Plant Circular RNA Database

Detail information of Solyc04g039600.1_circ_ig.1

			
						 General Information
					
						CircRNA Name
						Solyc04g039600.1_circ_ig.1
					
						ID in PlantcircBase
						sly_circ_001343
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 13631807-13635423  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						fruit
					
						Exon boundary  
						
							No-No							"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  
						
							AA-TG							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
						NA

General Information
CircRNA Name	Solyc04g039600.1_circ_ig.1
ID in PlantcircBase	sly_circ_001343
Alias	NA
Organism	Solanum lycopersicum
Position	chr4: 13631807-13635423 JBrowse»
Reference genome	SL2.50.38
Type	ig-circRNA
Identification method	Segemehl, CIRI
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	NA
Support reads	NA
Tissues	fruit
Exon boundary	No-No "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	AA-TG 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	NA

			
						 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  
						
							CTAGTATTTAAATATTTTTATGCATTGGGGACAATTGCATGTCTTTTTGTGGGGGTGGGGTAAA
TAGAAAGTGAGTGCTAGGGTGAAGTCTGAGTAGCCGacctatcactttagcaaaactttcatac
ttcaaaatcttctcttatccttcttttatgaagggactaccttctcaaacattaaacattttca
tatgtaac

									
								

					

						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
						
							ACCTATCACTTTAGCAAAACTTTCATACTTCAAAATCTTCTCTTATCCTTCTTTTATGAAGGGA
CTACCTTCTCAAACATTAAACATTTTCATATGTAACACTTTTTCACACATTAAAACTTCAAACA
AAGTCAAGAAAAATTTTCTCAAAATTCAAAAATCTATAGTGAACATCACTGTAACACTGTTAAG
CATGCTTAAAATTTTAAAATTCTATTATTTGAGAATTTCATAAGAAAAGGCCTGATCATATGAA
GTATTGTACTATATAAACTCATCTAATAACACATTGAAACCATAATTCATGAAAAATGCAATTT
CCTTATAATTTGGACTTACTTGCAATGAATTCAAAAATTCACTTTGTCCCATGCTTAAAATTTC
AATAATGCACCTTTCAAGCAACTTTAATAAGATGTCATGACAGTATAAGAGACAAGACTATACT
AACTTACTCCAAAGAGAATTGATAAGTTCCACTAAGTTCAATGTGAGAGTAGCATACCATACTA
CCACTCCCACTTAGTGACCCTTGAGGATATCTTTTGGACTAAGTACATTACATGCAATTCTACT
CAACTCATTCTCCCCCACTTAGGGTAAATCCATCTTCAACGTCTCATACTTAAAAGCACCATTA
TGCCTCTCACATAGAAAGGACTCACACAACCCTCAACTAATTCACATCAAGACTAAAATCCAAT
CCACTAGTCAAGCATAACACTCTCCTCTAAGGATTTAAGCCTAAAAGAAATCCCTTTAACGCCA
CCTCATTCAACTCTTAGGCGTCACTTAACTCAATTTCATGAAACAAAACTCCCTTACTAGGTAT
TCATACCAAATTTCCTCCATAGTGTAAACCTACACAAGAACCTCAACCAAATCACAAGAACAAC
TATTCAAACATTAACCACACAAGCGGGTTGTCCTCTACTCTTATAAAATCTCCACATTCTTTCA
ACATTCCTCAAATTTACACCTTAAAGCATTTCTACCATCATTGAATATAATCATAAGATAACTC
ATTTCCTCTCAAAGGCAATTTATTCAATCATTATAATTCTTAACATGCTTAGAACTACACCACC
