Plant Circular RNA Database

Detail information of AT1G50460_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT1G50460_circ_g.1
					
						ID in PlantcircBase
						ath_circ_006681
					
						Alias
						At_ciR2421
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 18695227-18696718  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder, circRNA_finder, find_circ
					
						Parent gene
						
							AT1G50460						
					
						Parent gene annotation
						
							Hexokinase-3
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G50460_circ_g.2 AT1G50460_circ_g.3 						
					
						Support reads
						3/2
					
						Tissues
						leaf/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
						AT1G50460.2:6
AT1G50460.1:6
AT1G50460.3:6

General Information
CircRNA Name	AT1G50460_circ_g.1
ID in PlantcircBase	ath_circ_006681
Alias	At_ciR2421
Organism	Arabidpsis thaliana
Position	chr1: 18695227-18696718 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, PcircRNA_finder, circRNA_finder, find_circ
Parent gene	AT1G50460
Parent gene annotation	Hexokinase-3
Parent gene strand	+
Alternative splicing	AT1G50460_circ_g.2 AT1G50460_circ_g.3
Support reads	3/2
Tissues	leaf/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	AT1G50460.2:6 AT1G50460.1:6 AT1G50460.3:6

			
						 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  
						
							ATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACC
CATCTCGCCCGTGTTATCTGAGCCTTACGTTCTAAGgagggagaaaggtacttattatgcactt
caccttggaggcacttattttaggattttaagggttcttctgggtgatcaaaggtcttatctag
atgttcaa

									
								

					

						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: 789
Transcript exons: 18695227-18695377,18695482-18695661,18695929-18696003,18
696150-18696305,18696396-18696494,18696591-18696718
GAGGGAGAAAGGTACTTATTATGCACTTCACCTTGGAGGCACTTATTTTAGGATTTTAAGGGTT
CTTCTGGGTGATCAAAGGTCTTATCTAGATGTTCAAGATGTTGAACGACACCCAATACCTTCAC
ATTTGATGAATAGCACCAGCGAGGTTCTTTTCAACTTTCTCGCCTTTTCCTTGGAAAGGTTTAT
TGAAAAGGAGGAAAACGGGTCCGATTCACAAGGTGTTAGAAGGGAACTTGCATTTACGTTCTCA
TTCCCTGTCAAGCATACTTCTATTTCTTCAGGAGTTCTAATTAAATGGACCAAAGGTTTTGAGA
TTAGTGAAATGGTTGGGCAAGATATAGCTGAATGTCTACAAGGAGCTCTGAACAGAAGAGGCCT
AGATATGCATGTTGCGGCTCTTGTGAATGATACTGTTGGAGCCTTGTCGCTTGGATATTATCAC
GATCCAGATACGGTTGTTGCGGTTGTATTTGGAACAGGTAGTAATGCATGTTACTTGGAAAGAA
CCGATGCCATAATCAAGTGTCAGGGTCTGCTTACAACTTCTGGAAGCATGGTGGTAAATATGGA
GTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAG
AGTTCAAATGCAAATGATATGGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTG
TTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGCCCGTGTT
ATCTGAGCCTTACGTTCTAAG
						
					

