Plant Circular RNA Database

Detail information of Solyc12g038400.1_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc12g038400.1_circ_g.3
					
						ID in PlantcircBase
						sly_circ_003633
					
						Alias
						Slcirc182
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr12: 48120404-48122121  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc12g038400.1						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc12g038400.1_circ_g.2 						
					
						Support reads
						19
					
						Tissues
						leaf
					
						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  
						
							CT-AC							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
						Solyc12g038400.1.1:3

General Information
CircRNA Name	Solyc12g038400.1_circ_g.3
ID in PlantcircBase	sly_circ_003633
Alias	Slcirc182
Organism	Solanum lycopersicum
Position	chr12: 48120404-48122121 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc12g038400.1
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc12g038400.1_circ_g.2
Support reads	19
Tissues	leaf
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	CT-AC 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	Solyc12g038400.1.1:3

			
						 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  
						
							AGCCAAGTAGATCACCACAGAATTAACATCCATCGGCATATCTATAGCTATGGCAGATCCTTTC
TCCAAACCCAGGCTTTCAAGAGCATATGCAACTTCCttggaatctttcactctgtctaaaaagt
caggccaagagatgtcaccatcacgtaattctatgctcaagctggagactctattgggaatcac
aattgcca

									
								

					

						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: 372
Transcript exons: 48120404-48120529,48120675-48120715,48121917-48122121
TTGGAATCTTTCACTCTGTCTAAAAAGTCAGGCCAAGAGATGTCACCATCACGTAATTCTATGC
TCAAGCTGGAGACTCTATTGGGAATCACAATTGCCATCGGTGAATGAGCTTCAACAACTCGACT
GTACAAGGGTATCTTTTTTTCTCCACGGGGAATAAAATCCTGAGTAAAAATTGCTTTTGCTTTT
GATAAGATGAGCCTTGTTGAAATTTCACTTGGGGCAAAACTATCAGCAATGGACACAACTACAT
AACCAGCAAGAACAATAGCCAAGTAGATCACCACAGAATTAACATCCATCGGCATATCTATAGC
TATGGCAGATCCTTTCTCCAAACCCAGGCTTTCAAGAGCATATGCAACTTCC
						
					

						Genomic sequence
						
							TTGGAATCTTTCACTCTGTCTAAAAAGTCAGGCCAAGAGATGTCACCATCACGTAATTCTATGC
TCAAGCTGGAGACTCTATTGGGAATCACAATTGCCATCGGTGAATGAGCTTCAACAACTCGACT
GCAGTTTTCAACGAGTGAGTCAAGAAAGAGAAGACATGAAAAAAGGGGAAATGCATAATTTACT
ACTGCCGCTAGAGGTTAAGCTTGCATGAACCTCGATACAGTTCATAATGTCTGAAGCAGAAAGG
GAGGAGAGAGATGACCTGTACAAGGGTATCTTTTTTTCTCCACGGGGAATAAAATCCTGTACAC
ATCATTGACAGAACGAAATTAAACAAGAAAAGGACCAATAAATAGTAATAACAAACAAATGGGA
AGCAAAATGAGTGCAGCTGCATATGCCAAAAGGAGTAATAAGAATGAGGAATAATGATTTGTAC
CGAATTTCACCATTTGAATTTTGTTGAACTTGAGGAATAAAATATAAATTAAAGTACAATTTGA
TCATAGGGGAGTCCATAAGAAGCAATGATCAAATAATAGAGCCATTAAATAGTGTTTCTGCAGT
AGATACTTCCATGAATGTTAGTCCAACTAGATTTTTGGAAGCCTGTCCGTAAAATACTGGAACT
CTTTGGAAATTCTTCAAATGCCCTTAGTAGAGAAAATTAGACAAAAAAGACCCAATGTTCATGA
GTATGAAGAATTTACTTCTCCACGATCAAACTGCTTTATTTTTTCGAAGTAGTAAAAATGAAGC
CATAACAAATTTGCTGGAAGCTAATATTTAAAATATTCCTACATTTCTTTATATATGTATTATT
TTTTAAGAATAAAAGAAAAAGTGTTTACCAGCTTTGAGTCTCAAATGAAGTTCTTTCATCATTT
CAACGCATCAACTGGACTTTACATGCTTAAAAAACTGAATTCTCCAAAAAGATTTTAAAATAAT
GAAACAAAATAAACTGATTAGGCAACTGCTCCATAATCTTCCTGATCATCTGTACGTAAATTGG
TTATATCCAATACTATCATATCTAAATATTTTAAGAAGATATTAACCCATGACTTTACAACCAT
CTCCTGTCCAGCTAATATGGTCTCACATATTATCTTCATATATTGCTTAATTTAATCTAAAATA
GAAACACAATATTTTTTAGAACTCATTTGTATCCACTTCTTTAATGCATACTATAGTTACATTT
TTTCCTCAATTCTTTGTTAATTTTGGGTTATTATCTGATATATTGTTGAATGACTGACTATAAA
ACCATCCGAGACCATAAGATTTTGAATGTAGTACTATGTTATCTGATGCATTAAAATCAATGCA
CTAGTGTGGGTCCTACCTTTACAACCCTGTCTTTTCTTAGTGTAGAACTGCTAGCATAGGAAGG
AGTTAGAAACTTGTATTCATCCAATGAAATTTTAATGACTTTAAAAGATAACATATATATGATA
CAATAGCTAAAAAGAATATCCTCAATCAATAAATAGAGCACCTGAGTAAAAATTGCTTTTGCTT
TTGATAAGATGAGCCTTGTTGAAATTTCACTTGGGGCAAAACTATCAGCAATGGACACAACTAC
ATAACCAGCAAGAACAATAGCCAAGTAGATCACCACAGAATTAACATCCATCGGCATATCTATA
GCTATGGCAGATCCTTTCTCCAAACCCAGGCTTTCAAGAGCATATGCAACTTCC
						
