Plant Circular RNA Database

Detail information of AT4G39910_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT4G39910_circ_g.2
					
						ID in PlantcircBase
						ath_circ_035780
					
						Alias
						4:18512428-18513611
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 18512428-18513611  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G39910						
					
						Parent gene annotation
						
							Ubiquitin carboxyl-terminal hydrolase 3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G39910_circ_g.3 						
					
						Support reads
						1/1
					
						Tissues
						seedling;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
						AT4G39910.1:4

General Information
CircRNA Name	AT4G39910_circ_g.2
ID in PlantcircBase	ath_circ_035780
Alias	4:18512428-18513611
Organism	Arabidpsis thaliana
Position	chr4: 18512428-18513611 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G39910
Parent gene annotation	Ubiquitin carboxyl-terminal hydrolase 3
Parent gene strand	-
Alternative splicing	AT4G39910_circ_g.3
Support reads	1/1
Tissues	seedling;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	AT4G39910.1:4

			
						 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  
						
							CCAGGCAGGTCATAAGATTCTCTTCAGCATCGGCCACGCTTTTATTACTGGTATAGTATTCGAG
CAGTTGTTCACGGAAAGGAACACAGAAATAAAGAGCctgcagcatttgtcacaaaagaatttgt
cttcagcgtgaagcgtctctgtggagctgaagtttttcaaacagctagttatcgaactgttctg
ttcgatat

						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
						
							CTGCAGCATTTGTCACAAAAGAATTTGTCTTCAGCGTGAAGCGTCTCTGTGGAGCTGAAGTTTT
TCAAACAGCTAGTTATCGAACTGTTCTGTTCGATATCAAGGCTTAGGTCTAGGAATGTTTCGTC
TCTTGCTGTCACTGTTTCACATCGCAGACACCTTGTCTCGTTGGTAAGTATGCCCTGTGTACAT
ACCCCGAATTTAAAATAAGCCAAAAATAGCACAACATAGTCGCACCTTATAAGGAGAAGTGAAC
CTTTTCATTAGAAACAACTGACCTGAAAAATATTGTGCACCCATGTAACAATAGGCTCCTTGTG
CACAACACCATTTGCCTGAGGAACTTTCAGTCCATTTGCTATCTTCTCGGGAGATGATGATGAC
GAGGTTTCATGTTCAGTTTTTGTAGCTTTTGCCTCTTTCTCCAGTATGTCAACAACTTCATTCA
GCAAATAATTCAGGAATTCATGTGCATCCTACATGAGATAAGAAACGTAAAATCAATCAAATGT
TAATTGCTTATCTCGCATCTTCTGTAAAATAGCTCCCGAAAAGATGGGGAGATTTGCAAAGATC
ACCTGGTGCATATAACTCCGAAACAGCTCATTTTGTTTCTTCAACCTCTGTACAAATCGCTTAG
GCGCAATAACACCTGTTTTCTTCTTCTGGGAACTTATCTACAGAATGAATAACTATGATCAGAC
TTATGATTACACCCTCTCTTTTTTTTCCACAGAATGACTAGCATACAATTATCTAAATGATGAT
GACAAGATATGATATACTAGGCACTTCATCAAGCACATTTAGTATCTCGAAGATATTTAACTAT
GTACACAATAATATCAAGTTCATGTAATGCCAAAAAAAACATTGACTTGTGCCTATAAATAATT
GATTAAATCCACTTATGATGTCAAGTGAGAAATCAAGTAAACCAACCTCAAGAGAAATATTGTC
AGAGAATACAAGATTGGTCACTTGAGTTAAGACAGTATGGAAGACCTCGAAAGGGTAGATAAAA
ATTAAACTCTCAAAAGGAAAAGAAAGCCAAAGATCACAAATACCTGCGAAAACAAGTCTGCCAG
GCAGGTCATAAGATTCTCTTCAGCATCGGCCACGCTTTTATTACTGGTATAGTATTCGAGCAGT
TGTTCACGGAAAGGAACACAGAAATAAAGAGC

Sequences
Splice junction sequence	CCAGGCAGGTCATAAGATTCTCTTCAGCATCGGCCACGCTTTTATTACTGGTATAGTATTCGAG CAGTTGTTCACGGAAAGGAACACAGAAATAAAGAGCctgcagcatttgtcacaaaagaatttgt cttcagcgtgaagcgtctctgtggagctgaagtttttcaaacagctagttatcgaactgttctg ttcgatat
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	CTGCAGCATTTGTCACAAAAGAATTTGTCTTCAGCGTGAAGCGTCTCTGTGGAGCTGAAGTTTT TCAAACAGCTAGTTATCGAACTGTTCTGTTCGATATCAAGGCTTAGGTCTAGGAATGTTTCGTC TCTTGCTGTCACTGTTTCACATCGCAGACACCTTGTCTCGTTGGTAAGTATGCCCTGTGTACAT ACCCCGAATTTAAAATAAGCCAAAAATAGCACAACATAGTCGCACCTTATAAGGAGAAGTGAAC CTTTTCATTAGAAACAACTGACCTGAAAAATATTGTGCACCCATGTAACAATAGGCTCCTTGTG CACAACACCATTTGCCTGAGGAACTTTCAGTCCATTTGCTATCTTCTCGGGAGATGATGATGAC GAGGTTTCATGTTCAGTTTTTGTAGCTTTTGCCTCTTTCTCCAGTATGTCAACAACTTCATTCA GCAAATAATTCAGGAATTCATGTGCATCCTACATGAGATAAGAAACGTAAAATCAATCAAATGT TAATTGCTTATCTCGCATCTTCTGTAAAATAGCTCCCGAAAAGATGGGGAGATTTGCAAAGATC ACCTGGTGCATATAACTCCGAAACAGCTCATTTTGTTTCTTCAACCTCTGTACAAATCGCTTAG GCGCAATAACACCTGTTTTCTTCTTCTGGGAACTTATCTACAGAATGAATAACTATGATCAGAC TTATGATTACACCCTCTCTTTTTTTTCCACAGAATGACTAGCATACAATTATCTAAATGATGAT GACAAGATATGATATACTAGGCACTTCATCAAGCACATTTAGTATCTCGAAGATATTTAACTAT GTACACAATAATATCAAGTTCATGTAATGCCAAAAAAAACATTGACTTGTGCCTATAAATAATT GATTAAATCCACTTATGATGTCAAGTGAGAAATCAAGTAAACCAACCTCAAGAGAAATATTGTC AGAGAATACAAGATTGGTCACTTGAGTTAAGACAGTATGGAAGACCTCGAAAGGGTAGATAAAA ATTAAACTCTCAAAAGGAAAAGAAAGCCAAAGATCACAAATACCTGCGAAAACAAGTCTGCCAG GCAGGTCATAAGATTCTCTTCAGCATCGGCCACGCTTTTATTACTGGTATAGTATTCGAGCAGT TGTTCACGGAAAGGAACACAGAAATAAAGAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.176846424

Conservation Information
Conserved circRNAs	NA
PMCS	0.176846424

			
						 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 AT4G39910_circ_g.2

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