Plant Circular RNA Database

Detail information of AT5G19390_circ_g.17

			
						 General Information
					
						CircRNA Name
						AT5G19390_circ_g.17
					
						ID in PlantcircBase
						ath_circ_039210
					
						Alias
						At_ciR2808, Ath_circ_FC3401
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 6536449-6537793  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ, CIRI-full
					
						Parent gene
						
							AT5G19390						
					
						Parent gene annotation
						
							Rho GTPase-activating protein 7
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G19390_circ_g.4 AT5G19390_circ_g.5 AT5G19390_circ_g.6 AT5G19390_circ_g.7 AT5G19390_circ_g.8 AT5G19390_circ_g.9 AT5G19390_circ_g.10 AT5G19390_circ_g.11 AT5G19390_circ_g.12 AT5G19390_circ_g.13 AT5G19390_circ_g.14 AT5G19390_circ_g.15 AT5G19390_circ_g.16 AT5G19390_circ_g.18 AT5G19390_circ_g.19 						
					
						Support reads
						3
					
						Tissues
						leaf
					
						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
						AT5G19390.3:6
AT5G19390.4:4
AT5G19390.2:6
AT5G19390.1:6

General Information
CircRNA Name	AT5G19390_circ_g.17
ID in PlantcircBase	ath_circ_039210
Alias	At_ciR2808, Ath_circ_FC3401
Organism	Arabidpsis thaliana
Position	chr5: 6536449-6537793 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ, CIRI-full
Parent gene	AT5G19390
Parent gene annotation	Rho GTPase-activating protein 7
Parent gene strand	+
Alternative splicing	AT5G19390_circ_g.4 AT5G19390_circ_g.5 AT5G19390_circ_g.6 AT5G19390_circ_g.7 AT5G19390_circ_g.8 AT5G19390_circ_g.9 AT5G19390_circ_g.10 AT5G19390_circ_g.11 AT5G19390_circ_g.12 AT5G19390_circ_g.13 AT5G19390_circ_g.14 AT5G19390_circ_g.15 AT5G19390_circ_g.16 AT5G19390_circ_g.18 AT5G19390_circ_g.19
Support reads	3
Tissues	leaf
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	AT5G19390.3:6 AT5G19390.4:4 AT5G19390.2:6 AT5G19390.1:6

			
						 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  
						
							AACTGACTCTAAAATCAGTGAAGAGTCTGGAAAGATATCCGTGGACAAGCTCTCATCCATAGAT
TCTCCATCTATTCCGTCGACTTCAAGAGTATTAGATgcttgctatacagaggctcgagaccaca
aaaaatgaactgcgacaacgaattgcaaaggaggtaatcatctactgctgaaatattattcttt
gccttcat

									
								

					

						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: 703
Transcript exons: 6536449-6536509,6536584-6536667,6536777-6536887,6536970-
6537139,6537433-6537502,6537587-6537793
GCTTGCTATACAGAGGCTCGAGACCACAAAAAATGAACTGCGACAACGAATTGCAAAGGAGGCC
AGAGGTAATGCAATATTACAGGCTAGCTTGGAGAGAAGGAAACAAGCACTGCATGAACGTCGTT
TGTCGCTTGAACAAGATGTGTCAAGATTACAAGAGCAGCTGCAAGCTGAAAGAGATCTCCGAGC
AGCACTGGAGGTTGGTTTGAGCATGTCTTCTGGACAATTCAGTTCACATGGTGTAGATTCAAAA
ACAAGGGCTGAGCTTGAGGAAATTGCTCTTGCTGAGGCTGATGTGGCCAGGCTGAAGCAGAAAG
TTGCAGAACTTCACCATCAGCTTAACCAGCAACGTCAGACTCATTTTGGTTCCTTCTCAGATGC
ACGTGATACTCATCAGTATCTCCAGAATCACAATCCTCAAAAAAGGTTTCTTCAGCAAGATTTT
GATTCCACTCTTGCCTATGTAAATCATGAAAGGAAACAAAGACACGAGGAGAATGTACTGGGAG
CGGAGTGGAGAAATAGTAAAGGGGCAGGATCTTTTGGTGTTGGCAATAGCAGGCAACCATCTCG
TAAACAAATACCAGAATCAACAAACACAACTGACTCTAAAATCAGTGAAGAGTCTGGAAAGATA
TCCGTGGACAAGCTCTCATCCATAGATTCTCCATCTATTCCGTCGACTTCAAGAGTATTAGAT
Transcript length: 268
Transcript exons: 6536449-6537793
GCTTGCTATACAGAGGCTCGAGACCACAAAAAATGAACTGCGACAACGAATTGCAAAGGAGGAG
AATGTACTGGGAGCGGAGTGGAGAAATAGTAAAGGGGCAGGATCTTTTGGTGTTGGCAATAGCA
GGCAACCATCTCGTAAACAAATACCAGAATCAACAAACACAACTGACTCTAAAATCAGTGAAGA
GTCTGGAAAGATATCCGTGGACAAGCTCTCATCCATAGATTCTCCATCTATTCCGTCGACTTCA
AGAGTATTAGAT
						
