Plant Circular RNA Database

Detail information of 3_circ_igg.3

			
						 General Information
					
						CircRNA Name
						3_circ_igg.3
					
						ID in PlantcircBase
						ath_circ_022457
					
						Alias
						3:6123280-6124589
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 6123280-6124589  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							igg-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							AT3G17880_circ_g.1 AT3G17880_circ_g.2 AT3G17880_circ_g.3 AT3G17880_circ_g.4 AT3G17880_circ_g.5 						
					
						Support reads
						2
					
						Tissues
						flower
					
						Exon boundary  
						
							NA-NA							"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
						NA

General Information
CircRNA Name	3_circ_igg.3
ID in PlantcircBase	ath_circ_022457
Alias	3:6123280-6124589
Organism	Arabidpsis thaliana
Position	chr3: 6123280-6124589 JBrowse»
Reference genome	TAIR10.38
Type	igg-circRNA
Identification method	find_circ; CIRI2
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	AT3G17880_circ_g.1 AT3G17880_circ_g.2 AT3G17880_circ_g.3 AT3G17880_circ_g.4 AT3G17880_circ_g.5
Support reads	2
Tissues	flower
Exon boundary	NA-NA "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	NA

			
						 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  
						
							GATAATACTCAATATTTGTGATTGTTGTCCTGCAGCTAGTGTGTTTTTAAAAGTTAAGAAGCCA
AATGCTGCAATTCGTGATGCCAACGTAGCGTTACAGcccatcaaggcccaatgtcttattgcac
aacgaaaagggatgttgcaaaagatgataaaccggatatgaattcagtcgcggttaagttaacg
cgaagaca

						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
						
							CCCATCAAGGCCCAATGTCTTATTGCACAACGAAAAGGGATGTTGCAAAAGATGATAAACCGGA
TATGAATTCAGTCGCGGTTAAGTTAACGCGAAGACAAAACCGGTTGGACATGTTCGGTTTTCGG
CGATGATTATTTCAACGTTTTTCAGTCTAATCAAAACCAATACGAGCAGACACAGCTCCGTACG
ATCACAAGGATTCACTGATTTCTAAGCTTTTCATAGAAAGAAGAAGAAAAAGGCGGAATTCGAT
GGTGGATGCGATTCAAGTAGCTGAGCTGAGAAGATTCGTCGAGCAGTTGAAATTGAATCCTTCG
ATTCTCCACGATCCTAGTCTGGTTTTCTTCAAAGAATATCTCCGAAGGTGATTCATTCTTCTCT
GACTTATCTTTCTTTCGGTGAATTTCATTTGTCAGTTGAATTTTTCCATGGAGCTGTGAGTTTC
TTTGTAATCGATGCTCGTTCCCGTCTTATCGTGTACAGTTTAGGAGCTCAAGTTCCGAAGATTG
AGAAAACTGTAAGTTGTCTTTCTTATGAATTATCGATGTTTAGGTTTCTCTTGTTTGTGCTACT
TGGGATTGAGTTCTTAATATCTTTGTGTTGAATTGATGTACAAAACCCTTTTCTAGGCTTCAAC
ACTATCTAAATGTTGATCGAATAGTTAACTATAAATTGCAGGAAAGAGATTATGAAGATAAGGC
TGAGACAAAACCCAGTTTCTCTCCTAAACATGATGATGATGATGATGATATTATGGAGTCTGAT
GTTGAACTCGACAACTCTGATGTAGTTGAACCAGACAATGAGCCTCCTCAGCCGGTAGGTGTTG
AAGTTATCATCTTTGGATATTATGTGGTGCTTGTGTCTCTATGCATTTTTTTACCTGATTGGAT
GATTTTACTTTCTTGTCTTAGATGGGAGACCCTACTGCTGAAGTGACCGATGAAAATAGGGATG
ATGCTCAGTCAGAGAAGAGCAAAGCTATGGAGGCAATCTCTGATGGTACATAACTACCGTTGAA
ATTGGTTTTGATTATCTACTTCATAAGATTTCTCCTTAATGCTTGATTGGTATACAGGGAGGTT
TGACGAAGCTATAGAGCATCTAACAAAAGCTGTCATGCTAAATCCTACTTCAGCGATTCTCTAC
GCCACTAGAGGTAACTTTCTTTTACTAGTTCACTCTCCCTTTTCGGCTGAATGTGGGTGATAAT
ACTCAATATTTGTGATTGTTGTCCTGCAGCTAGTGTGTTTTTAAAAGTTAAGAAGCCAAATGCT
GCAATTCGTGATGCCAACGTAGCGTTACAG

