Plant Circular RNA Database

Detail information of AT3G61420_circ_g.10

			
						 General Information
					
						CircRNA Name
						AT3G61420_circ_g.10
					
						ID in PlantcircBase
						ath_circ_028588
					
						Alias
						Ath_circ_FC2461, Ath_circ_FC2462, Ath_circ_FC2463, AT3G61420_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 22728135-22729216  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, MapSplice, PcircRNA_finder, CIRI2
					
						Parent gene
						
							AT3G61420						
					
						Parent gene annotation
						
							Probable RNA polymerase II transcription factor B subunit 1-3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G61420_circ_g.1 AT3G61420_circ_g.2 AT3G61420_circ_g.3 AT3G61420_circ_g.4 AT3G61420_circ_g.5 AT3G61420_circ_g.6 AT3G61420_circ_g.7 AT3G61420_circ_g.8 AT3G61420_circ_g.9 AT3G61420_circ_g.11 AT3G61420_circ_g.12 AT3G61420_circ_g.13 AT3G61420_circ_g.14 AT3G61420_circ_g.15 AT3G61420_circ_g.16 						
					
						Support reads
						3
					
						Tissues
						root, seed, whole_plant/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  
						
							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
						AT3G61420.2:5
AT3G61420.1:5

General Information
CircRNA Name	AT3G61420_circ_g.10
ID in PlantcircBase	ath_circ_028588
Alias	Ath_circ_FC2461, Ath_circ_FC2462, Ath_circ_FC2463, AT3G61420_C1
Organism	Arabidpsis thaliana
Position	chr3: 22728135-22729216 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, MapSplice, PcircRNA_finder, CIRI2
Parent gene	AT3G61420
Parent gene annotation	Probable RNA polymerase II transcription factor B subunit 1-3
Parent gene strand	-
Alternative splicing	AT3G61420_circ_g.1 AT3G61420_circ_g.2 AT3G61420_circ_g.3 AT3G61420_circ_g.4 AT3G61420_circ_g.5 AT3G61420_circ_g.6 AT3G61420_circ_g.7 AT3G61420_circ_g.8 AT3G61420_circ_g.9 AT3G61420_circ_g.11 AT3G61420_circ_g.12 AT3G61420_circ_g.13 AT3G61420_circ_g.14 AT3G61420_circ_g.15 AT3G61420_circ_g.16
Support reads	3
Tissues	root, seed, whole_plant/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	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	AT3G61420.2:5 AT3G61420.1:5

			
						 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  
						
							CAGCAGCATGACGATTAAGATCTTGTAAAAGTGACCTCTTAAGCTGGTCATTCTGTGGTTCAAT
AATGTCATTGGTGCCATCGCGCTGGATCCCGTGGTCatgtataacttcatccttagtggacttt
ggtaatctgtccagaaagctctcttgcgggttcttcccgagaatatttttggcagttgagatag
ttcgggtc

									
								

					

						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: 201
Transcript exons: 22728135-22728248,22729130-22729216
ATGTATAACTTCATCCTTAGTGGACTTTGGTAATCTGTCCAGAAAGCTCTCTTGCGGGTTCTTC
CCGAGAATATTTTTGGCAGTTGAGATAGTTCGGGTCAACGAACTGAAAACATTAAGATCTTGTA
AAAGTGACCTCTTAAGCTGGTCATTCTGTGGTTCAATAATGTCATTGGTGCCATCGCGCTGGAT
CCCGTGGTC
Transcript length: 597
Transcript exons: 22728135-22728248,22728344-22728517,22728606-22728733,22
728853-22728909,22729093-22729216
ATGTATAACTTCATCCTTAGTGGACTTTGGTAATCTGTCCAGAAAGCTCTCTTGCGGGTTCTTC
CCGAGAATATTTTTGGCAGTTGAGATAGTTCGGGTCAACGAACTGAAAACCTCAAAGGAAACTT
CAGGTTTAATCAACGGATCACTTAATCCCGTCATTCTAATCACCAAAATGGATTCTTTTAGTAA
TCCATAAGCTTCATGGACATTTCTTTTTGACGCCTTTGCTCCTCTGGGTTCACTGAGGATGTTT
CCTTGTTGAGATTCAAAGTAATCACGAGGGTCCTTGATAGAGAGTGGTGCTAATGGGAAGTTTT
GTGGTGCTTGAAGATCCTCCATTTCTGTTGCACGGGACATTCTCTCCAACCTCTCCTGATTAGC
GTCCTTGGTGATTTCACCATCAGCTTTGCTTACTTGTTTCGCCCGTGTGAGAGCCTCTGCAACA
ATTCTCGTATCTTCAGACTGAACATTGATGCATCTTCCTTCCAATACAACAGCAGCATGACGAT
TAAGATCTTGTAAAAGTGACCTCTTAAGCTGGTCATTCTGTGGTTCAATAATGTCATTGGTGCC
ATCGCGCTGGATCCCGTGGTC
						
