Plant Circular RNA Database

Detail information of AT3G05400_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT3G05400_circ_g.2
					
						ID in PlantcircBase
						ath_circ_019866
					
						Alias
						3:1549686-1553977
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 1549686-1553977  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G05400						
					
						Parent gene annotation
						
							Sugar transporter ERD6-like 12
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G05400_circ_g.1 AT3G05400_circ_g.3 AT3G05400_circ_g.4 AT3G05400_circ_g.5 AT3G05400_circ_g.6 AT3G05400_circ_g.7 AT3G05400_circ_g.8 AT3G05400_circ_g.9 AT3G05400_circ_g.10 AT3G05400_circ_g.11 						
					
						Support reads
						2/1/2
					
						Tissues
						seedling;flower
					
						Exon boundary  
						
							No-No							"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
						AT3G05400.1:17
AT3G05400.2:16

General Information
CircRNA Name	AT3G05400_circ_g.2
ID in PlantcircBase	ath_circ_019866
Alias	3:1549686-1553977
Organism	Arabidpsis thaliana
Position	chr3: 1549686-1553977 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G05400
Parent gene annotation	Sugar transporter ERD6-like 12
Parent gene strand	+
Alternative splicing	AT3G05400_circ_g.1 AT3G05400_circ_g.3 AT3G05400_circ_g.4 AT3G05400_circ_g.5 AT3G05400_circ_g.6 AT3G05400_circ_g.7 AT3G05400_circ_g.8 AT3G05400_circ_g.9 AT3G05400_circ_g.10 AT3G05400_circ_g.11
Support reads	2/1/2
Tissues	seedling;flower
Exon boundary	No-No "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	AT3G05400.1:17 AT3G05400.2:16

			
						 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  
						
							GCTTGGTGCCGGAGACTCGAAGATTAACGTTAGAAGAAATCCAACTGTCGTTTGTCAATGTTTA
GGGTTCATCGGAAGCATTCATATATACATCATAAAGggtttgattgaagaaaatggaaggagag
aataatatggagaaaggattgttattggcaaaaaaggaagacagtgcaaatacaactccacttc
ttatcttc

									
								

					

