Plant Circular RNA Database

Detail information of AT4G12460_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT4G12460_circ_g.1
					
						ID in PlantcircBase
						ath_circ_030555
					
						Alias
						4:7392688-7394557
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 7392688-7394557  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G12460						
					
						Parent gene annotation
						
							OSBP(oxysterol binding protein)-related protein 2B
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G12460_circ_g.2 AT4G12460_circ_g.3 AT4G12460_circ_g.4 						
					
						Support reads
						2
					
						Tissues
						leaf
					
						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  
						
							GT-AG							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
						AT4G12460.8:4
AT4G12460.9:4
AT4G12460.6:4
AT4G12460.2:4
AT4G12460.4:4
AT4G12460.5:4
AT4G12460.3:4
AT4G12460.1:4
AT4G12460.7:4

General Information
CircRNA Name	AT4G12460_circ_g.1
ID in PlantcircBase	ath_circ_030555
Alias	4:7392688-7394557
Organism	Arabidpsis thaliana
Position	chr4: 7392688-7394557 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G12460
Parent gene annotation	OSBP(oxysterol binding protein)-related protein 2B
Parent gene strand	+
Alternative splicing	AT4G12460_circ_g.2 AT4G12460_circ_g.3 AT4G12460_circ_g.4
Support reads	2
Tissues	leaf
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	GT-AG 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	AT4G12460.8:4 AT4G12460.9:4 AT4G12460.6:4 AT4G12460.2:4 AT4G12460.4:4 AT4G12460.5:4 AT4G12460.3:4 AT4G12460.1:4 AT4G12460.7:4

			
						 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  
						
							TTCCACCGAAGGACGACACTGTAAACCTTTCAACCCTTTGCTCGGAGAAACATATGAAGCTGAC
TTTCCTGAAAAGGGAATTCGTTTCTTCTCTGAGAAGcaggtttcatcttaccgagaaagcaagt
ctgatcatagaaagttttatatctttactgcaaccaagactctgcatctgaggactgattctag
aagtgata

									
								

					

						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: 954
Transcript exons: 7392688-7393053,7393489-7393585,7393842-7394176,7394402-
7394557
CAGGTTTCATCTTACCGAGAAAGCAAGTCTGATCATAGAAAGTTTTATATCTTTACTGCAACCA
AGACTCTGCATCTGAGGACTGATTCTAGAAGTGATAGAGCAGCATGGTTACAAGCTTTAGCATC
TACCAGGGGCATAGTTCCTCTCCAGTCAATTAATGGGGATTTCTCCTTCGTATCACCAAAGGAT
TTATCCATATCTACCGAGAGACTAAAGAAACGGTTGTTTGAAGAGGGAATGAACGAGAGTCTTG
TAAAAGAGTGCGAGCAGATCGTGGATTCAGAGTTCTGTGAAGTTCAAGAACAGATTAAACTTCT
TCACGAAGAGCGGAAAAAGTTGCTTGATGCTTTGAGGCAGCTAGAGATGGCCAACCTTGAAGCT
GAAGCCTCAGGGATCCATGACGATGTCTACCAATTAAGAAATCACAAGTATTCCAGCTTAGGAC
GTGGAAAATATAGTGAATGCAGTACAAGTGCTTCATCTGATGATAAGCAAGAGTTTGAGGATAT
CTCTGAGGAAGACGAGGCTTCCTTCCATGACACAAAGGAGTCATTTGGTGAACCTGATGTTGGT
TCTGTGCTCACGCATTTTAAGAGACGAACAAAGCTTCCTGATCCAGCAGAGAAAGAGAGAGGTG
TCAGTCTCTGGTCTATGATCAAAGACAATGTTGGAAAGGATCTCACACGAGTTTGTCTTCCTGT
TTATTTCAATGAACCAATATCTTCCCTCCAAAAGTGTTTTGAAGACTTGGAGTACTCTTATCTC
TTGGACCAAGCATATGAATACGGAAAATCCGGGAAGAGTCTCCTTAGAGCCCTCAATGTCGCTG
CTTTTGCAGTCTCTGGTTATGCTTCCACCGAAGGACGACACTGTAAACCTTTCAACCCTTTGCT
CGGAGAAACATATGAAGCTGACTTTCCTGAAAAGGGAATTCGTTTCTTCTCTGAGAAG
						
