Plant Circular RNA Database

Detail information of AT5G53740_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G53740_circ_g.1
					
						ID in PlantcircBase
						ath_circ_043977
					
						Alias
						5:21811769-21814216
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 21811769-21814216  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ie-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G53740						
					
						Parent gene annotation
						
							Putative uncharacterized protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							ENSRNA049493778_circ_g.1 ENSRNA049493778_circ_g.2 5_circ_ag.2 5_circ_ag.3 AT5G53740_circ_g.4 AT5G53740_circ_g.5 5_circ_ag.6 AT5G53760_circ_g.1 AT5G53770_circ_g.1 AT5G53770_circ_g.2 5_circ_ig.3 AT5G53850_circ_g.1 AT5G53850_circ_g.2 AT5G53850_circ_g.3 AT5G53850_circ_g.4 AT5G53850_circ_g.5 AT5G53860_circ_g.1 AT5G53860_circ_g.2 AT5G53860_circ_g.3 AT5G53860_circ_g.4 AT5G53860_circ_g.5 AT5G53860_circ_g.6 AT5G53860_circ_g.7 AT5G53860_circ_g.8 AT5G53860_circ_g.9 AT5G53860_circ_g.10 AT5G53860_circ_g.11 AT5G53880_circ_g.1 AT5G53905_circ_g.1 5_circ_ag.2 AT5G53905_circ_g.3 5_circ_ag.4 AT5G53920_circ_g.1 AT5G53940_circ_g.1 AT5G53940_circ_g.2 AT5G53970_circ_g.1 AT5G53970_circ_g.2 AT5G54000_circ_g.1 AT5G54060_circ_g.1 ENSRNA049493776_circ_g.1 ENSRNA049493776_circ_g.2 ENSRNA049493776_circ_g.3 5_circ_ag.4 5_circ_ag.5 5_circ_ag.6 AT5G54080_circ_g.1 AT5G54080_circ_g.2 AT5G54080_circ_g.3 AT5G54080_circ_g.4 AT5G54090_circ_g.1 AT5G54090_circ_g.2 AT5G54090_circ_g.3 AT5G54090_circ_g.4 AT5G54100_circ_g.1 AT5G54130_circ_g.1 AT5G54130_circ_g.2 AT5G54130_circ_g.3 AT5G54130_circ_g.4 AT5G54130_circ_g.5 AT5G54160_circ_g.1 AT5G54160_circ_g.2 AT5G54170_circ_g.1 ENSRNA049493783_circ_g.1 ENSRNA049493783_circ_g.2 ENSRNA049493783_circ_g.3 ENSRNA049493783_circ_g.4 						
					
						Support reads
						5/1/1
					
						Tissues
						root;flower
					
						Exon boundary  
						
							No-No							"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
						AT5G53740.1:6

General Information
CircRNA Name	AT5G53740_circ_g.1
ID in PlantcircBase	ath_circ_043977
Alias	5:21811769-21814216
Organism	Arabidpsis thaliana
Position	chr5: 21811769-21814216 JBrowse»
Reference genome	TAIR10.38
Type	ie-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G53740
Parent gene annotation	Putative uncharacterized protein
Parent gene strand	+
Alternative splicing	ENSRNA049493778_circ_g.1 ENSRNA049493778_circ_g.2 5_circ_ag.2 5_circ_ag.3 AT5G53740_circ_g.4 AT5G53740_circ_g.5 5_circ_ag.6 AT5G53760_circ_g.1 AT5G53770_circ_g.1 AT5G53770_circ_g.2 5_circ_ig.3 AT5G53850_circ_g.1 AT5G53850_circ_g.2 AT5G53850_circ_g.3 AT5G53850_circ_g.4 AT5G53850_circ_g.5 AT5G53860_circ_g.1 AT5G53860_circ_g.2 AT5G53860_circ_g.3 AT5G53860_circ_g.4 AT5G53860_circ_g.5 AT5G53860_circ_g.6 AT5G53860_circ_g.7 AT5G53860_circ_g.8 AT5G53860_circ_g.9 AT5G53860_circ_g.10 AT5G53860_circ_g.11 AT5G53880_circ_g.1 AT5G53905_circ_g.1 5_circ_ag.2 AT5G53905_circ_g.3 5_circ_ag.4 AT5G53920_circ_g.1 AT5G53940_circ_g.1 AT5G53940_circ_g.2 AT5G53970_circ_g.1 AT5G53970_circ_g.2 AT5G54000_circ_g.1 AT5G54060_circ_g.1 ENSRNA049493776_circ_g.1 ENSRNA049493776_circ_g.2 ENSRNA049493776_circ_g.3 5_circ_ag.4 5_circ_ag.5 5_circ_ag.6 AT5G54080_circ_g.1 AT5G54080_circ_g.2 AT5G54080_circ_g.3 AT5G54080_circ_g.4 AT5G54090_circ_g.1 AT5G54090_circ_g.2 AT5G54090_circ_g.3 AT5G54090_circ_g.4 AT5G54100_circ_g.1 AT5G54130_circ_g.1 AT5G54130_circ_g.2 AT5G54130_circ_g.3 AT5G54130_circ_g.4 AT5G54130_circ_g.5 AT5G54160_circ_g.1 AT5G54160_circ_g.2 AT5G54170_circ_g.1 ENSRNA049493783_circ_g.1 ENSRNA049493783_circ_g.2 ENSRNA049493783_circ_g.3 ENSRNA049493783_circ_g.4
Support reads	5/1/1
Tissues	root;flower
Exon boundary	No-No "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	AT5G53740.1:6

