Plant Circular RNA Database

Detail information of AT3G55880_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G55880_circ_g.3
					
						ID in PlantcircBase
						ath_circ_027757
					
						Alias
						AT3G55880_C1, AT3G55880_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 20737316-20738445  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							AT3G55880						
					
						Parent gene annotation
						
							SUE4
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G55880_circ_g.2 AT3G55880_circ_g.4 						
					
						Support reads
						NA
					
						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  
						
							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
						AT3G55880.1:1
AT3G55880.4:1
AT3G55880.3:2
AT3G55880.2:2

General Information
CircRNA Name	AT3G55880_circ_g.3
ID in PlantcircBase	ath_circ_027757
Alias	AT3G55880_C1, AT3G55880_C1
Organism	Arabidpsis thaliana
Position	chr3: 20737316-20738445 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	AT3G55880
Parent gene annotation	SUE4
Parent gene strand	+
Alternative splicing	AT3G55880_circ_g.2 AT3G55880_circ_g.4
Support reads	NA
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	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	AT3G55880.1:1 AT3G55880.4:1 AT3G55880.3:2 AT3G55880.2:2

			
						 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  
						
							TCGTCACATGTACATATATACTTACAGTACAAGCTACATGTATATAAATATACGTATCTATGCA
ACATCTACTGGGTTTTGGTCTCCTTTCATGTTCGAGgcgtttacgggctttgtgacggaccaaa
gttatcaaggggaccatatctgacaataacgatgatatgctcgatatcttcactgatatacgta
tcgttcaa

									
								

					

						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: 1130
Transcript exons: 20737316-20738445
GCGTTTACGGGCTTTGTGACGGACCAAAGTTATCAAGGGGACCATATCTGACAATAACGATGAT
ATGCTCGATATCTTCACTGATATACGTATCGTTCAAGGCAGCAATTGTATTCGGAGAGCCAGTG
ATCGGAGGATATTTCCGAACAGAGGAAATGGCTCTCTTTCTATGTTCTTGGATCTTAGCCATCG
GTCACATCGTTGTGGCGTACCGTACAAGTTGTAGAGAGAGACGAAAGCTCCTAGTCTTCAAAAT
CGACATCGAATCCGTAAGTTCACTTTGATTTTTCTTATTTTATTAACTTTTAGCCGTTACATAA
AGCATTATTAGCATTAAAAAAATGATATAGGCCGTATCAAAATTGTTTATTTTTCAAATCTAGC
ATTAGTTATTTGTTTTTATATCTTAAGATATTGTTCTTCTACCACTAATACAGATCAGACTCGG
TCAGAAATAGCATGTGACTTCAGATATTACATTATAGTCACCGTCTTGAATTAATTTTCACATT
TTTTTTGGTACCAAGTGTTATTGTAGGTTTGAAAATGACTAGTCAATTGAGAAGGTTTGATTTT
TCACTCCCAACAAAAACTAGAGGAAATTGTATTTTGATTAGCACTTTCTTATGTATAAAATCAC
TTTGATTCAAACCTAATTAGATAGTGACGAATAAATAGTATTAATTACTTATATATAATAAGAA
TAAGAATAAATCGACATTTTCCCTCGAATAAAAGAAAGAGTGAAACGGATGTTTCCGAGTGGGA
ACCGTGTGGGATGAATAATGATGGACGACTGCTTTATATAATCTTCGTATTTAATGTTACTTTC
AATTAAATTTTTATAAGATATTAATAGACATGACAACGTCACTAACACCTAAAACATGGCTCAT
GATTTTAGTTGAAGTGTGACTAATAAATATATATATTCCAATTTGCAGGTTTCAGCTTGTAAAA
ATGTGTTTCCCAGATATCAAAAAATCCTCCAACAAGAGAGACTCAAATAGCTAGCTATATTCGA
AGTCAATCGTCACATGTACATATATACTTACAGTACAAGCTACATGTATATAAATATACGTATC
TATGCAACATCTACTGGGTTTTGGTCTCCTTTCATGTTCGAG
Transcript length: 455
Transcript exons: 20737316-20737584,20738260-20738445
GCGTTTACGGGCTTTGTGACGGACCAAAGTTATCAAGGGGACCATATCTGACAATAACGATGAT
ATGCTCGATATCTTCACTGATATACGTATCGTTCAAGGCAGCAATTGTATTCGGAGAGCCAGTG
ATCGGAGGATATTTCCGAACAGAGGAAATGGCTCTCTTTCTATGTTCTTGGATCTTAGCCATCG
GTCACATCGTTGTGGCGTACCGTACAAGTTGTAGAGAGAGACGAAAGCTCCTAGTCTTCAAAAT
CGACATCGAATCCGTTTCAGCTTGTAAAAATGTGTTTCCCAGATATCAAAAAATCCTCCAACAA
GAGAGACTCAAATAGCTAGCTATATTCGAAGTCAATCGTCACATGTACATATATACTTACAGTA
CAAGCTACATGTATATAAATATACGTATCTATGCAACATCTACTGGGTTTTGGTCTCCTTTCAT
GTTCGAG
						
