Plant Circular RNA Database

Detail information of Solyc11g010600.1_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc11g010600.1_circ_g.2
					
						ID in PlantcircBase
						sly_circ_003275
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr11: 3665229-3667624  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc11g010600.1						
					
						Parent gene annotation
						
							Putative auxin growth promotor protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc11g010600.1_circ_g.1 Solyc11g010600.1_circ_g.3 						
					
						Support reads
						3
					
						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
						Solyc11g010600.1.1:7

General Information
CircRNA Name	Solyc11g010600.1_circ_g.2
ID in PlantcircBase	sly_circ_003275
Alias	NA
Organism	Solanum lycopersicum
Position	chr11: 3665229-3667624 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc11g010600.1
Parent gene annotation	Putative auxin growth promotor protein
Parent gene strand	+
Alternative splicing	Solyc11g010600.1_circ_g.1 Solyc11g010600.1_circ_g.3
Support reads	3
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	Solyc11g010600.1.1:7

			
						 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  
						
							CAAAGGAAAGGCTTCATTATTGGCTGCAGTTGATTATTATGTTGGCATGCACAGTGATATTTTT
GTTTCCGCCTCCCCTGGAAATATGCACAATGCAATGgatttgaatgctccaaaattcaggcact
cacgtcttgcgaagagtgctatacaacgccaaactgtgcgtaagaccttattgatcacactcac
ttgttcct

									
								

					