			
						 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  
						
							CGATCGTAGCCGTCAATCACGCTCTAGCCGCACGGTCATGGTTCATCAACCAGGGTAAAGGGCC
TGTCTCTTGAGAAATCAAGGAAACAGAGGTACGAGCctgtcagaccgccgtgcgaccaccccgg
ctagggtaaaccgagccgagtaacgatcctctacagcaccggatgcgtccgaggacaatcgtag
ccgtcaat

									
								

					

						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: 2448
Transcript exons: 21811769-21814216
CACCGGATGCGTCCGAGGACAATCGTAGCCGTCAATCACGCTCTAGCCGCACGGTCATGGTTCA
TCAACCAGGGTTTAGGGCCTGTCTCTTGAGAAATCAAGGAAACAGAGGTACGAGCCTATCAGAC
CGCCGTGCGACCACCCCGGCTAGGGTAAACCGAGCCGAGTAACGATCCTCTACAG
						
					

						Genomic sequence
						
							CTGTCAGACCGCCGTGCGACCACCCCGGCTAGGGTAAACCGAGCCGAGTAACGATCCTCTACAG
CACCGGATGCGTCCGAGGACAATCGTAGCCGTCAATCACGCTCTAGCCGCACGGTCATGGTTCA
TCAACCAGGGTTTAGGGCCTGTCTCTTGAGAAATCAAGGAAACAGAGGTACGAGCCTATAGAAC
AGATCCTGTTCAAGTAAGGTCGTGACCATTGCTGCTCTCTCAATGTTATATATCCGGCAACATT
GTTTTTCAAAATAGCGATGTGGGACAAAGTTATATAAAGATCACATTAGAAAAGCATGCATGGG
TCGTGATATATGGACTAAGGCCCACTTAATTATCATATAAAGCCCCTCCCTAAATTAGCGTTGA
AAATTATCATTAAGTCAATATGATTTGCGAAGTATAGGCGTATAGCTATTAAGTGTGATAAATT
CGTTCTCAATTATGTGCGGGTAACAAAGCTATCTTCATTATATCAGACGATGTTGAAACTTTTT
TTTTTGTTTTTCTGCCGATGTGAAGATATAACCTATTAGAACAAGCAAAGCAGTCATTCATGTC
CCAATCATTTTTTTATTTCATGCTATGATCCGAAAATTTTGTTCCTTTCTTGGATTACCAATGA
TGAAACCTAGAAGAACTACAGATTTGACGTCTCTCAGTGACTGCATAGCCGCTCGTTGTGATAG
CTTGCTTCTGGGGAAGTCTCACAGTAAACAGATATTAATTACATAATCTGTATAACCTTAAACG
CCAAACTAAATGTTGTGTTATAATACTCCTCCTTTCTAATGACAAACACTGAGCTTCTATACAA
CCATTACTAAACCCTAGAGAAAAATATTTCATATCATTTTGAAACTGAAGAATTGATGGAGGTT
