Plant Circular RNA Database

Detail information of AT3G13990_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT3G13990_circ_g.5
					
						ID in PlantcircBase
						ath_circ_021604
					
						Alias
						Ath_circ_FC1963
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 4628775-4629836  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT3G13990						
					
						Parent gene annotation
						
							AT3g13990/MDC16_11
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G13990_circ_g.1 AT3G13990_circ_g.2 3_circ_ag.3 AT3G13990_circ_g.4 AT3G13990_circ_g.6 AT3G13990_circ_g.7 AT3G14000_circ_g.1 AT3G14000_circ_g.2 AT3G14010_circ_g.1 AT3G14010_circ_g.2 AT3G14010_circ_g.3 AT3G14010_circ_g.4 AT3G14010_circ_g.5 AT3G14010_circ_g.6 AT3G14010_circ_g.7 AT3G14010_circ_g.8 AT3G14020_circ_g.1 AT3G14020_circ_g.2 AT3G14067_circ_g.1 AT3G14075_circ_g.1 AT3G14075_circ_g.2 AT3G14080_circ_g.1 AT3G14080_circ_g.2 AT3G14080_circ_g.3 AT3G14100_circ_g.1 AT3G14100_circ_g.2 AT3G14100_circ_g.3 AT3G14100_circ_g.4 AT3G14100_circ_g.5 AT3G14100_circ_g.6 AT3G14100_circ_g.7 AT3G14100_circ_g.8 AT3G14100_circ_g.9 AT3G14110_circ_g.1 AT3G14120_circ_g.1 AT3G14120_circ_g.2 AT3G14120_circ_g.3 3_circ_ag.4 AT3G14130_circ_g.1 AT3G14130_circ_g.2 AT3G14130_circ_g.3 AT3G14130_circ_g.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 AT3G14150_circ_g.1 AT3G14172_circ_g.1 AT3G14172_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						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  
						
							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
						AT3G13990.1:3
AT3G13990.2:3

General Information
CircRNA Name	AT3G13990_circ_g.5
ID in PlantcircBase	ath_circ_021604
Alias	Ath_circ_FC1963
Organism	Arabidpsis thaliana
Position	chr3: 4628775-4629836 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, PcircRNA_finder
Parent gene	AT3G13990
Parent gene annotation	AT3g13990/MDC16_11
Parent gene strand	-
Alternative splicing	AT3G13990_circ_g.1 AT3G13990_circ_g.2 3_circ_ag.3 AT3G13990_circ_g.4 AT3G13990_circ_g.6 AT3G13990_circ_g.7 AT3G14000_circ_g.1 AT3G14000_circ_g.2 AT3G14010_circ_g.1 AT3G14010_circ_g.2 AT3G14010_circ_g.3 AT3G14010_circ_g.4 AT3G14010_circ_g.5 AT3G14010_circ_g.6 AT3G14010_circ_g.7 AT3G14010_circ_g.8 AT3G14020_circ_g.1 AT3G14020_circ_g.2 AT3G14067_circ_g.1 AT3G14075_circ_g.1 AT3G14075_circ_g.2 AT3G14080_circ_g.1 AT3G14080_circ_g.2 AT3G14080_circ_g.3 AT3G14100_circ_g.1 AT3G14100_circ_g.2 AT3G14100_circ_g.3 AT3G14100_circ_g.4 AT3G14100_circ_g.5 AT3G14100_circ_g.6 AT3G14100_circ_g.7 AT3G14100_circ_g.8 AT3G14100_circ_g.9 AT3G14110_circ_g.1 AT3G14120_circ_g.1 AT3G14120_circ_g.2 AT3G14120_circ_g.3 3_circ_ag.4 AT3G14130_circ_g.1 AT3G14130_circ_g.2 AT3G14130_circ_g.3 AT3G14130_circ_g.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 AT3G14150_circ_g.1 AT3G14172_circ_g.1 AT3G14172_circ_g.2
Support reads	2
Tissues	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	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	AT3G13990.1:3 AT3G13990.2:3

			
						 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  
						
							GTTAAAAAGGAGAAGAACTGGGAACAAGATACCATAACAGTTATATGTAACCTCACCTCTTTTT
TCCTGTCTCTTTTTCTCTTCACCTCGTGAAATGGATcccaatttgttcacagtggcaaccactt
tgttaatatttgatccagaggactgggcagaagaatgcttcaactcttcatcaacatttggatt
agacctgt

						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: 349
Transcript exons: 4628775-4628907,4629247-4629418,4629793-4629836
CCCAATTTGTTCACAGTGGCAACCACTTTGTTAATATTTGATCCAGAGGACTGGGCAGAAGAAT
GCTTCAACTCTTCATCAACATTTGGATTAGACCTGTTGTCCCTAACAACGCGAAACTCTTTGTT
GGATCCAGTAGCAGGATTTCTAGGAGATGCATTTCGTTGAGCAGCGTTCCTGGGGAAGAAATTC
CTACTGTAGCCTCCTCTCCGAACATTATGTTCAGGCTGTGTACGAACTTTCACTTCACTGGTAA
CATTTTCAAGAGGTTTCTTTATGTTGGCAGGCTCAACAAATACTGTATCCTCTTTTTTCCTGTC
TCTTTTTCTCTTCACCTCGTGAAATGGAT
						
