Plant Circular RNA Database

Detail information of 4_circ_ig.3

			
						 General Information
					
						CircRNA Name
						4_circ_ig.3
					
						ID in PlantcircBase
						ath_circ_029910
					
						Alias
						Chr4:5059539|5060151
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 5059539-5060151  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						CIRCexplorer; CIRI
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							4_circ_ig.4 4_circ_ig.5 						
					
						Support reads
						12
					
						Tissues
						seedling
					
						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-TA							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	4_circ_ig.3
ID in PlantcircBase	ath_circ_029910
Alias	Chr4:5059539\|5060151
Organism	Arabidpsis thaliana
Position	chr4: 5059539-5060151 JBrowse»
Reference genome	TAIR10.38
Type	ig-circRNA
Identification method	CIRCexplorer; CIRI
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	4_circ_ig.4 4_circ_ig.5
Support reads	12
Tissues	seedling
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-TA 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  
						
							TTACTCTCATCATGCGATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGT
TGCATCCCTGCTGTTACTCCAGCTGTTATTCATTTCcctcagtagaatgttctggagatgtagt
catccatatctgcttgagtgtactcagcaagcatgaccggttcttgatgtggctccgccatctc
ctcgtcat

						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
						
							CCTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGA
CCGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTG
TGAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACCCTTAATTGATGAATGTACA
GTTCTAGCACTCTTCCTCCTCTTGTGTTCCATTGGCTCATGAGACGAGTGCCTTGCGGAAACTT
GTGGAACGGTGTGGTCCCTTTGTTGATAGGTGGATTGCCTTGGTGGGAGAAAGTCGTGGCAGCT
GGATGGCATGTCTTCAGGCGGGTTGTCATTGAAGTCCTGTCGGGCATTTTCACTTCTCCTTGCG
ATTGAGTGGTTTGGGCAATTCCACTAAGAGACCACTCGATCACACCACTTCCATGTTGCGATCG
AGTAGTTTGACATTTTTGTTGAGAAAGATGTTGTCCCAAAACCAGTAGATCGCACTCTCGAGCT
TTTACTCTCATCATGCGATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGG
TTGCATCCCTGCTGTTACTCCAGCTGTTATTCATTTC

Sequences
Splice junction sequence	TTACTCTCATCATGCGATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGT TGCATCCCTGCTGTTACTCCAGCTGTTATTCATTTCcctcagtagaatgttctggagatgtagt catccatatctgcttgagtgtactcagcaagcatgaccggttcttgatgtggctccgccatctc ctcgtcat
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	CCTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGA CCGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTG TGAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACCCTTAATTGATGAATGTACA GTTCTAGCACTCTTCCTCCTCTTGTGTTCCATTGGCTCATGAGACGAGTGCCTTGCGGAAACTT GTGGAACGGTGTGGTCCCTTTGTTGATAGGTGGATTGCCTTGGTGGGAGAAAGTCGTGGCAGCT GGATGGCATGTCTTCAGGCGGGTTGTCATTGAAGTCCTGTCGGGCATTTTCACTTCTCCTTGCG ATTGAGTGGTTTGGGCAATTCCACTAAGAGACCACTCGATCACACCACTTCCATGTTGCGATCG AGTAGTTTGACATTTTTGTTGAGAAAGATGTTGTCCCAAAACCAGTAGATCGCACTCTCGAGCT TTTACTCTCATCATGCGATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGG TTGCATCCCTGCTGTTACTCCAGCTGTTATTCATTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.124681104

Conservation Information
Conserved circRNAs	NA
PMCS	0.124681104

			
						 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
						responsive to methyl jasmonate

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	responsive to methyl jasmonate

			
						 Other Information
					
						References
						Zhang et al., 2020

circRNA

Detail information of 4_circ_ig.3

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