Plant Circular RNA Database

Detail information of AT4G24000_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT4G24000_circ_g.1
					
						ID in PlantcircBase
						ath_circ_032437
					
						Alias
						AT4G24000_C1, AT4G24000_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 12463423-12464298  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							AT4G24000						
					
						Parent gene annotation
						
							Glycosyltransferase (Fragment)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							4_circ_ag.5 4_circ_ag.6 4_circ_ag.7 4_circ_ag.2 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						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
						AT4G24000.2:3
AT4G24000.1:3

General Information
CircRNA Name	AT4G24000_circ_g.1
ID in PlantcircBase	ath_circ_032437
Alias	AT4G24000_C1, AT4G24000_C1
Organism	Arabidpsis thaliana
Position	chr4: 12463423-12464298 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	AT4G24000
Parent gene annotation	Glycosyltransferase (Fragment)
Parent gene strand	+
Alternative splicing	4_circ_ag.5 4_circ_ag.6 4_circ_ag.7 4_circ_ag.2
Support reads	NA
Tissues	leaf
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	AT4G24000.2:3 AT4G24000.1:3

			
						 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  
						
							TCGGATTGCCGATAAGCCCATTAAAGCCCAAGATATTTTGGCGTTGGCACACGATGTAGCAGGA
TGTAACTACGAGTGCAACACCAATTGGGGATCCAAGatgatgtacgaagacatgaagagtagag
tcgaacatgtggtcgagagcggaaaagttgagactgcgtttatcgcatgcgatcaatttagttg
tgtgttcg

									
								

					

						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: 702
Transcript exons: 12463423-12463572,12463663-12463770,12463855-12464298
ATGATGTACGAAGACATGAAGAGTAGAGTCGAACATGTGGTCGAGAGCGGAAAAGTTGAGACTG
CGTTTATCGCATGCGATCAATTTAGTTGTGTGTTCGATCTGTGGACAGATAAATTCACTCGTCA
TGACCATCCTACCATTATTATGGTGCTACAACATAACGAAACAGAGATGATGCCAAACCTTATA
TATGTTTCAAGAGAAAAGAGTAAAGTTTCACCACATCATTTCAAAGCCGGTGCTCTTAATACTT
TGTTACGTGTATCTGCCGTGATGACAAACTCACCAATCATTCTAACACTAGATTGTGACATGTA
CTCAAACAATCCTACAACACCACTTCATGCTCTGTGCTATTTGTCAGACCCTAAAATCAATTTT
GATTTAGGATTTGTGCAATTTCCTCAAAAATTTCAAGGAGTAAACAAAAATGATATTTATGCAT
CCGAGCTCAAACGCCCATTTGACATCAACACGGTTGGGTTTGATGGACTTATGGGACCAGTTCA
TATGGGAACTGGGTGTTTCTTCAATCGACGGGCGTTTTATGGGCCTCCGACTACTTTGATTTTG
CCTGAGATAGAAACATTTGGGCCAAATCGGATTGCCGATAAGCCCATTAAAGCCCAAGATATTT
TGGCGTTGGCACACGATGTAGCAGGATGTAACTACGAGTGCAACACCAATTGGGGATCCAAG
						
					

						Genomic sequence
						
							ATGATGTACGAAGACATGAAGAGTAGAGTCGAACATGTGGTCGAGAGCGGAAAAGTTGAGACTG
CGTTTATCGCATGCGATCAATTTAGTTGTGTGTTCGATCTGTGGACAGATAAATTCACTCGTCA
TGACCATCCTACCATTATTATGGTATGTAACTATTTTGTAATGCATGGTAAAAGTTTCGTCACA
AATTAATGTTTCTAAAAACTCGTTTTTATCTATTAATTTGTGGTGAAGGTGCTACAACATAACG
AAACAGAGATGATGCCAAACCTTATATATGTTTCAAGAGAAAAGAGTAAAGTTTCACCACATCA
TTTCAAAGCCGGTGCTCTTAATACTTTGGTATCAACTAATCCATATCTCGGTTAAACTGTCATT
TCTATATTTGTAATATTTCGTTAACCACAACATGTATTTTCTTTGTAGTTACGTGTATCTGCCG
TGATGACAAACTCACCAATCATTCTAACACTAGATTGTGACATGTACTCAAACAATCCTACAAC
ACCACTTCATGCTCTGTGCTATTTGTCAGACCCTAAAATCAATTTTGATTTAGGATTTGTGCAA
TTTCCTCAAAAATTTCAAGGAGTAAACAAAAATGATATTTATGCATCCGAGCTCAAACGCCCAT
TTGACATCAACACGGTTGGGTTTGATGGACTTATGGGACCAGTTCATATGGGAACTGGGTGTTT
CTTCAATCGACGGGCGTTTTATGGGCCTCCGACTACTTTGATTTTGCCTGAGATAGAAACATTT
GGGCCAAATCGGATTGCCGATAAGCCCATTAAAGCCCAAGATATTTTGGCGTTGGCACACGATG
TAGCAGGATGTAACTACGAGTGCAACACCAATTGGGGATCCAAG
						