ATAAAGTTTGTCATCACAACACTCCCCATCTTATAAATCACGGCTAGCCATAAATGGCATCATA
TCACAATTTTCAAATCTTACCTTCATATCTACTCTTCTAGCCAAAAAACCATCATAACAATAAA
ATATACCTTTTTCTCTAAATCAAACTTAGAAACATGTTCCTTTCCAAGCAATCACCCCTAGAAG
ACCACATATCAAGGGAACATAAGAGAGAGAGAGACCATATGGATTTGAGTTTTATGGCACTATT
CAAGAGTAATCGAGAAAGTGAAACTCTATTATTCTATATCATCTTGTCCAAGGATGTGTCGTAA
CTCACATCAATGATCAAGATACTACTAGACGTGGCTTGTAAAACCTTTAATACCTAAACTATTT
CCCATAACCTAATGCTTTGATACCAAGTCTGTCACGACCCGAAAGTACCCCCTAAAAGTTAGGG
AGAACCCTCGGTTCATGGCAACATGTACTTGACCTTTTGGTGTCTTGTACCATCCCTATAGCTA
TCGTTCATTACAAAAGACCTAAAAAGTAGTGCGGAATTCAAAATTTTTAAGATAATTAATAAAA
GCTAGTCTTTCATAAATATTTAGAGAATCTCATCATCACAAGCCAACATAAACACACGACATAA
TATATTAGGGACTCGGTCCTTTACATTAAAAATAAATACATAATAAGTCTTTCAATAAGAAAGA
AAGAAAAGGACTATGCCCTTGAATATATGAGGACATACTTTGTCTTGAGAGACACTTTCCCAAG
CTTTTCCTTCTAGTCTTCAACCATGCTTCAAACCTATAGTTAGATAGTATCGAAAAGTATGGGG
TTAGTACAAAATAATGTACTAAGTATGGCATATGCAAAAACATTCAAAAAAGGACATTTTTAGT
AAAATAACATTTCATCATGAACATATAAACATAATAACATAAGAAACATCATTTGACACATAGT
AGAAAGATATCATAATTTTAAAACTTATAGAACACATTGAAGTAACATCAGGACTATTACAATG
AATACATTATAGTGAATGTCATAGTGCAAATCATGTGAACCCTTTTCCTTTGAAGTTAACCTAA
CCCAAGTTATCCTAAGACTCCCTAAGGTAATACAAGAAGGGACCTCCCATACACTCCCTTCAAA
TCACAAAAAAGGTGTCCTTTAGACTACCAACCATAGGGTTACCTCATATGGGAATCAAATTCAC
ACTCATAACTAAACATATGCCAAATATTACTTCATACGGACTTCATGTAAGTACCTTTCTCCAA
TATTACTTATAGGTCATACTAAGTGAAATGTGAGAGTAGAATCCCGTACTACTACTTCCACTTA
GTGCTCCTAATGAGTTCTCTTGGATTTGAGCACATTACAATGACTATACAAAATACATTAAACT
ATACAAAACATTACAGTGAACTAAAGAGACTCCAAAGATAATGAATTTCAAATTGCCAATGAGG
AACTGAGCTCATTTCCCAAGGAGTTTCCCTACTGAGGTTATCCTAAGACTCTGCAAGGTAAGGT
ATGAAGGAAATGTCTTAACACCTCCTTCAATGCACACGAAGGAGATTCTTAAGACTACCCTCCA
AAAGCTTACTCCACTCAGGAGAACAAGTCACCACTCAAAACACAAGACATTAGAAGAACACTCA
ATAAACCACCAAAGACTTCCCTTTAAGAATGCCTCCTTAGTGCATTTGATAGATAGCGTCCTAT
ACCACCACCTATCTATGTAGTACACTCTTTTATAAGGTTTGGCACCAAGTCTTCCTTTTTGGAA
GGTACTACTTTGTGCAATGGATAGATAGCATCTAATACAATTGCCTACCCTAAGTAGCACATAC
TTTTAGAATACTTAGTTCATTCAATGTTTTTGTGGGGGTTTTCTTAACTGACATAGAACATGAG
AGCTAAATATGGAATCCTGATACTTCCCTTATCAGATAAGGGTCCCCTTATTTGCCTAGGGTGA
GGTCTTTTACCTTTACATGGCTTGCACATTAGCTACACCTATGCGGGCGCATAATTAAATGATA
AGTAGATTGCTATTAAGTAGCTCATTCTCTACTAACGAGGAGTACTCATCTCCAGAGGTACATT
AAAATACCACATCTCAACTCACAAATTGTAACCACTTTTTCTTCATATCCTCTCGGTTCTAAGC
TTAACTGATATACCTTGGTTTCACGGTATTATTAATACTTTATCTTAAGTTTAGTGTGTCCAAA
AGCCTTTTTGTGCTAATTTTTATGTAAGATAATCGTGGAGATCACGGGAGGCACTGCTGATAGT
GTTGTTGAGGCTGAGGACATCACTGAGGGTATCCAGATTATAGAGATAGCAGGTTCCGAGGAAC
CGGACCCACCAGCTTGCTGATCGTCGGCGCTTTGTGCACCAGGTTTTCTTCACCTACCACTCTA
GTATTTAAATATTTTTATGCATTGGGGACAATTGCATGTCTTTTTGTGGGGGTGGGGTAAATAG
AAAGTGAGTGCTAGGGTGAAGTCTGAGTAGCCG
						
