Plant Circular RNA Database

Detail information of Solyc12g019860.1_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc12g019860.1_circ_g.3
					
						ID in PlantcircBase
						sly_circ_003580
					
						Alias
						12:12005572|12008556
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr12: 12005572-12008556  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc12g019860.1						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc12g019860.1_circ_g.1 Solyc12g019860.1_circ_g.2 						
					
						Support reads
						4
					
						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
						Solyc12g019860.1.1:4

General Information
CircRNA Name	Solyc12g019860.1_circ_g.3
ID in PlantcircBase	sly_circ_003580
Alias	12:12005572\|12008556
Organism	Solanum lycopersicum
Position	chr12: 12005572-12008556 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc12g019860.1
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc12g019860.1_circ_g.1 Solyc12g019860.1_circ_g.2
Support reads	4
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	Solyc12g019860.1.1:4

			
						 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  
						
							CAGAAGCTGTAACTTCTTTTTGGTTTTCCAGGGTGTCACTGTTCCCAGTGCGGTTTTGAGTGTG
AAAACTTCTCTGGCCTCTCCACCTGCTCAAGCATCGgttggggagcttgaaagtcaaattgaca
atttcgaggctgaactggaaggactctcagttaaaaaagggaagcagaggcccccaagattggt
aagaagat

									
								

					

