Plant Circular RNA Database

Detail information of AT1G65220_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT1G65220_circ_g.4
					
						ID in PlantcircBase
						ath_circ_008755
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 24226846-24227753  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder
					
						Parent gene
						
							AT1G65220						
					
						Parent gene annotation
						
							ARM repeat superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							1_circ_ag.3 AT1G65080_circ_g.1 AT1G65130_circ_g.1 AT1G65220_circ_g.1 AT1G65220_circ_g.2 AT1G65220_circ_g.3 AT1G65220_circ_g.5 AT1G65220_circ_g.6 AT1G65230_circ_g.1 AT1G65230_circ_g.2 AT1G65230_circ_g.3 AT1G65230_circ_g.4 AT1G65230_circ_g.5 AT1G65260_circ_g.1 AT1G65260_circ_g.2 AT1G65260_circ_g.3 AT1G65260_circ_g.4 AT1G65260_circ_g.5 AT1G65260_circ_g.6 AT1G65260_circ_g.7 AT1G65260_circ_g.8 AT1G65260_circ_g.9 AT1G65260_circ_g.10 AT1G65260_circ_g.11 AT1G65260_circ_g.12 AT1G65260_circ_g.13 AT1G65260_circ_g.14 AT1G65260_circ_g.15 AT1G65270_circ_g.1 AT1G65270_circ_g.2 AT1G65270_circ_g.3 AT1G65270_circ_g.4 AT1G65270_circ_g.5 AT1G65270_circ_g.6 AT1G65280_circ_g.1 AT1G65280_circ_g.2 AT1G65280_circ_g.3 AT1G65290_circ_g.1 AT1G65290_circ_g.2 AT1G65295_circ_g.1 AT1G65320_circ_g.1 AT1G65350_circ_g.1 AT1G65370_circ_g.1 AT1G65370_circ_g.2 						
					
						Support reads
						22/NA
					
						Tissues
						inflorescences, whole_plant/leaf
					
						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
						AT1G65220.1:3

General Information
CircRNA Name	AT1G65220_circ_g.4
ID in PlantcircBase	ath_circ_008755
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 24226846-24227753 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder
Parent gene	AT1G65220
Parent gene annotation	ARM repeat superfamily protein
Parent gene strand	+
Alternative splicing	1_circ_ag.3 AT1G65080_circ_g.1 AT1G65130_circ_g.1 AT1G65220_circ_g.1 AT1G65220_circ_g.2 AT1G65220_circ_g.3 AT1G65220_circ_g.5 AT1G65220_circ_g.6 AT1G65230_circ_g.1 AT1G65230_circ_g.2 AT1G65230_circ_g.3 AT1G65230_circ_g.4 AT1G65230_circ_g.5 AT1G65260_circ_g.1 AT1G65260_circ_g.2 AT1G65260_circ_g.3 AT1G65260_circ_g.4 AT1G65260_circ_g.5 AT1G65260_circ_g.6 AT1G65260_circ_g.7 AT1G65260_circ_g.8 AT1G65260_circ_g.9 AT1G65260_circ_g.10 AT1G65260_circ_g.11 AT1G65260_circ_g.12 AT1G65260_circ_g.13 AT1G65260_circ_g.14 AT1G65260_circ_g.15 AT1G65270_circ_g.1 AT1G65270_circ_g.2 AT1G65270_circ_g.3 AT1G65270_circ_g.4 AT1G65270_circ_g.5 AT1G65270_circ_g.6 AT1G65280_circ_g.1 AT1G65280_circ_g.2 AT1G65280_circ_g.3 AT1G65290_circ_g.1 AT1G65290_circ_g.2 AT1G65295_circ_g.1 AT1G65320_circ_g.1 AT1G65350_circ_g.1 AT1G65370_circ_g.1 AT1G65370_circ_g.2
Support reads	22/NA
Tissues	inflorescences, whole_plant/leaf
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	AT1G65220.1:3

			
						 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  
						
							ACTTGATTTCTATTCTGAGGCGTGGCAAGATGGATGACAAACTCTTGGAGTTCCTGCCACCCAC
AAAGCGGACTACAGAAAGTTTTGCCGAGCATTTCACaggtacgcggattaagacccgcaaaagg
aatattgctgctcctctcgaccctgctgctttttctgatgcactagttcagatttatctggata
atgctggt

									
								

					

