Plant Circular RNA Database

Detail information of AT4G21380_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT4G21380_circ_g.2
					
						ID in PlantcircBase
						ath_circ_031976
					
						Alias
						At_ciR481, AT4G21380_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 11390206-11390688  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI2
					
						Parent gene
						
							AT4G21380						
					
						Parent gene annotation
						
							Receptor-like serine/threonine-protein kinase SD1-8
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G21380_circ_g.1 AT4G21380_circ_g.3 AT4G21380_circ_g.4 						
					
						Support reads
						10/7
					
						Tissues
						leaf/leaf, aerial
					
						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
						AT4G21380.1:2
AT4G21380.2:2

General Information
CircRNA Name	AT4G21380_circ_g.2
ID in PlantcircBase	ath_circ_031976
Alias	At_ciR481, AT4G21380_C1
Organism	Arabidpsis thaliana
Position	chr4: 11390206-11390688 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI2
Parent gene	AT4G21380
Parent gene annotation	Receptor-like serine/threonine-protein kinase SD1-8
Parent gene strand	-
Alternative splicing	AT4G21380_circ_g.1 AT4G21380_circ_g.3 AT4G21380_circ_g.4
Support reads	10/7
Tissues	leaf/leaf, aerial
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	AT4G21380.1:2 AT4G21380.2:2

			
						 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  
						
							AATTCGAGATCGTCTGTATTGTTTTCTCTAGATATGTGTCTCCTACTTGATATTACAACTTCGT
TCATTAGCAAATCTCGGCTTCTCAGTTGATGATCAAcaaatagatgagagtcgaggcttagatt
ttccaagtactcgtaaatcaacatcttctcacccgcatcgacgcaacatgcaagaagcctaaca
aggtttat

						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: 239
Transcript exons: 11390206-11390260,11390280-11390380,11390606-11390688
CAAATAGATGAGAGTCGAGGCTTAGATTTTCCAAGTACTCGTAAATCAACATCTTCATGCAAGA
AGCCTAACAAGGTTTATGTGCTGAAGCCTTGCAATCAACTTTACCTCATTCTTGAACTCATCAG
TCCCCTGAACTGATGTCTTTGATAGTCTATTGTTTTCTCTAGATATGTGTCTCCTACTTGATAT
TACAACTTCGTTCATTAGCAAATCTCGGCTTCTCAGTTGATGATCAA
Transcript length: 405
Transcript exons: 11390206-11390416,11390495-11390688
CAAATAGATGAGAGTCGAGGCTTAGATTTTCCAAGTACTCGTAAATCAACATCTTCTCACCCGC
ATCGACGCAACATGCAAGAAGCCTAACAAGGTTTATGTGCTGAAGCCTTGCAATCAACTTTACC
TCATTCTTGAACTCATCAGTCCCCTGAACTGATGTCTTTGATAGTCTCTTCACTGCCATTTCTT
GACCATCAAGTAACTTTCCCTTATAAACTATACCAAAACCACCTTGTCCTAGCTTGTTGGCGTT
AGAAAAATTGTTTGTGGCCATGGCAACTTCTTCAAACTCCATCAATGGCAATTCGAGATCGTCT
GTATTGTTTTCTCTAGATATGTGTCTCCTACTTGATATTACAACTTCGTTCATTAGCAAATCTC
GGCTTCTCAGTTGATGATCAA
						
						Genomic sequence
						
							CAAATAGATGAGAGTCGAGGCTTAGATTTTCCAAGTACTCGTAAATCAACATCTTCTCACCCGC
ATCGACGCAACATGCAAGAAGCCTAACAAGGTTTATGTGCTGAAGCCTTGCAATCAACTTTACC
TCATTCTTGAACTCATCAGTCCCCTGAACTGATGTCTTTGATAGTCTCTTCACTGCCATTTCTT
GACCATCAAGTAACTTTCCCTGTAACCCTTAATTTTGTTACACAACGAAATATTTGTCCAGCGA
TAGATTATGAATTAAGTTTTCAATCATTTTTACCTTATAAACTATACCAAAACCACCTTGTCCT
AGCTTGTTGGCGTTAGAAAAATTGTTTGTGGCCATGGCAACTTCTTCAAACTCCATCAATGGCA
ATTCGAGATCGTCTGTATTGTTTTCTCTAGATATGTGTCTCCTACTTGATATTACAACTTCGTT
CATTAGCAAATCTCGGCTTCTCAGTTGATGATCAA

