Plant Circular RNA Database

Detail information of AT2G39190_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT2G39190_circ_g.2
					
						ID in PlantcircBase
						ath_circ_017347
					
						Alias
						2:16350876-16352267
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 16350876-16352267  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT2G39190						
					
						Parent gene annotation
						
							Protein kinase superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G39190_circ_g.3 AT2G39190_circ_g.4 AT2G39190_circ_g.5 AT2G39190_circ_g.6 AT2G39190_circ_g.7 AT2G39190_circ_g.8 AT2G39190_circ_g.9 AT2G39190_circ_g.10 AT2G39190_circ_g.11 AT2G39190_circ_g.12 AT2G39190_circ_g.13 						
					
						Support reads
						1/1/1
					
						Tissues
						seedling;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  
						
							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
						AT2G39190.2:6
AT2G39190.1:6

General Information
CircRNA Name	AT2G39190_circ_g.2
ID in PlantcircBase	ath_circ_017347
Alias	2:16350876-16352267
Organism	Arabidpsis thaliana
Position	chr2: 16350876-16352267 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT2G39190
Parent gene annotation	Protein kinase superfamily protein
Parent gene strand	+
Alternative splicing	AT2G39190_circ_g.3 AT2G39190_circ_g.4 AT2G39190_circ_g.5 AT2G39190_circ_g.6 AT2G39190_circ_g.7 AT2G39190_circ_g.8 AT2G39190_circ_g.9 AT2G39190_circ_g.10 AT2G39190_circ_g.11 AT2G39190_circ_g.12 AT2G39190_circ_g.13
Support reads	1/1/1
Tissues	seedling;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	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	AT2G39190.2:6 AT2G39190.1:6

			
						 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  
						
							GAGAGAAAATGACATTCGTGTATATGCTGATGAGCTTGGAATGGGTTTGGCTGGAGAATTGGAC
TTTACTTTAGAGGCTGCCAATGCCTCTGAATTTCAGggctcactggggtggatttgttcatggc
tgatgtcaaagccttggagacatatgctggttacttttacagtctttctaagatgtggtcaaga
ccacttcc

									
								

					

						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: 746
Transcript exons: 16350876-16351051,16351238-16351379,16351503-16351555,16
351717-16351860,16351952-16352056,16352142-16352267
GGCTCACTGGGGTGGATTTGTTCATGGCTGATGTCAAAGCCTTGGAGACATATGCTGGTTACTT
TTACAGTCTTTCTAAGATGTGGTCAAGACCACTTCCTGAAGTTTATGATTCACAAGCTGTTGCA
GATTACTTTAATTGCAGGCCTCATGTCGTTGCCTTTAGGCTTCTCGAGGTATTTTCTGCGTTCA
CGATTGCTGCCATCAGATTACGAACATCAGCATCAGTTAAGGGCAAAAGTTTAGAAGCTTCAGA
GCAGATTTTTGGGATGGTGTTGAAAGAAACCATGCTACATTTGGGCCCAACTTTTATCAAAGTT
GGTCAATCGCTTTCCACGAGGCCAGATATCATTGGGACTGAAATCTCCAAGGCACTATCTGAAC
TGCATGACCGAATCCCTCCCTTTCCCTGGCCTGAGGCTGTAAAAATCCTTGAAGGGGAATTAGG
TGGTCCTGTCGAATCATTCTTTAGTCAGTTTTCGCAAGAAACTGTAGCAGCAGCATCCTTTGGT
CAGGTCTACCGAGGAAGGACCCTCGATGGTGCAGATGTTGCAGTGAAAGTTCAGCGCCCTGATC
TGAGACATGCAGTGCTACGCGACATCTACATTCTGCGACTTGGGTTAGGTGTATTGCGAAAGGT
AGCAAAGAGAGAAAATGACATTCGTGTATATGCTGATGAGCTTGGAATGGGTTTGGCTGGAGAA
TTGGACTTTACTTTAGAGGCTGCCAATGCCTCTGAATTTCAG
						
					

