Plant Circular RNA Database

Detail information of AT4G10770_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G10770_circ_g.3
					
						ID in PlantcircBase
						ath_circ_030266
					
						Alias
						AT4G10770_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 6632014-6632412  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, CIRI-full, CIRI2
					
						Parent gene
						
							AT4G10770						
					
						Parent gene annotation
						
							Oligopeptide transporter 7
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G10770_circ_g.2 AT4G10770_circ_g.4 						
					
						Support reads
						26
					
						Tissues
						root, 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  
						
							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
						AT4G10770.2:1
AT4G10770.1:1

General Information
CircRNA Name	AT4G10770_circ_g.3
ID in PlantcircBase	ath_circ_030266
Alias	AT4G10770_C1
Organism	Arabidpsis thaliana
Position	chr4: 6632014-6632412 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, CIRI-full, CIRI2
Parent gene	AT4G10770
Parent gene annotation	Oligopeptide transporter 7
Parent gene strand	-
Alternative splicing	AT4G10770_circ_g.2 AT4G10770_circ_g.4
Support reads	26
Tissues	root, 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	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	AT4G10770.2:1 AT4G10770.1:1

			
						 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  
						
							GAGATTGGTAAAAGAAGATCCTCTGTTTCATCTCTTGGTTCAGATGAAGATGAAGATGATGACG
CATATGATGGGTTTGTCAGATCTTTTGGGTTTGTTActggattcaacgtaaactgccactttga
tccttggaagaagactctatcggtgattttagcagccatgagacgaccaagtggtacgacggcg
atttgagc

									
								

					

						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: 225
Transcript exons: 6632014-6632113,6632269-6632369,6632389-6632412
CTGGATTCAACGTAAACTGCCACTTTGATCCTTGGAAGAAGACTCTATCGGTGATTTTAGCAGC
CATGAGACGACCAAGTGGTACGACGGCGATTTGAGCGTCGGATTGGTGAGTTCTCTTCTTCTTC
CTCCTCATTCTCGTCGGAGATTGGTAAAAGAAGATCCTCTGTTTCATCTCTTGGTTCAGATGAA
GATGAAGATTTGTCAGATCTTTTGGGTTTGTTA
Transcript length: 231
Transcript exons: 6632014-6632092,6632247-6632358,6632373-6632412
CTGGATTCAACGTAAACTGCCACTTTGATCCTTGGAAGAAGACTCTATCGGTGATTTTAGCAGC
CATGAGACGACCAAGGTCGGAACAGTGAGTGCTACTTGTCGGATTGGTGAGTTCTCTTCTTCTT
CCTCCTCATTCTCGTCGGAGATTGGTAAAAGAAGATCCTCTGTTTCATCTCTTGGTTCAGATGG
ACGCATATGATGGGTTTGTCAGATCTTTTGGGTTTGTTA
Transcript length: 331
Transcript exons: 6632014-6632086,6632123-6632223,6632250-6632350,6632357-
6632412
CTGGATTCAACGTAAACTGCCACTTTGATCCTTGGAAGAAGACTCTATCGGTGATTTTAGCAGC
CATGAGACGAGAGATAGTGAGAGGTTCTGTTCTATACCAGAAGAACTGATTGAGAAACGACAAG
AGGATGCAAGAGAGAGTTCCTAAGACCCACATGCGAAATGTTAAGAGGAACAGTGAGTGCTACT
TGTCGGATTGGTGAGTTCTCTTCTTCTTCCTCCTCATTCTCGTCGGAGATTGGTAAAAGAAGAT
CCTCTGTTTCATCTCTTGGTGAAGATGAAGATGATGACGCATATGATGGGTTTGTCAGATCTTT
TGGGTTTGTTA
Transcript length: 399
Transcript exons: 6632014-6632412
CTGGATTCAACGTAAACTGCCACTTTGATCCTTGGAAGAAGACTCTATCGGTGATTTTAGCAGC
CATGAGACGACCAAGTGGTACGACGGCGATTTGAGCGGAGATGGCAGAGATAGTGAGAGGTTCT
GTTCTATACCAGAAGAACTGATTGAGAAACGACAAGAGGATGCAAGAGAGAGTTCCTAAGACCC
ACATGCGAAATGTTAAGACAGGTAATGAAGGATCATCTGTTGTCGGAACAGTGAGTGCTACTTG
TCGGATTGGTGAGTTCTCTTCTTCTTCCTCCTCATTCTCGTCGGAGATTGGTAAAAGAAGATCC
TCTGTTTCATCTCTTGGTTCAGATGAAGATGAAGATGATGACGCATATGATGGGTTTGTCAGAT
CTTTTGGGTTTGTTA
						