						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
						
							GGTTTGATTGAAGAAAATGGAAGGAGAGAATAATATGGAGAAAGGATTGTTATTGGCAAAAAAG
GAAGACAGTGCAAATACAACTCCACTTCTTATCTTCTCCACCTTCATCATTGTCTCTGCCTCCT
TCACCTTTGGCGCTGCCGTATGTACCCATCTCTCTCTCTCTCTCTAGCTCTCTATTTCTTCTCT
ATATATGCACTCTCATATAGATGTTCCTATTAATTAGAACCAAATTCCAGATCTAGGCCAGAGG
TATAATGAGCTAAGGAACAGATTCAAACCACCAACTTCTTTTCTTTAGCATTAATGTTATATAC
TAAACTTTATTGTCTTTCAACAAGATTGTTGTTTAGAAATTATTTTAACGCAGATAATCAAAAC
CATGATGATTTTTGGCCTCAGATTTGTAATACTTAATTTCGAATTAAAAGCTAAGTTTATATAT
ATTGACAAAAGATGAAAAAGGTAATAATATAGTTTCTATACTATATATTATCTCTTCATATCTT
CAATCTTGTGGACCTCGAAAATGTTGGATTGATAGTACGTGCTACCTATAGCCATATCTTATCT
CGACATCTCTTTTAAATTTCAAGTTTCTAACCACAGTAAAGGTTAAAAAAAAATTCAAGTAATT
GTATTAAAGTAAGAGTTTATAACTTCATTATGTATATAGAGTTAAAAAAGAACAACTTAATTAT
TTCTATCATCTTATGGTTCACAGATAGGTTATACTGCAGATACAATGTCCTCCATTATGTCAGA
CTTGGATCTTTCTCTCGCACAAGTAAGTCCAACTTTCATCACAATTTTTATGGGAAACAACATT
AATATAATTTTTCAGTCAATTCTTCCAATTTTACAAGTGGATGGATACACGCAAACGTATACGT
ATTTTGTTGAAACTACTAGTTACATCGCTTTTTTTTTATATCAAATGAAAAATTATTTAGGGGT
AACAAAATAGAAAAAGTTGACTACTGTACGAGCTCATATTGTTACAGTGATGACTAGTTAATTT
TAATTTCTTGAGAACTATGTTTACAGTTTTCGCTGTTTGGTTCGTTGTCGACGTTTGGAGGAAT
GATCGGTGCAATATTCAGCGCCAAAGCTGCAAGTGCCTTCGGTCATAAAATGGTAAGTATCAAT
TATTCTCAAAATCACCCCTATCTTTCTTTTATTTTGTCGTAAGCCCAAAAATTTATATCGTAAA
TTTCTACACCCTCATTTTTTTTTGTCTTACAATATTTCTTAGACGTTGTGGGTGGCTGATTTAT
TCTGCATAACTGGTTGGCTTGCAATTTCACTAGCCAAGGTTCCCTCCATAACTTATATTCTTCT
TTATTTTTGCAAGTTTAACAAAATTGTATATTTTATCACCATTTTAGTAATATAGTCTATGTTT
TTTTGTAGTATATAATTCTTATTTTAAATTTCTTTTTTGGCACACAGGATATTATTTGGCTTGA
CATGGGGCGATTTTTGGTGGGAATTGGAGTTGGTCTCATTAGCTACGTGGTAAAGCTATTTCCT
GAAAAGATGACAAAAAAAATATATATATATATCGTCGTAACCATAAATATTTTCTGTATAGGTT
CCTGTATATATTGCAGAAATAACACCCAAGCACGTAAGAGGGGCTTTTACATTTAGCAATCAGG
TGACTTACCTATTTAAAATCGAAGTTTAGACGTATATTATCATTTTATACATAAATTTGACTTA
TTTATTCTAACATCAATACTTCACAGCTTTTGCAAAACTGTGGAGTTGCAGTCGTATATTACTT
TGGAAATTTCTTGTCATGGAGAACTTTAGCCATAATAGGTGATTCATTCCCATCAACTATCCCG
ATTTTAAAGATTCATTTCTCCTGATTATTATTTTATTTGCCCTAAACTAAAATATAGATATCTA
ATTAACCAGGTAGTATTCCATGTTGGATACAAGTTATTGGTTTGTTCTTCATACCTGAGTCTCC
AAGATGGCTGGTTAGTCATATAAATCAATCGTGAAAAACTTATATCCATGAACATGATTGTTGT
AATTTGTAAGTAAATATATAATAATATATGAACATAATATTTACAGGCGAAAAAAGGTCGTGAT
