Plant Circular RNA Database

Detail information of AT4G20300_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G20300_circ_g.3
					
						ID in PlantcircBase
						ath_circ_031823
					
						Alias
						At_ciR4431, AT4G20300_C3
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 10956285-10958269  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ, CIRI2
					
						Parent gene
						
							AT4G20300						
					
						Parent gene annotation
						
							Putative uncharacterized protein At4g20300
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G20300_circ_g.2 AT4G20300_circ_g.4 AT4G20300_circ_g.5 AT4G20300_circ_g.6 AT4G20300_circ_g.7 AT4G20300_circ_g.8 AT4G20300_circ_g.9 AT4G20300_circ_g.10 						
					
						Support reads
						3/1/3
					
						Tissues
						leaf/root/seedlings
					
						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
						AT4G20300.2:3
AT4G20300.1:3

General Information
CircRNA Name	AT4G20300_circ_g.3
ID in PlantcircBase	ath_circ_031823
Alias	At_ciR4431, AT4G20300_C3
Organism	Arabidpsis thaliana
Position	chr4: 10956285-10958269 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ, CIRI2
Parent gene	AT4G20300
Parent gene annotation	Putative uncharacterized protein At4g20300
Parent gene strand	+
Alternative splicing	AT4G20300_circ_g.2 AT4G20300_circ_g.4 AT4G20300_circ_g.5 AT4G20300_circ_g.6 AT4G20300_circ_g.7 AT4G20300_circ_g.8 AT4G20300_circ_g.9 AT4G20300_circ_g.10
Support reads	3/1/3
Tissues	leaf/root/seedlings
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	AT4G20300.2:3 AT4G20300.1:3

			
						 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  
						
							TAATTAATGTATTATTGTACAGTTTTGTTTTCCAGGGATGTGGTTATCTGATTTGACCAAGAAC
CGTTATGAAGTTAGGGAGAAGAAAAATGTGAAGAAGgtatcagagagtaagcccagattgtctt
cctctcacaaatggaggtaagaagccttacttacgaccatcaccatcaagagcaacaaacgaag
acaccacc

									
								

					

						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: 201
Transcript exons: 10956285-10956444,10958229-10958269
GTATCAGAGAGTAAGCCCAGATTGTCTTCCTCTCACAAATGGAGGTAAGAAGCCTTACTTACGA
CCATCACCATCAAGAGCAACAAACGAAGACACCACCACCACCACCGTCATTACCACAACCTCAA
TCGCCGGAAGAGGATTTAACGGCGGATCATGCAGAACCGTTATGAAGTTAGGGAGAAGAAAAAT
GTGAAGAAG
Transcript length: 994
Transcript exons: 10956285-10956818,10957705-10958086,10958192-10958269
GTATCAGAGAGTAAGCCCAGATTGTCTTCCTCTCACAAATGGAGGTAAGAAGCCTTACTTACGA
CCATCACCATCAAGAGCAACAAACGAAGACACCACCACCACCACCGTCATTACCACAACCTCAA
TCGCCGGAAGAGGATTTAACGGCGGATCATGCACAACCACCACCAACAACACCTCATCTCTAGA
CGGAGTCCCCAAAGGATTCCGATTCAGATCCACTCAACAGCAGCAACAACAACAAGATCCTAGT
CCTAGCCGTCGCGGCGGTGATGTACTGTTACAGTGGGGACAACGAAAACGATCGAGAGCCTCTA
GAGCTGAGATCCGATCCACCACCACCATCACAACCACCGCCGATGATTCTTCGTCTTCTTCAGG
TCAAGGTAAGATACAATCAAACAAACCGCAAAGAAGATCGATGAATCCTTCTATGCCACCTCCA
CCACCAGCTCCGCCGATTTTCTCGGGCCGGAGTACAAACCCTAGAAACGGTTTCGTTATCGGCA
AGGAATCTTTCTTCCCTTCCAGGAATCTAGAAGATCGATCAGCAAACGGATCACCATCAAGGAA
CAACATAAACGGCCGTATGATATCCAGATCGGGTGGCTCAAAGCGATCTCCACCGTCACCAGAC
CAAATCGAGAAGAGATCAAGCGTTAGAGATCAGAGACAAAACGGGTTTGATCATCAACAACAAC
AACATCAAAGAGTGAACAGATCAGAATCAACGGCTCAGGGTCATCAAGAAGTGGAGATAAATGG
AGAAAGAGAGAAAGCAACGCAAGAGTGGCCGAGGATCTACATTGCTTTGTCTAGGAAAGAGAAG
GAAGAAGATTTCTTGGTTATGAAAGGAACTAAGCTTCCTCATAGACCCAGGAAACGAGCTAAGA
ACATTGATAAAGCCCTTCAGTTTTGTTTTCCAGGGATGTGGTTATCTGATTTGACCAAGAACCG
TTATGAAGTTAGGGAGAAGAAAAATGTGAAGAAG
						