						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
						
							GTTGGGGAGCTTGAAAGTCAAATTGACAATTTCGAGGCTGAACTGGAAGGACTCTCAGTTAAAA
AAGGGAAGCAGAGGCCCCCAAGATTGGTAAGAAGATGTAAAATTAAGTGTGTATTGTGCATTTG
GCTTATCGTGCTTGATTAAAGGTTACTTCTTTTATGTTTTCCCTAGGTACATTTGGAAACATCT
ATTGCTCGGCACAAGGCTCATATAATGAAGTTAGAGTTAATTTTAAGATTACTGGATAATGATG
AGTTGAGTCCTGAGCAAGTCAACGATGTCAAGGATTTCCTCGACGATTATGTGGAAAGAAATCA
GGTATACTATTCTGTGCAATTTATTCCTCATGTGTCTGGTGTAGGTTACTGTGAAGAAATGAAG
CATAATTATCACTCTAACCTCTTAATTTAAATGGAATTCTGAAGCGCTGCTAGGTTGCTATCTC
TTTCTCTTCACTTGTTTCTGTTTATTTACTTCTGATGTGTTCTTAGGATTGCTCTTGAAGTAAT
GACATCTTTTTGGCATGTAATATTACCATTTGCTTGTACTGCTGTATTTTTGCAGGAGGATTTT
GATGAATTCAGTGATGTTGATGAGCTCTACAGCACTTTACCACTAGATAAGGTGGAGTCTCTTG
AAGATCTGGTTACCGTCGTTCCACCTGCTCTTGTCAAGGTAATATACATCCAAATCATCATTTC
TTCTAATTTTATTTTCTACTTAAATTATTCATTTATTGTTCATCTTTTATGTTTTGACTGATAT
ATTTGTCTCTTTTGCTATACTAAAATAATTGTGGTCATTTCTTAATTCGAATGTATGGGTGTAG
AATTATTTTGATCTTTAATGCATACCATTCCTGAACGCAATTCTTCTTAATATTTAGGCCAAAA
CCCTAAAACTAAAGGAAATCACGAAAGAGGTGTGACCTGTTATAGTGAAAAAACCAAAACATAT
AAGAAGCACTCAAATTAGCCCGGTAGGGAGAAGAGAGAAACAGAGAACTCTGTATCATTGCTAG
CATTTTAGCCCCTTAATCAGTCCAAAGTCGGGCGATTTTCCATTGTTGTGCTTGGTCCGAAGGG
TGGAAAAAATAAGCCATTTATTAGCTCAACCCAACCCATTAAATATTGGGTTGATTTGTAACCC
AAATTGACTCATTTTAAAAACTTGATGTGTTATATATGGCCATAATAAATATTTTTTATTAGGT
ACTAAAATATTTAAAAGAACAAATGAAATAATGAAAACTTAGTAAAAATTGGGTTGAGTTGGGT
CTTAACCCATTTTGACTGAAAAAGATTTGTGTTGGGTTTGGTCTTGACCTGTTTATTGGCTTGA
CCCATTATGATCCGTCCAAATTTTAACCAACTTGCCCAATTGCCATTGTTTGTCACTTAAGAGG
CCCATTGCCCTTTCACCATATGTAAATTTACTATTTGTGTGGATGTATATTGGAGTTTCTATTG
GCTCAAGTGAAGATTTTGCATATAGGGTTTTAGTTTGTGATTTTTAGATCTACATGAGTTCAGG
GTTTTGTGGTTGACAGCAAGCTGAGGATTTCAATGGAGCGATTTTAAATATGATAGAAGATGTT
AACAAGACTTTTAACATCTTCTATCATATTTATAGATTTGGACTAAAATTGTCCACTTTTTATA
AATATAAATATTACAATACACCAAAGTTTTGTAGCTGATACGAGTGTGGATCAAAAGTTTGGAT
GTTCCATTGCGTTAATTTTGAGATTTAAGGAAATGGATTCGAGTGCATCATACCAGTGCAAAGA
TACTATTAATTATTTAAACATGTTGAAAAACAACTTTTTTTCCTATTAAAAGGTAATTTAAATC
CATTTCTATTAATTGAGTTAAATGAAAAATGTCCACATCATTGTAACTCGCTAATATATATATA
TATATATACATATAAAGTTTGAATTGAGAAAAATATTTTTTTTCTGTTCAAAAAATTGGTTATC
AGTCTCTATTTATGCTTCTTGAGCTTTATATGTGACTCGAAAGCAAAAAGTATTTGTGGTAGAA
ATAATTGTGTTATTACTAACTAGAGCACAAAAAGTATCAAGTATTTGTGGTAAAATTTAAGTTC
AGTGTAAACACTTAAATTTTTTATTTATAAGCTATCTCGTACAAAAGCAAAGTGTTCTAGTACT
TTATGTGTTATATATGATATAAACCAAATTCAAACCAAATACACAATTATTCTATATTTCATGG
GAATATGTTTAGTCAAAAGCACCCAAGATAGGTTGACTAAATCCAGTGCTGATCCCACACCACA
CCCAAATTGTGTTGGATGACATGAGTTCAGAAAAGATTTTGAAGGATCTGGCTAGATAGATCAA
AACCTAAGTTGGAGCTCTAAATCCCTAAAGCTTGCCTTATCTATTATTAGAAAGGGAGGTGACT
ATGTCCTTCAGACACTTTGCCTTTACTCAAAAAAATGAGGGAAGTGACGAGGTACGCCTAAATT
ACATGGATGGAAGTTGTCTCCTTAAATCTCTTGAAATAAATAGGAACTAAACAAAGAACATTAC
TCAATATAAGCAAAGGTTATTACATAAGCTATTCCGATTACATGGTATTTTGACTTAGTTGTTG
TTATTAGGTTTGGATATGGGTAAGTGTGAGGTTTGGATAACCTTCAAGACAAATATTTTACCAC
TACTGGAATGAGTGGAGATCGAATAGAGTGAAACAGATATAGGTGATTCATCTCGGCAGCCACG
AGTTATTTGGCTAGAGACGTAATTATGGTTTATGCAAGTAGCAATTCCTTTCACTAGTTTCTTT
CGGTATTTTTTCAAGTAGAGGAAAGAAACTCTCTGCCCATCTATGTAGGGATGGGCCGTACAAC
CTTTGCAGAAGCTGTAACTTCTTTTTGGTTTTCCAGGGTGTCACTGTTCCCAGTGCGGTTTTGA
GTGTGAAAACTTCTCTGGCCTCTCCACCTGCTCAAGCATCG
						
					

			
		