Sequences
Splice junction sequence	GATAATACTCAATATTTGTGATTGTTGTCCTGCAGCTAGTGTGTTTTTAAAAGTTAAGAAGCCA AATGCTGCAATTCGTGATGCCAACGTAGCGTTACAGcccatcaaggcccaatgtcttattgcac aacgaaaagggatgttgcaaaagatgataaaccggatatgaattcagtcgcggttaagttaacg cgaagaca
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	CCCATCAAGGCCCAATGTCTTATTGCACAACGAAAAGGGATGTTGCAAAAGATGATAAACCGGA TATGAATTCAGTCGCGGTTAAGTTAACGCGAAGACAAAACCGGTTGGACATGTTCGGTTTTCGG CGATGATTATTTCAACGTTTTTCAGTCTAATCAAAACCAATACGAGCAGACACAGCTCCGTACG ATCACAAGGATTCACTGATTTCTAAGCTTTTCATAGAAAGAAGAAGAAAAAGGCGGAATTCGAT GGTGGATGCGATTCAAGTAGCTGAGCTGAGAAGATTCGTCGAGCAGTTGAAATTGAATCCTTCG ATTCTCCACGATCCTAGTCTGGTTTTCTTCAAAGAATATCTCCGAAGGTGATTCATTCTTCTCT GACTTATCTTTCTTTCGGTGAATTTCATTTGTCAGTTGAATTTTTCCATGGAGCTGTGAGTTTC TTTGTAATCGATGCTCGTTCCCGTCTTATCGTGTACAGTTTAGGAGCTCAAGTTCCGAAGATTG AGAAAACTGTAAGTTGTCTTTCTTATGAATTATCGATGTTTAGGTTTCTCTTGTTTGTGCTACT TGGGATTGAGTTCTTAATATCTTTGTGTTGAATTGATGTACAAAACCCTTTTCTAGGCTTCAAC ACTATCTAAATGTTGATCGAATAGTTAACTATAAATTGCAGGAAAGAGATTATGAAGATAAGGC TGAGACAAAACCCAGTTTCTCTCCTAAACATGATGATGATGATGATGATATTATGGAGTCTGAT GTTGAACTCGACAACTCTGATGTAGTTGAACCAGACAATGAGCCTCCTCAGCCGGTAGGTGTTG AAGTTATCATCTTTGGATATTATGTGGTGCTTGTGTCTCTATGCATTTTTTTACCTGATTGGAT GATTTTACTTTCTTGTCTTAGATGGGAGACCCTACTGCTGAAGTGACCGATGAAAATAGGGATG ATGCTCAGTCAGAGAAGAGCAAAGCTATGGAGGCAATCTCTGATGGTACATAACTACCGTTGAA ATTGGTTTTGATTATCTACTTCATAAGATTTCTCCTTAATGCTTGATTGGTATACAGGGAGGTT TGACGAAGCTATAGAGCATCTAACAAAAGCTGTCATGCTAAATCCTACTTCAGCGATTCTCTAC GCCACTAGAGGTAACTTTCTTTTACTAGTTCACTCTCCCTTTTCGGCTGAATGTGGGTGATAAT ACTCAATATTTGTGATTGTTGTCCTGCAGCTAGTGTGTTTTTAAAAGTTAAGAAGCCAAATGCT GCAATTCGTGATGCCAACGTAGCGTTACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.126892169

Conservation Information
Conserved circRNAs	NA
PMCS	0.126892169

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR5658 						
					
						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-miR5658
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of 3_circ_igg.3

Address

Any questions?

Supported by