Plant Circular RNA Database

Detail information of AT1G24070_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G24070_circ_g.3
					
						ID in PlantcircBase
						ath_circ_004119
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 8517575-8519063  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT1G24070						
					
						Parent gene annotation
						
							Probable mannan synthase 10
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G24070_circ_g.1 AT1G24070_circ_g.2 						
					
						Support reads
						41
					
						Tissues
						inflorescences
					
						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
						AT1G24070.1:5
AT1G24070.2:5

General Information
CircRNA Name	AT1G24070_circ_g.3
ID in PlantcircBase	ath_circ_004119
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 8517575-8519063 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT1G24070
Parent gene annotation	Probable mannan synthase 10
Parent gene strand	-
Alternative splicing	AT1G24070_circ_g.1 AT1G24070_circ_g.2
Support reads	41
Tissues	inflorescences
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	AT1G24070.1:5 AT1G24070.2:5

			
						 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  
						
							CCTTGATGGTTTGATCAGTGGAATCATCTAAAACTTGAACAATTAGGCGGTCCAATGGCCATAT
TAGTCTACATGCAGCACCTATAGATAATTGAAGGACcttattgcgaataatctccataatcatt
ttcctgaagagattagctggaccacaagaccatcgatgttgctggaatctaaaggccttaaact
tgcttggt

									
								

					

						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: 714
Transcript exons: 8517575-8517688,8518079-8518215,8518304-8518414,8518629-
8518881,8518965-8519063
CTTATTGCGAATAATCTCCATAATCATTTTCCTGAAGAGATTAGCTGGACCACAAGACCATCGA
TGTTGCTGGAATCTAAAGGCCTTAAACTTGCTTGGTAACTCGCTTTTCACCGTGAGGTCATTGA
GAAAGACAAATTTCCAGCCGAGAAGACCAGCACGAACGGCCAAGTCCATGTCCTCTACAGTAGT
CCGGTCATGCCATCCTCCAGCTTCTTCCATCGCGGCCATTCTCCATACACCCGCAGTTCCATTG
AAGCTAAAGAAGGCATGTCTAGTGGATCCAGATTCTTGCTCTGCCATAAAGTGGTAGTTGAGGG
ACATCTCTTGCATCCTCGTCATCAAGCACTTGTTTGCGTTCATGAATCTCCATCGGGCTTGAAC
CAGAGCGACCTCGGGGTTATGAACGAGGAAGGGGACAGAGTGTTGGAGGTAATCAGGCTCCGGT
TGGAAGTCTGCGTCGAAGATGACGACATAATTGCATAGCTTCACGTAGTTGTGCTTCATGCCTT
CTTTAAGAGCTCCGGCTTTGTAGCCATTTCTGTTGTCTCTCCTCTCACACTTTATATTTACACC
TTTGCTTTCCCATTTTGCACACTCTGTGTTCACCAGCTCCTTGATGGTTTGATCAGTGGAATCA
TCTAAAACTTGAACAATTAGGCGGTCCAATGGCCATATTAGTCTACATGCAGCACCTATAGATA
ATTGAAGGAC
						
					