					

						Genomic sequence
						
							GTATCAGAGAGTAAGCCCAGATTGTCTTCCTCTCACAAATGGAGGTAAGAAGCCTTACTTACGA
CCATCACCATCAAGAGCAACAAACGAAGACACCACCACCACCACCGTCATTACCACAACCTCAA
TCGCCGGAAGAGGATTTAACGGCGGATCATGCACAACCACCACCAACAACACCTCATCTCTAGA
CGGAGTCCCCAAAGGATTCCGATTCAGATCCACTCAACAGCAGCAACAACAACAAGATCCTAGT
CCTAGCCGTCGCGGCGGTGATGTACTGTTACAGTGGGGACAACGAAAACGATCGAGAGCCTCTA
GAGCTGAGATCCGATCCACCACCACCATCACAACCACCGCCGATGATTCTTCGTCTTCTTCAGG
TCAAGGTAAGATACAATCAAACAAACCGCAAAGAAGATCGATGAATCCTTCTATGCCACCTCCA
CCACCAGCTCCGCCGATTTTCTCGGGCCGGAGTACAAACCCTAGAAACGGTTTCGTTATCGGCA
AGGAATCTTTCTTCCCTTCCAGGTTTAGCCTCAAATCTTTCTTCATTCAATTAAATTTCCATAT
TTTGATATATTTACTTACCTTAAATGTTTTAGAATCGAGTTTGATTTGTCTTTTTTTACCTTTA
ATCGTTTAGATTTTGTTACTGTAAATTAATCCATATGATCGTGACTTCATTAGCTTCCATATAT
TTCTCTTTTTGTTCATCCATGTTATGTGATAAATAATGTGCCCTTGTTTTTATTTTTATATAAA
GTAAAGCTATTTTTGATTTTCAAGGTTTGATATATTCAATTTAAATGATTTTCGTTTTCTGGTT
TTTCATTTTTGAGATCTAAACAAACGTTTGGTTTCATCTTCTGTTAAAGCTTTAACGAAAGTTT
GGTGATCCAAAATTCCTTTTTGGGAAATGACAGTAATACCCTTGGAAGCACTAAGAAGCAGAGA
GTTGTGTCTCTTTTTCCTCAAGTGCTCAGTTTCTTAGGTTTTTCACTTGTTGTTTAGCTTTTGG
GGTGAAAAATATATAAACGATTTTTCTCAATCTAATTTTTTTTTTTGGGTTAAATATAAGATCT
CGTATTTTTCTTTGCCTTTCTTTGACCCAATCTTCAAATCTGGGCTACTTGTTTTGAAATCAAT
CGATTATAGATTTCTTCTTATTTTCTGTTTTGGTCCCTCTCTTTTAGTTTTATTGTGTGTGTGT
GTCTGCGTTTTGATTCTGATTCTTAAATATGTAAATGGGTACAACTAGTTTCCTTTTCTAAATT
TCTTCCTTATTTTTAACACAAGGAGAAAAAAAAATTCATTAAACTCTCTCAAAGTTTATAGAAC
TAACCTTTATTATACCAAAATTCAATCACCTGTGGATTTATTAAAGCTGTTCATCATCATCATC
AATCATGCACAGGAATCTAGAAGATCGATCAGCAAACGGATCACCATCAAGGAACAACATAAAC
GGCCGTATGATATCCAGATCGGGTGGCTCAAAGCGATCTCCACCGTCACCAGACCAAATCGAGA
AGAGATCAAGCGTTAGAGATCAGAGACAAAACGGGTTTGATCATCAACAACAACAACATCAAAG
AGTGAACAGATCAGAATCAACGGCTCAGGGTCATCAAGAAGTGGAGATAAATGGAGAAAGAGAG
AAAGCAACGCAAGAGTGGCCGAGGATCTACATTGCTTTGTCTAGGAAAGAGAAGGAAGAAGATT
TCTTGGTTATGAAAGGAACTAAGCTTCCTCATAGACCCAGGAAACGAGCTAAGAACATTGATAA
AGCCCTTCAGGTAAAATTCATTAAAAAAAAAGTATTTATTTTTATCTCACAAGAGTTAAAAACA
AAAAAAAAATCATAAATGAAAATATGTTTTAATTAATGTATTATTGTACAGTTTTGTTTTCCAG
GGATGTGGTTATCTGATTTGACCAAGAACCGTTATGAAGTTAGGGAGAAGAAAAATGTGAAGAA
G
						