					

						Genomic sequence
						
							CTGGATTCAACGTAAACTGCCACTTTGATCCTTGGAAGAAGACTCTATCGGTGATTTTAGCAGC
CATGAGACGACCAAGTGGTACGACGGCGATTTGAGCGGAGATGGCAGAGATAGTGAGAGGTTCT
GTTCTATACCAGAAGAACTGATTGAGAAACGACAAGAGGATGCAAGAGAGAGTTCCTAAGACCC
ACATGCGAAATGTTAAGACAGGTAATGAAGGATCATCTGTTGTCGGAACAGTGAGTGCTACTTG
TCGGATTGGTGAGTTCTCTTCTTCTTCCTCCTCATTCTCGTCGGAGATTGGTAAAAGAAGATCC
TCTGTTTCATCTCTTGGTTCAGATGAAGATGAAGATGATGACGCATATGATGGGTTTGTCAGAT
CTTTTGGGTTTGTTA
						
					

			
		

Sequences
Splice junction sequence	GAGATTGGTAAAAGAAGATCCTCTGTTTCATCTCTTGGTTCAGATGAAGATGAAGATGATGACG CATATGATGGGTTTGTCAGATCTTTTGGGTTTGTTActggattcaacgtaaactgccactttga tccttggaagaagactctatcggtgattttagcagccatgagacgaccaagtggtacgacggcg atttgagc
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: 225 Transcript exons: 6632014-6632113,6632269-6632369,6632389-6632412 CTGGATTCAACGTAAACTGCCACTTTGATCCTTGGAAGAAGACTCTATCGGTGATTTTAGCAGC CATGAGACGACCAAGTGGTACGACGGCGATTTGAGCGTCGGATTGGTGAGTTCTCTTCTTCTTC CTCCTCATTCTCGTCGGAGATTGGTAAAAGAAGATCCTCTGTTTCATCTCTTGGTTCAGATGAA GATGAAGATTTGTCAGATCTTTTGGGTTTGTTA Transcript length: 231 Transcript exons: 6632014-6632092,6632247-6632358,6632373-6632412 CTGGATTCAACGTAAACTGCCACTTTGATCCTTGGAAGAAGACTCTATCGGTGATTTTAGCAGC CATGAGACGACCAAGGTCGGAACAGTGAGTGCTACTTGTCGGATTGGTGAGTTCTCTTCTTCTT CCTCCTCATTCTCGTCGGAGATTGGTAAAAGAAGATCCTCTGTTTCATCTCTTGGTTCAGATGG ACGCATATGATGGGTTTGTCAGATCTTTTGGGTTTGTTA Transcript length: 331 Transcript exons: 6632014-6632086,6632123-6632223,6632250-6632350,6632357- 6632412 CTGGATTCAACGTAAACTGCCACTTTGATCCTTGGAAGAAGACTCTATCGGTGATTTTAGCAGC CATGAGACGAGAGATAGTGAGAGGTTCTGTTCTATACCAGAAGAACTGATTGAGAAACGACAAG AGGATGCAAGAGAGAGTTCCTAAGACCCACATGCGAAATGTTAAGAGGAACAGTGAGTGCTACT TGTCGGATTGGTGAGTTCTCTTCTTCTTCCTCCTCATTCTCGTCGGAGATTGGTAAAAGAAGAT CCTCTGTTTCATCTCTTGGTGAAGATGAAGATGATGACGCATATGATGGGTTTGTCAGATCTTT TGGGTTTGTTA Transcript length: 399 Transcript exons: 6632014-6632412 CTGGATTCAACGTAAACTGCCACTTTGATCCTTGGAAGAAGACTCTATCGGTGATTTTAGCAGC CATGAGACGACCAAGTGGTACGACGGCGATTTGAGCGGAGATGGCAGAGATAGTGAGAGGTTCT GTTCTATACCAGAAGAACTGATTGAGAAACGACAAGAGGATGCAAGAGAGAGTTCCTAAGACCC ACATGCGAAATGTTAAGACAGGTAATGAAGGATCATCTGTTGTCGGAACAGTGAGTGCTACTTG TCGGATTGGTGAGTTCTCTTCTTCTTCCTCCTCATTCTCGTCGGAGATTGGTAAAAGAAGATCC TCTGTTTCATCTCTTGGTTCAGATGAAGATGAAGATGATGACGCATATGATGGGTTTGTCAGAT CTTTTGGGTTTGTTA
Genomic sequence	CTGGATTCAACGTAAACTGCCACTTTGATCCTTGGAAGAAGACTCTATCGGTGATTTTAGCAGC CATGAGACGACCAAGTGGTACGACGGCGATTTGAGCGGAGATGGCAGAGATAGTGAGAGGTTCT GTTCTATACCAGAAGAACTGATTGAGAAACGACAAGAGGATGCAAGAGAGAGTTCCTAAGACCC ACATGCGAAATGTTAAGACAGGTAATGAAGGATCATCTGTTGTCGGAACAGTGAGTGCTACTTG TCGGATTGGTGAGTTCTCTTCTTCTTCCTCCTCATTCTCGTCGGAGATTGGTAAAAGAAGATCC TCTGTTTCATCTCTTGGTTCAGATGAAGATGAAGATGATGACGCATATGATGGGTTTGTCAGAT CTTTTGGGTTTGTTA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.639183396