						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
						
							GATTTGAATGCTCCAAAATTCAGGCACTCACGTCTTGCGAAGAGTGCTATACAACGCCAAACTG
TGCGTAAGACCTTATTGATCACACTCACTTGTTCCTCTTAAATTAACTTCTGTTCTCCTGTCAT
GAGTTTGTGTCTTGCTTGGTTTCTTCTATGTCTTTAGTCCAATGAAGAACAGTCACGGCTTTGG
ACACCTTTGGAACACCAAGGATGGAAACCTTGTACTAAATCTGATGCTGCATCCAGTGAGTGTC
TATGATCACATATTCTGATACATCTAAAATTTACATCTAGTTTGTGAAGGCTTGCTGTTAAGCA
ATAACTCGATTGAGCATCAGCGCGATCTTGCCTTCTAATTTTCCAATGACTAATTACTGTTCCT
TGCACTATGCAGCAGTACCTGAAAAATCTGAGGGATACGTTCAAGTGTTCCTTGATGGTGGACT
AAATCAACAGAGGATGGGGGTGCGTATTATGATTCCTTTGTTTGATTGTTCATAGAAACAACAT
TAATGAATAATGCTCAACTCCTTTAATTATAGAAACAAATTGTTTGACCCTTCATTACTGACAT
CTATATTTCTTGGAGAAGATCTGTGATGCAGTTGTCGTTGCCAAAATTCTGAATGCCACACTTG
TGATCCCTCAGTTGGAAGTAAATCCTGTTTGGCAAGATTCAAGGTATCTTAAGTATAGTGCTAA
AATTGGTTTTCTTTCAACTTTTAAAAACATATACAAGTTATCGTCCTCTTTCCTACAGCTCATT
CGAGGATATCTTTGATGTGGATCACTTCATCAATGCATTGAAAGACGACGTAGCTATAGTCAAA
GAGTTGCCTGATGAATTCTCTTGGAGCACACGAGAATATTATGGCATAGCTATCCGACCTACAA
GAATCAAGACTGCTCCAGTTCATGCTTCAGCAAATTGGTATTTAGAGAATGTGTCACCTGTACT
GCAGAGGTTAGTCACAACATTGTTTTTTTTGAAGATTTTGGTCTAGTTGTATGATAGTCATGTA
AACTGTGTTCAGTCTCTCAACCCACCCGTATGACAAAGTACATGTATAATTGGTAAATTACTGG
CAGGATTTAGTGCTCAAAACTTAAGGGAATTCTACAAAAGTTCCATTGCCCAGTATTTTACTAT
TCATTTTAAGTTGTATGTTCCCTTAAACCAAAAATTTAAGTTAGGCATGGACTAAACATTATGT
GTTTGATTTATTTCTTGATATGATCATATTTTGTTCGTTCAGTTATTAGCTTCTGAAGGTAGTA
ATTCTCTTATCAGCCTTTTGCTGGAATTTGTGACATTGCTTTGTATATTAATATTTTATGAATG
GATCAGTTATGGAATTGCTGCCATAGCTCCATTTTCTCACCGACTGACATTTGACAACATGCCC
AAGTACCTCCAACACCTACGATGTAAAGTCAACTTTCAAGCATTGGCCTTTGTTCCTCACATCA
GACAACTCGGGGATGCCCTTATCACTCGCCTTAGGTTTCCTCCTAGTGAAGACAACATGGTTAG
TAACAACTACCTTAGAGAGGTTACTGATCTAAAGCCCAAACAAGGAGTTGGCAAGTTTGCTGTT
CTTCACCTTCGCTTTGACAAGGTAAAAACACCTTACTGTTGTTGAACTACCTATCCTGCAATAT
CTCCCGATCAAATATTAGTACTTCCACTTTCCTGAAAAAATCAGCTTTCCTTTACTGCCTGTTA
AAGGCAATATAACACTACTTATTGATGAATATATCTCAGTACCGTATTTTTGCTGTATTTTTTA
GTTAATTTTACTCCACCCAAAGTGTCACATGATTTAAGAACCTTTGGACTTGTTATCTCTCCAG
GATATGGCTGCTCATTCAGCCTGTGATTTTGGTGGCGGCAAGGCTGAAAATTTGGCTCTAGCTA
AATACAGGCAAGTAATTTGGGGAGGAAGGGTCATCAACTCTCAATTTACTGATGAAGAATTAAG
GAGTCAAGGAAGGTGCCCATTGACTCCCGAAGAAGTTGGATTGCTGCTGGCAGCTTTGGGATTT
GACAACAACACTCGCCTATATCTTGCCTCCCATAAGGTCTTCACTGAAGTTCTGCATTTATAGA
AACAATATGCCTTTCTTTAAGGCTAGAATACTTGAAGTGTAAAGCTAATATCTTCGTGTCCTGA
AGCTTGTTCATGTTTTTTCTAGGTTTATGGCGGGGAACGCAGGGTTTCAGCCTTAAGAAGTTTG
TTTCCCCTGATGGAAGATAAAAAGAGCCTTGCTTCTTCTGAGGAAAGAGCTCTTATCAAAGGAA
AGGCTTCATTATTGGCTGCAGTTGATTATTATGTTGGCATGCACAGTGATATTTTTGTTTCCGC
CTCCCCTGGAAATATGCACAATGCAATG
						
					

			
		

