Plant Circular RNA Database

Detail information of AT1G53780_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT1G53780_circ_g.6
					
						ID in PlantcircBase
						ath_circ_007236
					
						Alias
						At_ciR488, AT1G53780_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 20076661-20076975  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT1G53780						
					
						Parent gene annotation
						
							26S proteasome regulatory complex ATPase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							1_circ_ag.2 1_circ_ag.3 AT1G53750_circ_g.4 1_circ_ag.5 AT1G53750_circ_g.6 AT1G53750_circ_g.7 1_circ_ag.8 AT1G53750_circ_g.9 1_circ_ag.10 1_circ_ag.11 1_circ_ag.12 1_circ_ag.13 1_circ_ag.14 AT1G53760_circ_g.1 AT1G53760_circ_g.2 AT1G53780_circ_g.1 AT1G53780_circ_g.2 AT1G53780_circ_g.3 AT1G53780_circ_g.4 AT1G53780_circ_g.5 AT1G53780_circ_g.7 AT1G53780_circ_g.8 AT1G53780_circ_g.9 AT1G53780_circ_g.10 						
					
						Support reads
						9/40/7
					
						Tissues
						leaf/leaf, inflorescences, whole_plant/seedlings
					
						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
						AT1G53780.3:1
AT1G53780.2:1
AT1G53780.4:1
AT1G53780.1:1

General Information
CircRNA Name	AT1G53780_circ_g.6
ID in PlantcircBase	ath_circ_007236
Alias	At_ciR488, AT1G53780_C1
Organism	Arabidpsis thaliana
Position	chr1: 20076661-20076975 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ, CIRI-full, CIRI2
Parent gene	AT1G53780
Parent gene annotation	26S proteasome regulatory complex ATPase
Parent gene strand	-
Alternative splicing	1_circ_ag.2 1_circ_ag.3 AT1G53750_circ_g.4 1_circ_ag.5 AT1G53750_circ_g.6 AT1G53750_circ_g.7 1_circ_ag.8 AT1G53750_circ_g.9 1_circ_ag.10 1_circ_ag.11 1_circ_ag.12 1_circ_ag.13 1_circ_ag.14 AT1G53760_circ_g.1 AT1G53760_circ_g.2 AT1G53780_circ_g.1 AT1G53780_circ_g.2 AT1G53780_circ_g.3 AT1G53780_circ_g.4 AT1G53780_circ_g.5 AT1G53780_circ_g.7 AT1G53780_circ_g.8 AT1G53780_circ_g.9 AT1G53780_circ_g.10
Support reads	9/40/7
Tissues	leaf/leaf, inflorescences, whole_plant/seedlings
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	AT1G53780.3:1 AT1G53780.2:1 AT1G53780.4:1 AT1G53780.1:1

			
						 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  
						
							GTCGTATCCTGATATCTTTATTTGGTCTGTTCTTCGCATCAACAGAAGCTTTGGCTATACAAGT
CAAAGTTTCAAACCCGCTGGTAATCTTCCCAAACACagaattaattgcaacttcaacaggattg
gcagccatttcggcgaaggcctcgtttagttccagaaagtcaaattctgcatcccttatatccc
aatcctct

						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: 189
Transcript exons: 20076661-20076824,20076951-20076975
AGAATTAATTGCAACTTCAACAGGATTGGCAGCCATTTCGGCGAAGGCCTCGTTTAGTTCCAGA
AAGTCAAATTCTGCATCCCTTATATCCCAATCCTCTCTGGGTTGCATGTCATCTGTGACCTCGA
CCTTCGGTTTTCCCTTGGGGGAAGCGTCTGGTATCAACCCGCTGGTAATCTTCCCAAACAC
Transcript length: 213
Transcript exons: 20076661-20076713,20076816-20076975
AGAATTAATTGCAACTTCAACAGGATTGGCAGCCATTTCGGCGAAGGCCTCGTCTGGTATCATC
TTAGCCAGTTGTGGGGGATCATCAAATGGATCTGTAAGTATATATGTGTGTCGTATCCTGATAT
CTTTATTTGGTCTGTTCTTCGCATCAACAGAAGCTTTGGCTATACAAGTCAAAGTTTCAAACCC
GCTGGTAATCTTCCCAAACAC
Transcript length: 315
Transcript exons: 20076661-20076975
AGAATTAATTGCAACTTCAACAGGATTGGCAGCCATTTCGGCGAAGGCCTCGTTTAGTTCCAGA
AAGTCAAATTCTGCATCCCTTATATCCCAATCCTCTCTGGGTTGCATGTCATCTGTGACCTCGA
CCTTCGGTTTTCCCTTGGGGGAAGCGTCTGGTATCATCTTAGCCAGTTGTGGGGGATCATCAAA
TGGATCTGTAAGTATATATGTGTGTCGTATCCTGATATCTTTATTTGGTCTGTTCTTCGCATCA
ACAGAAGCTTTGGCTATACAAGTCAAAGTTTCAAACCCGCTGGTAATCTTCCCAAACAC
						