						Genomic sequence
						
							GGCTCACTGGGGTGGATTTGTTCATGGCTGATGTCAAAGCCTTGGAGACATATGCTGGTTACTT
TTACAGTCTTTCTAAGATGTGGTCAAGACCACTTCCTGAAGTTTATGATTCACAAGCTGTTGCA
GATTACTTTAATTGCAGGCCTCATGTCGTTGCCTTTAGGCTTCTCGAGGTATTTGTTTAGAGTT
TTTGTTGGTTCTGCTACTAATCACTGGATGATTTGAAATTATGATAAATGCTTTAGAGATACTG
ATGTTTATCTGATGAAGTGTTTCGTTTAGCCTAACGCATTAGTATTCTTGTTTTTCTTGAGTGA
CGGAAAATTCGGATGTGATTTTAATTGATTCTTAAAATATAGGTATTTTCTGCGTTCACGATTG
CTGCCATCAGATTACGAACATCAGCATCAGTTAAGGGCAAAAGTTTAGAAGCTTCAGAGCAGAT
TTTTGGGATGGTGTTGAAAGAAACCATGCTACATTTGGGCCCAACTTTTATCAAAGGTCTGTGA
TTAGCTTATTATTTTTGAAGTGAAACTATCCATCAGTCACCATTTACATTTACTGCCATATATT
AGATACTTTGATCTGTTGTGAATGATTCTTCCCTCTCTTCTGCTGGTTCAGTTGGTCAATCGCT
TTCCACGAGGCCAGATATCATTGGGACTGAAATCTCCAAGGTCAGATAGAAGTTATGGTCACAT
TTGTCTAAATCTCTTAGCTTTTAATAGTGTCTTTCTGGTGCATGTTTCCATTGTTCTTTCTCTA
TTCTGCATGCTACATTTGGTTGTTCTTAGGGATGTAGCTGTCTGACTATGTTTGTTATGATTTG
AAACTGCAGGCACTATCTGAACTGCATGACCGAATCCCTCCCTTTCCCTGGCCTGAGGCTGTAA
AAATCCTTGAAGGGGAATTAGGTGGTCCTGTCGAATCATTCTTTAGTCAGTTTTCGCAAGAAAC
TGTAGCAGCAGCATCCTTTGGTCAGGTATTTACTCTGGTTTTTATCTTACAAGAAGTAAGCATC
ATATGAATCAACTTGTAGGATGCATGCCTTATACTTGATATGATATGTTAAGGTCTACCGAGGA
AGGACCCTCGATGGTGCAGATGTTGCAGTGAAAGTTCAGCGCCCTGATCTGAGACATGCAGTGC
TACGCGACATCTACATTCTGCGACTTGGGGTTCGTGTGAAATCTACCAAGTTATGACAAATCAA
TCTGCTTGAATCATGTCATAGTTATATGATATTTCTTTTGATTGTTGCAGTTAGGTGTATTGCG
AAAGGTAGCAAAGAGAGAAAATGACATTCGTGTATATGCTGATGAGCTTGGAATGGGTTTGGCT
GGAGAATTGGACTTTACTTTAGAGGCTGCCAATGCCTCTGAATTTCAG
						
					

			
		

