Plant Circular RNA Database

Detail information of AT1G28715_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G28715_circ_g.3
					
						ID in PlantcircBase
						ath_circ_004736
					
						Alias
						1:10097934-10101935
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 10097934-10101935  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G28715						
					
						Parent gene annotation
						
							lncRNA
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G28715_circ_g.1 AT1G28715_circ_g.2 AT1G28715_circ_g.4 AT1G28715_circ_g.5 						
					
						Support reads
						1/1
					
						Tissues
						root
					
						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
						AT1G28715.1:6

General Information
CircRNA Name	AT1G28715_circ_g.3
ID in PlantcircBase	ath_circ_004736
Alias	1:10097934-10101935
Organism	Arabidpsis thaliana
Position	chr1: 10097934-10101935 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G28715
Parent gene annotation	lncRNA
Parent gene strand	-
Alternative splicing	AT1G28715_circ_g.1 AT1G28715_circ_g.2 AT1G28715_circ_g.4 AT1G28715_circ_g.5
Support reads	1/1
Tissues	root
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	AT1G28715.1:6

			
						 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  
						
							CAATGGAATATAAGAGCATACCGTTGTCACGTCCTCTCAGTAAACTTCATGTAGGGGGGACTGT
CATCTTTTGTAAGAAGCCAGATCCAAAAAGAATGAGcttggctttcacgtcgtggagctagaaa
acacttttttggataatggattgaacacagaacatcgctagctgaattctgccatttcatgccc
cattaact

									
								

					

