Plant Circular RNA Database

Detail information of AT5G56190_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT5G56190_circ_g.2
					
						ID in PlantcircBase
						ath_circ_044351
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 22742525-22743787  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT5G56190						
					
						Parent gene annotation
						
							Transducin/WD40 repeat-like superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G56190_circ_g.1 AT5G56190_circ_g.3 AT5G56190_circ_g.4 AT5G56190_circ_g.5 AT5G56190_circ_g.6 						
					
						Support reads
						7
					
						Tissues
						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  
						
							GT-AG							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
						AT5G56190.3:6
AT5G56190.5:5
AT5G56190.2:5
AT5G56190.4:5
AT5G56190.6:5
AT5G56190.1:6
AT5G56190.7:6

General Information
CircRNA Name	AT5G56190_circ_g.2
ID in PlantcircBase	ath_circ_044351
Alias	NA
Organism	Arabidpsis thaliana
Position	chr5: 22742525-22743787 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT5G56190
Parent gene annotation	Transducin/WD40 repeat-like superfamily protein
Parent gene strand	+
Alternative splicing	AT5G56190_circ_g.1 AT5G56190_circ_g.3 AT5G56190_circ_g.4 AT5G56190_circ_g.5 AT5G56190_circ_g.6
Support reads	7
Tissues	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	GT-AG 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	AT5G56190.3:6 AT5G56190.5:5 AT5G56190.2:5 AT5G56190.4:5 AT5G56190.6:5 AT5G56190.1:6 AT5G56190.7:6

			
						 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  
						
							GAGTTTGTTGGAAGGATTTACAGAGACTCAAGTTAGCACTCTTGCAGTAAAAGAAAGGCTACTA
GTTGCTGGTGGATTCCAAGGAGAACTCATTTGCAAGgtttttggaagctaacttattgttggag
gtggagagatatggctgactttggtttgttctgtttcccttgtttaatggaagttgtttcatca
tcatcatc

									
								

					

						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: 665
Transcript exons: 22742525-22742575,22742685-22742800,22742896-22743060,22
743153-22743239,22743440-22743574,22743677-22743787
GTTTTTGGAAGCTAACTTATTGTTGGAGGTGGAGAGATATGGCTGACTTTGATGAATATATGGC
TGATGAGTATGACATGGATGATCTCGAGGATGATATGAATGCCGCGTTTGATGGAAGAGATATC
GATGCTTCTGATTCCGAAGTCGAAGATTTCGATCAATTGAACAAGGCTGCAGATACTTCTGCTG
CTCAAGCACGGAATGGGAAGGATATTCAGGGTATACCGTGGGATAGTCTTACTCTTACTAGAAA
AGATTACAGAAAAACTAGGCTAGAACAATATAAAAACTATGAAAATATACCCAATTCTGGTGAT
GAATCTGCCAAGAAATGCATGAATACTGAGAAAGGCAGCTCTTTCTATGAGTTCAGAAGGAATT
CTAGATCCGTGAGATCAACGATTCTCCATTTTCAGTTGAGGAATTTGGTCTGGGCTACCTCAAA
ACACGATGTTTATTTATTGTCCAACTACTCCATCAGCCACTGGTCTTCTTTGACAGGTTGTAGG
AGTGAAATTCTTAACGTTAAAGGTCATGTGGCTCCGTCTGAGAAACATCCCGAGAGTTTGTTGG
AAGGATTTACAGAGACTCAAGTTAGCACTCTTGCAGTAAAAGAAAGGCTACTAGTTGCTGGTGG
ATTCCAAGGAGAACTCATTTGCAAG
						
					

						Genomic sequence
						
							GTTTTTGGAAGCTAACTTATTGTTGGAGGTGGAGAGATATGGCTGACTTTGGTTTGTTCTGTTT
CCCTTGTTTAATGGAAGTTGTTTCATCATCATCATCATCTCTGTGATTGTAATTGATCTCACAC
CATGTCTGATTACAATGGTGATGATCTTGAAGATGAATATATGGCTGATGAGTATGACATGGAT
GATCTCGAGGATGATATGAATGCCGCGTTTGATGGAAGAGATATCGATGCTTCTGATTCCGAAG
TCGAAGATTTCGATCAATTGGTTTGTCTTCTTCCTCTGTTTCTCACACTCTTCAGCTTTGTGTT
CTCTGTATATTTTTCTTAACACACAATTGCTTGTATATGGAGTGTTTTCAGAACAAGGCTGCAG
ATACTTCTGCTGCTCAAGCACGGAATGGGAAGGATATTCAGGGTATACCGTGGGATAGTCTTAC
TCTTACTAGAAAAGATTACAGAAAAACTAGGCTAGAACAATATAAAAACTATGAAAATATACCC
AATTCTGGTGATGAATCTGCCAAGGTGAATTACATTTCATGTTTCTTTAAGGTTATTTATTAGT
AGATGCACCTATGTTGCTCTTTTCTCACTCTAGTCTTGTCTATTGGAACCAGAAATGCATGAAT
ACTGAGAAAGGCAGCTCTTTCTATGAGTTCAGAAGGAATTCTAGATCCGTGAGATCAACGATTC
TCCATTTTCAGGTTTGTCTAGTGCGTTATATAACCCCTGTCTCTATTATGCTTCCAACAATTTG
GTGGCTCTCTCGGGGTTTCTAAATGTAACTTGGTAGTTTTTTAATCATAATGTAGACCTTCCCT
GTGCTAGTATTGCTGATGGAACCATAGTTTTATGTGAAGCTGATCATAGTTAAGACTAAATTAT
GTTTGCTTCTTTGTTACAGTTGAGGAATTTGGTCTGGGCTACCTCAAAACACGATGTTTATTTA
TTGTCCAACTACTCCATCAGCCACTGGTCTTCTTTGACAGGTTGTAGGAGTGAAATTCTTAACG
TTAAAGGTCATGTGGCTCCGTCTGAGGTTCGTTTCTCAAGTCTTATCTAAACCATCTAATTAAT
TTGACTTGTGGTTTCCTTTCGTCTCTGCTGGGTTTAGCTAAAACCGATGTTCCGTATTTTTCAG
AAACATCCCGAGAGTTTGTTGGAAGGATTTACAGAGACTCAAGTTAGCACTCTTGCAGTAAAAG
AAAGGCTACTAGTTGCTGGTGGATTCCAAGGAGAACTCATTTGCAAG
						