Sequences
Splice junction sequence	AATTCGAGATCGTCTGTATTGTTTTCTCTAGATATGTGTCTCCTACTTGATATTACAACTTCGT TCATTAGCAAATCTCGGCTTCTCAGTTGATGATCAAcaaatagatgagagtcgaggcttagatt ttccaagtactcgtaaatcaacatcttctcacccgcatcgacgcaacatgcaagaagcctaaca aggtttat
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: 239 Transcript exons: 11390206-11390260,11390280-11390380,11390606-11390688 CAAATAGATGAGAGTCGAGGCTTAGATTTTCCAAGTACTCGTAAATCAACATCTTCATGCAAGA AGCCTAACAAGGTTTATGTGCTGAAGCCTTGCAATCAACTTTACCTCATTCTTGAACTCATCAG TCCCCTGAACTGATGTCTTTGATAGTCTATTGTTTTCTCTAGATATGTGTCTCCTACTTGATAT TACAACTTCGTTCATTAGCAAATCTCGGCTTCTCAGTTGATGATCAA Transcript length: 405 Transcript exons: 11390206-11390416,11390495-11390688 CAAATAGATGAGAGTCGAGGCTTAGATTTTCCAAGTACTCGTAAATCAACATCTTCTCACCCGC ATCGACGCAACATGCAAGAAGCCTAACAAGGTTTATGTGCTGAAGCCTTGCAATCAACTTTACC TCATTCTTGAACTCATCAGTCCCCTGAACTGATGTCTTTGATAGTCTCTTCACTGCCATTTCTT GACCATCAAGTAACTTTCCCTTATAAACTATACCAAAACCACCTTGTCCTAGCTTGTTGGCGTT AGAAAAATTGTTTGTGGCCATGGCAACTTCTTCAAACTCCATCAATGGCAATTCGAGATCGTCT GTATTGTTTTCTCTAGATATGTGTCTCCTACTTGATATTACAACTTCGTTCATTAGCAAATCTC GGCTTCTCAGTTGATGATCAA
Genomic sequence	CAAATAGATGAGAGTCGAGGCTTAGATTTTCCAAGTACTCGTAAATCAACATCTTCTCACCCGC ATCGACGCAACATGCAAGAAGCCTAACAAGGTTTATGTGCTGAAGCCTTGCAATCAACTTTACC TCATTCTTGAACTCATCAGTCCCCTGAACTGATGTCTTTGATAGTCTCTTCACTGCCATTTCTT GACCATCAAGTAACTTTCCCTGTAACCCTTAATTTTGTTACACAACGAAATATTTGTCCAGCGA TAGATTATGAATTAAGTTTTCAATCATTTTTACCTTATAAACTATACCAAAACCACCTTGTCCT AGCTTGTTGGCGTTAGAAAAATTGTTTGTGGCCATGGCAACTTCTTCAAACTCCATCAATGGCA ATTCGAGATCGTCTGTATTGTTTTCTCTAGATATGTGTCTCCTACTTGATATTACAACTTCGTT CATTAGCAAATCTCGGCTTCTCAGTTGATGATCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.43548235

Conservation Information
Conserved circRNAs	NA
PMCS	0.43548235

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11390657-11390208(-)
						
						Potential amino acid sequence
						
							MNEVVISSRRHISRENNTDDLELPLMEFEEVAMATNNFSNANKLGQGGFGIVYKGKLLDGQEMA
VKRLSKTSVQGTDEFKNEVKLIARLQHINLVRLLACCVDAGEKMLIYEYLENLSLDSHLFVDHQ
LRSRDLLMNEVVISSRRHISRENNTDDLELPLMEFEEVAMATNNFSNANKLGQGGFGIVYKGKL
LDGQEMAVKRLSKTSVQGTDEFKNEVKLIARLQHINLVRLLACCVDAGEKMLIYEYLENLSLDS
HLFVDHQLRSRDLLMNEVVISSRRHISRENNTDDLELPLMEFEEVAMATNNFSNANKLGQGGFG
IVYKGKLLDGQEMAVKRLSKTSVQGTDEFKNEVKLIARLQHINLVRLLACCVDAGEKMLIYEYL
ENLSLDSHLFVDHQLRSRDLLMNEVVISSRRHISRENNTDDLELPLMEFEEVAMATNNFSNANK
LGQGGFGIVYKGKLLDGQEMAVKRLSKTSVQGTDEFKNEVKLIARLQHINLVRLLACCVDAGEK
MLIYEYLENLSLDSHLF(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	11390657-11390208(-)
Potential amino acid sequence	MNEVVISSRRHISRENNTDDLELPLMEFEEVAMATNNFSNANKLGQGGFGIVYKGKLLDGQEMA VKRLSKTSVQGTDEFKNEVKLIARLQHINLVRLLACCVDAGEKMLIYEYLENLSLDSHLFVDHQ LRSRDLLMNEVVISSRRHISRENNTDDLELPLMEFEEVAMATNNFSNANKLGQGGFGIVYKGKL LDGQEMAVKRLSKTSVQGTDEFKNEVKLIARLQHINLVRLLACCVDAGEKMLIYEYLENLSLDS HLFVDHQLRSRDLLMNEVVISSRRHISRENNTDDLELPLMEFEEVAMATNNFSNANKLGQGGFG IVYKGKLLDGQEMAVKRLSKTSVQGTDEFKNEVKLIARLQHINLVRLLACCVDAGEKMLIYEYL ENLSLDSHLFVDHQLRSRDLLMNEVVISSRRHISRENNTDDLELPLMEFEEVAMATNNFSNANK LGQGGFGIVYKGKLLDGQEMAVKRLSKTSVQGTDEFKNEVKLIARLQHINLVRLLACCVDAGEK MLIYEYLENLSLDSHLF(-)
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;Zhang et al., 2019

circRNA

Detail information of AT4G21380_circ_g.2

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