Plant Circular RNA Database

Detail information of AT5G04540_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT5G04540_circ_g.5
					
						ID in PlantcircBase
						ath_circ_036404
					
						Alias
						Ath_circ_FC3149, Ath_circ_FC5339
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 1298850-1300404  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI-full
					
						Parent gene
						
							AT5G04540						
					
						Parent gene annotation
						
							Phosphatidylinositol-3-phosphatase myotubularin-2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G04540_circ_g.1 AT5G04540_circ_g.2 AT5G04540_circ_g.3 AT5G04540_circ_g.4 AT5G04540_circ_g.6 AT5G04540_circ_g.7 AT5G04540_circ_g.8 AT5G04540_circ_g.9 AT5G04540_circ_g.10 						
					
						Support reads
						2
					
						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  
						
							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
						AT5G04540.1:6

General Information
CircRNA Name	AT5G04540_circ_g.5
ID in PlantcircBase	ath_circ_036404
Alias	Ath_circ_FC3149, Ath_circ_FC5339
Organism	Arabidpsis thaliana
Position	chr5: 1298850-1300404 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI-full
Parent gene	AT5G04540
Parent gene annotation	Phosphatidylinositol-3-phosphatase myotubularin-2
Parent gene strand	-
Alternative splicing	AT5G04540_circ_g.1 AT5G04540_circ_g.2 AT5G04540_circ_g.3 AT5G04540_circ_g.4 AT5G04540_circ_g.6 AT5G04540_circ_g.7 AT5G04540_circ_g.8 AT5G04540_circ_g.9 AT5G04540_circ_g.10
Support reads	2
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	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	AT5G04540.1:6

			
						 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  
						
							AAGTACCACAACCACTGCATATCTACCTGGATGACACCACGAGATCACAGGTAAGCGACATCTT
GCCCGGAAAGTAGAAGTCTGGAGCAGCTCTTCATCActgcagtgcacaagaactgatgctgact
ccatagcaacacgtgcagcaatccatgctacaccagctaagatgctctgaatgtgactcaacca
accactat

									
								

					

						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: 588
Transcript exons: 1298850-1299019,1299363-1299476,1299562-1299661,1299988-
1300053,1300178-1300241,1300331-1300404
CTGCAGTGCACAAGAACTGATGCTGACTCCATAGCAACACGTGCAGCAATCCATGCTACACCAG
CTAAGATGCTCTGAATGTGACTCAACCAACCACTATCTCCAAGCACGGATACTGAAGCAGACAT
ACTACTGAGATTACCTCCACCCCACGTCCAGCCACCATGCCTCAAGAATGATGACGTCCCATCG
GATGATGTTGTACCATGCATATCTAAATAATCCCTAAGGCGGGAAAAGCTCTCTCTCATTGCAT
GTATGTTGTCTATCCCCAAAAAAACAATTTCAGATTGCAAATAATTTGAAGATGATTCTGAGCC
TCCTCCCTTTGCTCCATTTGCTAATGCATTTTTCCTAGGTCTTGCATCTACGATATAAAGCTTC
CTTCGTGCTCCCTTATGACCAGCTAATTGAGTGCAGAATGAAGCAACAAGTTTCTCATCAGAGT
TACTCCTCATGTTCATCATCAGACCAACTAAAGGTTGTGATGAGCGAGCAATCACAGCTCCACT
TCCTGGATGACACCACGAGATCACAGGTAAGCGACATCTTGCCCGGAAAGTAGAAGTCTGGAGC
AGCTCTTCATCA
Transcript length: 488
Transcript exons: 1298850-1300404
CTGCAGTGCACAAGAACTGATGCTGACTCCATAGCAACACGTGCAGCAATCCATGCTACACCAG
CTAAGATGCTCTGAATGTGACTCAACCAACCACTATCTCCAAGCACGGATACTGAAGCAGACAT
ACTACTGAGATTACCTCCACCCCACGTCCAGCCACCATGCCTCAAGAATGATGACGTCCCATCG
GATGATGTTGTACCATGCATATCTAAATAATCCCTAAGGCGGGAAAAGCTCTCTCTCATTGCAT
GTATGTTGTCTATCCCCAAAAAAACAATCTTCGTGCTCCCTTATGACCAGCTAATTGAGTGCAG
AATGAAGCAACAAGTTTCTCATCAGAGTTACTCCTCATGTTCATCATCAGACCAACTAAAGGTT
GTGATGAGCGAGCAATCACAGCTCCACTTCCTGGATGACACCACGAGATCACAGGTAAGCGACA
TCTTGCCCGGAAAGTAGAAGTCTGGAGCAGCTCTTCATCA
						