					

			
		

Sequences
Splice junction sequence	AGCCAAGTAGATCACCACAGAATTAACATCCATCGGCATATCTATAGCTATGGCAGATCCTTTC TCCAAACCCAGGCTTTCAAGAGCATATGCAACTTCCttggaatctttcactctgtctaaaaagt caggccaagagatgtcaccatcacgtaattctatgctcaagctggagactctattgggaatcac aattgcca
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: 372 Transcript exons: 48120404-48120529,48120675-48120715,48121917-48122121 TTGGAATCTTTCACTCTGTCTAAAAAGTCAGGCCAAGAGATGTCACCATCACGTAATTCTATGC TCAAGCTGGAGACTCTATTGGGAATCACAATTGCCATCGGTGAATGAGCTTCAACAACTCGACT GTACAAGGGTATCTTTTTTTCTCCACGGGGAATAAAATCCTGAGTAAAAATTGCTTTTGCTTTT GATAAGATGAGCCTTGTTGAAATTTCACTTGGGGCAAAACTATCAGCAATGGACACAACTACAT AACCAGCAAGAACAATAGCCAAGTAGATCACCACAGAATTAACATCCATCGGCATATCTATAGC TATGGCAGATCCTTTCTCCAAACCCAGGCTTTCAAGAGCATATGCAACTTCC
Genomic sequence	TTGGAATCTTTCACTCTGTCTAAAAAGTCAGGCCAAGAGATGTCACCATCACGTAATTCTATGC TCAAGCTGGAGACTCTATTGGGAATCACAATTGCCATCGGTGAATGAGCTTCAACAACTCGACT GCAGTTTTCAACGAGTGAGTCAAGAAAGAGAAGACATGAAAAAAGGGGAAATGCATAATTTACT ACTGCCGCTAGAGGTTAAGCTTGCATGAACCTCGATACAGTTCATAATGTCTGAAGCAGAAAGG GAGGAGAGAGATGACCTGTACAAGGGTATCTTTTTTTCTCCACGGGGAATAAAATCCTGTACAC ATCATTGACAGAACGAAATTAAACAAGAAAAGGACCAATAAATAGTAATAACAAACAAATGGGA AGCAAAATGAGTGCAGCTGCATATGCCAAAAGGAGTAATAAGAATGAGGAATAATGATTTGTAC CGAATTTCACCATTTGAATTTTGTTGAACTTGAGGAATAAAATATAAATTAAAGTACAATTTGA TCATAGGGGAGTCCATAAGAAGCAATGATCAAATAATAGAGCCATTAAATAGTGTTTCTGCAGT AGATACTTCCATGAATGTTAGTCCAACTAGATTTTTGGAAGCCTGTCCGTAAAATACTGGAACT CTTTGGAAATTCTTCAAATGCCCTTAGTAGAGAAAATTAGACAAAAAAGACCCAATGTTCATGA GTATGAAGAATTTACTTCTCCACGATCAAACTGCTTTATTTTTTCGAAGTAGTAAAAATGAAGC CATAACAAATTTGCTGGAAGCTAATATTTAAAATATTCCTACATTTCTTTATATATGTATTATT TTTTAAGAATAAAAGAAAAAGTGTTTACCAGCTTTGAGTCTCAAATGAAGTTCTTTCATCATTT CAACGCATCAACTGGACTTTACATGCTTAAAAAACTGAATTCTCCAAAAAGATTTTAAAATAAT GAAACAAAATAAACTGATTAGGCAACTGCTCCATAATCTTCCTGATCATCTGTACGTAAATTGG TTATATCCAATACTATCATATCTAAATATTTTAAGAAGATATTAACCCATGACTTTACAACCAT CTCCTGTCCAGCTAATATGGTCTCACATATTATCTTCATATATTGCTTAATTTAATCTAAAATA GAAACACAATATTTTTTAGAACTCATTTGTATCCACTTCTTTAATGCATACTATAGTTACATTT TTTCCTCAATTCTTTGTTAATTTTGGGTTATTATCTGATATATTGTTGAATGACTGACTATAAA ACCATCCGAGACCATAAGATTTTGAATGTAGTACTATGTTATCTGATGCATTAAAATCAATGCA CTAGTGTGGGTCCTACCTTTACAACCCTGTCTTTTCTTAGTGTAGAACTGCTAGCATAGGAAGG AGTTAGAAACTTGTATTCATCCAATGAAATTTTAATGACTTTAAAAGATAACATATATATGATA CAATAGCTAAAAAGAATATCCTCAATCAATAAATAGAGCACCTGAGTAAAAATTGCTTTTGCTT TTGATAAGATGAGCCTTGTTGAAATTTCACTTGGGGCAAAACTATCAGCAATGGACACAACTAC ATAACCAGCAAGAACAATAGCCAAGTAGATCACCACAGAATTAACATCCATCGGCATATCTATA GCTATGGCAGATCCTTTCTCCAAACCCAGGCTTTCAAGAGCATATGCAACTTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.572775219

