Plant Circular RNA Database

Detail information of 4_circ_ag.3

			
						 General Information
					
						CircRNA Name
						4_circ_ag.3
					
						ID in PlantcircBase
						ath_circ_031605
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 10358203-10362063  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							4_circ_ag.2 AT4G18905_circ_g.1 AT4G18905_circ_g.2 AT4G18905_circ_g.3 AT4G18905_circ_g.4 AT4G18905_circ_g.5 						
					
						Support reads
						23
					
						Tissues
						root, aerial, inflorescences, seed
					
						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
						NA

General Information
CircRNA Name	4_circ_ag.3
ID in PlantcircBase	ath_circ_031605
Alias	NA
Organism	Arabidpsis thaliana
Position	chr4: 10358203-10362063 JBrowse»
Reference genome	TAIR10.38
Type	ag-circRNA
Identification method	CIRI
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	4_circ_ag.2 AT4G18905_circ_g.1 AT4G18905_circ_g.2 AT4G18905_circ_g.3 AT4G18905_circ_g.4 AT4G18905_circ_g.5
Support reads	23
Tissues	root, aerial, inflorescences, seed
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	NA

			
						 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  
						
							TTGTTTATTGTTTGTATGATCACAGGTTCAAGCGGTTGCTTGGAACCATTATGCTCCAGAAGTG
CTTCTCAGTGGGTCGTTTGATCAAACTGTTGTCATGaaagacggaagacaaccttcacactcgg
gtttcaaatggtctgtcatgtccgatgttgaaagcttagcctgggatcctcatagtgaacactc
ctttgtgg

