Plant Circular RNA Database

Detail information of AT1G76990_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G76990_circ_g.2
					
						ID in PlantcircBase
						ath_circ_010565
					
						Alias
						At_ciR438, AT1G76990_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 28933339-28935187  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI2
					
						Parent gene
						
							AT1G76990						
					
						Parent gene annotation
						
							ACR3
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G76990_circ_g.1 AT1G76990_circ_g.3 AT1G76990_circ_g.4 						
					
						Support reads
						18/2
					
						Tissues
						leaf/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  
						
							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
						AT1G76990.3:6
AT1G76990.4:6
AT1G76990.5:6
AT1G76990.2:6
AT1G76990.1:6

General Information
CircRNA Name	AT1G76990_circ_g.2
ID in PlantcircBase	ath_circ_010565
Alias	At_ciR438, AT1G76990_C1
Organism	Arabidpsis thaliana
Position	chr1: 28933339-28935187 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI2
Parent gene	AT1G76990
Parent gene annotation	ACR3
Parent gene strand	+
Alternative splicing	AT1G76990_circ_g.1 AT1G76990_circ_g.3 AT1G76990_circ_g.4
Support reads	18/2
Tissues	leaf/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	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	AT1G76990.3:6 AT1G76990.4:6 AT1G76990.5:6 AT1G76990.2:6 AT1G76990.1:6

			
						 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  
						
							AATGGAAAGAAGAAGGTCAAGCCGGAACAGGAGGAGGATGGGCCAAAACCAGTTTCTTCTTTGG
GAATTTGCTGGAGAAGTTACTGCCTTGAGAGAAAAGaacaagtgaaagagcttaatatccacaa
gactcttgtttctttcttaaatggctaaagtttattggccttatttcgatcctgaatatgagaa
cttgagct

									
								

					

						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: 1418
Transcript exons: 28933339-28933457,28933540-28933585,28933667-28933781,28
933873-28933940,28934035-28934757,28934841-28935187
AACAAGTGAAAGAGCTTAATATCCACAAGACTCTTGTTTCTTTCTTAAATGGCTAAAGTTTATT
GGCCTTATTTCGATCCTGAATATGAGAACTTGAGCTCCAGAATCAATCCTCCAAGTGTTTCTAT
AGATAACACTAGCTGCAAAGAATGCACTCTTGTCAAGGTGGACAGTATGAACAAACCTGGAATA
CTACTTGAAGTTGTGCAAGTCCTAACCGATCTCGATCTCACTATCACTAAAGCTTATATCTCTT
CTGATGGTGGATGGTTCATGGACGTATTCCATGTCACCGATCAACAAGGAAACAAGGTTACTGA
TAGCAAAACCATCGATTACATCGAGAAGGTGTTAGGACCAAAGGGTCATGCTTCGGCTTCACAA
AACACTTGGCCTGGTAAAAGAGTCGGTGTCCATTCATTAGGCGACCACACATCGATAGAGATTA
TTGCTCGTGATCGTCCTGGTCTCTTGTCGGAGGTTTCAGCCGTACTAGCAGACCTCAACATTAA
TGTGGTGGCAGCTGAAGCATGGACTCACAACCGTAGGATTGCGTGTGTCCTCTATGTGAATGAC
AATGCAACTTCTAGAGCCGTTGATGATCCAGAAAGATTGTCTTCCATGGAAGAACAGCTTAACA
ATGTGCTGCGTGGGTGCGAAGAACAAGATGAGAAATTTGCTCGGACGAGTCTCTCCATTGGGTC
GACTCACGTTGATCGAAGGCTTCATCAGATGTTTTTCGCTGATAGAGACTACGAAGCAGTGACT
AAGCTTGATGATTCTGCTTCTTGCGGATTCGAGCCCAAAATCACGGTTGAGCATTGTGAAGAGA
AAGGTTACTCCGTGATAAACGTGAGCTGCGAGGATCGACCAAAGCTCATGTTTGACATTGTATG
CACGCTTACGGATATGCAATACATTGTGTTTCACGCCACGATTTCATCAAGCGGCTCTCATGCT
TCTCAGGAGTATTTCATCAGACACAAAGACGGTTGCACTCTTGACACAGAAGGAGAGAAAGAGA
GAGTTGTCAAATGTCTGGAAGCTGCAATCCATAGACGAGTCAGCGAGGGTTGGAGTTTGGAGCT
CTGCGCAAAGGACAGAGTTGGATTACTGTCGGAAGTGACAAGGATTCTGAGAGAGCACGGGCTA
TCAGTGTCGAGAGCTGGTGTGACAACAGTAGGAGAACAAGCCGTCAACGTTTTCTATGTGAAAG
ATGCTTCAGGGAATCCAGTGGATGTGAAGACGATTGAGGCGTTACGCGGAGAGATTGGACACAG
TATGATGATTGACTTCAAGAATAAAGTTCCGAGCAGAAAATGGAAAGAAGAAGGTCAAGCCGGA
ACAGGAGGAGGATGGGCCAAAACCAGTTTCTTCTTTGGGAATTTGCTGGAGAAGTTACTGCCTT
GAGAGAAAAG
						