AAAGAATGTGAAGAAGTTCTTCAAAAGTTAAGAGGAAGAAAATACGATATTGTGCCTGAAGCTT
GCGAAATCAAGGTACTCATACGTACAAATCAGTCCCACAAAATACAGATGTTTGACATAAATAT
ATTTAAAATCACTTGTAGTCTTGTAGATCATTCATTCACCAAAAGAAAAAAGAAAAACAATCTA
CTCCTAAGCAAAAATTCTCACTTATACTTGTTTTAAATTTGTAGATTTCAGTTGAAGCTTCGAA
GAAAAATTCGAATATCAACATTCGTAGTCTTTTCGAAAAGAGATATGCTCATCAACTTACAGTA
AGAAAAGAAGAGTTTTATTCATTCATTAAATATATTCTAGTGATCTTGATTTTTATATAAGAAC
TGAATAACAAATTATTTGTTTTGTTTGGATTCGGTTGATTTTTGTTTAGATCGGCATTGGTTTG
ATGCTTCTGCAACAGTTATGTGGAACTGCAGGAATAAGTTCTTACGGAAGCACTCTATTTAAAC
TTGCCGGTAATCAGATTTATTTCCTAATTGAATTGTTTATAATTTAGTTAGGAATTTGTTTTTT
GCTTTTCAAACTAATCCTTTGATTTTCTAGGGTTTCCTGCTCGGATTGGGATGATGGTGTTATC
TCTTATCGTCGTACGTAAAAATTTATTAGATAGATATTTTTCTGTTTTAAATGCACTTTGACAA
AAGAAAAAAAAAATATTATATATGATTGCTTCATTAATTGTATTCTCACATCCTGACCCCAATT
TCTTATTAATGATCATATGCATAGGTACCAAAATCTTTAATGGGTCTAATCCTCGTGGATCGAT
GGGGAAGACGCCCACTTCTTATGGTTAGAAAAATTTAAATCTTTTAGGTTCAGTCTATCTTTTT
TTTTACTGTGCAAGTAAAATAGTCCATAAATAAGATAAATTTTTATTTTCATACATCGAATTTG
CAGACTTCAGCGTTGGGGTTGTGTTTAAGCTGTATCACATTGGCAGTAGCGTTTGGAGTTAAAG
ATGTCCCGGGAATTGGAAAAATTACTCCAATTTTCTGTTTCATTGGAATATTGGTAAGTTTTTC
ACTATTTGAATTTCACTCTAATTTATAATCTAAAAACTCTATCAAACTATATATTTACACAAAC
TTCAAATGTGTTATTCTGTTTTTCTTTAATATCTCAAGTACACTAAACCAAATTAGACAGCCAT
TTTTTTTAGGCAATCATACTTGATCAAAAATAATATGAAAGTCAAAACTCACAATATATATATA
TATATATATATATATATTGATTATTGTTAAATTTTCAAAATTTTGACTAGCTATAACAATTTAT
CATTCAAACAGTCGTTTACGATGATGTTCGCAATTGGAATGGGAGCGTTACCATGGATTATAAT
GTCTGAGGTATACACATATGAGCAAACATACTATTTTACAGATGTTTTTGGATTATAGTCATAC
CGATGATCATTTGTTAATTATTATTATTTATGTTAATTACTTTCTTGGCAGATATTTCCAATGG
ATATAAAGGTATTAGCTGGGAGTTTAGTGACCATAGCAAATTGGTTCACTGGTTGGATCGCCAA
CTATGCTTTCAATTTTATGTTGGTTTGGAGCCCAAGCGGTGAGTAACATAAAGCATATACACAT
TCGATTACAAATCAAAATATTCTATTAGTTTTACTTGAATAAACCGAAGCAAATATATATACAA
ATGCATAAATGATTTGCTAAATCCTAAATCGCTGCCTAGGCATGTAGGCATGCATGCAAGTCTT
TTGTTTAATTCTTTCATGCATGCAAGTATACCGTATACGTCTCTAGTTTTTCTTTTATAACTTT
TTCTTTTAAGGATGTTAATTTTTCTTTCATATGTTAAATTTGAATTAACTAGACTAACATGTTC
TTTTTTCTTTTTGTATATATATAATACTAGACTAACATGCTTAATCGTGTGCTATAAGAAAAAA
GCAATGGCTAATCCTGTCTATATAAATAAAAATAACTTGCAGGGACTTTTATAATATCCGCTAT
AATCTGTGGAGCAACAATTGTATTCACATGGTGCTTGGTGCCGGAGACTCGAAGATTAACGTTA
GAAGAAATCCAACTGTCGTTTGTCAATGTTTAGGGTTCATCGGAAGCATTCATATATACATCAT
AAAG
						
