Plant Circular RNA Database

Detail information of Solyc11g062310.1_circ_g.4

			
						 General Information
					
						CircRNA Name
						Solyc11g062310.1_circ_g.4
					
						ID in PlantcircBase
						sly_circ_003412
					
						Alias
						11:46325333|46326934
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr11: 49241833-49243434  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc11g062310.1						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc11g062310.1_circ_g.1 Solyc11g062310.1_circ_g.2 Solyc11g062310.1_circ_g.3 Solyc11g062310.1_circ_g.5 Solyc11g062310.1_circ_g.6 						
					
						Support reads
						16
					
						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
						Solyc11g062310.1.1:3

General Information
CircRNA Name	Solyc11g062310.1_circ_g.4
ID in PlantcircBase	sly_circ_003412
Alias	11:46325333\|46326934
Organism	Solanum lycopersicum
Position	chr11: 49241833-49243434 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc11g062310.1
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc11g062310.1_circ_g.1 Solyc11g062310.1_circ_g.2 Solyc11g062310.1_circ_g.3 Solyc11g062310.1_circ_g.5 Solyc11g062310.1_circ_g.6
Support reads	16
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	Solyc11g062310.1.1:3

			
						 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  
						
							AACAGCTTGAAATAGAAGTCGCAGTAGCATGGTTGTAAATGGTTTGATATTTACGCCAACTTTC
TGCGCTAACAAGCTTATAAAATTTGCAACGCCAACCctcccatatgcgtccagggatttctttc
aagagggatgagaggagtacatggtgctgtgaggaaaccacctcaccaaggatgtcacagagct
tacttact

									
								

					

						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: 601
Transcript exons: 49241833-49241943,49242085-49242238,49243099-49243434
CTCCCATATGCGTCCAGGGATTTCTTTCAAGAGGGATGAGAGGAGTACATGGTGCTGTGAGGAA
ACCACCTCACCAAGGATGTCACAGAGCTTACTTACTGCCTGAGCAGCCTTCTGTTTTCGAGACC
ATGAGGATGACATAATTCCTCCACTGATAAGCTCAACGATCTCCCCCAAGTACAATTGAAGAGT
AACTCGTTCACTACTCATATTTTCCTCCCACATTTCTTCATACAGATTAGAAACAGATTTTTCA
TCCTCAAATCTTGAAATAAATATTACTGGCACAATCACATCATTATATCCACCCAAAACATCAG
CAGCTGAGGAAAAGTAGCTTTTCAATAAAACTGCACATGCAATCTGTTCATTCCTTTCCCCGAG
ATGTAAAGCAGCAGTGTCTTCAATCAACTTCTGGGCCTGGGAAGGAGTTGCATACTTCAGAACT
GTGGCACAAGCATTTGCAAATGCACGTTTTGAAGTAGCACTTCTTTCCTCCTTAACAGCTTGAA
ATAGAAGTCGCAGTAGCATGGTTGTAAATGGTTTGATATTTACGCCAACTTTCTGCGCTAACAA
GCTTATAAAATTTGCAACGCCAACC
						
					