Sequences
Splice junction sequence	CAAAGGAAAGGCTTCATTATTGGCTGCAGTTGATTATTATGTTGGCATGCACAGTGATATTTTT GTTTCCGCCTCCCCTGGAAATATGCACAATGCAATGgatttgaatgctccaaaattcaggcact cacgtcttgcgaagagtgctatacaacgccaaactgtgcgtaagaccttattgatcacactcac ttgttcct
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	GATTTGAATGCTCCAAAATTCAGGCACTCACGTCTTGCGAAGAGTGCTATACAACGCCAAACTG TGCGTAAGACCTTATTGATCACACTCACTTGTTCCTCTTAAATTAACTTCTGTTCTCCTGTCAT GAGTTTGTGTCTTGCTTGGTTTCTTCTATGTCTTTAGTCCAATGAAGAACAGTCACGGCTTTGG ACACCTTTGGAACACCAAGGATGGAAACCTTGTACTAAATCTGATGCTGCATCCAGTGAGTGTC TATGATCACATATTCTGATACATCTAAAATTTACATCTAGTTTGTGAAGGCTTGCTGTTAAGCA ATAACTCGATTGAGCATCAGCGCGATCTTGCCTTCTAATTTTCCAATGACTAATTACTGTTCCT TGCACTATGCAGCAGTACCTGAAAAATCTGAGGGATACGTTCAAGTGTTCCTTGATGGTGGACT AAATCAACAGAGGATGGGGGTGCGTATTATGATTCCTTTGTTTGATTGTTCATAGAAACAACAT TAATGAATAATGCTCAACTCCTTTAATTATAGAAACAAATTGTTTGACCCTTCATTACTGACAT CTATATTTCTTGGAGAAGATCTGTGATGCAGTTGTCGTTGCCAAAATTCTGAATGCCACACTTG TGATCCCTCAGTTGGAAGTAAATCCTGTTTGGCAAGATTCAAGGTATCTTAAGTATAGTGCTAA AATTGGTTTTCTTTCAACTTTTAAAAACATATACAAGTTATCGTCCTCTTTCCTACAGCTCATT CGAGGATATCTTTGATGTGGATCACTTCATCAATGCATTGAAAGACGACGTAGCTATAGTCAAA GAGTTGCCTGATGAATTCTCTTGGAGCACACGAGAATATTATGGCATAGCTATCCGACCTACAA GAATCAAGACTGCTCCAGTTCATGCTTCAGCAAATTGGTATTTAGAGAATGTGTCACCTGTACT GCAGAGGTTAGTCACAACATTGTTTTTTTTGAAGATTTTGGTCTAGTTGTATGATAGTCATGTA AACTGTGTTCAGTCTCTCAACCCACCCGTATGACAAAGTACATGTATAATTGGTAAATTACTGG CAGGATTTAGTGCTCAAAACTTAAGGGAATTCTACAAAAGTTCCATTGCCCAGTATTTTACTAT TCATTTTAAGTTGTATGTTCCCTTAAACCAAAAATTTAAGTTAGGCATGGACTAAACATTATGT GTTTGATTTATTTCTTGATATGATCATATTTTGTTCGTTCAGTTATTAGCTTCTGAAGGTAGTA ATTCTCTTATCAGCCTTTTGCTGGAATTTGTGACATTGCTTTGTATATTAATATTTTATGAATG GATCAGTTATGGAATTGCTGCCATAGCTCCATTTTCTCACCGACTGACATTTGACAACATGCCC AAGTACCTCCAACACCTACGATGTAAAGTCAACTTTCAAGCATTGGCCTTTGTTCCTCACATCA GACAACTCGGGGATGCCCTTATCACTCGCCTTAGGTTTCCTCCTAGTGAAGACAACATGGTTAG TAACAACTACCTTAGAGAGGTTACTGATCTAAAGCCCAAACAAGGAGTTGGCAAGTTTGCTGTT CTTCACCTTCGCTTTGACAAGGTAAAAACACCTTACTGTTGTTGAACTACCTATCCTGCAATAT CTCCCGATCAAATATTAGTACTTCCACTTTCCTGAAAAAATCAGCTTTCCTTTACTGCCTGTTA AAGGCAATATAACACTACTTATTGATGAATATATCTCAGTACCGTATTTTTGCTGTATTTTTTA GTTAATTTTACTCCACCCAAAGTGTCACATGATTTAAGAACCTTTGGACTTGTTATCTCTCCAG GATATGGCTGCTCATTCAGCCTGTGATTTTGGTGGCGGCAAGGCTGAAAATTTGGCTCTAGCTA AATACAGGCAAGTAATTTGGGGAGGAAGGGTCATCAACTCTCAATTTACTGATGAAGAATTAAG GAGTCAAGGAAGGTGCCCATTGACTCCCGAAGAAGTTGGATTGCTGCTGGCAGCTTTGGGATTT GACAACAACACTCGCCTATATCTTGCCTCCCATAAGGTCTTCACTGAAGTTCTGCATTTATAGA AACAATATGCCTTTCTTTAAGGCTAGAATACTTGAAGTGTAAAGCTAATATCTTCGTGTCCTGA AGCTTGTTCATGTTTTTTCTAGGTTTATGGCGGGGAACGCAGGGTTTCAGCCTTAAGAAGTTTG TTTCCCCTGATGGAAGATAAAAAGAGCCTTGCTTCTTCTGAGGAAAGAGCTCTTATCAAAGGAA AGGCTTCATTATTGGCTGCAGTTGATTATTATGTTGGCATGCACAGTGATATTTTTGTTTCCGC CTCCCCTGGAAATATGCACAATGCAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.193638456

