Plant Circular RNA Database

Detail information of AT3G24180_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT3G24180_circ_g.4
					
						ID in PlantcircBase
						ath_circ_023589
					
						Alias
						3:8738129-8739350
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 8738129-8739350  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G24180						
					
						Parent gene annotation
						
							Non-lysosomal glucosylceramidase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G24180_circ_g.2 AT3G24180_circ_g.3 						
					
						Support reads
						1/2
					
						Tissues
						leaf;flower
					
						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
						AT3G24180.2:4
AT3G24180.1:4

General Information
CircRNA Name	AT3G24180_circ_g.4
ID in PlantcircBase	ath_circ_023589
Alias	3:8738129-8739350
Organism	Arabidpsis thaliana
Position	chr3: 8738129-8739350 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G24180
Parent gene annotation	Non-lysosomal glucosylceramidase
Parent gene strand	-
Alternative splicing	AT3G24180_circ_g.2 AT3G24180_circ_g.3
Support reads	1/2
Tissues	leaf;flower
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	AT3G24180.2:4 AT3G24180.1:4

			
						 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  
						
							TGCTCTTCTATATAATGTACATCAAGTAATTCAGATGTCAACTCACCGCCCATGTGAAAAGAAG
GCTGACTTTTGCCCTTTCCTTTCCAGTGTTCACCAActgttccattgtatcccacatatctttc
gctgtaaaagaactatcttcagacaatccaaagcatggtaaaacagttacattaacattctgag
tctcagaa

									
								

					

						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: 291
Transcript exons: 8738129-8738270,8739033-8739071,8739159-8739214,8739297-
8739350
CTGTTCCATTGTATCCCACATATCTTTCGCTGTAAAAGAACTATCTTCAGACAATCCAAAGCAT
GGTAAAACAGTTACATTAACATTCTGAGTCTCAGAAGCAGCAATCGCAAATGTAACAGGAGGAT
TTCCTTTGCCTGTCTTGTGATGTAAGAGGACGCCAGAGACCCCATCTTCACCTATGAATGGCTC
ATTCACATGACCCCCTGACATATGTGAAGTCCCACCCATTGAATTCGCCCATGTGAAAAGAAGG
CTGACTTTTGCCCTTTCCTTTCCAGTGTTCACCAA
						
					

						Genomic sequence
						
							CTGTTCCATTGTATCCCACATATCTTTCGCTGTAAAAGAACTATCTTCAGACAATCCAAAGCAT
GGTAAAACAGTTACATTAACATTCTGAGTCTCAGAAGCAGCAATCGCAAATGTAACAGGAGGAT
TTCCTTTGCCTGTCCTGCAAAATCAGCACACATTCAAAACAAATATATCCGCTTAGAGTAAAGA
ACACAACCTTCTCCTGCAATAAGCATATATTCTAGCAGATTCAACTTCATCAAGGGCGCATGGC
GCATGTGAATAGATAAGCCAGTAAAGAATGTCATACACTCAAGAAGCATATATAGAGAAAGAAT
ATGACTAGACTATTCAGGCAGACACAGGTATAACACAACTACAAGCTTCAACAGGAAGCAGACT
GCACCGGGTAAGTTGATGTTCCGAGATAAATTGTCAACTAATCACACAGCAGTAGAACAAATCA
CACTAAAAAGACTTGGAAGATAAGGAGACGCGCATACACTTGGACAGATAATGCAACAAGATAA
GAGCGGTACATTTATAGTCTGAATGCAGTACACTAAGCCTTCACACTTAAAGAAAAGTCTACCT
AGGGAACATTTTGGTGCTAATAACTGCATGGGAGACTCCGGCCTCAACTATCTATTTTCTCTGT
TTTGTGCATTAACTATTGACCGATAAGGTGTACTTAGTTGGCGGACTTTCTAATTATGTGTAGG
TACCATTTTATCTTTTGCTAAGTTTATCAGATCAATTATTAACAATAACACTTAAGGTACTGCC
ATTTCGTAACCGTCCTCCATTTAACCAATAAGAAATAATGGTACAATGGACCACATTTTTCAAA
TCGTTGAATCTACCGCGAGATATATGCAAACCAACCGTAATATATAGTTAATATTAAGGTAAGA
TGACTTGCTTGTGATGTAAGAGGACGCCAGAGACCCCATCTTCACCTCTGAAAAGAAAAAGGAA
CCAAAAATAAATAAACATCAACTTGAAGCAATAATCATTTATGGAAAAGACGGCACATATTTTG
TCTTACATGAATGGCTCATTCACATGACCCCCTGACATATGTGAAGTCCCACCCATTGAATTCT
GCACAACATAAAGGTGATAAACATATCTTCCCTCTGCTCTTCTATATAATGTACATCAAGTAAT
TCAGATGTCAACTCACCGCCCATGTGAAAAGAAGGCTGACTTTTGCCCTTTCCTTTCCAGTGTT
CACCAA
						