						Genomic sequence
						
							CTCCCATATGCGTCCAGGGATTTCTTTCAAGAGGGATGAGAGGAGTACATGGTGCTGTGAGGAA
ACCACCTCACCAAGGATGTCACAGAGCTTACTTACTGCCTGAGCAGCCTGCATGATAAATAAGA
TAGTAAAACTCTTGAAACAGCCCAACATACCTTTTTCTTTGAGGTGCAAGGGAAAACTGCAGAT
AGTTAAACTTTCATGCACTTATCTAAGCTTGGGAGTGAATATAAGAAAGATCATTAGTACCTTC
TGTTTTCGAGACCATGAGGATGACATAATTCCTCCACTGATAAGCTCAACGATCTCCCCCAAGT
ACAATTGAAGAGTAACTCGTTCACTACTCATATTTTCCTCCCACATTTCTTCATACAGATTAGA
AACAGATTTTTCATCCTCAAATCTGCATAAGATTATATAATAGTGTCCACTGATAAGCACTAGT
CATAGAAAATACTGTTAGGAGAAATTTAAAATACTTGGCTTTACAACCGGACAAAACTTGCAAG
CTCAAGTAGAAGGTTCAATTATGTAAATATTTTTGCAAGTATGTATATATTGTTCTAAAGGAGG
GCAATGGGGGTACTTGTTACCATTTCCCAATAAAAAGGGAAGGTGGTGGTCTGGTGGAGGTAGA
ATAAACAGAAAGTTCAGAGTTCAAATTGACTACTACATCAGGCTGTCCTACAACTAGAAAGTTC
AAGAACTTCATAACACTTCCATTTCAAAATGACATACAATATTTGTCAAAGGTGGCCCTTAAGT
CAGTAGCCAACAAATAAGGCACAGGATTTAATCAGAATTACCAAGGAAGGATACCAGATAAACC
AGCTCCCTATCTATGCTACTCCGGAGAGAGGAATTAAGTCCATTTTATGCATTTGAAACAGGAT
AATATAATATTCTTGAATTTGCTGTCCCAGTAATCTTGAATATGTTGTCATGTCATGTCAAGGG
AAGTTAGCATTGTCCCATCATCCCAAATCCATACTGCTTATAGGTTGTCATGTAAATTATTATG
TTCATTTTTACAATTCTATTCTTCGTTTGAACAAGATAACATGGCAATATATAGATTCTTCGAT
AATTAAGGTTACCTCATTTTATACACATAGATACGTTCTCATGTAAGAAGTGACAGCAAATTCA
AGATTACTGGGACATGCTAACTTCTCTTGGGAAAATTGATATAACATGAAACAAGATTACATAA
AAATTCACCATCACAGGCTATGAAATAGAGAAAGGAAAATAGAGTCTGACCTTGAAATAAATAT
TACTGGCACAATCACATCATTATATCCACCCAAAACATCAGCAGCTGAGGAAAAGTAGCTTTTC
AATAAAACTGCACATGCAATCTGTTCATTCCTTTCCCCGAGATGTAAAGCAGCAGTGTCTTCAA
TCAACTTCTGGGCCTGGGAAGGAGTTGCATACTTCAGAACTGTGGCACAAGCATTTGCAAATGC
ACGTTTTGAAGTAGCACTTCTTTCCTCCTTAACAGCTTGAAATAGAAGTCGCAGTAGCATGGTT
GTAAATGGTTTGATATTTACGCCAACTTTCTGCGCTAACAAGCTTATAAAATTTGCAACGCCAA
CC
						
					

			
		