						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
						
							CTTGGCTTTCACGTCGTGGAGCTAGAAAACACTTTTTTGGATAATGGATTGAACACAGAACATC
GCTAGCTGAATTCTGCCATTTCATGCCCCATTAACTTTGTAAGCGAACTATTTAAGTTCCAGCT
AGGAAATGTTTTCCATATAAGGTTGTCCTTTTGTTCATATTCTTCAAAGATAACAGTGGGCATT
TACCTGATATTTCATCAAGATTAGATTACAATACTCCAACTTGACTATTACGTAGTGGAAGACA
ACATAAAGAACTAGATCTAAAATGTAGCTATCTTTTTAGATTTCTCAACAAGAATACATTTTAA
TAACAGATACAAGAACCAAATGTAAAATAGTTTTAACTTACACTAACTGTACTTTTCCACAACA
TATTAGATGGATTAAACACTCTTTTATACCATAGTATTCGAACCAGAGGAACTACACTAGGAGA
TCCTAAAATAGATTACACTAAGAAGAAAAAAACTTCTACCAAGAATTATTCAGGTTAGGGAATT
AAATTCAGCAGATAACATCTAGCCTAAAGCCTCTGGACTAACTACTAAGTACTAACTGATGAAA
GAAATAAGAAGAAACTATCTTTACATCCGATACTGCAAATCTAAATAGATCCTAACATCATGGT
TTCAGCTCGTGCTACAGATTCTAATGCCAACAACTTGTGCTGCAGATATAAAGTGTGAAACGGA
TTTAAACAAACAACAGGGCATTTGGTCTAGTGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCC
GAGTTCGATTCTCGGAATGCCCCTTTGACTTTTTGGAAAACAAATGTTCCAAACGCCAGCTAAC
ATTTCATCAATACTAAATTACAGACTATCCACCTTACAATTAAGCCCTGAAAGTCAACTGATAG
ATCCCAGATCTAAAAAGTAATTTCTGTCTTAGAAGATCTAAACAAGAAACCATTTGAACGCCAT
ATTCAAAATTAATTAAAGAATAGTTTGAACTTACTGCATCTTGCCTGCTTAATCCCGAATAGAG
CCCTCAAAAGATAAACAAACCATCAAGAGTGAATTTCCTGTAATAATAGACTGAAGCATGAATT
CTCTTTTCCACATGATTAACAACATCACAGTGCTACAATGTAACTATATTAACAACAGGGCATT
TGGTCTAGTGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGAGTTCGATTCTCGGAATGCCC
CGTTATAATTTTTCTTAATAAATGTGTCCAAACCAAAATGAGATATGCATGAACAAAGAGGTTT
TTTTTTTTTTTTCTCTACTGCAAACCGTACATTTCAAGTAACGTAAATGCAACTGATCTTTTTA
ATTGGATTTCATTCGAAACAGATCTCATAGATTTCACTAACAAACATTCTACAAAGACTAAAAT
ATTTCTTTAGTAGAAGTCAACTAAGAAACCGAGATCAGAATGTGACCAAATCTTAAACTTTTTA
ACTACATTGCTTAACAAGAGGGCATTTGGTCTAGTGGTATGATTCTCGCTTAGGGTGCGAGAGG
TCCCGAGTTCAATTCTCGGAATGCCCCAATGACTTTTTATATTAACATGTTATATATCTGTTTT
AAATGCCAGCTTGCTTAAAAACCAACTGTAGACCATATGTTTCAATCCTAACATTTTTCACAAT
CTTAGAGTTTCATAATTAACTACATAATGCAAAACAAATAACTTACCACAGTTCCGCGTCCAAT
CTATATGTCTTTTTAATTAATAAAGACAGACGTTTTGTATGCTGCCAGAGATTGTGCTGCAGAA
ATAGCAAAACAATCCTTAATAAGCATCTAACGAAAGCAAAGGGAAGCAAATATTCTCGTGAAGA
AAAAGTAGAATGCGTTAATTTAACAAGAATAAGAACAGGGCATTTGGTCTAGTGGTATGATTCT
CGCTTTGGGTGCGAGAGGTCCCGAGTTCGATTCTCGGAATGCCCCATTGACTTTTTCCAAAAAC
ATTTGTTCTAAATGCCAGCTACATATCCCCATTGAATTTTTCAACAAAACAATGCATGTACAAA
TATTTTTTATTTATCTCAGCAAGAGGAAACAAAATAACACCTCCCCATAAGGTTTCATTATTTA
ACAGCTTTAGTGCCAAGGAAGATAAGAACGTACCACTGTTTTAACGAGTAACTACATATAGGTC
GGCCCTTCACATTTTGTAAGCTGCCGATTTCACAAAGTATGATCTGCATAAATAATAAAGGAGT
CATCATTAAGCATATAACTGAATGCAAAAGGTAAAAAAATATCTCTAAACGAAAGGCTAGAATG
CTAATAGAAGGCATTAACTGAACAACATATAAACAGGGCATTTGGTCTAGTGGTATGATTCTCG
CTTTGGGTGCGAGAGGTCCCGAGTTCGATTCTCGGAATGCCCCCATTGACTTTTTGTAAAACAT
ACGTTCTAAATGCCAGCTCAAACTAATTTGCATACAACTTTGTACTTGCTTCTGGATTTGCCAC
AGATCACATTCATCATTTCAACGATGTGTATCTACCTAAAACTCCACCAACACTAATTTACAAA
CAATCCACCGGAAAGTCAACTGATGGAATTTCAGATGGTTCAATTATCATCTTCAAGCACCAGA
TGTATAATAGACTGAATCTAAGCTAACTGTAAGTTTTAAAAGTATAGACGAGCATAGAAAATGT
TTGAACCATAATGCATATACAACAGGGCATTTGGCCTTGTGGTATGATTTTCGCTTTGGGTGCT
AGAGGTCCCGAGTAAGATCTTTATTTAGTCCTAGTGCTTTCGCAATCAAATCCAAGTAAGAACC
ATATATTACCATCTCATTTCAGTAAGTTAGTTAAGGTGCCAAAGGAAAAGAAGAACATACCGGT
CTTCACGTACAATCAACAAATCTTTTTAACCAGTAACCTTCATAAAGGGGGGACCATAATGTTT
TGTACGCAGCCAGCTTCACCAAAAATGAGCTGCATAAGCAGAAATGGATGTTCGATTGAGTATC
TACTGGAAAAGCAAACGGAGCAAAAAAATCACTGAAACAAAATGGAAATTGCTTATAGGAGGCA
TTAACTGAACAACATATAAACAGGGCATTTGGTCTAGTGGTATGATTCTCGCTTTGGGTGCGAG
AGGTCCCGAGTTCGATTCTCGGAATGCCCCTTTGACTTTTTGTGAAACCATACATTGTAAGTTC
CAGTTCAGAATTTTTGCATAGAAATTAATATTTGGTGCCAGGTTTTCACAGATCACATTCAGGA
GTTCAACTATCAGTTTTTACCTTTAACTTCAGCAACTCTGGGTATTGTCTAGAGAGTCAGTCAA
TAGCTAAGCATTTGATATGGCAGAATGATCAGTCAACTGTTAAAACAAACAAAATCATAGGACT
AACTCTTCTAATGATTTTTAGCAGTAGAGGTTTAAACAACTGGACCAATATATTTCTGGAGTAT
TTCCATACGTAGTACTACAATACAAACCAGATATTCAAACAAAAATGCAAAGAAAAATTGACTG
GGATTTCAGTTGAAAGAGATTAAGAGATCTCATAGATTAGAACTAGGAACATCCTACTACTAAA
ATATTCATTTTGTAGTCAACTAAGACAACAGGATCAAAATCTGACCAAATCTACAACTTTTAAA
CTAAATTGCTTAATAACAGGGCATTTGGTCTAGTGGTATGATTCTCGCTTTGGGTGCGAGAGGT
CCCGAGTTCGATTCTCGGAATGCCCCATTGACTTTTTTGTTAAATGATCTAAATTCAAGCAGCA
AATTGGTTTATTCAGTGCTAGTTCTATCGTAGATCATGATCCAAGTAAGAACCACATATTACCC
TTTCATTTCAGCTAGAGAAAATACAAACAAAATGCACCTTAAATTTTTATTAGTGCTTAATGCA
ATGGAATATAAGAGCATACCGTTGTCACGTCCTCTCAGTAAACTTCATGTAGGGGGGACTGTCA
TCTTTTGTAAGAAGCCAGATCCAAAAAGAATGAG
						