						Genomic sequence
						
							CTTATTGCGAATAATCTCCATAATCATTTTCCTGAAGAGATTAGCTGGACCACAAGACCATCGA
TGTTGCTGGAATCTAAAGGCCTTAAACTTGCTTGGTAACTCGCTTTTCACCTACAAACTCAGTG
TTCATATACATAATGTAATGATTATAATTTAGTAATTATTATTTTATAGCAATGCATCACTATA
TATATATATAGAATTATAGATATCATTGCACATCAAGACAAGAGTGCCACACTAGTCAGAAACT
ATGTCCATAACCAAATTCTATAAAATCTACCACAATAACTATAGTTCAAAAGGGGAGTTTCTAT
GTGACTTTAATAAAGTTATAGTTTCAAAAGTGGAAGCATACAAAAAAAAAGTGGGAGTGTCTAT
GTAAAGAAAGCACTAGTAAATGTTGGATATTAAATCCACATGGGAACAGTTACATAATGTACGA
AAGATGCAATGAGGGCTTATTTACAGCAATTAATAGGTAGGGATAAAATCAAGTACCGTGAGGT
CATTGAGAAAGACAAATTTCCAGCCGAGAAGACCAGCACGAACGGCCAAGTCCATGTCCTCTAC
AGTAGTCCGGTCATGCCATCCTCCAGCTTCTTCCATCGCGGCCATTCTCCATACACCCGCAGTT
CCTGAAAGAGATATACCAAAACCATATTTATAAAATAAGTACCTAAAATTTATCAAAAATTCAA
AACATGTAATGATAACCAAATACACCATTGAAGCTAAAGAAGGCATGTCTAGTGGATCCAGATT
CTTGCTCTGCCATAAAGTGGTAGTTGAGGGACATCTCTTGCATCCTCGTCATCAAGCACTTGTT
TGCGTTCACTGCAATGAACCCCACACACACATACAATCACTCAGTTTGAAAATAAACTTTGTTA
GGATCCTTAATTATGTACATAGCATTGTTACGAAAGATATAAGTTCAGTTTATCACAACCTAGA
TATGGAGTAAAAATTTACAAATATTGATAGTCTCATATAAGTTAATAGTTGTAAATGTTTAGGT
ACGTAAAATTGTCTACCATAATGTACGTACTGAATCTCCATCGGGCTTGAACCAGAGCGACCTC
GGGGTTATGAACGAGGAAGGGGACAGAGTGTTGGAGGTAATCAGGCTCCGGTTGGAAGTCTGCG
TCGAAGATGACGACATAATTGCATAGCTTCACGTAGTTGTGCTTCATGCCTTCTTTAAGAGCTC
CGGCTTTGTAGCCATTTCTGTTGTCTCTCCTCTCACACTTTATATTTACACCTTTGCTTTCCCA
TTTTGCACACTCTGTGTTCACCAGCTCCTGAAACTCAATCCTCCTCACATTAAATATCTTACAA
TACATTATATGTGTTCAAATAAATCAACAAACTTGGTCGGCAAGACCTTGATGGTTTGATCAGT
GGAATCATCTAAAACTTGAACAATTAGGCGGTCCAATGGCCATATTAGTCTACATGCAGCACCT
ATAGATAATTGAAGGAC
						
					

			
		

