Plant Circular RNA Database

Detail information of AT5G20840_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT5G20840_circ_g.2
					
						ID in PlantcircBase
						ath_circ_039556
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 7062278-7065409  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT5G20840						
					
						Parent gene annotation
						
							Phosphoinositide phosphatase SAC4
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G20840_circ_g.1 AT5G20840_circ_g.3 AT5G20840_circ_g.4 						
					
						Support reads
						1
					
						Tissues
						aerial
					
						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
						AT5G20840.1:6

General Information
CircRNA Name	AT5G20840_circ_g.2
ID in PlantcircBase	ath_circ_039556
Alias	NA
Organism	Arabidpsis thaliana
Position	chr5: 7062278-7065409 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT5G20840
Parent gene annotation	Phosphoinositide phosphatase SAC4
Parent gene strand	-
Alternative splicing	AT5G20840_circ_g.1 AT5G20840_circ_g.3 AT5G20840_circ_g.4
Support reads	1
Tissues	aerial
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	AT5G20840.1:6

			
						 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  
						
							ATCACCATTTGCAACATTCTTACTTGGGCGGCAATTCTTCTCTAATGAGTCATAATCCCTACTA
TCATCATCAGAACTATTATGTGGAGACGTGTCGGCActtcctgctgcttgatccactctctctc
atagctggcgtcaattgttttacttcagtgatgatattctctgatgaagacgtctctgcggttg
aatatatt

									
								

					

						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: 1069
Transcript exons: 7062278-7062392,7062683-7062859,7063144-7063335,7063884-
7063994,7064097-7064218,7065058-7065409
CTTCCTGCTGCTTGATCCACTCTCTCTCATAGCTGGCGTCAATTGTTTTACTTCAGTGATGATA
TTCTCTGATGAAGACGTCTCTGCGGTTGAATATATTGTAAGCGCTGACGGCCTGGACAAGTGAT
CGTTCTCACATAGATTTTCTGACGACGAAAGCCACTCAATATCAACGAAATTTGAGACACTAGA
CATATCTTCTTGCTCGGACAAGTAAATGGAGCTACTACCATTATGTTGAACTTTTTGGACATCT
CCAAAAAAATGTGTGCTAGGCATTGACGGAGTACACCTCGATAATGTTACATCACCGGCAGCTG
GCATATCTGGTGATGATTCTGAAATTATATGAGTACGAGTCACTTGGTGTGACGACACAAAACC
TCTATGTGATATGCTTTCATTCTTTCTACTCATTGCAGACATCGGAGTGTGACTTTCATGGAGA
ATATTCCCATCTGATAAGCACCTCTTTACAAGAAACTTTTCATCTTCCCCCATGCTTATCTCTC
CACTTCGTCCATTAGAGTGGGAATCTGAACGCAACTCCCAAACCGCCTGGCTCCCTTGTTCAGG
CCGGAAAGTACCAAGAAATATATTAATGGCATCTTGTTTATCCGCATCCATATATGCGTTATTA
TAATAACGTTGCAGAGTCCTCAAGAACTCTTGTGACTGGGTTGCTGCTCTCCACTGGCCTCGCC
TTTCACTAAAAACCTTATTGTGGGCTGCAGATCCACCATATTGATAAGCTAGTGTGTCTCCCAT
TCTCTCGTATAACCCCATTAAAGTACTAGACAAAGGATCATCAAGTTCTATTGTTGGAGCATCT
CTAATTCCTAAAGCATGAAGCTGTTGCCCTAGAGCAGCCCAACCATATGCATATTGGGCAACAT
TTGTACGATCAAGGCAATCTATGCAGTTGGTCCGCAGCACTCCACTCTGGAGCCTGCTAGGCTT
GACATCATAATCACCATTTGCAACATTCTTACTTGGGCGGCAATTCTTCTCTAATGAGTCATAA
TCCCTACTATCATCATCAGAACTATTATGTGGAGACGTGTCGGCA
						
					

