Plant Circular RNA Database

Detail information of Solyc01g081070.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc01g081070.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_000210
					
						Alias
						1:72915416|72922249
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 80404610-80411443  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc01g081070.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc01g081070.2_circ_g.1 Solyc01g081070.2_circ_g.2 						
					
						Support reads
						2/2
					
						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  
						
							GC-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
						Solyc01g081070.2.1:5

General Information
CircRNA Name	Solyc01g081070.2_circ_g.3
ID in PlantcircBase	sly_circ_000210
Alias	1:72915416\|72922249
Organism	Solanum lycopersicum
Position	chr1: 80404610-80411443 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc01g081070.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc01g081070.2_circ_g.1 Solyc01g081070.2_circ_g.2
Support reads	2/2
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	GC-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	Solyc01g081070.2.1:5

			
						 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  
						
							AAAAATATTCTTCTCCAGTTATCAGCACAGTAGCGGACAAATGAGACTTCGGGTTACCACTCTT
TCTAGAAGATGGGTTGCTGGACCTGGAAGTGTACAGattgtgtcgaagattttatctgagccca
taaggtctcacaaggatctggacaaagattctgcaccattgtatcataaggctgtgaagtttta
cgagggaa

						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: 639
Transcript exons: 80404610-80404771,80405903-80406045,80410938-80411013,80
411093-80411268,80411362-80411443
ATTGTGTCGAAGATTTTATCTGAGCCCATAAGGTCTCACAAGGATCTGGACAAAGATTCTGCAC
CATTGTATCATAAGGCTGTGAAGTTTTACGAGGGAATTTCAAAGCAACTTGTGCATCAAGGGCA
TGTGTTGGATGTTTTTGCTTGTGCACTTGAACAGGTCGGCCTTGCTGAAATTAAAGTTGCATGT
GAGAAAACTGGTGGACTTGTTGTTCTTGCAGAAAGTTTTGGCCATAGTGTTTTCAAGGATTCTC
TGAAACAAGTTTTCCAGTCAGGTGGCAATGATCTTGGACTGGCATCAAACGGTATTTTTGAGGT
AAATTGCTCAAAAGATATCAAAGTTCAGGGAGTTATTGGTCCTTCTGCATCACTTGAAAAGAAA
GGTCCTTTGTGCTCTGAGGTTGTCGTAGGTCAGGGAAATACAACAGCTTGGAAGATGTGTGGTC
TTGATAAATCTTCAACGTTTTGTTTAATATTTGAAGTTGCCAAGAAGGAGAGCCCAGATGCAAT
TGCTCAATCTGCAAATCCACAGTTTTATTTCCAGTTTTTGACATATTATCAGCACAGTAGCGGA
CAAATGAGACTTCGGGTTACCACTCTTTCTAGAAGATGGGTTGCTGGACCTGGAAGTGTACAG
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AAAAATATTCTTCTCCAGTTATCAGCACAGTAGCGGACAAATGAGACTTCGGGTTACCACTCTT TCTAGAAGATGGGTTGCTGGACCTGGAAGTGTACAGattgtgtcgaagattttatctgagccca taaggtctcacaaggatctggacaaagattctgcaccattgtatcataaggctgtgaagtttta cgagggaa
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: 639 Transcript exons: 80404610-80404771,80405903-80406045,80410938-80411013,80 411093-80411268,80411362-80411443 ATTGTGTCGAAGATTTTATCTGAGCCCATAAGGTCTCACAAGGATCTGGACAAAGATTCTGCAC CATTGTATCATAAGGCTGTGAAGTTTTACGAGGGAATTTCAAAGCAACTTGTGCATCAAGGGCA TGTGTTGGATGTTTTTGCTTGTGCACTTGAACAGGTCGGCCTTGCTGAAATTAAAGTTGCATGT GAGAAAACTGGTGGACTTGTTGTTCTTGCAGAAAGTTTTGGCCATAGTGTTTTCAAGGATTCTC TGAAACAAGTTTTCCAGTCAGGTGGCAATGATCTTGGACTGGCATCAAACGGTATTTTTGAGGT AAATTGCTCAAAAGATATCAAAGTTCAGGGAGTTATTGGTCCTTCTGCATCACTTGAAAAGAAA GGTCCTTTGTGCTCTGAGGTTGTCGTAGGTCAGGGAAATACAACAGCTTGGAAGATGTGTGGTC TTGATAAATCTTCAACGTTTTGTTTAATATTTGAAGTTGCCAAGAAGGAGAGCCCAGATGCAAT TGCTCAATCTGCAAATCCACAGTTTTATTTCCAGTTTTTGACATATTATCAGCACAGTAGCGGA CAAATGAGACTTCGGGTTACCACTCTTTCTAGAAGATGGGTTGCTGGACCTGGAAGTGTACAG
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.682898725

