Plant Circular RNA Database

Detail information of AT3G15220_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G15220_circ_g.1
					
						ID in PlantcircBase
						ath_circ_021888
					
						Alias
						At_ciR5973
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 5128633-5129927  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, find_circ, CIRI-full
					
						Parent gene
						
							AT3G15220						
					
						Parent gene annotation
						
							MAP kinase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G15220_circ_g.2 						
					
						Support reads
						2/1
					
						Tissues
						leaf/whole_plant
					
						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
						AT3G15220.1:6

General Information
CircRNA Name	AT3G15220_circ_g.1
ID in PlantcircBase	ath_circ_021888
Alias	At_ciR5973
Organism	Arabidpsis thaliana
Position	chr3: 5128633-5129927 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, find_circ, CIRI-full
Parent gene	AT3G15220
Parent gene annotation	MAP kinase
Parent gene strand	-
Alternative splicing	AT3G15220_circ_g.2
Support reads	2/1
Tissues	leaf/whole_plant
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	AT3G15220.1:6

			
						 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  
						
							AGAAGTGAAGCTCAGTATATAGGCGAGATACCTTCTCATTATACCCTTCTGAGTTCTGAATAAC
TTCTGGTGCCATCCAAAATGGGGTTCCTACAAAAGTctcttcgtggaagccatcttcatggtca
ttctgaaaagggtgtcttctgacaaaacctccttcagaagcttcagaaattgtactcccagtcg
cagatgac

									
								

					

						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: 732
Transcript exons: 5128633-5128900,5128976-5129104,5129287-5129366,5129456-
5129524,5129611-5129727,5129859-5129927
CTCTTCGTGGAAGCCATCTTCATGGTCATTCTGAAAAGGGTGTCTTCTGACAAAACCTCCTTCA
GAAGCTTCAGAAATTGTACTCCCAGTCGCAGATGACCATTGATTACCACTAGGTCTTGTTGTTC
TTTGCGAAATCCGATTAGGAGAAACTTCTTGGCGCCTCTCCCTTGCTTGAGGAGGTTTTAAAGC
ACGAACTGTTCCAATACTCTGTGACCCCCCAACGGTAAAGTCCCATCCAGCATTTTTGACGGTA
TTCCCCTGAAAACTATATCCAGGCGCGCCTTGGCTTCTTTCATCTCTAGCTATCCTAACAGTAC
CAGATGATTCAACTGGAGCTTTGGCCCCATTCCTAGGAGTCTCTTCATCTTCTTTTACTTGGTA
CTTTGGCCGCTCTCTTATCCTCTCAAGAAGTTTCGGACTTTTCCTAGCATTCTTAATAAATCTG
TGTTTAATAAGTTCTTTGGCACTTGGTCTCTCGGCAGGGGCCTTCTTCAGGCATAATGAAACAA
ACTCCTTTACTTGACGGGAAAAATGCTCATCTAACTGTGGTGGAGTTTCTCGAGGAATGATAAA
AAGCACTCTCATGGGATGAAGGTCAGCTAGGGGAGGTTCTCCTTTTGCCATCTCAATAACTGTT
ATTCCGAGCGACCAAATATCTGCCTTCTCATTATACCCTTCTGAGTTCTGAATAACTTCTGGTG
CCATCCAAAATGGGGTTCCTACAAAAGT
Transcript length: 337
Transcript exons: 5128633-5129927
CTCTTCGTGGAAGCCATCTTCATGGTCATTCTGAAAAGGGTGTCTTCTGACAAAACCTCCTTCA
GAAGCTTCAGAAATTGTACTCCCAGTCGCAGATGACCATTGATTACCACTAGGTCTTGTTGTTC
TTTGCGAAATCCGATTAGGAGAAACTTCTTGGCGCCTCTCCCTTGCTTGAGGAGGTTTTAAAGC
ACGAACTGTTCCAATACTCTGTGACCCCCCAACGGTAAAGTCCCATCCAGCATTTTTGACGGTA
TTCCCCTGAAAACTTCTCATTATACCCTTCTGAGTTCTGAATAACTTCTGGTGCCATCCAAAAT
GGGGTTCCTACAAAAGT
						
					