Sequences
Splice junction sequence	CAGAAGCTGTAACTTCTTTTTGGTTTTCCAGGGTGTCACTGTTCCCAGTGCGGTTTTGAGTGTG AAAACTTCTCTGGCCTCTCCACCTGCTCAAGCATCGgttggggagcttgaaagtcaaattgaca atttcgaggctgaactggaaggactctcagttaaaaaagggaagcagaggcccccaagattggt aagaagat
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	GTTGGGGAGCTTGAAAGTCAAATTGACAATTTCGAGGCTGAACTGGAAGGACTCTCAGTTAAAA AAGGGAAGCAGAGGCCCCCAAGATTGGTAAGAAGATGTAAAATTAAGTGTGTATTGTGCATTTG GCTTATCGTGCTTGATTAAAGGTTACTTCTTTTATGTTTTCCCTAGGTACATTTGGAAACATCT ATTGCTCGGCACAAGGCTCATATAATGAAGTTAGAGTTAATTTTAAGATTACTGGATAATGATG AGTTGAGTCCTGAGCAAGTCAACGATGTCAAGGATTTCCTCGACGATTATGTGGAAAGAAATCA GGTATACTATTCTGTGCAATTTATTCCTCATGTGTCTGGTGTAGGTTACTGTGAAGAAATGAAG CATAATTATCACTCTAACCTCTTAATTTAAATGGAATTCTGAAGCGCTGCTAGGTTGCTATCTC TTTCTCTTCACTTGTTTCTGTTTATTTACTTCTGATGTGTTCTTAGGATTGCTCTTGAAGTAAT GACATCTTTTTGGCATGTAATATTACCATTTGCTTGTACTGCTGTATTTTTGCAGGAGGATTTT GATGAATTCAGTGATGTTGATGAGCTCTACAGCACTTTACCACTAGATAAGGTGGAGTCTCTTG AAGATCTGGTTACCGTCGTTCCACCTGCTCTTGTCAAGGTAATATACATCCAAATCATCATTTC TTCTAATTTTATTTTCTACTTAAATTATTCATTTATTGTTCATCTTTTATGTTTTGACTGATAT ATTTGTCTCTTTTGCTATACTAAAATAATTGTGGTCATTTCTTAATTCGAATGTATGGGTGTAG AATTATTTTGATCTTTAATGCATACCATTCCTGAACGCAATTCTTCTTAATATTTAGGCCAAAA CCCTAAAACTAAAGGAAATCACGAAAGAGGTGTGACCTGTTATAGTGAAAAAACCAAAACATAT AAGAAGCACTCAAATTAGCCCGGTAGGGAGAAGAGAGAAACAGAGAACTCTGTATCATTGCTAG CATTTTAGCCCCTTAATCAGTCCAAAGTCGGGCGATTTTCCATTGTTGTGCTTGGTCCGAAGGG TGGAAAAAATAAGCCATTTATTAGCTCAACCCAACCCATTAAATATTGGGTTGATTTGTAACCC AAATTGACTCATTTTAAAAACTTGATGTGTTATATATGGCCATAATAAATATTTTTTATTAGGT ACTAAAATATTTAAAAGAACAAATGAAATAATGAAAACTTAGTAAAAATTGGGTTGAGTTGGGT CTTAACCCATTTTGACTGAAAAAGATTTGTGTTGGGTTTGGTCTTGACCTGTTTATTGGCTTGA CCCATTATGATCCGTCCAAATTTTAACCAACTTGCCCAATTGCCATTGTTTGTCACTTAAGAGG CCCATTGCCCTTTCACCATATGTAAATTTACTATTTGTGTGGATGTATATTGGAGTTTCTATTG GCTCAAGTGAAGATTTTGCATATAGGGTTTTAGTTTGTGATTTTTAGATCTACATGAGTTCAGG GTTTTGTGGTTGACAGCAAGCTGAGGATTTCAATGGAGCGATTTTAAATATGATAGAAGATGTT AACAAGACTTTTAACATCTTCTATCATATTTATAGATTTGGACTAAAATTGTCCACTTTTTATA AATATAAATATTACAATACACCAAAGTTTTGTAGCTGATACGAGTGTGGATCAAAAGTTTGGAT GTTCCATTGCGTTAATTTTGAGATTTAAGGAAATGGATTCGAGTGCATCATACCAGTGCAAAGA TACTATTAATTATTTAAACATGTTGAAAAACAACTTTTTTTCCTATTAAAAGGTAATTTAAATC CATTTCTATTAATTGAGTTAAATGAAAAATGTCCACATCATTGTAACTCGCTAATATATATATA TATATATACATATAAAGTTTGAATTGAGAAAAATATTTTTTTTCTGTTCAAAAAATTGGTTATC AGTCTCTATTTATGCTTCTTGAGCTTTATATGTGACTCGAAAGCAAAAAGTATTTGTGGTAGAA ATAATTGTGTTATTACTAACTAGAGCACAAAAAGTATCAAGTATTTGTGGTAAAATTTAAGTTC AGTGTAAACACTTAAATTTTTTATTTATAAGCTATCTCGTACAAAAGCAAAGTGTTCTAGTACT TTATGTGTTATATATGATATAAACCAAATTCAAACCAAATACACAATTATTCTATATTTCATGG GAATATGTTTAGTCAAAAGCACCCAAGATAGGTTGACTAAATCCAGTGCTGATCCCACACCACA CCCAAATTGTGTTGGATGACATGAGTTCAGAAAAGATTTTGAAGGATCTGGCTAGATAGATCAA AACCTAAGTTGGAGCTCTAAATCCCTAAAGCTTGCCTTATCTATTATTAGAAAGGGAGGTGACT ATGTCCTTCAGACACTTTGCCTTTACTCAAAAAAATGAGGGAAGTGACGAGGTACGCCTAAATT ACATGGATGGAAGTTGTCTCCTTAAATCTCTTGAAATAAATAGGAACTAAACAAAGAACATTAC TCAATATAAGCAAAGGTTATTACATAAGCTATTCCGATTACATGGTATTTTGACTTAGTTGTTG TTATTAGGTTTGGATATGGGTAAGTGTGAGGTTTGGATAACCTTCAAGACAAATATTTTACCAC TACTGGAATGAGTGGAGATCGAATAGAGTGAAACAGATATAGGTGATTCATCTCGGCAGCCACG AGTTATTTGGCTAGAGACGTAATTATGGTTTATGCAAGTAGCAATTCCTTTCACTAGTTTCTTT CGGTATTTTTTCAAGTAGAGGAAAGAAACTCTCTGCCCATCTATGTAGGGATGGGCCGTACAAC CTTTGCAGAAGCTGTAACTTCTTTTTGGTTTTCCAGGGTGTCACTGTTCCCAGTGCGGTTTTGA GTGTGAAAACTTCTCTGGCCTCTCCACCTGCTCAAGCATCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.148253953

