Plant Circular RNA Database

Detail information of AT2G38020_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT2G38020_circ_g.4
					
						ID in PlantcircBase
						ath_circ_017152
					
						Alias
						At_ciR364, AT2G38020_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 15910564-15910878  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, find_circ, circseq_cup, CIRI-full, CIRI2
					
						Parent gene
						
							AT2G38020						
					
						Parent gene annotation
						
							Protein VACUOLELESS1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT2G38020_circ_g.1 AT2G38020_circ_g.2 AT2G38020_circ_g.3 AT2G38020_circ_g.5 AT2G38020_circ_g.6 						
					
						Support reads
						10/7
					
						Tissues
						leaf/root, aerial, whole_plant
					
						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
						AT2G38020.2:2
AT2G38020.1:2

General Information
CircRNA Name	AT2G38020_circ_g.4
ID in PlantcircBase	ath_circ_017152
Alias	At_ciR364, AT2G38020_C1
Organism	Arabidpsis thaliana
Position	chr2: 15910564-15910878 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, find_circ, circseq_cup, CIRI-full, CIRI2
Parent gene	AT2G38020
Parent gene annotation	Protein VACUOLELESS1
Parent gene strand	-
Alternative splicing	AT2G38020_circ_g.1 AT2G38020_circ_g.2 AT2G38020_circ_g.3 AT2G38020_circ_g.5 AT2G38020_circ_g.6
Support reads	10/7
Tissues	leaf/root, aerial, whole_plant
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	AT2G38020.2:2 AT2G38020.1:2

			
						 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  
						
							ACGGTTATTACCCAGGACAATACATGTGCGTATAGTATCATTGATGCTTGAATCAACAAAGATA
GCCTGCTTCGTACTAGCTTCTAGCTCATGTTGTATCccattggtggtctcttttccttcgaaaa
cttttcaagcgctgcccagtctttgattgtagcgagagcaaatgctttaagccaataccatctt
ttatcact

									
								

					

						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: 139
Transcript exons: 15910564-15910601,15910778-15910878
CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCCACGGTTATTACCCAGGACAATACAT
GTGCGTATAGTATCATTGATGCTTGAATCAACAAAGATAGCCTGCTTCGTACTAGCTTCTAGCT
CATGTTGTATC
Transcript length: 175
Transcript exons: 15910564-15910620,15910761-15910878
CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGCTTCACT
TTTATTGCAGCACGGTTATTACCCAGGACAATACATGTGCGTATAGTATCATTGATGCTTGAAT
CAACAAAGATAGCCTGCTTCGTACTAGCTTCTAGCTCATGTTGTATC
Transcript length: 205
Transcript exons: 15910564-15910637,15910748-15910878
CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGTAGCGAG
AGCAAATGCTCCTTGAATTCTGTCTTCACTTTTATTGCAGCACGGTTATTACCCAGGACAATAC
ATGTGCGTATAGTATCATTGATGCTTGAATCAACAAAGATAGCCTGCTTCGTACTAGCTTCTAG
CTCATGTTGTATC
Transcript length: 211
Transcript exons: 15910564-15910644,15910749-15910878
CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGTAGCGAG
AGCAAATGCTTTAAGCCCTTGAATTCTGTCTTCACTTTTATTGCAGCACGGTTATTACCCAGGA
CAATACATGTGCGTATAGTATCATTGATGCTTGAATCAACAAAGATAGCCTGCTTCGTACTAGC
TTCTAGCTCATGTTGTATC
Transcript length: 213
Transcript exons: 15910564-15910646,15910749-15910878
CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGTAGCGAG
AGCAAATGCTTTAAGCCAACTTGAATTCTGTCTTCACTTTTATTGCAGCACGGTTATTACCCAG
GACAATACATGTGCGTATAGTATCATTGATGCTTGAATCAACAAAGATAGCCTGCTTCGTACTA
GCTTCTAGCTCATGTTGTATC
Transcript length: 216
Transcript exons: 15910564-15910649,15910749-15910878
CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGTAGCGAG
AGCAAATGCTTTAAGCCAATACCTTGAATTCTGTCTTCACTTTTATTGCAGCACGGTTATTACC
CAGGACAATACATGTGCGTATAGTATCATTGATGCTTGAATCAACAAAGATAGCCTGCTTCGTA
CTAGCTTCTAGCTCATGTTGTATC
Transcript length: 233
Transcript exons: 15910564-15910666,15910749-15910878
CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGTAGCGAG
AGCAAATGCTTTAAGCCAATACCATCTTTTATCACTGACCTTGAATTCTGTCTTCACTTTTATT
GCAGCACGGTTATTACCCAGGACAATACATGTGCGTATAGTATCATTGATGCTTGAATCAACAA
AGATAGCCTGCTTCGTACTAGCTTCTAGCTCATGTTGTATC
						
					

