Plant Circular RNA Database

Detail information of AT1G16880_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT1G16880_circ_g.4
					
						ID in PlantcircBase
						ath_circ_002980
					
						Alias
						1:5774332-5775981
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 5774332-5775981  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G16880						
					
						Parent gene annotation
						
							ACR11
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G16880_circ_g.2 AT1G16880_circ_g.3 AT1G16880_circ_g.5 AT1G16880_circ_g.6 AT1G16880_circ_g.7 AT1G16880_circ_g.8 AT1G16880_circ_g.9 						
					
						Support reads
						1/1
					
						Tissues
						leaf;flower
					
						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
						AT1G16880.2:5
AT1G16880.1:8

General Information
CircRNA Name	AT1G16880_circ_g.4
ID in PlantcircBase	ath_circ_002980
Alias	1:5774332-5775981
Organism	Arabidpsis thaliana
Position	chr1: 5774332-5775981 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G16880
Parent gene annotation	ACR11
Parent gene strand	+
Alternative splicing	AT1G16880_circ_g.2 AT1G16880_circ_g.3 AT1G16880_circ_g.5 AT1G16880_circ_g.6 AT1G16880_circ_g.7 AT1G16880_circ_g.8 AT1G16880_circ_g.9
Support reads	1/1
Tissues	leaf;flower
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	AT1G16880.2:5 AT1G16880.1:8

			
						 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  
						
							TGCTTCTTCTTGTTGTATGTGAAACAAAAAGGGTTTGTTGGCTAAGGTGAAGTTTCATGTAAGC
TACAGGAACAAAGCCCTAATCAAGCCTCTCCAGCAGattatccactttgaagattagagcatca
aatgctactgctgtggaggtatgaaaatgaaatgattacacaaggacactagtaatttgaatag
acttttta

									
								

					

						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
						
							ATTATCCACTTTGAAGATTAGAGCATCAAATGCTACTGCTGTGGAGGTATGAAAATGAAATGAT
TACACAAGGACACTAGTAATTTGAATAGACTTTTTAAAGTTTATATGTTTTTGTTTTTGATTTT
GAAGAATGGAAAGCAAGAAGGAAGTGCTGCTGATTCTGATAAAGTTCCAACTCCAGTTGTTATA
ATCGACCAAGATTCTGACCCTGATGCAACCGTTCTTGAAGTTACATTCGGAGATCGTCTTGGAG
CTTTACTTGACACTGTAAGGAAGGATACCTTCTTCTTACTCACTTGTTGCTAGCTCTGCATAAT
CGACCAACATTCACAAAAGCTTCTTACTTCCTTTCCTGCTTTTTTGACTGCTTCTTGATCTGAT
CAACTTTGCCCTTCTAGATGAATGCGCTCAAAAACTTGGGATTGAATGTCGTCAAGGCAAATGT
TTACCTTGATTCTTCCGGCAAGCACAACAAATTTGCCATTACTAGAGCGTATGTCTTTTCATAT
CATCAAAGAGTATTTTGAGCTCCAAGAGTCGTTTAGATAGTTAATGTTGCTTTGAATCGATTGA
CTCTGTCAAATAGTTGACTTTAGATTGAGTTTTGAGCTGACTGTAATTGTTGTTACAACAGAGA
TAGTGGAAGAAAAGTAGAAGACCCTGAATTGCTTGAGGCCATTCGTCTCACAGTCATAAACAAT
CTGCTTGAGTTTCATCCTGTAACTACTTCACATCCTAATATCCTCTCTTTCTATTTTTCCTATA
TCTTGCATAATTTTTTAACTCACACATTGCTTCTCGATGATTTGGATCAGGAATCAAGTTCTCA
GTTGGCAATGGGAGCAGCTTTTGGTGTTCTTCCTCCAACTGAACCGGTAAAAACCTTAAACTGT
GATGCTCTTTTTATAACCTTATCCACTTCTTTTGTATTGCACTAATTCTTCAAGTAGTTAGCAT
CCTCGAACATAAAGGTCAAGACTGCTTGTCGTTTCCTCGGTCACGTACAGATAAGAAACAATAA
TAGAGAAAACAAAGACTTAACTAATAATCAACATATTTGGATTTGGCGGGTCAATGTAGAGTAC
AAGTATTAAACTTCATTATAGTATTAATCACTTTGATGAAGAAGGGAATACCCACGCAACTTCA
AAGTAGCTTCAAAATTCATTTTCCTTCTTCTGTATTTTGGATTGGGATGTTGACAGATTGACGT
GGACATAGCAACACATATAACCATTGAAGATGATGGACCAGACCGCAGGTAATGTATACCCATA
CCTTATCTCAACTCTAGAACCTTATCCAAATGCTTTTATTCTTATGATATATGATCTGATCATT
GATCCATAATTATTTGTTGATGATGCAGTTTACTCTTCATAGAATCAGCGGATAGACCTGGACT
ATTAGTTGAGCTGGTGAAGATCATTTCAGATATCAGCGTCGCTGTTGAATCTGGAGAATTCGAC
ACCGAGGTATCTAATAATCCTGTTTTTTAATGTCTAAAACATATACCCTCCGCTATAATATCGC
TCTGTTTCTCATGTTGCTTCTTCTTGTTGTATGTGAAACAAAAAGGGTTTGTTGGCTAAGGTGA
AGTTTCATGTAAGCTACAGGAACAAAGCCCTAATCAAGCCTCTCCAGCAG
						