					

						Genomic sequence
						
							GCGTTTACGGGCTTTGTGACGGACCAAAGTTATCAAGGGGACCATATCTGACAATAACGATGAT
ATGCTCGATATCTTCACTGATATACGTATCGTTCAAGGCAGCAATTGTATTCGGAGAGCCAGTG
ATCGGAGGATATTTCCGAACAGAGGAAATGGCTCTCTTTCTATGTTCTTGGATCTTAGCCATCG
GTCACATCGTTGTGGCGTACCGTACAAGTTGTAGAGAGAGACGAAAGCTCCTAGTCTTCAAAAT
CGACATCGAATCCGTAAGTTCACTTTGATTTTTCTTATTTTATTAACTTTTAGCCGTTACATAA
AGCATTATTAGCATTAAAAAAATGATATAGGCCGTATCAAAATTGTTTATTTTTCAAATCTAGC
ATTAGTTATTTGTTTTTATATCTTAAGATATTGTTCTTCTACCACTAATACAGATCAGACTCGG
TCAGAAATAGCATGTGACTTCAGATATTACATTATAGTCACCGTCTTGAATTAATTTTCACATT
TTTTTTGGTACCAAGTGTTATTGTAGGTTTGAAAATGACTAGTCAATTGAGAAGGTTTGATTTT
TCACTCCCAACAAAAACTAGAGGAAATTGTATTTTGATTAGCACTTTCTTATGTATAAAATCAC
TTTGATTCAAACCTAATTAGATAGTGACGAATAAATAGTATTAATTACTTATATATAATAAGAA
TAAGAATAAATCGACATTTTCCCTCGAATAAAAGAAAGAGTGAAACGGATGTTTCCGAGTGGGA
ACCGTGTGGGATGAATAATGATGGACGACTGCTTTATATAATCTTCGTATTTAATGTTACTTTC
AATTAAATTTTTATAAGATATTAATAGACATGACAACGTCACTAACACCTAAAACATGGCTCAT
GATTTTAGTTGAAGTGTGACTAATAAATATATATATTCCAATTTGCAGGTTTCAGCTTGTAAAA
ATGTGTTTCCCAGATATCAAAAAATCCTCCAACAAGAGAGACTCAAATAGCTAGCTATATTCGA
AGTCAATCGTCACATGTACATATATACTTACAGTACAAGCTACATGTATATAAATATACGTATC
TATGCAACATCTACTGGGTTTTGGTCTCCTTTCATGTTCGAG
						
					

			
		

