Plant Circular RNA Database

Detail information of AT3G57300_circ_g.10

			
						 General Information
					
						CircRNA Name
						AT3G57300_circ_g.10
					
						ID in PlantcircBase
						ath_circ_027950
					
						Alias
						Ath_circ_FC2418
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 21205692-21207218  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT3G57300						
					
						Parent gene annotation
						
							DNA helicase INO80-like protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G57300_circ_g.9 AT3G57300_circ_g.11 AT3G57300_circ_g.12 						
					
						Support reads
						18
					
						Tissues
						root, 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  
						
							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
						AT3G57300.2:6
AT3G57300.1:6
AT3G57300.3:2
AT3G57300.4:6

General Information
CircRNA Name	AT3G57300_circ_g.10
ID in PlantcircBase	ath_circ_027950
Alias	Ath_circ_FC2418
Organism	Arabidpsis thaliana
Position	chr3: 21205692-21207218 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT3G57300
Parent gene annotation	DNA helicase INO80-like protein
Parent gene strand	+
Alternative splicing	AT3G57300_circ_g.9 AT3G57300_circ_g.11 AT3G57300_circ_g.12
Support reads	18
Tissues	root, 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	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	AT3G57300.2:6 AT3G57300.1:6 AT3G57300.3:2 AT3G57300.4:6

			
						 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  
						
							AGGAGATGCAACTTTGGAAGAGTTAGAAGATGTTGACCGACAGGATAACGGACAGGAACCTTTG
GAAGAACCGGAAAAGCCAAAATCCAGTAATAAAAAGgtaagcattcattgctcggacagaaatt
cggcatacagagttacagaagaattacatcaaccatggcttaagagactattaatcggttttgc
acgaacgt

									
								

					

						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: 981
Transcript exons: 21205692-21205952,21206038-21206145,21206262-21206356,21
206440-21206596,21206780-21206989,21207069-21207218
GTAAGCATTCATTGCTCGGACAGAAATTCGGCATACAGAGTTACAGAAGAATTACATCAACCAT
GGCTTAAGAGACTATTAATCGGTTTTGCACGAACGTCAGAAGCTAATGGACCCAGGAAGCCTAA
CAGCTTTCCACATCCTTTAATCCAAGAAATTGATTCAGAACTTCCAGTTGTGCAGCCTGCGCTT
CAACTGACACACAGAATATTTGGTTCTTGCCCTCCAATGCAAAGTTTTGACCCAGCAAAGTTGC
TCACGGACTCTGGGAAGCTGCAGACACTTGATATATTATTGAAGCGGCTTCGAGCTGGAAATCA
CAGGGTGCTCCTGTTTGCACAAATGACAAAGATGCTGAACATTCTCGAGGATTATATGAACTAT
AGAAAGTACAAGTACCTCAGGCTTGATGGATCCTCCACCATCATGGATCGCCGAGATATGGTTA
GGGATTTTCAGCATAGGAGCGATATTTTTGTATTCTTGCTGAGCACCAGAGCTGGAGGACTTGG
TATCAACTTGACGGCTGCAGACACTGTCATTTTCTATGAAAGTGATTGGAATCCCACCTTGGAT
TTACAAGCTATGGACAGGGCTCATCGTCTTGGACAGACAAAAGATGTTACTGTTTATCGTCTCA
TCTGTAAGGAGACGGTGGAAGAGAAAATTTTGCACAGGGCAAGTCAGAAAAATACAGTTCAACA
GCTTGTTATGACTGGAGGGCATGTTCAGGGTGATGATTTTCTTGGAGCTGCGGATGTGGTATCT
CTGCTAATGGATGATGCGGAGGCAGCACAACTGGAGCAGAAATTCAGAGAACTACCATTACAGG
TAAAGGACAGGCAGAAGAAAAAGACGAAACGTATCAGAATAGATGCTGAAGGAGATGCAACTTT
GGAAGAGTTAGAAGATGTTGACCGACAGGATAACGGACAGGAACCTTTGGAAGAACCGGAAAAG
CCAAAATCCAGTAATAAAAAG
						
