Plant Circular RNA Database

Detail information of 3_circ_igg.20

			
						 General Information
					
						CircRNA Name
						3_circ_igg.20
					
						ID in PlantcircBase
						ath_circ_026305
					
						Alias
						At_ciR3740, AtciR48
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 17173528-17174520  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							igg-circRNA							
									
						Identification method
						CIRI, circRNA_finder, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							AT3G46614_circ_g.1 AT3G46614_circ_g.2 AT3G46614_circ_g.3 AT3G46614_circ_g.4 AT3G46614_circ_g.5 AT3G46614_circ_g.6 AT3G46614_circ_g.7 3_circ_igg.8 AT3G46614_circ_g.9 AT3G46614_circ_g.10 3_circ_ig.11 3_circ_igg.12 3_circ_ig.13 3_circ_ig.14 3_circ_igg.15 3_circ_ig.16 3_circ_igg.17 3_circ_ag.18 3_circ_igg.19 3_circ_igg.21 3_circ_igg.22 3_circ_igg.23 						
					
						Support reads
						2/10
					
						Tissues
						leaf/root, aerial, inflorescences, whole_plant
					
						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  
						
							CT-AC							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.20
ID in PlantcircBase	ath_circ_026305
Alias	At_ciR3740, AtciR48
Organism	Arabidpsis thaliana
Position	chr3: 17173528-17174520 JBrowse»
Reference genome	TAIR10.38
Type	igg-circRNA
Identification method	CIRI, circRNA_finder, find_circ, CIRI-full, CIRI2
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	AT3G46614_circ_g.1 AT3G46614_circ_g.2 AT3G46614_circ_g.3 AT3G46614_circ_g.4 AT3G46614_circ_g.5 AT3G46614_circ_g.6 AT3G46614_circ_g.7 3_circ_igg.8 AT3G46614_circ_g.9 AT3G46614_circ_g.10 3_circ_ig.11 3_circ_igg.12 3_circ_ig.13 3_circ_ig.14 3_circ_igg.15 3_circ_ig.16 3_circ_igg.17 3_circ_ag.18 3_circ_igg.19 3_circ_igg.21 3_circ_igg.22 3_circ_igg.23
Support reads	2/10
Tissues	leaf/root, aerial, inflorescences, whole_plant
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	CT-AC 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  
						
							CCTTTGTGAAGTATGTATTGAGTAGAAATAGATAAACTTCACCTTATAACTCTAGCTTTTATCT
TGCATTTTGAATCATCACCGAGCTTCCCTGATATGTctctcatatgcacttggttacatattca
ccttcgaaattttgttctcttgacctgaaaattaccagcaagaggccggaaacacgacccctcg
tttgcctc

									
								

					

						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: 171
Transcript exons: 17173528-17173649,17174472-17174520
CTCTCATATGCACTTGGTTACATATTCACCTTCGAAATTTTGTTCTCTTGACCTGAAAATTACC
AGCAAGAGGCCGGAAACACGACCCCTCGTTTGCCTCTTGGCTACTAAACCAAAATTTCCTAGCT
TTTATCTTGCATTTTGAATCATCACCGAGCTTCCCTGATATGT
Transcript length: 385
Transcript exons: 17173528-17174520
CTCTCATATGCACTTGGTTACATATTCACCTTCGAAATTTTGTTCTCTTGACCTGAAAATTACC
AGCAAGAGGCCGGAAACACGACCCCTCGTTTGCCTCTTGGCTACTAAACCAAAATTTCACTGAG
CCAAAATCTGACTGCATGCTACTTTACAGATCATGCTTTATAATGAAGAACCCAACTGATATTT
CCTTTCTCCGAGGCAACTGAAGTACTTTCCTAAGTTTAGTTATATTCAGCTTAAGGGTCGTCCA
TCTTGATACAAAATCATTAAATTCTGATCCAAGCCTGATTCGACTTCTTTGCTCCTGTTGTTTC
TGTTAATCTTATAACTCTAGCTTTTATCTTGCATTTTGAATCATCACCGAGCTTCCCTGATATG
T
						
					

						Genomic sequence
						
							CTCTCATATGCACTTGGTTACATATTCACCTTCGAAATTTTGTTCTCTTGACCTGAAAATTACC
AGCAAGAGGCCGGAAACACGACCCCTCGTTTGCCTCTTGGCTACTAAACCAAAATTTCACCTGA
AAGTACAACACAAACAATAAATTGAAACCACAAATCAATGCCAAAATAAATAAAAAAACACTAG
GTAGAGTCTTACTGAGCCAAAATCTGACTGCATGCTACTTTACAGATCATGCTTTATAATGAAG
AACCCAACTGAAAACATAACTCTTCAAGTTAGAAAAACAATCTAACTCCAGAGGAATATAAACT
GCAATATCGTACCTTGGAAATCGAGATCTATATGATATGTTTTTTTAGTTGATATCACTTAAAC
ACGTTAGAAATTAGTAGAAAACATTGTATCAAAGTGTGTTTATCTACCTGACCCTTCTTTTTAC
GGAGAGATTGAATAGCTTTCTTAAATTTGGTTCTTTTCCACTTAAGAATCGCCTATCCTGGTAC
AGAACCATTATGTTAGCAGTATACACAAGACCATTAGAAAACTACAAAAACTCTGAAAAGAGAT
GAAGGTAGTTTATCTACCTGATATTTCCTTTCTCCGAGGCAACTGAAGTACTTTCCTAAGTTTA
GTTATATTCAGCTTAAGGGTCGTCCATCTTGATACAAAATCATTCTAATAGCAGTAACTATATA
CATAAGACTGTAAAATTAAATCACAAAATAATGCTAATTAAGAAACTTACAAATTCTGATCCAA
GCCTGATTCGACTTCTTTGCTCCTGTTGTTTCTGTTAATCTTGACAAAGGAAACAATGTCCACA
ACTCAAATATTGAACATGCTTATTAAGTTTGAATAAAACAAGTTTTTACGAGTGCATTTGTCCT
TTGTGAAGTATGTATTGAGTAGAAATAGATAAACTTCACCTTATAACTCTAGCTTTTATCTTGC
ATTTTGAATCATCACCGAGCTTCCCTGATATGT
						