						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: 669
Transcript exons: 24226846-24226951,24227053-24227121,24227260-24227753
AGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCT
GATGCACTAGTTCAGATTTATCTGGATAATGCTGGTGATCTGGAACTTGTTGCCAGAAGTTTAG
AGTCATCTGATCTTAATTTCTCAAGATACGGTGATATTTTCTTTGAGGTTGTTTTCATTGGAGG
ACGTACTCAAACTGGTTCAGTGAAATCTGATGAAGGGGAACGCCACCCTTACTCTATAATCGAC
TGTGAACCAAAGCGTGAAGCTATTTTACCATCAGTTGTATACATACAGAAAATTTTGCGGAGGA
AAGCCTTCCTTATTAAGAACCTTGAGAATGTTACACGGAGATTCTTACAGTCACTGGAGCTTTT
TGAGGAGAATGAGAGGAAGAAGCTTGCAATATTCACAGCACTTGCATTTTCACAGAAGCTCTCA
GGATTACCTGCAGAGACTGTCTTCCAGCCATTGCTTAAGGATACTCTTGTTGCCAAAGGGATAG
TTCTCAATTTTGTAACAGACTTCTTCAATGAATATTTGGTTGAGAACAGTCTTGATGACTTGAT
TTCTATTCTGAGGCGTGGCAAGATGGATGACAAACTCTTGGAGTTCCTGCCACCCACAAAGCGG
ACTACAGAAAGTTTTGCCGAGCATTTCAC
						
					

						Genomic sequence
						
							AGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCT
GATGCACTAGTTCAGATTTATCTGGATAATGCTGGTGATCTGGTACTTTTTTTTTCGTGTTTTA
AGTATTTATTTATCTGTTTTTATTTGCTTGTAAAATGTCGTGCACCTTAACTTATGACTTTGTT
TTTGTTTTGTCTTAGGAACTTGTTGCCAGAAGTTTAGAGTCATCTGATCTTAATTTCTCAAGAT
ACGGTGATATTTTCTTTGAGGTAAATTCTCCATATATCAATACTGTCTCAGCTATCTTCTATTG
CCTGTGTATTTTTTGTTTTCTTGTAGCAAGGGGCTTTTTGTTTTGCTTGTCTTTCCGAGATTTA
ATAATTGATGGATCTCTTTTATTATATAAGGTTGTTTTCATTGGAGGACGTACTCAAACTGGTT
CAGTGAAATCTGATGAAGGGGAACGCCACCCTTACTCTATAATCGACTGTGAACCAAAGCGTGA
AGCTATTTTACCATCAGTTGTATACATACAGAAAATTTTGCGGAGGAAAGCCTTCCTTATTAAG
AACCTTGAGAATGTTACACGGAGATTCTTACAGTCACTGGAGCTTTTTGAGGAGAATGAGAGGA
AGAAGCTTGCAATATTCACAGCACTTGCATTTTCACAGAAGCTCTCAGGATTACCTGCAGAGAC
TGTCTTCCAGCCATTGCTTAAGGATACTCTTGTTGCCAAAGGGATAGTTCTCAATTTTGTAACA
GACTTCTTCAATGAATATTTGGTTGAGAACAGTCTTGATGACTTGATTTCTATTCTGAGGCGTG
GCAAGATGGATGACAAACTCTTGGAGTTCCTGCCACCCACAAAGCGGACTACAGAAAGTTTTGC
CGAGCATTTCAC
						
					

			
		

Sequences
Splice junction sequence	ACTTGATTTCTATTCTGAGGCGTGGCAAGATGGATGACAAACTCTTGGAGTTCCTGCCACCCAC AAAGCGGACTACAGAAAGTTTTGCCGAGCATTTCACaggtacgcggattaagacccgcaaaagg aatattgctgctcctctcgaccctgctgctttttctgatgcactagttcagatttatctggata atgctggt
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: 669 Transcript exons: 24226846-24226951,24227053-24227121,24227260-24227753 AGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCT GATGCACTAGTTCAGATTTATCTGGATAATGCTGGTGATCTGGAACTTGTTGCCAGAAGTTTAG AGTCATCTGATCTTAATTTCTCAAGATACGGTGATATTTTCTTTGAGGTTGTTTTCATTGGAGG ACGTACTCAAACTGGTTCAGTGAAATCTGATGAAGGGGAACGCCACCCTTACTCTATAATCGAC TGTGAACCAAAGCGTGAAGCTATTTTACCATCAGTTGTATACATACAGAAAATTTTGCGGAGGA AAGCCTTCCTTATTAAGAACCTTGAGAATGTTACACGGAGATTCTTACAGTCACTGGAGCTTTT TGAGGAGAATGAGAGGAAGAAGCTTGCAATATTCACAGCACTTGCATTTTCACAGAAGCTCTCA GGATTACCTGCAGAGACTGTCTTCCAGCCATTGCTTAAGGATACTCTTGTTGCCAAAGGGATAG TTCTCAATTTTGTAACAGACTTCTTCAATGAATATTTGGTTGAGAACAGTCTTGATGACTTGAT TTCTATTCTGAGGCGTGGCAAGATGGATGACAAACTCTTGGAGTTCCTGCCACCCACAAAGCGG ACTACAGAAAGTTTTGCCGAGCATTTCAC
Genomic sequence	AGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCT GATGCACTAGTTCAGATTTATCTGGATAATGCTGGTGATCTGGTACTTTTTTTTTCGTGTTTTA AGTATTTATTTATCTGTTTTTATTTGCTTGTAAAATGTCGTGCACCTTAACTTATGACTTTGTT TTTGTTTTGTCTTAGGAACTTGTTGCCAGAAGTTTAGAGTCATCTGATCTTAATTTCTCAAGAT ACGGTGATATTTTCTTTGAGGTAAATTCTCCATATATCAATACTGTCTCAGCTATCTTCTATTG CCTGTGTATTTTTTGTTTTCTTGTAGCAAGGGGCTTTTTGTTTTGCTTGTCTTTCCGAGATTTA ATAATTGATGGATCTCTTTTATTATATAAGGTTGTTTTCATTGGAGGACGTACTCAAACTGGTT CAGTGAAATCTGATGAAGGGGAACGCCACCCTTACTCTATAATCGACTGTGAACCAAAGCGTGA AGCTATTTTACCATCAGTTGTATACATACAGAAAATTTTGCGGAGGAAAGCCTTCCTTATTAAG AACCTTGAGAATGTTACACGGAGATTCTTACAGTCACTGGAGCTTTTTGAGGAGAATGAGAGGA AGAAGCTTGCAATATTCACAGCACTTGCATTTTCACAGAAGCTCTCAGGATTACCTGCAGAGAC TGTCTTCCAGCCATTGCTTAAGGATACTCTTGTTGCCAAAGGGATAGTTCTCAATTTTGTAACA GACTTCTTCAATGAATATTTGGTTGAGAACAGTCTTGATGACTTGATTTCTATTCTGAGGCGTG GCAAGATGGATGACAAACTCTTGGAGTTCCTGCCACCCACAAAGCGGACTACAGAAAGTTTTGC CGAGCATTTCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.347168469