						Genomic sequence
						
							CTTCCTGCTGCTTGATCCACTCTCTCTCATAGCTGGCGTCAATTGTTTTACTTCAGTGATGATA
TTCTCTGATGAAGACGTCTCTGCGGTTGAATATATTGTAAGCGCTGACGGCCTGCCAAAATAAT
GCAATGAGACTTGCACAGTAAAATTGACCAAACCGTGATTAAAAAAATTGTTGATCATTCATGA
TGAATATTATTGTTATATTAGACATACGCAGATGGATATTTGAAAATTTTGGTTTTAACATTTT
CAGATGGAACATAATCAGATGGATTTTTAGATTGATGGACGATATAATGCTATAGATGTGAAAT
TTTAAGCTTCTATGTGACGACATCTGGTTGCTCTATTGACTGCTTAAAATCGTGAATTGATCTC
TTTAGTGCACAGTAATTTTACCTGGACAAGTGATCGTTCTCACATAGATTTTCTGACGACGAAA
GCCACTCAATATCAACGAAATTTGAGACACTAGACATATCTTCTTGCTCGGACAAGTAAATGGA
GCTACTACCATTATGTTGAACTTTTTGGACATCTCCAAAAAAATGTGTGCTAGGCATTGACGGA
GTACACCTACAAAGATTTTATAGCTGAATATTAAGACCAACAACAAAGACGAGTATTATTATGT
ACTAGTACACACAAAATCTTAAGCTACATGAAGCATAAAGAGTAAAGACAACCACCTCATGAAT
AATATATGAGCTATAATCATGGATAGAATTGACAAGCACAATAGAGCTTGACCCAGGAAAATTA
TAATGCATACACAGCATGGACACTCAAGCTAAATGTACCAGCAGTACATATTTTATCTAGCTAT
AATGAAGAAAAATGTAAGAAAGATTTAAACAAACCTCGATAATGTTACATCACCGGCAGCTGGC
ATATCTGGTGATGATTCTGAAATTATATGAGTACGAGTCACTTGGTGTGACGACACAAAACCTC
TATGTGATATGCTTTCATTCTTTCTACTCATTGCAGACATCGGAGTGTGACTTTCATGGAGAAT
ATTCCCATCTGATAAGCACCTCTTTACAAGAAACCTGGAAACACAGTAATAAGAGCTATGATAT
AGATGCGAAACAAAATCAATATATTTTTGTTCACTTTTAGAGGAAGGCTAATAGAGTTGGAAAC
TTCATATACTAAAAAACAGAGCATTCTTAAGCTAGCAGAGAGTACAGATTTTGGTACAGTTCGA
TGCAGTTAACAAACCAATCCTAGTTTCCCATGACCCCATATGTCTATAACAAAAGCCCATACCT
CCTTGTATCTAAATCCTATGTTAATTTCGTATGATTAGGGTCACAACAGTTTTGTAGGATCTAA
ACTGGAAGTTATGGTGGAGAATAAAATTCCAGTGAATGGATAATGTCGAGATATGTAGAGCCTA
TATTTTTCAAATTCGTAAACTTAATGCATAGCAAATAGGTATAAGATATTAGAACTCATGTGAC
TCATAAATCATCAAAATATGTCTAAAGAAGAAAATGGAAACCTCAAAACCTTTCTACCTACATG