					

			
		

Sequences
Splice junction sequence	CTAGTATTTAAATATTTTTATGCATTGGGGACAATTGCATGTCTTTTTGTGGGGGTGGGGTAAA TAGAAAGTGAGTGCTAGGGTGAAGTCTGAGTAGCCGacctatcactttagcaaaactttcatac ttcaaaatcttctcttatccttcttttatgaagggactaccttctcaaacattaaacattttca tatgtaac
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	ACCTATCACTTTAGCAAAACTTTCATACTTCAAAATCTTCTCTTATCCTTCTTTTATGAAGGGA CTACCTTCTCAAACATTAAACATTTTCATATGTAACACTTTTTCACACATTAAAACTTCAAACA AAGTCAAGAAAAATTTTCTCAAAATTCAAAAATCTATAGTGAACATCACTGTAACACTGTTAAG CATGCTTAAAATTTTAAAATTCTATTATTTGAGAATTTCATAAGAAAAGGCCTGATCATATGAA GTATTGTACTATATAAACTCATCTAATAACACATTGAAACCATAATTCATGAAAAATGCAATTT CCTTATAATTTGGACTTACTTGCAATGAATTCAAAAATTCACTTTGTCCCATGCTTAAAATTTC AATAATGCACCTTTCAAGCAACTTTAATAAGATGTCATGACAGTATAAGAGACAAGACTATACT AACTTACTCCAAAGAGAATTGATAAGTTCCACTAAGTTCAATGTGAGAGTAGCATACCATACTA CCACTCCCACTTAGTGACCCTTGAGGATATCTTTTGGACTAAGTACATTACATGCAATTCTACT CAACTCATTCTCCCCCACTTAGGGTAAATCCATCTTCAACGTCTCATACTTAAAAGCACCATTA TGCCTCTCACATAGAAAGGACTCACACAACCCTCAACTAATTCACATCAAGACTAAAATCCAAT CCACTAGTCAAGCATAACACTCTCCTCTAAGGATTTAAGCCTAAAAGAAATCCCTTTAACGCCA CCTCATTCAACTCTTAGGCGTCACTTAACTCAATTTCATGAAACAAAACTCCCTTACTAGGTAT TCATACCAAATTTCCTCCATAGTGTAAACCTACACAAGAACCTCAACCAAATCACAAGAACAAC TATTCAAACATTAACCACACAAGCGGGTTGTCCTCTACTCTTATAAAATCTCCACATTCTTTCA ACATTCCTCAAATTTACACCTTAAAGCATTTCTACCATCATTGAATATAATCATAAGATAACTC ATTTCCTCTCAAAGGCAATTTATTCAATCATTATAATTCTTAACATGCTTAGAACTACACCACC ATAAAGTTTGTCATCACAACACTCCCCATCTTATAAATCACGGCTAGCCATAAATGGCATCATA TCACAATTTTCAAATCTTACCTTCATATCTACTCTTCTAGCCAAAAAACCATCATAACAATAAA ATATACCTTTTTCTCTAAATCAAACTTAGAAACATGTTCCTTTCCAAGCAATCACCCCTAGAAG ACCACATATCAAGGGAACATAAGAGAGAGAGAGACCATATGGATTTGAGTTTTATGGCACTATT CAAGAGTAATCGAGAAAGTGAAACTCTATTATTCTATATCATCTTGTCCAAGGATGTGTCGTAA CTCACATCAATGATCAAGATACTACTAGACGTGGCTTGTAAAACCTTTAATACCTAAACTATTT CCCATAACCTAATGCTTTGATACCAAGTCTGTCACGACCCGAAAGTACCCCCTAAAAGTTAGGG AGAACCCTCGGTTCATGGCAACATGTACTTGACCTTTTGGTGTCTTGTACCATCCCTATAGCTA TCGTTCATTACAAAAGACCTAAAAAGTAGTGCGGAATTCAAAATTTTTAAGATAATTAATAAAA GCTAGTCTTTCATAAATATTTAGAGAATCTCATCATCACAAGCCAACATAAACACACGACATAA TATATTAGGGACTCGGTCCTTTACATTAAAAATAAATACATAATAAGTCTTTCAATAAGAAAGA AAGAAAAGGACTATGCCCTTGAATATATGAGGACATACTTTGTCTTGAGAGACACTTTCCCAAG