					

						Genomic sequence
						
							CAGGTTTCATCTTACCGAGAAAGCAAGTCTGATCATAGAAAGTTTTATATCTTTACTGCAACCA
AGACTCTGCATCTGAGGACTGATTCTAGAAGTGATAGAGCAGCATGGTTACAAGCTTTAGCATC
TACCAGGGGCATAGTTCCTCTCCAGTCAATTAATGGGGATTTCTCCTTCGTATCACCAAAGGAT
TTATCCATATCTACCGAGAGACTAAAGAAACGGTTGTTTGAAGAGGGAATGAACGAGAGTCTTG
TAAAAGAGTGCGAGCAGATCGTGGATTCAGAGTTCTGTGAAGTTCAAGAACAGATTAAACTTCT
TCACGAAGAGCGGAAAAAGTTGCTTGATGCTTTGAGGCAGCTAGAGGTAAAGCTGAATTTTTGG
TCTTCTTTTATGATCGTTTTGGTTTGGTTGAGCTGTTTAGTGTGGTCTCGGTCATTGTTTCCTT
TCATATAATGACTTAGTATTCCACGGGCTTTACAGTGCAGTTGCATTGGTAACAGCGAGTCTAT
GCACAAAGGCATGCTAGTTTATTTGTCATGTAATCACGAACGGGACGGTTATTTTAATATATGT
TTTACATTCTTTTATCTCCATTCATGTGGATATTTTGTTAATTGAGTTGATAATTTCTGAACTT
CATATATCCATGCCTAGGCATAACACAAAAATTATGTATCATGCATTAAAAACTTGAATGTCAA
GTTATGATTATTATGAATCTTGCGAAAGATCCCTCCCCGCTTTTTATAATTCTGTTATTTGTTG
GCTATTCTACACTGAGAGTTTCTTTATGTACAGATGGCCAACCTTGAAGCTGAAGCCTCAGGGA
TCCATGACGATGTCTACCAATTAAGAAATCACAAGTATTCCAGCTTAGGACGTGGAAAATATAG
TGGTACACAAAATTTCTATCGCGTAATTGTTCTTTTATTCACTGCATCTCTTTCTCTTTCTCTG
TTTTAGTTTTGCCATTAAATATTGATGAAGCCAGCTGGCGAGGATCTCGTTACTGCATAGTAGA
ACAATAATTTCTGATACGATATTCAATTATTTGTTTCCTAAATTTTCCTCCTTATGCTTCTTTT
ACATAGCTTCAGTGGAGTTGCATTTAGCTTCCTGTGTTGTTTTGCTTGACAATATTTAATTTCT
AGAATGCAGTACAAGTGCTTCATCTGATGATAAGCAAGAGTTTGAGGATATCTCTGAGGAAGAC
GAGGCTTCCTTCCATGACACAAAGGAGTCATTTGGTGAACCTGATGTTGGTTCTGTGCTCACGC
ATTTTAAGAGACGAACAAAGCTTCCTGATCCAGCAGAGAAAGAGAGAGGTGTCAGTCTCTGGTC
TATGATCAAAGACAATGTTGGAAAGGATCTCACACGAGTTTGTCTTCCTGTTTATTTCAATGAA
CCAATATCTTCCCTCCAAAAGTGTTTTGAAGACTTGGAGTACTCTTATCTCTTGGACCAAGCAT
ATGAATACGGAAAATCCGTAAGTGATTTCAAAAAACTTACTGTTGTATGTAATTCGCTTCCTTC
TGGAAATGCAAACGTTTTCTCTACTCTTAACTTTTATTTAATTCCAATTACTAAAGTAATTTAA
CTACATAGTTTGAGCTTCTATGCTCTTGCATGATATGATATGTGGTCTATACTTATCTTTTTAT
CTTAAATTGACCTCTCAGTTTGTTATATTAACAGAGTTTTTCATCATCAGGGGAAGAGTCTCCT
TAGAGCCCTCAATGTCGCTGCTTTTGCAGTCTCTGGTTATGCTTCCACCGAAGGACGACACTGT
AAACCTTTCAACCCTTTGCTCGGAGAAACATATGAAGCTGACTTTCCTGAAAAGGGAATTCGTT
TCTTCTCTGAGAAG
						