						Genomic sequence
						
							CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGTAGCGAG
AGCAAATGCTTTAAGCCAATACCATCTTTTATCACTGACCTGAAAATTCAAACAGTACAGTGGT
GAGATCGCGTTCTTACAGTCATCCATTGCACAGAAGGGGTTAAAATCCAATTAGAACCTTGAAT
TCTGTCTTCACTTTTATTGCAGCACGGTTATTACCCAGGACAATACATGTGCGTATAGTATCAT
TGATGCTTGAATCAACAAAGATAGCCTGCTTCGTACTAGCTTCTAGCTCATGTTGTATC
						
					

			
		

Sequences
Splice junction sequence	ACGGTTATTACCCAGGACAATACATGTGCGTATAGTATCATTGATGCTTGAATCAACAAAGATA GCCTGCTTCGTACTAGCTTCTAGCTCATGTTGTATCccattggtggtctcttttccttcgaaaa cttttcaagcgctgcccagtctttgattgtagcgagagcaaatgctttaagccaataccatctt ttatcact
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: 139 Transcript exons: 15910564-15910601,15910778-15910878 CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCCACGGTTATTACCCAGGACAATACAT GTGCGTATAGTATCATTGATGCTTGAATCAACAAAGATAGCCTGCTTCGTACTAGCTTCTAGCT CATGTTGTATC Transcript length: 175 Transcript exons: 15910564-15910620,15910761-15910878 CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGCTTCACT TTTATTGCAGCACGGTTATTACCCAGGACAATACATGTGCGTATAGTATCATTGATGCTTGAAT CAACAAAGATAGCCTGCTTCGTACTAGCTTCTAGCTCATGTTGTATC Transcript length: 205 Transcript exons: 15910564-15910637,15910748-15910878 CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGTAGCGAG AGCAAATGCTCCTTGAATTCTGTCTTCACTTTTATTGCAGCACGGTTATTACCCAGGACAATAC ATGTGCGTATAGTATCATTGATGCTTGAATCAACAAAGATAGCCTGCTTCGTACTAGCTTCTAG CTCATGTTGTATC Transcript length: 211 Transcript exons: 15910564-15910644,15910749-15910878 CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGTAGCGAG AGCAAATGCTTTAAGCCCTTGAATTCTGTCTTCACTTTTATTGCAGCACGGTTATTACCCAGGA CAATACATGTGCGTATAGTATCATTGATGCTTGAATCAACAAAGATAGCCTGCTTCGTACTAGC TTCTAGCTCATGTTGTATC Transcript length: 213 Transcript exons: 15910564-15910646,15910749-15910878 CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGTAGCGAG AGCAAATGCTTTAAGCCAACTTGAATTCTGTCTTCACTTTTATTGCAGCACGGTTATTACCCAG GACAATACATGTGCGTATAGTATCATTGATGCTTGAATCAACAAAGATAGCCTGCTTCGTACTA GCTTCTAGCTCATGTTGTATC Transcript length: 216 Transcript exons: 15910564-15910649,15910749-15910878 CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGTAGCGAG AGCAAATGCTTTAAGCCAATACCTTGAATTCTGTCTTCACTTTTATTGCAGCACGGTTATTACC CAGGACAATACATGTGCGTATAGTATCATTGATGCTTGAATCAACAAAGATAGCCTGCTTCGTA CTAGCTTCTAGCTCATGTTGTATC Transcript length: 233 Transcript exons: 15910564-15910666,15910749-15910878 CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGTAGCGAG AGCAAATGCTTTAAGCCAATACCATCTTTTATCACTGACCTTGAATTCTGTCTTCACTTTTATT GCAGCACGGTTATTACCCAGGACAATACATGTGCGTATAGTATCATTGATGCTTGAATCAACAA AGATAGCCTGCTTCGTACTAGCTTCTAGCTCATGTTGTATC
Genomic sequence	CCATTGGTGGTCTCTTTTCCTTCGAAAACTTTTCAAGCGCTGCCCAGTCTTTGATTGTAGCGAG AGCAAATGCTTTAAGCCAATACCATCTTTTATCACTGACCTGAAAATTCAAACAGTACAGTGGT GAGATCGCGTTCTTACAGTCATCCATTGCACAGAAGGGGTTAAAATCCAATTAGAACCTTGAAT TCTGTCTTCACTTTTATTGCAGCACGGTTATTACCCAGGACAATACATGTGCGTATAGTATCAT TGATGCTTGAATCAACAAAGATAGCCTGCTTCGTACTAGCTTCTAGCTCATGTTGTATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.744629076

Conservation Information
Conserved circRNAs	NA
PMCS	0.744629076

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress; regulation of development and senescence of leaves

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress; regulation of development and senescence of leaves

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Liu et al., 2017;Zhang et al., 2019

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Detail information of AT2G38020_circ_g.4

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