					

			
		

Sequences
Splice junction sequence	GAGTTTGTTGGAAGGATTTACAGAGACTCAAGTTAGCACTCTTGCAGTAAAAGAAAGGCTACTA GTTGCTGGTGGATTCCAAGGAGAACTCATTTGCAAGgtttttggaagctaacttattgttggag gtggagagatatggctgactttggtttgttctgtttcccttgtttaatggaagttgtttcatca tcatcatc
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: 665 Transcript exons: 22742525-22742575,22742685-22742800,22742896-22743060,22 743153-22743239,22743440-22743574,22743677-22743787 GTTTTTGGAAGCTAACTTATTGTTGGAGGTGGAGAGATATGGCTGACTTTGATGAATATATGGC TGATGAGTATGACATGGATGATCTCGAGGATGATATGAATGCCGCGTTTGATGGAAGAGATATC GATGCTTCTGATTCCGAAGTCGAAGATTTCGATCAATTGAACAAGGCTGCAGATACTTCTGCTG CTCAAGCACGGAATGGGAAGGATATTCAGGGTATACCGTGGGATAGTCTTACTCTTACTAGAAA AGATTACAGAAAAACTAGGCTAGAACAATATAAAAACTATGAAAATATACCCAATTCTGGTGAT GAATCTGCCAAGAAATGCATGAATACTGAGAAAGGCAGCTCTTTCTATGAGTTCAGAAGGAATT CTAGATCCGTGAGATCAACGATTCTCCATTTTCAGTTGAGGAATTTGGTCTGGGCTACCTCAAA ACACGATGTTTATTTATTGTCCAACTACTCCATCAGCCACTGGTCTTCTTTGACAGGTTGTAGG AGTGAAATTCTTAACGTTAAAGGTCATGTGGCTCCGTCTGAGAAACATCCCGAGAGTTTGTTGG AAGGATTTACAGAGACTCAAGTTAGCACTCTTGCAGTAAAAGAAAGGCTACTAGTTGCTGGTGG ATTCCAAGGAGAACTCATTTGCAAG
Genomic sequence	GTTTTTGGAAGCTAACTTATTGTTGGAGGTGGAGAGATATGGCTGACTTTGGTTTGTTCTGTTT CCCTTGTTTAATGGAAGTTGTTTCATCATCATCATCATCTCTGTGATTGTAATTGATCTCACAC CATGTCTGATTACAATGGTGATGATCTTGAAGATGAATATATGGCTGATGAGTATGACATGGAT GATCTCGAGGATGATATGAATGCCGCGTTTGATGGAAGAGATATCGATGCTTCTGATTCCGAAG TCGAAGATTTCGATCAATTGGTTTGTCTTCTTCCTCTGTTTCTCACACTCTTCAGCTTTGTGTT CTCTGTATATTTTTCTTAACACACAATTGCTTGTATATGGAGTGTTTTCAGAACAAGGCTGCAG ATACTTCTGCTGCTCAAGCACGGAATGGGAAGGATATTCAGGGTATACCGTGGGATAGTCTTAC TCTTACTAGAAAAGATTACAGAAAAACTAGGCTAGAACAATATAAAAACTATGAAAATATACCC AATTCTGGTGATGAATCTGCCAAGGTGAATTACATTTCATGTTTCTTTAAGGTTATTTATTAGT AGATGCACCTATGTTGCTCTTTTCTCACTCTAGTCTTGTCTATTGGAACCAGAAATGCATGAAT ACTGAGAAAGGCAGCTCTTTCTATGAGTTCAGAAGGAATTCTAGATCCGTGAGATCAACGATTC TCCATTTTCAGGTTTGTCTAGTGCGTTATATAACCCCTGTCTCTATTATGCTTCCAACAATTTG GTGGCTCTCTCGGGGTTTCTAAATGTAACTTGGTAGTTTTTTAATCATAATGTAGACCTTCCCT GTGCTAGTATTGCTGATGGAACCATAGTTTTATGTGAAGCTGATCATAGTTAAGACTAAATTAT GTTTGCTTCTTTGTTACAGTTGAGGAATTTGGTCTGGGCTACCTCAAAACACGATGTTTATTTA TTGTCCAACTACTCCATCAGCCACTGGTCTTCTTTGACAGGTTGTAGGAGTGAAATTCTTAACG TTAAAGGTCATGTGGCTCCGTCTGAGGTTCGTTTCTCAAGTCTTATCTAAACCATCTAATTAAT TTGACTTGTGGTTTCCTTTCGTCTCTGCTGGGTTTAGCTAAAACCGATGTTCCGTATTTTTCAG AAACATCCCGAGAGTTTGTTGGAAGGATTTACAGAGACTCAAGTTAGCACTCTTGCAGTAAAAG AAAGGCTACTAGTTGCTGGTGGATTCCAAGGAGAACTCATTTGCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.183783817

Conservation Information
Conserved circRNAs	NA
PMCS	0.183783817

			
						 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 AT5G56190_circ_g.2

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