Plant Circular RNA Database

Detail information of AT5G37475_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G37475_circ_g.1
					
						ID in PlantcircBase
						ath_circ_041344
					
						Alias
						5:14866574-14867806
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 14866574-14867806  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G37475						
					
						Parent gene annotation
						
							Eukaryotic translation initiation factor 3 subunit J
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G37475_circ_g.2 AT5G37475_circ_g.3 AT5G37475_circ_g.4 AT5G37475_circ_g.5 						
					
						Support reads
						1/1
					
						Tissues
						root
					
						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
						AT5G37475.3:5
AT5G37475.1:5
AT5G37475.2:5

General Information
CircRNA Name	AT5G37475_circ_g.1
ID in PlantcircBase	ath_circ_041344
Alias	5:14866574-14867806
Organism	Arabidpsis thaliana
Position	chr5: 14866574-14867806 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G37475
Parent gene annotation	Eukaryotic translation initiation factor 3 subunit J
Parent gene strand	-
Alternative splicing	AT5G37475_circ_g.2 AT5G37475_circ_g.3 AT5G37475_circ_g.4 AT5G37475_circ_g.5
Support reads	1/1
Tissues	root
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	AT5G37475.3:5 AT5G37475.1:5 AT5G37475.2:5

			
						 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  
						
							GTATTGAACAATTCTTAATGTAAGTCTTACCCCAATCATCCATATGTGTCGCCGATTATCTAGA
AGAAGTACAAGCTGCTATCTGAATCCAACTGAAAACctgacttctttttgccagcagcagcttc
tttctccgccttcaatttttcatttgctatagctgtaatggacgaagcaacgtctttaacatct
gctgcttt

									
								

					

						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: 646
Transcript exons: 14866574-14866733,14866855-14867002,14867155-14867303,14
867398-14867516,14867737-14867806
CTGACTTCTTTTTGCCAGCAGCAGCTTCTTTCTCCGCCTTCAATTTTTCATTTGCTATAGCTGT
AATGGACGAAGCAACGTCTTTAACATCTGCTGCTTTCATATTAGCCACAGAAAGTCTCATCACT
GCTTTGAGTAGCCCGATATAGTGAAAGCTTTTCTCAAATGGTACAAGTCTCTGAGATATCAACT
CAGCATAATCCAAGAAATCGCTTTCAGACTTCGGAATTAACATATCGACGCTTTTCTCTTCAGT
CTTTACTCCAAAGAGTTCAGCAGTTGATTGGTAATCAGCTTCCTCTACAAGCCTCTGCATGCGA
AGTTTCTCAGCAATAGGATCTAGAGGTTCTTCCCTTGATGTTCCTTTCGGAGCTTCAACAGTTT
TAACCTTCTTTTCAACAGCTTTTACTGCTGGTTTCTTTGGAGCCTTCTCAGAAGCAGGCTTTAC
TATAGGTGGCGGAGCAGATACATCTTCCTCCTCCCACGAGTCCTTGATATCATTCTCATCCACA
TCCTCATCATCCCAGTTACTTTTCAGTTCAACTTTTGAGGGAAGTGGTTGAAAGTCCTCGGCCT
CCCAATCATCCATATGTGTCGCCGATTATCTAGAAGAAGTACAAGCTGCTATCTGAATCCAACT
GAAAAC
						
					

						Genomic sequence
						
							CTGACTTCTTTTTGCCAGCAGCAGCTTCTTTCTCCGCCTTCAATTTTTCATTTGCTATAGCTGT
AATGGACGAAGCAACGTCTTTAACATCTGCTGCTTTCATATTAGCCACAGAAAGTCTCATCACT
GCTTTGAGTAGCCCGATATAGTGAAAGCTTTTCTGCGAAATAGTAGACATAGTTAAAATGCAGA
CGAATTGGTCTTAATATGATATTTGGTCATATAGAAATAAGTGACAGTTAGCTAAGACAAGAAA
GTAACAGGAAATGAAAATAGCATACCTCAAATGGTACAAGTCTCTGAGATATCAACTCAGCATA
ATCCAAGAAATCGCTTTCAGACTTCGGAATTAACATATCGACGCTTTTCTCTTCAGTCTTTACT
CCAAAGAGTTCAGCAGTTGATTGGTAATCAGCTTCCTCTACAAGCCTAAGATAAGAAGAATATT
AAAAATTAGCACAATGGCCTTCCTCAGTGACATGCTTCTTACACTACTAGAAAACATTTTTCAT
CCCATTCAACCAAACCAATGCAGAACCAACAGTAGAAGCATATGTAAGTGAACTATTATTACAC
TCTACCTCTGCATGCGAAGTTTCTCAGCAATAGGATCTAGAGGTTCTTCCCTTGATGTTCCTTT
CGGAGCTTCAACAGTTTTAACCTTCTTTTCAACAGCTTTTACTGCTGGTTTCTTTGGAGCCTTC
TCAGAAGCAGGCTTTACTATAGGTGGCTACAGGAGAAACAAAGATTGTTAGCCGCAATCTCAAA
AACAAATAACAAACAAAACCCAATGACTAAAAGTATATAATGAAAGAAAAATATACCGGAGCAG
ATACATCTTCCTCCTCCCACGAGTCCTTGATATCATTCTCATCCACATCCTCATCATCCCAGTT
ACTTTTCAGTTCAACTTTTGAGGGAAGTGGTTGAAAGTCCTCGGCCTCTGAAATCAGAAAGGAA
AACCTAAAAGTGAGAATTCTAATATATTTCCCATATGAAAACTTCAATAAAACAACAATAAAGC
CTATCATCTTAGAGAACATAGTAAAATATATATAGCTGTATACAGCCTGTACTACTTTTTACAT
ATTCAAAGAGATTAATGCAACACCTAGAGAACAAGAAAGTATTGTGTATTGAACAATTCTTAAT
GTAAGTCTTACCCCAATCATCCATATGTGTCGCCGATTATCTAGAAGAAGTACAAGCTGCTATC
TGAATCCAACTGAAAAC
						