					

						Genomic sequence
						
							AACAAGTGAAAGAGCTTAATATCCACAAGACTCTTGTTTCTTTCTTAAATGGCTAAAGTTTATT
GGCCTTATTTCGATCCTGAATATGAGAACTTGAGCTCCAGAATCAATCCTCCAAGGTAAATCAT
TATTACATTTCACACTTGAAACCCATTGATGCTACTTCCAAGAAGCTCATACTTTTTTTCTATG
TTGTTGCAGTGTTTCTATAGATAACACTAGCTGCAAAGAATGCACTCTTGTCAAGGTAAGCATC
TTCTTCCTCTGATTTTAGTTGATTCGATGATTAAACTGAGATTTTGATGCATTTGTGACTGTTA
ATTATTAGGTGGACAGTATGAACAAACCTGGAATACTACTTGAAGTTGTGCAAGTCCTAACCGA
TCTCGATCTCACTATCACTAAAGCTTATATCTCTTCTGATGGTGGATGGTTCATGGACGGTACT
AATTTTGCATATATGTATATACATTCATAACTTATTATTTCATTACAATGAAGCATCTCACTGA
TTCTATTTTCACATCTTTTTAGTATTCCATGTCACCGATCAACAAGGAAACAAGGTTACTGATA
GCAAAACCATCGATTACATCGAGAAGGTATATTCATATAAGCAGTAGTTTGTATAATATATGCA
ATTGGTTTGTTATGACATTATATGTGATTCTTTTTTTTTCTTTTTTCTTTTAAAAGGTGTTAGG
ACCAAAGGGTCATGCTTCGGCTTCACAAAACACTTGGCCTGGTAAAAGAGTCGGTGTCCATTCA
TTAGGCGACCACACATCGATAGAGATTATTGCTCGTGATCGTCCTGGTCTCTTGTCGGAGGTTT
CAGCCGTACTAGCAGACCTCAACATTAATGTGGTGGCAGCTGAAGCATGGACTCACAACCGTAG
GATTGCGTGTGTCCTCTATGTGAATGACAATGCAACTTCTAGAGCCGTTGATGATCCAGAAAGA
TTGTCTTCCATGGAAGAACAGCTTAACAATGTGCTGCGTGGGTGCGAAGAACAAGATGAGAAAT
TTGCTCGGACGAGTCTCTCCATTGGGTCGACTCACGTTGATCGAAGGCTTCATCAGATGTTTTT
CGCTGATAGAGACTACGAAGCAGTGACTAAGCTTGATGATTCTGCTTCTTGCGGATTCGAGCCC
AAAATCACGGTTGAGCATTGTGAAGAGAAAGGTTACTCCGTGATAAACGTGAGCTGCGAGGATC
GACCAAAGCTCATGTTTGACATTGTATGCACGCTTACGGATATGCAATACATTGTGTTTCACGC
CACGATTTCATCAAGCGGCTCTCATGCTTCTCAGGAGTATTTCATCAGACACAAAGACGGTTGC
ACTCTTGACACAGAAGGAGAGAAAGAGAGAGTTGTCAAATGTCTGGAAGCTGCAATCCATAGAC
GAGTCAGCGAGGTAAGTAAACACATTTTGTTGGTGTATGTTTCTTGCGTTAGAAGCAACAATAC
CTTAAGTTATTGTCTGAAATTTGATTATAGGGTTGGAGTTTGGAGCTCTGCGCAAAGGACAGAG
TTGGATTACTGTCGGAAGTGACAAGGATTCTGAGAGAGCACGGGCTATCAGTGTCGAGAGCTGG
TGTGACAACAGTAGGAGAACAAGCCGTCAACGTTTTCTATGTGAAAGATGCTTCAGGGAATCCA
GTGGATGTGAAGACGATTGAGGCGTTACGCGGAGAGATTGGACACAGTATGATGATTGACTTCA
AGAATAAAGTTCCGAGCAGAAAATGGAAAGAAGAAGGTCAAGCCGGAACAGGAGGAGGATGGGC
CAAAACCAGTTTCTTCTTTGGGAATTTGCTGGAGAAGTTACTGCCTTGAGAGAAAAG
						
