Plant Circular RNA Database

Detail information of Solyc07g044760.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc07g044760.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_002340
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr7: 57808113-57810250  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc07g044760.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc07g044760.2_circ_g.1 Solyc07g044760.2_circ_g.3 						
					
						Support reads
						11
					
						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
						Solyc07g044760.2.1:5

General Information
CircRNA Name	Solyc07g044760.2_circ_g.2
ID in PlantcircBase	sly_circ_002340
Alias	NA
Organism	Solanum lycopersicum
Position	chr7: 57808113-57810250 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc07g044760.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc07g044760.2_circ_g.1 Solyc07g044760.2_circ_g.3
Support reads	11
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	Solyc07g044760.2.1:5

			
						 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  
						
							GCGTGCTGGGAAGAAAGGAAGTGCAATTCTGATTCATTCGTCAGGCCAACATAGGGATGTGAAA
GGAATCGAACGTGATGTAGGATGCAGATTTATCGAGagagctgttctggaaccagcaatgcaag
gatctgacatgataggtcgagctagaactggaactgggaagacactagcttttgggattcccat
catggata

									
								

					

						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
						
							AGAGCTGTTCTGGAACCAGCAATGCAAGGATCTGACATGATAGGTCGAGCTAGAACTGGAACTG
GGAAGACACTAGCTTTTGGGATTCCCATCATGGATAAGATCATTCGCTTCAATGAGAAACATGG
GTTTGTCCAGTCTGCTTTCTCTCTGGGCTTTTATAGTTTTAGTAGTGCAAATATGATAGCAGCA
TTATGTAATGTTTTTTCATCTGCTAGGCTTGGCAACTTTATTAAAGTTTGATTCTGAATATTTG
TTGCGAATTTTGACCTAATTACAGTTGTAAAATACTAACAATGTGTTTATTCTCTATAATGTAG
ACGTGGAAGGAATCCTTTGGCTTTAATCTTGGCGCCTACCAGAGAACTTGCTAAACAAGTGGAT
AAAGAATTTTTTGAATCTGCTCCTGGTCTGGATACGCTGTGTGTTTATGGTGGTGTTCCCATTT
CACGCCAAATGAGTTCCCTGGACAGGGGAGTTGATGTTGTTGTGGGAACGCCAGGTCGGATTAT
TGATCTGCTGAAGAGGGGTGCTTTGAATTTGGCAGAAATCCAGTTTGTTGTTCTAGATGAAGCT
GATCAAATGCTTAATGTGGGTTTTGCGGAGGATGTCGAGACCATATTAGAAAATGTTCCGCAGA
AGCACCAGACACTGATGTTTTCAGCCACAATGCCCAGTTGGATATTAAAAATTACCAACAAGTT
CCTGAAAAATCCAGTTCACATTGATCTTGTGAGACTATAAATGCTCAACATTTTAATACAAATT
TCCTTAATTTTTTAGAACTTTGGAGGCTAATTTTTCGATATATCCCAGGTAGGAGATTCTGATC
AGAAACTGGCTGATGGGATTTCCTTGTTTTCAATTGCTTGTGATATGCATCAGAAACCCGCAAT
TCTTGGACCTCTGATAACTGTATGGAGATATACCTTCAGTCTCCTCTGTCTCACCTTATACATA
TCATATTGTTCTAAGTCGCTCTCTATTTATTTCCACCAACATAAAGATAATGGCCTTTCTGTTG
TCTAATTTTTTGATAATCCTTAATCTCTGAAACTAATTGAGCATTTCATTTTTGCAGGAGCATG
CAAAAGGAGGCAAGTGCATTGTTTTTACTCAAACTAAACGTGATGCTGATAAATTGTCGTATGT
AATGCAAAAGAGTTTCAACTGTGAAGCTTTGCACGGGGACATCTCACAAACCCAGAGGGAGAGA
ACTTTATCAGGTTTTCGCCAAGGTCAATTCAATGTTTTGGTGGCTACTGATGTTGCTGCTCGAG
GACTTGATGTACCTAATGTTGATCTGGTTGGTCTTTTGTTCTCATATTTGTGATTTTAAGTTCA
ATAATCACTGCATTTCTTCTCTTTCATCTGTACTATCCAGCAATAGAGCAGGCAACATATTAGA
AAACCCTCTGTTAGAACCTGTTGATCAACAAACCAATAACATGACATGTAATAGAAGGGGTTCA
GTGGAAGTTGCATATTTAAATAGCAACCTTACCTGATCCTTCATGTTTTTAAGGTTTATCATTT
AATAACTCAATACCACTTTACTTGAATGCAGACTAAGCAATTTCTTCAGTTTCCTCTCCTTTGA
AACACTTTTTGTAGGGGTCTTTATATAGTCTATGTTTGATGTTGTACATCTCTAAAGCATTTGT
CAATTGTGAGAAGATGTATCTGAAAGTAGCAGTCTTTTCTACATATTTAAAGCAATAAGGTACG
ATCATGGGTGAAGCTATGTAGAACCAAGGAGATTCTGTTGATATCCTTCGTCAGAAACTAAACT
CCGCAAATAGGTCAAGAACGAGTGCTTTAATTATACATAGACTATTGAATCCCCTTGAGATAAA
AGAGCATTCTAGTTTAGTGGGAATGGGATTGCTTTAGATCCCACAGGTTTGCTCCCAAATGTGA
TATTCTAGTAATATTTTGGATTCCCTGCATAAACTTGGAAATATTTTGCTACTCAGGTGGTACA
TTATGAGCTTCCAAACTCATCAGAGATCTTTGTTCATCGATCTGGTCGAACTGGGCGTGCTGGG
AAGAAAGGAAGTGCAATTCTGATTCATTCGTCAGGCCAACATAGGGATGTGAAAGGAATCGAAC
GTGATGTAGGATGCAGATTTATCGAG
						