					

			
		

Sequences
Splice junction sequence	CAATGGAATATAAGAGCATACCGTTGTCACGTCCTCTCAGTAAACTTCATGTAGGGGGGACTGT CATCTTTTGTAAGAAGCCAGATCCAAAAAGAATGAGcttggctttcacgtcgtggagctagaaa acacttttttggataatggattgaacacagaacatcgctagctgaattctgccatttcatgccc cattaact
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	CTTGGCTTTCACGTCGTGGAGCTAGAAAACACTTTTTTGGATAATGGATTGAACACAGAACATC GCTAGCTGAATTCTGCCATTTCATGCCCCATTAACTTTGTAAGCGAACTATTTAAGTTCCAGCT AGGAAATGTTTTCCATATAAGGTTGTCCTTTTGTTCATATTCTTCAAAGATAACAGTGGGCATT TACCTGATATTTCATCAAGATTAGATTACAATACTCCAACTTGACTATTACGTAGTGGAAGACA ACATAAAGAACTAGATCTAAAATGTAGCTATCTTTTTAGATTTCTCAACAAGAATACATTTTAA TAACAGATACAAGAACCAAATGTAAAATAGTTTTAACTTACACTAACTGTACTTTTCCACAACA TATTAGATGGATTAAACACTCTTTTATACCATAGTATTCGAACCAGAGGAACTACACTAGGAGA TCCTAAAATAGATTACACTAAGAAGAAAAAAACTTCTACCAAGAATTATTCAGGTTAGGGAATT AAATTCAGCAGATAACATCTAGCCTAAAGCCTCTGGACTAACTACTAAGTACTAACTGATGAAA GAAATAAGAAGAAACTATCTTTACATCCGATACTGCAAATCTAAATAGATCCTAACATCATGGT TTCAGCTCGTGCTACAGATTCTAATGCCAACAACTTGTGCTGCAGATATAAAGTGTGAAACGGA TTTAAACAAACAACAGGGCATTTGGTCTAGTGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCC GAGTTCGATTCTCGGAATGCCCCTTTGACTTTTTGGAAAACAAATGTTCCAAACGCCAGCTAAC ATTTCATCAATACTAAATTACAGACTATCCACCTTACAATTAAGCCCTGAAAGTCAACTGATAG ATCCCAGATCTAAAAAGTAATTTCTGTCTTAGAAGATCTAAACAAGAAACCATTTGAACGCCAT ATTCAAAATTAATTAAAGAATAGTTTGAACTTACTGCATCTTGCCTGCTTAATCCCGAATAGAG CCCTCAAAAGATAAACAAACCATCAAGAGTGAATTTCCTGTAATAATAGACTGAAGCATGAATT CTCTTTTCCACATGATTAACAACATCACAGTGCTACAATGTAACTATATTAACAACAGGGCATT TGGTCTAGTGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGAGTTCGATTCTCGGAATGCCC CGTTATAATTTTTCTTAATAAATGTGTCCAAACCAAAATGAGATATGCATGAACAAAGAGGTTT TTTTTTTTTTTTCTCTACTGCAAACCGTACATTTCAAGTAACGTAAATGCAACTGATCTTTTTA ATTGGATTTCATTCGAAACAGATCTCATAGATTTCACTAACAAACATTCTACAAAGACTAAAAT ATTTCTTTAGTAGAAGTCAACTAAGAAACCGAGATCAGAATGTGACCAAATCTTAAACTTTTTA ACTACATTGCTTAACAAGAGGGCATTTGGTCTAGTGGTATGATTCTCGCTTAGGGTGCGAGAGG TCCCGAGTTCAATTCTCGGAATGCCCCAATGACTTTTTATATTAACATGTTATATATCTGTTTT AAATGCCAGCTTGCTTAAAAACCAACTGTAGACCATATGTTTCAATCCTAACATTTTTCACAAT CTTAGAGTTTCATAATTAACTACATAATGCAAAACAAATAACTTACCACAGTTCCGCGTCCAAT CTATATGTCTTTTTAATTAATAAAGACAGACGTTTTGTATGCTGCCAGAGATTGTGCTGCAGAA ATAGCAAAACAATCCTTAATAAGCATCTAACGAAAGCAAAGGGAAGCAAATATTCTCGTGAAGA AAAAGTAGAATGCGTTAATTTAACAAGAATAAGAACAGGGCATTTGGTCTAGTGGTATGATTCT CGCTTTGGGTGCGAGAGGTCCCGAGTTCGATTCTCGGAATGCCCCATTGACTTTTTCCAAAAAC