Plant Circular RNA Database

Detail information of AT2G25880_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT2G25880_circ_g.1
					
						ID in PlantcircBase
						ath_circ_014842
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 11035244-11036352  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT2G25880						
					
						Parent gene annotation
						
							ataurora2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT2G25880_circ_g.2 AT2G25880_circ_g.3 AT2G25880_circ_g.4 						
					
						Support reads
						22
					
						Tissues
						root, inflorescences, whole_plant
					
						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
						AT2G25880.3:6
AT2G25880.2:5
AT2G25880.4:6
AT2G25880.1:6

General Information
CircRNA Name	AT2G25880_circ_g.1
ID in PlantcircBase	ath_circ_014842
Alias	NA
Organism	Arabidpsis thaliana
Position	chr2: 11035244-11036352 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, PcircRNA_finder
Parent gene	AT2G25880
Parent gene annotation	ataurora2
Parent gene strand	-
Alternative splicing	AT2G25880_circ_g.2 AT2G25880_circ_g.3 AT2G25880_circ_g.4
Support reads	22
Tissues	root, inflorescences, whole_plant
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	AT2G25880.3:6 AT2G25880.2:5 AT2G25880.4:6 AT2G25880.1:6

			
						 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  
						
							CTCTTGCTAGATAAACATGGCCAAACTTTCCTCTACCAAGTGGCTTTCCGATATCGAAATCGCT
TGTAGTCCATCTCTTTTGTGCAGCCTCTGAAGCCGCcttttgtatgtctctgaatgctccctgg
cctcaaaaggaggaacaccataaagaaattcgtagcagagaattcctagactccatatatcgac
actcgcat

									
								

					

						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: 566
Transcript exons: 11035244-11035361,11035450-11035546,11035816-11035911,11
036008-11036154,11036245-11036352
CTTTTGTATGTCTCTGAATGCTCCCTGGCCTCAAAAGGAGGAACACCATAAAGAAATTCGTAGC
AGAGAATTCCTAGACTCCATATATCGACACTCGCATCATGTTCAACGCTTTCCACCATCTCAGG
TGGAAGGTAATCCAAAGTGCCACACATAGTCCTTCTACGGTTGAATGTGTGTACTGACCATCCA
AAATCTGCAATCTTGAGCTCACCAGTTGCTGCTCGACGTTCGCTGAAGTACTTGCACTTCTGAA
GCTCTTTATAAAGCTCACCCCTTACAGCATACTCCAAAATCAAATAAACTCTTTTCTGATCATA
GAAGTAACCGTAGAGCCGCAGAATATTGGGATGCCGAAGATGAGATTGAATCTCTACTTCCCTT
CGTAACTGGTGTTCAACTTGAGATTGTTGAAGCTGAGCCTTAAAAAGAACCTTTAAAGCCACAA
TGTGATCGCTCCGTTTCTCTCTTGCTAGATAAACATGGCCAAACTTTCCTCTACCAAGTGGCTT
TCCGATATCGAAATCGCTTGTAGTCCATCTCTTTTGTGCAGCCTCTGAAGCCGC
Transcript length: 662
Transcript exons: 11035244-11035361,11035450-11035546,11035639-11035734,11
035816-11035911,11036008-11036154,11036245-11036352
CTTTTGTATGTCTCTGAATGCTCCCTGGCCTCAAAAGGAGGAACACCATAAAGAAATTCGTAGC
AGAGAATTCCTAGACTCCATATATCGACACTCGCATCATGTTCAACGCTTTCCACCATCTCAGG
TGGAAGGTAATCCAAAGTGCCACACATAGTCCTTCTACGGTTGAATGTGTGTACTGACCATCCA
AAATCTGCAATCTTGAGCTCACCCTGAGCACCAATCAACAGATTTTCAGGTTTTATATCTCTGT
GAATTACATGCTTTCCATGGCAATAGATGAGGGCTCTAGCCAATGACGCAACATAAGTTGCTGC
TCGACGTTCGCTGAAGTACTTGCACTTCTGAAGCTCTTTATAAAGCTCACCCCTTACAGCATAC
TCCAAAATCAAATAAACTCTTTTCTGATCATAGAAGTAACCGTAGAGCCGCAGAATATTGGGAT
GCCGAAGATGAGATTGAATCTCTACTTCCCTTCGTAACTGGTGTTCAACTTGAGATTGTTGAAG
CTGAGCCTTAAAAAGAACCTTTAAAGCCACAATGTGATCGCTCCGTTTCTCTCTTGCTAGATAA
ACATGGCCAAACTTTCCTCTACCAAGTGGCTTTCCGATATCGAAATCGCTTGTAGTCCATCTCT
TTTGTGCAGCCTCTGAAGCCGC
						