					

			
		

Sequences
Splice junction sequence	GCGTGCTGGGAAGAAAGGAAGTGCAATTCTGATTCATTCGTCAGGCCAACATAGGGATGTGAAA GGAATCGAACGTGATGTAGGATGCAGATTTATCGAGagagctgttctggaaccagcaatgcaag gatctgacatgataggtcgagctagaactggaactgggaagacactagcttttgggattcccat catggata
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	AGAGCTGTTCTGGAACCAGCAATGCAAGGATCTGACATGATAGGTCGAGCTAGAACTGGAACTG GGAAGACACTAGCTTTTGGGATTCCCATCATGGATAAGATCATTCGCTTCAATGAGAAACATGG GTTTGTCCAGTCTGCTTTCTCTCTGGGCTTTTATAGTTTTAGTAGTGCAAATATGATAGCAGCA TTATGTAATGTTTTTTCATCTGCTAGGCTTGGCAACTTTATTAAAGTTTGATTCTGAATATTTG TTGCGAATTTTGACCTAATTACAGTTGTAAAATACTAACAATGTGTTTATTCTCTATAATGTAG ACGTGGAAGGAATCCTTTGGCTTTAATCTTGGCGCCTACCAGAGAACTTGCTAAACAAGTGGAT AAAGAATTTTTTGAATCTGCTCCTGGTCTGGATACGCTGTGTGTTTATGGTGGTGTTCCCATTT CACGCCAAATGAGTTCCCTGGACAGGGGAGTTGATGTTGTTGTGGGAACGCCAGGTCGGATTAT TGATCTGCTGAAGAGGGGTGCTTTGAATTTGGCAGAAATCCAGTTTGTTGTTCTAGATGAAGCT GATCAAATGCTTAATGTGGGTTTTGCGGAGGATGTCGAGACCATATTAGAAAATGTTCCGCAGA AGCACCAGACACTGATGTTTTCAGCCACAATGCCCAGTTGGATATTAAAAATTACCAACAAGTT CCTGAAAAATCCAGTTCACATTGATCTTGTGAGACTATAAATGCTCAACATTTTAATACAAATT TCCTTAATTTTTTAGAACTTTGGAGGCTAATTTTTCGATATATCCCAGGTAGGAGATTCTGATC AGAAACTGGCTGATGGGATTTCCTTGTTTTCAATTGCTTGTGATATGCATCAGAAACCCGCAAT TCTTGGACCTCTGATAACTGTATGGAGATATACCTTCAGTCTCCTCTGTCTCACCTTATACATA TCATATTGTTCTAAGTCGCTCTCTATTTATTTCCACCAACATAAAGATAATGGCCTTTCTGTTG TCTAATTTTTTGATAATCCTTAATCTCTGAAACTAATTGAGCATTTCATTTTTGCAGGAGCATG CAAAAGGAGGCAAGTGCATTGTTTTTACTCAAACTAAACGTGATGCTGATAAATTGTCGTATGT AATGCAAAAGAGTTTCAACTGTGAAGCTTTGCACGGGGACATCTCACAAACCCAGAGGGAGAGA ACTTTATCAGGTTTTCGCCAAGGTCAATTCAATGTTTTGGTGGCTACTGATGTTGCTGCTCGAG GACTTGATGTACCTAATGTTGATCTGGTTGGTCTTTTGTTCTCATATTTGTGATTTTAAGTTCA ATAATCACTGCATTTCTTCTCTTTCATCTGTACTATCCAGCAATAGAGCAGGCAACATATTAGA AAACCCTCTGTTAGAACCTGTTGATCAACAAACCAATAACATGACATGTAATAGAAGGGGTTCA GTGGAAGTTGCATATTTAAATAGCAACCTTACCTGATCCTTCATGTTTTTAAGGTTTATCATTT AATAACTCAATACCACTTTACTTGAATGCAGACTAAGCAATTTCTTCAGTTTCCTCTCCTTTGA AACACTTTTTGTAGGGGTCTTTATATAGTCTATGTTTGATGTTGTACATCTCTAAAGCATTTGT CAATTGTGAGAAGATGTATCTGAAAGTAGCAGTCTTTTCTACATATTTAAAGCAATAAGGTACG ATCATGGGTGAAGCTATGTAGAACCAAGGAGATTCTGTTGATATCCTTCGTCAGAAACTAAACT CCGCAAATAGGTCAAGAACGAGTGCTTTAATTATACATAGACTATTGAATCCCCTTGAGATAAA AGAGCATTCTAGTTTAGTGGGAATGGGATTGCTTTAGATCCCACAGGTTTGCTCCCAAATGTGA TATTCTAGTAATATTTTGGATTCCCTGCATAAACTTGGAAATATTTTGCTACTCAGGTGGTACA TTATGAGCTTCCAAACTCATCAGAGATCTTTGTTCATCGATCTGGTCGAACTGGGCGTGCTGGG AAGAAAGGAAGTGCAATTCTGATTCATTCGTCAGGCCAACATAGGGATGTGAAAGGAATCGAAC GTGATGTAGGATGCAGATTTATCGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.196864835

