Plant Circular RNA Database

Detail information of AT5G20840_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G20840_circ_g.4
					
						ID in PlantcircBase
						ath_circ_039558
					
						Alias
						At_ciR1610
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 7063144-7065409  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, find_circ
					
						Parent gene
						
							AT5G20840						
					
						Parent gene annotation
						
							Phosphoinositide phosphatase SAC4
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G20840_circ_g.1 AT5G20840_circ_g.2 AT5G20840_circ_g.3 						
					
						Support reads
						6/1
					
						Tissues
						leaf/inflorescences
					
						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
						AT5G20840.1:4

General Information
CircRNA Name	AT5G20840_circ_g.4
ID in PlantcircBase	ath_circ_039558
Alias	At_ciR1610
Organism	Arabidpsis thaliana
Position	chr5: 7063144-7065409 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, find_circ
Parent gene	AT5G20840
Parent gene annotation	Phosphoinositide phosphatase SAC4
Parent gene strand	-
Alternative splicing	AT5G20840_circ_g.1 AT5G20840_circ_g.2 AT5G20840_circ_g.3
Support reads	6/1
Tissues	leaf/inflorescences
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	AT5G20840.1:4

			
						 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  
						
							ATCACCATTTGCAACATTCTTACTTGGGCGGCAATTCTTCTCTAATGAGTCATAATCCCTACTA
TCATCATCAGAACTATTATGTGGAGACGTGTCGGCActcgataatgttacatcaccggcagctg
gcatatctggtgatgattctgaaattatatgagtacgagtcacttggtgtgacgacacaaaacc
tctatgtg

									
								

					

						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: 777
Transcript exons: 7063144-7063335,7063884-7063994,7064097-7064218,7065058-
7065409
CTCGATAATGTTACATCACCGGCAGCTGGCATATCTGGTGATGATTCTGAAATTATATGAGTAC
GAGTCACTTGGTGTGACGACACAAAACCTCTATGTGATATGCTTTCATTCTTTCTACTCATTGC
AGACATCGGAGTGTGACTTTCATGGAGAATATTCCCATCTGATAAGCACCTCTTTACAAGAAAC
TTTTCATCTTCCCCCATGCTTATCTCTCCACTTCGTCCATTAGAGTGGGAATCTGAACGCAACT
CCCAAACCGCCTGGCTCCCTTGTTCAGGCCGGAAAGTACCAAGAAATATATTAATGGCATCTTG
TTTATCCGCATCCATATATGCGTTATTATAATAACGTTGCAGAGTCCTCAAGAACTCTTGTGAC
TGGGTTGCTGCTCTCCACTGGCCTCGCCTTTCACTAAAAACCTTATTGTGGGCTGCAGATCCAC
CATATTGATAAGCTAGTGTGTCTCCCATTCTCTCGTATAACCCCATTAAAGTACTAGACAAAGG
ATCATCAAGTTCTATTGTTGGAGCATCTCTAATTCCTAAAGCATGAAGCTGTTGCCCTAGAGCA
GCCCAACCATATGCATATTGGGCAACATTTGTACGATCAAGGCAATCTATGCAGTTGGTCCGCA
GCACTCCACTCTGGAGCCTGCTAGGCTTGACATCATAATCACCATTTGCAACATTCTTACTTGG
GCGGCAATTCTTCTCTAATGAGTCATAATCCCTACTATCATCATCAGAACTATTATGTGGAGAC
GTGTCGGCA
						
					