Sequences
Splice junction sequence	TCGTCACATGTACATATATACTTACAGTACAAGCTACATGTATATAAATATACGTATCTATGCA ACATCTACTGGGTTTTGGTCTCCTTTCATGTTCGAGgcgtttacgggctttgtgacggaccaaa gttatcaaggggaccatatctgacaataacgatgatatgctcgatatcttcactgatatacgta tcgttcaa
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: 1130 Transcript exons: 20737316-20738445 GCGTTTACGGGCTTTGTGACGGACCAAAGTTATCAAGGGGACCATATCTGACAATAACGATGAT ATGCTCGATATCTTCACTGATATACGTATCGTTCAAGGCAGCAATTGTATTCGGAGAGCCAGTG ATCGGAGGATATTTCCGAACAGAGGAAATGGCTCTCTTTCTATGTTCTTGGATCTTAGCCATCG GTCACATCGTTGTGGCGTACCGTACAAGTTGTAGAGAGAGACGAAAGCTCCTAGTCTTCAAAAT CGACATCGAATCCGTAAGTTCACTTTGATTTTTCTTATTTTATTAACTTTTAGCCGTTACATAA AGCATTATTAGCATTAAAAAAATGATATAGGCCGTATCAAAATTGTTTATTTTTCAAATCTAGC ATTAGTTATTTGTTTTTATATCTTAAGATATTGTTCTTCTACCACTAATACAGATCAGACTCGG TCAGAAATAGCATGTGACTTCAGATATTACATTATAGTCACCGTCTTGAATTAATTTTCACATT TTTTTTGGTACCAAGTGTTATTGTAGGTTTGAAAATGACTAGTCAATTGAGAAGGTTTGATTTT TCACTCCCAACAAAAACTAGAGGAAATTGTATTTTGATTAGCACTTTCTTATGTATAAAATCAC TTTGATTCAAACCTAATTAGATAGTGACGAATAAATAGTATTAATTACTTATATATAATAAGAA TAAGAATAAATCGACATTTTCCCTCGAATAAAAGAAAGAGTGAAACGGATGTTTCCGAGTGGGA ACCGTGTGGGATGAATAATGATGGACGACTGCTTTATATAATCTTCGTATTTAATGTTACTTTC AATTAAATTTTTATAAGATATTAATAGACATGACAACGTCACTAACACCTAAAACATGGCTCAT GATTTTAGTTGAAGTGTGACTAATAAATATATATATTCCAATTTGCAGGTTTCAGCTTGTAAAA ATGTGTTTCCCAGATATCAAAAAATCCTCCAACAAGAGAGACTCAAATAGCTAGCTATATTCGA AGTCAATCGTCACATGTACATATATACTTACAGTACAAGCTACATGTATATAAATATACGTATC TATGCAACATCTACTGGGTTTTGGTCTCCTTTCATGTTCGAG Transcript length: 455 Transcript exons: 20737316-20737584,20738260-20738445 GCGTTTACGGGCTTTGTGACGGACCAAAGTTATCAAGGGGACCATATCTGACAATAACGATGAT ATGCTCGATATCTTCACTGATATACGTATCGTTCAAGGCAGCAATTGTATTCGGAGAGCCAGTG ATCGGAGGATATTTCCGAACAGAGGAAATGGCTCTCTTTCTATGTTCTTGGATCTTAGCCATCG GTCACATCGTTGTGGCGTACCGTACAAGTTGTAGAGAGAGACGAAAGCTCCTAGTCTTCAAAAT CGACATCGAATCCGTTTCAGCTTGTAAAAATGTGTTTCCCAGATATCAAAAAATCCTCCAACAA GAGAGACTCAAATAGCTAGCTATATTCGAAGTCAATCGTCACATGTACATATATACTTACAGTA CAAGCTACATGTATATAAATATACGTATCTATGCAACATCTACTGGGTTTTGGTCTCCTTTCAT GTTCGAG
Genomic sequence	GCGTTTACGGGCTTTGTGACGGACCAAAGTTATCAAGGGGACCATATCTGACAATAACGATGAT ATGCTCGATATCTTCACTGATATACGTATCGTTCAAGGCAGCAATTGTATTCGGAGAGCCAGTG ATCGGAGGATATTTCCGAACAGAGGAAATGGCTCTCTTTCTATGTTCTTGGATCTTAGCCATCG GTCACATCGTTGTGGCGTACCGTACAAGTTGTAGAGAGAGACGAAAGCTCCTAGTCTTCAAAAT CGACATCGAATCCGTAAGTTCACTTTGATTTTTCTTATTTTATTAACTTTTAGCCGTTACATAA AGCATTATTAGCATTAAAAAAATGATATAGGCCGTATCAAAATTGTTTATTTTTCAAATCTAGC ATTAGTTATTTGTTTTTATATCTTAAGATATTGTTCTTCTACCACTAATACAGATCAGACTCGG TCAGAAATAGCATGTGACTTCAGATATTACATTATAGTCACCGTCTTGAATTAATTTTCACATT TTTTTTGGTACCAAGTGTTATTGTAGGTTTGAAAATGACTAGTCAATTGAGAAGGTTTGATTTT TCACTCCCAACAAAAACTAGAGGAAATTGTATTTTGATTAGCACTTTCTTATGTATAAAATCAC TTTGATTCAAACCTAATTAGATAGTGACGAATAAATAGTATTAATTACTTATATATAATAAGAA TAAGAATAAATCGACATTTTCCCTCGAATAAAAGAAAGAGTGAAACGGATGTTTCCGAGTGGGA ACCGTGTGGGATGAATAATGATGGACGACTGCTTTATATAATCTTCGTATTTAATGTTACTTTC AATTAAATTTTTATAAGATATTAATAGACATGACAACGTCACTAACACCTAAAACATGGCTCAT GATTTTAGTTGAAGTGTGACTAATAAATATATATATTCCAATTTGCAGGTTTCAGCTTGTAAAA ATGTGTTTCCCAGATATCAAAAAATCCTCCAACAAGAGAGACTCAAATAGCTAGCTATATTCGA AGTCAATCGTCACATGTACATATATACTTACAGTACAAGCTACATGTATATAAATATACGTATC TATGCAACATCTACTGGGTTTTGGTCTCCTTTCATGTTCGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.239140722

Conservation Information
Conserved circRNAs	NA
PMCS	0.239140722

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20738354-20737363(+)
						
						Potential amino acid sequence
						
							MYIYTYSTSYMYINIRIYATSTGFWSPFMFEAFTGFVTDQSYQGDHI*
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	20738354-20737363(+)
Potential amino acid sequence	MYIYTYSTSYMYINIRIYATSTGFWSPFMFEAFTGFVTDQSYQGDHI*
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

			
						 Other Information
					
						References
						Zhang et al., 2019

circRNA

Detail information of AT3G55880_circ_g.3

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