					

			
		

Sequences
Splice junction sequence	TGCTTCTTCTTGTTGTATGTGAAACAAAAAGGGTTTGTTGGCTAAGGTGAAGTTTCATGTAAGC TACAGGAACAAAGCCCTAATCAAGCCTCTCCAGCAGattatccactttgaagattagagcatca aatgctactgctgtggaggtatgaaaatgaaatgattacacaaggacactagtaatttgaatag acttttta
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	ATTATCCACTTTGAAGATTAGAGCATCAAATGCTACTGCTGTGGAGGTATGAAAATGAAATGAT TACACAAGGACACTAGTAATTTGAATAGACTTTTTAAAGTTTATATGTTTTTGTTTTTGATTTT GAAGAATGGAAAGCAAGAAGGAAGTGCTGCTGATTCTGATAAAGTTCCAACTCCAGTTGTTATA ATCGACCAAGATTCTGACCCTGATGCAACCGTTCTTGAAGTTACATTCGGAGATCGTCTTGGAG CTTTACTTGACACTGTAAGGAAGGATACCTTCTTCTTACTCACTTGTTGCTAGCTCTGCATAAT CGACCAACATTCACAAAAGCTTCTTACTTCCTTTCCTGCTTTTTTGACTGCTTCTTGATCTGAT CAACTTTGCCCTTCTAGATGAATGCGCTCAAAAACTTGGGATTGAATGTCGTCAAGGCAAATGT TTACCTTGATTCTTCCGGCAAGCACAACAAATTTGCCATTACTAGAGCGTATGTCTTTTCATAT CATCAAAGAGTATTTTGAGCTCCAAGAGTCGTTTAGATAGTTAATGTTGCTTTGAATCGATTGA CTCTGTCAAATAGTTGACTTTAGATTGAGTTTTGAGCTGACTGTAATTGTTGTTACAACAGAGA TAGTGGAAGAAAAGTAGAAGACCCTGAATTGCTTGAGGCCATTCGTCTCACAGTCATAAACAAT CTGCTTGAGTTTCATCCTGTAACTACTTCACATCCTAATATCCTCTCTTTCTATTTTTCCTATA TCTTGCATAATTTTTTAACTCACACATTGCTTCTCGATGATTTGGATCAGGAATCAAGTTCTCA GTTGGCAATGGGAGCAGCTTTTGGTGTTCTTCCTCCAACTGAACCGGTAAAAACCTTAAACTGT GATGCTCTTTTTATAACCTTATCCACTTCTTTTGTATTGCACTAATTCTTCAAGTAGTTAGCAT CCTCGAACATAAAGGTCAAGACTGCTTGTCGTTTCCTCGGTCACGTACAGATAAGAAACAATAA TAGAGAAAACAAAGACTTAACTAATAATCAACATATTTGGATTTGGCGGGTCAATGTAGAGTAC AAGTATTAAACTTCATTATAGTATTAATCACTTTGATGAAGAAGGGAATACCCACGCAACTTCA AAGTAGCTTCAAAATTCATTTTCCTTCTTCTGTATTTTGGATTGGGATGTTGACAGATTGACGT GGACATAGCAACACATATAACCATTGAAGATGATGGACCAGACCGCAGGTAATGTATACCCATA CCTTATCTCAACTCTAGAACCTTATCCAAATGCTTTTATTCTTATGATATATGATCTGATCATT GATCCATAATTATTTGTTGATGATGCAGTTTACTCTTCATAGAATCAGCGGATAGACCTGGACT ATTAGTTGAGCTGGTGAAGATCATTTCAGATATCAGCGTCGCTGTTGAATCTGGAGAATTCGAC ACCGAGGTATCTAATAATCCTGTTTTTTAATGTCTAAAACATATACCCTCCGCTATAATATCGC TCTGTTTCTCATGTTGCTTCTTCTTGTTGTATGTGAAACAAAAAGGGTTTGTTGGCTAAGGTGA AGTTTCATGTAAGCTACAGGAACAAAGCCCTAATCAAGCCTCTCCAGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.114233389

Conservation Information
Conserved circRNAs	NA
PMCS	0.114233389

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR171b-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-miR171b-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT1G16880_circ_g.4

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