						Genomic sequence
						
							CTCGATAATGTTACATCACCGGCAGCTGGCATATCTGGTGATGATTCTGAAATTATATGAGTAC
GAGTCACTTGGTGTGACGACACAAAACCTCTATGTGATATGCTTTCATTCTTTCTACTCATTGC
AGACATCGGAGTGTGACTTTCATGGAGAATATTCCCATCTGATAAGCACCTCTTTACAAGAAAC
CTGGAAACACAGTAATAAGAGCTATGATATAGATGCGAAACAAAATCAATATATTTTTGTTCAC
TTTTAGAGGAAGGCTAATAGAGTTGGAAACTTCATATACTAAAAAACAGAGCATTCTTAAGCTA
GCAGAGAGTACAGATTTTGGTACAGTTCGATGCAGTTAACAAACCAATCCTAGTTTCCCATGAC
CCCATATGTCTATAACAAAAGCCCATACCTCCTTGTATCTAAATCCTATGTTAATTTCGTATGA
TTAGGGTCACAACAGTTTTGTAGGATCTAAACTGGAAGTTATGGTGGAGAATAAAATTCCAGTG
AATGGATAATGTCGAGATATGTAGAGCCTATATTTTTCAAATTCGTAAACTTAATGCATAGCAA
ATAGGTATAAGATATTAGAACTCATGTGACTCATAAATCATCAAAATATGTCTAAAGAAGAAAA
TGGAAACCTCAAAACCTTTCTACCTACATGACAGCAACTAATTATATAGGCATATTATTGTTGA
ATTTATGAAATCCAAGTTAGCAGTCACAGAACCTACTTTTCATCTTCCCCCATGCTTATCTCTC
CACTTCGTCCATTAGAGTGGGAATCTGAACGCAACTCCCAAACCGCCTGGCTCCCTTGTTCAGG
CCGGAAAGTACCAAGAAATCTGCATATAGAAATTCACAAAGGCCCAAAGAATTTCTGTAAGACT
CTAAGAGATCATCGCGTAACATGGATATATACGAGAGAGTGACATAGAGCAGCTTACATATTAA
TGGCATCTTGTTTATCCGCATCCATATATGCGTTATTATAATAACGTTGCAGAGTCCTCAAGAA
CTCTTGTGACTGGGTTGCTGCTCTCCACTGGCCTCGCCTTTCACTAAAAACCTATTACACACCA
AAAATTCTAGGAATCAACAAAGTGTATCCCAACAATAGTGAACATAATGGGAACTTGAGTCGGC
TGCAGAAGATCAATACATCATAATTCAGTGCAGAACAATGAGACAGATTACAAAATGAATGTTA
ACTAAGTCTGATATCCTTTTTTTTTTTTTTTTTTTTTGTTTGTTGTCACCAAGTCTGATATCCT
TCCAAGACAGTAAAATAACGAGGGCACAGTTGTGATTAAGATATAATATAGATCACATAACCCT
TGTAATTCTTGGACTTCAAAGACCAAGATCAGAAAATAGACCAGATTTTCTTACAGCAATATCA
TCACAAATGATGAATTCCAAAAATTCAAAAAGAAAAACATTTTAAAATTTGCCAATCATGTATA
TGCTGCTTCTAACATAAGAATCAGATCATAATAATAATGTCAGCTGAAAAGTGTCAGCTACAGA
GAGGTTCAAATATAAGAGATGATTGATCAGCATGCATGACGGATTCCTGTTGTTAGACCGAGCA
ACAAGGATGTACAAAGAACACTAGATTTTTCATGAGCTTAGATTTACTTTAAGGTAAGGCTTGT
TATTTTAATTGTAAACAATAAAAAATGTTGACGAGAAAAGGGATACAAATCATCTCATGGAGCC
AGTCATGAATCATTCCCAACCGAGACTAAATGGAATCTATTTTGTGCATAATTAACAGTCCAGC
GTTTAGTATCAACTAACTGTCTCTAGCAGAAGACTTAATATGAGACAGTTCCATATGAACATGA
ACAAAATTAGTCTGCTGCCATGTCAAGACTTATAAAAACAAAGTAAGCATAATAATACCTTATT
GTGGGCTGCAGATCCACCATATTGATAAGCTAGTGTGTCTCCCATTCTCTCGTATAACCCCATT
AAAGTACTAGACAAAGGATCATCAAGTTCTATTGTTGGAGCATCTCTAATTCCTAAAGCATGAA
GCTGTTGCCCTAGAGCAGCCCAACCATATGCATATTGGGCAACATTTGTACGATCAAGGCAATC
TATGCAGTTGGTCCGCAGCACTCCACTCTGGAGCCTGCTAGGCTTGACATCATAATCACCATTT
GCAACATTCTTACTTGGGCGGCAATTCTTCTCTAATGAGTCATAATCCCTACTATCATCATCAG
AACTATTATGTGGAGACGTGTCGGCA
						
