Plant Circular RNA Database

Detail information of AT3G62030_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G62030_circ_g.1
					
						ID in PlantcircBase
						ath_circ_028719
					
						Alias
						Ath_circ_FC2473
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 22973956-22974876  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT3G62030						
					
						Parent gene annotation
						
							Rotamase CYP 4
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G62030_circ_g.2 AT3G62030_circ_g.3 AT3G62030_circ_g.4 AT3G62030_circ_g.5 AT3G62030_circ_g.6 AT3G62030_circ_g.7 						
					
						Support reads
						236
					
						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
						AT3G62030.2:5
AT3G62030.3:5
AT3G62030.1:5

General Information
CircRNA Name	AT3G62030_circ_g.1
ID in PlantcircBase	ath_circ_028719
Alias	Ath_circ_FC2473
Organism	Arabidpsis thaliana
Position	chr3: 22973956-22974876 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT3G62030
Parent gene annotation	Rotamase CYP 4
Parent gene strand	+
Alternative splicing	AT3G62030_circ_g.2 AT3G62030_circ_g.3 AT3G62030_circ_g.4 AT3G62030_circ_g.5 AT3G62030_circ_g.6 AT3G62030_circ_g.7
Support reads	236
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	AT3G62030.2:5 AT3G62030.3:5 AT3G62030.1:5

			
						 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  
						
							TTCCGCATTTGCAGTGAAGCATACTGGACCTGGAATCTTGAGCATGGCAAACGCTGGTCCTAAT
ACTAATGGAAGCCAGTTTTTCATTTGTACCGTCAAGattgggttcggtgttaagtcgcaattag
tttctgcaaatcgaacaactcaatcagtttgctttggagctcgttcctctggaattgcattatc
ttcgagat

									
								

					

						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: 573
Transcript exons: 22973956-22974144,22974222-22974375,22974463-22974551,22
974643-22974697,22974791-22974876
ATTGGGTTCGGTGTTAAGTCGCAATTAGTTTCTGCAAATCGAACAACTCAATCAGTTTGCTTTG
GAGCTCGTTCCTCTGGAATTGCATTATCTTCGAGATTGCACTATGCATCACCCATTAAGCAATT
TTCTGGGGTTTATGCGACCACCAAGCATCAGAGAACCGCTTGTGTTAAATCCATGGCTGCTGAG
GAAGAAGAAGTAATCGAACCTCAAGCTAAAGTGACAAACAAGGTTTACTTTGATGTGGAAATTG
GAGGTGAAGTTGCTGGCAGAATTGTGATGGGTCTCTTTGGAGAAGTTGTGCCTAAAACCGTTGA
AAACTTCCGTGCCTTGTGTACTGGTGAGAAGAAATACGGGTACAAGGGTTCCTCTTTCCATCGT
ATTATTAAGGATTTCATGATCCAAGGAGGTGATTTCACCGAGGGAAATGGTACTGGAGGTATTA
GTATTTACGGTGCCAAGTTCGAAGATGAAAACTTCACCCTGAAGCATACTGGACCTGGAATCTT
GAGCATGGCAAACGCTGGTCCTAATACTAATGGAAGCCAGTTTTTCATTTGTACCGTCAAG
						
					

						Genomic sequence
						
							ATTGGGTTCGGTGTTAAGTCGCAATTAGTTTCTGCAAATCGAACAACTCAATCAGTTTGCTTTG
GAGCTCGTTCCTCTGGAATTGCATTATCTTCGAGATTGCACTATGCATCACCCATTAAGCAATT
TTCTGGGGTTTATGCGACCACCAAGCATCAGAGAACCGCTTGTGTTAAATCCATGGCTGCTGTA
AGTTACTTTTTTCATAAATCATTCATGTTCTGTTGCCTTATGGATTCGTGTTGATTTTTGAACT
TGGTTTGTAGGAGGAAGAAGAAGTAATCGAACCTCAAGCTAAAGTGACAAACAAGGTTTACTTT
GATGTGGAAATTGGAGGTGAAGTTGCTGGCAGAATTGTGATGGGTCTCTTTGGAGAAGTTGTGC
CTAAAACCGTTGAAAACTTCCGTGCCTTGTGTACTGGTAAGCTCCTTATCAAAATGATGTTTAA
AGTTTGGAACTTTATAGACACAATCAAAACCATTGTCTAAAGGAAATTGATTTCTTCAGGTGAG
AAGAAATACGGGTACAAGGGTTCCTCTTTCCATCGTATTATTAAGGATTTCATGATCCAAGGAG
GTGATTTCACCGAGGGAAATGTAAGTTCTTTCCAACAAGTTACATTTCAGACTGTTTGTTTGTT
ATTTTGATATTTCTTTCTAAATCGTCTTTTTCGATATGGTCTCACAGGGTACTGGAGGTATTAG
TATTTACGGTGCCAAGTTCGAAGATGAAAACTTCACCCGTAAGTACTCACAAACAAAGAAAAAC
TCTGGTTTTCTGCAAATATGGCATTACTTCTTTGAGGTATTAATGGTTTTGTTTTCCGCATTTG
CAGTGAAGCATACTGGACCTGGAATCTTGAGCATGGCAAACGCTGGTCCTAATACTAATGGAAG
CCAGTTTTTCATTTGTACCGTCAAG
						