ATTTGTTCTAAATGCCAGCTACATATCCCCATTGAATTTTTCAACAAAACAATGCATGTACAAA TATTTTTTATTTATCTCAGCAAGAGGAAACAAAATAACACCTCCCCATAAGGTTTCATTATTTA ACAGCTTTAGTGCCAAGGAAGATAAGAACGTACCACTGTTTTAACGAGTAACTACATATAGGTC GGCCCTTCACATTTTGTAAGCTGCCGATTTCACAAAGTATGATCTGCATAAATAATAAAGGAGT CATCATTAAGCATATAACTGAATGCAAAAGGTAAAAAAATATCTCTAAACGAAAGGCTAGAATG CTAATAGAAGGCATTAACTGAACAACATATAAACAGGGCATTTGGTCTAGTGGTATGATTCTCG CTTTGGGTGCGAGAGGTCCCGAGTTCGATTCTCGGAATGCCCCCATTGACTTTTTGTAAAACAT ACGTTCTAAATGCCAGCTCAAACTAATTTGCATACAACTTTGTACTTGCTTCTGGATTTGCCAC AGATCACATTCATCATTTCAACGATGTGTATCTACCTAAAACTCCACCAACACTAATTTACAAA CAATCCACCGGAAAGTCAACTGATGGAATTTCAGATGGTTCAATTATCATCTTCAAGCACCAGA TGTATAATAGACTGAATCTAAGCTAACTGTAAGTTTTAAAAGTATAGACGAGCATAGAAAATGT TTGAACCATAATGCATATACAACAGGGCATTTGGCCTTGTGGTATGATTTTCGCTTTGGGTGCT AGAGGTCCCGAGTAAGATCTTTATTTAGTCCTAGTGCTTTCGCAATCAAATCCAAGTAAGAACC ATATATTACCATCTCATTTCAGTAAGTTAGTTAAGGTGCCAAAGGAAAAGAAGAACATACCGGT CTTCACGTACAATCAACAAATCTTTTTAACCAGTAACCTTCATAAAGGGGGGACCATAATGTTT TGTACGCAGCCAGCTTCACCAAAAATGAGCTGCATAAGCAGAAATGGATGTTCGATTGAGTATC TACTGGAAAAGCAAACGGAGCAAAAAAATCACTGAAACAAAATGGAAATTGCTTATAGGAGGCA TTAACTGAACAACATATAAACAGGGCATTTGGTCTAGTGGTATGATTCTCGCTTTGGGTGCGAG AGGTCCCGAGTTCGATTCTCGGAATGCCCCTTTGACTTTTTGTGAAACCATACATTGTAAGTTC CAGTTCAGAATTTTTGCATAGAAATTAATATTTGGTGCCAGGTTTTCACAGATCACATTCAGGA GTTCAACTATCAGTTTTTACCTTTAACTTCAGCAACTCTGGGTATTGTCTAGAGAGTCAGTCAA TAGCTAAGCATTTGATATGGCAGAATGATCAGTCAACTGTTAAAACAAACAAAATCATAGGACT AACTCTTCTAATGATTTTTAGCAGTAGAGGTTTAAACAACTGGACCAATATATTTCTGGAGTAT TTCCATACGTAGTACTACAATACAAACCAGATATTCAAACAAAAATGCAAAGAAAAATTGACTG GGATTTCAGTTGAAAGAGATTAAGAGATCTCATAGATTAGAACTAGGAACATCCTACTACTAAA ATATTCATTTTGTAGTCAACTAAGACAACAGGATCAAAATCTGACCAAATCTACAACTTTTAAA CTAAATTGCTTAATAACAGGGCATTTGGTCTAGTGGTATGATTCTCGCTTTGGGTGCGAGAGGT CCCGAGTTCGATTCTCGGAATGCCCCATTGACTTTTTTGTTAAATGATCTAAATTCAAGCAGCA AATTGGTTTATTCAGTGCTAGTTCTATCGTAGATCATGATCCAAGTAAGAACCACATATTACCC TTTCATTTCAGCTAGAGAAAATACAAACAAAATGCACCTTAAATTTTTATTAGTGCTTAATGCA ATGGAATATAAGAGCATACCGTTGTCACGTCCTCTCAGTAAACTTCATGTAGGGGGGACTGTCA TCTTTTGTAAGAAGCCAGATCCAAAAAGAATGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.105055631

Conservation Information
Conserved circRNAs	NA
PMCS	0.105055631

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

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT1G28715_circ_g.3

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