					

			
		

Sequences
Splice junction sequence	TTCCACCGAAGGACGACACTGTAAACCTTTCAACCCTTTGCTCGGAGAAACATATGAAGCTGAC TTTCCTGAAAAGGGAATTCGTTTCTTCTCTGAGAAGcaggtttcatcttaccgagaaagcaagt ctgatcatagaaagttttatatctttactgcaaccaagactctgcatctgaggactgattctag aagtgata
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: 954 Transcript exons: 7392688-7393053,7393489-7393585,7393842-7394176,7394402- 7394557 CAGGTTTCATCTTACCGAGAAAGCAAGTCTGATCATAGAAAGTTTTATATCTTTACTGCAACCA AGACTCTGCATCTGAGGACTGATTCTAGAAGTGATAGAGCAGCATGGTTACAAGCTTTAGCATC TACCAGGGGCATAGTTCCTCTCCAGTCAATTAATGGGGATTTCTCCTTCGTATCACCAAAGGAT TTATCCATATCTACCGAGAGACTAAAGAAACGGTTGTTTGAAGAGGGAATGAACGAGAGTCTTG TAAAAGAGTGCGAGCAGATCGTGGATTCAGAGTTCTGTGAAGTTCAAGAACAGATTAAACTTCT TCACGAAGAGCGGAAAAAGTTGCTTGATGCTTTGAGGCAGCTAGAGATGGCCAACCTTGAAGCT GAAGCCTCAGGGATCCATGACGATGTCTACCAATTAAGAAATCACAAGTATTCCAGCTTAGGAC GTGGAAAATATAGTGAATGCAGTACAAGTGCTTCATCTGATGATAAGCAAGAGTTTGAGGATAT CTCTGAGGAAGACGAGGCTTCCTTCCATGACACAAAGGAGTCATTTGGTGAACCTGATGTTGGT TCTGTGCTCACGCATTTTAAGAGACGAACAAAGCTTCCTGATCCAGCAGAGAAAGAGAGAGGTG TCAGTCTCTGGTCTATGATCAAAGACAATGTTGGAAAGGATCTCACACGAGTTTGTCTTCCTGT TTATTTCAATGAACCAATATCTTCCCTCCAAAAGTGTTTTGAAGACTTGGAGTACTCTTATCTC TTGGACCAAGCATATGAATACGGAAAATCCGGGAAGAGTCTCCTTAGAGCCCTCAATGTCGCTG CTTTTGCAGTCTCTGGTTATGCTTCCACCGAAGGACGACACTGTAAACCTTTCAACCCTTTGCT CGGAGAAACATATGAAGCTGACTTTCCTGAAAAGGGAATTCGTTTCTTCTCTGAGAAG
Genomic sequence	CAGGTTTCATCTTACCGAGAAAGCAAGTCTGATCATAGAAAGTTTTATATCTTTACTGCAACCA AGACTCTGCATCTGAGGACTGATTCTAGAAGTGATAGAGCAGCATGGTTACAAGCTTTAGCATC TACCAGGGGCATAGTTCCTCTCCAGTCAATTAATGGGGATTTCTCCTTCGTATCACCAAAGGAT TTATCCATATCTACCGAGAGACTAAAGAAACGGTTGTTTGAAGAGGGAATGAACGAGAGTCTTG TAAAAGAGTGCGAGCAGATCGTGGATTCAGAGTTCTGTGAAGTTCAAGAACAGATTAAACTTCT TCACGAAGAGCGGAAAAAGTTGCTTGATGCTTTGAGGCAGCTAGAGGTAAAGCTGAATTTTTGG