Plant Circular RNA Database

Detail information of AT3G17880_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT3G17880_circ_g.5
					
						ID in PlantcircBase
						ath_circ_022462
					
						Alias
						At_ciR2422
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 6124749-6125089  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT3G17880						
					
						Parent gene annotation
						
							TPR repeat-containing thioredoxin TDX
							
						Parent gene strand
						+
					
						Alternative splicing
						
							3_circ_igg.3 AT3G17880_circ_g.1 AT3G17880_circ_g.2 AT3G17880_circ_g.3 AT3G17880_circ_g.4 						
					
						Support reads
						3
					
						Tissues
						leaf
					
						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
						AT3G17880.2:2
AT3G17880.1:2

General Information
CircRNA Name	AT3G17880_circ_g.5
ID in PlantcircBase	ath_circ_022462
Alias	At_ciR2422
Organism	Arabidpsis thaliana
Position	chr3: 6124749-6125089 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ
Parent gene	AT3G17880
Parent gene annotation	TPR repeat-containing thioredoxin TDX
Parent gene strand	+
Alternative splicing	3_circ_igg.3 AT3G17880_circ_g.1 AT3G17880_circ_g.2 AT3G17880_circ_g.3 AT3G17880_circ_g.4
Support reads	3
Tissues	leaf
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	AT3G17880.2:2 AT3G17880.1:2

			
						 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  
						
							AAAGAGAATCGAAGAACACCGCAGGAAATACCAACGCCTGAGGAAAGAAAAGGAGCTCCAAAGG
GCTGAACGCGAGAGACGGAAACAGCAAGAAGCCCAGttcaactctgattcagctaaggggtaca
aatcacgaggtatggctaaggccatgttaggccaatgggaagaggctgcagctgatctacatgt
cgcatcaa

						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: 255
Transcript exons: 6124749-6124889,6124976-6125089
TTCAACTCTGATTCAGCTAAGGGGTACAAATCACGAGGTATGGCTAAGGCCATGTTAGGCCAAT
GGGAAGAGGCTGCAGCTGATCTACATGTCGCATCAAAATTAGATTACGATGAGGAGATAGGGAC
AATGCTTAAGAAGGTTGAACCCAATGCAAAGAGAATCGAAGAACACCGCAGGAAATACCAACGC
CTGAGGAAAGAAAAGGAGCTCCAAAGGGCTGAACGCGAGAGACGGAAACAGCAAGAAGCCCAG
						
						Genomic sequence
						
							TTCAACTCTGATTCAGCTAAGGGGTACAAATCACGAGGTATGGCTAAGGCCATGTTAGGCCAAT
GGGAAGAGGCTGCAGCTGATCTACATGTCGCATCAAAATTAGATTACGATGAGGAGATAGGGAC
AATGCTTAAGAAGGTAATTGCGGAAACCTCTTGATATCACTGTATGGTCCTTGAGTTTTACAGT
ACCAAATATATATGCTGAAAATGTGTACTTCCCAGGTTGAACCCAATGCAAAGAGAATCGAAGA
ACACCGCAGGAAATACCAACGCCTGAGGAAAGAAAAGGAGCTCCAAAGGGCTGAACGCGAGAGA
CGGAAACAGCAAGAAGCCCAG

Sequences
Splice junction sequence	AAAGAGAATCGAAGAACACCGCAGGAAATACCAACGCCTGAGGAAAGAAAAGGAGCTCCAAAGG GCTGAACGCGAGAGACGGAAACAGCAAGAAGCCCAGttcaactctgattcagctaaggggtaca aatcacgaggtatggctaaggccatgttaggccaatgggaagaggctgcagctgatctacatgt cgcatcaa
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: 255 Transcript exons: 6124749-6124889,6124976-6125089 TTCAACTCTGATTCAGCTAAGGGGTACAAATCACGAGGTATGGCTAAGGCCATGTTAGGCCAAT GGGAAGAGGCTGCAGCTGATCTACATGTCGCATCAAAATTAGATTACGATGAGGAGATAGGGAC AATGCTTAAGAAGGTTGAACCCAATGCAAAGAGAATCGAAGAACACCGCAGGAAATACCAACGC CTGAGGAAAGAAAAGGAGCTCCAAAGGGCTGAACGCGAGAGACGGAAACAGCAAGAAGCCCAG
Genomic sequence	TTCAACTCTGATTCAGCTAAGGGGTACAAATCACGAGGTATGGCTAAGGCCATGTTAGGCCAAT GGGAAGAGGCTGCAGCTGATCTACATGTCGCATCAAAATTAGATTACGATGAGGAGATAGGGAC AATGCTTAAGAAGGTAATTGCGGAAACCTCTTGATATCACTGTATGGTCCTTGAGTTTTACAGT ACCAAATATATATGCTGAAAATGTGTACTTCCCAGGTTGAACCCAATGCAAAGAGAATCGAAGA ACACCGCAGGAAATACCAACGCCTGAGGAAAGAAAAGGAGCTCCAAAGGGCTGAACGCGAGAGA CGGAAACAGCAAGAAGCCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.279328684

Conservation Information
Conserved circRNAs	NA
PMCS	0.279328684

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6124788-6125086(+)
						
						Potential amino acid sequence
						
							MAKAMLGQWEEAAADLHVASKLDYDEEIGTMLKKVEPNAKRIEEHRRKYQRLRKEKELQRAERE
RRKQQEAQFNSDSAKGYKSRGMAKAMLGQWEEAAADLHVASKLDYDEEIGTMLKKVEPNAKRIE
EHRRKYQRLRKEKELQRAERERRKQQEAQFNSDSAKGYKSRGMAKAMLGQWEEAAADLHVASKL
DYDEEIGTMLKKVEPNAKRIEEHRRKYQRLRKEKELQRAERERRKQQEAQFNSDSAKGYKSRGM
AKAMLGQWEEAAADLHVASKLDYDEEIGTMLKKVEPNAKRIEEHRRKYQRLRKEKELQRAERER
RKQQEAQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6124788-6125086(+)
Potential amino acid sequence	MAKAMLGQWEEAAADLHVASKLDYDEEIGTMLKKVEPNAKRIEEHRRKYQRLRKEKELQRAERE RRKQQEAQFNSDSAKGYKSRGMAKAMLGQWEEAAADLHVASKLDYDEEIGTMLKKVEPNAKRIE EHRRKYQRLRKEKELQRAERERRKQQEAQFNSDSAKGYKSRGMAKAMLGQWEEAAADLHVASKL DYDEEIGTMLKKVEPNAKRIEEHRRKYQRLRKEKELQRAERERRKQQEAQFNSDSAKGYKSRGM AKAMLGQWEEAAADLHVASKLDYDEEIGTMLKKVEPNAKRIEEHRRKYQRLRKEKELQRAERER RKQQEAQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT3G17880_circ_g.5

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