					

			
		

Sequences
Splice junction sequence	TTCCGCATTTGCAGTGAAGCATACTGGACCTGGAATCTTGAGCATGGCAAACGCTGGTCCTAAT ACTAATGGAAGCCAGTTTTTCATTTGTACCGTCAAGattgggttcggtgttaagtcgcaattag tttctgcaaatcgaacaactcaatcagtttgctttggagctcgttcctctggaattgcattatc ttcgagat
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: 573 Transcript exons: 22973956-22974144,22974222-22974375,22974463-22974551,22 974643-22974697,22974791-22974876 ATTGGGTTCGGTGTTAAGTCGCAATTAGTTTCTGCAAATCGAACAACTCAATCAGTTTGCTTTG GAGCTCGTTCCTCTGGAATTGCATTATCTTCGAGATTGCACTATGCATCACCCATTAAGCAATT TTCTGGGGTTTATGCGACCACCAAGCATCAGAGAACCGCTTGTGTTAAATCCATGGCTGCTGAG GAAGAAGAAGTAATCGAACCTCAAGCTAAAGTGACAAACAAGGTTTACTTTGATGTGGAAATTG GAGGTGAAGTTGCTGGCAGAATTGTGATGGGTCTCTTTGGAGAAGTTGTGCCTAAAACCGTTGA AAACTTCCGTGCCTTGTGTACTGGTGAGAAGAAATACGGGTACAAGGGTTCCTCTTTCCATCGT ATTATTAAGGATTTCATGATCCAAGGAGGTGATTTCACCGAGGGAAATGGTACTGGAGGTATTA GTATTTACGGTGCCAAGTTCGAAGATGAAAACTTCACCCTGAAGCATACTGGACCTGGAATCTT GAGCATGGCAAACGCTGGTCCTAATACTAATGGAAGCCAGTTTTTCATTTGTACCGTCAAG
Genomic sequence	ATTGGGTTCGGTGTTAAGTCGCAATTAGTTTCTGCAAATCGAACAACTCAATCAGTTTGCTTTG GAGCTCGTTCCTCTGGAATTGCATTATCTTCGAGATTGCACTATGCATCACCCATTAAGCAATT TTCTGGGGTTTATGCGACCACCAAGCATCAGAGAACCGCTTGTGTTAAATCCATGGCTGCTGTA AGTTACTTTTTTCATAAATCATTCATGTTCTGTTGCCTTATGGATTCGTGTTGATTTTTGAACT TGGTTTGTAGGAGGAAGAAGAAGTAATCGAACCTCAAGCTAAAGTGACAAACAAGGTTTACTTT GATGTGGAAATTGGAGGTGAAGTTGCTGGCAGAATTGTGATGGGTCTCTTTGGAGAAGTTGTGC CTAAAACCGTTGAAAACTTCCGTGCCTTGTGTACTGGTAAGCTCCTTATCAAAATGATGTTTAA AGTTTGGAACTTTATAGACACAATCAAAACCATTGTCTAAAGGAAATTGATTTCTTCAGGTGAG AAGAAATACGGGTACAAGGGTTCCTCTTTCCATCGTATTATTAAGGATTTCATGATCCAAGGAG GTGATTTCACCGAGGGAAATGTAAGTTCTTTCCAACAAGTTACATTTCAGACTGTTTGTTTGTT ATTTTGATATTTCTTTCTAAATCGTCTTTTTCGATATGGTCTCACAGGGTACTGGAGGTATTAG TATTTACGGTGCCAAGTTCGAAGATGAAAACTTCACCCGTAAGTACTCACAAACAAAGAAAAAC TCTGGTTTTCTGCAAATATGGCATTACTTCTTTGAGGTATTAATGGTTTTGTTTTCCGCATTTG CAGTGAAGCATACTGGACCTGGAATCTTGAGCATGGCAAACGCTGGTCCTAATACTAATGGAAG CCAGTTTTTCATTTGTACCGTCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.222652651