Conservation Information
Conserved circRNAs	NA
PMCS	0.682898725

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							80411151-80411440(+)
80404640-80411367(-)
80404678-80411411(-)
						
						Potential amino acid sequence
						
							MCGLDKSSTFCLIFEVAKKESPDAIAQSANPQFYFQFLTYYQHSSGQMRLRVTTLSRRWVAGPG
SVQIVSKILSEPIRSHKDLDKDSAPLYHKAVKFYEGISKQLVHQGHVLDVFACALEQVGLAEIK
VACEKTGGLVVLAESFGHSVFKDSLKQVFQSGGNDLGLASNGIFEVNCSKDIKVQGVIGPSASL
EKKGPLCSEVVVGQGNTTAWKMCGLDKSSTFCLIFEVAKKESPDAIAQSANPQFYFQFLTYYQH
SSGQMRLRVTTLSRRWVAGPGSVQIVSKILSEPIRSHKDLDKDSAPLYHKAVKFYEGISKQLVH
QGHVLDVFACALEQVGLAEIKVACEKTGGLVVLAESFGHSVFKDSLKQVFQSGGNDLGLASNGI
FEVNCSKDIKVQGVIGPSASLEKKGPLCSEVVVGQGNTTAWKMCGLDKSSTFCLIFEVAKKESP
DAIAQSANPQFYFQFLTYYQHSSGQMRLRVTTLSRRWVAGPGSVQIVSKILSEPIRSHKDLDKD
SAPLYHKAVKFYEGISKQLVHQGHVLDVFACALEQVGLAEIKVACEKTGGLVVLAESFGHSVFK
DSLKQVFQSGGNDLGLASNGIFEVNCSKDIKVQGVIGPSASLEKKGPLCSEVVVGQGNTTAWKM
CGLDKSSTFCLIFEVAKKESPDAIAQSANPQFYFQFLTYYQHSSGQMRLRVTTLSRRWVAGPGS
VQ(+)
MGSDKIFDTICTLPGPATHLLERVVTRSLICPLLC*(-)
MVQNLCPDPCETLWAQIKSSTQSVHFQVQQPIF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	80411151-80411440(+) 80404640-80411367(-) 80404678-80411411(-)
Potential amino acid sequence	MCGLDKSSTFCLIFEVAKKESPDAIAQSANPQFYFQFLTYYQHSSGQMRLRVTTLSRRWVAGPG SVQIVSKILSEPIRSHKDLDKDSAPLYHKAVKFYEGISKQLVHQGHVLDVFACALEQVGLAEIK VACEKTGGLVVLAESFGHSVFKDSLKQVFQSGGNDLGLASNGIFEVNCSKDIKVQGVIGPSASL EKKGPLCSEVVVGQGNTTAWKMCGLDKSSTFCLIFEVAKKESPDAIAQSANPQFYFQFLTYYQH SSGQMRLRVTTLSRRWVAGPGSVQIVSKILSEPIRSHKDLDKDSAPLYHKAVKFYEGISKQLVH QGHVLDVFACALEQVGLAEIKVACEKTGGLVVLAESFGHSVFKDSLKQVFQSGGNDLGLASNGI FEVNCSKDIKVQGVIGPSASLEKKGPLCSEVVVGQGNTTAWKMCGLDKSSTFCLIFEVAKKESP DAIAQSANPQFYFQFLTYYQHSSGQMRLRVTTLSRRWVAGPGSVQIVSKILSEPIRSHKDLDKD SAPLYHKAVKFYEGISKQLVHQGHVLDVFACALEQVGLAEIKVACEKTGGLVVLAESFGHSVFK DSLKQVFQSGGNDLGLASNGIFEVNCSKDIKVQGVIGPSASLEKKGPLCSEVVVGQGNTTAWKM CGLDKSSTFCLIFEVAKKESPDAIAQSANPQFYFQFLTYYQHSSGQMRLRVTTLSRRWVAGPGS VQ(+) MGSDKIFDTICTLPGPATHLLERVVTRSLICPLLC(-) MVQNLCPDPCETLWAQIKSSTQSVHFQVQQPIF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Solyc01g081070.2_circ_g.3

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