						Genomic sequence
						
							CTCTTCGTGGAAGCCATCTTCATGGTCATTCTGAAAAGGGTGTCTTCTGACAAAACCTCCTTCA
GAAGCTTCAGAAATTGTACTCCCAGTCGCAGATGACCATTGATTACCACTAGGTCTTGTTGTTC
TTTGCGAAATCCGATTAGGAGAAACTTCTTGGCGCCTCTCCCTTGCTTGAGGAGGTTTTAAAGC
ACGAACTGTTCCAATACTCTGTGACCCCCCAACGGTAAAGTCCCATCCAGCATTTTTGACGGTA
TTCCCCTGAAAACTGTAGCTACGAGTTAATAAAGATTTTATCAAACAAGCAACAGAAGAAAACC
AAAGCGCAGAACATTCATCCAACCTATATCCAGGCGCGCCTTGGCTTCTTTCATCTCTAGCTAT
CCTAACAGTACCAGATGATTCAACTGGAGCTTTGGCCCCATTCCTAGGAGTCTCTTCATCTTCT
TTTACTTGGTACTTTGGCCGCTCTCTTTAAAGAGGAAAAAAGGACAGAATAACAATCGTGCTTA
TTCTGGATTTTCTTTTGGCATATAAAAGATCAAAACAAACATACGGGAAACCATCTAAATGTTA
CTTTTGACATACAACTGAATTAGGAAAGTCATAATTGAAATCACATGCCAAAGCTGTTGAAGAG
AAAAAGTATCAAACCTTATCCTCTCAAGAAGTTTCGGACTTTTCCTAGCATTCTTAATAAATCT
GTGTTTAATAAGTTCTTTGGCACTTGGTCTCTGAAAGTATAAGACTTGAATAAGAGATCTTGAA
ATGCCACTGCTGCCAATAAAGAAAGCAAAGATTACAAGGATTGCATTGCAAGTACCTCGGCAGG
GGCCTTCTTCAGGCATAATGAAACAAACTCCTTTACTTGACGGGAAAAATGCTCATCTAACTGC
CCAGAAAAGGTAAAATTCTGCTGAGGCAAAGCACAGTGACCAGTATAACTTTTATCATGTTTAA
AATGAAAATATGTGAAACCTGTGGTGGAGTTTCTCGAGGAATGATAAAAAGCACTCTCATGGGA
TGAAGGTCAGCTAGGGGAGGTTCTCCTTTTGCCATCTCAATAACTGTTATTCCGAGCGACCAAA
TATCTGCCTAAATGACAACAATCCCAGCAACAGAAAAAGAAGGCAAAAAATATTAGATATGCTA
AGGAAACAAGTATAGCCTCTACAAACACACATGTCAAGCTAGGAGAAGTGAAGCTCAGTATATA
GGCGAGATACCTTCTCATTATACCCTTCTGAGTTCTGAATAACTTCTGGTGCCATCCAAAATGG
GGTTCCTACAAAAGT
						
					

			
		