						Genomic sequence
						
							AGAATTAATTGCAACTTCAACAGGATTGGCAGCCATTTCGGCGAAGGCCTCGTTTAGTTCCAGA
AAGTCAAATTCTGCATCCCTTATATCCCAATCCTCTCTGGGTTGCATGTCATCTGTGACCTCGA
CCTTCGGTTTTCCCTTGGGGGAAGCGTCTGGTATCATCTTAGCCAGTTGTGGGGGATCATCAAA
TGGATCTGTAAGTATATATGTGTGTCGTATCCTGATATCTTTATTTGGTCTGTTCTTCGCATCA
ACAGAAGCTTTGGCTATACAAGTCAAAGTTTCAAACCCGCTGGTAATCTTCCCAAACAC

Sequences
Splice junction sequence	GTCGTATCCTGATATCTTTATTTGGTCTGTTCTTCGCATCAACAGAAGCTTTGGCTATACAAGT CAAAGTTTCAAACCCGCTGGTAATCTTCCCAAACACagaattaattgcaacttcaacaggattg gcagccatttcggcgaaggcctcgtttagttccagaaagtcaaattctgcatcccttatatccc aatcctct
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: 189 Transcript exons: 20076661-20076824,20076951-20076975 AGAATTAATTGCAACTTCAACAGGATTGGCAGCCATTTCGGCGAAGGCCTCGTTTAGTTCCAGA AAGTCAAATTCTGCATCCCTTATATCCCAATCCTCTCTGGGTTGCATGTCATCTGTGACCTCGA CCTTCGGTTTTCCCTTGGGGGAAGCGTCTGGTATCAACCCGCTGGTAATCTTCCCAAACAC Transcript length: 213 Transcript exons: 20076661-20076713,20076816-20076975 AGAATTAATTGCAACTTCAACAGGATTGGCAGCCATTTCGGCGAAGGCCTCGTCTGGTATCATC TTAGCCAGTTGTGGGGGATCATCAAATGGATCTGTAAGTATATATGTGTGTCGTATCCTGATAT CTTTATTTGGTCTGTTCTTCGCATCAACAGAAGCTTTGGCTATACAAGTCAAAGTTTCAAACCC GCTGGTAATCTTCCCAAACAC Transcript length: 315 Transcript exons: 20076661-20076975 AGAATTAATTGCAACTTCAACAGGATTGGCAGCCATTTCGGCGAAGGCCTCGTTTAGTTCCAGA AAGTCAAATTCTGCATCCCTTATATCCCAATCCTCTCTGGGTTGCATGTCATCTGTGACCTCGA CCTTCGGTTTTCCCTTGGGGGAAGCGTCTGGTATCATCTTAGCCAGTTGTGGGGGATCATCAAA TGGATCTGTAAGTATATATGTGTGTCGTATCCTGATATCTTTATTTGGTCTGTTCTTCGCATCA ACAGAAGCTTTGGCTATACAAGTCAAAGTTTCAAACCCGCTGGTAATCTTCCCAAACAC
Genomic sequence	AGAATTAATTGCAACTTCAACAGGATTGGCAGCCATTTCGGCGAAGGCCTCGTTTAGTTCCAGA AAGTCAAATTCTGCATCCCTTATATCCCAATCCTCTCTGGGTTGCATGTCATCTGTGACCTCGA CCTTCGGTTTTCCCTTGGGGGAAGCGTCTGGTATCATCTTAGCCAGTTGTGGGGGATCATCAAA TGGATCTGTAAGTATATATGTGTGTCGTATCCTGATATCTTTATTTGGTCTGTTCTTCGCATCA ACAGAAGCTTTGGCTATACAAGTCAAAGTTTCAAACCCGCTGGTAATCTTCCCAAACAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.501835582