					

						Genomic sequence
						
							GTAAGCATTCATTGCTCGGACAGAAATTCGGCATACAGAGTTACAGAAGAATTACATCAACCAT
GGCTTAAGAGACTATTAATCGGTTTTGCACGAACGTCAGAAGCTAATGGACCCAGGAAGCCTAA
CAGCTTTCCACATCCTTTAATCCAAGAAATTGATTCAGAACTTCCAGTTGTGCAGCCTGCGCTT
CAACTGACACACAGAATATTTGGTTCTTGCCCTCCAATGCAAAGTTTTGACCCAGCAAAGTTGC
TCACGGTAGTTTCTTTTCTGTTGCAACTTCCTTTTAAATTTAGTTGCTTTAATATGAGCCCATG
TTTCTAATCACAAATTTGGATTGTAGGACTCTGGGAAGCTGCAGACACTTGATATATTATTGAA
GCGGCTTCGAGCTGGAAATCACAGGGTGCTCCTGTTTGCACAAATGACAAAGATGCTGAACATT
CTCGAGGTAGTATCTAGACACAAGTCTTTGACCTCACTGTACAAATGAATTTGTAATTACATAT
AACAAGCATCCCTATCTACACCTTTGCTTTACATTTCTTTTATTTTATGTTTATGCAGGATTAT
ATGAACTATAGAAAGTACAAGTACCTCAGGCTTGATGGATCCTCCACCATCATGGATCGCCGAG
ATATGGTTAGGGATTTTCAGCATAGGTAGGATTTAACTTTCTCAAGCTTTTTTTTTTACGTTCC
CATGAGGCTTTCTGTGCACAATTGTAAACCATATATGGTTGCAGGAGCGATATTTTTGTATTCT
TGCTGAGCACCAGAGCTGGAGGACTTGGTATCAACTTGACGGCTGCAGACACTGTCATTTTCTA
TGAAAGTGATTGGAATCCCACCTTGGATTTACAAGCTATGGACAGGGCTCATCGTCTTGGACAG
ACAAAAGATGTCAGTGATTATTCTCTGCTTTTATTATTCTAATCGCTTTCATTTCCCAAAAAAA
AACTGTGCATTGAGAACCAATTTCTTTGTTGCTTCCTTATATAACCAAAGCTTCATACAAGTGA
ACAAGCATCTGCCAATGGGGTTATTTTCCTGATCTTTTTTTTCTGAAATGAAACCTCTTAATAG
GTTACTGTTTATCGTCTCATCTGTAAGGAGACGGTGGAAGAGAAAATTTTGCACAGGGCAAGTC
AGAAAAATACAGTTCAACAGCTTGTTATGACTGGAGGGCATGTTCAGGGTGATGATTTTCTTGG
AGCTGCGGATGTGGTATCTCTGCTAATGGATGATGCGGAGGCAGCACAACTGGAGCAGAAATTC
AGAGAACTACCATTACAGGTGGGGACGACATGCTTCTTACATTTAATATTTCACGAACTTAGAA
TTCTGCCACTCATAAATTCTTTACATCATCCAGGTAAAGGACAGGCAGAAGAAAAAGACGAAAC
GTATCAGAATAGATGCTGAAGGAGATGCAACTTTGGAAGAGTTAGAAGATGTTGACCGACAGGA
TAACGGACAGGAACCTTTGGAAGAACCGGAAAAGCCAAAATCCAGTAATAAAAAG
						
					

			
		