Sequences
Splice junction sequence	AGAAGTGAAGCTCAGTATATAGGCGAGATACCTTCTCATTATACCCTTCTGAGTTCTGAATAAC TTCTGGTGCCATCCAAAATGGGGTTCCTACAAAAGTctcttcgtggaagccatcttcatggtca ttctgaaaagggtgtcttctgacaaaacctccttcagaagcttcagaaattgtactcccagtcg cagatgac
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: 732 Transcript exons: 5128633-5128900,5128976-5129104,5129287-5129366,5129456- 5129524,5129611-5129727,5129859-5129927 CTCTTCGTGGAAGCCATCTTCATGGTCATTCTGAAAAGGGTGTCTTCTGACAAAACCTCCTTCA GAAGCTTCAGAAATTGTACTCCCAGTCGCAGATGACCATTGATTACCACTAGGTCTTGTTGTTC TTTGCGAAATCCGATTAGGAGAAACTTCTTGGCGCCTCTCCCTTGCTTGAGGAGGTTTTAAAGC ACGAACTGTTCCAATACTCTGTGACCCCCCAACGGTAAAGTCCCATCCAGCATTTTTGACGGTA TTCCCCTGAAAACTATATCCAGGCGCGCCTTGGCTTCTTTCATCTCTAGCTATCCTAACAGTAC CAGATGATTCAACTGGAGCTTTGGCCCCATTCCTAGGAGTCTCTTCATCTTCTTTTACTTGGTA CTTTGGCCGCTCTCTTATCCTCTCAAGAAGTTTCGGACTTTTCCTAGCATTCTTAATAAATCTG TGTTTAATAAGTTCTTTGGCACTTGGTCTCTCGGCAGGGGCCTTCTTCAGGCATAATGAAACAA ACTCCTTTACTTGACGGGAAAAATGCTCATCTAACTGTGGTGGAGTTTCTCGAGGAATGATAAA AAGCACTCTCATGGGATGAAGGTCAGCTAGGGGAGGTTCTCCTTTTGCCATCTCAATAACTGTT ATTCCGAGCGACCAAATATCTGCCTTCTCATTATACCCTTCTGAGTTCTGAATAACTTCTGGTG CCATCCAAAATGGGGTTCCTACAAAAGT Transcript length: 337 Transcript exons: 5128633-5129927 CTCTTCGTGGAAGCCATCTTCATGGTCATTCTGAAAAGGGTGTCTTCTGACAAAACCTCCTTCA GAAGCTTCAGAAATTGTACTCCCAGTCGCAGATGACCATTGATTACCACTAGGTCTTGTTGTTC TTTGCGAAATCCGATTAGGAGAAACTTCTTGGCGCCTCTCCCTTGCTTGAGGAGGTTTTAAAGC ACGAACTGTTCCAATACTCTGTGACCCCCCAACGGTAAAGTCCCATCCAGCATTTTTGACGGTA TTCCCCTGAAAACTTCTCATTATACCCTTCTGAGTTCTGAATAACTTCTGGTGCCATCCAAAAT GGGGTTCCTACAAAAGT
Genomic sequence	CTCTTCGTGGAAGCCATCTTCATGGTCATTCTGAAAAGGGTGTCTTCTGACAAAACCTCCTTCA GAAGCTTCAGAAATTGTACTCCCAGTCGCAGATGACCATTGATTACCACTAGGTCTTGTTGTTC TTTGCGAAATCCGATTAGGAGAAACTTCTTGGCGCCTCTCCCTTGCTTGAGGAGGTTTTAAAGC ACGAACTGTTCCAATACTCTGTGACCCCCCAACGGTAAAGTCCCATCCAGCATTTTTGACGGTA TTCCCCTGAAAACTGTAGCTACGAGTTAATAAAGATTTTATCAAACAAGCAACAGAAGAAAACC AAAGCGCAGAACATTCATCCAACCTATATCCAGGCGCGCCTTGGCTTCTTTCATCTCTAGCTAT CCTAACAGTACCAGATGATTCAACTGGAGCTTTGGCCCCATTCCTAGGAGTCTCTTCATCTTCT TTTACTTGGTACTTTGGCCGCTCTCTTTAAAGAGGAAAAAAGGACAGAATAACAATCGTGCTTA TTCTGGATTTTCTTTTGGCATATAAAAGATCAAAACAAACATACGGGAAACCATCTAAATGTTA CTTTTGACATACAACTGAATTAGGAAAGTCATAATTGAAATCACATGCCAAAGCTGTTGAAGAG AAAAAGTATCAAACCTTATCCTCTCAAGAAGTTTCGGACTTTTCCTAGCATTCTTAATAAATCT GTGTTTAATAAGTTCTTTGGCACTTGGTCTCTGAAAGTATAAGACTTGAATAAGAGATCTTGAA ATGCCACTGCTGCCAATAAAGAAAGCAAAGATTACAAGGATTGCATTGCAAGTACCTCGGCAGG GGCCTTCTTCAGGCATAATGAAACAAACTCCTTTACTTGACGGGAAAAATGCTCATCTAACTGC CCAGAAAAGGTAAAATTCTGCTGAGGCAAAGCACAGTGACCAGTATAACTTTTATCATGTTTAA AATGAAAATATGTGAAACCTGTGGTGGAGTTTCTCGAGGAATGATAAAAAGCACTCTCATGGGA TGAAGGTCAGCTAGGGGAGGTTCTCCTTTTGCCATCTCAATAACTGTTATTCCGAGCGACCAAA TATCTGCCTAAATGACAACAATCCCAGCAACAGAAAAAGAAGGCAAAAAATATTAGATATGCTA AGGAAACAAGTATAGCCTCTACAAACACACATGTCAAGCTAGGAGAAGTGAAGCTCAGTATATA GGCGAGATACCTTCTCATTATACCCTTCTGAGTTCTGAATAACTTCTGGTGCCATCCAAAATGG GGTTCCTACAAAAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.278432035

Conservation Information
Conserved circRNAs	NA
PMCS	0.278432035

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5129904-5128635(-)
						