					

						Genomic sequence
						
							CTTTTGTATGTCTCTGAATGCTCCCTGGCCTCAAAAGGAGGAACACCATAAAGAAATTCGTAGC
AGAGAATTCCTAGACTCCATATATCGACACTCGCATCATGTTCAACGCTTTCCACTGTGAATCC
AAAAGCAGAAAAGTCAATTAGCTGGTTGCCGAAGAAAGTAATTTAGAATCACACAAGAGAGAGA
GAGCTTTCTCTTACCCATCTCAGGTGGAAGGTAATCCAAAGTGCCACACATAGTCCTTCTACGG
TTGAATGTGTGTACTGACCATCCAAAATCTGCAATCTTGAGCTCACCCTGAAAACATATATCCA
TGAATACATAAACACATAAGCTAACTGCAATCACATGGCGTTGATGGAGAAAGATAACCAGATT
CAATTTGTTACCTGAGCACCAATCAACAGATTTTCAGGTTTTATATCTCTGTGAATTACATGCT
TTCCATGGCAATAGATGAGGGCTCTAGCCAATGACGCAACATACTGCCACAATAAACGTAAGGG
TATGACTACACAGATTCACATTAACATGCTAGAATAAGTTCAATTATCACTAGGACTTACAGTT
GCTGCTCGACGTTCGCTGAAGTACTTGCACTTCTGAAGCTCTTTATAAAGCTCACCCCTTACAG
CATACTCCAAAATCAAATAAACTCTTTTCTGCAACAACGGTATCCCAAAAACTATGTTAACCTC
ACAGAGCCAAACATTGTATGTCAACAAGAAGTTCTTTTACAAGCACAGATAACACAAAACCTGA
TCATAGAAGTAACCGTAGAGCCGCAGAATATTGGGATGCCGAAGATGAGATTGAATCTCTACTT
CCCTTCGTAACTGGTGTTCAACTTGAGATTGTTGAAGCTGAGCCTTAAAAAGAACCTTTAAAGC
CACAATGTGATCGCTCTGTTTGCAAAGACACATAGAAGACAGCTTGGTTAAAAAAGACATCAAA
TTAATTCTGCTTGTTTAACATAATTGTGAAGAAACACTAACCCGTTTCTCTCTTGCTAGATAAA
CATGGCCAAACTTTCCTCTACCAAGTGGCTTTCCGATATCGAAATCGCTTGTAGTCCATCTCTT
TTGTGCAGCCTCTGAAGCCGC
						
					

			
		