Sequences
Splice junction sequence	AACAGCTTGAAATAGAAGTCGCAGTAGCATGGTTGTAAATGGTTTGATATTTACGCCAACTTTC TGCGCTAACAAGCTTATAAAATTTGCAACGCCAACCctcccatatgcgtccagggatttctttc aagagggatgagaggagtacatggtgctgtgaggaaaccacctcaccaaggatgtcacagagct tacttact
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: 601 Transcript exons: 49241833-49241943,49242085-49242238,49243099-49243434 CTCCCATATGCGTCCAGGGATTTCTTTCAAGAGGGATGAGAGGAGTACATGGTGCTGTGAGGAA ACCACCTCACCAAGGATGTCACAGAGCTTACTTACTGCCTGAGCAGCCTTCTGTTTTCGAGACC ATGAGGATGACATAATTCCTCCACTGATAAGCTCAACGATCTCCCCCAAGTACAATTGAAGAGT AACTCGTTCACTACTCATATTTTCCTCCCACATTTCTTCATACAGATTAGAAACAGATTTTTCA TCCTCAAATCTTGAAATAAATATTACTGGCACAATCACATCATTATATCCACCCAAAACATCAG CAGCTGAGGAAAAGTAGCTTTTCAATAAAACTGCACATGCAATCTGTTCATTCCTTTCCCCGAG ATGTAAAGCAGCAGTGTCTTCAATCAACTTCTGGGCCTGGGAAGGAGTTGCATACTTCAGAACT GTGGCACAAGCATTTGCAAATGCACGTTTTGAAGTAGCACTTCTTTCCTCCTTAACAGCTTGAA ATAGAAGTCGCAGTAGCATGGTTGTAAATGGTTTGATATTTACGCCAACTTTCTGCGCTAACAA GCTTATAAAATTTGCAACGCCAACC
Genomic sequence	CTCCCATATGCGTCCAGGGATTTCTTTCAAGAGGGATGAGAGGAGTACATGGTGCTGTGAGGAA ACCACCTCACCAAGGATGTCACAGAGCTTACTTACTGCCTGAGCAGCCTGCATGATAAATAAGA TAGTAAAACTCTTGAAACAGCCCAACATACCTTTTTCTTTGAGGTGCAAGGGAAAACTGCAGAT AGTTAAACTTTCATGCACTTATCTAAGCTTGGGAGTGAATATAAGAAAGATCATTAGTACCTTC TGTTTTCGAGACCATGAGGATGACATAATTCCTCCACTGATAAGCTCAACGATCTCCCCCAAGT ACAATTGAAGAGTAACTCGTTCACTACTCATATTTTCCTCCCACATTTCTTCATACAGATTAGA AACAGATTTTTCATCCTCAAATCTGCATAAGATTATATAATAGTGTCCACTGATAAGCACTAGT CATAGAAAATACTGTTAGGAGAAATTTAAAATACTTGGCTTTACAACCGGACAAAACTTGCAAG CTCAAGTAGAAGGTTCAATTATGTAAATATTTTTGCAAGTATGTATATATTGTTCTAAAGGAGG GCAATGGGGGTACTTGTTACCATTTCCCAATAAAAAGGGAAGGTGGTGGTCTGGTGGAGGTAGA ATAAACAGAAAGTTCAGAGTTCAAATTGACTACTACATCAGGCTGTCCTACAACTAGAAAGTTC AAGAACTTCATAACACTTCCATTTCAAAATGACATACAATATTTGTCAAAGGTGGCCCTTAAGT CAGTAGCCAACAAATAAGGCACAGGATTTAATCAGAATTACCAAGGAAGGATACCAGATAAACC AGCTCCCTATCTATGCTACTCCGGAGAGAGGAATTAAGTCCATTTTATGCATTTGAAACAGGAT AATATAATATTCTTGAATTTGCTGTCCCAGTAATCTTGAATATGTTGTCATGTCATGTCAAGGG AAGTTAGCATTGTCCCATCATCCCAAATCCATACTGCTTATAGGTTGTCATGTAAATTATTATG TTCATTTTTACAATTCTATTCTTCGTTTGAACAAGATAACATGGCAATATATAGATTCTTCGAT AATTAAGGTTACCTCATTTTATACACATAGATACGTTCTCATGTAAGAAGTGACAGCAAATTCA AGATTACTGGGACATGCTAACTTCTCTTGGGAAAATTGATATAACATGAAACAAGATTACATAA AAATTCACCATCACAGGCTATGAAATAGAGAAAGGAAAATAGAGTCTGACCTTGAAATAAATAT TACTGGCACAATCACATCATTATATCCACCCAAAACATCAGCAGCTGAGGAAAAGTAGCTTTTC AATAAAACTGCACATGCAATCTGTTCATTCCTTTCCCCGAGATGTAAAGCAGCAGTGTCTTCAA TCAACTTCTGGGCCTGGGAAGGAGTTGCATACTTCAGAACTGTGGCACAAGCATTTGCAAATGC ACGTTTTGAAGTAGCACTTCTTTCCTCCTTAACAGCTTGAAATAGAAGTCGCAGTAGCATGGTT GTAAATGGTTTGATATTTACGCCAACTTTCTGCGCTAACAAGCTTATAAAATTTGCAACGCCAA CC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.816388804

Conservation Information
Conserved circRNAs	NA
PMCS	0.816388804

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							49243364-49241868(+)
49243366-49243335(-)
						
						Potential amino acid sequence
						
							MVVNGLIFTPTFCANKLIKFATPTLPYASRDFFQEG*(+)
MLLRLLFQAVKEERSATSKRAFANACATVLKYATPSQAQKLIEDTAALHLGERNEQIACAVLLK
SYFSSAADVLGGYNDVIVPVIFISRFEDEKSVSNLYEEMWEENMSSERVTLQLYLGEIVELISG
GIMSSSWSRKQKAAQAVSKLCDILGEVVSSQHHVLLSSLLKEIPGRIWEGWRCKFYKLVSAESW
RKYQTIYNHATATSISSC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	49243364-49241868(+) 49243366-49243335(-)
Potential amino acid sequence	MVVNGLIFTPTFCANKLIKFATPTLPYASRDFFQEG(+) MLLRLLFQAVKEERSATSKRAFANACATVLKYATPSQAQKLIEDTAALHLGERNEQIACAVLLK SYFSSAADVLGGYNDVIVPVIFISRFEDEKSVSNLYEEMWEENMSSERVTLQLYLGEIVELISG GIMSSSWSRKQKAAQAVSKLCDILGEVVSSQHHVLLSSLLKEIPGRIWEGWRCKFYKLVSAESW RKYQTIYNHATATSISSC(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc11g062310.1_circ_g.4

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