGTAGAAGTACCTGCAGCTTCTTGGC
CAGTCATTGCATCCACAACAAGTAAAACCTCTGTGGGGTTCAGTACCCGTTTCACGTCTTTTAA
TTCATCCATCATAGTTTTATCTATCTACAAGAACTAAGAGAAAGGTTTAAATACAACTACTAGA
AAAAGTTATAGTGGAATTCAAAAACTAAGATGATATGACCTGAAGTCTTCCAGCTGTATCCATT
ATGACTACATCTACATTCTTCTTTTTGGCCTCTTGTAATCCTTGTCGGGCTATTTCTGCAGGTT
TTACATCTGTTCCTGCTGCATAAACAGGTACATCAACCTGTTCCCCCACTTATCAGTGAACATG
AGAATGGATGAAGTTGTGTTTAGATATTCTGTGTACTCGTAAAGAAGATATATAGATAAAGATT
GTTAAGGTGTAGAAGAACAGAAAGAAGCATCTAAAATAAAATGATATATAATCTTATTGTTGCT
AATGTGACATGGCACACCTGTTTACCCAAAATAACAAGTTGGTCAATAGCAGCAGGTCTGTACA
CGTCTCCAGCAATCAGCATGCAACTCTTACCCTGCAGACCATGCCACCAGTGCCCATAAATGGT
TTGACAATAGAATGAGAAAAAGGGAAAATGCTAATATTAGAAGGCACTTGGAGAAATGCAGGTT
CTACGACCATATATGTAAATTGCAATAGAATGAGCAAGAGAGAGGGGAGTGAGAGAAAGTAAAG
GAAGGTCAGGAAAGGGAGAAGGTGAAGTTTGGAAGTCCACCTGCTTCTTTAGATATAAAGCTAA
CTTTGCACTAACAGTTGTCTTCCCAACACCTTGTAGACCGGCCAATAGTATTACGGTGGGCTTA
GATTTAGCAAAAACCAGTTCAGAAACCTCTCCACCCATCAGTTTCACAAGCTCGTCACGTACAG
TCTACACCAACCAAATGAGACAAAGAAAATGTTCAGATCGAGCTGATAGCAAATTGTGCAAGCA
ATTAACAACAGAAGGGTGACCGTCTGTTATCAATGTACAAATGTGTATTGTTCAGAGTCATCAG
TTCAAAAATACATACCTTAACTAGTTGCTGATCTGGTTTTACACCTCGAATCAAACCAGTGCCA
ACGGCTTCTTCACTAACAGACTGAACAAACCTTCTGACAACTGGGAGACTAACCTGCCGATTAA
AGTTAAATAAGCGGCGAAATTTTATGTATAGAGATTAGTTGTTGAAACAGTAAGCAACATACAT
CAGCTTCTAAAAGAGCCCTCCTGATGTCCCTCATAGGTTCCACGATGTTTTCCTTGGTCAAAAC
CT
						
					

			
		