Conservation Information
Conserved circRNAs	NA
PMCS	0.148253953

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12005789-12008553(+)
						
						Potential amino acid sequence
						
							MKLELILRLLDNDELSPEQVNDVKDFLDDYVERNQEDFDEFSDVDELYSTLPLDKVESLEDLVT
VVPPALVKGVTVPSAVLSVKTSLASPPAQASVGELESQIDNFEAELEGLSVKKGKQRPPRLVHL
ETSIARHKAHIMKLELILRLLDNDELSPEQVNDVKDFLDDYVERNQEDFDEFSDVDELYSTLPL
DKVESLEDLVTVVPPALVKGVTVPSAVLSVKTSLASPPAQASVGELESQIDNFEAELEGLSVKK
GKQRPPRLVHLETSIARHKAHIMKLELILRLLDNDELSPEQVNDVKDFLDDYVERNQEDFDEFS
DVDELYSTLPLDKVESLEDLVTVVPPALVKGVTVPSAVLSVKTSLASPPAQASVGELESQIDNF
EAELEGLSVKKGKQRPPRLVHLETSIARHKAHIMKLELILRLLDNDELSPEQVNDVKDFLDDYV
ERNQEDFDEFSDVDELYSTLPLDKVESLEDLVTVVPPALVKGVTVPSAVLSVKTSLASPPAQAS
(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	12005789-12008553(+)
Potential amino acid sequence	MKLELILRLLDNDELSPEQVNDVKDFLDDYVERNQEDFDEFSDVDELYSTLPLDKVESLEDLVT VVPPALVKGVTVPSAVLSVKTSLASPPAQASVGELESQIDNFEAELEGLSVKKGKQRPPRLVHL ETSIARHKAHIMKLELILRLLDNDELSPEQVNDVKDFLDDYVERNQEDFDEFSDVDELYSTLPL DKVESLEDLVTVVPPALVKGVTVPSAVLSVKTSLASPPAQASVGELESQIDNFEAELEGLSVKK GKQRPPRLVHLETSIARHKAHIMKLELILRLLDNDELSPEQVNDVKDFLDDYVERNQEDFDEFS DVDELYSTLPLDKVESLEDLVTVVPPALVKGVTVPSAVLSVKTSLASPPAQASVGELESQIDNF EAELEGLSVKKGKQRPPRLVHLETSIARHKAHIMKLELILRLLDNDELSPEQVNDVKDFLDDYV ERNQEDFDEFSDVDELYSTLPLDKVESLEDLVTVVPPALVKGVTVPSAVLSVKTSLASPPAQAS (+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Zuo et al., 2016; Tan et al., 2017; Yin et al., 2018

circRNA

Detail information of Solyc12g019860.1_circ_g.3

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