					

			
		

Sequences
Splice junction sequence	ATCACCATTTGCAACATTCTTACTTGGGCGGCAATTCTTCTCTAATGAGTCATAATCCCTACTA TCATCATCAGAACTATTATGTGGAGACGTGTCGGCActcgataatgttacatcaccggcagctg gcatatctggtgatgattctgaaattatatgagtacgagtcacttggtgtgacgacacaaaacc tctatgtg
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: 777 Transcript exons: 7063144-7063335,7063884-7063994,7064097-7064218,7065058- 7065409 CTCGATAATGTTACATCACCGGCAGCTGGCATATCTGGTGATGATTCTGAAATTATATGAGTAC GAGTCACTTGGTGTGACGACACAAAACCTCTATGTGATATGCTTTCATTCTTTCTACTCATTGC AGACATCGGAGTGTGACTTTCATGGAGAATATTCCCATCTGATAAGCACCTCTTTACAAGAAAC TTTTCATCTTCCCCCATGCTTATCTCTCCACTTCGTCCATTAGAGTGGGAATCTGAACGCAACT CCCAAACCGCCTGGCTCCCTTGTTCAGGCCGGAAAGTACCAAGAAATATATTAATGGCATCTTG TTTATCCGCATCCATATATGCGTTATTATAATAACGTTGCAGAGTCCTCAAGAACTCTTGTGAC TGGGTTGCTGCTCTCCACTGGCCTCGCCTTTCACTAAAAACCTTATTGTGGGCTGCAGATCCAC CATATTGATAAGCTAGTGTGTCTCCCATTCTCTCGTATAACCCCATTAAAGTACTAGACAAAGG ATCATCAAGTTCTATTGTTGGAGCATCTCTAATTCCTAAAGCATGAAGCTGTTGCCCTAGAGCA GCCCAACCATATGCATATTGGGCAACATTTGTACGATCAAGGCAATCTATGCAGTTGGTCCGCA GCACTCCACTCTGGAGCCTGCTAGGCTTGACATCATAATCACCATTTGCAACATTCTTACTTGG GCGGCAATTCTTCTCTAATGAGTCATAATCCCTACTATCATCATCAGAACTATTATGTGGAGAC GTGTCGGCA
Genomic sequence	CTCGATAATGTTACATCACCGGCAGCTGGCATATCTGGTGATGATTCTGAAATTATATGAGTAC GAGTCACTTGGTGTGACGACACAAAACCTCTATGTGATATGCTTTCATTCTTTCTACTCATTGC AGACATCGGAGTGTGACTTTCATGGAGAATATTCCCATCTGATAAGCACCTCTTTACAAGAAAC CTGGAAACACAGTAATAAGAGCTATGATATAGATGCGAAACAAAATCAATATATTTTTGTTCAC TTTTAGAGGAAGGCTAATAGAGTTGGAAACTTCATATACTAAAAAACAGAGCATTCTTAAGCTA GCAGAGAGTACAGATTTTGGTACAGTTCGATGCAGTTAACAAACCAATCCTAGTTTCCCATGAC CCCATATGTCTATAACAAAAGCCCATACCTCCTTGTATCTAAATCCTATGTTAATTTCGTATGA TTAGGGTCACAACAGTTTTGTAGGATCTAAACTGGAAGTTATGGTGGAGAATAAAATTCCAGTG AATGGATAATGTCGAGATATGTAGAGCCTATATTTTTCAAATTCGTAAACTTAATGCATAGCAA