Conservation Information
Conserved circRNAs	NA
PMCS	0.196864835

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							57808135-57810247(+)
57808221-57810186(-)
						
					

						Potential amino acid sequence
						
							MQGSDMIGRARTGTGKTLAFGIPIMDKIIRFNEKHGRGRNPLALILAPTRELAKQVDKEFFESA
PGLDTLCVYGGVPISRQMSSLDRGVDVVVGTPGRIIDLLKRGALNLAEIQFVVLDEADQMLNVG
FAEDVETILENVPQKHQTLMFSATMPSWILKITNKFLKNPVHIDLVGDSDQKLADGISLFSIAC
DMHQKPAILGPLITEHAKGGKCIVFTQTKRDADKLSYVMQKSFNCEALHGDISQTQRERTLSGF
RQGQFNVLVATDVAARGLDVPNVDLVVHYELPNSSEIFVHRSGRTGRAGKKGSAILIHSSGQHR
DVKGIERDVGCRFIERAVLEPAMQGSDMIGRARTGTGKTLAFGIPIMDKIIRFNEKHGRGRNPL
ALILAPTRELAKQVDKEFFESAPGLDTLCVYGGVPISRQMSSLDRGVDVVVGTPGRIIDLLKRG
ALNLAEIQFVVLDEADQMLNVGFAEDVETILENVPQKHQTLMFSATMPSWILKITNKFLKNPVH
IDLVGDSDQKLADGISLFSIACDMHQKPAILGPLITEHAKGGKCIVFTQTKRDADKLSYVMQKS
FNCEALHGDISQTQRERTLSGFRQGQFNVLVATDVAARGLDVPNVDLVVHYELPNSSEIFVHRS
GRTGRAGKKGSAILIHSSGQHRDVKGIERDVGCRFIERAVLEPAMQGSDMIGRARTGTGKTLAF
GIPIMDKIIRFNEKHGRGRNPLALILAPTRELAKQVDKEFFESAPGLDTLCVYGGVPISRQMSS
LDRGVDVVVGTPGRIIDLLKRGALNLAEIQFVVLDEADQMLNVGFAEDVETILENVPQKHQTLM
FSATMPSWILKITNKFLKNPVHIDLVGDSDQKLADGISLFSIACDMHQKPAILGPLITEHAKGG
KCIVFTQTKRDADKLSYVMQKSFNCEALHGDISQTQRERTLSGFRQGQFNVLVATDVAARGLDV
PNVDLVVHYELPNSSEIFVHRSGRTGRAGKKGSAILIHSSGQHRDVKGIERDVGCRFIERAVLE
PAMQGSDMIGRARTGTGKTLAFGIPIMDKIIRFNEKHGRGRNPLALILAPTRELAKQVDKEFFE
SAPGLDTLCVYGGVPISRQMSSLDRGVDVVVGTPGRIIDLLKRGALNLAEIQFVVLDEADQMLN
VGFAEDVETILENVPQKHQTLMFSATMPSWILKITNKFLKNPVHIDLVGDSDQKLADGISLFSI
ACDMHQKPAILGPLITEHAKGGKCIVFTQTKRDADKLSYVMQKSFNCEALHGDISQTQRERTLS
GFRQGQFNVLVATDVAARGLDVPNVDLVVHYELPNSSEIFVHRSGRTGRAGKKGSAILIHSSGQ
HRDVKGIERDVGCRFIE(+)