Conservation Information
Conserved circRNAs	NA
PMCS	0.347168469

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24227683-24227750(+)
						
						Potential amino acid sequence
						
							MDDKLLEFLPPTKRTTESFAEHFTGTRIKTRKRNIAAPLDPAAFSDALVQIYLDNAGDLELVAR
SLESSDLNFSRYGDIFFEVVFIGGRTQTGSVKSDEGERHPYSIIDCEPKREAILPSVVYIQKIL
RRKAFLIKNLENVTRRFLQSLELFEENERKKLAIFTALAFSQKLSGLPAETVFQPLLKDTLVAK
GIVLNFVTDFFNEYLVENSLDDLISILRRGKMDDKLLEFLPPTKRTTESFAEHFTGTRIKTRKR
NIAAPLDPAAFSDALVQIYLDNAGDLELVARSLESSDLNFSRYGDIFFEVVFIGGRTQTGSVKS
DEGERHPYSIIDCEPKREAILPSVVYIQKILRRKAFLIKNLENVTRRFLQSLELFEENERKKLA
IFTALAFSQKLSGLPAETVFQPLLKDTLVAKGIVLNFVTDFFNEYLVENSLDDLISILRRGKMD
DKLLEFLPPTKRTTESFAEHFTGTRIKTRKRNIAAPLDPAAFSDALVQIYLDNAGDLELVARSL
ESSDLNFSRYGDIFFEVVFIGGRTQTGSVKSDEGERHPYSIIDCEPKREAILPSVVYIQKILRR
KAFLIKNLENVTRRFLQSLELFEENERKKLAIFTALAFSQKLSGLPAETVFQPLLKDTLVAKGI
VLNFVTDFFNEYLVENSLDDLISILRRGKMDDKLLEFLPPTKRTTESFAEHF(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24227683-24227750(+)
Potential amino acid sequence	MDDKLLEFLPPTKRTTESFAEHFTGTRIKTRKRNIAAPLDPAAFSDALVQIYLDNAGDLELVAR SLESSDLNFSRYGDIFFEVVFIGGRTQTGSVKSDEGERHPYSIIDCEPKREAILPSVVYIQKIL RRKAFLIKNLENVTRRFLQSLELFEENERKKLAIFTALAFSQKLSGLPAETVFQPLLKDTLVAK GIVLNFVTDFFNEYLVENSLDDLISILRRGKMDDKLLEFLPPTKRTTESFAEHFTGTRIKTRKR NIAAPLDPAAFSDALVQIYLDNAGDLELVARSLESSDLNFSRYGDIFFEVVFIGGRTQTGSVKS DEGERHPYSIIDCEPKREAILPSVVYIQKILRRKAFLIKNLENVTRRFLQSLELFEENERKKLA IFTALAFSQKLSGLPAETVFQPLLKDTLVAKGIVLNFVTDFFNEYLVENSLDDLISILRRGKMD DKLLEFLPPTKRTTESFAEHFTGTRIKTRKRNIAAPLDPAAFSDALVQIYLDNAGDLELVARSL ESSDLNFSRYGDIFFEVVFIGGRTQTGSVKSDEGERHPYSIIDCEPKREAILPSVVYIQKILRR KAFLIKNLENVTRRFLQSLELFEENERKKLAIFTALAFSQKLSGLPAETVFQPLLKDTLVAKGI VLNFVTDFFNEYLVENSLDDLISILRRGKMDDKLLEFLPPTKRTTESFAEHF(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Liu et al., 2017

circRNA

Detail information of AT1G65220_circ_g.4

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