					

						Genomic sequence
						
							GCTTGCTATACAGAGGCTCGAGACCACAAAAAATGAACTGCGACAACGAATTGCAAAGGAGGTA
ATCATCTACTGCTGAAATATTATTCTTTGCCTTCATAAAGTCATTAACACTGGTCACCGTTATT
GTTATAGGCCAGAGGTAATGCAATATTACAGGCTAGCTTGGAGAGAAGGAAACAAGCACTGCAT
GAACGTCGTTTGTCGCTTGAACAAGATGTAAAGAATTTCTCTTTAAAACTATCAGTGTTTATAA
ATCTCGTCTCTCCACTATTAATCCTAATGTCAAAGGAATCTTCTTCTGATTTGATGAAAAATAC
TTATTTAGGTGTCAAGATTACAAGAGCAGCTGCAAGCTGAAAGAGATCTCCGAGCAGCACTGGA
GGTTGGTTTGAGCATGTCTTCTGGACAATTCAGTTCACATGGTGTAGATTCAAAAGTAAGTATA
CATTTTAAGGAAATGGTATCTTTCTTTATAACAATTAGCTCGTAAAAAATACTTACAATCCAAG
TATTTGAAGACAAGGGCTGAGCTTGAGGAAATTGCTCTTGCTGAGGCTGATGTGGCCAGGCTGA
AGCAGAAAGTTGCAGAACTTCACCATCAGCTTAACCAGCAACGTCAGACTCATTTTGGTTCCTT
CTCAGATGCACGTGATACTCATCAGTATCTCCAGAATCACAATCCTCAAAAGTGAGTTGTATCA
CTATCCCTGTTTCCTCACACTGAGGAGCTTGTAGTCCAAGTTATTTTTTGTGATAACTTACCCT
TATTTCTGTAAATCTTTTATGCTTGAATTACTGGCTTGTTTCTTTAGCTAGTGAAGATGTTTAA
CAAATATCTCAGATTAACTTATCCAGCATTAATCTTCAACTCAGTACAGCTGTGAGAATTATGT
TTGAAGTAACCTTTGCACAACATATCTTGTACTATGATTGGTTCACATCTGTGTTTCTTCTCTA
ATACCATGTTATGTATTTCCGCAGAAGGTTTCTTCAGCAAGATTTTGATTCCACTCTTGCCTAT
GTAAATCATGAAAGGAAACAAAGACACGAGGTACTTCTTACTGATATTTCTGTCATCAATCATC
ATCTTTCATAGTTTAGATCAAACCTATAGAATTTACTGTTTGGCCTACAGGAGAATGTACTGGG
AGCGGAGTGGAGAAATAGTAAAGGGGCAGGATCTTTTGGTGTTGGCAATAGCAGGCAACCATCT
CGTAAACAAATACCAGAATCAACAAACACAACTGACTCTAAAATCAGTGAAGAGTCTGGAAAGA
TATCCGTGGACAAGCTCTCATCCATAGATTCTCCATCTATTCCGTCGACTTCAAGAGTATTAGA
T
						
					

			
		