					

						Genomic sequence
						
							CTGCAGTGCACAAGAACTGATGCTGACTCCATAGCAACACGTGCAGCAATCCATGCTACACCAG
CTAAGATGCTCTGAATGTGACTCAACCAACCACTATCTCCAAGCACGGATACTGAAGCAGACAT
ACTACTGAGATTACCTCCACCCCACGTCCAGCCACCATGCCTCTACAGATTTCACACAAAAAGA
ATTATCCACTTTAAGCAAGGGACGAAAAAAACTAAGTATGGTAAATCATGATGTAAGATATCTG
TAAATTAATTTAGACGTTCTCCATGACATTGAAAAAGAAACTAAGGTTGCAAATATTAACTTGA
TAGATAATGTAAAATCATATCCACATGCTTAAGCTTAATTCAATTGAAGGATATCTGATTTAGT
TACTGAAACCATTTAGATGTTGTGTGCTAGAAAACTTGGAAAGTGTCGTTGATATGTTAAGAAA
CTTTAACTGCTTTTGAAATTCTCTGCCAACTACAATTACTGAATTCCCTGGAATTCAATACTTA
CCAAGAATGATGACGTCCCATCGGATGATGTTGTACCATGCATATCTAAATAATCCCTAAGGCG
GGAAAAGCTCTCTCTCATTGCATGTATGTTGTCTATCCCCAAAAAAACAATCTGAAGAAAAAAC
ATTGTCAGTCAAAACAAGCAGTTCCAGAAGACAAAATATTGAGCTCCAAACCACTTTAGGCCAT
GTACAGACTTCAGATTGCAAATAATTTGAAGATGATTCTGAGCCTCCTCCCTTTGCTCCATTTG
CTAATGCATTTTTCCTAGGTCTTGCATCTACGATATAAAGCTTCCTATGACATAAAAACAAAGG
AGAGTACGTGAATATTTTTAATAACCAGGTATCAACATTCAACCACATTGCAGATATGAAACAG
CAGAGTATTTTTTTATTCTAACCAAACAGACTTTTCTTAACATTTCAGAAAATAATCCCACGAG
CAATGGGGTCAACAAGAGTGGTTATTTCAAAGTATATACATGTAATTTATGATTTTTAACACAA
AAGCATGCGAGAAATGAAAACACAAAGAGGAGTCATGGTACTATGAGATGACAAAAAGAGCATC
AGTAAATCAAATGTAAATTTTAACCAAACGACGGAAAATCAGAAGCTCACCTTCGTGCTCCCTT
ATGACCAGCTAATTGAGTGCAGAATGAAGCAACAAGTTTCTCATCAGAGTTACTGTAGAAAATG
GGTGAAATATATCAAAACTTCAGAATCCATCATTTTAAGCACTTTGAGAATCCAAATAAGCAAC
TAAATTATCATGCACAAGTCTGGTCATAAAATTAAAACTTCTATATACCTCCTCATGTTCATCA
TCAGACCAACTAAAGGTTGTGATGAGCGAGCAATCACAGCTCCACTTCCTGCAATTGAGATAAA
AAAAAGGAACATGTAAATGTGGAACTATGCCAACAAAGTTCAAACAGAAGTACCACAACCACTG
CATATCTACCTGGATGACACCACGAGATCACAGGTAAGCGACATCTTGCCCGGAAAGTAGAAGT
CTGGAGCAGCTCTTCATCA
						
					

			
		

