Plant Circular RNA Database

Detail information of 3_circ_ag.4

			
						 General Information
					
						CircRNA Name
						3_circ_ag.4
					
						ID in PlantcircBase
						ath_circ_020388
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 2497918-2503284  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRI, find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							3_circ_ag.3 						
					
						Support reads
						17
					
						Tissues
						inflorescences
					
						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
						NA

General Information
CircRNA Name	3_circ_ag.4
ID in PlantcircBase	ath_circ_020388
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 2497918-2503284 JBrowse»
Reference genome	TAIR10.38
Type	ag-circRNA
Identification method	CIRI, find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	3_circ_ag.3
Support reads	17
Tissues	inflorescences
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	NA

			
						 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  
						
							CCGTCATCTCGATCTCACCAAGCTTGAACTCACCCTTTGTGATCACCACCTTGCTCGCTGTCGG
AGCTTGGCATGCTGATGTGAATGCTTTCAGAAGTGCctgagtaatatcagaacctgatgaagaa
ccaatggtgaatacctcagcattggctgaaattcccaacaaacagataataaaaattgtagaaa
ctccaaaa

						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: 382
Transcript exons: 2497918-2498082,2500159-2500350,2503260-2503284
CTGAGTAATATCAGAACCTGATGAAGAACCAATGGTGAATACCTCAGCATTGGCTGAAATTCCC
AACAAACAGATAATAAAAATTGTAGAAACTCCAAAATATCCACCCATTTTTTCCCCAAAAAAAT
AAAAAAATTACTACTAATATTACTATTTGTTATTCTAGTTGATAATGGAGACCCCGACACTTCT
TCCCAAGTGGATCCCGTCAGTGTTGGGGCTCTCTGCTGGAGCCATGATCTTGACGTTGTCAAAG
GTCATGTTCTTGGCGCCAATCACGTTGATGTGAAAGTTCTTGGCATCGATTGAGGATATGTCTC
TGATCTCAGCGTTCGTCACGAAATCAAACCTTATACTCTGATGTGAATGCTTTCAGAAGTGC
Transcript length: 484
Transcript exons: 2497918-2498089,2500146-2500350,2500439-2500488,2500715-
2500747,2503261-2503284
CTGAGTAATATCAGAACCTGATGAAGAACCAATGGTGAATACCTCAGCATTGGCTGAAATTCCC
AACAAACAGATAATAAAAATTGTAGAAACTCCAAAATATCCACCCATTTTTTCCCCAAAAAAAT
AAAAAAATTACTACTAATATTACTATTTGTTATTCTATTTTTTGTGGAGATCCTAGAGTTGATA
ATGGAGACCCCGACACTTCTTCCCAAGTGGATCCCGTCAGTGTTGGGGCTCTCTGCTGGAGCCA
TGATCTTGACGTTGTCAAAGGTCATGTTCTTGGCGCCAATCACGTTGATGTGAAAGTTCTTGGC
ATCGATTGAGGATATGTCTCTGATCTCAGCGTTCGTCACGAAATCAAACCTTATACTGATGGGA
AGTTTCTTGCACTCGAAAGTCTTGTGACAGTTATTGACCCTCCGCATGCCGTTGTGAATGCTCT
CAGAAGCGCCTGTGATGTGAATGCTTTCAGAAGTGC
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CCGTCATCTCGATCTCACCAAGCTTGAACTCACCCTTTGTGATCACCACCTTGCTCGCTGTCGG AGCTTGGCATGCTGATGTGAATGCTTTCAGAAGTGCctgagtaatatcagaacctgatgaagaa ccaatggtgaatacctcagcattggctgaaattcccaacaaacagataataaaaattgtagaaa ctccaaaa
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: 382 Transcript exons: 2497918-2498082,2500159-2500350,2503260-2503284 CTGAGTAATATCAGAACCTGATGAAGAACCAATGGTGAATACCTCAGCATTGGCTGAAATTCCC AACAAACAGATAATAAAAATTGTAGAAACTCCAAAATATCCACCCATTTTTTCCCCAAAAAAAT AAAAAAATTACTACTAATATTACTATTTGTTATTCTAGTTGATAATGGAGACCCCGACACTTCT TCCCAAGTGGATCCCGTCAGTGTTGGGGCTCTCTGCTGGAGCCATGATCTTGACGTTGTCAAAG GTCATGTTCTTGGCGCCAATCACGTTGATGTGAAAGTTCTTGGCATCGATTGAGGATATGTCTC TGATCTCAGCGTTCGTCACGAAATCAAACCTTATACTCTGATGTGAATGCTTTCAGAAGTGC Transcript length: 484 Transcript exons: 2497918-2498089,2500146-2500350,2500439-2500488,2500715- 2500747,2503261-2503284 CTGAGTAATATCAGAACCTGATGAAGAACCAATGGTGAATACCTCAGCATTGGCTGAAATTCCC AACAAACAGATAATAAAAATTGTAGAAACTCCAAAATATCCACCCATTTTTTCCCCAAAAAAAT AAAAAAATTACTACTAATATTACTATTTGTTATTCTATTTTTTGTGGAGATCCTAGAGTTGATA ATGGAGACCCCGACACTTCTTCCCAAGTGGATCCCGTCAGTGTTGGGGCTCTCTGCTGGAGCCA TGATCTTGACGTTGTCAAAGGTCATGTTCTTGGCGCCAATCACGTTGATGTGAAAGTTCTTGGC ATCGATTGAGGATATGTCTCTGATCTCAGCGTTCGTCACGAAATCAAACCTTATACTGATGGGA AGTTTCTTGCACTCGAAAGTCTTGTGACAGTTATTGACCCTCCGCATGCCGTTGTGAATGCTCT CAGAAGCGCCTGTGATGTGAATGCTTTCAGAAGTGC
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.372990026

Conservation Information
Conserved circRNAs	NA
PMCS	0.372990026

			
						 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

circRNA

Detail information of 3_circ_ag.4

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