Sequences
Splice junction sequence	AGGAGATGCAACTTTGGAAGAGTTAGAAGATGTTGACCGACAGGATAACGGACAGGAACCTTTG GAAGAACCGGAAAAGCCAAAATCCAGTAATAAAAAGgtaagcattcattgctcggacagaaatt cggcatacagagttacagaagaattacatcaaccatggcttaagagactattaatcggttttgc acgaacgt
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: 981 Transcript exons: 21205692-21205952,21206038-21206145,21206262-21206356,21 206440-21206596,21206780-21206989,21207069-21207218 GTAAGCATTCATTGCTCGGACAGAAATTCGGCATACAGAGTTACAGAAGAATTACATCAACCAT GGCTTAAGAGACTATTAATCGGTTTTGCACGAACGTCAGAAGCTAATGGACCCAGGAAGCCTAA CAGCTTTCCACATCCTTTAATCCAAGAAATTGATTCAGAACTTCCAGTTGTGCAGCCTGCGCTT CAACTGACACACAGAATATTTGGTTCTTGCCCTCCAATGCAAAGTTTTGACCCAGCAAAGTTGC TCACGGACTCTGGGAAGCTGCAGACACTTGATATATTATTGAAGCGGCTTCGAGCTGGAAATCA CAGGGTGCTCCTGTTTGCACAAATGACAAAGATGCTGAACATTCTCGAGGATTATATGAACTAT AGAAAGTACAAGTACCTCAGGCTTGATGGATCCTCCACCATCATGGATCGCCGAGATATGGTTA GGGATTTTCAGCATAGGAGCGATATTTTTGTATTCTTGCTGAGCACCAGAGCTGGAGGACTTGG TATCAACTTGACGGCTGCAGACACTGTCATTTTCTATGAAAGTGATTGGAATCCCACCTTGGAT TTACAAGCTATGGACAGGGCTCATCGTCTTGGACAGACAAAAGATGTTACTGTTTATCGTCTCA TCTGTAAGGAGACGGTGGAAGAGAAAATTTTGCACAGGGCAAGTCAGAAAAATACAGTTCAACA GCTTGTTATGACTGGAGGGCATGTTCAGGGTGATGATTTTCTTGGAGCTGCGGATGTGGTATCT CTGCTAATGGATGATGCGGAGGCAGCACAACTGGAGCAGAAATTCAGAGAACTACCATTACAGG TAAAGGACAGGCAGAAGAAAAAGACGAAACGTATCAGAATAGATGCTGAAGGAGATGCAACTTT GGAAGAGTTAGAAGATGTTGACCGACAGGATAACGGACAGGAACCTTTGGAAGAACCGGAAAAG CCAAAATCCAGTAATAAAAAG
Genomic sequence	GTAAGCATTCATTGCTCGGACAGAAATTCGGCATACAGAGTTACAGAAGAATTACATCAACCAT GGCTTAAGAGACTATTAATCGGTTTTGCACGAACGTCAGAAGCTAATGGACCCAGGAAGCCTAA CAGCTTTCCACATCCTTTAATCCAAGAAATTGATTCAGAACTTCCAGTTGTGCAGCCTGCGCTT CAACTGACACACAGAATATTTGGTTCTTGCCCTCCAATGCAAAGTTTTGACCCAGCAAAGTTGC TCACGGTAGTTTCTTTTCTGTTGCAACTTCCTTTTAAATTTAGTTGCTTTAATATGAGCCCATG TTTCTAATCACAAATTTGGATTGTAGGACTCTGGGAAGCTGCAGACACTTGATATATTATTGAA GCGGCTTCGAGCTGGAAATCACAGGGTGCTCCTGTTTGCACAAATGACAAAGATGCTGAACATT CTCGAGGTAGTATCTAGACACAAGTCTTTGACCTCACTGTACAAATGAATTTGTAATTACATAT AACAAGCATCCCTATCTACACCTTTGCTTTACATTTCTTTTATTTTATGTTTATGCAGGATTAT ATGAACTATAGAAAGTACAAGTACCTCAGGCTTGATGGATCCTCCACCATCATGGATCGCCGAG ATATGGTTAGGGATTTTCAGCATAGGTAGGATTTAACTTTCTCAAGCTTTTTTTTTTACGTTCC CATGAGGCTTTCTGTGCACAATTGTAAACCATATATGGTTGCAGGAGCGATATTTTTGTATTCT TGCTGAGCACCAGAGCTGGAGGACTTGGTATCAACTTGACGGCTGCAGACACTGTCATTTTCTA TGAAAGTGATTGGAATCCCACCTTGGATTTACAAGCTATGGACAGGGCTCATCGTCTTGGACAG ACAAAAGATGTCAGTGATTATTCTCTGCTTTTATTATTCTAATCGCTTTCATTTCCCAAAAAAA AACTGTGCATTGAGAACCAATTTCTTTGTTGCTTCCTTATATAACCAAAGCTTCATACAAGTGA ACAAGCATCTGCCAATGGGGTTATTTTCCTGATCTTTTTTTTCTGAAATGAAACCTCTTAATAG GTTACTGTTTATCGTCTCATCTGTAAGGAGACGGTGGAAGAGAAAATTTTGCACAGGGCAAGTC AGAAAAATACAGTTCAACAGCTTGTTATGACTGGAGGGCATGTTCAGGGTGATGATTTTCTTGG AGCTGCGGATGTGGTATCTCTGCTAATGGATGATGCGGAGGCAGCACAACTGGAGCAGAAATTC AGAGAACTACCATTACAGGTGGGGACGACATGCTTCTTACATTTAATATTTCACGAACTTAGAA TTCTGCCACTCATAAATTCTTTACATCATCCAGGTAAAGGACAGGCAGAAGAAAAAGACGAAAC GTATCAGAATAGATGCTGAAGGAGATGCAACTTTGGAAGAGTTAGAAGATGTTGACCGACAGGA TAACGGACAGGAACCTTTGGAAGAACCGGAAAAGCCAAAATCCAGTAATAAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.228361285