Sequences
Splice junction sequence	GAGATTAGTTGTTGAAACAGTAAGCAACATACATCAGCTTCTAAAAGAGCCCTCCTGATGTCCC TCATAGGTTCCACGATGTTTTCCTTGGTCAAAACCTcaacttcttgggctttctcaacaaacga tagaacatctcccattcctaaaatacgtccagccatgcggtcaggatagaaaggttcaaggtcc tccatacg
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	CAACTTCTTGGGCTTTCTCAACAAACGATAGAACATCTCCCATTCCTAAAATACGTCCAGCCAT GCGGTCAGGATAGAAAGGTTCAAGGTCCTCCATACGTTCACCCCTTCCTACGAGCTTGATTGGC TTTCCTGATACCTGTGGTAGTGAACATATAATTGTGATGCACAATCTTAGTTCATTTAACCAAA AACCTGACCGTTAAAGAGCAATCAGTGATTTTTTTTGTCTATACATATGATTCGTGTACAATCT CTACCCCATAAAAGGTAGGAGTAAGATCTGCTTACATCCTCCCCTCCCCATTACACACATGTCG GACTACACTGGGTTGTTGTTCTGTTGTAACTTGTGACCCATATTGGCAACATTTGACACAACCA CTTAAACAGATATCATCAATTGCCTATTGGCTTCAAATCTATTCCATTCAGTTTAAACCTTGAC AAAAGTAAATTTCTTCCAAGATAATACGCAAAAGACATGTTGAACATAGAGGAAATCTGAAGTT TGTGGTCCAATCACTCTTTACGTTTTAGTATTTGTTTCGCCGCATGATCCCTTCAAGGAAGAAA AGCTTTTGGATATTTATAATCATCTACTTCCATCATTAACTCTCCTTCATCTTTGCTGCTCTAA GTTCAAAAGTAGAAATGTTGACTTTGCTAATCAAGAGAAGTTGAAGCAAAGTAAACTGCAAGGT TAAACTTAGAACAAGGAAAAAACGAATGTATGTGTCGTGTAGTAAAAAGACCCCACCTCCTTGA CACTTAAAGCTGCTCCACCCCTAGAATCTCCATCTAGCTTCGTCAAGATGGCACCAGTAATTCC AATTTCGAGATTGAATGTTGTGACCAAAGCTACAATTTCATCAATGTGAACGATAAGAGAGAAA ACAAATCGGAATTTTCTGTTTTCAACATGAAATGATTGGTATAGGGCAGAAATTATGTCCTTGT GTCAGTAATAACTCAATGAAAGTGCAGTACTATGATTTCTGTTTTGAGATGTTACAGAATTTTA ATGCACTATCTAGTAACAAATTTCAAGAGTTCAGATTCATTTAACAACTCAGATATGGAATGCC TCTCTCCATTAACCTCAAAAAACCAATTCCGTTTATTTTTTTCTGACTAAAAAAGTTTCAAGTA AATGAAACTAATTCCTTAAACTCCATATCAACCAAGCATGTCGCGTGAATAGAGGGAGTATTAA AATAGTTAAACAGCTTCAGATTATCAAAGATAACATCCATATTTATGTAATGAAGTCCCAAAAA TAACTTATATTCGTACAAGACAAGCACAAGAAAGAAATTAACTGTCATATACAGCTGTGCTATA AGTCTCCAAGCTTCGATGAGAAGCAATATAACGTTCTCTTGAGAAAAACGCTCGGTGGCAACAT TACACAAACAACAGATATTTTGCTCTCTCTGTGAGAAGCAGACCTCAGATAACAGAATGGCCTG GATTGTTAAGGAAAGTTTTTCGTATCAGACGGTTAGTTCTTGGAACATGAAAATGCAAGTGTGG TAAGTCAAAAGTATGCATGGCAAGATACACTTCTTTGGCAATATGTGAATGTCCATGGTTAAGA AAAAAAAGATGTTCCTCAACGATCAACCACAGAGCATAAATATTAGTGCGACCTTGCTGTAGAT CAAAGCATGTGAAAAGTGATATGACCATGCTAGTCAAAAGCCATATTTCACAAGAAGCGAACTG TCTGTGGCATGTAATAGATCATTTGCATGTTTTATGAGTGTAGAAGTACCTGCAGCTTCTTGGC CAGTCATTGCATCCACAACAAGTAAAACCTCTGTGGGGTTCAGTACCCGTTTCACGTCTTTTAA TTCATCCATCATAGTTTTATCTATCTACAAGAACTAAGAGAAAGGTTTAAATACAACTACTAGA AAAAGTTATAGTGGAATTCAAAAACTAAGATGATATGACCTGAAGTCTTCCAGCTGTATCCATT ATGACTACATCTACATTCTTCTTTTTGGCCTCTTGTAATCCTTGTCGGGCTATTTCTGCAGGTT TTACATCTGTTCCTGCTGCATAAACAGGTACATCAACCTGTTCCCCCACTTATCAGTGAACATG AGAATGGATGAAGTTGTGTTTAGATATTCTGTGTACTCGTAAAGAAGATATATAGATAAAGATT GTTAAGGTGTAGAAGAACAGAAAGAAGCATCTAAAATAAAATGATATATAATCTTATTGTTGCT AATGTGACATGGCACACCTGTTTACCCAAAATAACAAGTTGGTCAATAGCAGCAGGTCTGTACA CGTCTCCAGCAATCAGCATGCAACTCTTACCCTGCAGACCATGCCACCAGTGCCCATAAATGGT TTGACAATAGAATGAGAAAAAGGGAAAATGCTAATATTAGAAGGCACTTGGAGAAATGCAGGTT CTACGACCATATATGTAAATTGCAATAGAATGAGCAAGAGAGAGGGGAGTGAGAGAAAGTAAAG GAAGGTCAGGAAAGGGAGAAGGTGAAGTTTGGAAGTCCACCTGCTTCTTTAGATATAAAGCTAA CTTTGCACTAACAGTTGTCTTCCCAACACCTTGTAGACCGGCCAATAGTATTACGGTGGGCTTA GATTTAGCAAAAACCAGTTCAGAAACCTCTCCACCCATCAGTTTCACAAGCTCGTCACGTACAG TCTACACCAACCAAATGAGACAAAGAAAATGTTCAGATCGAGCTGATAGCAAATTGTGCAAGCA ATTAACAACAGAAGGGTGACCGTCTGTTATCAATGTACAAATGTGTATTGTTCAGAGTCATCAG TTCAAAAATACATACCTTAACTAGTTGCTGATCTGGTTTTACACCTCGAATCAAACCAGTGCCA ACGGCTTCTTCACTAACAGACTGAACAAACCTTCTGACAACTGGGAGACTAACCTGCCGATTAA AGTTAAATAAGCGGCGAAATTTTATGTATAGAGATTAGTTGTTGAAACAGTAAGCAACATACAT CAGCTTCTAAAAGAGCCCTCCTGATGTCCCTCATAGGTTCCACGATGTTTTCCTTGGTCAAAAC CT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.192446682

Conservation Information
Conserved circRNAs	NA
PMCS	0.192446682

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to low-temperature stress

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to low-temperature stress

			
						 Other Information
					
						References
						Yang et al., 2020

circRNA

Detail information of Solyc09g009940.2_circ_g.1

Address

Any questions?

Supported by