Plant Circular RNA Database

Detail information of AT5G65440_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G65440_circ_g.4
					
						ID in PlantcircBase
						ath_circ_045962
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 26154253-26155224  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT5G65440						
					
						Parent gene annotation
						
							unknown protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G65440_circ_g.5 						
					
						Support reads
						4
					
						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
						AT5G65440.3:4
AT5G65440.4:4
AT5G65440.1:4
AT5G65440.7:4
AT5G65440.6:4
AT5G65440.9:4
AT5G65440.5:4
AT5G65440.8:4
AT5G65440.2:4

General Information
CircRNA Name	AT5G65440_circ_g.4
ID in PlantcircBase	ath_circ_045962
Alias	NA
Organism	Arabidpsis thaliana
Position	chr5: 26154253-26155224 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder
Parent gene	AT5G65440
Parent gene annotation	unknown protein
Parent gene strand	+
Alternative splicing	AT5G65440_circ_g.5
Support reads	4
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	AT5G65440.3:4 AT5G65440.4:4 AT5G65440.1:4 AT5G65440.7:4 AT5G65440.6:4 AT5G65440.9:4 AT5G65440.5:4 AT5G65440.8:4 AT5G65440.2:4

			
						 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  
						
							TTCTTCTCGTTTGGCCTCCTCCTGGACCATCACCTGCGGTTGTTGATTTAGTTATTACAACTGC
TGACTTTCAGAGAGATCTCTCTAGCTGGCACATAAAatatctttcttatgtcatggatgtcgca
tcgcctaccaaggactgtcttgatctgatacatgattttctattccctattataatgacaagca
accacagg

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							ATATCTTTCTTATGTCATGGATGTCGCATCGCCTACCAAGGACTGTCTTGATCTGATACATGAT
TTTCTATTCCCTATTATAATGACAAGCAACCACAGGGCTGTATTGAGTCATCAAGAGGTGGGTT
AGCTTTGATCATCAAATTGTTATATTTTCAGTATTCAAGTAGCTTACTTCAACTTTTGGTCCTT
TGGTCAGAATCGGTTACTTGGGGAAATTGACGAACAAATTCAGCAGATTCTCGCTTCAGCATTT
GAGAATTATAAATCACTTGCTGAACTGTCTTTCTCCGGGATGAAAGATGTTTTTGAGTCTGCTA
CGGGGACTCCAGCACCTGCTATAGAATCAGCTGTCAAGCTTTATGGTCTTCTCAACGATGTATT
AACCCCCGAGGCACAGTTGAAACTCTGCAGATACTTTCAGGTATTAATCAAACTTGTATCTGTT
TCTTATCCATCTTTTCTGAAGTTGTATATGTGATTCATCACCTACGGAAACCACTTCAGGCTGC
TTCAAAGAAGAGGTCAAGAAGACATTTATTGGACACAAACGATTTACTTAACAACCGTAGTGAA
GGTGTACCAGTTGATCCCATGGTGCTTGCAGCTTCGTATCAAAAGATGAAGTCTCTAATCTTAA
GCCTTAAAAATGAAATATCCACTGACATAGCGATTCATGACTGCAATGTGCTCCCAAGGTTTGT
TTAAGACTCAAGTAAAAAATATGCAGCACATATGTTAACTATCAAACAGCTTTATCTTTTATCT
TTTTTAATGATTTTCTCGCCGTCAACTATCAATCAGCTTTATAGACCTTCCAAATCATTCAGCG
GCAATATATAGTGTTGATGTCTGCAATAGGCTCCGGGAATTTCTTCTCGTTTGGCCTCCTCCTG
GACCATCACCTGCGGTTGTTGATTTAGTTATTACAACTGCTGACTTTCAGAGAGATCTCTCTAG
CTGGCACATAAA

Sequences
Splice junction sequence	TTCTTCTCGTTTGGCCTCCTCCTGGACCATCACCTGCGGTTGTTGATTTAGTTATTACAACTGC TGACTTTCAGAGAGATCTCTCTAGCTGGCACATAAAatatctttcttatgtcatggatgtcgca tcgcctaccaaggactgtcttgatctgatacatgattttctattccctattataatgacaagca accacagg
Assembled circRNA sequence	NA 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	NA
Genomic sequence	ATATCTTTCTTATGTCATGGATGTCGCATCGCCTACCAAGGACTGTCTTGATCTGATACATGAT TTTCTATTCCCTATTATAATGACAAGCAACCACAGGGCTGTATTGAGTCATCAAGAGGTGGGTT AGCTTTGATCATCAAATTGTTATATTTTCAGTATTCAAGTAGCTTACTTCAACTTTTGGTCCTT TGGTCAGAATCGGTTACTTGGGGAAATTGACGAACAAATTCAGCAGATTCTCGCTTCAGCATTT GAGAATTATAAATCACTTGCTGAACTGTCTTTCTCCGGGATGAAAGATGTTTTTGAGTCTGCTA CGGGGACTCCAGCACCTGCTATAGAATCAGCTGTCAAGCTTTATGGTCTTCTCAACGATGTATT AACCCCCGAGGCACAGTTGAAACTCTGCAGATACTTTCAGGTATTAATCAAACTTGTATCTGTT TCTTATCCATCTTTTCTGAAGTTGTATATGTGATTCATCACCTACGGAAACCACTTCAGGCTGC TTCAAAGAAGAGGTCAAGAAGACATTTATTGGACACAAACGATTTACTTAACAACCGTAGTGAA GGTGTACCAGTTGATCCCATGGTGCTTGCAGCTTCGTATCAAAAGATGAAGTCTCTAATCTTAA GCCTTAAAAATGAAATATCCACTGACATAGCGATTCATGACTGCAATGTGCTCCCAAGGTTTGT TTAAGACTCAAGTAAAAAATATGCAGCACATATGTTAACTATCAAACAGCTTTATCTTTTATCT TTTTTAATGATTTTCTCGCCGTCAACTATCAATCAGCTTTATAGACCTTCCAAATCATTCAGCG GCAATATATAGTGTTGATGTCTGCAATAGGCTCCGGGAATTTCTTCTCGTTTGGCCTCCTCCTG GACCATCACCTGCGGTTGTTGATTTAGTTATTACAACTGCTGACTTTCAGAGAGATCTCTCTAG CTGGCACATAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.175209662

