Plant Circular RNA Database

Detail information of 3_circ_ig.11

			
						 General Information
					
						CircRNA Name
						3_circ_ig.11
					
						ID in PlantcircBase
						ath_circ_024190
					
						Alias
						3:10486190-10487122
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 10486190-10487122  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							3_circ_igg.2 3_circ_igg.3 3_circ_ig.4 3_circ_ig.5 3_circ_igg.6 3_circ_igg.7 3_circ_igg.8 3_circ_igg.9 3_circ_igg.10 						
					
						Support reads
						1/1
					
						Tissues
						seedling;root
					
						Exon boundary  
						
							NA-NA							"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_ig.11
ID in PlantcircBase	ath_circ_024190
Alias	3:10486190-10487122
Organism	Arabidpsis thaliana
Position	chr3: 10486190-10487122 JBrowse»
Reference genome	TAIR10.38
Type	ig-circRNA
Identification method	find_circ; CIRI2
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	3_circ_igg.2 3_circ_igg.3 3_circ_ig.4 3_circ_ig.5 3_circ_igg.6 3_circ_igg.7 3_circ_igg.8 3_circ_igg.9 3_circ_igg.10
Support reads	1/1
Tissues	seedling;root
Exon boundary	NA-NA "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  
						
							CTCACATTTTTTCTCATTTTAACCTGGAGCTGCACCTGCACACAACAACCGACCAAGATTTCCT
CTGACTTGTCTAGTTCTTCTAGAACTTCTATCTCTTcagttccatttggttggatacgtttatt
agccccttccagaattttattacagcttcaattggatccaaacgtatctacaaaaatttaaaac
actcagtt

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							CAGTTCCATTTGGTTGGATACGTTTATTAGCCCCTTCCAGAATTTTATTACAGCTTCAATTGGA
TCCAAACGTATCTACAAAAATTTAAAACACTCAGTTTCAACTCTACAGCTTAGAATAATTTTTT
CACAAAAGAATTGTTAGCAACAAAAAAAGATTTCAAAATCAGGAATCTCAAAGCCTTTTTACCG
ACGTCTATCTAACTCTCTTCGGTGCCGCAGTCCCCTGATGAACAACAGACAAGTAAAAACAAGA
AATCTAAAAGACCATCCACAAAAATGAACCAAACAAACACATGTTAGGCAAAGCAGAAGTAGCT
TAAAAGGAATTCGTAAGTTTCAAAAGTGAGACACCAAAGTCATCAACTGCCGAAACAATCCAGA
ATAAGCCTTCACTATGAACCTTGGGATTGTTGTGCTCTTTCATGATTCTGCAAAGCTACAAACA
AAAGTCATGAATCATCATTGTGATCAGATTAAAATGAAAGTCGATAGAAAATTTACCGAACCAG
CACAAACCCTTTCGATCAGCTGCTTCACAAAAAGAAGTAGGCCACTTCATTGTAGAGGCTCATA
TCTTTATATCTGAAACTGAGCCAAGAAAGAATTTTGTAAGAAAAAGATAAAACTGACGTCTAAA
TACAGCATTCAGTTTCTAAAAGTTACTTTTTCTTCTTCTATTACTAACCTGTAATGCAAAGTAT
GACACATTTCTTTTGCCGCAGTTGAAGATATGAGTGATGATTTGCAGAACCTGCTTTTCCAAGT
AATATTCTCAGGGAATAATTCGATAATTACATATAAGAAGATTTTAAATGGAGTAACAAGCATA
CCTCACATTTTTTCTCATTTTAACCTGGAGCTGCACCTGCACACAACAACCGACCAAGATTTCC
TCTGACTTGTCTAGTTCTTCTAGAACTTCTATCTCTT

Sequences
Splice junction sequence	CTCACATTTTTTCTCATTTTAACCTGGAGCTGCACCTGCACACAACAACCGACCAAGATTTCCT CTGACTTGTCTAGTTCTTCTAGAACTTCTATCTCTTcagttccatttggttggatacgtttatt agccccttccagaattttattacagcttcaattggatccaaacgtatctacaaaaatttaaaac actcagtt
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CAGTTCCATTTGGTTGGATACGTTTATTAGCCCCTTCCAGAATTTTATTACAGCTTCAATTGGA TCCAAACGTATCTACAAAAATTTAAAACACTCAGTTTCAACTCTACAGCTTAGAATAATTTTTT CACAAAAGAATTGTTAGCAACAAAAAAAGATTTCAAAATCAGGAATCTCAAAGCCTTTTTACCG ACGTCTATCTAACTCTCTTCGGTGCCGCAGTCCCCTGATGAACAACAGACAAGTAAAAACAAGA AATCTAAAAGACCATCCACAAAAATGAACCAAACAAACACATGTTAGGCAAAGCAGAAGTAGCT TAAAAGGAATTCGTAAGTTTCAAAAGTGAGACACCAAAGTCATCAACTGCCGAAACAATCCAGA ATAAGCCTTCACTATGAACCTTGGGATTGTTGTGCTCTTTCATGATTCTGCAAAGCTACAAACA AAAGTCATGAATCATCATTGTGATCAGATTAAAATGAAAGTCGATAGAAAATTTACCGAACCAG CACAAACCCTTTCGATCAGCTGCTTCACAAAAAGAAGTAGGCCACTTCATTGTAGAGGCTCATA TCTTTATATCTGAAACTGAGCCAAGAAAGAATTTTGTAAGAAAAAGATAAAACTGACGTCTAAA TACAGCATTCAGTTTCTAAAAGTTACTTTTTCTTCTTCTATTACTAACCTGTAATGCAAAGTAT GACACATTTCTTTTGCCGCAGTTGAAGATATGAGTGATGATTTGCAGAACCTGCTTTTCCAAGT AATATTCTCAGGGAATAATTCGATAATTACATATAAGAAGATTTTAAATGGAGTAACAAGCATA CCTCACATTTTTTCTCATTTTAACCTGGAGCTGCACCTGCACACAACAACCGACCAAGATTTCC TCTGACTTGTCTAGTTCTTCTAGAACTTCTATCTCTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.175152528

Conservation Information
Conserved circRNAs	NA
PMCS	0.175152528

			
						 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 3_circ_ig.11

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