					

			
		

Sequences
Splice junction sequence	GCTTGGTGCCGGAGACTCGAAGATTAACGTTAGAAGAAATCCAACTGTCGTTTGTCAATGTTTA GGGTTCATCGGAAGCATTCATATATACATCATAAAGggtttgattgaagaaaatggaaggagag aataatatggagaaaggattgttattggcaaaaaaggaagacagtgcaaatacaactccacttc ttatcttc
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	GGTTTGATTGAAGAAAATGGAAGGAGAGAATAATATGGAGAAAGGATTGTTATTGGCAAAAAAG GAAGACAGTGCAAATACAACTCCACTTCTTATCTTCTCCACCTTCATCATTGTCTCTGCCTCCT TCACCTTTGGCGCTGCCGTATGTACCCATCTCTCTCTCTCTCTCTAGCTCTCTATTTCTTCTCT ATATATGCACTCTCATATAGATGTTCCTATTAATTAGAACCAAATTCCAGATCTAGGCCAGAGG TATAATGAGCTAAGGAACAGATTCAAACCACCAACTTCTTTTCTTTAGCATTAATGTTATATAC TAAACTTTATTGTCTTTCAACAAGATTGTTGTTTAGAAATTATTTTAACGCAGATAATCAAAAC CATGATGATTTTTGGCCTCAGATTTGTAATACTTAATTTCGAATTAAAAGCTAAGTTTATATAT ATTGACAAAAGATGAAAAAGGTAATAATATAGTTTCTATACTATATATTATCTCTTCATATCTT CAATCTTGTGGACCTCGAAAATGTTGGATTGATAGTACGTGCTACCTATAGCCATATCTTATCT CGACATCTCTTTTAAATTTCAAGTTTCTAACCACAGTAAAGGTTAAAAAAAAATTCAAGTAATT GTATTAAAGTAAGAGTTTATAACTTCATTATGTATATAGAGTTAAAAAAGAACAACTTAATTAT TTCTATCATCTTATGGTTCACAGATAGGTTATACTGCAGATACAATGTCCTCCATTATGTCAGA CTTGGATCTTTCTCTCGCACAAGTAAGTCCAACTTTCATCACAATTTTTATGGGAAACAACATT AATATAATTTTTCAGTCAATTCTTCCAATTTTACAAGTGGATGGATACACGCAAACGTATACGT ATTTTGTTGAAACTACTAGTTACATCGCTTTTTTTTTATATCAAATGAAAAATTATTTAGGGGT AACAAAATAGAAAAAGTTGACTACTGTACGAGCTCATATTGTTACAGTGATGACTAGTTAATTT TAATTTCTTGAGAACTATGTTTACAGTTTTCGCTGTTTGGTTCGTTGTCGACGTTTGGAGGAAT GATCGGTGCAATATTCAGCGCCAAAGCTGCAAGTGCCTTCGGTCATAAAATGGTAAGTATCAAT TATTCTCAAAATCACCCCTATCTTTCTTTTATTTTGTCGTAAGCCCAAAAATTTATATCGTAAA TTTCTACACCCTCATTTTTTTTTGTCTTACAATATTTCTTAGACGTTGTGGGTGGCTGATTTAT TCTGCATAACTGGTTGGCTTGCAATTTCACTAGCCAAGGTTCCCTCCATAACTTATATTCTTCT TTATTTTTGCAAGTTTAACAAAATTGTATATTTTATCACCATTTTAGTAATATAGTCTATGTTT TTTTGTAGTATATAATTCTTATTTTAAATTTCTTTTTTGGCACACAGGATATTATTTGGCTTGA CATGGGGCGATTTTTGGTGGGAATTGGAGTTGGTCTCATTAGCTACGTGGTAAAGCTATTTCCT GAAAAGATGACAAAAAAAATATATATATATATCGTCGTAACCATAAATATTTTCTGTATAGGTT CCTGTATATATTGCAGAAATAACACCCAAGCACGTAAGAGGGGCTTTTACATTTAGCAATCAGG TGACTTACCTATTTAAAATCGAAGTTTAGACGTATATTATCATTTTATACATAAATTTGACTTA TTTATTCTAACATCAATACTTCACAGCTTTTGCAAAACTGTGGAGTTGCAGTCGTATATTACTT TGGAAATTTCTTGTCATGGAGAACTTTAGCCATAATAGGTGATTCATTCCCATCAACTATCCCG ATTTTAAAGATTCATTTCTCCTGATTATTATTTTATTTGCCCTAAACTAAAATATAGATATCTA ATTAACCAGGTAGTATTCCATGTTGGATACAAGTTATTGGTTTGTTCTTCATACCTGAGTCTCC AAGATGGCTGGTTAGTCATATAAATCAATCGTGAAAAACTTATATCCATGAACATGATTGTTGT AATTTGTAAGTAAATATATAATAATATATGAACATAATATTTACAGGCGAAAAAAGGTCGTGAT AAAGAATGTGAAGAAGTTCTTCAAAAGTTAAGAGGAAGAAAATACGATATTGTGCCTGAAGCTT