Conservation Information
Conserved circRNAs	NA
PMCS	0.228361285

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21205920-21207215(+)
						
						Potential amino acid sequence
						
							MQSFDPAKLLTDSGKLQTLDILLKRLRAGNHRVLLFAQMTKMLNILEDYMNYRKYKYLRLDGSS
TIMDRRDMVRDFQHRSDIFVFLLSTRAGGLGINLTAADTVIFYESDWNPTLDLQAMDRAHRLGQ
TKDVTVYRLICKETVEEKILHRASQKNTVQQLVMTGGHVQGDDFLGAADVVSLLMDDAEAAQLE
QKFRELPLQVKDRQKKKTKRIRIDAEGDATLEELEDVDRQDNGQEPLEEPEKPKSSNKKVSIHC
SDRNSAYRVTEELHQPWLKRLLIGFARTSEANGPRKPNSFPHPLIQEIDSELPVVQPALQLTHR
IFGSCPPMQSFDPAKLLTDSGKLQTLDILLKRLRAGNHRVLLFAQMTKMLNILEDYMNYRKYKY
LRLDGSSTIMDRRDMVRDFQHRSDIFVFLLSTRAGGLGINLTAADTVIFYESDWNPTLDLQAMD
RAHRLGQTKDVTVYRLICKETVEEKILHRASQKNTVQQLVMTGGHVQGDDFLGAADVVSLLMDD
AEAAQLEQKFRELPLQVKDRQKKKTKRIRIDAEGDATLEELEDVDRQDNGQEPLEEPEKPKSSN
KKVSIHCSDRNSAYRVTEELHQPWLKRLLIGFARTSEANGPRKPNSFPHPLIQEIDSELPVVQP
ALQLTHRIFGSCPPMQSFDPAKLLTDSGKLQTLDILLKRLRAGNHRVLLFAQMTKMLNILEDYM
NYRKYKYLRLDGSSTIMDRRDMVRDFQHRSDIFVFLLSTRAGGLGINLTAADTVIFYESDWNPT
LDLQAMDRAHRLGQTKDVTVYRLICKETVEEKILHRASQKNTVQQLVMTGGHVQGDDFLGAADV
VSLLMDDAEAAQLEQKFRELPLQVKDRQKKKTKRIRIDAEGDATLEELEDVDRQDNGQEPLEEP
EKPKSSNKKVSIHCSDRNSAYRVTEELHQPWLKRLLIGFARTSEANGPRKPNSFPHPLIQEIDS
ELPVVQPALQLTHRIFGSCPPMQSFDPAKLLTDSGKLQTLDILLKRLRAGNHRVLLFAQMTKML
NILEDYMNYRKYKYLRLDGSSTIMDRRDMVRDFQHRSDIFVFLLSTRAGGLGINLTAADTVIFY
ESDWNPTLDLQAMDRAHRLGQTKDVTVYRLICKETVEEKILHRASQKNTVQQLVMTGGHVQGDD
FLGAADVVSLLMDDAEAAQLEQKFRELPLQVKDRQKKKTKRIRIDAEGDATLEELEDVDRQDNG