					

			
		

Sequences
Splice junction sequence	GTATTGAACAATTCTTAATGTAAGTCTTACCCCAATCATCCATATGTGTCGCCGATTATCTAGA AGAAGTACAAGCTGCTATCTGAATCCAACTGAAAACctgacttctttttgccagcagcagcttc tttctccgccttcaatttttcatttgctatagctgtaatggacgaagcaacgtctttaacatct gctgcttt
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: 646 Transcript exons: 14866574-14866733,14866855-14867002,14867155-14867303,14 867398-14867516,14867737-14867806 CTGACTTCTTTTTGCCAGCAGCAGCTTCTTTCTCCGCCTTCAATTTTTCATTTGCTATAGCTGT AATGGACGAAGCAACGTCTTTAACATCTGCTGCTTTCATATTAGCCACAGAAAGTCTCATCACT GCTTTGAGTAGCCCGATATAGTGAAAGCTTTTCTCAAATGGTACAAGTCTCTGAGATATCAACT CAGCATAATCCAAGAAATCGCTTTCAGACTTCGGAATTAACATATCGACGCTTTTCTCTTCAGT CTTTACTCCAAAGAGTTCAGCAGTTGATTGGTAATCAGCTTCCTCTACAAGCCTCTGCATGCGA AGTTTCTCAGCAATAGGATCTAGAGGTTCTTCCCTTGATGTTCCTTTCGGAGCTTCAACAGTTT TAACCTTCTTTTCAACAGCTTTTACTGCTGGTTTCTTTGGAGCCTTCTCAGAAGCAGGCTTTAC TATAGGTGGCGGAGCAGATACATCTTCCTCCTCCCACGAGTCCTTGATATCATTCTCATCCACA TCCTCATCATCCCAGTTACTTTTCAGTTCAACTTTTGAGGGAAGTGGTTGAAAGTCCTCGGCCT CCCAATCATCCATATGTGTCGCCGATTATCTAGAAGAAGTACAAGCTGCTATCTGAATCCAACT GAAAAC
Genomic sequence	CTGACTTCTTTTTGCCAGCAGCAGCTTCTTTCTCCGCCTTCAATTTTTCATTTGCTATAGCTGT AATGGACGAAGCAACGTCTTTAACATCTGCTGCTTTCATATTAGCCACAGAAAGTCTCATCACT GCTTTGAGTAGCCCGATATAGTGAAAGCTTTTCTGCGAAATAGTAGACATAGTTAAAATGCAGA CGAATTGGTCTTAATATGATATTTGGTCATATAGAAATAAGTGACAGTTAGCTAAGACAAGAAA GTAACAGGAAATGAAAATAGCATACCTCAAATGGTACAAGTCTCTGAGATATCAACTCAGCATA ATCCAAGAAATCGCTTTCAGACTTCGGAATTAACATATCGACGCTTTTCTCTTCAGTCTTTACT CCAAAGAGTTCAGCAGTTGATTGGTAATCAGCTTCCTCTACAAGCCTAAGATAAGAAGAATATT AAAAATTAGCACAATGGCCTTCCTCAGTGACATGCTTCTTACACTACTAGAAAACATTTTTCAT CCCATTCAACCAAACCAATGCAGAACCAACAGTAGAAGCATATGTAAGTGAACTATTATTACAC TCTACCTCTGCATGCGAAGTTTCTCAGCAATAGGATCTAGAGGTTCTTCCCTTGATGTTCCTTT CGGAGCTTCAACAGTTTTAACCTTCTTTTCAACAGCTTTTACTGCTGGTTTCTTTGGAGCCTTC TCAGAAGCAGGCTTTACTATAGGTGGCTACAGGAGAAACAAAGATTGTTAGCCGCAATCTCAAA AACAAATAACAAACAAAACCCAATGACTAAAAGTATATAATGAAAGAAAAATATACCGGAGCAG ATACATCTTCCTCCTCCCACGAGTCCTTGATATCATTCTCATCCACATCCTCATCATCCCAGTT ACTTTTCAGTTCAACTTTTGAGGGAAGTGGTTGAAAGTCCTCGGCCTCTGAAATCAGAAAGGAA AACCTAAAAGTGAGAATTCTAATATATTTCCCATATGAAAACTTCAATAAAACAACAATAAAGC CTATCATCTTAGAGAACATAGTAAAATATATATAGCTGTATACAGCCTGTACTACTTTTTACAT ATTCAAAGAGATTAATGCAACACCTAGAGAACAAGAAAGTATTGTGTATTGAACAATTCTTAAT GTAAGTCTTACCCCAATCATCCATATGTGTCGCCGATTATCTAGAAGAAGTACAAGCTGCTATC TGAATCCAACTGAAAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.243642822

Conservation Information
Conserved circRNAs	NA
PMCS	0.243642822

			
						 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 AT5G37475_circ_g.1

Address

Any questions?

Supported by