Plant Circular RNA Database

Detail information of AT1G55350_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT1G55350_circ_g.5
					
						ID in PlantcircBase
						ath_circ_007493
					
						Alias
						1:20656563-20657343
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 20656563-20657343  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G55350						
					
						Parent gene annotation
						
							Calpain-type cysteine protease family
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G55350_circ_g.4 						
					
						Support reads
						2/1
					
						Tissues
						seedling
					
						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
						AT1G55350.4:2
AT1G55350.2:2
AT1G55350.5:2
AT1G55350.1:2
AT1G55350.6:2
AT1G55350.3:2

General Information
CircRNA Name	AT1G55350_circ_g.5
ID in PlantcircBase	ath_circ_007493
Alias	1:20656563-20657343
Organism	Arabidpsis thaliana
Position	chr1: 20656563-20657343 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G55350
Parent gene annotation	Calpain-type cysteine protease family
Parent gene strand	-
Alternative splicing	AT1G55350_circ_g.4
Support reads	2/1
Tissues	seedling
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	AT1G55350.4:2 AT1G55350.2:2 AT1G55350.5:2 AT1G55350.1:2 AT1G55350.6:2 AT1G55350.3:2

			
						 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  
						
							ACTTAGAGGTAACCCATTCTGGTAGCCATCAAACCCACCATCTATGTAACAAGTAGCTTCCCCC
GCATCAGCATCAATTGTGATTGTCACTGTATGCCACctgcaattttgatgggggattttgtgta
tccacaaataaagagcgatcatttggaggaaattcctggtcagtaaattgcttatcacctcgtg
cagagaga

						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: 670
Transcript exons: 20656563-20656880,20656992-20657343
CTGCAATTTTGATGGGGGATTTTGTGTATCCACAAATAAAGAGCGATCATTTGGAGGAAATTCC
TGGTCAGTAAATTGCTTATCACCTCGTGCAGAGAGAGCTTCTTTGACAGCCAACTCAACTGAAC
GCATTCTTTGATTTATATCTTCTTGTGTCTCCATCCTGGGTTTCCTGTGTCTCCTGGCAAAGGA
ATCGACACTCATTACAAAATCCCGACCTGATCTTCTTTTCCTCCCACTGGAATATTGTCCATCC
CAATCTACGTCATCCCTATCATAGAGATCAACATCGGCAGGATCACTATCCCAACCATCGACTC
TGGGGGGTGAATCCGTCCATTGCCAATTGTCATCAGACAAATCAATCATGTCTAAGTCAGCCAT
GCCAATGGCTGCATGCAAAGAAGCGGCCTCTTCTTCACTTAAGCATTTCCCCCAAAGGAAAACA
TCCATAATATGCATCTTTGATTCGACGCCATCACTATCTGATCTCCCGAATGCATCAACATCTA
TAGGTGGCCTAACACCCAACCAAACTTCAGCTCCTTGTTCCCAAATGGCACTGCCAATACTTAG
AGGTAACCCATTCTGGTAGCCATCAAACCCACCATCTATGTAACAAGTAGCTTCCCCCGCATCA
GCATCAATTGTGATTGTCACTGTATGCCAC
						
						Genomic sequence
						
							CTGCAATTTTGATGGGGGATTTTGTGTATCCACAAATAAAGAGCGATCATTTGGAGGAAATTCC
TGGTCAGTAAATTGCTTATCACCTCGTGCAGAGAGAGCTTCTTTGACAGCCAACTCAACTGAAC
GCATTCTTTGATTTATATCTTCTTGTGTCTCCATCCTGGGTTTCCTGTGTCTCCTGGCAAAGGA
ATCGACACTCATTACAAAATCCCGACCTGATCTTCTTTTCCTCCCACTGGAATATTGTCCATCC
CAATCTACGTCATCCCTATCATAGAGATCAACATCGGCAGGATCACTATCCCAACCATCGACCT
GGTAAAAAGAGAAAGGAATCAACAAAAATTAGAATAGGTTTTAACATTAGCCTTTTAACAAACA
TCGGACTGAAAAAATATGCCAACAGTCAACAGAAGGAAAACATACTCTGGGGGGTGAATCCGTC
CATTGCCAATTGTCATCAGACAAATCAATCATGTCTAAGTCAGCCATGCCAATGGCTGCATGCA
AAGAAGCGGCCTCTTCTTCACTTAAGCATTTCCCCCAAAGGAAAACATCCATAATATGCATCTT
TGATTCGACGCCATCACTATCTGATCTCCCGAATGCATCAACATCTATAGGTGGCCTAACACCC
AACCAAACTTCAGCTCCTTGTTCCCAAATGGCACTGCCAATACTTAGAGGTAACCCATTCTGGT
AGCCATCAAACCCACCATCTATGTAACAAGTAGCTTCCCCCGCATCAGCATCAATTGTGATTGT
CACTGTATGCCAC

