Plant Circular RNA Database

Detail information of AT3G27090_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G27090_circ_g.1
					
						ID in PlantcircBase
						ath_circ_024018
					
						Alias
						Chr3:9990008|9991140
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 9990008-9991140  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer; CIRI
					
						Parent gene
						
							AT3G27090						
					
						Parent gene annotation
						
							AT3g27090/MOJ10_18
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G27090_circ_g.2 AT3G27090_circ_g.3 AT3G27090_circ_g.4 						
					
						Support reads
						4
					
						Tissues
						seedling
					
						Exon boundary  
						
							No-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-TA							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
						AT3G27090.1:4
AT3G27090.2:4
AT3G27090.3:4

General Information
CircRNA Name	AT3G27090_circ_g.1
ID in PlantcircBase	ath_circ_024018
Alias	Chr3:9990008\|9991140
Organism	Arabidpsis thaliana
Position	chr3: 9990008-9991140 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer; CIRI
Parent gene	AT3G27090
Parent gene annotation	AT3g27090/MOJ10_18
Parent gene strand	+
Alternative splicing	AT3G27090_circ_g.2 AT3G27090_circ_g.3 AT3G27090_circ_g.4
Support reads	4
Tissues	seedling
Exon boundary	No-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-TA 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	AT3G27090.1:4 AT3G27090.2:4 AT3G27090.3:4

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							YES							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   
						
							Convergent:(F):AGGTCAGACGAGAGCATCAGAG
(R):AAGAGTCTCCGAAGCAGGCAAG.Divergent:(F):GCAAAGCCTTGGAAGAGGACTC
(R)CTCTGCATCGAAGTCTTCCCCA
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	YES 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	Convergent:(F):AGGTCAGACGAGAGCATCAGAG (R):AAGAGTCTCCGAAGCAGGCAAG.Divergent:(F):GCAAAGCCTTGGAAGAGGACTC (R)CTCTGCATCGAAGTCTTCCCCA 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  
						
							AGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCACCACTATGAT
GGTCCAAAATTCCGCCTTGAGCTCTCTGTTCCTGAGgccttttgagatatggacagcttctggc
aattaggtgatgagctacgaggtcagacgagagcatcagaggatcacaaatggtctactgttgc
aacgaagc

						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
						
							GCCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTCAGACGAGAGCAT
CAGAGGATCACAAATGGTCTACTGTTGCAACGAAGCTAGCTGAGCAAACTAGAATGAAAGGGGA
GAGGATGAACAATCTTGATCTCTCCAAAGGTTACACTGAGTTTAGACCAAGTGAGAAATTCAGT
TTCCAGGAGAACAATCTTAACTTCAACATGTTGAATTTGGATGGTAAATTTGGTGAAAGCATCA
TGGGGAAGACTTCGATGCAGAGCAATGTTTATAATATGAATACTGTTTTCCAGAAGAATGACTT
TAAGAGTGGAGGCAACATGAAAGTTAACAAGTATAATGGTAATGTTGTTGCTAACAAGGAGATG
AGCAACAACAAACATAACAACAACTGCAATGATAATGGGAATATGAATTTGGCTGTTGACAAGA
GGTTTAAAACCTTGCCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTT
TGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGGTAATTTCCCAATA
CCCTTTTCTAGTGTTTTACTGATATTCAAACTGCAAGTAAATAACTTTTTGACTTTCATCATTG
TTCAGGTTTACCTCCAAGATACAGAGACTCTGTTCGAGCTATAACACCTGGATTGCCTCTGTTT
CTTTACAACTACACCACTCACCAGCTTCATGGTATCTTTGAGGTTTGTTCTCGTGCTTTTTTTT
TGTCATAACAATGGTTTTGATGCTACCATTTACTGAAAATTTGATGTTCGAATTATTCCGTGAA
TGATTCCTTGTTTAGGCAACAACTTTTGGAGGTACTAATATTGATGCTACTGCTTGGGAAGACA
AAAAGTGCAAAGGAGAGTCAAGGTTTCCGGCTCAGGTGAAACTTAAATCACAATGACTTTCATT
GTTTTAAGTCTTTATTTTGATATCTTGTACTAATATAACTTCTTTCTCTTAAATTGTAACAGGT
AAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCAC
CACTATGATGGTCCAAAATTCCGCCTTGAGCTCTCTGTTCCTGAG

Sequences
Splice junction sequence	AGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCACCACTATGAT GGTCCAAAATTCCGCCTTGAGCTCTCTGTTCCTGAGgccttttgagatatggacagcttctggc aattaggtgatgagctacgaggtcagacgagagcatcagaggatcacaaatggtctactgttgc aacgaagc
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	GCCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTCAGACGAGAGCAT CAGAGGATCACAAATGGTCTACTGTTGCAACGAAGCTAGCTGAGCAAACTAGAATGAAAGGGGA GAGGATGAACAATCTTGATCTCTCCAAAGGTTACACTGAGTTTAGACCAAGTGAGAAATTCAGT TTCCAGGAGAACAATCTTAACTTCAACATGTTGAATTTGGATGGTAAATTTGGTGAAAGCATCA TGGGGAAGACTTCGATGCAGAGCAATGTTTATAATATGAATACTGTTTTCCAGAAGAATGACTT TAAGAGTGGAGGCAACATGAAAGTTAACAAGTATAATGGTAATGTTGTTGCTAACAAGGAGATG AGCAACAACAAACATAACAACAACTGCAATGATAATGGGAATATGAATTTGGCTGTTGACAAGA GGTTTAAAACCTTGCCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTT TGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGGTAATTTCCCAATA CCCTTTTCTAGTGTTTTACTGATATTCAAACTGCAAGTAAATAACTTTTTGACTTTCATCATTG TTCAGGTTTACCTCCAAGATACAGAGACTCTGTTCGAGCTATAACACCTGGATTGCCTCTGTTT CTTTACAACTACACCACTCACCAGCTTCATGGTATCTTTGAGGTTTGTTCTCGTGCTTTTTTTT TGTCATAACAATGGTTTTGATGCTACCATTTACTGAAAATTTGATGTTCGAATTATTCCGTGAA TGATTCCTTGTTTAGGCAACAACTTTTGGAGGTACTAATATTGATGCTACTGCTTGGGAAGACA AAAAGTGCAAAGGAGAGTCAAGGTTTCCGGCTCAGGTGAAACTTAAATCACAATGACTTTCATT GTTTTAAGTCTTTATTTTGATATCTTGTACTAATATAACTTCTTTCTCTTAAATTGTAACAGGT AAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCAC CACTATGATGGTCCAAAATTCCGCCTTGAGCTCTCTGTTCCTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.201422544

Conservation Information
Conserved circRNAs	NA
PMCS	0.201422544

			
						 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
						responsive to methyl jasmonate (validated)

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	responsive to methyl jasmonate (validated)

			
						 Other Information
					
						References
						Zhang et al., 2020

circRNA

Detail information of AT3G27090_circ_g.1

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