						Potential amino acid sequence
						
							MAPEVIQNSEGYNEKADIWSLGITVIEMAKGEPPLADLHPMRVLFIIPRETPPQLDEHFSRQVK
EFVSLCLKKAPAERPSAKELIKHRFIKNARKSPKLLERIRERPKYQVKEDEETPRNGAKAPVES
SGTVRIARDERSQGAPGYSFQGNTVKNAGWDFTVGGSQSIGTVRALKPPQARERRQEVSPNRIS
QRTTRPSGNQWSSATGSTISEASEGGFVRRHPFQNDHEDGFHEETFVGTPFWMAPEVIQNSEGY
NEKADIWSLGITVIEMAKGEPPLADLHPMRVLFIIPRETPPQLDEHFSRQVKEFVSLCLKKAPA
ERPSAKELIKHRFIKNARKSPKLLERIRERPKYQVKEDEETPRNGAKAPVESSGTVRIARDERS
QGAPGYSFQGNTVKNAGWDFTVGGSQSIGTVRALKPPQARERRQEVSPNRISQRTTRPSGNQWS
SATGSTISEASEGGFVRRHPFQNDHEDGFHEETFVGTPFWMAPEVIQNSEGYNEKADIWSLGIT
VIEMAKGEPPLADLHPMRVLFIIPRETPPQLDEHFSRQVKEFVSLCLKKAPAERPSAKELIKHR
FIKNARKSPKLLERIRERPKYQVKEDEETPRNGAKAPVESSGTVRIARDERSQGAPGYSFQGNT
VKNAGWDFTVGGSQSIGTVRALKPPQARERRQEVSPNRISQRTTRPSGNQWSSATGSTISEASE
GGFVRRHPFQNDHEDGFHEETFVGTPFWMAPEVIQNSEGYNEKADIWSLGITVIEMAKGEPPLA
DLHPMRVLFIIPRETPPQLDEHFSRQVKEFVSLCLKKAPAERPSAKELIKHRFIKNARKSPKLL
ERIRERPKYQVKEDEETPRNGAKAPVESSGTVRIARDERSQGAPGYSFQGNTVKNAGWDFTVGG
SQSIGTVRALKPPQARERRQEVSPNRISQRTTRPSGNQWSSATGSTISEASEGGFVRRHPFQND
HEDGFHEE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5129904-5128635(-)
Potential amino acid sequence	MAPEVIQNSEGYNEKADIWSLGITVIEMAKGEPPLADLHPMRVLFIIPRETPPQLDEHFSRQVK EFVSLCLKKAPAERPSAKELIKHRFIKNARKSPKLLERIRERPKYQVKEDEETPRNGAKAPVES SGTVRIARDERSQGAPGYSFQGNTVKNAGWDFTVGGSQSIGTVRALKPPQARERRQEVSPNRIS QRTTRPSGNQWSSATGSTISEASEGGFVRRHPFQNDHEDGFHEETFVGTPFWMAPEVIQNSEGY NEKADIWSLGITVIEMAKGEPPLADLHPMRVLFIIPRETPPQLDEHFSRQVKEFVSLCLKKAPA ERPSAKELIKHRFIKNARKSPKLLERIRERPKYQVKEDEETPRNGAKAPVESSGTVRIARDERS QGAPGYSFQGNTVKNAGWDFTVGGSQSIGTVRALKPPQARERRQEVSPNRISQRTTRPSGNQWS SATGSTISEASEGGFVRRHPFQNDHEDGFHEETFVGTPFWMAPEVIQNSEGYNEKADIWSLGIT VIEMAKGEPPLADLHPMRVLFIIPRETPPQLDEHFSRQVKEFVSLCLKKAPAERPSAKELIKHR FIKNARKSPKLLERIRERPKYQVKEDEETPRNGAKAPVESSGTVRIARDERSQGAPGYSFQGNT VKNAGWDFTVGGSQSIGTVRALKPPQARERRQEVSPNRISQRTTRPSGNQWSSATGSTISEASE GGFVRRHPFQNDHEDGFHEETFVGTPFWMAPEVIQNSEGYNEKADIWSLGITVIEMAKGEPPLA DLHPMRVLFIIPRETPPQLDEHFSRQVKEFVSLCLKKAPAERPSAKELIKHRFIKNARKSPKLL ERIRERPKYQVKEDEETPRNGAKAPVESSGTVRIARDERSQGAPGYSFQGNTVKNAGWDFTVGG SQSIGTVRALKPPQARERRQEVSPNRISQRTTRPSGNQWSSATGSTISEASEGGFVRRHPFQND HEDGFHEE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of AT3G15220_circ_g.1

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