Conservation Information
Conserved circRNAs	NA
PMCS	0.572775219

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							48122072-48120511(+)
48122112-48120708(+)
48122062-48120406(-)
						
						Potential amino acid sequence
						
							MADPFSKPRLSRAYATSLESFTLSKKSGQEMSPSRNSMLKLETLLGITIAIGE*(+)
MQLPWNLSLCLKSQAKRCHHHVILCSSWRLYWESQLPSVNELQQLDCTRVSFFLHGE*(+)
MPMDVNSVVIYLAIVLAGYVVVSIADSFAPSEISTRLILSKAKAIFTQDFIPRGEKKIPLYSRV
VEAHSPMAIVIPNRVSSLSIELRDGDISWPDFLDRVKDSKEVAYALESLGLEKGSAIAIDMPMD
VNSVVIYLAIVLAGYVVVSIADSFAPSEISTRLILSKAKAIFTQDFIPRGEKKIPLYSRVVEAH
SPMAIVIPNRVSSLSIELRDGDISWPDFLDRVKDSKEVAYALESLGLEKGSAIAIDMPMDVNSV
VIYLAIVLAGYVVVSIADSFAPSEISTRLILSKAKAIFTQDFIPRGEKKIPLYSRVVEAHSPMA
IVIPNRVSSLSIELRDGDISWPDFLDRVKDSKEVAYALESLGLEKGSAIAIDMPMDVNSVVIYL
AIVLAGYVVVSIADSFAPSEISTRLILSKAKAIFTQDFIPRGEKKIPLYSRVVEAHSPMAIVIP
NRVSSLSIELRDGDISWPDFLDRVKDS(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	48122072-48120511(+) 48122112-48120708(+) 48122062-48120406(-)
Potential amino acid sequence	MADPFSKPRLSRAYATSLESFTLSKKSGQEMSPSRNSMLKLETLLGITIAIGE(+) MQLPWNLSLCLKSQAKRCHHHVILCSSWRLYWESQLPSVNELQQLDCTRVSFFLHGE(+) MPMDVNSVVIYLAIVLAGYVVVSIADSFAPSEISTRLILSKAKAIFTQDFIPRGEKKIPLYSRV VEAHSPMAIVIPNRVSSLSIELRDGDISWPDFLDRVKDSKEVAYALESLGLEKGSAIAIDMPMD VNSVVIYLAIVLAGYVVVSIADSFAPSEISTRLILSKAKAIFTQDFIPRGEKKIPLYSRVVEAH SPMAIVIPNRVSSLSIELRDGDISWPDFLDRVKDSKEVAYALESLGLEKGSAIAIDMPMDVNSV VIYLAIVLAGYVVVSIADSFAPSEISTRLILSKAKAIFTQDFIPRGEKKIPLYSRVVEAHSPMA IVIPNRVSSLSIELRDGDISWPDFLDRVKDSKEVAYALESLGLEKGSAIAIDMPMDVNSVVIYL AIVLAGYVVVSIADSFAPSEISTRLILSKAKAIFTQDFIPRGEKKIPLYSRVVEAHSPMAIVIP NRVSSLSIELRDGDISWPDFLDRVKDS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Wang et al., 2018b

circRNA

Detail information of Solyc12g038400.1_circ_g.3

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