ATAGGTATAAGATATTAGAACTCATGTGACTCATAAATCATCAAAATATGTCTAAAGAAGAAAA TGGAAACCTCAAAACCTTTCTACCTACATGACAGCAACTAATTATATAGGCATATTATTGTTGA ATTTATGAAATCCAAGTTAGCAGTCACAGAACCTACTTTTCATCTTCCCCCATGCTTATCTCTC CACTTCGTCCATTAGAGTGGGAATCTGAACGCAACTCCCAAACCGCCTGGCTCCCTTGTTCAGG CCGGAAAGTACCAAGAAATCTGCATATAGAAATTCACAAAGGCCCAAAGAATTTCTGTAAGACT CTAAGAGATCATCGCGTAACATGGATATATACGAGAGAGTGACATAGAGCAGCTTACATATTAA TGGCATCTTGTTTATCCGCATCCATATATGCGTTATTATAATAACGTTGCAGAGTCCTCAAGAA CTCTTGTGACTGGGTTGCTGCTCTCCACTGGCCTCGCCTTTCACTAAAAACCTATTACACACCA AAAATTCTAGGAATCAACAAAGTGTATCCCAACAATAGTGAACATAATGGGAACTTGAGTCGGC TGCAGAAGATCAATACATCATAATTCAGTGCAGAACAATGAGACAGATTACAAAATGAATGTTA ACTAAGTCTGATATCCTTTTTTTTTTTTTTTTTTTTTGTTTGTTGTCACCAAGTCTGATATCCT TCCAAGACAGTAAAATAACGAGGGCACAGTTGTGATTAAGATATAATATAGATCACATAACCCT TGTAATTCTTGGACTTCAAAGACCAAGATCAGAAAATAGACCAGATTTTCTTACAGCAATATCA TCACAAATGATGAATTCCAAAAATTCAAAAAGAAAAACATTTTAAAATTTGCCAATCATGTATA TGCTGCTTCTAACATAAGAATCAGATCATAATAATAATGTCAGCTGAAAAGTGTCAGCTACAGA GAGGTTCAAATATAAGAGATGATTGATCAGCATGCATGACGGATTCCTGTTGTTAGACCGAGCA ACAAGGATGTACAAAGAACACTAGATTTTTCATGAGCTTAGATTTACTTTAAGGTAAGGCTTGT TATTTTAATTGTAAACAATAAAAAATGTTGACGAGAAAAGGGATACAAATCATCTCATGGAGCC AGTCATGAATCATTCCCAACCGAGACTAAATGGAATCTATTTTGTGCATAATTAACAGTCCAGC GTTTAGTATCAACTAACTGTCTCTAGCAGAAGACTTAATATGAGACAGTTCCATATGAACATGA ACAAAATTAGTCTGCTGCCATGTCAAGACTTATAAAAACAAAGTAAGCATAATAATACCTTATT GTGGGCTGCAGATCCACCATATTGATAAGCTAGTGTGTCTCCCATTCTCTCGTATAACCCCATT AAAGTACTAGACAAAGGATCATCAAGTTCTATTGTTGGAGCATCTCTAATTCCTAAAGCATGAA GCTGTTGCCCTAGAGCAGCCCAACCATATGCATATTGGGCAACATTTGTACGATCAAGGCAATC TATGCAGTTGGTCCGCAGCACTCCACTCTGGAGCCTGCTAGGCTTGACATCATAATCACCATTT GCAACATTCTTACTTGGGCGGCAATTCTTCTCTAATGAGTCATAATCCCTACTATCATCATCAG AACTATTATGTGGAGACGTGTCGGCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.292543766