CTTTTCCTTCTAGTCTTCAACCATGCTTCAAACCTATAGTTAGATAGTATCGAAAAGTATGGGG TTAGTACAAAATAATGTACTAAGTATGGCATATGCAAAAACATTCAAAAAAGGACATTTTTAGT AAAATAACATTTCATCATGAACATATAAACATAATAACATAAGAAACATCATTTGACACATAGT AGAAAGATATCATAATTTTAAAACTTATAGAACACATTGAAGTAACATCAGGACTATTACAATG AATACATTATAGTGAATGTCATAGTGCAAATCATGTGAACCCTTTTCCTTTGAAGTTAACCTAA CCCAAGTTATCCTAAGACTCCCTAAGGTAATACAAGAAGGGACCTCCCATACACTCCCTTCAAA TCACAAAAAAGGTGTCCTTTAGACTACCAACCATAGGGTTACCTCATATGGGAATCAAATTCAC ACTCATAACTAAACATATGCCAAATATTACTTCATACGGACTTCATGTAAGTACCTTTCTCCAA TATTACTTATAGGTCATACTAAGTGAAATGTGAGAGTAGAATCCCGTACTACTACTTCCACTTA GTGCTCCTAATGAGTTCTCTTGGATTTGAGCACATTACAATGACTATACAAAATACATTAAACT ATACAAAACATTACAGTGAACTAAAGAGACTCCAAAGATAATGAATTTCAAATTGCCAATGAGG AACTGAGCTCATTTCCCAAGGAGTTTCCCTACTGAGGTTATCCTAAGACTCTGCAAGGTAAGGT ATGAAGGAAATGTCTTAACACCTCCTTCAATGCACACGAAGGAGATTCTTAAGACTACCCTCCA AAAGCTTACTCCACTCAGGAGAACAAGTCACCACTCAAAACACAAGACATTAGAAGAACACTCA ATAAACCACCAAAGACTTCCCTTTAAGAATGCCTCCTTAGTGCATTTGATAGATAGCGTCCTAT ACCACCACCTATCTATGTAGTACACTCTTTTATAAGGTTTGGCACCAAGTCTTCCTTTTTGGAA GGTACTACTTTGTGCAATGGATAGATAGCATCTAATACAATTGCCTACCCTAAGTAGCACATAC TTTTAGAATACTTAGTTCATTCAATGTTTTTGTGGGGGTTTTCTTAACTGACATAGAACATGAG AGCTAAATATGGAATCCTGATACTTCCCTTATCAGATAAGGGTCCCCTTATTTGCCTAGGGTGA GGTCTTTTACCTTTACATGGCTTGCACATTAGCTACACCTATGCGGGCGCATAATTAAATGATA AGTAGATTGCTATTAAGTAGCTCATTCTCTACTAACGAGGAGTACTCATCTCCAGAGGTACATT AAAATACCACATCTCAACTCACAAATTGTAACCACTTTTTCTTCATATCCTCTCGGTTCTAAGC TTAACTGATATACCTTGGTTTCACGGTATTATTAATACTTTATCTTAAGTTTAGTGTGTCCAAA AGCCTTTTTGTGCTAATTTTTATGTAAGATAATCGTGGAGATCACGGGAGGCACTGCTGATAGT GTTGTTGAGGCTGAGGACATCACTGAGGGTATCCAGATTATAGAGATAGCAGGTTCCGAGGAAC CGGACCCACCAGCTTGCTGATCGTCGGCGCTTTGTGCACCAGGTTTTCTTCACCTACCACTCTA GTATTTAAATATTTTTATGCATTGGGGACAATTGCATGTCTTTTTGTGGGGGTGGGGTAAATAG AAAGTGAGTGCTAGGGTGAAGTCTGAGTAGCCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.092664224

Conservation Information
Conserved circRNAs	NA
PMCS	0.092664224

			
						 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
						NA

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	NA

			
						 Other Information
					
						References
						Tan et al., 2017

circRNA

Detail information of Solyc04g039600.1_circ_ig.1

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