Plant Circular RNA Database

Detail information of AT3G61440_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G61440_circ_g.3
					
						ID in PlantcircBase
						ath_circ_028607
					
						Alias
						3:22736179-22736783
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 22736179-22736783  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G61440						
					
						Parent gene annotation
						
							Bifunctional L-3-cyanoalanine synthase/cysteine synthase C1, mit
ochondrial
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G61440_circ_g.4 AT3G61440_circ_g.5 AT3G61440_circ_g.6 AT3G61440_circ_g.7 AT3G61440_circ_g.8 AT3G61440_circ_g.9 						
					
						Support reads
						1/1/1/1/3
					
						Tissues
						seedling;root;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  
						
							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
						AT3G61440.2:3
AT3G61440.3:2
AT3G61440.4:3
AT3G61440.1:3

General Information
CircRNA Name	AT3G61440_circ_g.3
ID in PlantcircBase	ath_circ_028607
Alias	3:22736179-22736783
Organism	Arabidpsis thaliana
Position	chr3: 22736179-22736783 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G61440
Parent gene annotation	Bifunctional L-3-cyanoalanine synthase/cysteine synthase C1, mit ochondrial
Parent gene strand	+
Alternative splicing	AT3G61440_circ_g.4 AT3G61440_circ_g.5 AT3G61440_circ_g.6 AT3G61440_circ_g.7 AT3G61440_circ_g.8 AT3G61440_circ_g.9
Support reads	1/1/1/1/3
Tissues	seedling;root;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	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	AT3G61440.2:3 AT3G61440.3:2 AT3G61440.4:3 AT3G61440.1:3

			
						 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  
						
							CAAAGGAATGGGTGGAACTGTTAAGAAAGCTTATGACCTCCTTGATAGTACTCCTGATGCTTTC
ATGTGTCAACAGTTTGCTAATCCTGCAAACACTCAGcttattgggaaaacgcctcttgtgttcc
tcaacaaagtcactgaaggttgtgaagcgtatgttgcagccaaacaagaacatttccagccaac
ttgtagca

									
								

					

						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: 374
Transcript exons: 22736179-22736288,22736520-22736783
CTTATTGGGAAAACGCCTCTTGTGTTCCTCAACAAAGTCACTGAAGGTTGTGAAGCGTATGTTG
CAGCCAAACAAGAACATTTCCAGCCAACTTGTAGCATTAAAGACAGACAACACTGATAGAGCCT
ACTTCAGGAAACATGGGAATCAGTTTGGCTTTCATGGCTGCTATGAAAGGGTACAGGATTATAA
TGACGATGCCTTCGTACACTAGCTTGGAGAGGAGAGTGACGATGAGATCCTTTGGTGCTGAGCT
TGTTCTCACTGATCCAGCCAAAGGAATGGGTGGAACTGTTAAGAAAGCTTATGACCTCCTTGAT
AGTACTCCTGATGCTTTCATGTGTCAACAGTTTGCTAATCCTGCAAACACTCAG
Transcript length: 432
Transcript exons: 22736179-22736288,22736370-22736427,22736520-22736783
CTTATTGGGAAAACGCCTCTTGTGTTCCTCAACAAAGTCACTGAAGGTTGTGAAGCGTATGTTG
CAGCCAAACAAGAACATTTCCAGCCAACTTGTAGCATTAAAGACAGACCAGCTATAGCCATGAT
TGCAGATGCAGAGAAGAAAAAACTAATCATCCCTGGAAAAACAACACTGATAGAGCCTACTTCA
GGAAACATGGGAATCAGTTTGGCTTTCATGGCTGCTATGAAAGGGTACAGGATTATAATGACGA
TGCCTTCGTACACTAGCTTGGAGAGGAGAGTGACGATGAGATCCTTTGGTGCTGAGCTTGTTCT
CACTGATCCAGCCAAAGGAATGGGTGGAACTGTTAAGAAAGCTTATGACCTCCTTGATAGTACT
CCTGATGCTTTCATGTGTCAACAGTTTGCTAATCCTGCAAACACTCAG
						
					