Conservation Information
Conserved circRNAs	NA
PMCS	0.222652651

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22974136-22974873(+)
						
						Potential amino acid sequence
						
							MAAEEEEVIEPQAKVTNKVYFDVEIGGEVAGRIVMGLFGEVVPKTVENFRALCTGEKKYGYKGS
SFHRIIKDFMIQGGDFTEGNGTGGISIYGAKFEDENFTLKHTGPGILSMANAGPNTNGSQFFIC
TVKIGFGVKSQLVSANRTTQSVCFGARSSGIALSSRLHYASPIKQFSGVYATTKHQRTACVKSM
AAEEEEVIEPQAKVTNKVYFDVEIGGEVAGRIVMGLFGEVVPKTVENFRALCTGEKKYGYKGSS
FHRIIKDFMIQGGDFTEGNGTGGISIYGAKFEDENFTLKHTGPGILSMANAGPNTNGSQFFICT
VKIGFGVKSQLVSANRTTQSVCFGARSSGIALSSRLHYASPIKQFSGVYATTKHQRTACVKSMA
AEEEEVIEPQAKVTNKVYFDVEIGGEVAGRIVMGLFGEVVPKTVENFRALCTGEKKYGYKGSSF
HRIIKDFMIQGGDFTEGNGTGGISIYGAKFEDENFTLKHTGPGILSMANAGPNTNGSQFFICTV
KIGFGVKSQLVSANRTTQSVCFGARSSGIALSSRLHYASPIKQFSGVYATTKHQRTACVKSMAA
EEEEVIEPQAKVTNKVYFDVEIGGEVAGRIVMGLFGEVVPKTVENFRALCTGEKKYGYKGSSFH
RIIKDFMIQGGDFTEGNGTGGISIYGAKFEDENFTLKHTGPGILSMANAGPNTNGSQFFICTVK
(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22974136-22974873(+)
Potential amino acid sequence	MAAEEEEVIEPQAKVTNKVYFDVEIGGEVAGRIVMGLFGEVVPKTVENFRALCTGEKKYGYKGS SFHRIIKDFMIQGGDFTEGNGTGGISIYGAKFEDENFTLKHTGPGILSMANAGPNTNGSQFFIC TVKIGFGVKSQLVSANRTTQSVCFGARSSGIALSSRLHYASPIKQFSGVYATTKHQRTACVKSM AAEEEEVIEPQAKVTNKVYFDVEIGGEVAGRIVMGLFGEVVPKTVENFRALCTGEKKYGYKGSS FHRIIKDFMIQGGDFTEGNGTGGISIYGAKFEDENFTLKHTGPGILSMANAGPNTNGSQFFICT VKIGFGVKSQLVSANRTTQSVCFGARSSGIALSSRLHYASPIKQFSGVYATTKHQRTACVKSMA AEEEEVIEPQAKVTNKVYFDVEIGGEVAGRIVMGLFGEVVPKTVENFRALCTGEKKYGYKGSSF HRIIKDFMIQGGDFTEGNGTGGISIYGAKFEDENFTLKHTGPGILSMANAGPNTNGSQFFICTV KIGFGVKSQLVSANRTTQSVCFGARSSGIALSSRLHYASPIKQFSGVYATTKHQRTACVKSMAA EEEEVIEPQAKVTNKVYFDVEIGGEVAGRIVMGLFGEVVPKTVENFRALCTGEKKYGYKGSSFH RIIKDFMIQGGDFTEGNGTGGISIYGAKFEDENFTLKHTGPGILSMANAGPNTNGSQFFICTVK (+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT3G62030_circ_g.1

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