						Genomic sequence
						
							GAGGGAGAAAGGTACTTATTATGCACTTCACCTTGGAGGCACTTATTTTAGGATTTTAAGGGTT
CTTCTGGGTGATCAAAGGTCTTATCTAGATGTTCAAGATGTTGAACGACACCCAATACCTTCAC
ATTTGATGAATAGCACCAGCGAGGTGACTATTTTGCTGTTTATTTCGTACCAGTCTTTGCTTGT
TATGTAATATGCAAGCTGCTTAATTGAGTCTGTGTTGTTCTTTTTTTTTTTACATGGTTGCAGG
TTCTTTTCAACTTTCTCGCCTTTTCCTTGGAAAGGTTTATTGAAAAGGAGGAAAACGGGTCCGA
TTCACAAGGTGTTAGAAGGGAACTTGCATTTACGTTCTCATTCCCTGTCAAGCATACTTCTATT
TCTTCAGGAGTTCTAATTAAATGGACCAAAGGTTTTGAGATTAGTGAAATGGTTAGTACAGGGA
TGCTTACATTGCTTCTTATATTCTCTGCAAACTGTGACTTGTCTTTGAAATATCCTTCCAAATC
TATTAACTTGATATCCTGACGCACTCTTCGGTTGACAGGAGTTGATGCCCTTGAGCTTTAAATT
ATTACTTGAGTTGTAATTTTGTGAAAATGGAATCCATCTCTTGGTGTTTTCCTGTTTGGTGTGA
GTCAAACATATTCAAATTTCAAGTTATTTAATCGTATAACAAGCAAATCCTTATTATTTTAGGT
TGGGCAAGATATAGCTGAATGTCTACAAGGAGCTCTGAACAGAAGAGGCCTAGATATGCATGTT
GCGGCTCTTGTAAGTGCTTTGTCACTCTGCAACAGCATCATTTCCTTGGCAAAATTCTGGCACT
ACCACCAAAAAATTTCAATCTTTCTTTTTGTTTTCCTTACCTTTTTCTTTATGAAAATATCATG
AAATGTTTCAGTTTTCTCTATGAGCAGGTGAATGATACTGTTGGAGCCTTGTCGCTTGGATATT
ATCACGATCCAGATACGGTTGTTGCGGTTGTATTTGGAACAGGTAGTAATGCATGTTACTTGGA
AAGAACCGATGCCATAATCAAGTGTCAGGGTCTGCTTACAACTTCTGGAAGCATGGTACTAAGA
ATCATTGCATGGTCTATTTTTAGAAACCAGCTTTAGACCCAAAAGAAACATGTTTAAGATTGAT
TCCCTCTTATGTTTCAGGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAG
AACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATGGTAATCTTTGCC
ATACTTCCCTGTTTTTCCGATTTGGTATTGCGTTATTAGTTTTTAACCAATTAACATCAACATC
ATTTGGGGTTTCTTACATAGGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGT
TCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGCCCGTGTTA
TCTGAGCCTTACGTTCTAAG
						
					

			
		

