Plant Circular RNA Database

Detail information of Solyc12g008390.1_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc12g008390.1_circ_g.2
					
						ID in PlantcircBase
						sly_circ_003508
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr12: 1829352-1830657  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc12g008390.1						
					
						Parent gene annotation
						
							Golgin candidate 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						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
						Solyc12g008390.1.1:4

General Information
CircRNA Name	Solyc12g008390.1_circ_g.2
ID in PlantcircBase	sly_circ_003508
Alias	NA
Organism	Solanum lycopersicum
Position	chr12: 1829352-1830657 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc12g008390.1
Parent gene annotation	Golgin candidate 1
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
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	Solyc12g008390.1.1:4

			
						 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  
						
							CATTAATGGGTAATTTTTTGATTGACTGTAGGCTGAAATGCAAAAGTTAAGAGTTGAAACAGCT
GCCATGAAAAGGGATGCTGAACATTACTCTCGCCCGagaacagctgatgaaaggactgccaagg
caacagagtttgagcagaaggtggcactgcttgaggtaaataatatttttttggatgtcatcct
ttaggtga

						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
						
							AGAACAGCTGATGAAAGGACTGCCAAGGCAACAGAGTTTGAGCAGAAGGTGGCACTGCTTGAGG
TAAATAATATTTTTTTGGATGTCATCCTTTAGGTGACTCTTACCTTATCAAAAAAGAAAATCCT
TTATGTGGCTCTTTGGCTTAATTGGAAATGATGATACCTAAAAGAATAATGAAAGGATTTCTTC
AGCACTTCTCAACTTATCCAAGGGTGTCTGAATCTTGCAGGTTGAATGTGCAACTCTAAATCAA
GAACTGCAAGACATGGAAGCTCGTACTCGTCGTGGACAAAAGAAGTCCTCAGAAGAGGCAAATC
AAGTGCTTCAGGTTCTATATCTGTCATTAACCTGAATGCATTTTGAAGTAACATGAGAGAACCA
CAGATACAAGTAGACGTAAAATCGTTGGTGGCTGCAAGACACTTGAGTTAGAAAAAGATATACA
AAGAGATAAATTCTCATCTTACTAAGTGAATTATTATACTCCTGATATTGAAGTTACAAGTCAT
GCTAAATTAGGTGTTTTCATGCCTACTTTACATATTACGCCTGGTGAACTGTCCTGGAATCTTG
TGAATATGAAATTTACGATTCTTAACTTAGACAAGGGACCTTGTGTTTGACATTATCAGCCATG
CTTGCTGCAGTTAAAAAGTTTACACTTGAGTTAGAAAAAGATTACAAAGAGAAAAATTCTCATC
TTACTAAGTAAATTGTTATGCTCTGATATTGAAGTTGTAACTCATGCAAAATTGATATTGAAGT
TGTAACTCATGCAAAACTATGTGCTTTCATGCCCCTATTGTACATTATCAGTCACGTGCGCAGC
AGTCAAAAAGTTTACACATGCAACTGGATCCTTGATATACATAGGTGCTTCCATCAATTCTCAT
AATCCTTTGTTCAGTTGCAACCTGAGACTGTTTGAAACTGTATCATCACAGTAAGCTCGATAAA
ACAGACACCCTGCAGATGTCTGTTTTAACTTCATTTTCTGAACATGCAGGTGCAGGCATGGCAA
GAAGAAGTGGAGCGTGCACGCCAAGGTCAGAGGGAAGCTGAAAGCAAGCTTGCTTCTTTGGAGG
CAAGTTTATAGCTCTATAGTTTGGCTCAATAACTAACTAGTGTGCTATTATTGTACTTGTTCGT
TTTTTATCGTAACTATAATTATCTTTTGCTCTAAGTATCAGCCTTAATGATGATCATTAATGGG
TAATTTTTTGATTGACTGTAGGCTGAAATGCAAAAGTTAAGAGTTGAAACAGCTGCCATGAAAA
GGGATGCTGAACATTACTCTCGCCCG

Sequences
Splice junction sequence	CATTAATGGGTAATTTTTTGATTGACTGTAGGCTGAAATGCAAAAGTTAAGAGTTGAAACAGCT GCCATGAAAAGGGATGCTGAACATTACTCTCGCCCGagaacagctgatgaaaggactgccaagg caacagagtttgagcagaaggtggcactgcttgaggtaaataatatttttttggatgtcatcct ttaggtga
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	AGAACAGCTGATGAAAGGACTGCCAAGGCAACAGAGTTTGAGCAGAAGGTGGCACTGCTTGAGG TAAATAATATTTTTTTGGATGTCATCCTTTAGGTGACTCTTACCTTATCAAAAAAGAAAATCCT TTATGTGGCTCTTTGGCTTAATTGGAAATGATGATACCTAAAAGAATAATGAAAGGATTTCTTC AGCACTTCTCAACTTATCCAAGGGTGTCTGAATCTTGCAGGTTGAATGTGCAACTCTAAATCAA GAACTGCAAGACATGGAAGCTCGTACTCGTCGTGGACAAAAGAAGTCCTCAGAAGAGGCAAATC AAGTGCTTCAGGTTCTATATCTGTCATTAACCTGAATGCATTTTGAAGTAACATGAGAGAACCA CAGATACAAGTAGACGTAAAATCGTTGGTGGCTGCAAGACACTTGAGTTAGAAAAAGATATACA AAGAGATAAATTCTCATCTTACTAAGTGAATTATTATACTCCTGATATTGAAGTTACAAGTCAT GCTAAATTAGGTGTTTTCATGCCTACTTTACATATTACGCCTGGTGAACTGTCCTGGAATCTTG TGAATATGAAATTTACGATTCTTAACTTAGACAAGGGACCTTGTGTTTGACATTATCAGCCATG CTTGCTGCAGTTAAAAAGTTTACACTTGAGTTAGAAAAAGATTACAAAGAGAAAAATTCTCATC TTACTAAGTAAATTGTTATGCTCTGATATTGAAGTTGTAACTCATGCAAAATTGATATTGAAGT TGTAACTCATGCAAAACTATGTGCTTTCATGCCCCTATTGTACATTATCAGTCACGTGCGCAGC AGTCAAAAAGTTTACACATGCAACTGGATCCTTGATATACATAGGTGCTTCCATCAATTCTCAT AATCCTTTGTTCAGTTGCAACCTGAGACTGTTTGAAACTGTATCATCACAGTAAGCTCGATAAA ACAGACACCCTGCAGATGTCTGTTTTAACTTCATTTTCTGAACATGCAGGTGCAGGCATGGCAA GAAGAAGTGGAGCGTGCACGCCAAGGTCAGAGGGAAGCTGAAAGCAAGCTTGCTTCTTTGGAGG CAAGTTTATAGCTCTATAGTTTGGCTCAATAACTAACTAGTGTGCTATTATTGTACTTGTTCGT TTTTTATCGTAACTATAATTATCTTTTGCTCTAAGTATCAGCCTTAATGATGATCATTAATGGG TAATTTTTTGATTGACTGTAGGCTGAAATGCAAAAGTTAAGAGTTGAAACAGCTGCCATGAAAA GGGATGCTGAACATTACTCTCGCCCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.162400664

