Plant Circular RNA Database

Detail information of AT1G01100_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT1G01100_circ_g.1
					
						ID in PlantcircBase
						ath_circ_000018
					
						Alias
						1:50419-50631
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 50419-50631  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G01100						
					
						Parent gene annotation
						
							60S acidic ribosomal protein P1-1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G01100_circ_g.2 AT1G01100_circ_g.3 						
					
						Support reads
						1/1
					
						Tissues
						leaf;flower
					
						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
						AT1G01100.4:1
AT1G01100.1:1
AT1G01100.3:2
AT1G01100.2:1

General Information
CircRNA Name	AT1G01100_circ_g.1
ID in PlantcircBase	ath_circ_000018
Alias	1:50419-50631
Organism	Arabidpsis thaliana
Position	chr1: 50419-50631 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G01100
Parent gene annotation	60S acidic ribosomal protein P1-1
Parent gene strand	-
Alternative splicing	AT1G01100_circ_g.2 AT1G01100_circ_g.3
Support reads	1/1
Tissues	leaf;flower
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	AT1G01100.4:1 AT1G01100.1:1 AT1G01100.3:2 AT1G01100.2:1

			
						 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  
						
							CAGTCACGTTACGTTTCTCAGCCATCTTGGCGAATAGCATTGGCCAGTATGACTCAATACTAAC
ACCAGCAGCTTTCACCAAGGTCGCGATTTTGTCAGCcttcttcttctcctcagcagcaggagca
gctgccgcaccaccgccagcagctggagcagcagctgcaaccggagcaccacctccaccaccag
caccaacg

						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: 165
Transcript exons: 50419-50447,50496-50631
CTTCTTCTTCTCCTCAGCAGCAGGAGCAGCACCTCCACCACCAGCACCAACGTTCATGATGAGA
TCAGTCACGTTACGTTTCTCAGCCATCTTGGCGAATAGCATTGGCCAGTATGACTCAATACTAA
CACCAGCAGCTTTCACCAAGGTCGCGATTTTGTCAGC
Transcript length: 213
Transcript exons: 50419-50631
CTTCTTCTTCTCCTCAGCAGCAGGAGCAGCTGCCGCACCACCGCCAGCAGCTGGAGCAGCAGCT
GCAACCGGAGCACCACCTCCACCACCAGCACCAACGTTCATGATGAGATCAGTCACGTTACGTT
TCTCAGCCATCTTGGCGAATAGCATTGGCCAGTATGACTCAATACTAACACCAGCAGCTTTCAC
CAAGGTCGCGATTTTGTCAGC
						
						Genomic sequence
						
							CTTCTTCTTCTCCTCAGCAGCAGGAGCAGCTGCCGCACCACCGCCAGCAGCTGGAGCAGCAGCT
GCAACCGGAGCACCACCTCCACCACCAGCACCAACGTTCATGATGAGATCAGTCACGTTACGTT
TCTCAGCCATCTTGGCGAATAGCATTGGCCAGTATGACTCAATACTAACACCAGCAGCTTTCAC
CAAGGTCGCGATTTTGTCAGC

Sequences
Splice junction sequence	CAGTCACGTTACGTTTCTCAGCCATCTTGGCGAATAGCATTGGCCAGTATGACTCAATACTAAC ACCAGCAGCTTTCACCAAGGTCGCGATTTTGTCAGCcttcttcttctcctcagcagcaggagca gctgccgcaccaccgccagcagctggagcagcagctgcaaccggagcaccacctccaccaccag caccaacg
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: 165 Transcript exons: 50419-50447,50496-50631 CTTCTTCTTCTCCTCAGCAGCAGGAGCAGCACCTCCACCACCAGCACCAACGTTCATGATGAGA TCAGTCACGTTACGTTTCTCAGCCATCTTGGCGAATAGCATTGGCCAGTATGACTCAATACTAA CACCAGCAGCTTTCACCAAGGTCGCGATTTTGTCAGC Transcript length: 213 Transcript exons: 50419-50631 CTTCTTCTTCTCCTCAGCAGCAGGAGCAGCTGCCGCACCACCGCCAGCAGCTGGAGCAGCAGCT GCAACCGGAGCACCACCTCCACCACCAGCACCAACGTTCATGATGAGATCAGTCACGTTACGTT TCTCAGCCATCTTGGCGAATAGCATTGGCCAGTATGACTCAATACTAACACCAGCAGCTTTCAC CAAGGTCGCGATTTTGTCAGC
Genomic sequence	CTTCTTCTTCTCCTCAGCAGCAGGAGCAGCTGCCGCACCACCGCCAGCAGCTGGAGCAGCAGCT GCAACCGGAGCACCACCTCCACCACCAGCACCAACGTTCATGATGAGATCAGTCACGTTACGTT TCTCAGCCATCTTGGCGAATAGCATTGGCCAGTATGACTCAATACTAACACCAGCAGCTTTCAC CAAGGTCGCGATTTTGTCAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.467478124

Conservation Information
Conserved circRNAs	NA
PMCS	0.467478124

			
						 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 AT1G01100_circ_g.1

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