Plant Circular RNA Database

Detail information of AT2G28290_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT2G28290_circ_g.3
					
						ID in PlantcircBase
						ath_circ_015314
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 12058560-12059623  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT2G28290						
					
						Parent gene annotation
						
							P-loop containing nucleoside triphosphate hydrolases superfamily
 protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						1
					
						Tissues
						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  
						
							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
						AT2G28290.5:4
AT2G28290.6:4
AT2G28290.4:4
AT2G28290.1:4
AT2G28290.3:4
AT2G28290.2:4

General Information
CircRNA Name	AT2G28290_circ_g.3
ID in PlantcircBase	ath_circ_015314
Alias	NA
Organism	Arabidpsis thaliana
Position	chr2: 12058560-12059623 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT2G28290
Parent gene annotation	P-loop containing nucleoside triphosphate hydrolases superfamily protein
Parent gene strand	+
Alternative splicing	NA
Support reads	1
Tissues	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	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	AT2G28290.5:4 AT2G28290.6:4 AT2G28290.4:4 AT2G28290.1:4 AT2G28290.3:4 AT2G28290.2:4

			
						 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  
						
							TATGGGTCGACAGAATAAGAGACTATTGGTTGATCGTAGTTGGTCCCTTAAACAGCAGAAAGCC
GACCAGGCAATTGGTTCACGGTTCAATGAGTTGAAGtgtggctggcagagcagtgaagccacag
caatcaggcctgcaattcataaagaacctggaaataatgttgcaggagagggattcctgccttc
aggttcac

									
								

					

						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: 777
Transcript exons: 12058560-12058720,12058808-12058872,12058955-12059347,12
059466-12059623
TGTGGCTGGCAGAGCAGTGAAGCCACAGCAATCAGGCCTGCAATTCATAAAGAACCTGGAAATA
ATGTTGCAGGAGAGGGATTCCTGCCTTCAGGTTCACCTTTTAGAGAGCAACAACTGAAGCAGCT
CAGAGCCCAGTGCCTTGTGTTTCTAGCTCTTAGAAATGGTTTGGTACCGAAGAAACTTCACGTA
GAGATTGCCCTTCGAAATACTTTCCGCGAAGAAGATGGTTTCCGCGGAGAATTGTTTGATCCGA
AAGGGAGAACACATACGTCCAGTGATCTGGGTGGCATTCCTGACGTCTCTGCACTGTTGTCAAG
AACAGACAATCCCACTGGAAGATTGGATGAAATGGACTTCTCATCCAAAGAAACTGAGAGATCA
AGACTAGGGGAAAAAAGTTTCGCAAATACTGTATTTTCTGACGGGCAAAAGCTTCTAGCATCTA
GAATTCCCAGCTCTCAAGCACAAACTCAGGTTGCTGTTAGTCATTCTCAACTAACGTTTTCTCC
TGGTTTGACCAAAAACACACCATCAGAGATGGTGGGGTGGACTGGAGTAATCAAAACTAATGAC
CTCTCAACTTCTGCTGTTCAACTCGACGAATTTCATTCTTCTGATGAAGAGGAAGGTAATTTGC
AACCGTCGCCTAAGTACACCATGTCACAGAAATGGATTATGGGTCGACAGAATAAGAGACTATT
GGTTGATCGTAGTTGGTCCCTTAAACAGCAGAAAGCCGACCAGGCAATTGGTTCACGGTTCAAT
GAGTTGAAG
Transcript length: 780
Transcript exons: 12058560-12058720,12058808-12058872,12058955-12059347,12
059463-12059623
TGTGGCTGGCAGAGCAGTGAAGCCACAGCAATCAGGCCTGCAATTCATAAAGAACCTGGAAATA
ATGTTGCAGGAGAGGGATTCCTGCCTTCAGGTTCACCTTTTAGAGAGCAACAACTGAAGCAGCT
CAGAGCCCAGTGCCTTGTGTTTCTAGCTCTTAGAAATGGTTTGGTACCGAAGAAACTTCACGTA
GAGATTGCCCTTCGAAATACTTTCCGCGAAGAAGATGGTTTCCGCGGAGAATTGTTTGATCCGA
AAGGGAGAACACATACGTCCAGTGATCTGGGTGGCATTCCTGACGTCTCTGCACTGTTGTCAAG
AACAGACAATCCCACTGGAAGATTGGATGAAATGGACTTCTCATCCAAAGAAACTGAGAGATCA
AGACTAGGGGAAAAAAGTTTCGCAAATACTGTATTTTCTGACGGGCAAAAGCTTCTAGCATCTA
GAATTCCCAGCTCTCAAGCACAAACTCAGGTTGCTGTTAGTCATTCTCAACTAACGTTTTCTCC
TGGTTTGACCAAAAACACACCATCAGAGATGGTGGGGTGGACTGGAGTAATCAAAACTAATGAC
CTCTCAACTTCTGCTGTTCAACTCGACGAATTTCATTCTTCTGCAGATGAAGAGGAAGGTAATT
TGCAACCGTCGCCTAAGTACACCATGTCACAGAAATGGATTATGGGTCGACAGAATAAGAGACT
ATTGGTTGATCGTAGTTGGTCCCTTAAACAGCAGAAAGCCGACCAGGCAATTGGTTCACGGTTC
AATGAGTTGAAG
						
