Plant Circular RNA Database

Detail information of AT4G02760_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT4G02760_circ_g.4
					
						ID in PlantcircBase
						ath_circ_029448
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 1225791-1226691  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT4G02760						
					
						Parent gene annotation
						
							RNI-like superfamily protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G02760_circ_g.2 AT4G02760_circ_g.3 						
					
						Support reads
						1
					
						Tissues
						aerial
					
						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
						AT4G02760.5:5
AT4G02760.6:5
AT4G02760.9:5
AT4G02760.8:5
AT4G02760.4:5
AT4G02760.7:5
AT4G02760.2:5
AT4G02760.1:5
AT4G02760.3:5

General Information
CircRNA Name	AT4G02760_circ_g.4
ID in PlantcircBase	ath_circ_029448
Alias	NA
Organism	Arabidpsis thaliana
Position	chr4: 1225791-1226691 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT4G02760
Parent gene annotation	RNI-like superfamily protein
Parent gene strand	-
Alternative splicing	AT4G02760_circ_g.2 AT4G02760_circ_g.3
Support reads	1
Tissues	aerial
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	AT4G02760.5:5 AT4G02760.6:5 AT4G02760.9:5 AT4G02760.8:5 AT4G02760.4:5 AT4G02760.7:5 AT4G02760.2:5 AT4G02760.1:5 AT4G02760.3:5

			
						 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  
						
							CTTCAAATCAGTGAGATTTAAACAAGCTGACAACACAGGAGATAAGGACCCGCAATCTATCATT
CTGAGATGGTAAAGGTGTAGGCTTCTCAAATGACCCctcctttaggatatagcagtcacgcaat
atcagagtctccaatggactatctttgccgcaaagttccaaacccctaccaacaaaaccttagg
ccataaat

						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: 448
Transcript exons: 1225791-1225863,1225949-1226013,1226111-1226223,1226312-
1226397,1226581-1226691
CTCCTTTAGGATATAGCAGTCACGCAATATCAGAGTCTCCAATGGACTATCTTTGCCGCAAAGT
TCCAAACCCCTGAAAAAGCAACCACTAATTTCAGGCGAACTCGACAGATTAATGTGCTTCAGTC
GACGAAAACCCTTAATTAATTTTTGTAATATTGCGTCATTTAGCAGAAAACCTAGGAGCGATAT
CGAACTTAAGTTGGGGCAATTGGCCGCAAACTCTAACAAGCTTGAATCTGTTATAAGGCCTGCT
GCACCATATATCTCTATGAACAGGTGCTCTATCAAGCGACAATTTCTCGTGAGTAAACCTAACT
GCTCAAGTGGATTATCCAGTCCAACAATCTTCAAATCAGTGAGATTTAAACAAGCTGACAACAC
AGGAGATAAGGACCCGCAATCTATCATTCTGAGATGGTAAAGGTGTAGGCTTCTCAAATGACCC
						
						Genomic sequence
						
							CTCCTTTAGGATATAGCAGTCACGCAATATCAGAGTCTCCAATGGACTATCTTTGCCGCAAAGT
TCCAAACCCCTACCAACAAAACCTTAGGCCATAAATAGTTTGCTACCAAAGACTTACAGATATC
ACCATTAACATTTACTCAAACGACACTAACCTGAAAAAGCAACCACTAATTTCAGGCGAACTCG
ACAGATTAATGTGCTTCAGTCGACGAAAACCCTGCAAAACATCACAATTTTATTTCGGTTTTGT
AAAATGTATTAGATGATACCAAATGAAAAGAAAAGAAATAACAACAAAACTAGAGGAGCCATAC
CTTAATTAATTTTTGTAATATTGCGTCATTTAGCAGAAAACCTAGGAGCGATATCGAACTTAAG
TTGGGGCAATTGGCCGCAAACTCTAACAAGCTTGAATCTGTTATAAGGCCTATACTACCAGTCA
AAAAGTAGGTAACCTTGAGCAAACACTCAGATGAAAAATACAAAGAGGAAATCTTCATAGCAGA
AATATTTACCTGCTGCACCATATATCTCTATGAACAGGTGCTCTATCAAGCGACAATTTCTCGT
GAGTAAACCTAACTGCTCAAGTGGATTATCCCTGCTTCCTGAAATACTAAATAATGCAAAAAAA
AGTAATTACCATAAGGAATCAGCAGAATTTAAAGTGAACAGGCATTCAAGTTACAAAAACAGTT
AAAAGCATAGACGGAGGCGCCTCCAGGCAAAGTAAAGTAAAGCAATAATGAATTGGAGAATTCC
TGAATGATCCAAAACAGCTTACAGTCCAACAATCTTCAAATCAGTGAGATTTAAACAAGCTGAC
AACACAGGAGATAAGGACCCGCAATCTATCATTCTGAGATGGTAAAGGTGTAGGCTTCTCAAAT
GACCC

