Plant Circular RNA Database

Detail information of AT1G63940_circ_g.8

			
						 General Information
					
						CircRNA Name
						AT1G63940_circ_g.8
					
						ID in PlantcircBase
						ath_circ_008585
					
						Alias
						1:23731827-23732342
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 23731827-23732342  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G63940						
					
						Parent gene annotation
						
							MDAR6
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G63940_circ_g.1 AT1G63940_circ_g.2 AT1G63940_circ_g.3 AT1G63940_circ_g.4 AT1G63940_circ_g.5 AT1G63940_circ_g.6 AT1G63940_circ_g.7 						
					
						Support reads
						1/1
					
						Tissues
						root;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
						AT1G63940.4:3
AT1G63940.1:3
AT1G63940.3:3
AT1G63940.2:3

General Information
CircRNA Name	AT1G63940_circ_g.8
ID in PlantcircBase	ath_circ_008585
Alias	1:23731827-23732342
Organism	Arabidpsis thaliana
Position	chr1: 23731827-23732342 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G63940
Parent gene annotation	MDAR6
Parent gene strand	+
Alternative splicing	AT1G63940_circ_g.1 AT1G63940_circ_g.2 AT1G63940_circ_g.3 AT1G63940_circ_g.4 AT1G63940_circ_g.5 AT1G63940_circ_g.6 AT1G63940_circ_g.7
Support reads	1/1
Tissues	root;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	AT1G63940.4:3 AT1G63940.1:3 AT1G63940.3:3 AT1G63940.2:3

			
						 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  
						
							GTGTATCCTTACTTTACAGGTTGTAATTGGAATTGGAGCTAAGCCTGCTATTGGCCCCTTTGAA
ACTTTGGCCATGAACAAATCAATTGGAGGAATTCAGattgtattccctgaagatcagcttttgc
aaagattgttcactccatcgcttgctcagaaatatgaagaactgtaccgtcaaaatggtgttaa
gtttgtca

						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: 273
Transcript exons: 23731827-23731928,23732041-23732130,23732262-23732342
ATTGTATTCCCTGAAGATCAGCTTTTGCAAAGATTGTTCACTCCATCGCTTGCTCAGAAATATG
AAGAACTGTACCGTCAAAATGGTGTTAAGTTTGTCAAGGGCGCTTCCATAAATAACTTGGAAGC
AGGTTCGGATGGGCGTGTATCAGCTGTTAAGCTTGCTGATGGGTCTACAATTGAGGCAGACACG
GTTGTAATTGGAATTGGAGCTAAGCCTGCTATTGGCCCCTTTGAAACTTTGGCCATGAACAAAT
CAATTGGAGGAATTCAG
						
						Genomic sequence
						
							ATTGTATTCCCTGAAGATCAGCTTTTGCAAAGATTGTTCACTCCATCGCTTGCTCAGAAATATG
AAGAACTGTACCGTCAAAATGGTGTTAAGTTTGTCAAGGTAAGATATCAGCACACGATCAACAC
CTTATACTGAAGCCTTTGCTTTCCTGCAAACCTAAGAATTTCAGAAACACAGTGTGCAAACTTG
AATTTCTCTTTCTGTTGAACAGGGCGCTTCCATAAATAACTTGGAAGCAGGTTCGGATGGGCGT
GTATCAGCTGTTAAGCTTGCTGATGGGTCTACAATTGAGGCAGACACGGTATAGTTGTAGCTCA
GCTTCACTTTTTTCTTTCTCAAATGATGCAAATTCAACAACTTTGATCAAATGAAAACTGTGAA
GGGTCAATGTAATACTGACTTTTGTACGACCTGTGTATCCTTACTTTACAGGTTGTAATTGGAA
TTGGAGCTAAGCCTGCTATTGGCCCCTTTGAAACTTTGGCCATGAACAAATCAATTGGAGGAAT
TCAG

Sequences
Splice junction sequence	GTGTATCCTTACTTTACAGGTTGTAATTGGAATTGGAGCTAAGCCTGCTATTGGCCCCTTTGAA ACTTTGGCCATGAACAAATCAATTGGAGGAATTCAGattgtattccctgaagatcagcttttgc aaagattgttcactccatcgcttgctcagaaatatgaagaactgtaccgtcaaaatggtgttaa gtttgtca
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: 273 Transcript exons: 23731827-23731928,23732041-23732130,23732262-23732342 ATTGTATTCCCTGAAGATCAGCTTTTGCAAAGATTGTTCACTCCATCGCTTGCTCAGAAATATG AAGAACTGTACCGTCAAAATGGTGTTAAGTTTGTCAAGGGCGCTTCCATAAATAACTTGGAAGC AGGTTCGGATGGGCGTGTATCAGCTGTTAAGCTTGCTGATGGGTCTACAATTGAGGCAGACACG GTTGTAATTGGAATTGGAGCTAAGCCTGCTATTGGCCCCTTTGAAACTTTGGCCATGAACAAAT CAATTGGAGGAATTCAG
Genomic sequence	ATTGTATTCCCTGAAGATCAGCTTTTGCAAAGATTGTTCACTCCATCGCTTGCTCAGAAATATG AAGAACTGTACCGTCAAAATGGTGTTAAGTTTGTCAAGGTAAGATATCAGCACACGATCAACAC CTTATACTGAAGCCTTTGCTTTCCTGCAAACCTAAGAATTTCAGAAACACAGTGTGCAAACTTG AATTTCTCTTTCTGTTGAACAGGGCGCTTCCATAAATAACTTGGAAGCAGGTTCGGATGGGCGT GTATCAGCTGTTAAGCTTGCTGATGGGTCTACAATTGAGGCAGACACGGTATAGTTGTAGCTCA GCTTCACTTTTTTCTTTCTCAAATGATGCAAATTCAACAACTTTGATCAAATGAAAACTGTGAA GGGTCAATGTAATACTGACTTTTGTACGACCTGTGTATCCTTACTTTACAGGTTGTAATTGGAA TTGGAGCTAAGCCTGCTATTGGCCCCTTTGAAACTTTGGCCATGAACAAATCAATTGGAGGAAT TCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.234075924

Conservation Information
Conserved circRNAs	NA
PMCS	0.234075924

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

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT1G63940_circ_g.8

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