					

			
		

Sequences
Splice junction sequence	AATGGAAAGAAGAAGGTCAAGCCGGAACAGGAGGAGGATGGGCCAAAACCAGTTTCTTCTTTGG GAATTTGCTGGAGAAGTTACTGCCTTGAGAGAAAAGaacaagtgaaagagcttaatatccacaa gactcttgtttctttcttaaatggctaaagtttattggccttatttcgatcctgaatatgagaa cttgagct
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: 1418 Transcript exons: 28933339-28933457,28933540-28933585,28933667-28933781,28 933873-28933940,28934035-28934757,28934841-28935187 AACAAGTGAAAGAGCTTAATATCCACAAGACTCTTGTTTCTTTCTTAAATGGCTAAAGTTTATT GGCCTTATTTCGATCCTGAATATGAGAACTTGAGCTCCAGAATCAATCCTCCAAGTGTTTCTAT AGATAACACTAGCTGCAAAGAATGCACTCTTGTCAAGGTGGACAGTATGAACAAACCTGGAATA CTACTTGAAGTTGTGCAAGTCCTAACCGATCTCGATCTCACTATCACTAAAGCTTATATCTCTT CTGATGGTGGATGGTTCATGGACGTATTCCATGTCACCGATCAACAAGGAAACAAGGTTACTGA TAGCAAAACCATCGATTACATCGAGAAGGTGTTAGGACCAAAGGGTCATGCTTCGGCTTCACAA AACACTTGGCCTGGTAAAAGAGTCGGTGTCCATTCATTAGGCGACCACACATCGATAGAGATTA TTGCTCGTGATCGTCCTGGTCTCTTGTCGGAGGTTTCAGCCGTACTAGCAGACCTCAACATTAA TGTGGTGGCAGCTGAAGCATGGACTCACAACCGTAGGATTGCGTGTGTCCTCTATGTGAATGAC AATGCAACTTCTAGAGCCGTTGATGATCCAGAAAGATTGTCTTCCATGGAAGAACAGCTTAACA ATGTGCTGCGTGGGTGCGAAGAACAAGATGAGAAATTTGCTCGGACGAGTCTCTCCATTGGGTC GACTCACGTTGATCGAAGGCTTCATCAGATGTTTTTCGCTGATAGAGACTACGAAGCAGTGACT AAGCTTGATGATTCTGCTTCTTGCGGATTCGAGCCCAAAATCACGGTTGAGCATTGTGAAGAGA AAGGTTACTCCGTGATAAACGTGAGCTGCGAGGATCGACCAAAGCTCATGTTTGACATTGTATG CACGCTTACGGATATGCAATACATTGTGTTTCACGCCACGATTTCATCAAGCGGCTCTCATGCT TCTCAGGAGTATTTCATCAGACACAAAGACGGTTGCACTCTTGACACAGAAGGAGAGAAAGAGA GAGTTGTCAAATGTCTGGAAGCTGCAATCCATAGACGAGTCAGCGAGGGTTGGAGTTTGGAGCT CTGCGCAAAGGACAGAGTTGGATTACTGTCGGAAGTGACAAGGATTCTGAGAGAGCACGGGCTA TCAGTGTCGAGAGCTGGTGTGACAACAGTAGGAGAACAAGCCGTCAACGTTTTCTATGTGAAAG ATGCTTCAGGGAATCCAGTGGATGTGAAGACGATTGAGGCGTTACGCGGAGAGATTGGACACAG TATGATGATTGACTTCAAGAATAAAGTTCCGAGCAGAAAATGGAAAGAAGAAGGTCAAGCCGGA ACAGGAGGAGGATGGGCCAAAACCAGTTTCTTCTTTGGGAATTTGCTGGAGAAGTTACTGCCTT GAGAGAAAAG