Conservation Information
Conserved circRNAs	NA
PMCS	0.175209662

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							26154269-26155221(+)
						
						Potential amino acid sequence
						
							MDVASPTKDCLDLIHDFLFPIIMTSNHRAVLSHQENRLLGEIDEQIQQILASAFENYKSLAELS
FSGMKDVFESATGTPAPAIESAVKLYGLLNDVLTPEAQLKLCRYFQAASKKRSRRHLLDTNDLL
NNRSEGVPVDPMVLAASYQKMKSLILSLKNEISTDIAIHDCNVLPSFIDLPNHSAAIYSVDVCN
RLREFLLVWPPPGPSPAVVDLVITTADFQRDLSSWHIKYLSYVMDVASPTKDCLDLIHDFLFPI
IMTSNHRAVLSHQENRLLGEIDEQIQQILASAFENYKSLAELSFSGMKDVFESATGTPAPAIES
AVKLYGLLNDVLTPEAQLKLCRYFQAASKKRSRRHLLDTNDLLNNRSEGVPVDPMVLAASYQKM
KSLILSLKNEISTDIAIHDCNVLPSFIDLPNHSAAIYSVDVCNRLREFLLVWPPPGPSPAVVDL
VITTADFQRDLSSWHIKYLSYVMDVASPTKDCLDLIHDFLFPIIMTSNHRAVLSHQENRLLGEI
DEQIQQILASAFENYKSLAELSFSGMKDVFESATGTPAPAIESAVKLYGLLNDVLTPEAQLKLC
RYFQAASKKRSRRHLLDTNDLLNNRSEGVPVDPMVLAASYQKMKSLILSLKNEISTDIAIHDCN
VLPSFIDLPNHSAAIYSVDVCNRLREFLLVWPPPGPSPAVVDLVITTADFQRDLSSWHIKYLSY
VMDVASPTKDCLDLIHDFLFPIIMTSNHRAVLSHQENRLLGEIDEQIQQILASAFENYKSLAEL
SFSGMKDVFESATGTPAPAIESAVKLYGLLNDVLTPEAQLKLCRYFQAASKKRSRRHLLDTNDL
LNNRSEGVPVDPMVLAASYQKMKSLILSLKNEISTDIAIHDCNVLPSFIDLPNHSAAIYSVDVC
NRLREFLLVWPPPGPSPAVVDLVITTADFQRDLSSWHI(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	26154269-26155221(+)
Potential amino acid sequence	MDVASPTKDCLDLIHDFLFPIIMTSNHRAVLSHQENRLLGEIDEQIQQILASAFENYKSLAELS FSGMKDVFESATGTPAPAIESAVKLYGLLNDVLTPEAQLKLCRYFQAASKKRSRRHLLDTNDLL NNRSEGVPVDPMVLAASYQKMKSLILSLKNEISTDIAIHDCNVLPSFIDLPNHSAAIYSVDVCN RLREFLLVWPPPGPSPAVVDLVITTADFQRDLSSWHIKYLSYVMDVASPTKDCLDLIHDFLFPI IMTSNHRAVLSHQENRLLGEIDEQIQQILASAFENYKSLAELSFSGMKDVFESATGTPAPAIES AVKLYGLLNDVLTPEAQLKLCRYFQAASKKRSRRHLLDTNDLLNNRSEGVPVDPMVLAASYQKM KSLILSLKNEISTDIAIHDCNVLPSFIDLPNHSAAIYSVDVCNRLREFLLVWPPPGPSPAVVDL VITTADFQRDLSSWHIKYLSYVMDVASPTKDCLDLIHDFLFPIIMTSNHRAVLSHQENRLLGEI DEQIQQILASAFENYKSLAELSFSGMKDVFESATGTPAPAIESAVKLYGLLNDVLTPEAQLKLC RYFQAASKKRSRRHLLDTNDLLNNRSEGVPVDPMVLAASYQKMKSLILSLKNEISTDIAIHDCN VLPSFIDLPNHSAAIYSVDVCNRLREFLLVWPPPGPSPAVVDLVITTADFQRDLSSWHIKYLSY VMDVASPTKDCLDLIHDFLFPIIMTSNHRAVLSHQENRLLGEIDEQIQQILASAFENYKSLAEL SFSGMKDVFESATGTPAPAIESAVKLYGLLNDVLTPEAQLKLCRYFQAASKKRSRRHLLDTNDL LNNRSEGVPVDPMVLAASYQKMKSLILSLKNEISTDIAIHDCNVLPSFIDLPNHSAAIYSVDVC NRLREFLLVWPPPGPSPAVVDLVITTADFQRDLSSWHI(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT5G65440_circ_g.4

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