					

			
		

Sequences
Splice junction sequence	TAATTAATGTATTATTGTACAGTTTTGTTTTCCAGGGATGTGGTTATCTGATTTGACCAAGAAC CGTTATGAAGTTAGGGAGAAGAAAAATGTGAAGAAGgtatcagagagtaagcccagattgtctt cctctcacaaatggaggtaagaagccttacttacgaccatcaccatcaagagcaacaaacgaag acaccacc
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: 201 Transcript exons: 10956285-10956444,10958229-10958269 GTATCAGAGAGTAAGCCCAGATTGTCTTCCTCTCACAAATGGAGGTAAGAAGCCTTACTTACGA CCATCACCATCAAGAGCAACAAACGAAGACACCACCACCACCACCGTCATTACCACAACCTCAA TCGCCGGAAGAGGATTTAACGGCGGATCATGCAGAACCGTTATGAAGTTAGGGAGAAGAAAAAT GTGAAGAAG Transcript length: 994 Transcript exons: 10956285-10956818,10957705-10958086,10958192-10958269 GTATCAGAGAGTAAGCCCAGATTGTCTTCCTCTCACAAATGGAGGTAAGAAGCCTTACTTACGA CCATCACCATCAAGAGCAACAAACGAAGACACCACCACCACCACCGTCATTACCACAACCTCAA TCGCCGGAAGAGGATTTAACGGCGGATCATGCACAACCACCACCAACAACACCTCATCTCTAGA CGGAGTCCCCAAAGGATTCCGATTCAGATCCACTCAACAGCAGCAACAACAACAAGATCCTAGT CCTAGCCGTCGCGGCGGTGATGTACTGTTACAGTGGGGACAACGAAAACGATCGAGAGCCTCTA GAGCTGAGATCCGATCCACCACCACCATCACAACCACCGCCGATGATTCTTCGTCTTCTTCAGG TCAAGGTAAGATACAATCAAACAAACCGCAAAGAAGATCGATGAATCCTTCTATGCCACCTCCA CCACCAGCTCCGCCGATTTTCTCGGGCCGGAGTACAAACCCTAGAAACGGTTTCGTTATCGGCA AGGAATCTTTCTTCCCTTCCAGGAATCTAGAAGATCGATCAGCAAACGGATCACCATCAAGGAA CAACATAAACGGCCGTATGATATCCAGATCGGGTGGCTCAAAGCGATCTCCACCGTCACCAGAC CAAATCGAGAAGAGATCAAGCGTTAGAGATCAGAGACAAAACGGGTTTGATCATCAACAACAAC AACATCAAAGAGTGAACAGATCAGAATCAACGGCTCAGGGTCATCAAGAAGTGGAGATAAATGG AGAAAGAGAGAAAGCAACGCAAGAGTGGCCGAGGATCTACATTGCTTTGTCTAGGAAAGAGAAG GAAGAAGATTTCTTGGTTATGAAAGGAACTAAGCTTCCTCATAGACCCAGGAAACGAGCTAAGA ACATTGATAAAGCCCTTCAGTTTTGTTTTCCAGGGATGTGGTTATCTGATTTGACCAAGAACCG TTATGAAGTTAGGGAGAAGAAAAATGTGAAGAAG
Genomic sequence	GTATCAGAGAGTAAGCCCAGATTGTCTTCCTCTCACAAATGGAGGTAAGAAGCCTTACTTACGA CCATCACCATCAAGAGCAACAAACGAAGACACCACCACCACCACCGTCATTACCACAACCTCAA TCGCCGGAAGAGGATTTAACGGCGGATCATGCACAACCACCACCAACAACACCTCATCTCTAGA CGGAGTCCCCAAAGGATTCCGATTCAGATCCACTCAACAGCAGCAACAACAACAAGATCCTAGT CCTAGCCGTCGCGGCGGTGATGTACTGTTACAGTGGGGACAACGAAAACGATCGAGAGCCTCTA GAGCTGAGATCCGATCCACCACCACCATCACAACCACCGCCGATGATTCTTCGTCTTCTTCAGG