Sequences
Splice junction sequence	ACTTAGAGGTAACCCATTCTGGTAGCCATCAAACCCACCATCTATGTAACAAGTAGCTTCCCCC GCATCAGCATCAATTGTGATTGTCACTGTATGCCACctgcaattttgatgggggattttgtgta tccacaaataaagagcgatcatttggaggaaattcctggtcagtaaattgcttatcacctcgtg cagagaga
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: 670 Transcript exons: 20656563-20656880,20656992-20657343 CTGCAATTTTGATGGGGGATTTTGTGTATCCACAAATAAAGAGCGATCATTTGGAGGAAATTCC TGGTCAGTAAATTGCTTATCACCTCGTGCAGAGAGAGCTTCTTTGACAGCCAACTCAACTGAAC GCATTCTTTGATTTATATCTTCTTGTGTCTCCATCCTGGGTTTCCTGTGTCTCCTGGCAAAGGA ATCGACACTCATTACAAAATCCCGACCTGATCTTCTTTTCCTCCCACTGGAATATTGTCCATCC CAATCTACGTCATCCCTATCATAGAGATCAACATCGGCAGGATCACTATCCCAACCATCGACTC TGGGGGGTGAATCCGTCCATTGCCAATTGTCATCAGACAAATCAATCATGTCTAAGTCAGCCAT GCCAATGGCTGCATGCAAAGAAGCGGCCTCTTCTTCACTTAAGCATTTCCCCCAAAGGAAAACA TCCATAATATGCATCTTTGATTCGACGCCATCACTATCTGATCTCCCGAATGCATCAACATCTA TAGGTGGCCTAACACCCAACCAAACTTCAGCTCCTTGTTCCCAAATGGCACTGCCAATACTTAG AGGTAACCCATTCTGGTAGCCATCAAACCCACCATCTATGTAACAAGTAGCTTCCCCCGCATCA GCATCAATTGTGATTGTCACTGTATGCCAC
Genomic sequence	CTGCAATTTTGATGGGGGATTTTGTGTATCCACAAATAAAGAGCGATCATTTGGAGGAAATTCC TGGTCAGTAAATTGCTTATCACCTCGTGCAGAGAGAGCTTCTTTGACAGCCAACTCAACTGAAC GCATTCTTTGATTTATATCTTCTTGTGTCTCCATCCTGGGTTTCCTGTGTCTCCTGGCAAAGGA ATCGACACTCATTACAAAATCCCGACCTGATCTTCTTTTCCTCCCACTGGAATATTGTCCATCC CAATCTACGTCATCCCTATCATAGAGATCAACATCGGCAGGATCACTATCCCAACCATCGACCT GGTAAAAAGAGAAAGGAATCAACAAAAATTAGAATAGGTTTTAACATTAGCCTTTTAACAAACA TCGGACTGAAAAAATATGCCAACAGTCAACAGAAGGAAAACATACTCTGGGGGGTGAATCCGTC CATTGCCAATTGTCATCAGACAAATCAATCATGTCTAAGTCAGCCATGCCAATGGCTGCATGCA AAGAAGCGGCCTCTTCTTCACTTAAGCATTTCCCCCAAAGGAAAACATCCATAATATGCATCTT TGATTCGACGCCATCACTATCTGATCTCCCGAATGCATCAACATCTATAGGTGGCCTAACACCC AACCAAACTTCAGCTCCTTGTTCCCAAATGGCACTGCCAATACTTAGAGGTAACCCATTCTGGT AGCCATCAAACCCACCATCTATGTAACAAGTAGCTTCCCCCGCATCAGCATCAATTGTGATTGT CACTGTATGCCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.498638351

Conservation Information
Conserved circRNAs	NA
PMCS	0.498638351

			
						 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 AT1G55350_circ_g.5

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