					

						Genomic sequence
						
							ATGTATAACTTCATCCTTAGTGGACTTTGGTAATCTGTCCAGAAAGCTCTCTTGCGGGTTCTTC
CCGAGAATATTTTTGGCAGTTGAGATAGTTCGGGTCAACGAACTGAAAACCTGGATAGGGTTTA
GCAATATTTAGCTCAGGGAACAAAGCAATAAGCCATGGTTTCTTTAGGCAGCATGCATTTTATA
TTGAGATAGAATAGCACCTCAAAGGAAACTTCAGGTTTAATCAACGGATCACTTAATCCCGTCA
TTCTAATCACCAAAATGGATTCTTTTAGTAATCCATAAGCTTCATGGACATTTCTTTTTGACGC
CTTTGCTCCTCTGGGTTCACTGAGGATGTTTCCTTGTTGAGATTCAAAGTAATCACGAGGGTCC
TGATTCCAAACAAGAGAAGGTACGAGGATTTACGCACCATCTTTCATCATCAACAGTGTAAACC
TATTTATCACAAAAAGCCAAGACCTTGATAGAGAGTGGTGCTAATGGGAAGTTTTGTGGTGCTT
GAAGATCCTCCATTTCTGTTGCACGGGACATTCTCTCCAACCTCTCCTGATTAGCGTCCTTGGT
GATTTCACCATCAGCTTTGCTTACTACCAGGGGTAATAGACATGGATACCTAGGTCAGATGAAT
ATGAATTGCAGCATTGGCCATTGATCAGCATAGAAAAAGAAAAAGATAAGTAGAGCATATCATA
ATGAAACAGCAAACCTTGTTTCGCCCGTGTGAGAGCCTCTGCAACAATTCTCGTATCTTCAGAC
TGAACATCTACTTTCCAGTATAAAAGAATAAGTGAGTATCATTGTATACTTTACCACCAAGAAC
TAAAAGCAGAGGGCCAAAATACATGTTTATCCCTCATCAACTATCTGTTGGGAAGTCATTTGAT
GGCTATTTTTTATACTGTTACACAAAACACCAGATGAAACAATCAGAGTTGAAAGTGTTTACTG
ATGCATCTTCCTTCCAATACAACAGCAGCATGACGATTAAGATCTTGTAAAAGTGACCTCTTAA
GCTGGTCATTCTGTGGTTCAATAATGTCATTGGTGCCATCGCGCTGGATCCCGTGGTC
						
					

			
		

