Plant Circular RNA Database

Detail information of AT3G11880_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G11880_circ_g.1
					
						ID in PlantcircBase
						ath_circ_021087
					
						Alias
						3:3752331-3753421
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 3752331-3753421  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G11880						
					
						Parent gene annotation
						
							F26K24.17 protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G11880_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						seedling
					
						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
						AT3G11880.4:4
AT3G11880.2:5
AT3G11880.3:4
AT3G11880.1:5

General Information
CircRNA Name	AT3G11880_circ_g.1
ID in PlantcircBase	ath_circ_021087
Alias	3:3752331-3753421
Organism	Arabidpsis thaliana
Position	chr3: 3752331-3753421 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G11880
Parent gene annotation	F26K24.17 protein
Parent gene strand	+
Alternative splicing	AT3G11880_circ_g.2
Support reads	2
Tissues	seedling
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	AT3G11880.4:4 AT3G11880.2:5 AT3G11880.3:4 AT3G11880.1:5

			
						 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  
						
							AAAGCTTGTAGATGAAAGGGGTGATATTTCCATCAAACTAGCATCATCACCGAGTCATAAATTC
ACACTCAATCAAACTATGGAGAGCATCAGGCTAAAAgtagcagtatttgttgcactagcaatgg
tattgcgtaatgaacctaatactttggttattgtattgccgactctcaaggaagacgagtatca
aggacatg

									
								

					

						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: 762
Transcript exons: 3752331-3752465,3752565-3752701,3752771-3752903,3752977-
3753106,3753195-3753421
GTAGCAGTATTTGTTGCACTAGCAATGGTATTGCGTAATGAACCTAATACTTTGGTTATTGTAT
TGCCGACTCTCAAGGAAGACGAGTATCAAGGACATGACAAGCTTCCGATTTTAGTTTGGATGAT
GGCTCAGGCCTCCCAAGGTGATTTATCTGTAGGCTTGTATTCATGGTCGTGTAACTTGTTACCA
GTATTTTACCAAGAAAACTTGTTACCAGTATCCCGTAGCAACTCTCAGTCAATGGATCTCATCC
TGCAGTTGGCTGAGATGATTTTGTCTAATCTTGATGCTCGGACTATACTTGTAAACGGAACCGT
TATAGATAAACAGCGACTGATTTCACCTTATGCATTTGAGCTCTTGATGCGGCTTACATTCCCT
GCTTCATCTGAAAGAGTAAAGGCTACAGAGAGGTTTGAGGCAATTTATCCCTTGTTGAAGGAAG
TGGCTCTTGCCTGTGAACCAGGAAGCGAGTTAATGAAACAAGTCACTCAACAAATATTCCATTA
TTCTTTGATAATAGCTGGAAGAAGAAATCTTGTTTTAGCCAAGGAAGCTACAGCAATCGCTGTC
TGGTCTCTGACCGAAAACGTAGATTGCTGCAAGCAGTGGGAAAAACTCTATTGGGAGAATAAAG
AAGCTAGTGTTGCTGTTCTTAAAAAGCTTGTAGATGAAAGGGGTGATATTTCCATCAAACTAGC
ATCATCACCGAGTCATAAATTCACACTCAATCAAACTATGGAGAGCATCAGGCTAAAA
						
					

						Genomic sequence
						
							GTAGCAGTATTTGTTGCACTAGCAATGGTATTGCGTAATGAACCTAATACTTTGGTTATTGTAT
TGCCGACTCTCAAGGAAGACGAGTATCAAGGACATGACAAGCTTCCGATTTTAGTTTGGATGAT
GGCTCAGGTTCATGTGATCTTTTGTTCCCCTTATGTCTAGTGTCGAAATTTGTGTGCTTTTGTC
ATCTGTATTCTCAAAGTTAATTCAACTGTAAAATGTGGTCAGGCCTCCCAAGGTGATTTATCTG
TAGGCTTGTATTCATGGTCGTGTAACTTGTTACCAGTATTTTACCAAGAAAACTTGTTACCAGT
ATCCCGTAGCAACTCTCAGTCAATGGATCTCATCCTGCAGTTGGCTGAGATGTGAGTCGAAAAT
TTTCTTGTCATTTCCTTTGCTATATATATACAATCATCTGATCATTTTCTTGGCAGGATTTTGT
CTAATCTTGATGCTCGGACTATACTTGTAAACGGAACCGTTATAGATAAACAGCGACTGATTTC
ACCTTATGCATTTGAGCTCTTGATGCGGCTTACATTCCCTGCTTCATCTGAAAGAGTAAAGGTA
AGCACTAGTGTCAGACTTTATGATGCGTTTGTCAATTCTGATCACAAGCATGGTCTCTATACGC
ACACAGGCTACAGAGAGGTTTGAGGCAATTTATCCCTTGTTGAAGGAAGTGGCTCTTGCCTGTG
AACCAGGAAGCGAGTTAATGAAACAAGTCACTCAACAAATATTCCATTATTCTTTGATAATAGC
TGGAAGAAGTAATAGTAAATGGAATCTTTAATCCCTGAGTTTCTAGTTCCCTCTCTCTTCTCCA
AATAGAGTTCTTATGTTTACCCTTTGTTACAGGAAATCTTGTTTTAGCCAAGGAAGCTACAGCA
ATCGCTGTCTGGTCTCTGACCGAAAACGTAGATTGCTGCAAGCAGTGGGAAAAACTCTATTGGG
AGAATAAAGAAGCTAGTGTTGCTGTTCTTAAAAAGCTTGTAGATGAAAGGGGTGATATTTCCAT
CAAACTAGCATCATCACCGAGTCATAAATTCACACTCAATCAAACTATGGAGAGCATCAGGCTA
AAA
						