MILSMMGIPKASVFPVPVLARPIMSDPCIAGSRTALSINLHPTSRSIPFTSLCWPDE*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	57808135-57810247(+) 57808221-57810186(-)
Potential amino acid sequence	MQGSDMIGRARTGTGKTLAFGIPIMDKIIRFNEKHGRGRNPLALILAPTRELAKQVDKEFFESA PGLDTLCVYGGVPISRQMSSLDRGVDVVVGTPGRIIDLLKRGALNLAEIQFVVLDEADQMLNVG FAEDVETILENVPQKHQTLMFSATMPSWILKITNKFLKNPVHIDLVGDSDQKLADGISLFSIAC DMHQKPAILGPLITEHAKGGKCIVFTQTKRDADKLSYVMQKSFNCEALHGDISQTQRERTLSGF RQGQFNVLVATDVAARGLDVPNVDLVVHYELPNSSEIFVHRSGRTGRAGKKGSAILIHSSGQHR DVKGIERDVGCRFIERAVLEPAMQGSDMIGRARTGTGKTLAFGIPIMDKIIRFNEKHGRGRNPL ALILAPTRELAKQVDKEFFESAPGLDTLCVYGGVPISRQMSSLDRGVDVVVGTPGRIIDLLKRG ALNLAEIQFVVLDEADQMLNVGFAEDVETILENVPQKHQTLMFSATMPSWILKITNKFLKNPVH IDLVGDSDQKLADGISLFSIACDMHQKPAILGPLITEHAKGGKCIVFTQTKRDADKLSYVMQKS FNCEALHGDISQTQRERTLSGFRQGQFNVLVATDVAARGLDVPNVDLVVHYELPNSSEIFVHRS GRTGRAGKKGSAILIHSSGQHRDVKGIERDVGCRFIERAVLEPAMQGSDMIGRARTGTGKTLAF GIPIMDKIIRFNEKHGRGRNPLALILAPTRELAKQVDKEFFESAPGLDTLCVYGGVPISRQMSS LDRGVDVVVGTPGRIIDLLKRGALNLAEIQFVVLDEADQMLNVGFAEDVETILENVPQKHQTLM FSATMPSWILKITNKFLKNPVHIDLVGDSDQKLADGISLFSIACDMHQKPAILGPLITEHAKGG KCIVFTQTKRDADKLSYVMQKSFNCEALHGDISQTQRERTLSGFRQGQFNVLVATDVAARGLDV PNVDLVVHYELPNSSEIFVHRSGRTGRAGKKGSAILIHSSGQHRDVKGIERDVGCRFIERAVLE PAMQGSDMIGRARTGTGKTLAFGIPIMDKIIRFNEKHGRGRNPLALILAPTRELAKQVDKEFFE SAPGLDTLCVYGGVPISRQMSSLDRGVDVVVGTPGRIIDLLKRGALNLAEIQFVVLDEADQMLN VGFAEDVETILENVPQKHQTLMFSATMPSWILKITNKFLKNPVHIDLVGDSDQKLADGISLFSI ACDMHQKPAILGPLITEHAKGGKCIVFTQTKRDADKLSYVMQKSFNCEALHGDISQTQRERTLS GFRQGQFNVLVATDVAARGLDVPNVDLVVHYELPNSSEIFVHRSGRTGRAGKKGSAILIHSSGQ HRDVKGIERDVGCRFIE(+) MILSMMGIPKASVFPVPVLARPIMSDPCIAGSRTALSINLHPTSRSIPFTSLCWPDE*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc07g044760.2_circ_g.2

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