Sequences
Splice junction sequence	CAGCAGCATGACGATTAAGATCTTGTAAAAGTGACCTCTTAAGCTGGTCATTCTGTGGTTCAAT AATGTCATTGGTGCCATCGCGCTGGATCCCGTGGTCatgtataacttcatccttagtggacttt ggtaatctgtccagaaagctctcttgcgggttcttcccgagaatatttttggcagttgagatag ttcgggtc
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: 201 Transcript exons: 22728135-22728248,22729130-22729216 ATGTATAACTTCATCCTTAGTGGACTTTGGTAATCTGTCCAGAAAGCTCTCTTGCGGGTTCTTC CCGAGAATATTTTTGGCAGTTGAGATAGTTCGGGTCAACGAACTGAAAACATTAAGATCTTGTA AAAGTGACCTCTTAAGCTGGTCATTCTGTGGTTCAATAATGTCATTGGTGCCATCGCGCTGGAT CCCGTGGTC Transcript length: 597 Transcript exons: 22728135-22728248,22728344-22728517,22728606-22728733,22 728853-22728909,22729093-22729216 ATGTATAACTTCATCCTTAGTGGACTTTGGTAATCTGTCCAGAAAGCTCTCTTGCGGGTTCTTC CCGAGAATATTTTTGGCAGTTGAGATAGTTCGGGTCAACGAACTGAAAACCTCAAAGGAAACTT CAGGTTTAATCAACGGATCACTTAATCCCGTCATTCTAATCACCAAAATGGATTCTTTTAGTAA TCCATAAGCTTCATGGACATTTCTTTTTGACGCCTTTGCTCCTCTGGGTTCACTGAGGATGTTT CCTTGTTGAGATTCAAAGTAATCACGAGGGTCCTTGATAGAGAGTGGTGCTAATGGGAAGTTTT GTGGTGCTTGAAGATCCTCCATTTCTGTTGCACGGGACATTCTCTCCAACCTCTCCTGATTAGC GTCCTTGGTGATTTCACCATCAGCTTTGCTTACTTGTTTCGCCCGTGTGAGAGCCTCTGCAACA ATTCTCGTATCTTCAGACTGAACATTGATGCATCTTCCTTCCAATACAACAGCAGCATGACGAT TAAGATCTTGTAAAAGTGACCTCTTAAGCTGGTCATTCTGTGGTTCAATAATGTCATTGGTGCC ATCGCGCTGGATCCCGTGGTC
Genomic sequence	ATGTATAACTTCATCCTTAGTGGACTTTGGTAATCTGTCCAGAAAGCTCTCTTGCGGGTTCTTC CCGAGAATATTTTTGGCAGTTGAGATAGTTCGGGTCAACGAACTGAAAACCTGGATAGGGTTTA GCAATATTTAGCTCAGGGAACAAAGCAATAAGCCATGGTTTCTTTAGGCAGCATGCATTTTATA TTGAGATAGAATAGCACCTCAAAGGAAACTTCAGGTTTAATCAACGGATCACTTAATCCCGTCA TTCTAATCACCAAAATGGATTCTTTTAGTAATCCATAAGCTTCATGGACATTTCTTTTTGACGC CTTTGCTCCTCTGGGTTCACTGAGGATGTTTCCTTGTTGAGATTCAAAGTAATCACGAGGGTCC TGATTCCAAACAAGAGAAGGTACGAGGATTTACGCACCATCTTTCATCATCAACAGTGTAAACC TATTTATCACAAAAAGCCAAGACCTTGATAGAGAGTGGTGCTAATGGGAAGTTTTGTGGTGCTT GAAGATCCTCCATTTCTGTTGCACGGGACATTCTCTCCAACCTCTCCTGATTAGCGTCCTTGGT GATTTCACCATCAGCTTTGCTTACTACCAGGGGTAATAGACATGGATACCTAGGTCAGATGAAT ATGAATTGCAGCATTGGCCATTGATCAGCATAGAAAAAGAAAAAGATAAGTAGAGCATATCATA ATGAAACAGCAAACCTTGTTTCGCCCGTGTGAGAGCCTCTGCAACAATTCTCGTATCTTCAGAC TGAACATCTACTTTCCAGTATAAAAGAATAAGTGAGTATCATTGTATACTTTACCACCAAGAAC TAAAAGCAGAGGGCCAAAATACATGTTTATCCCTCATCAACTATCTGTTGGGAAGTCATTTGAT GGCTATTTTTTATACTGTTACACAAAACACCAGATGAAACAATCAGAGTTGAAAGTGTTTACTG ATGCATCTTCCTTCCAATACAACAGCAGCATGACGATTAAGATCTTGTAAAAGTGACCTCTTAA GCTGGTCATTCTGTGGTTCAATAATGTCATTGGTGCCATCGCGCTGGATCCCGTGGTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.483385176