Sequences
Splice junction sequence	AAGTACCACAACCACTGCATATCTACCTGGATGACACCACGAGATCACAGGTAAGCGACATCTT GCCCGGAAAGTAGAAGTCTGGAGCAGCTCTTCATCActgcagtgcacaagaactgatgctgact ccatagcaacacgtgcagcaatccatgctacaccagctaagatgctctgaatgtgactcaacca accactat
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: 588 Transcript exons: 1298850-1299019,1299363-1299476,1299562-1299661,1299988- 1300053,1300178-1300241,1300331-1300404 CTGCAGTGCACAAGAACTGATGCTGACTCCATAGCAACACGTGCAGCAATCCATGCTACACCAG CTAAGATGCTCTGAATGTGACTCAACCAACCACTATCTCCAAGCACGGATACTGAAGCAGACAT ACTACTGAGATTACCTCCACCCCACGTCCAGCCACCATGCCTCAAGAATGATGACGTCCCATCG GATGATGTTGTACCATGCATATCTAAATAATCCCTAAGGCGGGAAAAGCTCTCTCTCATTGCAT GTATGTTGTCTATCCCCAAAAAAACAATTTCAGATTGCAAATAATTTGAAGATGATTCTGAGCC TCCTCCCTTTGCTCCATTTGCTAATGCATTTTTCCTAGGTCTTGCATCTACGATATAAAGCTTC CTTCGTGCTCCCTTATGACCAGCTAATTGAGTGCAGAATGAAGCAACAAGTTTCTCATCAGAGT TACTCCTCATGTTCATCATCAGACCAACTAAAGGTTGTGATGAGCGAGCAATCACAGCTCCACT TCCTGGATGACACCACGAGATCACAGGTAAGCGACATCTTGCCCGGAAAGTAGAAGTCTGGAGC AGCTCTTCATCA Transcript length: 488 Transcript exons: 1298850-1300404 CTGCAGTGCACAAGAACTGATGCTGACTCCATAGCAACACGTGCAGCAATCCATGCTACACCAG CTAAGATGCTCTGAATGTGACTCAACCAACCACTATCTCCAAGCACGGATACTGAAGCAGACAT ACTACTGAGATTACCTCCACCCCACGTCCAGCCACCATGCCTCAAGAATGATGACGTCCCATCG GATGATGTTGTACCATGCATATCTAAATAATCCCTAAGGCGGGAAAAGCTCTCTCTCATTGCAT GTATGTTGTCTATCCCCAAAAAAACAATCTTCGTGCTCCCTTATGACCAGCTAATTGAGTGCAG AATGAAGCAACAAGTTTCTCATCAGAGTTACTCCTCATGTTCATCATCAGACCAACTAAAGGTT GTGATGAGCGAGCAATCACAGCTCCACTTCCTGGATGACACCACGAGATCACAGGTAAGCGACA TCTTGCCCGGAAAGTAGAAGTCTGGAGCAGCTCTTCATCA
Genomic sequence	CTGCAGTGCACAAGAACTGATGCTGACTCCATAGCAACACGTGCAGCAATCCATGCTACACCAG CTAAGATGCTCTGAATGTGACTCAACCAACCACTATCTCCAAGCACGGATACTGAAGCAGACAT ACTACTGAGATTACCTCCACCCCACGTCCAGCCACCATGCCTCTACAGATTTCACACAAAAAGA ATTATCCACTTTAAGCAAGGGACGAAAAAAACTAAGTATGGTAAATCATGATGTAAGATATCTG TAAATTAATTTAGACGTTCTCCATGACATTGAAAAAGAAACTAAGGTTGCAAATATTAACTTGA TAGATAATGTAAAATCATATCCACATGCTTAAGCTTAATTCAATTGAAGGATATCTGATTTAGT TACTGAAACCATTTAGATGTTGTGTGCTAGAAAACTTGGAAAGTGTCGTTGATATGTTAAGAAA CTTTAACTGCTTTTGAAATTCTCTGCCAACTACAATTACTGAATTCCCTGGAATTCAATACTTA CCAAGAATGATGACGTCCCATCGGATGATGTTGTACCATGCATATCTAAATAATCCCTAAGGCG GGAAAAGCTCTCTCTCATTGCATGTATGTTGTCTATCCCCAAAAAAACAATCTGAAGAAAAAAC ATTGTCAGTCAAAACAAGCAGTTCCAGAAGACAAAATATTGAGCTCCAAACCACTTTAGGCCAT GTACAGACTTCAGATTGCAAATAATTTGAAGATGATTCTGAGCCTCCTCCCTTTGCTCCATTTG CTAATGCATTTTTCCTAGGTCTTGCATCTACGATATAAAGCTTCCTATGACATAAAAACAAAGG AGAGTACGTGAATATTTTTAATAACCAGGTATCAACATTCAACCACATTGCAGATATGAAACAG CAGAGTATTTTTTTATTCTAACCAAACAGACTTTTCTTAACATTTCAGAAAATAATCCCACGAG CAATGGGGTCAACAAGAGTGGTTATTTCAAAGTATATACATGTAATTTATGATTTTTAACACAA AAGCATGCGAGAAATGAAAACACAAAGAGGAGTCATGGTACTATGAGATGACAAAAAGAGCATC AGTAAATCAAATGTAAATTTTAACCAAACGACGGAAAATCAGAAGCTCACCTTCGTGCTCCCTT ATGACCAGCTAATTGAGTGCAGAATGAAGCAACAAGTTTCTCATCAGAGTTACTGTAGAAAATG GGTGAAATATATCAAAACTTCAGAATCCATCATTTTAAGCACTTTGAGAATCCAAATAAGCAAC TAAATTATCATGCACAAGTCTGGTCATAAAATTAAAACTTCTATATACCTCCTCATGTTCATCA TCAGACCAACTAAAGGTTGTGATGAGCGAGCAATCACAGCTCCACTTCCTGCAATTGAGATAAA AAAAAGGAACATGTAAATGTGGAACTATGCCAACAAAGTTCAAACAGAAGTACCACAACCACTG CATATCTACCTGGATGACACCACGAGATCACAGGTAAGCGACATCTTGCCCGGAAAGTAGAAGT CTGGAGCAGCTCTTCATCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.227183266

