Plant Circular RNA Database

Detail information of AT1G03780_circ_g.29

			
						 General Information
					
						CircRNA Name
						AT1G03780_circ_g.29
					
						ID in PlantcircBase
						ath_circ_000484
					
						Alias
						Ath_circ_FC0157, Ath_circ_FC0158
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 949883-951211  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT1G03780						
					
						Parent gene annotation
						
							Protein TPX2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G03780_circ_g.1 AT1G03780_circ_g.2 AT1G03780_circ_g.3 AT1G03780_circ_g.4 AT1G03780_circ_g.5 AT1G03780_circ_g.6 AT1G03780_circ_g.7 AT1G03780_circ_g.8 AT1G03780_circ_g.9 AT1G03780_circ_g.10 AT1G03780_circ_g.11 AT1G03780_circ_g.12 AT1G03780_circ_g.13 AT1G03780_circ_g.14 AT1G03780_circ_g.15 AT1G03780_circ_g.16 AT1G03780_circ_g.17 AT1G03780_circ_g.18 AT1G03780_circ_g.19 AT1G03780_circ_g.20 AT1G03780_circ_g.21 AT1G03780_circ_g.22 AT1G03780_circ_g.23 AT1G03780_circ_g.24 AT1G03780_circ_g.25 AT1G03780_circ_g.26 AT1G03780_circ_g.27 AT1G03780_circ_g.28 AT1G03780_circ_g.30 AT1G03780_circ_g.31 AT1G03780_circ_g.32 AT1G03780_circ_g.33 AT1G03780_circ_g.34 						
					
						Support reads
						4
					
						Tissues
						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
						AT1G03780.2:6
AT1G03780.1:6
AT1G03780.3:6

General Information
CircRNA Name	AT1G03780_circ_g.29
ID in PlantcircBase	ath_circ_000484
Alias	Ath_circ_FC0157, Ath_circ_FC0158
Organism	Arabidpsis thaliana
Position	chr1: 949883-951211 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT1G03780
Parent gene annotation	Protein TPX2
Parent gene strand	-
Alternative splicing	AT1G03780_circ_g.1 AT1G03780_circ_g.2 AT1G03780_circ_g.3 AT1G03780_circ_g.4 AT1G03780_circ_g.5 AT1G03780_circ_g.6 AT1G03780_circ_g.7 AT1G03780_circ_g.8 AT1G03780_circ_g.9 AT1G03780_circ_g.10 AT1G03780_circ_g.11 AT1G03780_circ_g.12 AT1G03780_circ_g.13 AT1G03780_circ_g.14 AT1G03780_circ_g.15 AT1G03780_circ_g.16 AT1G03780_circ_g.17 AT1G03780_circ_g.18 AT1G03780_circ_g.19 AT1G03780_circ_g.20 AT1G03780_circ_g.21 AT1G03780_circ_g.22 AT1G03780_circ_g.23 AT1G03780_circ_g.24 AT1G03780_circ_g.25 AT1G03780_circ_g.26 AT1G03780_circ_g.27 AT1G03780_circ_g.28 AT1G03780_circ_g.30 AT1G03780_circ_g.31 AT1G03780_circ_g.32 AT1G03780_circ_g.33 AT1G03780_circ_g.34
Support reads	4
Tissues	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	AT1G03780.2:6 AT1G03780.1:6 AT1G03780.3:6

			
						 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  
						
							TGTAAGAAAAAAACCTTGAGCGTCTCTTCTTCAGCTTCATTGAAGTTGCACATGGCCTCTACCT
TGAACGATCTCCTTGCTTTGATTCTAGGAACCGAAGcttcttgttcacaggtcgagctttaaac
ttgggaatctttgccaacatctcttcctcaagttctgcactgctcttaactctcaaaggacgag
ctcgttgg

									
								

					

						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: 914
Transcript exons: 949883-950125,950198-950311,950404-950500,950582-950794,
950881-951041,951126-951211
CTTCTTGTTCACAGGTCGAGCTTTAAACTTGGGAATCTTTGCCAACATCTCTTCCTCAAGTTCT
GCACTGCTCTTAACTCTCAAAGGACGAGCTCGTTGGGACGTCACAAATTCGGGTTCCTTTGGTC
TTGTCAGTGTCAGCTTAGGTCGATTCTGGACGAATAGGTCTCGCGTGCTTGTTTGGAACTTCTT
CATCAATTCAGCAGTTGAAACAAAAGGTGCAATTTGCTCACGAACATAAACCTTTCTGTTTTCC
TTCGGAGTGTGCTTAGTGACTGAAGGGCATAAGTTGAAACCAGTGTTAACAAGACCATTTCTTG
TCTTGTGGAGCAGAGTTGCTGGTTTTGGATTGAGAATCTGTCTTGATTTTCCATCATCTAGCTT
TTGCCTTTTGATGGCTTGATTTTCTTGAATCAGATTGGTAGTGCTAGCTATGTTGTTAAGATTC
GTTTCCCCTTTCACACTTTTCTGATGACTGCCTTTGGCTTGAGACTGGTTTTTAGGCCTTAGTG
TAGATGGATTCTTCAGCAGACTAGCTATCTTTCTAGCAGTTTGCTGCTTCTTAAGATCCACCGA
CTTTGCCCCTAGAGAAAACTGCATTGGTGGTTTGGGTGTGCAAGCAGGAGCAATGTTCTCCTTG
TCTTCTATTGGCTCAGTCGTCGGATCGCTGGCATCTACGGTCTTGTTGTTGACCTCTGCGTCCT
TGGAACTGATGCGAGACGGCTTAACAGTGCTTGCTTTAGAAGGAGCAACTTCTGCTTTCTTGGC
CTGAGAAGGCTGCGATTGTAAAGAAACAATTGGAACTACTGGTTCTAACGGCTCTTTATCCTTG
AGCGTCTCTTCTTCAGCTTCATTGAAGTTGCACATGGCCTCTACCTTGAACGATCTCCTTGCTT
TGATTCTAGGAACCGAAG
						