					

						Genomic sequence
						
							TGTGGCTGGCAGAGCAGTGAAGCCACAGCAATCAGGCCTGCAATTCATAAAGAACCTGGAAATA
ATGTTGCAGGAGAGGGATTCCTGCCTTCAGGTTCACCTTTTAGAGAGCAACAACTGAAGCAGCT
CAGAGCCCAGTGCCTTGTGTTTCTAGCTCTTAGGTACCTTACAGTCTCCTAGCCTCTGTATACT
CCTTTTGGTGCGGCAATTGTAACTCTAAAAATTTCTGGTTGATTTTCATCTCGTAGAAATGGTT
TGGTACCGAAGAAACTTCACGTAGAGATTGCCCTTCGAAATACTTTCCGCGAAGAAGGTAATGT
TGGTGCTCACTGAAGTTACTTTCGAATCCACTTTTTACATGCTTTCCCTTGGATCATAATTGGT
CTTCATTACAGATGGTTTCCGCGGAGAATTGTTTGATCCGAAAGGGAGAACACATACGTCCAGT
GATCTGGGTGGCATTCCTGACGTCTCTGCACTGTTGTCAAGAACAGACAATCCCACTGGAAGAT
TGGATGAAATGGACTTCTCATCCAAAGAAACTGAGAGATCAAGACTAGGGGAAAAAAGTTTCGC
AAATACTGTATTTTCTGACGGGCAAAAGCTTCTAGCATCTAGAATTCCCAGCTCTCAAGCACAA
ACTCAGGTTGCTGTTAGTCATTCTCAACTAACGTTTTCTCCTGGTTTGACCAAAAACACACCAT
CAGAGATGGTGGGGTGGACTGGAGTAATCAAAACTAATGACCTCTCAACTTCTGCTGTTCAACT
CGACGAATTTCATTCTTCTGGTTAGTGACTATCTTAGATGGGATTGTTTTAACTGATGGGTCTT
TCCCTTTTGGAGTGTAGTATTGTTAACTAATTTGATTGATAACTCTTCGAATATGGATATATGG
CACATAGCAGATGAAGAGGAAGGTAATTTGCAACCGTCGCCTAAGTACACCATGTCACAGAAAT
GGATTATGGGTCGACAGAATAAGAGACTATTGGTTGATCGTAGTTGGTCCCTTAAACAGCAGAA
AGCCGACCAGGCAATTGGTTCACGGTTCAATGAGTTGAAG
						
					

			
		