Conservation Information
Conserved circRNAs	NA
PMCS	0.227183266

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1300195-1298852(-)
						
						Potential amino acid sequence
						
							MMNMRSNSDEKLVASFCTQLAGHKGARRKLYIVDARPRKNALANGAKGGGSESSSNYLQSEIVF
LGIDNIHAMRESFSRLRDYLDMHGTTSSDGTSSFLRHGGWTWGGGNLSSMSASVSVLGDSGWLS
HIQSILAGVAWIAARVAMESASVLVHCSDEELLQTSTFRARCRLPVISWCHPGSGAVIARSSQP
LVGLMMNMRSNSDEKLVASFCTQLAGHKGARRKLYIVDARPRKNALANGAKGGGSESSSNYLQS
EIVFLGIDNIHAMRESFSRLRDYLDMHGTTSSDGTSSFLRHGGWTWGGGNLSSMSASVSVLGDS
GWLSHIQSILAGVAWIAARVAMESASVLVHCSDEELLQTSTFRARCRLPVISWCHPGSGAVIAR
SSQPLVGLMMNMRSNSDEKLVASFCTQLAGHKGARRKLYIVDARPRKNALANGAKGGGSESSSN
YLQSEIVFLGIDNIHAMRESFSRLRDYLDMHGTTSSDGTSSFLRHGGWTWGGGNLSSMSASVSV
LGDSGWLSHIQSILAGVAWIAARVAMESASVLVHCSDEELLQTSTFRARCRLPVISWCHPGSGA
VIARSSQPLVGLMMNMRSNSDEKLVASFCTQLAGHKGARRKLYIVDARPRKNALANGAKGGGSE
SSSNYLQSEIVFLGIDNIHAMRESFSRLRDYLDMHGTTSSDGTSSFLRHGGWTWGGGNLSSMSA
SVSVLGDSGWLSHIQSILAGVAWIAARVAMESASVLVHC(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1300195-1298852(-)
Potential amino acid sequence	MMNMRSNSDEKLVASFCTQLAGHKGARRKLYIVDARPRKNALANGAKGGGSESSSNYLQSEIVF LGIDNIHAMRESFSRLRDYLDMHGTTSSDGTSSFLRHGGWTWGGGNLSSMSASVSVLGDSGWLS HIQSILAGVAWIAARVAMESASVLVHCSDEELLQTSTFRARCRLPVISWCHPGSGAVIARSSQP LVGLMMNMRSNSDEKLVASFCTQLAGHKGARRKLYIVDARPRKNALANGAKGGGSESSSNYLQS EIVFLGIDNIHAMRESFSRLRDYLDMHGTTSSDGTSSFLRHGGWTWGGGNLSSMSASVSVLGDS GWLSHIQSILAGVAWIAARVAMESASVLVHCSDEELLQTSTFRARCRLPVISWCHPGSGAVIAR SSQPLVGLMMNMRSNSDEKLVASFCTQLAGHKGARRKLYIVDARPRKNALANGAKGGGSESSSN YLQSEIVFLGIDNIHAMRESFSRLRDYLDMHGTTSSDGTSSFLRHGGWTWGGGNLSSMSASVSV LGDSGWLSHIQSILAGVAWIAARVAMESASVLVHCSDEELLQTSTFRARCRLPVISWCHPGSGA VIARSSQPLVGLMMNMRSNSDEKLVASFCTQLAGHKGARRKLYIVDARPRKNALANGAKGGGSE SSSNYLQSEIVFLGIDNIHAMRESFSRLRDYLDMHGTTSSDGTSSFLRHGGWTWGGGNLSSMSA SVSVLGDSGWLSHIQSILAGVAWIAARVAMESASVLVHC(-)
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 AT5G04540_circ_g.5

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