					

			
		

Sequences
Splice junction sequence	TGCTCTTCTATATAATGTACATCAAGTAATTCAGATGTCAACTCACCGCCCATGTGAAAAGAAG GCTGACTTTTGCCCTTTCCTTTCCAGTGTTCACCAActgttccattgtatcccacatatctttc gctgtaaaagaactatcttcagacaatccaaagcatggtaaaacagttacattaacattctgag tctcagaa
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: 291 Transcript exons: 8738129-8738270,8739033-8739071,8739159-8739214,8739297- 8739350 CTGTTCCATTGTATCCCACATATCTTTCGCTGTAAAAGAACTATCTTCAGACAATCCAAAGCAT GGTAAAACAGTTACATTAACATTCTGAGTCTCAGAAGCAGCAATCGCAAATGTAACAGGAGGAT TTCCTTTGCCTGTCTTGTGATGTAAGAGGACGCCAGAGACCCCATCTTCACCTATGAATGGCTC ATTCACATGACCCCCTGACATATGTGAAGTCCCACCCATTGAATTCGCCCATGTGAAAAGAAGG CTGACTTTTGCCCTTTCCTTTCCAGTGTTCACCAA
Genomic sequence	CTGTTCCATTGTATCCCACATATCTTTCGCTGTAAAAGAACTATCTTCAGACAATCCAAAGCAT GGTAAAACAGTTACATTAACATTCTGAGTCTCAGAAGCAGCAATCGCAAATGTAACAGGAGGAT TTCCTTTGCCTGTCCTGCAAAATCAGCACACATTCAAAACAAATATATCCGCTTAGAGTAAAGA ACACAACCTTCTCCTGCAATAAGCATATATTCTAGCAGATTCAACTTCATCAAGGGCGCATGGC GCATGTGAATAGATAAGCCAGTAAAGAATGTCATACACTCAAGAAGCATATATAGAGAAAGAAT ATGACTAGACTATTCAGGCAGACACAGGTATAACACAACTACAAGCTTCAACAGGAAGCAGACT GCACCGGGTAAGTTGATGTTCCGAGATAAATTGTCAACTAATCACACAGCAGTAGAACAAATCA CACTAAAAAGACTTGGAAGATAAGGAGACGCGCATACACTTGGACAGATAATGCAACAAGATAA GAGCGGTACATTTATAGTCTGAATGCAGTACACTAAGCCTTCACACTTAAAGAAAAGTCTACCT AGGGAACATTTTGGTGCTAATAACTGCATGGGAGACTCCGGCCTCAACTATCTATTTTCTCTGT TTTGTGCATTAACTATTGACCGATAAGGTGTACTTAGTTGGCGGACTTTCTAATTATGTGTAGG TACCATTTTATCTTTTGCTAAGTTTATCAGATCAATTATTAACAATAACACTTAAGGTACTGCC ATTTCGTAACCGTCCTCCATTTAACCAATAAGAAATAATGGTACAATGGACCACATTTTTCAAA TCGTTGAATCTACCGCGAGATATATGCAAACCAACCGTAATATATAGTTAATATTAAGGTAAGA TGACTTGCTTGTGATGTAAGAGGACGCCAGAGACCCCATCTTCACCTCTGAAAAGAAAAAGGAA CCAAAAATAAATAAACATCAACTTGAAGCAATAATCATTTATGGAAAAGACGGCACATATTTTG TCTTACATGAATGGCTCATTCACATGACCCCCTGACATATGTGAAGTCCCACCCATTGAATTCT GCACAACATAAAGGTGATAAACATATCTTCCCTCTGCTCTTCTATATAATGTACATCAAGTAAT TCAGATGTCAACTCACCGCCCATGTGAAAAGAAGGCTGACTTTTGCCCTTTCCTTTCCAGTGTT CACCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.190420785

Conservation Information
Conserved circRNAs	NA
PMCS	0.190420785

			
						 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 AT3G24180_circ_g.4

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