Sequences
Splice junction sequence	CCTTGATGGTTTGATCAGTGGAATCATCTAAAACTTGAACAATTAGGCGGTCCAATGGCCATAT TAGTCTACATGCAGCACCTATAGATAATTGAAGGACcttattgcgaataatctccataatcatt ttcctgaagagattagctggaccacaagaccatcgatgttgctggaatctaaaggccttaaact tgcttggt
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: 714 Transcript exons: 8517575-8517688,8518079-8518215,8518304-8518414,8518629- 8518881,8518965-8519063 CTTATTGCGAATAATCTCCATAATCATTTTCCTGAAGAGATTAGCTGGACCACAAGACCATCGA TGTTGCTGGAATCTAAAGGCCTTAAACTTGCTTGGTAACTCGCTTTTCACCGTGAGGTCATTGA GAAAGACAAATTTCCAGCCGAGAAGACCAGCACGAACGGCCAAGTCCATGTCCTCTACAGTAGT CCGGTCATGCCATCCTCCAGCTTCTTCCATCGCGGCCATTCTCCATACACCCGCAGTTCCATTG AAGCTAAAGAAGGCATGTCTAGTGGATCCAGATTCTTGCTCTGCCATAAAGTGGTAGTTGAGGG ACATCTCTTGCATCCTCGTCATCAAGCACTTGTTTGCGTTCATGAATCTCCATCGGGCTTGAAC CAGAGCGACCTCGGGGTTATGAACGAGGAAGGGGACAGAGTGTTGGAGGTAATCAGGCTCCGGT TGGAAGTCTGCGTCGAAGATGACGACATAATTGCATAGCTTCACGTAGTTGTGCTTCATGCCTT CTTTAAGAGCTCCGGCTTTGTAGCCATTTCTGTTGTCTCTCCTCTCACACTTTATATTTACACC TTTGCTTTCCCATTTTGCACACTCTGTGTTCACCAGCTCCTTGATGGTTTGATCAGTGGAATCA TCTAAAACTTGAACAATTAGGCGGTCCAATGGCCATATTAGTCTACATGCAGCACCTATAGATA ATTGAAGGAC
Genomic sequence	CTTATTGCGAATAATCTCCATAATCATTTTCCTGAAGAGATTAGCTGGACCACAAGACCATCGA TGTTGCTGGAATCTAAAGGCCTTAAACTTGCTTGGTAACTCGCTTTTCACCTACAAACTCAGTG TTCATATACATAATGTAATGATTATAATTTAGTAATTATTATTTTATAGCAATGCATCACTATA TATATATATAGAATTATAGATATCATTGCACATCAAGACAAGAGTGCCACACTAGTCAGAAACT ATGTCCATAACCAAATTCTATAAAATCTACCACAATAACTATAGTTCAAAAGGGGAGTTTCTAT GTGACTTTAATAAAGTTATAGTTTCAAAAGTGGAAGCATACAAAAAAAAAGTGGGAGTGTCTAT GTAAAGAAAGCACTAGTAAATGTTGGATATTAAATCCACATGGGAACAGTTACATAATGTACGA AAGATGCAATGAGGGCTTATTTACAGCAATTAATAGGTAGGGATAAAATCAAGTACCGTGAGGT CATTGAGAAAGACAAATTTCCAGCCGAGAAGACCAGCACGAACGGCCAAGTCCATGTCCTCTAC AGTAGTCCGGTCATGCCATCCTCCAGCTTCTTCCATCGCGGCCATTCTCCATACACCCGCAGTT CCTGAAAGAGATATACCAAAACCATATTTATAAAATAAGTACCTAAAATTTATCAAAAATTCAA AACATGTAATGATAACCAAATACACCATTGAAGCTAAAGAAGGCATGTCTAGTGGATCCAGATT CTTGCTCTGCCATAAAGTGGTAGTTGAGGGACATCTCTTGCATCCTCGTCATCAAGCACTTGTT TGCGTTCACTGCAATGAACCCCACACACACATACAATCACTCAGTTTGAAAATAAACTTTGTTA GGATCCTTAATTATGTACATAGCATTGTTACGAAAGATATAAGTTCAGTTTATCACAACCTAGA TATGGAGTAAAAATTTACAAATATTGATAGTCTCATATAAGTTAATAGTTGTAAATGTTTAGGT ACGTAAAATTGTCTACCATAATGTACGTACTGAATCTCCATCGGGCTTGAACCAGAGCGACCTC GGGGTTATGAACGAGGAAGGGGACAGAGTGTTGGAGGTAATCAGGCTCCGGTTGGAAGTCTGCG TCGAAGATGACGACATAATTGCATAGCTTCACGTAGTTGTGCTTCATGCCTTCTTTAAGAGCTC CGGCTTTGTAGCCATTTCTGTTGTCTCTCCTCTCACACTTTATATTTACACCTTTGCTTTCCCA TTTTGCACACTCTGTGTTCACCAGCTCCTGAAACTCAATCCTCCTCACATTAAATATCTTACAA TACATTATATGTGTTCAAATAAATCAACAAACTTGGTCGGCAAGACCTTGATGGTTTGATCAGT GGAATCATCTAAAACTTGAACAATTAGGCGGTCCAATGGCCATATTAGTCTACATGCAGCACCT ATAGATAATTGAAGGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.191743432

Conservation Information
Conserved circRNAs	NA
PMCS	0.191743432

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8518774-8517577(-)
						