ACAGCAACTAATTATATAGGCATATTATTGTTGAATTTATGAAATCCAAGTTAGCAGTCACAGA
ACCTACTTTTCATCTTCCCCCATGCTTATCTCTCCACTTCGTCCATTAGAGTGGGAATCTGAAC
GCAACTCCCAAACCGCCTGGCTCCCTTGTTCAGGCCGGAAAGTACCAAGAAATCTGCATATAGA
AATTCACAAAGGCCCAAAGAATTTCTGTAAGACTCTAAGAGATCATCGCGTAACATGGATATAT
ACGAGAGAGTGACATAGAGCAGCTTACATATTAATGGCATCTTGTTTATCCGCATCCATATATG
CGTTATTATAATAACGTTGCAGAGTCCTCAAGAACTCTTGTGACTGGGTTGCTGCTCTCCACTG
GCCTCGCCTTTCACTAAAAACCTATTACACACCAAAAATTCTAGGAATCAACAAAGTGTATCCC
AACAATAGTGAACATAATGGGAACTTGAGTCGGCTGCAGAAGATCAATACATCATAATTCAGTG
CAGAACAATGAGACAGATTACAAAATGAATGTTAACTAAGTCTGATATCCTTTTTTTTTTTTTT
TTTTTTTGTTTGTTGTCACCAAGTCTGATATCCTTCCAAGACAGTAAAATAACGAGGGCACAGT
TGTGATTAAGATATAATATAGATCACATAACCCTTGTAATTCTTGGACTTCAAAGACCAAGATC
AGAAAATAGACCAGATTTTCTTACAGCAATATCATCACAAATGATGAATTCCAAAAATTCAAAA
AGAAAAACATTTTAAAATTTGCCAATCATGTATATGCTGCTTCTAACATAAGAATCAGATCATA
ATAATAATGTCAGCTGAAAAGTGTCAGCTACAGAGAGGTTCAAATATAAGAGATGATTGATCAG
CATGCATGACGGATTCCTGTTGTTAGACCGAGCAACAAGGATGTACAAAGAACACTAGATTTTT
CATGAGCTTAGATTTACTTTAAGGTAAGGCTTGTTATTTTAATTGTAAACAATAAAAAATGTTG
ACGAGAAAAGGGATACAAATCATCTCATGGAGCCAGTCATGAATCATTCCCAACCGAGACTAAA
TGGAATCTATTTTGTGCATAATTAACAGTCCAGCGTTTAGTATCAACTAACTGTCTCTAGCAGA
AGACTTAATATGAGACAGTTCCATATGAACATGAACAAAATTAGTCTGCTGCCATGTCAAGACT
TATAAAAACAAAGTAAGCATAATAATACCTTATTGTGGGCTGCAGATCCACCATATTGATAAGC
TAGTGTGTCTCCCATTCTCTCGTATAACCCCATTAAAGTACTAGACAAAGGATCATCAAGTTCT
ATTGTTGGAGCATCTCTAATTCCTAAAGCATGAAGCTGTTGCCCTAGAGCAGCCCAACCATATG
CATATTGGGCAACATTTGTACGATCAAGGCAATCTATGCAGTTGGTCCGCAGCACTCCACTCTG
GAGCCTGCTAGGCTTGACATCATAATCACCATTTGCAACATTCTTACTTGGGCGGCAATTCTTC
TCTAATGAGTCATAATCCCTACTATCATCATCAGAACTATTATGTGGAGACGTGTCGGCA
						