Genomic sequence	AACAAGTGAAAGAGCTTAATATCCACAAGACTCTTGTTTCTTTCTTAAATGGCTAAAGTTTATT GGCCTTATTTCGATCCTGAATATGAGAACTTGAGCTCCAGAATCAATCCTCCAAGGTAAATCAT TATTACATTTCACACTTGAAACCCATTGATGCTACTTCCAAGAAGCTCATACTTTTTTTCTATG TTGTTGCAGTGTTTCTATAGATAACACTAGCTGCAAAGAATGCACTCTTGTCAAGGTAAGCATC TTCTTCCTCTGATTTTAGTTGATTCGATGATTAAACTGAGATTTTGATGCATTTGTGACTGTTA ATTATTAGGTGGACAGTATGAACAAACCTGGAATACTACTTGAAGTTGTGCAAGTCCTAACCGA TCTCGATCTCACTATCACTAAAGCTTATATCTCTTCTGATGGTGGATGGTTCATGGACGGTACT AATTTTGCATATATGTATATACATTCATAACTTATTATTTCATTACAATGAAGCATCTCACTGA TTCTATTTTCACATCTTTTTAGTATTCCATGTCACCGATCAACAAGGAAACAAGGTTACTGATA GCAAAACCATCGATTACATCGAGAAGGTATATTCATATAAGCAGTAGTTTGTATAATATATGCA ATTGGTTTGTTATGACATTATATGTGATTCTTTTTTTTTCTTTTTTCTTTTAAAAGGTGTTAGG ACCAAAGGGTCATGCTTCGGCTTCACAAAACACTTGGCCTGGTAAAAGAGTCGGTGTCCATTCA TTAGGCGACCACACATCGATAGAGATTATTGCTCGTGATCGTCCTGGTCTCTTGTCGGAGGTTT CAGCCGTACTAGCAGACCTCAACATTAATGTGGTGGCAGCTGAAGCATGGACTCACAACCGTAG GATTGCGTGTGTCCTCTATGTGAATGACAATGCAACTTCTAGAGCCGTTGATGATCCAGAAAGA TTGTCTTCCATGGAAGAACAGCTTAACAATGTGCTGCGTGGGTGCGAAGAACAAGATGAGAAAT TTGCTCGGACGAGTCTCTCCATTGGGTCGACTCACGTTGATCGAAGGCTTCATCAGATGTTTTT CGCTGATAGAGACTACGAAGCAGTGACTAAGCTTGATGATTCTGCTTCTTGCGGATTCGAGCCC AAAATCACGGTTGAGCATTGTGAAGAGAAAGGTTACTCCGTGATAAACGTGAGCTGCGAGGATC GACCAAAGCTCATGTTTGACATTGTATGCACGCTTACGGATATGCAATACATTGTGTTTCACGC CACGATTTCATCAAGCGGCTCTCATGCTTCTCAGGAGTATTTCATCAGACACAAAGACGGTTGC ACTCTTGACACAGAAGGAGAGAAAGAGAGAGTTGTCAAATGTCTGGAAGCTGCAATCCATAGAC GAGTCAGCGAGGTAAGTAAACACATTTTGTTGGTGTATGTTTCTTGCGTTAGAAGCAACAATAC CTTAAGTTATTGTCTGAAATTTGATTATAGGGTTGGAGTTTGGAGCTCTGCGCAAAGGACAGAG TTGGATTACTGTCGGAAGTGACAAGGATTCTGAGAGAGCACGGGCTATCAGTGTCGAGAGCTGG TGTGACAACAGTAGGAGAACAAGCCGTCAACGTTTTCTATGTGAAAGATGCTTCAGGGAATCCA GTGGATGTGAAGACGATTGAGGCGTTACGCGGAGAGATTGGACACAGTATGATGATTGACTTCA AGAATAAAGTTCCGAGCAGAAAATGGAAAGAAGAAGGTCAAGCCGGAACAGGAGGAGGATGGGC CAAAACCAGTTTCTTCTTTGGGAATTTGCTGGAGAAGTTACTGCCTTGAGAGAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.341411123

Conservation Information
Conserved circRNAs	NA
PMCS	0.341411123

			
						 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;Zhang et al., 2019

circRNA

Detail information of AT1G76990_circ_g.2

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