Sequences
Splice junction sequence	ATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACC CATCTCGCCCGTGTTATCTGAGCCTTACGTTCTAAGgagggagaaaggtacttattatgcactt caccttggaggcacttattttaggattttaagggttcttctgggtgatcaaaggtcttatctag atgttcaa
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: 789 Transcript exons: 18695227-18695377,18695482-18695661,18695929-18696003,18 696150-18696305,18696396-18696494,18696591-18696718 GAGGGAGAAAGGTACTTATTATGCACTTCACCTTGGAGGCACTTATTTTAGGATTTTAAGGGTT CTTCTGGGTGATCAAAGGTCTTATCTAGATGTTCAAGATGTTGAACGACACCCAATACCTTCAC ATTTGATGAATAGCACCAGCGAGGTTCTTTTCAACTTTCTCGCCTTTTCCTTGGAAAGGTTTAT TGAAAAGGAGGAAAACGGGTCCGATTCACAAGGTGTTAGAAGGGAACTTGCATTTACGTTCTCA TTCCCTGTCAAGCATACTTCTATTTCTTCAGGAGTTCTAATTAAATGGACCAAAGGTTTTGAGA TTAGTGAAATGGTTGGGCAAGATATAGCTGAATGTCTACAAGGAGCTCTGAACAGAAGAGGCCT AGATATGCATGTTGCGGCTCTTGTGAATGATACTGTTGGAGCCTTGTCGCTTGGATATTATCAC GATCCAGATACGGTTGTTGCGGTTGTATTTGGAACAGGTAGTAATGCATGTTACTTGGAAAGAA CCGATGCCATAATCAAGTGTCAGGGTCTGCTTACAACTTCTGGAAGCATGGTGGTAAATATGGA GTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAG AGTTCAAATGCAAATGATATGGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTG TTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGCCCGTGTT ATCTGAGCCTTACGTTCTAAG
Genomic sequence	GAGGGAGAAAGGTACTTATTATGCACTTCACCTTGGAGGCACTTATTTTAGGATTTTAAGGGTT CTTCTGGGTGATCAAAGGTCTTATCTAGATGTTCAAGATGTTGAACGACACCCAATACCTTCAC ATTTGATGAATAGCACCAGCGAGGTGACTATTTTGCTGTTTATTTCGTACCAGTCTTTGCTTGT TATGTAATATGCAAGCTGCTTAATTGAGTCTGTGTTGTTCTTTTTTTTTTTACATGGTTGCAGG TTCTTTTCAACTTTCTCGCCTTTTCCTTGGAAAGGTTTATTGAAAAGGAGGAAAACGGGTCCGA TTCACAAGGTGTTAGAAGGGAACTTGCATTTACGTTCTCATTCCCTGTCAAGCATACTTCTATT TCTTCAGGAGTTCTAATTAAATGGACCAAAGGTTTTGAGATTAGTGAAATGGTTAGTACAGGGA TGCTTACATTGCTTCTTATATTCTCTGCAAACTGTGACTTGTCTTTGAAATATCCTTCCAAATC TATTAACTTGATATCCTGACGCACTCTTCGGTTGACAGGAGTTGATGCCCTTGAGCTTTAAATT ATTACTTGAGTTGTAATTTTGTGAAAATGGAATCCATCTCTTGGTGTTTTCCTGTTTGGTGTGA GTCAAACATATTCAAATTTCAAGTTATTTAATCGTATAACAAGCAAATCCTTATTATTTTAGGT TGGGCAAGATATAGCTGAATGTCTACAAGGAGCTCTGAACAGAAGAGGCCTAGATATGCATGTT GCGGCTCTTGTAAGTGCTTTGTCACTCTGCAACAGCATCATTTCCTTGGCAAAATTCTGGCACT ACCACCAAAAAATTTCAATCTTTCTTTTTGTTTTCCTTACCTTTTTCTTTATGAAAATATCATG AAATGTTTCAGTTTTCTCTATGAGCAGGTGAATGATACTGTTGGAGCCTTGTCGCTTGGATATT ATCACGATCCAGATACGGTTGTTGCGGTTGTATTTGGAACAGGTAGTAATGCATGTTACTTGGA AAGAACCGATGCCATAATCAAGTGTCAGGGTCTGCTTACAACTTCTGGAAGCATGGTACTAAGA ATCATTGCATGGTCTATTTTTAGAAACCAGCTTTAGACCCAAAAGAAACATGTTTAAGATTGAT TCCCTCTTATGTTTCAGGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAG AACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATGGTAATCTTTGCC ATACTTCCCTGTTTTTCCGATTTGGTATTGCGTTATTAGTTTTTAACCAATTAACATCAACATC ATTTGGGGTTTCTTACATAGGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGT TCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGCCCGTGTTA TCTGAGCCTTACGTTCTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.266666225

Conservation Information
Conserved circRNAs	NA
PMCS	0.266666225

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18695360-18696715(+)
						