					

			
		

Sequences
Splice junction sequence	TCGGATTGCCGATAAGCCCATTAAAGCCCAAGATATTTTGGCGTTGGCACACGATGTAGCAGGA TGTAACTACGAGTGCAACACCAATTGGGGATCCAAGatgatgtacgaagacatgaagagtagag tcgaacatgtggtcgagagcggaaaagttgagactgcgtttatcgcatgcgatcaatttagttg tgtgttcg
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: 702 Transcript exons: 12463423-12463572,12463663-12463770,12463855-12464298 ATGATGTACGAAGACATGAAGAGTAGAGTCGAACATGTGGTCGAGAGCGGAAAAGTTGAGACTG CGTTTATCGCATGCGATCAATTTAGTTGTGTGTTCGATCTGTGGACAGATAAATTCACTCGTCA TGACCATCCTACCATTATTATGGTGCTACAACATAACGAAACAGAGATGATGCCAAACCTTATA TATGTTTCAAGAGAAAAGAGTAAAGTTTCACCACATCATTTCAAAGCCGGTGCTCTTAATACTT TGTTACGTGTATCTGCCGTGATGACAAACTCACCAATCATTCTAACACTAGATTGTGACATGTA CTCAAACAATCCTACAACACCACTTCATGCTCTGTGCTATTTGTCAGACCCTAAAATCAATTTT GATTTAGGATTTGTGCAATTTCCTCAAAAATTTCAAGGAGTAAACAAAAATGATATTTATGCAT CCGAGCTCAAACGCCCATTTGACATCAACACGGTTGGGTTTGATGGACTTATGGGACCAGTTCA TATGGGAACTGGGTGTTTCTTCAATCGACGGGCGTTTTATGGGCCTCCGACTACTTTGATTTTG CCTGAGATAGAAACATTTGGGCCAAATCGGATTGCCGATAAGCCCATTAAAGCCCAAGATATTT TGGCGTTGGCACACGATGTAGCAGGATGTAACTACGAGTGCAACACCAATTGGGGATCCAAG
Genomic sequence	ATGATGTACGAAGACATGAAGAGTAGAGTCGAACATGTGGTCGAGAGCGGAAAAGTTGAGACTG CGTTTATCGCATGCGATCAATTTAGTTGTGTGTTCGATCTGTGGACAGATAAATTCACTCGTCA TGACCATCCTACCATTATTATGGTATGTAACTATTTTGTAATGCATGGTAAAAGTTTCGTCACA AATTAATGTTTCTAAAAACTCGTTTTTATCTATTAATTTGTGGTGAAGGTGCTACAACATAACG AAACAGAGATGATGCCAAACCTTATATATGTTTCAAGAGAAAAGAGTAAAGTTTCACCACATCA TTTCAAAGCCGGTGCTCTTAATACTTTGGTATCAACTAATCCATATCTCGGTTAAACTGTCATT TCTATATTTGTAATATTTCGTTAACCACAACATGTATTTTCTTTGTAGTTACGTGTATCTGCCG TGATGACAAACTCACCAATCATTCTAACACTAGATTGTGACATGTACTCAAACAATCCTACAAC ACCACTTCATGCTCTGTGCTATTTGTCAGACCCTAAAATCAATTTTGATTTAGGATTTGTGCAA TTTCCTCAAAAATTTCAAGGAGTAAACAAAAATGATATTTATGCATCCGAGCTCAAACGCCCAT TTGACATCAACACGGTTGGGTTTGATGGACTTATGGGACCAGTTCATATGGGAACTGGGTGTTT CTTCAATCGACGGGCGTTTTATGGGCCTCCGACTACTTTGATTTTGCCTGAGATAGAAACATTT GGGCCAAATCGGATTGCCGATAAGCCCATTAAAGCCCAAGATATTTTGGCGTTGGCACACGATG TAGCAGGATGTAACTACGAGTGCAACACCAATTGGGGATCCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.233378438

Conservation Information
Conserved circRNAs	NA
PMCS	0.233378438

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12463424-12464295(+)
						