Sequences
Splice junction sequence	GAGAGAAAATGACATTCGTGTATATGCTGATGAGCTTGGAATGGGTTTGGCTGGAGAATTGGAC TTTACTTTAGAGGCTGCCAATGCCTCTGAATTTCAGggctcactggggtggatttgttcatggc tgatgtcaaagccttggagacatatgctggttacttttacagtctttctaagatgtggtcaaga ccacttcc
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: 746 Transcript exons: 16350876-16351051,16351238-16351379,16351503-16351555,16 351717-16351860,16351952-16352056,16352142-16352267 GGCTCACTGGGGTGGATTTGTTCATGGCTGATGTCAAAGCCTTGGAGACATATGCTGGTTACTT TTACAGTCTTTCTAAGATGTGGTCAAGACCACTTCCTGAAGTTTATGATTCACAAGCTGTTGCA GATTACTTTAATTGCAGGCCTCATGTCGTTGCCTTTAGGCTTCTCGAGGTATTTTCTGCGTTCA CGATTGCTGCCATCAGATTACGAACATCAGCATCAGTTAAGGGCAAAAGTTTAGAAGCTTCAGA GCAGATTTTTGGGATGGTGTTGAAAGAAACCATGCTACATTTGGGCCCAACTTTTATCAAAGTT GGTCAATCGCTTTCCACGAGGCCAGATATCATTGGGACTGAAATCTCCAAGGCACTATCTGAAC TGCATGACCGAATCCCTCCCTTTCCCTGGCCTGAGGCTGTAAAAATCCTTGAAGGGGAATTAGG TGGTCCTGTCGAATCATTCTTTAGTCAGTTTTCGCAAGAAACTGTAGCAGCAGCATCCTTTGGT CAGGTCTACCGAGGAAGGACCCTCGATGGTGCAGATGTTGCAGTGAAAGTTCAGCGCCCTGATC TGAGACATGCAGTGCTACGCGACATCTACATTCTGCGACTTGGGTTAGGTGTATTGCGAAAGGT AGCAAAGAGAGAAAATGACATTCGTGTATATGCTGATGAGCTTGGAATGGGTTTGGCTGGAGAA TTGGACTTTACTTTAGAGGCTGCCAATGCCTCTGAATTTCAG
Genomic sequence	GGCTCACTGGGGTGGATTTGTTCATGGCTGATGTCAAAGCCTTGGAGACATATGCTGGTTACTT TTACAGTCTTTCTAAGATGTGGTCAAGACCACTTCCTGAAGTTTATGATTCACAAGCTGTTGCA GATTACTTTAATTGCAGGCCTCATGTCGTTGCCTTTAGGCTTCTCGAGGTATTTGTTTAGAGTT TTTGTTGGTTCTGCTACTAATCACTGGATGATTTGAAATTATGATAAATGCTTTAGAGATACTG ATGTTTATCTGATGAAGTGTTTCGTTTAGCCTAACGCATTAGTATTCTTGTTTTTCTTGAGTGA CGGAAAATTCGGATGTGATTTTAATTGATTCTTAAAATATAGGTATTTTCTGCGTTCACGATTG CTGCCATCAGATTACGAACATCAGCATCAGTTAAGGGCAAAAGTTTAGAAGCTTCAGAGCAGAT TTTTGGGATGGTGTTGAAAGAAACCATGCTACATTTGGGCCCAACTTTTATCAAAGGTCTGTGA TTAGCTTATTATTTTTGAAGTGAAACTATCCATCAGTCACCATTTACATTTACTGCCATATATT AGATACTTTGATCTGTTGTGAATGATTCTTCCCTCTCTTCTGCTGGTTCAGTTGGTCAATCGCT TTCCACGAGGCCAGATATCATTGGGACTGAAATCTCCAAGGTCAGATAGAAGTTATGGTCACAT TTGTCTAAATCTCTTAGCTTTTAATAGTGTCTTTCTGGTGCATGTTTCCATTGTTCTTTCTCTA TTCTGCATGCTACATTTGGTTGTTCTTAGGGATGTAGCTGTCTGACTATGTTTGTTATGATTTG AAACTGCAGGCACTATCTGAACTGCATGACCGAATCCCTCCCTTTCCCTGGCCTGAGGCTGTAA AAATCCTTGAAGGGGAATTAGGTGGTCCTGTCGAATCATTCTTTAGTCAGTTTTCGCAAGAAAC TGTAGCAGCAGCATCCTTTGGTCAGGTATTTACTCTGGTTTTTATCTTACAAGAAGTAAGCATC ATATGAATCAACTTGTAGGATGCATGCCTTATACTTGATATGATATGTTAAGGTCTACCGAGGA AGGACCCTCGATGGTGCAGATGTTGCAGTGAAAGTTCAGCGCCCTGATCTGAGACATGCAGTGC TACGCGACATCTACATTCTGCGACTTGGGGTTCGTGTGAAATCTACCAAGTTATGACAAATCAA TCTGCTTGAATCATGTCATAGTTATATGATATTTCTTTTGATTGTTGCAGTTAGGTGTATTGCG AAAGGTAGCAAAGAGAGAAAATGACATTCGTGTATATGCTGATGAGCTTGGAATGGGTTTGGCT GGAGAATTGGACTTTACTTTAGAGGCTGCCAATGCCTCTGAATTTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.334854506

Conservation Information
Conserved circRNAs	NA
PMCS	0.334854506

			
						 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 AT2G39190_circ_g.2

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