						Potential amino acid sequence
						
							MNSTSEVLFNFLAFSLERFIEKEENGSDSQGVRRELAFTFSFPVKHTSISSGVLIKWTKGFEIS
EMVGQDIAECLQGALNRRGLDMHVAALVNDTVGALSLGYYHDPDTVVAVVFGTGSNACYLERTD
AIIKCQGLLTTSGSMVVNMEWGNFWSSHLPRTSYDIDLDAESSNANDMGFEKMISGMYLGDIVR
RVILRMSEDSDIFGPISPVLSEPYVLRREKGTYYALHLGGTYFRILRVLLGDQRSYLDVQDVER
HPIPSHLMNSTSEVLFNFLAFSLERFIEKEENGSDSQGVRRELAFTFSFPVKHTSISSGVLIKW
TKGFEISEMVGQDIAECLQGALNRRGLDMHVAALVNDTVGALSLGYYHDPDTVVAVVFGTGSNA
CYLERTDAIIKCQGLLTTSGSMVVNMEWGNFWSSHLPRTSYDIDLDAESSNANDMGFEKMISGM
YLGDIVRRVILRMSEDSDIFGPISPVLSEPYVLRREKGTYYALHLGGTYFRILRVLLGDQRSYL
DVQDVERHPIPSHLMNSTSEVLFNFLAFSLERFIEKEENGSDSQGVRRELAFTFSFPVKHTSIS
SGVLIKWTKGFEISEMVGQDIAECLQGALNRRGLDMHVAALVNDTVGALSLGYYHDPDTVVAVV
FGTGSNACYLERTDAIIKCQGLLTTSGSMVVNMEWGNFWSSHLPRTSYDIDLDAESSNANDMGF
EKMISGMYLGDIVRRVILRMSEDSDIFGPISPVLSEPYVLRREKGTYYALHLGGTYFRILRVLL
GDQRSYLDVQDVERHPIPSHLMNSTSEVLFNFLAFSLERFIEKEENGSDSQGVRRELAFTFSFP
VKHTSISSGVLIKWTKGFEISEMVGQDIAECLQGALNRRGLDMHVAALVNDTVGALSLGYYHDP
DTVVAVVFGTGSNACYLERTDAIIKCQGLLTTSGSMVVNMEWGNFWSSHLPRTSYDIDLDAESS
NANDMGFEKMISGMYLGDIVRRVILRMSEDSDIFGPISPVLSEPYVL(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18695360-18696715(+)
Potential amino acid sequence	MNSTSEVLFNFLAFSLERFIEKEENGSDSQGVRRELAFTFSFPVKHTSISSGVLIKWTKGFEIS EMVGQDIAECLQGALNRRGLDMHVAALVNDTVGALSLGYYHDPDTVVAVVFGTGSNACYLERTD AIIKCQGLLTTSGSMVVNMEWGNFWSSHLPRTSYDIDLDAESSNANDMGFEKMISGMYLGDIVR RVILRMSEDSDIFGPISPVLSEPYVLRREKGTYYALHLGGTYFRILRVLLGDQRSYLDVQDVER HPIPSHLMNSTSEVLFNFLAFSLERFIEKEENGSDSQGVRRELAFTFSFPVKHTSISSGVLIKW TKGFEISEMVGQDIAECLQGALNRRGLDMHVAALVNDTVGALSLGYYHDPDTVVAVVFGTGSNA CYLERTDAIIKCQGLLTTSGSMVVNMEWGNFWSSHLPRTSYDIDLDAESSNANDMGFEKMISGM YLGDIVRRVILRMSEDSDIFGPISPVLSEPYVLRREKGTYYALHLGGTYFRILRVLLGDQRSYL DVQDVERHPIPSHLMNSTSEVLFNFLAFSLERFIEKEENGSDSQGVRRELAFTFSFPVKHTSIS SGVLIKWTKGFEISEMVGQDIAECLQGALNRRGLDMHVAALVNDTVGALSLGYYHDPDTVVAVV FGTGSNACYLERTDAIIKCQGLLTTSGSMVVNMEWGNFWSSHLPRTSYDIDLDAESSNANDMGF EKMISGMYLGDIVRRVILRMSEDSDIFGPISPVLSEPYVLRREKGTYYALHLGGTYFRILRVLL GDQRSYLDVQDVERHPIPSHLMNSTSEVLFNFLAFSLERFIEKEENGSDSQGVRRELAFTFSFP VKHTSISSGVLIKWTKGFEISEMVGQDIAECLQGALNRRGLDMHVAALVNDTVGALSLGYYHDP DTVVAVVFGTGSNACYLERTDAIIKCQGLLTTSGSMVVNMEWGNFWSSHLPRTSYDIDLDAESS NANDMGFEKMISGMYLGDIVRRVILRMSEDSDIFGPISPVLSEPYVL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of AT1G50460_circ_g.1

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