Sequences
Splice junction sequence	CTTCAAATCAGTGAGATTTAAACAAGCTGACAACACAGGAGATAAGGACCCGCAATCTATCATT CTGAGATGGTAAAGGTGTAGGCTTCTCAAATGACCCctcctttaggatatagcagtcacgcaat atcagagtctccaatggactatctttgccgcaaagttccaaacccctaccaacaaaaccttagg ccataaat
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: 448 Transcript exons: 1225791-1225863,1225949-1226013,1226111-1226223,1226312- 1226397,1226581-1226691 CTCCTTTAGGATATAGCAGTCACGCAATATCAGAGTCTCCAATGGACTATCTTTGCCGCAAAGT TCCAAACCCCTGAAAAAGCAACCACTAATTTCAGGCGAACTCGACAGATTAATGTGCTTCAGTC GACGAAAACCCTTAATTAATTTTTGTAATATTGCGTCATTTAGCAGAAAACCTAGGAGCGATAT CGAACTTAAGTTGGGGCAATTGGCCGCAAACTCTAACAAGCTTGAATCTGTTATAAGGCCTGCT GCACCATATATCTCTATGAACAGGTGCTCTATCAAGCGACAATTTCTCGTGAGTAAACCTAACT GCTCAAGTGGATTATCCAGTCCAACAATCTTCAAATCAGTGAGATTTAAACAAGCTGACAACAC AGGAGATAAGGACCCGCAATCTATCATTCTGAGATGGTAAAGGTGTAGGCTTCTCAAATGACCC
Genomic sequence	CTCCTTTAGGATATAGCAGTCACGCAATATCAGAGTCTCCAATGGACTATCTTTGCCGCAAAGT TCCAAACCCCTACCAACAAAACCTTAGGCCATAAATAGTTTGCTACCAAAGACTTACAGATATC ACCATTAACATTTACTCAAACGACACTAACCTGAAAAAGCAACCACTAATTTCAGGCGAACTCG ACAGATTAATGTGCTTCAGTCGACGAAAACCCTGCAAAACATCACAATTTTATTTCGGTTTTGT AAAATGTATTAGATGATACCAAATGAAAAGAAAAGAAATAACAACAAAACTAGAGGAGCCATAC CTTAATTAATTTTTGTAATATTGCGTCATTTAGCAGAAAACCTAGGAGCGATATCGAACTTAAG TTGGGGCAATTGGCCGCAAACTCTAACAAGCTTGAATCTGTTATAAGGCCTATACTACCAGTCA AAAAGTAGGTAACCTTGAGCAAACACTCAGATGAAAAATACAAAGAGGAAATCTTCATAGCAGA AATATTTACCTGCTGCACCATATATCTCTATGAACAGGTGCTCTATCAAGCGACAATTTCTCGT GAGTAAACCTAACTGCTCAAGTGGATTATCCCTGCTTCCTGAAATACTAAATAATGCAAAAAAA AGTAATTACCATAAGGAATCAGCAGAATTTAAAGTGAACAGGCATTCAAGTTACAAAAACAGTT AAAAGCATAGACGGAGGCGCCTCCAGGCAAAGTAAAGTAAAGCAATAATGAATTGGAGAATTCC TGAATGATCCAAAACAGCTTACAGTCCAACAATCTTCAAATCAGTGAGATTTAAACAAGCTGAC AACACAGGAGATAAGGACCCGCAATCTATCATTCTGAGATGGTAAAGGTGTAGGCTTCTCAAAT GACCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.234507197

Conservation Information
Conserved circRNAs	NA
PMCS	0.234507197

			
						 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
						NA

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	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT4G02760_circ_g.4

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