Sequences
Splice junction sequence	CTCTTGCTAGATAAACATGGCCAAACTTTCCTCTACCAAGTGGCTTTCCGATATCGAAATCGCT TGTAGTCCATCTCTTTTGTGCAGCCTCTGAAGCCGCcttttgtatgtctctgaatgctccctgg cctcaaaaggaggaacaccataaagaaattcgtagcagagaattcctagactccatatatcgac actcgcat
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: 566 Transcript exons: 11035244-11035361,11035450-11035546,11035816-11035911,11 036008-11036154,11036245-11036352 CTTTTGTATGTCTCTGAATGCTCCCTGGCCTCAAAAGGAGGAACACCATAAAGAAATTCGTAGC AGAGAATTCCTAGACTCCATATATCGACACTCGCATCATGTTCAACGCTTTCCACCATCTCAGG TGGAAGGTAATCCAAAGTGCCACACATAGTCCTTCTACGGTTGAATGTGTGTACTGACCATCCA AAATCTGCAATCTTGAGCTCACCAGTTGCTGCTCGACGTTCGCTGAAGTACTTGCACTTCTGAA GCTCTTTATAAAGCTCACCCCTTACAGCATACTCCAAAATCAAATAAACTCTTTTCTGATCATA GAAGTAACCGTAGAGCCGCAGAATATTGGGATGCCGAAGATGAGATTGAATCTCTACTTCCCTT CGTAACTGGTGTTCAACTTGAGATTGTTGAAGCTGAGCCTTAAAAAGAACCTTTAAAGCCACAA TGTGATCGCTCCGTTTCTCTCTTGCTAGATAAACATGGCCAAACTTTCCTCTACCAAGTGGCTT TCCGATATCGAAATCGCTTGTAGTCCATCTCTTTTGTGCAGCCTCTGAAGCCGC Transcript length: 662 Transcript exons: 11035244-11035361,11035450-11035546,11035639-11035734,11 035816-11035911,11036008-11036154,11036245-11036352 CTTTTGTATGTCTCTGAATGCTCCCTGGCCTCAAAAGGAGGAACACCATAAAGAAATTCGTAGC AGAGAATTCCTAGACTCCATATATCGACACTCGCATCATGTTCAACGCTTTCCACCATCTCAGG TGGAAGGTAATCCAAAGTGCCACACATAGTCCTTCTACGGTTGAATGTGTGTACTGACCATCCA AAATCTGCAATCTTGAGCTCACCCTGAGCACCAATCAACAGATTTTCAGGTTTTATATCTCTGT GAATTACATGCTTTCCATGGCAATAGATGAGGGCTCTAGCCAATGACGCAACATAAGTTGCTGC TCGACGTTCGCTGAAGTACTTGCACTTCTGAAGCTCTTTATAAAGCTCACCCCTTACAGCATAC TCCAAAATCAAATAAACTCTTTTCTGATCATAGAAGTAACCGTAGAGCCGCAGAATATTGGGAT GCCGAAGATGAGATTGAATCTCTACTTCCCTTCGTAACTGGTGTTCAACTTGAGATTGTTGAAG CTGAGCCTTAAAAAGAACCTTTAAAGCCACAATGTGATCGCTCCGTTTCTCTCTTGCTAGATAA ACATGGCCAAACTTTCCTCTACCAAGTGGCTTTCCGATATCGAAATCGCTTGTAGTCCATCTCT TTTGTGCAGCCTCTGAAGCCGC
Genomic sequence	CTTTTGTATGTCTCTGAATGCTCCCTGGCCTCAAAAGGAGGAACACCATAAAGAAATTCGTAGC AGAGAATTCCTAGACTCCATATATCGACACTCGCATCATGTTCAACGCTTTCCACTGTGAATCC AAAAGCAGAAAAGTCAATTAGCTGGTTGCCGAAGAAAGTAATTTAGAATCACACAAGAGAGAGA GAGCTTTCTCTTACCCATCTCAGGTGGAAGGTAATCCAAAGTGCCACACATAGTCCTTCTACGG TTGAATGTGTGTACTGACCATCCAAAATCTGCAATCTTGAGCTCACCCTGAAAACATATATCCA TGAATACATAAACACATAAGCTAACTGCAATCACATGGCGTTGATGGAGAAAGATAACCAGATT CAATTTGTTACCTGAGCACCAATCAACAGATTTTCAGGTTTTATATCTCTGTGAATTACATGCT TTCCATGGCAATAGATGAGGGCTCTAGCCAATGACGCAACATACTGCCACAATAAACGTAAGGG TATGACTACACAGATTCACATTAACATGCTAGAATAAGTTCAATTATCACTAGGACTTACAGTT GCTGCTCGACGTTCGCTGAAGTACTTGCACTTCTGAAGCTCTTTATAAAGCTCACCCCTTACAG CATACTCCAAAATCAAATAAACTCTTTTCTGCAACAACGGTATCCCAAAAACTATGTTAACCTC ACAGAGCCAAACATTGTATGTCAACAAGAAGTTCTTTTACAAGCACAGATAACACAAAACCTGA TCATAGAAGTAACCGTAGAGCCGCAGAATATTGGGATGCCGAAGATGAGATTGAATCTCTACTT CCCTTCGTAACTGGTGTTCAACTTGAGATTGTTGAAGCTGAGCCTTAAAAAGAACCTTTAAAGC CACAATGTGATCGCTCTGTTTGCAAAGACACATAGAAGACAGCTTGGTTAAAAAAGACATCAAA TTAATTCTGCTTGTTTAACATAATTGTGAAGAAACACTAACCCGTTTCTCTCTTGCTAGATAAA CATGGCCAAACTTTCCTCTACCAAGTGGCTTTCCGATATCGAAATCGCTTGTAGTCCATCTCTT TTGTGCAGCCTCTGAAGCCGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.448918134

Conservation Information
Conserved circRNAs	NA
PMCS	0.448918134

			
						 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
						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	responsive to methyl jasmonate

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT2G25880_circ_g.1

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