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							AAAGACGGAAGACAACCTTCACACTCGGGTTTCAAATGGTCTGTCATGTCCGATGTTGAAAGCT
TAGCCTGGGATCCTCATAGTGAACACTCCTTTGTGGTACGTTACACTTTAAGTCTTTAATTAAT
ATATACAATGTGTTTTTTTTGGCGGTTTAAAGAATTTTTTTTCTTCGGTTTCTTATCCCTTGTG
GCCTTGCTTATATATAGGTAAGTCTCGAAGATGGAACTGTCAAGGGCTTTGATGTACGTCAAGC
CTCCATTTCAGCCTCTGAATCAAATCCAAGCTTCACTATTAATGGACATGACGAAGCAGCTACT
TCCGTCTCATACAACATTTCGGCACCTAATGTAAGCGTCTCTTTCTCATTATTTGTTTCGTTTC
GATTCAAAAATATGAATAATTAACTCATAAATTCTAAACTTTGAAAACATATTTCTTATTCCCC
TTTGTCTACTCTCTCTTGTGTCATTGTTCTTTGTTATGTATGTTTTACTAGTTCTCACCATTTT
GGAGCTGTAATTGAACAGCTTTTGGCAACGGGATCTAAGGATAGAACGGTAAAGCTTTGGGATC
TTTCAAACAATGAGCCTTCATGCATTGCTACACACAATCCAAATGCTGTAAGAACCAATAATCG
ACCATTTAAAAAAAATAAAATTGGTTTCGTTATCTTAACTTGATTATTAATTTGTTCATATATA
TGATTCCAACACTTTTGATATCACACAGGGAGGCTTATTCTTCATTGCTTTCTCTCCGGACAAT
CCTTTCTTACTCGCTATGGGTGGCGTAATGGGGGAGTTAAAACTTTGGGATACACTTTCGGACA
CTAATGTCTCCAGCAGATACGGAAGCAGAGAAGTCCGACCGTGAAAAGTCCAAGCTAAACTTTG
ATTGGTCGTCACATTCGAACACAACTTAACCACAATTTTGTTTAGTTTCTTTCTTTCATTAATG
TTCGTTTTATTTCTTGTGTAATGGCTATAATTATTATTTCTGGCTCAATGTTTAATCAGACCCA
TACGAAATAGCCCATTAGTTTATCAGAAGTAGCTCAGAATATTTTAGTTAATTAATGGTTATTT
TACAAACATATGTGGTTAGGATAGACCAAATTAGTCATGGCTTATTGGTAAACCATAAGGGTTT
AAGATATGTAAATGGTCACTAAAATTTAGTTTTAAAGTAAGGTATCACTTCTGCAATTTATTAA
GAATTTTATCTTTAATTAATATTTTTAGTGAAATTTTTAGTGGAATTGCCTTTGTTCGAGTGAT
TGACCAAATGTTTATTAATACTTCTACATCTAAGTCTACGATTCGAGTTCCAAAAAAAACGCAG
TCTCTTGCAGATGAATGATGCAAATCTTATTGGAGATCCATAGTGCAGTATGCATAGTCGTTCG
TAGTGGTCTGAATGTTGTAGGGAGAGCTTATCCATCGTAAAAATATCGTATATGCAGAATCGTC
CGCTGAAGATCAGAATGTTGTGAGGAGAGAGCTGCATCTTGGAATCGTTGTTCGTGGAAACTGT
TCATCATAAATAAAATATAAAATTAACAGTTTCAACTTTCAAAAGGTTTTCTATGTACATTTTT
GAAGTTAAAGGTCTTTAATTCAATAACTAAATAGTTTTGGGCTTTTAAGAAATTTTCCCTTAAG
TTGTTTCTTCCTCTTCTTCGCTCAGCGCCGCTATACTCACTCTCGGCAAAAAAAAAGTTCCTCA
GAAGCAAACAAATCTTCAATTGTTAAACCCTAAACCTACAAAAGTCTTGACTTTGTTTGTTGCT
CATCTTCGTTCTTCTCTCTCGATTAAATTCGTTCCGAGAAAGTTAGGTCCCGTTTCTAAACGTA
AGTTCTCTTTTATTACTTTTCAATGATCATAGCTTTAACCCAGCTTTGAAATTCTTGTATGTGG
TTTATCAAATGACGCAAAAACCCTAATTTCGAGCTGCCCTCTACCCAAGAACCAGCCTTTGAGA
TTTTTTACCGATTTGATGATTCTCTCTCTGTTTTGAATATTTGCAGAATGATAACTGCAGTGTC
ATGGATACCAAAAGGGAATCTAAAAGCTGTTCCTGATGTTGCTGAGCCTCCGTCAAAGGAAGAA
CTTAAAGAGCTCATTGAGAGTGGTGCTTTTGCAAGAAAGTGAGATTTTTAACTTAGTATTGTTC
CTGTTTCTCTAAATTTAGGACTTGTGGAGATTGTGATTGATATTGGTTATAATATATAGCGTGG
AAGGTAGTAACGAGGATGAAGAAGAAGAGATTGAAGAAGATGGAGAAGAGATAAGTGAAGTTGA
TCATGCCAAGGCTGTAGCTGAAGCTTTGGGTAAATCTTCTAAAAGCAAGGCTGTTTCTTCTTCA
ATGGAGGTTGATGAGGTTTCTCAAGGATTGAAAGAACTTGACATGGATAATTATGATGAAGAGG
ATGATGGTACGTTTAGTTGGCCTTTTGGTGTTTGTTCTGCAATTCTACAAGTGATCATTTTGAT
TAGCAGAGATAGTTTGGTGTGTTCCTTATGTAAACGTTACCTTTTTTTTTGGTTGTGTTTGGAT
TCAGAAATTGAACTTTTCAGTTCTGGAATGGGGGATCTTTATTATCCAAGTAATGAGATGGATC
CATATCTGAAAGATGTTGATGTAAGCCATTTCACTGTTTCTATTTCACAATGAAACATATCGTG
TTTAAATTGTTTTGTATGAAGATGATGTTTGGTCTTTTTAGGATGAAGATGATGAAGAGGATAT
TGATGACACGACAGTCAAGCCGACCGATTCGGTGATTATTTGTGCTAGGAATGAAGATGATGTT
AGCCATCTAGAGGTATGGTCAGTCCTTCTCGCTGTGTAGGTTACATGTTAAACATTAGGGCTCA
TATGAAAGCTATATATATATGAACAGGTTTATTTATACGAGGAATCGTCTGGCTCTCCAAACAT
GTATGTTCATCATCACATAATTATACCAGAATTCCCATTGTGTACTGCATGGCTTGATTGTCCT
CTTAAAGGAGGGGAAAAAGGTTAGTGTACGCTTTTATTGTTCATATGAGGCAGGTTTTTTCCTT
CTTGCTATGGATGAAATCTTATTCTTACTCTGTGGTTTGCCTTGGTACTGTCAGGGAATTTTGT
AGCTATTGGTTCAAAGGATACACCGACAATCGAGATATGGGATCTTGACGTTGTATGTAATTAT
AACAGACTATGTATTTATCTTTGCCTTTATCGATTATGAGTCTATTGATAAGGTTATTATAATG
CTTCAGAGGGACGAGGTGCTACCTTGTATACAACTAGGAGGAATAGAGGAGATGATAGTGAGTA
AGAAAAAGAAGAGCAAGAAACAGAAACCGGTGTGTGCATCAAACTCGTCTATCTCTAGTTCGTC
TATGGCAAGTTCGTATGTATTTATTTATTTAATTTTGAGGTCTGTCTTTTACTTTACAGAAATT
CAAAGAAGGTAGCCATACTGAGTCAGTACTTGGTCTTGCTTGGAACAAGGAGTTTCGGTATGTC
TAAGCTTACTAGTGCTCATTAATTTTAAGTTTTTTTTTTCTGGTTTGCTCTTTAGGCGTGTCTG
ATTTTCTTTTGATTTGTTTGGATAAAAGGAACATACTTGCTAGTGCTAGTGCCGACAAAAAAGT
TAAGGTCTGGGATGTGGCTACTGGGACGTGTAAGATTACTATGGAGCATCACACAAAGGAGGTA
AAAACGAGAGTCGTAGAAGGAGAAAATTCTTTATTATATGGCATTCTCATTGTTTATTGTTTGT
ATGATCACAGGTTCAAGCGGTTGCTTGGAACCATTATGCTCCAGAAGTGCTTCTCAGTGGGTCG
TTTGATCAAACTGTTGTCATG
						