					

						Genomic sequence
						
							CTTCTTGTTCACAGGTCGAGCTTTAAACTTGGGAATCTTTGCCAACATCTCTTCCTCAAGTTCT
GCACTGCTCTTAACTCTCAAAGGACGAGCTCGTTGGGACGTCACAAATTCGGGTTCCTTTGGTC
TTGTCAGTGTCAGCTTAGGTCGATTCTGGACGAATAGGTCTCGCGTGCTTGTTTGGAACTTCTT
CATCAATTCAGCAGTTGAAACAAAAGGTGCAATTTGCTCACGAACATAAACCTGAAAAGTGAAA
ACAAGGTTTGAGAGGGTCTGACAGAAAAAGTATACAAGCAACCATGAAGCACAACACACCTTTC
TGTTTTCCTTCGGAGTGTGCTTAGTGACTGAAGGGCATAAGTTGAAACCAGTGTTAACAAGACC
ATTTCTTGTCTTGTGGAGCAGAGTTGCTGGTTTTGGATTGAGAATCTAGATAAATCAATGATAA
GAAGGAAAAAGTTTCAGTCATGCAGTGAGGTATGGAGTGAATGACATGCTGATTTTAAAACAAT
TTGGCTCACCTGTCTTGATTTTCCATCATCTAGCTTTTGCCTTTTGATGGCTTGATTTTCTTGA
ATCAGATTGGTAGTGCTAGCTATGTTGTTAAGATTCGTTTCCCTGCAGTGAGACAATCAACACA
TTAAAACAACTATCACAAGAGAAACGTGAACCAGATTGGTTATTAAGAATGTGAGGTACCCTTT
CACACTTTTCTGATGACTGCCTTTGGCTTGAGACTGGTTTTTAGGCCTTAGTGTAGATGGATTC
TTCAGCAGACTAGCTATCTTTCTAGCAGTTTGCTGCTTCTTAAGATCCACCGACTTTGCCCCTA
GAGAAAACTGCATTGGTGGTTTGGGTGTGCAAGCAGGAGCAATGTTCTCCTTGTCTTCTATTGG
CTCAGTCGTCGGATCGCTGTTAAATGAAAAAGAAGAAAGATCATTAGAATTGCCTCTTACTCAC
TTAACAGCGATACAATCTCCCAAAGAACGATGGAGAACCTGGCATCTACGGTCTTGTTGTTGAC
CTCTGCGTCCTTGGAACTGATGCGAGACGGCTTAACAGTGCTTGCTTTAGAAGGAGCAACTTCT
GCTTTCTTGGCCTGAGAAGGCTGCGATTGTAAAGAAACAATTGGAACTACTGGTTCTAACGGCT
CTTTATCCTGCAATAATCAGAATGATTAAAAAATGATCTTTCCTTGATCTTGTAATGGATGATA
AATCAGTGTTGATTGTAAGAAAAAAACCTTGAGCGTCTCTTCTTCAGCTTCATTGAAGTTGCAC
ATGGCCTCTACCTTGAACGATCTCCTTGCTTTGATTCTAGGAACCGAAG
						
					

			
		