Conservation Information
Conserved circRNAs	NA
PMCS	0.162400664

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1829621-1830654(+)
1830636-1829599(+)
1830372-1829354(-)
						
						Potential amino acid sequence
						
							MEARTRRGQKKSSEEANQVLQVQAWQEEVERARQGQREAESKLASLEAEMQKLRVETAAMKRDA
EHYSRPRTADERTAKATEFEQKVALLEVECATLNQELQDMEARTRRGQKKSSEEANQVLQVQAW
QEEVERARQGQREAESKLASLEAEMQKLRVETAAMKRDAEHYSRPRTADERTAKATEFEQKVAL
LEVECATLNQELQDMEARTRRGQKKSSEEANQVLQVQAWQEEVERARQGQREAESKLASLEAEM
QKLRVETAAMKRDAEHYSRPRTADERTAKATEFEQKVALLEVECATLNQELQDMEARTRRGQKK
SSEEANQVLQVQAWQEEVERARQGQREAESKLASLEAEMQKLRVETAAMKRDAEHYSRP(+)
MLNITLAREQLMKGLPRQQSLSRRWHCLRLNVQL*(+)
MPAPEALDLPLLRTSFVHDEYELPCLAVLDLELHIQPQAVPPSAQTLLPWQSFHQLFSGESNVQ
HPFSWQLFQLLTFAFQPPKKQACFQLPSDLGVHAPLLLAMPAPEALDLPLLRTSFVHDEYELPC
LAVLDLELHIQPQAVPPSAQTLLPWQSFHQLFSGESNVQHPFSWQLFQLLTFAFQPPKKQACFQ
LPSDLGVHAPLLLAMPAPEALDLPLLRTSFVHDEYELPCLAVLDLELHIQPQAVPPSAQTLLPW
QSFHQLFSGESNVQHPFSWQLFQLLTFAFQPPKKQACFQLPSDLGVHAPLLLAMPAPEALDLPL
LRTSFVHDEYELPCLAVLDLELHIQPQAVPPSAQTLLPWQSFHQLF(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1829621-1830654(+) 1830636-1829599(+) 1830372-1829354(-)
Potential amino acid sequence	MEARTRRGQKKSSEEANQVLQVQAWQEEVERARQGQREAESKLASLEAEMQKLRVETAAMKRDA EHYSRPRTADERTAKATEFEQKVALLEVECATLNQELQDMEARTRRGQKKSSEEANQVLQVQAW QEEVERARQGQREAESKLASLEAEMQKLRVETAAMKRDAEHYSRPRTADERTAKATEFEQKVAL LEVECATLNQELQDMEARTRRGQKKSSEEANQVLQVQAWQEEVERARQGQREAESKLASLEAEM QKLRVETAAMKRDAEHYSRPRTADERTAKATEFEQKVALLEVECATLNQELQDMEARTRRGQKK SSEEANQVLQVQAWQEEVERARQGQREAESKLASLEAEMQKLRVETAAMKRDAEHYSRP(+) MLNITLAREQLMKGLPRQQSLSRRWHCLRLNVQL*(+) MPAPEALDLPLLRTSFVHDEYELPCLAVLDLELHIQPQAVPPSAQTLLPWQSFHQLFSGESNVQ HPFSWQLFQLLTFAFQPPKKQACFQLPSDLGVHAPLLLAMPAPEALDLPLLRTSFVHDEYELPC LAVLDLELHIQPQAVPPSAQTLLPWQSFHQLFSGESNVQHPFSWQLFQLLTFAFQPPKKQACFQ LPSDLGVHAPLLLAMPAPEALDLPLLRTSFVHDEYELPCLAVLDLELHIQPQAVPPSAQTLLPW QSFHQLFSGESNVQHPFSWQLFQLLTFAFQPPKKQACFQLPSDLGVHAPLLLAMPAPEALDLPL LRTSFVHDEYELPCLAVLDLELHIQPQAVPPSAQTLLPWQSFHQLF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017

circRNA

Detail information of Solyc12g008390.1_circ_g.2

Address

Any questions?

Supported by