QEPLEEPEKPKSSNKK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21205920-21207215(+)
Potential amino acid sequence	MQSFDPAKLLTDSGKLQTLDILLKRLRAGNHRVLLFAQMTKMLNILEDYMNYRKYKYLRLDGSS TIMDRRDMVRDFQHRSDIFVFLLSTRAGGLGINLTAADTVIFYESDWNPTLDLQAMDRAHRLGQ TKDVTVYRLICKETVEEKILHRASQKNTVQQLVMTGGHVQGDDFLGAADVVSLLMDDAEAAQLE QKFRELPLQVKDRQKKKTKRIRIDAEGDATLEELEDVDRQDNGQEPLEEPEKPKSSNKKVSIHC SDRNSAYRVTEELHQPWLKRLLIGFARTSEANGPRKPNSFPHPLIQEIDSELPVVQPALQLTHR IFGSCPPMQSFDPAKLLTDSGKLQTLDILLKRLRAGNHRVLLFAQMTKMLNILEDYMNYRKYKY LRLDGSSTIMDRRDMVRDFQHRSDIFVFLLSTRAGGLGINLTAADTVIFYESDWNPTLDLQAMD RAHRLGQTKDVTVYRLICKETVEEKILHRASQKNTVQQLVMTGGHVQGDDFLGAADVVSLLMDD AEAAQLEQKFRELPLQVKDRQKKKTKRIRIDAEGDATLEELEDVDRQDNGQEPLEEPEKPKSSN KKVSIHCSDRNSAYRVTEELHQPWLKRLLIGFARTSEANGPRKPNSFPHPLIQEIDSELPVVQP ALQLTHRIFGSCPPMQSFDPAKLLTDSGKLQTLDILLKRLRAGNHRVLLFAQMTKMLNILEDYM NYRKYKYLRLDGSSTIMDRRDMVRDFQHRSDIFVFLLSTRAGGLGINLTAADTVIFYESDWNPT LDLQAMDRAHRLGQTKDVTVYRLICKETVEEKILHRASQKNTVQQLVMTGGHVQGDDFLGAADV VSLLMDDAEAAQLEQKFRELPLQVKDRQKKKTKRIRIDAEGDATLEELEDVDRQDNGQEPLEEP EKPKSSNKKVSIHCSDRNSAYRVTEELHQPWLKRLLIGFARTSEANGPRKPNSFPHPLIQEIDS ELPVVQPALQLTHRIFGSCPPMQSFDPAKLLTDSGKLQTLDILLKRLRAGNHRVLLFAQMTKML NILEDYMNYRKYKYLRLDGSSTIMDRRDMVRDFQHRSDIFVFLLSTRAGGLGINLTAADTVIFY ESDWNPTLDLQAMDRAHRLGQTKDVTVYRLICKETVEEKILHRASQKNTVQQLVMTGGHVQGDD FLGAADVVSLLMDDAEAAQLEQKFRELPLQVKDRQKKKTKRIRIDAEGDATLEELEDVDRQDNG QEPLEEPEKPKSSNKK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT3G57300_circ_g.10

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