						Genomic sequence
						
							CCCAATTTGTTCACAGTGGCAACCACTTTGTTAATATTTGATCCAGAGGACTGGGCAGAAGAAT
GCTTCAACTCTTCATCAACATTTGGATTAGACCTGTTGTCCCTAACAACGCGAAACTCTTTGTT
GGATCCTGCACTAACATGAAACGAACAAATTACAAACAGACAGAAAAACATTTCTAGGTGAATA
TGGTCAATACATTACATAAAACTTGAAGGCCTCACGCCAATGGCCAATAACAAAGATTAAAAAA
AAAAAACAAATCAACGCAAAACAATTTCTTCTACGTTTCCTTTGCTTGCCTGCATATATTTTTC
TGGATTTAACCAAGTTCATTTGATACTGCCGTTATATAGATTATGTTTACGAACCATTCAAAAG
ACAGCTTAAAACAAATTAAAGATTTTTAGTACAACTGTACAAGCATGCGAAAGAAACTGGCAAG
TATATCATCATCAAATTGATTTACCAGTAGCAGGATTTCTAGGAGATGCATTTCGTTGAGCAGC
GTTCCTGGGGAAGAAATTCCTACTGTAGCCTCCTCTCCGAACATTATGTTCAGGCTGTGTACGA
ACTTTCACTTCACTGGTAACATTTTCAAGAGGTTTCTTTATGTTGGCAGGCTCAACAAATACTG
TATCCTGAAACCAAAGGAACGCCCTAAAAATCAGAGGTTATACAAGAGGTGTCTTGATGATCTC
TACAAATTCATCAAACTATTTGAATGGCTAGAAAAGTTGAAATTTTTTTTGACGATCAATTAAA
TTAGAAGGCACACAAAATACTAAACAAAACAAAAAAAAAATATAGCTTGCCACAGCAGACATCC
GATGAGATATAATAGTCACACAAGCACAACTAACATTATGAAAAATCTAGTCACCTTCTTCAAA
TGCAGTTTCGAAAAGACTAAGGAGAGTCAAACAAAAAAACTACAATGTGGTTGCATTGGCAAAA
ATGTTAAAAAGGAGAAGAACTGGGAACAAGATACCATAACAGTTATATGTAACCTCACCTCTTT
TTTCCTGTCTCTTTTTCTCTTCACCTCGTGAAATGGAT

Sequences
Splice junction sequence	GTTAAAAAGGAGAAGAACTGGGAACAAGATACCATAACAGTTATATGTAACCTCACCTCTTTTT TCCTGTCTCTTTTTCTCTTCACCTCGTGAAATGGATcccaatttgttcacagtggcaaccactt tgttaatatttgatccagaggactgggcagaagaatgcttcaactcttcatcaacatttggatt agacctgt
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: 349 Transcript exons: 4628775-4628907,4629247-4629418,4629793-4629836 CCCAATTTGTTCACAGTGGCAACCACTTTGTTAATATTTGATCCAGAGGACTGGGCAGAAGAAT GCTTCAACTCTTCATCAACATTTGGATTAGACCTGTTGTCCCTAACAACGCGAAACTCTTTGTT GGATCCAGTAGCAGGATTTCTAGGAGATGCATTTCGTTGAGCAGCGTTCCTGGGGAAGAAATTC CTACTGTAGCCTCCTCTCCGAACATTATGTTCAGGCTGTGTACGAACTTTCACTTCACTGGTAA CATTTTCAAGAGGTTTCTTTATGTTGGCAGGCTCAACAAATACTGTATCCTCTTTTTTCCTGTC TCTTTTTCTCTTCACCTCGTGAAATGGAT
Genomic sequence	CCCAATTTGTTCACAGTGGCAACCACTTTGTTAATATTTGATCCAGAGGACTGGGCAGAAGAAT GCTTCAACTCTTCATCAACATTTGGATTAGACCTGTTGTCCCTAACAACGCGAAACTCTTTGTT GGATCCTGCACTAACATGAAACGAACAAATTACAAACAGACAGAAAAACATTTCTAGGTGAATA TGGTCAATACATTACATAAAACTTGAAGGCCTCACGCCAATGGCCAATAACAAAGATTAAAAAA AAAAAACAAATCAACGCAAAACAATTTCTTCTACGTTTCCTTTGCTTGCCTGCATATATTTTTC TGGATTTAACCAAGTTCATTTGATACTGCCGTTATATAGATTATGTTTACGAACCATTCAAAAG ACAGCTTAAAACAAATTAAAGATTTTTAGTACAACTGTACAAGCATGCGAAAGAAACTGGCAAG TATATCATCATCAAATTGATTTACCAGTAGCAGGATTTCTAGGAGATGCATTTCGTTGAGCAGC GTTCCTGGGGAAGAAATTCCTACTGTAGCCTCCTCTCCGAACATTATGTTCAGGCTGTGTACGA ACTTTCACTTCACTGGTAACATTTTCAAGAGGTTTCTTTATGTTGGCAGGCTCAACAAATACTG TATCCTGAAACCAAAGGAACGCCCTAAAAATCAGAGGTTATACAAGAGGTGTCTTGATGATCTC TACAAATTCATCAAACTATTTGAATGGCTAGAAAAGTTGAAATTTTTTTTGACGATCAATTAAA TTAGAAGGCACACAAAATACTAAACAAAACAAAAAAAAAATATAGCTTGCCACAGCAGACATCC GATGAGATATAATAGTCACACAAGCACAACTAACATTATGAAAAATCTAGTCACCTTCTTCAAA TGCAGTTTCGAAAAGACTAAGGAGAGTCAAACAAAAAAACTACAATGTGGTTGCATTGGCAAAA ATGTTAAAAAGGAGAAGAACTGGGAACAAGATACCATAACAGTTATATGTAACCTCACCTCTTT TTTCCTGTCTCTTTTTCTCTTCACCTCGTGAAATGGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.293539509

Conservation Information
Conserved circRNAs	NA
PMCS	0.293539509

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
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 AT3G13990_circ_g.5

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