						Potential amino acid sequence
						
							MMYEDMKSRVEHVVESGKVETAFIACDQFSCVFDLWTDKFTRHDHPTIIMVLQHNETEMMPNLI
YVSREKSKVSPHHFKAGALNTLLRVSAVMTNSPIILTLDCDMYSNNPTTPLHALCYLSDPKINF
DLGFVQFPQKFQGVNKNDIYASELKRPFDINTVGFDGLMGPVHMGTGCFFNRRAFYGPPTTLIL
PEIETFGPNRIADKPIKAQDILALAHDVAGCNYECNTNWGSKMMYEDMKSRVEHVVESGKVETA
FIACDQFSCVFDLWTDKFTRHDHPTIIMVLQHNETEMMPNLIYVSREKSKVSPHHFKAGALNTL
LRVSAVMTNSPIILTLDCDMYSNNPTTPLHALCYLSDPKINFDLGFVQFPQKFQGVNKNDIYAS
ELKRPFDINTVGFDGLMGPVHMGTGCFFNRRAFYGPPTTLILPEIETFGPNRIADKPIKAQDIL
ALAHDVAGCNYECNTNWGSKMMYEDMKSRVEHVVESGKVETAFIACDQFSCVFDLWTDKFTRHD
HPTIIMVLQHNETEMMPNLIYVSREKSKVSPHHFKAGALNTLLRVSAVMTNSPIILTLDCDMYS
NNPTTPLHALCYLSDPKINFDLGFVQFPQKFQGVNKNDIYASELKRPFDINTVGFDGLMGPVHM
GTGCFFNRRAFYGPPTTLILPEIETFGPNRIADKPIKAQDILALAHDVAGCNYECNTNWGSKMM
YEDMKSRVEHVVESGKVETAFIACDQFSCVFDLWTDKFTRHDHPTIIMVLQHNETEMMPNLIYV
SREKSKVSPHHFKAGALNTLLRVSAVMTNSPIILTLDCDMYSNNPTTPLHALCYLSDPKINFDL
GFVQFPQKFQGVNKNDIYASELKRPFDINTVGFDGLMGPVHMGTGCFFNRRAFYGPPTTLILPE
IETFGPNRIADKPIKAQDILALAHDVAGCNYECNTNWGSK
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	12463424-12464295(+)
Potential amino acid sequence	MMYEDMKSRVEHVVESGKVETAFIACDQFSCVFDLWTDKFTRHDHPTIIMVLQHNETEMMPNLI YVSREKSKVSPHHFKAGALNTLLRVSAVMTNSPIILTLDCDMYSNNPTTPLHALCYLSDPKINF DLGFVQFPQKFQGVNKNDIYASELKRPFDINTVGFDGLMGPVHMGTGCFFNRRAFYGPPTTLIL PEIETFGPNRIADKPIKAQDILALAHDVAGCNYECNTNWGSKMMYEDMKSRVEHVVESGKVETA FIACDQFSCVFDLWTDKFTRHDHPTIIMVLQHNETEMMPNLIYVSREKSKVSPHHFKAGALNTL LRVSAVMTNSPIILTLDCDMYSNNPTTPLHALCYLSDPKINFDLGFVQFPQKFQGVNKNDIYAS ELKRPFDINTVGFDGLMGPVHMGTGCFFNRRAFYGPPTTLILPEIETFGPNRIADKPIKAQDIL ALAHDVAGCNYECNTNWGSKMMYEDMKSRVEHVVESGKVETAFIACDQFSCVFDLWTDKFTRHD HPTIIMVLQHNETEMMPNLIYVSREKSKVSPHHFKAGALNTLLRVSAVMTNSPIILTLDCDMYS NNPTTPLHALCYLSDPKINFDLGFVQFPQKFQGVNKNDIYASELKRPFDINTVGFDGLMGPVHM GTGCFFNRRAFYGPPTTLILPEIETFGPNRIADKPIKAQDILALAHDVAGCNYECNTNWGSKMM YEDMKSRVEHVVESGKVETAFIACDQFSCVFDLWTDKFTRHDHPTIIMVLQHNETEMMPNLIYV SREKSKVSPHHFKAGALNTLLRVSAVMTNSPIILTLDCDMYSNNPTTPLHALCYLSDPKINFDL GFVQFPQKFQGVNKNDIYASELKRPFDINTVGFDGLMGPVHMGTGCFFNRRAFYGPPTTLILPE IETFGPNRIADKPIKAQDILALAHDVAGCNYECNTNWGSK
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

			
						 Other Information
					
						References
						Zhang et al., 2019

circRNA

Detail information of AT4G24000_circ_g.1

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