TCAAGGTAAGATACAATCAAACAAACCGCAAAGAAGATCGATGAATCCTTCTATGCCACCTCCA CCACCAGCTCCGCCGATTTTCTCGGGCCGGAGTACAAACCCTAGAAACGGTTTCGTTATCGGCA AGGAATCTTTCTTCCCTTCCAGGTTTAGCCTCAAATCTTTCTTCATTCAATTAAATTTCCATAT TTTGATATATTTACTTACCTTAAATGTTTTAGAATCGAGTTTGATTTGTCTTTTTTTACCTTTA ATCGTTTAGATTTTGTTACTGTAAATTAATCCATATGATCGTGACTTCATTAGCTTCCATATAT TTCTCTTTTTGTTCATCCATGTTATGTGATAAATAATGTGCCCTTGTTTTTATTTTTATATAAA GTAAAGCTATTTTTGATTTTCAAGGTTTGATATATTCAATTTAAATGATTTTCGTTTTCTGGTT TTTCATTTTTGAGATCTAAACAAACGTTTGGTTTCATCTTCTGTTAAAGCTTTAACGAAAGTTT GGTGATCCAAAATTCCTTTTTGGGAAATGACAGTAATACCCTTGGAAGCACTAAGAAGCAGAGA GTTGTGTCTCTTTTTCCTCAAGTGCTCAGTTTCTTAGGTTTTTCACTTGTTGTTTAGCTTTTGG GGTGAAAAATATATAAACGATTTTTCTCAATCTAATTTTTTTTTTTGGGTTAAATATAAGATCT CGTATTTTTCTTTGCCTTTCTTTGACCCAATCTTCAAATCTGGGCTACTTGTTTTGAAATCAAT CGATTATAGATTTCTTCTTATTTTCTGTTTTGGTCCCTCTCTTTTAGTTTTATTGTGTGTGTGT GTCTGCGTTTTGATTCTGATTCTTAAATATGTAAATGGGTACAACTAGTTTCCTTTTCTAAATT TCTTCCTTATTTTTAACACAAGGAGAAAAAAAAATTCATTAAACTCTCTCAAAGTTTATAGAAC TAACCTTTATTATACCAAAATTCAATCACCTGTGGATTTATTAAAGCTGTTCATCATCATCATC AATCATGCACAGGAATCTAGAAGATCGATCAGCAAACGGATCACCATCAAGGAACAACATAAAC GGCCGTATGATATCCAGATCGGGTGGCTCAAAGCGATCTCCACCGTCACCAGACCAAATCGAGA AGAGATCAAGCGTTAGAGATCAGAGACAAAACGGGTTTGATCATCAACAACAACAACATCAAAG AGTGAACAGATCAGAATCAACGGCTCAGGGTCATCAAGAAGTGGAGATAAATGGAGAAAGAGAG AAAGCAACGCAAGAGTGGCCGAGGATCTACATTGCTTTGTCTAGGAAAGAGAAGGAAGAAGATT TCTTGGTTATGAAAGGAACTAAGCTTCCTCATAGACCCAGGAAACGAGCTAAGAACATTGATAA AGCCCTTCAGGTAAAATTCATTAAAAAAAAAGTATTTATTTTTATCTCACAAGAGTTAAAAACA AAAAAAAAATCATAAATGAAAATATGTTTTAATTAATGTATTATTGTACAGTTTTGTTTTCCAG GGATGTGGTTATCTGATTTGACCAAGAACCGTTATGAAGTTAGGGAGAAGAAAAATGTGAAGAA G

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.256719976

Conservation Information
Conserved circRNAs	NA
PMCS	0.256719976

			
						 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

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

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

circRNA

Detail information of AT4G20300_circ_g.3

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