Plant Circular RNA Database

Detail information of AT5G43010_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G43010_circ_g.3
					
						ID in PlantcircBase
						ath_circ_042149
					
						Alias
						5:17249977-17250588
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 17249977-17250588  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G43010						
					
						Parent gene annotation
						
							26S proteasome regulatory subunit 10B homolog A
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G43010_circ_g.1 AT5G43010_circ_g.2 AT5G43010_circ_g.4 AT5G43010_circ_g.5 						
					
						Support reads
						1/1
					
						Tissues
						root
					
						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  
						
							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
						AT5G43010.1:3

General Information
CircRNA Name	AT5G43010_circ_g.3
ID in PlantcircBase	ath_circ_042149
Alias	5:17249977-17250588
Organism	Arabidpsis thaliana
Position	chr5: 17249977-17250588 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G43010
Parent gene annotation	26S proteasome regulatory subunit 10B homolog A
Parent gene strand	-
Alternative splicing	AT5G43010_circ_g.1 AT5G43010_circ_g.2 AT5G43010_circ_g.4 AT5G43010_circ_g.5
Support reads	1/1
Tissues	root
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	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	AT5G43010.1:3

			
						 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  
						
							CGAAGCACTTCTCCAATAATCTGCCCAACACTTTGAAGAGACTTGAGATCATCCTCGGTTTTGT
TGAATTCCTTTTTAGCTCCTCTTAAGTTCTCCCTAGctttggaggtttgatccctactctgagg
aaaagctcaggattcatgagagggagctcaatagattccctgagttctctgatctgatcaccta
accctccg

						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: 419
Transcript exons: 17249977-17250138,17250235-17250371,17250469-17250588
CTTTGGAGGTTTGATCCCTACTCTGAGGAAAAGCTCAGGATTCATGAGAGGGAGCTCAATAGAT
TCCCTGAGTTCTCTGATCTGATCACCTAACCCTCCGACAGCGGAGTAGCTAATGTTGCCAGGGT
CTTCATGAAGCATGTTATAAACAACAGGATCAACTTCTCGGGGAAGGGCTCGCATAATTGTTAG
TGTTGTCATATCGAGAACAACTCGAGTTCCGGAGGTTAGCTTTTCCTTATCCACTTTGCTTCGG
CAACCCACCACATAACGTGGACCACTGCTCGCTTTCACAATCAATCTTTCATTATCCAGGGGTC
GAAGCACTTCTCCAATAATCTGCCCAACACTTTGAAGAGACTTGAGATCATCCTCGGTTTTGTT
GAATTCCTTTTTAGCTCCTCTTAAGTTCTCCCTAG
						
						Genomic sequence
						
							CTTTGGAGGTTTGATCCCTACTCTGAGGAAAAGCTCAGGATTCATGAGAGGGAGCTCAATAGAT
TCCCTGAGTTCTCTGATCTGATCACCTAACCCTCCGACAGCGGAGTAGCTAATGTTGCCAGGGT
CTTCATGAAGCATGTTATAAACAACAGGATCAACCTACCATCAACATAAAAAACCACATTATTA
TCAAGAGAAATACACTACAAGAGTATAACTATAACAGAACCGAACACATGTCCAAATCGAACTT
ACTTCTCGGGGAAGGGCTCGCATAATTGTTAGTGTTGTCATATCGAGAACAACTCGAGTTCCGG
AGGTTAGCTTTTCCTTATCCACTTTGCTTCGGCAACCCACCACATAACGTGGACCACTGCTCGC
TTTCACAATCACTAAAACACAAAACATTTAAAATTTAACCAAGGGTCCAATGAGCAAAAATCTC
AAAAGATAAAAAAGAAGGGTATTAGGTCGAGGAAAAATGATTACATCTTTCATTATCCAGGGGT
CGAAGCACTTCTCCAATAATCTGCCCAACACTTTGAAGAGACTTGAGATCATCCTCGGTTTTGT
TGAATTCCTTTTTAGCTCCTCTTAAGTTCTCCCTAG

Sequences
Splice junction sequence	CGAAGCACTTCTCCAATAATCTGCCCAACACTTTGAAGAGACTTGAGATCATCCTCGGTTTTGT TGAATTCCTTTTTAGCTCCTCTTAAGTTCTCCCTAGctttggaggtttgatccctactctgagg aaaagctcaggattcatgagagggagctcaatagattccctgagttctctgatctgatcaccta accctccg
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: 419 Transcript exons: 17249977-17250138,17250235-17250371,17250469-17250588 CTTTGGAGGTTTGATCCCTACTCTGAGGAAAAGCTCAGGATTCATGAGAGGGAGCTCAATAGAT TCCCTGAGTTCTCTGATCTGATCACCTAACCCTCCGACAGCGGAGTAGCTAATGTTGCCAGGGT CTTCATGAAGCATGTTATAAACAACAGGATCAACTTCTCGGGGAAGGGCTCGCATAATTGTTAG TGTTGTCATATCGAGAACAACTCGAGTTCCGGAGGTTAGCTTTTCCTTATCCACTTTGCTTCGG CAACCCACCACATAACGTGGACCACTGCTCGCTTTCACAATCAATCTTTCATTATCCAGGGGTC GAAGCACTTCTCCAATAATCTGCCCAACACTTTGAAGAGACTTGAGATCATCCTCGGTTTTGTT GAATTCCTTTTTAGCTCCTCTTAAGTTCTCCCTAG
Genomic sequence	CTTTGGAGGTTTGATCCCTACTCTGAGGAAAAGCTCAGGATTCATGAGAGGGAGCTCAATAGAT TCCCTGAGTTCTCTGATCTGATCACCTAACCCTCCGACAGCGGAGTAGCTAATGTTGCCAGGGT CTTCATGAAGCATGTTATAAACAACAGGATCAACCTACCATCAACATAAAAAACCACATTATTA TCAAGAGAAATACACTACAAGAGTATAACTATAACAGAACCGAACACATGTCCAAATCGAACTT ACTTCTCGGGGAAGGGCTCGCATAATTGTTAGTGTTGTCATATCGAGAACAACTCGAGTTCCGG AGGTTAGCTTTTCCTTATCCACTTTGCTTCGGCAACCCACCACATAACGTGGACCACTGCTCGC TTTCACAATCACTAAAACACAAAACATTTAAAATTTAACCAAGGGTCCAATGAGCAAAAATCTC AAAAGATAAAAAAGAAGGGTATTAGGTCGAGGAAAAATGATTACATCTTTCATTATCCAGGGGT CGAAGCACTTCTCCAATAATCTGCCCAACACTTTGAAGAGACTTGAGATCATCCTCGGTTTTGT TGAATTCCTTTTTAGCTCCTCTTAAGTTCTCCCTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.346229882

Conservation Information
Conserved circRNAs	NA
PMCS	0.346229882

			
						 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 AT5G43010_circ_g.3

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