					

			
		

Sequences
Splice junction sequence	AAAGCTTGTAGATGAAAGGGGTGATATTTCCATCAAACTAGCATCATCACCGAGTCATAAATTC ACACTCAATCAAACTATGGAGAGCATCAGGCTAAAAgtagcagtatttgttgcactagcaatgg tattgcgtaatgaacctaatactttggttattgtattgccgactctcaaggaagacgagtatca aggacatg
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: 762 Transcript exons: 3752331-3752465,3752565-3752701,3752771-3752903,3752977- 3753106,3753195-3753421 GTAGCAGTATTTGTTGCACTAGCAATGGTATTGCGTAATGAACCTAATACTTTGGTTATTGTAT TGCCGACTCTCAAGGAAGACGAGTATCAAGGACATGACAAGCTTCCGATTTTAGTTTGGATGAT GGCTCAGGCCTCCCAAGGTGATTTATCTGTAGGCTTGTATTCATGGTCGTGTAACTTGTTACCA GTATTTTACCAAGAAAACTTGTTACCAGTATCCCGTAGCAACTCTCAGTCAATGGATCTCATCC TGCAGTTGGCTGAGATGATTTTGTCTAATCTTGATGCTCGGACTATACTTGTAAACGGAACCGT TATAGATAAACAGCGACTGATTTCACCTTATGCATTTGAGCTCTTGATGCGGCTTACATTCCCT GCTTCATCTGAAAGAGTAAAGGCTACAGAGAGGTTTGAGGCAATTTATCCCTTGTTGAAGGAAG TGGCTCTTGCCTGTGAACCAGGAAGCGAGTTAATGAAACAAGTCACTCAACAAATATTCCATTA TTCTTTGATAATAGCTGGAAGAAGAAATCTTGTTTTAGCCAAGGAAGCTACAGCAATCGCTGTC TGGTCTCTGACCGAAAACGTAGATTGCTGCAAGCAGTGGGAAAAACTCTATTGGGAGAATAAAG AAGCTAGTGTTGCTGTTCTTAAAAAGCTTGTAGATGAAAGGGGTGATATTTCCATCAAACTAGC ATCATCACCGAGTCATAAATTCACACTCAATCAAACTATGGAGAGCATCAGGCTAAAA
Genomic sequence	GTAGCAGTATTTGTTGCACTAGCAATGGTATTGCGTAATGAACCTAATACTTTGGTTATTGTAT TGCCGACTCTCAAGGAAGACGAGTATCAAGGACATGACAAGCTTCCGATTTTAGTTTGGATGAT GGCTCAGGTTCATGTGATCTTTTGTTCCCCTTATGTCTAGTGTCGAAATTTGTGTGCTTTTGTC ATCTGTATTCTCAAAGTTAATTCAACTGTAAAATGTGGTCAGGCCTCCCAAGGTGATTTATCTG TAGGCTTGTATTCATGGTCGTGTAACTTGTTACCAGTATTTTACCAAGAAAACTTGTTACCAGT ATCCCGTAGCAACTCTCAGTCAATGGATCTCATCCTGCAGTTGGCTGAGATGTGAGTCGAAAAT TTTCTTGTCATTTCCTTTGCTATATATATACAATCATCTGATCATTTTCTTGGCAGGATTTTGT CTAATCTTGATGCTCGGACTATACTTGTAAACGGAACCGTTATAGATAAACAGCGACTGATTTC ACCTTATGCATTTGAGCTCTTGATGCGGCTTACATTCCCTGCTTCATCTGAAAGAGTAAAGGTA AGCACTAGTGTCAGACTTTATGATGCGTTTGTCAATTCTGATCACAAGCATGGTCTCTATACGC ACACAGGCTACAGAGAGGTTTGAGGCAATTTATCCCTTGTTGAAGGAAGTGGCTCTTGCCTGTG AACCAGGAAGCGAGTTAATGAAACAAGTCACTCAACAAATATTCCATTATTCTTTGATAATAGC TGGAAGAAGTAATAGTAAATGGAATCTTTAATCCCTGAGTTTCTAGTTCCCTCTCTCTTCTCCA AATAGAGTTCTTATGTTTACCCTTTGTTACAGGAAATCTTGTTTTAGCCAAGGAAGCTACAGCA ATCGCTGTCTGGTCTCTGACCGAAAACGTAGATTGCTGCAAGCAGTGGGAAAAACTCTATTGGG AGAATAAAGAAGCTAGTGTTGCTGTTCTTAAAAAGCTTGTAGATGAAAGGGGTGATATTTCCAT CAAACTAGCATCATCACCGAGTCATAAATTCACACTCAATCAAACTATGGAGAGCATCAGGCTA AAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.191107142

Conservation Information
Conserved circRNAs	NA
PMCS	0.191107142

			
						 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 AT3G11880_circ_g.1

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