Conservation Information
Conserved circRNAs	NA
PMCS	0.483385176

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22728678-22728137(-)
						
						Potential amino acid sequence
						
							MSRATEMEDLQAPQNFPLAPLSIKDPRDYFESQQGNILSEPRGAKASKRNVHEAYGLLKESILV
IRMTGLSDPLIKPEVSFEVFSSLTRTISTAKNILGKNPQESFLDRLPKSTKDEVIHDHGIQRDG
TNDIIEPQNDQLKRSLLQDLNRHAAVVLEGRCINVQSEDTRIVAEALTRAKQVSKADGEITKDA
NQERLERMSRATEMEDLQAPQNFPLAPLSIKDPRDYFESQQGNILSEPRGAKASKRNVHEAYGL
LKESILVIRMTGLSDPLIKPEVSFEVFSSLTRTISTAKNILGKNPQESFLDRLPKSTKDEVIHD
HGIQRDGTNDIIEPQNDQLKRSLLQDLNRHAAVVLEGRCINVQSEDTRIVAEALTRAKQVSKAD
GEITKDANQERLERMSRATEMEDLQAPQNFPLAPLSIKDPRDYFESQQGNILSEPRGAKASKRN
VHEAYGLLKESILVIRMTGLSDPLIKPEVSFEVFSSLTRTISTAKNILGKNPQESFLDRLPKST
KDEVIHDHGIQRDGTNDIIEPQNDQLKRSLLQDLNRHAAVVLEGRCINVQSEDTRIVAEALTRA
KQVSKADGEITKDANQERLERMSRATEMEDLQAPQNFPLAPLSIKDPRDYFESQQGNILSEPRG
AKASKRNVHEAYGLLKESILVIRMTGLSDPLIKPEVSFEVFSSLTRTISTAKNILGKNPQESFL
DRLPKSTKDEVIH(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	22728678-22728137(-)
Potential amino acid sequence	MSRATEMEDLQAPQNFPLAPLSIKDPRDYFESQQGNILSEPRGAKASKRNVHEAYGLLKESILV IRMTGLSDPLIKPEVSFEVFSSLTRTISTAKNILGKNPQESFLDRLPKSTKDEVIHDHGIQRDG TNDIIEPQNDQLKRSLLQDLNRHAAVVLEGRCINVQSEDTRIVAEALTRAKQVSKADGEITKDA NQERLERMSRATEMEDLQAPQNFPLAPLSIKDPRDYFESQQGNILSEPRGAKASKRNVHEAYGL LKESILVIRMTGLSDPLIKPEVSFEVFSSLTRTISTAKNILGKNPQESFLDRLPKSTKDEVIHD HGIQRDGTNDIIEPQNDQLKRSLLQDLNRHAAVVLEGRCINVQSEDTRIVAEALTRAKQVSKAD GEITKDANQERLERMSRATEMEDLQAPQNFPLAPLSIKDPRDYFESQQGNILSEPRGAKASKRN VHEAYGLLKESILVIRMTGLSDPLIKPEVSFEVFSSLTRTISTAKNILGKNPQESFLDRLPKST KDEVIHDHGIQRDGTNDIIEPQNDQLKRSLLQDLNRHAAVVLEGRCINVQSEDTRIVAEALTRA KQVSKADGEITKDANQERLERMSRATEMEDLQAPQNFPLAPLSIKDPRDYFESQQGNILSEPRG AKASKRNVHEAYGLLKESILVIRMTGLSDPLIKPEVSFEVFSSLTRTISTAKNILGKNPQESFL DRLPKSTKDEVIH(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a;Liu et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT3G61420_circ_g.10

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