Conservation Information
Conserved circRNAs	NA
PMCS	0.292543766

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7065127-7063146(-)
						
						Potential amino acid sequence
						
							MGLYERMGDTLAYQYGGSAAHNKVFSERRGQWRAATQSQEFLRTLQRYYNNAYMDADKQDAINI
FLGTFRPEQGSQAVWELRSDSHSNGRSGEISMGEDEKFLVKRCLSDGNILHESHTPMSAMSRKN
ESISHRGFVSSHQVTRTHIISESSPDMPAAGDVTLSSADTSPHNSSDDDSRDYDSLEKNCRPSK
NVANGDYDVKPSRLQSGVLRTNCIDCLDRTNVAQYAYGWAALGQQLHALGIRDAPTIELDDPLS
STLMGLYERMGDTLAYQYGGSAAHNKVFSERRGQWRAATQSQEFLRTLQRYYNNAYMDADKQDA
INIFLGTFRPEQGSQAVWELRSDSHSNGRSGEISMGEDEKFLVKRCLSDGNILHESHTPMSAMS
RKNESISHRGFVSSHQVTRTHIISESSPDMPAAGDVTLSSADTSPHNSSDDDSRDYDSLEKNCR
PSKNVANGDYDVKPSRLQSGVLRTNCIDCLDRTNVAQYAYGWAALGQQLHALGIRDAPTIELDD
PLSSTLMGLYERMGDTLAYQYGGSAAHNKVFSERRGQWRAATQSQEFLRTLQRYYNNAYMDADK
QDAINIFLGTFRPEQGSQAVWELRSDSHSNGRSGEISMGEDEKFLVKRCLSDGNILHESHTPMS
AMSRKNESISHRGFVSSHQVTRTHIISESSPDMPAAGDVTLSSADTSPHNSSDDDSRDYDSLEK
NCRPSKNVANGDYDVKPSRLQSGVLRTNCIDCLDRTNVAQYAYGWAALGQQLHALGIRDAPTIE
LDDPLSSTLMGLYERMGDTLAYQYGGSAAHNKVFSERRGQWRAATQSQEFLRTLQRYYNNAYMD
ADKQDAINIFLGTFRPEQGSQAVWELRSDSHSNGRSGEISMGEDEKFLVKRCLSDGNILHESHT
PMSAMSRKNESISHRGFVSSHQVTRTHIISESSPDMPAAGDVTLS(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7065127-7063146(-)
Potential amino acid sequence	MGLYERMGDTLAYQYGGSAAHNKVFSERRGQWRAATQSQEFLRTLQRYYNNAYMDADKQDAINI FLGTFRPEQGSQAVWELRSDSHSNGRSGEISMGEDEKFLVKRCLSDGNILHESHTPMSAMSRKN ESISHRGFVSSHQVTRTHIISESSPDMPAAGDVTLSSADTSPHNSSDDDSRDYDSLEKNCRPSK NVANGDYDVKPSRLQSGVLRTNCIDCLDRTNVAQYAYGWAALGQQLHALGIRDAPTIELDDPLS STLMGLYERMGDTLAYQYGGSAAHNKVFSERRGQWRAATQSQEFLRTLQRYYNNAYMDADKQDA INIFLGTFRPEQGSQAVWELRSDSHSNGRSGEISMGEDEKFLVKRCLSDGNILHESHTPMSAMS RKNESISHRGFVSSHQVTRTHIISESSPDMPAAGDVTLSSADTSPHNSSDDDSRDYDSLEKNCR PSKNVANGDYDVKPSRLQSGVLRTNCIDCLDRTNVAQYAYGWAALGQQLHALGIRDAPTIELDD PLSSTLMGLYERMGDTLAYQYGGSAAHNKVFSERRGQWRAATQSQEFLRTLQRYYNNAYMDADK QDAINIFLGTFRPEQGSQAVWELRSDSHSNGRSGEISMGEDEKFLVKRCLSDGNILHESHTPMS AMSRKNESISHRGFVSSHQVTRTHIISESSPDMPAAGDVTLSSADTSPHNSSDDDSRDYDSLEK NCRPSKNVANGDYDVKPSRLQSGVLRTNCIDCLDRTNVAQYAYGWAALGQQLHALGIRDAPTIE LDDPLSSTLMGLYERMGDTLAYQYGGSAAHNKVFSERRGQWRAATQSQEFLRTLQRYYNNAYMD ADKQDAINIFLGTFRPEQGSQAVWELRSDSHSNGRSGEISMGEDEKFLVKRCLSDGNILHESHT PMSAMSRKNESISHRGFVSSHQVTRTHIISESSPDMPAAGDVTLS(-)
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 AT5G20840_circ_g.4

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