Sequences
Splice junction sequence	AACTGACTCTAAAATCAGTGAAGAGTCTGGAAAGATATCCGTGGACAAGCTCTCATCCATAGAT TCTCCATCTATTCCGTCGACTTCAAGAGTATTAGATgcttgctatacagaggctcgagaccaca aaaaatgaactgcgacaacgaattgcaaaggaggtaatcatctactgctgaaatattattcttt gccttcat
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: 703 Transcript exons: 6536449-6536509,6536584-6536667,6536777-6536887,6536970- 6537139,6537433-6537502,6537587-6537793 GCTTGCTATACAGAGGCTCGAGACCACAAAAAATGAACTGCGACAACGAATTGCAAAGGAGGCC AGAGGTAATGCAATATTACAGGCTAGCTTGGAGAGAAGGAAACAAGCACTGCATGAACGTCGTT TGTCGCTTGAACAAGATGTGTCAAGATTACAAGAGCAGCTGCAAGCTGAAAGAGATCTCCGAGC AGCACTGGAGGTTGGTTTGAGCATGTCTTCTGGACAATTCAGTTCACATGGTGTAGATTCAAAA ACAAGGGCTGAGCTTGAGGAAATTGCTCTTGCTGAGGCTGATGTGGCCAGGCTGAAGCAGAAAG TTGCAGAACTTCACCATCAGCTTAACCAGCAACGTCAGACTCATTTTGGTTCCTTCTCAGATGC ACGTGATACTCATCAGTATCTCCAGAATCACAATCCTCAAAAAAGGTTTCTTCAGCAAGATTTT GATTCCACTCTTGCCTATGTAAATCATGAAAGGAAACAAAGACACGAGGAGAATGTACTGGGAG CGGAGTGGAGAAATAGTAAAGGGGCAGGATCTTTTGGTGTTGGCAATAGCAGGCAACCATCTCG TAAACAAATACCAGAATCAACAAACACAACTGACTCTAAAATCAGTGAAGAGTCTGGAAAGATA TCCGTGGACAAGCTCTCATCCATAGATTCTCCATCTATTCCGTCGACTTCAAGAGTATTAGAT Transcript length: 268 Transcript exons: 6536449-6537793 GCTTGCTATACAGAGGCTCGAGACCACAAAAAATGAACTGCGACAACGAATTGCAAAGGAGGAG AATGTACTGGGAGCGGAGTGGAGAAATAGTAAAGGGGCAGGATCTTTTGGTGTTGGCAATAGCA GGCAACCATCTCGTAAACAAATACCAGAATCAACAAACACAACTGACTCTAAAATCAGTGAAGA GTCTGGAAAGATATCCGTGGACAAGCTCTCATCCATAGATTCTCCATCTATTCCGTCGACTTCA AGAGTATTAGAT
Genomic sequence	GCTTGCTATACAGAGGCTCGAGACCACAAAAAATGAACTGCGACAACGAATTGCAAAGGAGGTA ATCATCTACTGCTGAAATATTATTCTTTGCCTTCATAAAGTCATTAACACTGGTCACCGTTATT GTTATAGGCCAGAGGTAATGCAATATTACAGGCTAGCTTGGAGAGAAGGAAACAAGCACTGCAT GAACGTCGTTTGTCGCTTGAACAAGATGTAAAGAATTTCTCTTTAAAACTATCAGTGTTTATAA ATCTCGTCTCTCCACTATTAATCCTAATGTCAAAGGAATCTTCTTCTGATTTGATGAAAAATAC TTATTTAGGTGTCAAGATTACAAGAGCAGCTGCAAGCTGAAAGAGATCTCCGAGCAGCACTGGA GGTTGGTTTGAGCATGTCTTCTGGACAATTCAGTTCACATGGTGTAGATTCAAAAGTAAGTATA CATTTTAAGGAAATGGTATCTTTCTTTATAACAATTAGCTCGTAAAAAATACTTACAATCCAAG TATTTGAAGACAAGGGCTGAGCTTGAGGAAATTGCTCTTGCTGAGGCTGATGTGGCCAGGCTGA AGCAGAAAGTTGCAGAACTTCACCATCAGCTTAACCAGCAACGTCAGACTCATTTTGGTTCCTT CTCAGATGCACGTGATACTCATCAGTATCTCCAGAATCACAATCCTCAAAAGTGAGTTGTATCA CTATCCCTGTTTCCTCACACTGAGGAGCTTGTAGTCCAAGTTATTTTTTGTGATAACTTACCCT TATTTCTGTAAATCTTTTATGCTTGAATTACTGGCTTGTTTCTTTAGCTAGTGAAGATGTTTAA CAAATATCTCAGATTAACTTATCCAGCATTAATCTTCAACTCAGTACAGCTGTGAGAATTATGT TTGAAGTAACCTTTGCACAACATATCTTGTACTATGATTGGTTCACATCTGTGTTTCTTCTCTA ATACCATGTTATGTATTTCCGCAGAAGGTTTCTTCAGCAAGATTTTGATTCCACTCTTGCCTAT GTAAATCATGAAAGGAAACAAAGACACGAGGTACTTCTTACTGATATTTCTGTCATCAATCATC ATCTTTCATAGTTTAGATCAAACCTATAGAATTTACTGTTTGGCCTACAGGAGAATGTACTGGG AGCGGAGTGGAGAAATAGTAAAGGGGCAGGATCTTTTGGTGTTGGCAATAGCAGGCAACCATCT CGTAAACAAATACCAGAATCAACAAACACAACTGACTCTAAAATCAGTGAAGAGTCTGGAAAGA TATCCGTGGACAAGCTCTCATCCATAGATTCTCCATCTATTCCGTCGACTTCAAGAGTATTAGA T

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.297406314

Conservation Information
Conserved circRNAs	NA
PMCS	0.297406314

			
						 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
						Ye et al., 2015;Chen et al., 2017a

circRNA

Detail information of AT5G19390_circ_g.17

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