Sequences
Splice junction sequence	TGTAAGAAAAAAACCTTGAGCGTCTCTTCTTCAGCTTCATTGAAGTTGCACATGGCCTCTACCT TGAACGATCTCCTTGCTTTGATTCTAGGAACCGAAGcttcttgttcacaggtcgagctttaaac ttgggaatctttgccaacatctcttcctcaagttctgcactgctcttaactctcaaaggacgag ctcgttgg
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: 914 Transcript exons: 949883-950125,950198-950311,950404-950500,950582-950794, 950881-951041,951126-951211 CTTCTTGTTCACAGGTCGAGCTTTAAACTTGGGAATCTTTGCCAACATCTCTTCCTCAAGTTCT GCACTGCTCTTAACTCTCAAAGGACGAGCTCGTTGGGACGTCACAAATTCGGGTTCCTTTGGTC TTGTCAGTGTCAGCTTAGGTCGATTCTGGACGAATAGGTCTCGCGTGCTTGTTTGGAACTTCTT CATCAATTCAGCAGTTGAAACAAAAGGTGCAATTTGCTCACGAACATAAACCTTTCTGTTTTCC TTCGGAGTGTGCTTAGTGACTGAAGGGCATAAGTTGAAACCAGTGTTAACAAGACCATTTCTTG TCTTGTGGAGCAGAGTTGCTGGTTTTGGATTGAGAATCTGTCTTGATTTTCCATCATCTAGCTT TTGCCTTTTGATGGCTTGATTTTCTTGAATCAGATTGGTAGTGCTAGCTATGTTGTTAAGATTC GTTTCCCCTTTCACACTTTTCTGATGACTGCCTTTGGCTTGAGACTGGTTTTTAGGCCTTAGTG TAGATGGATTCTTCAGCAGACTAGCTATCTTTCTAGCAGTTTGCTGCTTCTTAAGATCCACCGA CTTTGCCCCTAGAGAAAACTGCATTGGTGGTTTGGGTGTGCAAGCAGGAGCAATGTTCTCCTTG TCTTCTATTGGCTCAGTCGTCGGATCGCTGGCATCTACGGTCTTGTTGTTGACCTCTGCGTCCT TGGAACTGATGCGAGACGGCTTAACAGTGCTTGCTTTAGAAGGAGCAACTTCTGCTTTCTTGGC CTGAGAAGGCTGCGATTGTAAAGAAACAATTGGAACTACTGGTTCTAACGGCTCTTTATCCTTG AGCGTCTCTTCTTCAGCTTCATTGAAGTTGCACATGGCCTCTACCTTGAACGATCTCCTTGCTT TGATTCTAGGAACCGAAG
Genomic sequence	CTTCTTGTTCACAGGTCGAGCTTTAAACTTGGGAATCTTTGCCAACATCTCTTCCTCAAGTTCT GCACTGCTCTTAACTCTCAAAGGACGAGCTCGTTGGGACGTCACAAATTCGGGTTCCTTTGGTC TTGTCAGTGTCAGCTTAGGTCGATTCTGGACGAATAGGTCTCGCGTGCTTGTTTGGAACTTCTT CATCAATTCAGCAGTTGAAACAAAAGGTGCAATTTGCTCACGAACATAAACCTGAAAAGTGAAA ACAAGGTTTGAGAGGGTCTGACAGAAAAAGTATACAAGCAACCATGAAGCACAACACACCTTTC TGTTTTCCTTCGGAGTGTGCTTAGTGACTGAAGGGCATAAGTTGAAACCAGTGTTAACAAGACC ATTTCTTGTCTTGTGGAGCAGAGTTGCTGGTTTTGGATTGAGAATCTAGATAAATCAATGATAA GAAGGAAAAAGTTTCAGTCATGCAGTGAGGTATGGAGTGAATGACATGCTGATTTTAAAACAAT TTGGCTCACCTGTCTTGATTTTCCATCATCTAGCTTTTGCCTTTTGATGGCTTGATTTTCTTGA ATCAGATTGGTAGTGCTAGCTATGTTGTTAAGATTCGTTTCCCTGCAGTGAGACAATCAACACA TTAAAACAACTATCACAAGAGAAACGTGAACCAGATTGGTTATTAAGAATGTGAGGTACCCTTT CACACTTTTCTGATGACTGCCTTTGGCTTGAGACTGGTTTTTAGGCCTTAGTGTAGATGGATTC TTCAGCAGACTAGCTATCTTTCTAGCAGTTTGCTGCTTCTTAAGATCCACCGACTTTGCCCCTA GAGAAAACTGCATTGGTGGTTTGGGTGTGCAAGCAGGAGCAATGTTCTCCTTGTCTTCTATTGG CTCAGTCGTCGGATCGCTGTTAAATGAAAAAGAAGAAAGATCATTAGAATTGCCTCTTACTCAC TTAACAGCGATACAATCTCCCAAAGAACGATGGAGAACCTGGCATCTACGGTCTTGTTGTTGAC CTCTGCGTCCTTGGAACTGATGCGAGACGGCTTAACAGTGCTTGCTTTAGAAGGAGCAACTTCT GCTTTCTTGGCCTGAGAAGGCTGCGATTGTAAAGAAACAATTGGAACTACTGGTTCTAACGGCT CTTTATCCTGCAATAATCAGAATGATTAAAAAATGATCTTTCCTTGATCTTGTAATGGATGATA AATCAGTGTTGATTGTAAGAAAAAAACCTTGAGCGTCTCTTCTTCAGCTTCATTGAAGTTGCAC ATGGCCTCTACCTTGAACGATCTCCTTGCTTTGATTCTAGGAACCGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.500572179

Conservation Information
Conserved circRNAs	NA
PMCS	0.500572179

			
						 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;Chen et al., 2017a

circRNA

Detail information of AT1G03780_circ_g.29

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