TATTATTTAGTAATAAACCTTTCCAAAAATAGGCGTATGCCGTTTAAAAGCAGAGAGAACACGA
TATTCTTTAGTAAAAGGCGAAAGAATAGTTCGCTATGCCCTCACTGCACGGCTCCGTGAGTCTT
ACCGAGTTGCTCTCGCTCTCTTTATATACTTTGTTTTACTCTGTTCCTGAGTATCCTGCCCGAT
GTGGGATCTAGCAAATCAATTAGCAAGCTTTTGATAGATTAATAAGGGCTTAAACTGATCCTTA
TAGCCCATTTCAGTTAAGCCCAACTATGTTGTTAATGTTCTGCCATGACGGAGCTAGATTGAAA
GGAATGAATCCTAGAAATGCTGAAGAAAGAAAGTACAGTATATATGTTTTGCTGTTATTACATA
AAACTGTTACATATTAAAGTCGTTGATTAAGCATGTTTCTAACAAAAATACAATGTAAACAGTC
AACGTAGTTTTTTTTTTCTTTCTTTTATATTCTCTTGAATTTATTGTTTAGAACCTATATACAA
CTTGAGTGAGTCAATTTGTAACAGTGTAACACTTCCATGTTTTTATTCAAAGATTGTCAAAACG
GATGACTCAAGGGTAACTCTCGGATTTAACTTGAGCTACTCTATAAATTGTTCATTTCTTTTGA
ATACCAAAACCATCCCAGTCAAGCAATTTCACTCTATCTCCTCTGACTCAAAAGAAAAATAAGG
AAACAATATATACGTGCAATGGAAGGTAGGATCGAAGCTCTTCTCTCCACTATTCTAGTTGTGA
CGACTCTGTGTGCCAACTACTCTATTGACACCAGGACAAGCCGAGGGACTCGTGACACCGCAAT
TTCTTTCTATTCCTGGTTCTCCAATTGATCTCACAAAATGTTGGTCATCACTCCTCAACATTCA
AGGTTGTAAAATCGAGATCTTTAAATCTGTTTTTAAGTGGTAAGTTTGAAAACGTTGGACCAAC
ATGCTGCAAGGCGTTTACGGAGGTGGATGCAAAGTGTTGGCCAAAAATGTTTCCGTTGAATCCA
TTATTCCCTCCTCTTCTCAAGGATGGTTGCTCTCGCATCATCTCTGGCGCACCAACACACACGA
AACCTCAATTCCTTGTCATCCCTGGTTCTCCGATCGATCTCACAAAATGTTTGTCATCACTTGT
TAACGTTGAAGGTTGCGTAACTGAAATCTACAAATCAGTTTTCACAGGAAAGTTTGGTAATGTT
GGATATATGTGCTGCAAGGCGTTTTCAGCTGTGGATGTAAAATGTTGGCCACAAATGTTTCCGC
TAAATCCGTTCTTCCCTCCTCTTCTCAAGAAGGAATGTTCTCCTATCAACGCAGCCACTCCTAC
ACACAAATGAAAGTAACTACAAAACCTGTCAGACCGCCGTGCGACCACCCCAGCAAGGTAGAAC
CGAACCGAGTAACGATCCTCTACAGCACCGAATGCGTCCGAGGACGATCGTAGCCGTCAATCAC
GCTCTAGCCGCACGGTCATGGTTCATCAACCAGGGTAAAGGGCCTGTCTCTTGAGAAATCAAGG
AAACAGAGGTACGAGC
						
					

			
		