Sequences
Splice junction sequence	TATGGGTCGACAGAATAAGAGACTATTGGTTGATCGTAGTTGGTCCCTTAAACAGCAGAAAGCC GACCAGGCAATTGGTTCACGGTTCAATGAGTTGAAGtgtggctggcagagcagtgaagccacag caatcaggcctgcaattcataaagaacctggaaataatgttgcaggagagggattcctgccttc aggttcac
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: 777 Transcript exons: 12058560-12058720,12058808-12058872,12058955-12059347,12 059466-12059623 TGTGGCTGGCAGAGCAGTGAAGCCACAGCAATCAGGCCTGCAATTCATAAAGAACCTGGAAATA ATGTTGCAGGAGAGGGATTCCTGCCTTCAGGTTCACCTTTTAGAGAGCAACAACTGAAGCAGCT CAGAGCCCAGTGCCTTGTGTTTCTAGCTCTTAGAAATGGTTTGGTACCGAAGAAACTTCACGTA GAGATTGCCCTTCGAAATACTTTCCGCGAAGAAGATGGTTTCCGCGGAGAATTGTTTGATCCGA AAGGGAGAACACATACGTCCAGTGATCTGGGTGGCATTCCTGACGTCTCTGCACTGTTGTCAAG AACAGACAATCCCACTGGAAGATTGGATGAAATGGACTTCTCATCCAAAGAAACTGAGAGATCA AGACTAGGGGAAAAAAGTTTCGCAAATACTGTATTTTCTGACGGGCAAAAGCTTCTAGCATCTA GAATTCCCAGCTCTCAAGCACAAACTCAGGTTGCTGTTAGTCATTCTCAACTAACGTTTTCTCC TGGTTTGACCAAAAACACACCATCAGAGATGGTGGGGTGGACTGGAGTAATCAAAACTAATGAC CTCTCAACTTCTGCTGTTCAACTCGACGAATTTCATTCTTCTGATGAAGAGGAAGGTAATTTGC AACCGTCGCCTAAGTACACCATGTCACAGAAATGGATTATGGGTCGACAGAATAAGAGACTATT GGTTGATCGTAGTTGGTCCCTTAAACAGCAGAAAGCCGACCAGGCAATTGGTTCACGGTTCAAT GAGTTGAAG Transcript length: 780 Transcript exons: 12058560-12058720,12058808-12058872,12058955-12059347,12 059463-12059623 TGTGGCTGGCAGAGCAGTGAAGCCACAGCAATCAGGCCTGCAATTCATAAAGAACCTGGAAATA ATGTTGCAGGAGAGGGATTCCTGCCTTCAGGTTCACCTTTTAGAGAGCAACAACTGAAGCAGCT CAGAGCCCAGTGCCTTGTGTTTCTAGCTCTTAGAAATGGTTTGGTACCGAAGAAACTTCACGTA GAGATTGCCCTTCGAAATACTTTCCGCGAAGAAGATGGTTTCCGCGGAGAATTGTTTGATCCGA AAGGGAGAACACATACGTCCAGTGATCTGGGTGGCATTCCTGACGTCTCTGCACTGTTGTCAAG AACAGACAATCCCACTGGAAGATTGGATGAAATGGACTTCTCATCCAAAGAAACTGAGAGATCA AGACTAGGGGAAAAAAGTTTCGCAAATACTGTATTTTCTGACGGGCAAAAGCTTCTAGCATCTA GAATTCCCAGCTCTCAAGCACAAACTCAGGTTGCTGTTAGTCATTCTCAACTAACGTTTTCTCC TGGTTTGACCAAAAACACACCATCAGAGATGGTGGGGTGGACTGGAGTAATCAAAACTAATGAC CTCTCAACTTCTGCTGTTCAACTCGACGAATTTCATTCTTCTGCAGATGAAGAGGAAGGTAATT TGCAACCGTCGCCTAAGTACACCATGTCACAGAAATGGATTATGGGTCGACAGAATAAGAGACT ATTGGTTGATCGTAGTTGGTCCCTTAAACAGCAGAAAGCCGACCAGGCAATTGGTTCACGGTTC AATGAGTTGAAG
Genomic sequence	TGTGGCTGGCAGAGCAGTGAAGCCACAGCAATCAGGCCTGCAATTCATAAAGAACCTGGAAATA ATGTTGCAGGAGAGGGATTCCTGCCTTCAGGTTCACCTTTTAGAGAGCAACAACTGAAGCAGCT CAGAGCCCAGTGCCTTGTGTTTCTAGCTCTTAGGTACCTTACAGTCTCCTAGCCTCTGTATACT CCTTTTGGTGCGGCAATTGTAACTCTAAAAATTTCTGGTTGATTTTCATCTCGTAGAAATGGTT TGGTACCGAAGAAACTTCACGTAGAGATTGCCCTTCGAAATACTTTCCGCGAAGAAGGTAATGT TGGTGCTCACTGAAGTTACTTTCGAATCCACTTTTTACATGCTTTCCCTTGGATCATAATTGGT CTTCATTACAGATGGTTTCCGCGGAGAATTGTTTGATCCGAAAGGGAGAACACATACGTCCAGT GATCTGGGTGGCATTCCTGACGTCTCTGCACTGTTGTCAAGAACAGACAATCCCACTGGAAGAT TGGATGAAATGGACTTCTCATCCAAAGAAACTGAGAGATCAAGACTAGGGGAAAAAAGTTTCGC AAATACTGTATTTTCTGACGGGCAAAAGCTTCTAGCATCTAGAATTCCCAGCTCTCAAGCACAA ACTCAGGTTGCTGTTAGTCATTCTCAACTAACGTTTTCTCCTGGTTTGACCAAAAACACACCAT CAGAGATGGTGGGGTGGACTGGAGTAATCAAAACTAATGACCTCTCAACTTCTGCTGTTCAACT CGACGAATTTCATTCTTCTGGTTAGTGACTATCTTAGATGGGATTGTTTTAACTGATGGGTCTT TCCCTTTTGGAGTGTAGTATTGTTAACTAATTTGATTGATAACTCTTCGAATATGGATATATGG CACATAGCAGATGAAGAGGAAGGTAATTTGCAACCGTCGCCTAAGTACACCATGTCACAGAAAT GGATTATGGGTCGACAGAATAAGAGACTATTGGTTGATCGTAGTTGGTCCCTTAAACAGCAGAA AGCCGACCAGGCAATTGGTTCACGGTTCAATGAGTTGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.311695463