					

			
		

Sequences
Splice junction sequence	ATCACCATTTGCAACATTCTTACTTGGGCGGCAATTCTTCTCTAATGAGTCATAATCCCTACTA TCATCATCAGAACTATTATGTGGAGACGTGTCGGCActtcctgctgcttgatccactctctctc atagctggcgtcaattgttttacttcagtgatgatattctctgatgaagacgtctctgcggttg aatatatt
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: 1069 Transcript exons: 7062278-7062392,7062683-7062859,7063144-7063335,7063884- 7063994,7064097-7064218,7065058-7065409 CTTCCTGCTGCTTGATCCACTCTCTCTCATAGCTGGCGTCAATTGTTTTACTTCAGTGATGATA TTCTCTGATGAAGACGTCTCTGCGGTTGAATATATTGTAAGCGCTGACGGCCTGGACAAGTGAT CGTTCTCACATAGATTTTCTGACGACGAAAGCCACTCAATATCAACGAAATTTGAGACACTAGA CATATCTTCTTGCTCGGACAAGTAAATGGAGCTACTACCATTATGTTGAACTTTTTGGACATCT CCAAAAAAATGTGTGCTAGGCATTGACGGAGTACACCTCGATAATGTTACATCACCGGCAGCTG GCATATCTGGTGATGATTCTGAAATTATATGAGTACGAGTCACTTGGTGTGACGACACAAAACC TCTATGTGATATGCTTTCATTCTTTCTACTCATTGCAGACATCGGAGTGTGACTTTCATGGAGA ATATTCCCATCTGATAAGCACCTCTTTACAAGAAACTTTTCATCTTCCCCCATGCTTATCTCTC CACTTCGTCCATTAGAGTGGGAATCTGAACGCAACTCCCAAACCGCCTGGCTCCCTTGTTCAGG CCGGAAAGTACCAAGAAATATATTAATGGCATCTTGTTTATCCGCATCCATATATGCGTTATTA TAATAACGTTGCAGAGTCCTCAAGAACTCTTGTGACTGGGTTGCTGCTCTCCACTGGCCTCGCC TTTCACTAAAAACCTTATTGTGGGCTGCAGATCCACCATATTGATAAGCTAGTGTGTCTCCCAT TCTCTCGTATAACCCCATTAAAGTACTAGACAAAGGATCATCAAGTTCTATTGTTGGAGCATCT CTAATTCCTAAAGCATGAAGCTGTTGCCCTAGAGCAGCCCAACCATATGCATATTGGGCAACAT TTGTACGATCAAGGCAATCTATGCAGTTGGTCCGCAGCACTCCACTCTGGAGCCTGCTAGGCTT GACATCATAATCACCATTTGCAACATTCTTACTTGGGCGGCAATTCTTCTCTAATGAGTCATAA TCCCTACTATCATCATCAGAACTATTATGTGGAGACGTGTCGGCA
Genomic sequence	CTTCCTGCTGCTTGATCCACTCTCTCTCATAGCTGGCGTCAATTGTTTTACTTCAGTGATGATA TTCTCTGATGAAGACGTCTCTGCGGTTGAATATATTGTAAGCGCTGACGGCCTGCCAAAATAAT GCAATGAGACTTGCACAGTAAAATTGACCAAACCGTGATTAAAAAAATTGTTGATCATTCATGA TGAATATTATTGTTATATTAGACATACGCAGATGGATATTTGAAAATTTTGGTTTTAACATTTT CAGATGGAACATAATCAGATGGATTTTTAGATTGATGGACGATATAATGCTATAGATGTGAAAT TTTAAGCTTCTATGTGACGACATCTGGTTGCTCTATTGACTGCTTAAAATCGTGAATTGATCTC TTTAGTGCACAGTAATTTTACCTGGACAAGTGATCGTTCTCACATAGATTTTCTGACGACGAAA GCCACTCAATATCAACGAAATTTGAGACACTAGACATATCTTCTTGCTCGGACAAGTAAATGGA GCTACTACCATTATGTTGAACTTTTTGGACATCTCCAAAAAAATGTGTGCTAGGCATTGACGGA GTACACCTACAAAGATTTTATAGCTGAATATTAAGACCAACAACAAAGACGAGTATTATTATGT ACTAGTACACACAAAATCTTAAGCTACATGAAGCATAAAGAGTAAAGACAACCACCTCATGAAT AATATATGAGCTATAATCATGGATAGAATTGACAAGCACAATAGAGCTTGACCCAGGAAAATTA TAATGCATACACAGCATGGACACTCAAGCTAAATGTACCAGCAGTACATATTTTATCTAGCTAT AATGAAGAAAAATGTAAGAAAGATTTAAACAAACCTCGATAATGTTACATCACCGGCAGCTGGC ATATCTGGTGATGATTCTGAAATTATATGAGTACGAGTCACTTGGTGTGACGACACAAAACCTC