Conservation Information
Conserved circRNAs	NA
PMCS	0.501835582

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20076826-20076663(-)
20076770-20076972(+)
						
						Potential amino acid sequence
						
							MIPDASPKGKPKVEVTDDMQPREDWDIRDAEFDFLELNEAFAEMAANPVEVAINSVFGKITSGF
ETLTCIAKASVDAKNRPNKDIRIRHTYILTDPFDDPPQLAKMIPDASPKGKPKVEVTDDMQPRE
DWDIRDAEFDFLELNEAFAEMAANPVEVAINSVFGKITSGFETLTCIAKASVDAKNRPNKDIRI
RHTYILTDPFDDPPQLAKMIPDASPKGKPKVEVTDDMQPREDWDIRDAEFDFLELNEAFAEMAA
NPVEVAINSVFGKITSGFETLTCIAKASVDAKNRPNKDIRIRHTYILTDPFDDPPQLAKMIPDA
SPKGKPKVEVTDDMQPREDWDIRDAEFDFLELNEAFAEMAANPVEVAINS(-)
MSSVTSTFGFPLGEASGIILASCGGSSNGSVSIYVCRILISLFGLFFASTEALAIQVKVSNPLV
IFPNTELIATSTGLAAISAKASFSSRKSNSASLISQSSLGCMSSVTSTFGFPLGEASGIILASC
GGSSNGSVSIYVCRILISLFGLFFASTEALAIQVKVSNPLVIFPNTELIATSTGLAAISAKASF
SSRKSNSASLISQSSLGCMSSVTSTFGFPLGEASGIILASCGGSSNGSVSIYVCRILISLFGLF
FASTEALAIQVKVSNPLVIFPNTELIATSTGLAAISAKASFSSRKSNSASLISQSSLGCMSSVT
STFGFPLGEASGIILASCGGSSNGSVSIYVCRILISLFGLFFASTEALAIQVKVSNPLVIFPN(
+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress; responsive to heat stress

Functional Information
Coding potential	Y
Potential coding position	20076826-20076663(-) 20076770-20076972(+)
Potential amino acid sequence	MIPDASPKGKPKVEVTDDMQPREDWDIRDAEFDFLELNEAFAEMAANPVEVAINSVFGKITSGF ETLTCIAKASVDAKNRPNKDIRIRHTYILTDPFDDPPQLAKMIPDASPKGKPKVEVTDDMQPRE DWDIRDAEFDFLELNEAFAEMAANPVEVAINSVFGKITSGFETLTCIAKASVDAKNRPNKDIRI RHTYILTDPFDDPPQLAKMIPDASPKGKPKVEVTDDMQPREDWDIRDAEFDFLELNEAFAEMAA NPVEVAINSVFGKITSGFETLTCIAKASVDAKNRPNKDIRIRHTYILTDPFDDPPQLAKMIPDA SPKGKPKVEVTDDMQPREDWDIRDAEFDFLELNEAFAEMAANPVEVAINS(-) MSSVTSTFGFPLGEASGIILASCGGSSNGSVSIYVCRILISLFGLFFASTEALAIQVKVSNPLV IFPNTELIATSTGLAAISAKASFSSRKSNSASLISQSSLGCMSSVTSTFGFPLGEASGIILASC GGSSNGSVSIYVCRILISLFGLFFASTEALAIQVKVSNPLVIFPNTELIATSTGLAAISAKASF SSRKSNSASLISQSSLGCMSSVTSTFGFPLGEASGIILASCGGSSNGSVSIYVCRILISLFGLF FASTEALAIQVKVSNPLVIFPNTELIATSTGLAAISAKASFSSRKSNSASLISQSSLGCMSSVT STFGFPLGEASGIILASCGGSSNGSVSIYVCRILISLFGLFFASTEALAIQVKVSNPLVIFPN( +)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress; responsive to heat stress

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Pan et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT1G53780_circ_g.6

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