Conservation Information
Conserved circRNAs	NA
PMCS	0.311695463

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12059080-12059620(+)
						
						Potential amino acid sequence
						
							MDFSSKETERSRLGEKSFANTVFSDGQKLLASRIPSSQAQTQVAVSHSQLTFSPGLTKNTPSEM
VGWTGVIKTNDLSTSAVQLDEFHSSDEEEGNLQPSPKYTMSQKWIMGRQNKRLLVDRSWSLKQQ
KADQAIGSRFNELKCGWQSSEATAIRPAIHKEPGNNVAGEGFLPSGSPFREQQLKQLRAQCLVF
LALRNGLVPKKLHVEIALRNTFREEDGFRGELFDPKGRTHTSSDLGGIPDVSALLSRTDNPTGR
LDEMDFSSKETERSRLGEKSFANTVFSDGQKLLASRIPSSQAQTQVAVSHSQLTFSPGLTKNTP
SEMVGWTGVIKTNDLSTSAVQLDEFHSSDEEEGNLQPSPKYTMSQKWIMGRQNKRLLVDRSWSL
KQQKADQAIGSRFNELKCGWQSSEATAIRPAIHKEPGNNVAGEGFLPSGSPFREQQLKQLRAQC
LVFLALRNGLVPKKLHVEIALRNTFREEDGFRGELFDPKGRTHTSSDLGGIPDVSALLSRTDNP
TGRLDEMDFSSKETERSRLGEKSFANTVFSDGQKLLASRIPSSQAQTQVAVSHSQLTFSPGLTK
NTPSEMVGWTGVIKTNDLSTSAVQLDEFHSSDEEEGNLQPSPKYTMSQKWIMGRQNKRLLVDRS
WSLKQQKADQAIGSRFNELKCGWQSSEATAIRPAIHKEPGNNVAGEGFLPSGSPFREQQLKQLR
AQCLVFLALRNGLVPKKLHVEIALRNTFREEDGFRGELFDPKGRTHTSSDLGGIPDVSALLSRT
DNPTGRLDEMDFSSKETERSRLGEKSFANTVFSDGQKLLASRIPSSQAQTQVAVSHSQLTFSPG
LTKNTPSEMVGWTGVIKTNDLSTSAVQLDEFHSSDEEEGNLQPSPKYTMSQKWIMGRQNKRLLV
DRSWSLKQQKADQAIGSRFNELK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	12059080-12059620(+)
Potential amino acid sequence	MDFSSKETERSRLGEKSFANTVFSDGQKLLASRIPSSQAQTQVAVSHSQLTFSPGLTKNTPSEM VGWTGVIKTNDLSTSAVQLDEFHSSDEEEGNLQPSPKYTMSQKWIMGRQNKRLLVDRSWSLKQQ KADQAIGSRFNELKCGWQSSEATAIRPAIHKEPGNNVAGEGFLPSGSPFREQQLKQLRAQCLVF LALRNGLVPKKLHVEIALRNTFREEDGFRGELFDPKGRTHTSSDLGGIPDVSALLSRTDNPTGR LDEMDFSSKETERSRLGEKSFANTVFSDGQKLLASRIPSSQAQTQVAVSHSQLTFSPGLTKNTP SEMVGWTGVIKTNDLSTSAVQLDEFHSSDEEEGNLQPSPKYTMSQKWIMGRQNKRLLVDRSWSL KQQKADQAIGSRFNELKCGWQSSEATAIRPAIHKEPGNNVAGEGFLPSGSPFREQQLKQLRAQC LVFLALRNGLVPKKLHVEIALRNTFREEDGFRGELFDPKGRTHTSSDLGGIPDVSALLSRTDNP TGRLDEMDFSSKETERSRLGEKSFANTVFSDGQKLLASRIPSSQAQTQVAVSHSQLTFSPGLTK NTPSEMVGWTGVIKTNDLSTSAVQLDEFHSSDEEEGNLQPSPKYTMSQKWIMGRQNKRLLVDRS WSLKQQKADQAIGSRFNELKCGWQSSEATAIRPAIHKEPGNNVAGEGFLPSGSPFREQQLKQLR AQCLVFLALRNGLVPKKLHVEIALRNTFREEDGFRGELFDPKGRTHTSSDLGGIPDVSALLSRT DNPTGRLDEMDFSSKETERSRLGEKSFANTVFSDGQKLLASRIPSSQAQTQVAVSHSQLTFSPG LTKNTPSEMVGWTGVIKTNDLSTSAVQLDEFHSSDEEEGNLQPSPKYTMSQKWIMGRQNKRLLV DRSWSLKQQKADQAIGSRFNELK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT2G28290_circ_g.3

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