TATGTGATATGCTTTCATTCTTTCTACTCATTGCAGACATCGGAGTGTGACTTTCATGGAGAAT ATTCCCATCTGATAAGCACCTCTTTACAAGAAACCTGGAAACACAGTAATAAGAGCTATGATAT AGATGCGAAACAAAATCAATATATTTTTGTTCACTTTTAGAGGAAGGCTAATAGAGTTGGAAAC TTCATATACTAAAAAACAGAGCATTCTTAAGCTAGCAGAGAGTACAGATTTTGGTACAGTTCGA TGCAGTTAACAAACCAATCCTAGTTTCCCATGACCCCATATGTCTATAACAAAAGCCCATACCT CCTTGTATCTAAATCCTATGTTAATTTCGTATGATTAGGGTCACAACAGTTTTGTAGGATCTAA ACTGGAAGTTATGGTGGAGAATAAAATTCCAGTGAATGGATAATGTCGAGATATGTAGAGCCTA TATTTTTCAAATTCGTAAACTTAATGCATAGCAAATAGGTATAAGATATTAGAACTCATGTGAC TCATAAATCATCAAAATATGTCTAAAGAAGAAAATGGAAACCTCAAAACCTTTCTACCTACATG ACAGCAACTAATTATATAGGCATATTATTGTTGAATTTATGAAATCCAAGTTAGCAGTCACAGA ACCTACTTTTCATCTTCCCCCATGCTTATCTCTCCACTTCGTCCATTAGAGTGGGAATCTGAAC GCAACTCCCAAACCGCCTGGCTCCCTTGTTCAGGCCGGAAAGTACCAAGAAATCTGCATATAGA AATTCACAAAGGCCCAAAGAATTTCTGTAAGACTCTAAGAGATCATCGCGTAACATGGATATAT ACGAGAGAGTGACATAGAGCAGCTTACATATTAATGGCATCTTGTTTATCCGCATCCATATATG CGTTATTATAATAACGTTGCAGAGTCCTCAAGAACTCTTGTGACTGGGTTGCTGCTCTCCACTG GCCTCGCCTTTCACTAAAAACCTATTACACACCAAAAATTCTAGGAATCAACAAAGTGTATCCC AACAATAGTGAACATAATGGGAACTTGAGTCGGCTGCAGAAGATCAATACATCATAATTCAGTG CAGAACAATGAGACAGATTACAAAATGAATGTTAACTAAGTCTGATATCCTTTTTTTTTTTTTT TTTTTTTGTTTGTTGTCACCAAGTCTGATATCCTTCCAAGACAGTAAAATAACGAGGGCACAGT TGTGATTAAGATATAATATAGATCACATAACCCTTGTAATTCTTGGACTTCAAAGACCAAGATC AGAAAATAGACCAGATTTTCTTACAGCAATATCATCACAAATGATGAATTCCAAAAATTCAAAA AGAAAAACATTTTAAAATTTGCCAATCATGTATATGCTGCTTCTAACATAAGAATCAGATCATA ATAATAATGTCAGCTGAAAAGTGTCAGCTACAGAGAGGTTCAAATATAAGAGATGATTGATCAG CATGCATGACGGATTCCTGTTGTTAGACCGAGCAACAAGGATGTACAAAGAACACTAGATTTTT CATGAGCTTAGATTTACTTTAAGGTAAGGCTTGTTATTTTAATTGTAAACAATAAAAAATGTTG ACGAGAAAAGGGATACAAATCATCTCATGGAGCCAGTCATGAATCATTCCCAACCGAGACTAAA TGGAATCTATTTTGTGCATAATTAACAGTCCAGCGTTTAGTATCAACTAACTGTCTCTAGCAGA AGACTTAATATGAGACAGTTCCATATGAACATGAACAAAATTAGTCTGCTGCCATGTCAAGACT TATAAAAACAAAGTAAGCATAATAATACCTTATTGTGGGCTGCAGATCCACCATATTGATAAGC TAGTGTGTCTCCCATTCTCTCGTATAACCCCATTAAAGTACTAGACAAAGGATCATCAAGTTCT ATTGTTGGAGCATCTCTAATTCCTAAAGCATGAAGCTGTTGCCCTAGAGCAGCCCAACCATATG CATATTGGGCAACATTTGTACGATCAAGGCAATCTATGCAGTTGGTCCGCAGCACTCCACTCTG GAGCCTGCTAGGCTTGACATCATAATCACCATTTGCAACATTCTTACTTGGGCGGCAATTCTTC TCTAATGAGTCATAATCCCTACTATCATCATCAGAACTATTATGTGGAGACGTGTCGGCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.231232788

Conservation Information
Conserved circRNAs	NA
PMCS	0.231232788

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT5G20840_circ_g.2

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