GCGAAATCAAGGTACTCATACGTACAAATCAGTCCCACAAAATACAGATGTTTGACATAAATAT ATTTAAAATCACTTGTAGTCTTGTAGATCATTCATTCACCAAAAGAAAAAAGAAAAACAATCTA CTCCTAAGCAAAAATTCTCACTTATACTTGTTTTAAATTTGTAGATTTCAGTTGAAGCTTCGAA GAAAAATTCGAATATCAACATTCGTAGTCTTTTCGAAAAGAGATATGCTCATCAACTTACAGTA AGAAAAGAAGAGTTTTATTCATTCATTAAATATATTCTAGTGATCTTGATTTTTATATAAGAAC TGAATAACAAATTATTTGTTTTGTTTGGATTCGGTTGATTTTTGTTTAGATCGGCATTGGTTTG ATGCTTCTGCAACAGTTATGTGGAACTGCAGGAATAAGTTCTTACGGAAGCACTCTATTTAAAC TTGCCGGTAATCAGATTTATTTCCTAATTGAATTGTTTATAATTTAGTTAGGAATTTGTTTTTT GCTTTTCAAACTAATCCTTTGATTTTCTAGGGTTTCCTGCTCGGATTGGGATGATGGTGTTATC TCTTATCGTCGTACGTAAAAATTTATTAGATAGATATTTTTCTGTTTTAAATGCACTTTGACAA AAGAAAAAAAAAATATTATATATGATTGCTTCATTAATTGTATTCTCACATCCTGACCCCAATT TCTTATTAATGATCATATGCATAGGTACCAAAATCTTTAATGGGTCTAATCCTCGTGGATCGAT GGGGAAGACGCCCACTTCTTATGGTTAGAAAAATTTAAATCTTTTAGGTTCAGTCTATCTTTTT TTTTACTGTGCAAGTAAAATAGTCCATAAATAAGATAAATTTTTATTTTCATACATCGAATTTG CAGACTTCAGCGTTGGGGTTGTGTTTAAGCTGTATCACATTGGCAGTAGCGTTTGGAGTTAAAG ATGTCCCGGGAATTGGAAAAATTACTCCAATTTTCTGTTTCATTGGAATATTGGTAAGTTTTTC ACTATTTGAATTTCACTCTAATTTATAATCTAAAAACTCTATCAAACTATATATTTACACAAAC TTCAAATGTGTTATTCTGTTTTTCTTTAATATCTCAAGTACACTAAACCAAATTAGACAGCCAT TTTTTTTAGGCAATCATACTTGATCAAAAATAATATGAAAGTCAAAACTCACAATATATATATA TATATATATATATATATTGATTATTGTTAAATTTTCAAAATTTTGACTAGCTATAACAATTTAT CATTCAAACAGTCGTTTACGATGATGTTCGCAATTGGAATGGGAGCGTTACCATGGATTATAAT GTCTGAGGTATACACATATGAGCAAACATACTATTTTACAGATGTTTTTGGATTATAGTCATAC CGATGATCATTTGTTAATTATTATTATTTATGTTAATTACTTTCTTGGCAGATATTTCCAATGG ATATAAAGGTATTAGCTGGGAGTTTAGTGACCATAGCAAATTGGTTCACTGGTTGGATCGCCAA CTATGCTTTCAATTTTATGTTGGTTTGGAGCCCAAGCGGTGAGTAACATAAAGCATATACACAT TCGATTACAAATCAAAATATTCTATTAGTTTTACTTGAATAAACCGAAGCAAATATATATACAA ATGCATAAATGATTTGCTAAATCCTAAATCGCTGCCTAGGCATGTAGGCATGCATGCAAGTCTT TTGTTTAATTCTTTCATGCATGCAAGTATACCGTATACGTCTCTAGTTTTTCTTTTATAACTTT TTCTTTTAAGGATGTTAATTTTTCTTTCATATGTTAAATTTGAATTAACTAGACTAACATGTTC TTTTTTCTTTTTGTATATATATAATACTAGACTAACATGCTTAATCGTGTGCTATAAGAAAAAA GCAATGGCTAATCCTGTCTATATAAATAAAAATAACTTGCAGGGACTTTTATAATATCCGCTAT AATCTGTGGAGCAACAATTGTATTCACATGGTGCTTGGTGCCGGAGACTCGAAGATTAACGTTA GAAGAAATCCAACTGTCGTTTGTCAATGTTTAGGGTTCATCGGAAGCATTCATATATACATCAT AAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.294595799

Conservation Information
Conserved circRNAs	NA
PMCS	0.294595799

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR870-5p 						
					
						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	ath-miR870-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT3G05400_circ_g.2

Address

Any questions?

Supported by