Conservation Information
Conserved circRNAs	NA
PMCS	0.639183396

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6632210-6632016(-)
						
						Potential amino acid sequence
						
							MWVLGTLSCILLSFLNQFFWYRTEPLTISAISAQIAVVPLGRLMAAKITDRVFFQGSKWQFTLN
PVTNPKDLTNPSYASSSSSSSEPRDETEDLLLPISDENEEEEEENSPIRQVALTVPTTDDPSLP
VLTFRMWVLGTLSCILLSFLNQFFWYRTEPLTISAISAQIAVVPLGRLMAAKITDRVFFQGSKW
QFTLNPVTNPKDLTNPSYASSSSSSSEPRDETEDLLLPISDENEEEEEENSPIRQVALTVPTTD
DPSLPVLTFRMWVLGTLSCILLSFLNQFFWYRTEPLTISAISAQIAVVPLGRLMAAKITDRVFF
QGSKWQFTLNPVTNPKDLTNPSYASSSSSSSEPRDETEDLLLPISDENEEEEEENSPIRQVALT
VPTTDDPSLPVLTFRMWVLGTLSCILLSFLNQFFWYRTEPLTISAISAQIAVVPLGRLMAAKIT
DRVFFQGSKWQFTLNP(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6632210-6632016(-)
Potential amino acid sequence	MWVLGTLSCILLSFLNQFFWYRTEPLTISAISAQIAVVPLGRLMAAKITDRVFFQGSKWQFTLN PVTNPKDLTNPSYASSSSSSSEPRDETEDLLLPISDENEEEEEENSPIRQVALTVPTTDDPSLP VLTFRMWVLGTLSCILLSFLNQFFWYRTEPLTISAISAQIAVVPLGRLMAAKITDRVFFQGSKW QFTLNPVTNPKDLTNPSYASSSSSSSEPRDETEDLLLPISDENEEEEEENSPIRQVALTVPTTD DPSLPVLTFRMWVLGTLSCILLSFLNQFFWYRTEPLTISAISAQIAVVPLGRLMAAKITDRVFF QGSKWQFTLNPVTNPKDLTNPSYASSSSSSSEPRDETEDLLLPISDENEEEEEENSPIRQVALT VPTTDDPSLPVLTFRMWVLGTLSCILLSFLNQFFWYRTEPLTISAISAQIAVVPLGRLMAAKIT DRVFFQGSKWQFTLNP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Liu et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT4G10770_circ_g.3

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