Conservation Information
Conserved circRNAs	NA
PMCS	0.193638456

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							3666632-3667621(+)
3667564-3665232(+)
3665838-3667563(-)
						
					

						Potential amino acid sequence
						
							MPKYLQHLRCKVNFQALAFVPHIRQLGDALITRLRFPPSEDNMVSNNYLREVTDLKPKQGVGKF
AVLHLRFDKDMAAHSACDFGGGKAENLALAKYRQVIWGGRVINSQFTDEELRSQGRCPLTPEEV
GLLLAALGFDNNTRLYLASHKVYGGERRVSALRSLFPLMEDKKSLASSEERALIKGKASLLAAV
DYYVGMHSDIFVSASPGNMHNAMDLNAPKFRHSRLAKSAIQRQTSNEEQSRLWTPLEHQGWKPC
TKSDAASIVVAKILNATLVIPQLEVNPVWQDSSSFEDIFDVDHFINALKDDVAIVKELPDEFSW
STREYYGIAIRPTRIKTAPVHASANWYLENVSPVLQSYGIAAIAPFSHRLTFDNMPKYLQHLRC
KVNFQALAFVPHIRQLGDALITRLRFPPSEDNMVSNNYLREVTDLKPKQGVGKFAVLHLRFDKD
MAAHSACDFGGGKAENLALAKYRQVIWGGRVINSQFTDEELRSQGRCPLTPEEVGLLLAALGFD
NNTRLYLASHKVYGGERRVSALRSLFPLMEDKKSLASSEERALIKGKASLLAAVDYYVGMHSDI
FVSASPGNMHNAMDLNAPKFRHSRLAKSAIQRQTSNEEQSRLWTPLEHQGWKPCTKSDAASIVV
AKILNATLVIPQLEVNPVWQDSSSFEDIFDVDHFINALKDDVAIVKELPDEFSWSTREYYGIAI
RPTRIKTAPVHASANWYLENVSPVLQSYGIAAIAPFSHRLTFDNMPKYLQHLRCKVNFQALAFV
PHIRQLGDALITRLRFPPSEDNMVSNNYLREVTDLKPKQGVGKFAVLHLRFDKDMAAHSACDFG
GGKAENLALAKYRQVIWGGRVINSQFTDEELRSQGRCPLTPEEVGLLLAALGFDNNTRLYLASH
KVYGGERRVSALRSLFPLMEDKKSLASSEERALIKGKASLLAAVDYYVGMHSDIFVSASPGNMH
NAMDLNAPKFRHSRLAKSAIQRQTSNEEQSRLWTPLEHQGWKPCTKSDAASIVVAKILNATLVI
PQLEVNPVWQDSSSFEDIFDVDHFINALKDDVAIVKELPDEFSWSTREYYGIAIRPTRIKTAPV
HASANWYLENVSPVLQSYGIAAIAPFSHRLTFDNMPKYLQHLRCKVNFQALAFVPHIRQLGDAL
ITRLRFPPSEDNMVSNNYLREVTDLKPKQGVGKFAVLHLRFDKDMAAHSACDFGGGKAENLALA
KYRQVIWGGRVINSQFTDEELRSQGRCPLTPEEVGLLLAALGFDNNTRLYLASHKVYGGERRVS
ALRSLFPLMEDKKSLASSEERALIKGKASLLAAVDYYVGMHSDIFVSASPGNMHNAM(+)
MLACTVIFLFPPPLEICTMQWI*(+)
MDAASDLVQGFHPWCSKGVQSRDCSSLEVWRCIALFARRECLNFGAFKSIALCIFPGEAETKIS