						Genomic sequence
						
							CTTATTGGGAAAACGCCTCTTGTGTTCCTCAACAAAGTCACTGAAGGTTGTGAAGCGTATGTTG
CAGCCAAACAAGAACATTTCCAGCCAACTTGTAGCATTAAAGACAGGTGCTTTGTGAAATCTTA
GTCTTCAAATCCTTCAAAAGCACTAGTAGCAAGTATTGATTTTGTTCCATTTCCTGTCTTTAGA
CCAGCTATAGCCATGATTGCAGATGCAGAGAAGAAAAAACTAATCATCCCTGGAAAAGTTAATA
GCTTTTTTCTTTTCTCTTAGTTAATTCTCAAATTAATGGTGAATCAAGAGTTTCTTACCCTCTG
AATTTGATGCTTAATTTTCAGACAACACTGATAGAGCCTACTTCAGGAAACATGGGAATCAGTT
TGGCTTTCATGGCTGCTATGAAAGGGTACAGGATTATAATGACGATGCCTTCGTACACTAGCTT
GGAGAGGAGAGTGACGATGAGATCCTTTGGTGCTGAGCTTGTTCTCACTGATCCAGCCAAAGGA
ATGGGTGGAACTGTTAAGAAAGCTTATGACCTCCTTGATAGTACTCCTGATGCTTTCATGTGTC
AACAGTTTGCTAATCCTGCAAACACTCAG
						
					

			
		

Sequences
Splice junction sequence	CAAAGGAATGGGTGGAACTGTTAAGAAAGCTTATGACCTCCTTGATAGTACTCCTGATGCTTTC ATGTGTCAACAGTTTGCTAATCCTGCAAACACTCAGcttattgggaaaacgcctcttgtgttcc tcaacaaagtcactgaaggttgtgaagcgtatgttgcagccaaacaagaacatttccagccaac ttgtagca
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: 374 Transcript exons: 22736179-22736288,22736520-22736783 CTTATTGGGAAAACGCCTCTTGTGTTCCTCAACAAAGTCACTGAAGGTTGTGAAGCGTATGTTG CAGCCAAACAAGAACATTTCCAGCCAACTTGTAGCATTAAAGACAGACAACACTGATAGAGCCT ACTTCAGGAAACATGGGAATCAGTTTGGCTTTCATGGCTGCTATGAAAGGGTACAGGATTATAA TGACGATGCCTTCGTACACTAGCTTGGAGAGGAGAGTGACGATGAGATCCTTTGGTGCTGAGCT TGTTCTCACTGATCCAGCCAAAGGAATGGGTGGAACTGTTAAGAAAGCTTATGACCTCCTTGAT AGTACTCCTGATGCTTTCATGTGTCAACAGTTTGCTAATCCTGCAAACACTCAG Transcript length: 432 Transcript exons: 22736179-22736288,22736370-22736427,22736520-22736783 CTTATTGGGAAAACGCCTCTTGTGTTCCTCAACAAAGTCACTGAAGGTTGTGAAGCGTATGTTG CAGCCAAACAAGAACATTTCCAGCCAACTTGTAGCATTAAAGACAGACCAGCTATAGCCATGAT TGCAGATGCAGAGAAGAAAAAACTAATCATCCCTGGAAAAACAACACTGATAGAGCCTACTTCA GGAAACATGGGAATCAGTTTGGCTTTCATGGCTGCTATGAAAGGGTACAGGATTATAATGACGA TGCCTTCGTACACTAGCTTGGAGAGGAGAGTGACGATGAGATCCTTTGGTGCTGAGCTTGTTCT CACTGATCCAGCCAAAGGAATGGGTGGAACTGTTAAGAAAGCTTATGACCTCCTTGATAGTACT CCTGATGCTTTCATGTGTCAACAGTTTGCTAATCCTGCAAACACTCAG
Genomic sequence	CTTATTGGGAAAACGCCTCTTGTGTTCCTCAACAAAGTCACTGAAGGTTGTGAAGCGTATGTTG CAGCCAAACAAGAACATTTCCAGCCAACTTGTAGCATTAAAGACAGGTGCTTTGTGAAATCTTA GTCTTCAAATCCTTCAAAAGCACTAGTAGCAAGTATTGATTTTGTTCCATTTCCTGTCTTTAGA CCAGCTATAGCCATGATTGCAGATGCAGAGAAGAAAAAACTAATCATCCCTGGAAAAGTTAATA GCTTTTTTCTTTTCTCTTAGTTAATTCTCAAATTAATGGTGAATCAAGAGTTTCTTACCCTCTG AATTTGATGCTTAATTTTCAGACAACACTGATAGAGCCTACTTCAGGAAACATGGGAATCAGTT TGGCTTTCATGGCTGCTATGAAAGGGTACAGGATTATAATGACGATGCCTTCGTACACTAGCTT GGAGAGGAGAGTGACGATGAGATCCTTTGGTGCTGAGCTTGTTCTCACTGATCCAGCCAAAGGA ATGGGTGGAACTGTTAAGAAAGCTTATGACCTCCTTGATAGTACTCCTGATGCTTTCATGTGTC AACAGTTTGCTAATCCTGCAAACACTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.312247248

Conservation Information
Conserved circRNAs	NA
PMCS	0.312247248

			
						 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 AT3G61440_circ_g.3

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