TCTTCTTTTATGATCGTTTTGGTTTGGTTGAGCTGTTTAGTGTGGTCTCGGTCATTGTTTCCTT TCATATAATGACTTAGTATTCCACGGGCTTTACAGTGCAGTTGCATTGGTAACAGCGAGTCTAT GCACAAAGGCATGCTAGTTTATTTGTCATGTAATCACGAACGGGACGGTTATTTTAATATATGT TTTACATTCTTTTATCTCCATTCATGTGGATATTTTGTTAATTGAGTTGATAATTTCTGAACTT CATATATCCATGCCTAGGCATAACACAAAAATTATGTATCATGCATTAAAAACTTGAATGTCAA GTTATGATTATTATGAATCTTGCGAAAGATCCCTCCCCGCTTTTTATAATTCTGTTATTTGTTG GCTATTCTACACTGAGAGTTTCTTTATGTACAGATGGCCAACCTTGAAGCTGAAGCCTCAGGGA TCCATGACGATGTCTACCAATTAAGAAATCACAAGTATTCCAGCTTAGGACGTGGAAAATATAG TGGTACACAAAATTTCTATCGCGTAATTGTTCTTTTATTCACTGCATCTCTTTCTCTTTCTCTG TTTTAGTTTTGCCATTAAATATTGATGAAGCCAGCTGGCGAGGATCTCGTTACTGCATAGTAGA ACAATAATTTCTGATACGATATTCAATTATTTGTTTCCTAAATTTTCCTCCTTATGCTTCTTTT ACATAGCTTCAGTGGAGTTGCATTTAGCTTCCTGTGTTGTTTTGCTTGACAATATTTAATTTCT AGAATGCAGTACAAGTGCTTCATCTGATGATAAGCAAGAGTTTGAGGATATCTCTGAGGAAGAC GAGGCTTCCTTCCATGACACAAAGGAGTCATTTGGTGAACCTGATGTTGGTTCTGTGCTCACGC ATTTTAAGAGACGAACAAAGCTTCCTGATCCAGCAGAGAAAGAGAGAGGTGTCAGTCTCTGGTC TATGATCAAAGACAATGTTGGAAAGGATCTCACACGAGTTTGTCTTCCTGTTTATTTCAATGAA CCAATATCTTCCCTCCAAAAGTGTTTTGAAGACTTGGAGTACTCTTATCTCTTGGACCAAGCAT ATGAATACGGAAAATCCGTAAGTGATTTCAAAAAACTTACTGTTGTATGTAATTCGCTTCCTTC TGGAAATGCAAACGTTTTCTCTACTCTTAACTTTTATTTAATTCCAATTACTAAAGTAATTTAA CTACATAGTTTGAGCTTCTATGCTCTTGCATGATATGATATGTGGTCTATACTTATCTTTTTAT CTTAAATTGACCTCTCAGTTTGTTATATTAACAGAGTTTTTCATCATCAGGGGAAGAGTCTCCT TAGAGCCCTCAATGTCGCTGCTTTTGCAGTCTCTGGTTATGCTTCCACCGAAGGACGACACTGT AAACCTTTCAACCCTTTGCTCGGAGAAACATATGAAGCTGACTTTCCTGAAAAGGGAATTCGTT TCTTCTCTGAGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.218587547

Conservation Information
Conserved circRNAs	NA
PMCS	0.218587547

			
						 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 AT4G12460_circ_g.1

Address

Any questions?

Supported by