					

			
		

Sequences
Splice junction sequence	CCTTTGTGAAGTATGTATTGAGTAGAAATAGATAAACTTCACCTTATAACTCTAGCTTTTATCT TGCATTTTGAATCATCACCGAGCTTCCCTGATATGTctctcatatgcacttggttacatattca ccttcgaaattttgttctcttgacctgaaaattaccagcaagaggccggaaacacgacccctcg tttgcctc
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: 171 Transcript exons: 17173528-17173649,17174472-17174520 CTCTCATATGCACTTGGTTACATATTCACCTTCGAAATTTTGTTCTCTTGACCTGAAAATTACC AGCAAGAGGCCGGAAACACGACCCCTCGTTTGCCTCTTGGCTACTAAACCAAAATTTCCTAGCT TTTATCTTGCATTTTGAATCATCACCGAGCTTCCCTGATATGT Transcript length: 385 Transcript exons: 17173528-17174520 CTCTCATATGCACTTGGTTACATATTCACCTTCGAAATTTTGTTCTCTTGACCTGAAAATTACC AGCAAGAGGCCGGAAACACGACCCCTCGTTTGCCTCTTGGCTACTAAACCAAAATTTCACTGAG CCAAAATCTGACTGCATGCTACTTTACAGATCATGCTTTATAATGAAGAACCCAACTGATATTT CCTTTCTCCGAGGCAACTGAAGTACTTTCCTAAGTTTAGTTATATTCAGCTTAAGGGTCGTCCA TCTTGATACAAAATCATTAAATTCTGATCCAAGCCTGATTCGACTTCTTTGCTCCTGTTGTTTC TGTTAATCTTATAACTCTAGCTTTTATCTTGCATTTTGAATCATCACCGAGCTTCCCTGATATG T
Genomic sequence	CTCTCATATGCACTTGGTTACATATTCACCTTCGAAATTTTGTTCTCTTGACCTGAAAATTACC AGCAAGAGGCCGGAAACACGACCCCTCGTTTGCCTCTTGGCTACTAAACCAAAATTTCACCTGA AAGTACAACACAAACAATAAATTGAAACCACAAATCAATGCCAAAATAAATAAAAAAACACTAG GTAGAGTCTTACTGAGCCAAAATCTGACTGCATGCTACTTTACAGATCATGCTTTATAATGAAG AACCCAACTGAAAACATAACTCTTCAAGTTAGAAAAACAATCTAACTCCAGAGGAATATAAACT GCAATATCGTACCTTGGAAATCGAGATCTATATGATATGTTTTTTTAGTTGATATCACTTAAAC ACGTTAGAAATTAGTAGAAAACATTGTATCAAAGTGTGTTTATCTACCTGACCCTTCTTTTTAC GGAGAGATTGAATAGCTTTCTTAAATTTGGTTCTTTTCCACTTAAGAATCGCCTATCCTGGTAC AGAACCATTATGTTAGCAGTATACACAAGACCATTAGAAAACTACAAAAACTCTGAAAAGAGAT GAAGGTAGTTTATCTACCTGATATTTCCTTTCTCCGAGGCAACTGAAGTACTTTCCTAAGTTTA GTTATATTCAGCTTAAGGGTCGTCCATCTTGATACAAAATCATTCTAATAGCAGTAACTATATA CATAAGACTGTAAAATTAAATCACAAAATAATGCTAATTAAGAAACTTACAAATTCTGATCCAA GCCTGATTCGACTTCTTTGCTCCTGTTGTTTCTGTTAATCTTGACAAAGGAAACAATGTCCACA ACTCAAATATTGAACATGCTTATTAAGTTTGAATAAAACAAGTTTTTACGAGTGCATTTGTCCT TTGTGAAGTATGTATTGAGTAGAAATAGATAAACTTCACCTTATAACTCTAGCTTTTATCTTGC ATTTTGAATCATCACCGAGCTTCCCTGATATGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.349229248

Conservation Information
Conserved circRNAs	NA
PMCS	0.349229248

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress; responsive to methyl jasmonate

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress; responsive to methyl jasmonate

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Zhang et al., 2019

circRNA

Detail information of 3_circ_igg.20

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