Sequences
Splice junction sequence	CGATCGTAGCCGTCAATCACGCTCTAGCCGCACGGTCATGGTTCATCAACCAGGGTAAAGGGCC TGTCTCTTGAGAAATCAAGGAAACAGAGGTACGAGCctgtcagaccgccgtgcgaccaccccgg ctagggtaaaccgagccgagtaacgatcctctacagcaccggatgcgtccgaggacaatcgtag ccgtcaat
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: 2448 Transcript exons: 21811769-21814216 CACCGGATGCGTCCGAGGACAATCGTAGCCGTCAATCACGCTCTAGCCGCACGGTCATGGTTCA TCAACCAGGGTTTAGGGCCTGTCTCTTGAGAAATCAAGGAAACAGAGGTACGAGCCTATCAGAC CGCCGTGCGACCACCCCGGCTAGGGTAAACCGAGCCGAGTAACGATCCTCTACAG
Genomic sequence	CTGTCAGACCGCCGTGCGACCACCCCGGCTAGGGTAAACCGAGCCGAGTAACGATCCTCTACAG CACCGGATGCGTCCGAGGACAATCGTAGCCGTCAATCACGCTCTAGCCGCACGGTCATGGTTCA TCAACCAGGGTTTAGGGCCTGTCTCTTGAGAAATCAAGGAAACAGAGGTACGAGCCTATAGAAC AGATCCTGTTCAAGTAAGGTCGTGACCATTGCTGCTCTCTCAATGTTATATATCCGGCAACATT GTTTTTCAAAATAGCGATGTGGGACAAAGTTATATAAAGATCACATTAGAAAAGCATGCATGGG TCGTGATATATGGACTAAGGCCCACTTAATTATCATATAAAGCCCCTCCCTAAATTAGCGTTGA AAATTATCATTAAGTCAATATGATTTGCGAAGTATAGGCGTATAGCTATTAAGTGTGATAAATT CGTTCTCAATTATGTGCGGGTAACAAAGCTATCTTCATTATATCAGACGATGTTGAAACTTTTT TTTTTGTTTTTCTGCCGATGTGAAGATATAACCTATTAGAACAAGCAAAGCAGTCATTCATGTC CCAATCATTTTTTTATTTCATGCTATGATCCGAAAATTTTGTTCCTTTCTTGGATTACCAATGA TGAAACCTAGAAGAACTACAGATTTGACGTCTCTCAGTGACTGCATAGCCGCTCGTTGTGATAG CTTGCTTCTGGGGAAGTCTCACAGTAAACAGATATTAATTACATAATCTGTATAACCTTAAACG CCAAACTAAATGTTGTGTTATAATACTCCTCCTTTCTAATGACAAACACTGAGCTTCTATACAA CCATTACTAAACCCTAGAGAAAAATATTTCATATCATTTTGAAACTGAAGAATTGATGGAGGTT TATTATTTAGTAATAAACCTTTCCAAAAATAGGCGTATGCCGTTTAAAAGCAGAGAGAACACGA TATTCTTTAGTAAAAGGCGAAAGAATAGTTCGCTATGCCCTCACTGCACGGCTCCGTGAGTCTT ACCGAGTTGCTCTCGCTCTCTTTATATACTTTGTTTTACTCTGTTCCTGAGTATCCTGCCCGAT GTGGGATCTAGCAAATCAATTAGCAAGCTTTTGATAGATTAATAAGGGCTTAAACTGATCCTTA TAGCCCATTTCAGTTAAGCCCAACTATGTTGTTAATGTTCTGCCATGACGGAGCTAGATTGAAA GGAATGAATCCTAGAAATGCTGAAGAAAGAAAGTACAGTATATATGTTTTGCTGTTATTACATA AAACTGTTACATATTAAAGTCGTTGATTAAGCATGTTTCTAACAAAAATACAATGTAAACAGTC AACGTAGTTTTTTTTTTCTTTCTTTTATATTCTCTTGAATTTATTGTTTAGAACCTATATACAA CTTGAGTGAGTCAATTTGTAACAGTGTAACACTTCCATGTTTTTATTCAAAGATTGTCAAAACG GATGACTCAAGGGTAACTCTCGGATTTAACTTGAGCTACTCTATAAATTGTTCATTTCTTTTGA ATACCAAAACCATCCCAGTCAAGCAATTTCACTCTATCTCCTCTGACTCAAAAGAAAAATAAGG AAACAATATATACGTGCAATGGAAGGTAGGATCGAAGCTCTTCTCTCCACTATTCTAGTTGTGA CGACTCTGTGTGCCAACTACTCTATTGACACCAGGACAAGCCGAGGGACTCGTGACACCGCAAT TTCTTTCTATTCCTGGTTCTCCAATTGATCTCACAAAATGTTGGTCATCACTCCTCAACATTCA AGGTTGTAAAATCGAGATCTTTAAATCTGTTTTTAAGTGGTAAGTTTGAAAACGTTGGACCAAC ATGCTGCAAGGCGTTTACGGAGGTGGATGCAAAGTGTTGGCCAAAAATGTTTCCGTTGAATCCA TTATTCCCTCCTCTTCTCAAGGATGGTTGCTCTCGCATCATCTCTGGCGCACCAACACACACGA AACCTCAATTCCTTGTCATCCCTGGTTCTCCGATCGATCTCACAAAATGTTTGTCATCACTTGT TAACGTTGAAGGTTGCGTAACTGAAATCTACAAATCAGTTTTCACAGGAAAGTTTGGTAATGTT GGATATATGTGCTGCAAGGCGTTTTCAGCTGTGGATGTAAAATGTTGGCCACAAATGTTTCCGC TAAATCCGTTCTTCCCTCCTCTTCTCAAGAAGGAATGTTCTCCTATCAACGCAGCCACTCCTAC ACACAAATGAAAGTAACTACAAAACCTGTCAGACCGCCGTGCGACCACCCCAGCAAGGTAGAAC CGAACCGAGTAACGATCCTCTACAGCACCGAATGCGTCCGAGGACGATCGTAGCCGTCAATCAC GCTCTAGCCGCACGGTCATGGTTCATCAACCAGGGTAAAGGGCCTGTCTCTTGAGAAATCAAGG AAACAGAGGTACGAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.336488134

Conservation Information
Conserved circRNAs	NA
PMCS	0.336488134

			
						 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
						NA

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	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT5G53740_circ_g.1

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