						Potential amino acid sequence
						
							MKHNYVKLCNYVVIFDADFQPEPDYLQHSVPFLVHNPEVALVQARWRFMNANKCLMTRMQEMSL
NYHFMAEQESGSTRHAFFSFNGTAGVWRMAAMEEAGGWHDRTTVEDMDLAVRAGLLGWKFVFLN
DLTVKSELPSKFKAFRFQQHRWSCGPANLFRKMIMEIIRNKVLQLSIGAACRLIWPLDRLIVQV
LDDSTDQTIKELVNTECAKWESKGVNIKCERRDNRNGYKAGALKEGMKHNYVKLCNYVVIFDAD
FQPEPDYLQHSVPFLVHNPEVALVQARWRFMNANKCLMTRMQEMSLNYHFMAEQESGSTRHAFF
SFNGTAGVWRMAAMEEAGGWHDRTTVEDMDLAVRAGLLGWKFVFLNDLTVKSELPSKFKAFRFQ
QHRWSCGPANLFRKMIMEIIRNKVLQLSIGAACRLIWPLDRLIVQVLDDSTDQTIKELVNTECA
KWESKGVNIKCERRDNRNGYKAGALKEGMKHNYVKLCNYVVIFDADFQPEPDYLQHSVPFLVHN
PEVALVQARWRFMNANKCLMTRMQEMSLNYHFMAEQESGSTRHAFFSFNGTAGVWRMAAMEEAG
GWHDRTTVEDMDLAVRAGLLGWKFVFLNDLTVKSELPSKFKAFRFQQHRWSCGPANLFRKMIME
IIRNKVLQLSIGAACRLIWPLDRLIVQVLDDSTDQTIKELVNTECAKWESKGVNIKCERRDNRN
GYKAGALKEGMKHNYVKLCNYVVIFDADFQPEPDYLQHSVPFLVHNPEVALVQARWRFMNANKC
LMTRMQEMSLNYHFMAEQESGSTRHAFFSFNGTAGVWRMAAMEEAGGWHDRTTVEDMDLAVRAG
LLGWKFVFLNDLTVKSELPSKFKAFRFQQHRWSCGPANLFRKMIMEIIRNK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8518774-8517577(-)
Potential amino acid sequence	MKHNYVKLCNYVVIFDADFQPEPDYLQHSVPFLVHNPEVALVQARWRFMNANKCLMTRMQEMSL NYHFMAEQESGSTRHAFFSFNGTAGVWRMAAMEEAGGWHDRTTVEDMDLAVRAGLLGWKFVFLN DLTVKSELPSKFKAFRFQQHRWSCGPANLFRKMIMEIIRNKVLQLSIGAACRLIWPLDRLIVQV LDDSTDQTIKELVNTECAKWESKGVNIKCERRDNRNGYKAGALKEGMKHNYVKLCNYVVIFDAD FQPEPDYLQHSVPFLVHNPEVALVQARWRFMNANKCLMTRMQEMSLNYHFMAEQESGSTRHAFF SFNGTAGVWRMAAMEEAGGWHDRTTVEDMDLAVRAGLLGWKFVFLNDLTVKSELPSKFKAFRFQ QHRWSCGPANLFRKMIMEIIRNKVLQLSIGAACRLIWPLDRLIVQVLDDSTDQTIKELVNTECA KWESKGVNIKCERRDNRNGYKAGALKEGMKHNYVKLCNYVVIFDADFQPEPDYLQHSVPFLVHN PEVALVQARWRFMNANKCLMTRMQEMSLNYHFMAEQESGSTRHAFFSFNGTAGVWRMAAMEEAG GWHDRTTVEDMDLAVRAGLLGWKFVFLNDLTVKSELPSKFKAFRFQQHRWSCGPANLFRKMIME IIRNKVLQLSIGAACRLIWPLDRLIVQVLDDSTDQTIKELVNTECAKWESKGVNIKCERRDNRN GYKAGALKEGMKHNYVKLCNYVVIFDADFQPEPDYLQHSVPFLVHNPEVALVQARWRFMNANKC LMTRMQEMSLNYHFMAEQESGSTRHAFFSFNGTAGVWRMAAMEEAGGWHDRTTVEDMDLAVRAG LLGWKFVFLNDLTVKSELPSKFKAFRFQQHRWSCGPANLFRKMIMEIIRNK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G24070_circ_g.3

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