LCMPT*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	3666632-3667621(+) 3667564-3665232(+) 3665838-3667563(-)
Potential amino acid sequence	MPKYLQHLRCKVNFQALAFVPHIRQLGDALITRLRFPPSEDNMVSNNYLREVTDLKPKQGVGKF AVLHLRFDKDMAAHSACDFGGGKAENLALAKYRQVIWGGRVINSQFTDEELRSQGRCPLTPEEV GLLLAALGFDNNTRLYLASHKVYGGERRVSALRSLFPLMEDKKSLASSEERALIKGKASLLAAV DYYVGMHSDIFVSASPGNMHNAMDLNAPKFRHSRLAKSAIQRQTSNEEQSRLWTPLEHQGWKPC TKSDAASIVVAKILNATLVIPQLEVNPVWQDSSSFEDIFDVDHFINALKDDVAIVKELPDEFSW STREYYGIAIRPTRIKTAPVHASANWYLENVSPVLQSYGIAAIAPFSHRLTFDNMPKYLQHLRC KVNFQALAFVPHIRQLGDALITRLRFPPSEDNMVSNNYLREVTDLKPKQGVGKFAVLHLRFDKD MAAHSACDFGGGKAENLALAKYRQVIWGGRVINSQFTDEELRSQGRCPLTPEEVGLLLAALGFD NNTRLYLASHKVYGGERRVSALRSLFPLMEDKKSLASSEERALIKGKASLLAAVDYYVGMHSDI FVSASPGNMHNAMDLNAPKFRHSRLAKSAIQRQTSNEEQSRLWTPLEHQGWKPCTKSDAASIVV AKILNATLVIPQLEVNPVWQDSSSFEDIFDVDHFINALKDDVAIVKELPDEFSWSTREYYGIAI RPTRIKTAPVHASANWYLENVSPVLQSYGIAAIAPFSHRLTFDNMPKYLQHLRCKVNFQALAFV PHIRQLGDALITRLRFPPSEDNMVSNNYLREVTDLKPKQGVGKFAVLHLRFDKDMAAHSACDFG GGKAENLALAKYRQVIWGGRVINSQFTDEELRSQGRCPLTPEEVGLLLAALGFDNNTRLYLASH KVYGGERRVSALRSLFPLMEDKKSLASSEERALIKGKASLLAAVDYYVGMHSDIFVSASPGNMH NAMDLNAPKFRHSRLAKSAIQRQTSNEEQSRLWTPLEHQGWKPCTKSDAASIVVAKILNATLVI PQLEVNPVWQDSSSFEDIFDVDHFINALKDDVAIVKELPDEFSWSTREYYGIAIRPTRIKTAPV HASANWYLENVSPVLQSYGIAAIAPFSHRLTFDNMPKYLQHLRCKVNFQALAFVPHIRQLGDAL ITRLRFPPSEDNMVSNNYLREVTDLKPKQGVGKFAVLHLRFDKDMAAHSACDFGGGKAENLALA KYRQVIWGGRVINSQFTDEELRSQGRCPLTPEEVGLLLAALGFDNNTRLYLASHKVYGGERRVS ALRSLFPLMEDKKSLASSEERALIKGKASLLAAVDYYVGMHSDIFVSASPGNMHNAM(+) MLACTVIFLFPPPLEICTMQWI(+) MDAASDLVQGFHPWCSKGVQSRDCSSLEVWRCIALFARRECLNFGAFKSIALCIFPGEAETKIS LCMPT(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc11g010600.1_circ_g.2

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