					

			
		

Sequences
Splice junction sequence	TTGTTTATTGTTTGTATGATCACAGGTTCAAGCGGTTGCTTGGAACCATTATGCTCCAGAAGTG CTTCTCAGTGGGTCGTTTGATCAAACTGTTGTCATGaaagacggaagacaaccttcacactcgg gtttcaaatggtctgtcatgtccgatgttgaaagcttagcctgggatcctcatagtgaacactc ctttgtgg
Assembled circRNA sequence	NA 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	NA
Genomic sequence	AAAGACGGAAGACAACCTTCACACTCGGGTTTCAAATGGTCTGTCATGTCCGATGTTGAAAGCT TAGCCTGGGATCCTCATAGTGAACACTCCTTTGTGGTACGTTACACTTTAAGTCTTTAATTAAT ATATACAATGTGTTTTTTTTGGCGGTTTAAAGAATTTTTTTTCTTCGGTTTCTTATCCCTTGTG GCCTTGCTTATATATAGGTAAGTCTCGAAGATGGAACTGTCAAGGGCTTTGATGTACGTCAAGC CTCCATTTCAGCCTCTGAATCAAATCCAAGCTTCACTATTAATGGACATGACGAAGCAGCTACT TCCGTCTCATACAACATTTCGGCACCTAATGTAAGCGTCTCTTTCTCATTATTTGTTTCGTTTC GATTCAAAAATATGAATAATTAACTCATAAATTCTAAACTTTGAAAACATATTTCTTATTCCCC TTTGTCTACTCTCTCTTGTGTCATTGTTCTTTGTTATGTATGTTTTACTAGTTCTCACCATTTT GGAGCTGTAATTGAACAGCTTTTGGCAACGGGATCTAAGGATAGAACGGTAAAGCTTTGGGATC TTTCAAACAATGAGCCTTCATGCATTGCTACACACAATCCAAATGCTGTAAGAACCAATAATCG ACCATTTAAAAAAAATAAAATTGGTTTCGTTATCTTAACTTGATTATTAATTTGTTCATATATA TGATTCCAACACTTTTGATATCACACAGGGAGGCTTATTCTTCATTGCTTTCTCTCCGGACAAT CCTTTCTTACTCGCTATGGGTGGCGTAATGGGGGAGTTAAAACTTTGGGATACACTTTCGGACA CTAATGTCTCCAGCAGATACGGAAGCAGAGAAGTCCGACCGTGAAAAGTCCAAGCTAAACTTTG ATTGGTCGTCACATTCGAACACAACTTAACCACAATTTTGTTTAGTTTCTTTCTTTCATTAATG TTCGTTTTATTTCTTGTGTAATGGCTATAATTATTATTTCTGGCTCAATGTTTAATCAGACCCA TACGAAATAGCCCATTAGTTTATCAGAAGTAGCTCAGAATATTTTAGTTAATTAATGGTTATTT TACAAACATATGTGGTTAGGATAGACCAAATTAGTCATGGCTTATTGGTAAACCATAAGGGTTT AAGATATGTAAATGGTCACTAAAATTTAGTTTTAAAGTAAGGTATCACTTCTGCAATTTATTAA GAATTTTATCTTTAATTAATATTTTTAGTGAAATTTTTAGTGGAATTGCCTTTGTTCGAGTGAT TGACCAAATGTTTATTAATACTTCTACATCTAAGTCTACGATTCGAGTTCCAAAAAAAACGCAG TCTCTTGCAGATGAATGATGCAAATCTTATTGGAGATCCATAGTGCAGTATGCATAGTCGTTCG TAGTGGTCTGAATGTTGTAGGGAGAGCTTATCCATCGTAAAAATATCGTATATGCAGAATCGTC CGCTGAAGATCAGAATGTTGTGAGGAGAGAGCTGCATCTTGGAATCGTTGTTCGTGGAAACTGT TCATCATAAATAAAATATAAAATTAACAGTTTCAACTTTCAAAAGGTTTTCTATGTACATTTTT GAAGTTAAAGGTCTTTAATTCAATAACTAAATAGTTTTGGGCTTTTAAGAAATTTTCCCTTAAG TTGTTTCTTCCTCTTCTTCGCTCAGCGCCGCTATACTCACTCTCGGCAAAAAAAAAGTTCCTCA GAAGCAAACAAATCTTCAATTGTTAAACCCTAAACCTACAAAAGTCTTGACTTTGTTTGTTGCT CATCTTCGTTCTTCTCTCTCGATTAAATTCGTTCCGAGAAAGTTAGGTCCCGTTTCTAAACGTA AGTTCTCTTTTATTACTTTTCAATGATCATAGCTTTAACCCAGCTTTGAAATTCTTGTATGTGG TTTATCAAATGACGCAAAAACCCTAATTTCGAGCTGCCCTCTACCCAAGAACCAGCCTTTGAGA TTTTTTACCGATTTGATGATTCTCTCTCTGTTTTGAATATTTGCAGAATGATAACTGCAGTGTC ATGGATACCAAAAGGGAATCTAAAAGCTGTTCCTGATGTTGCTGAGCCTCCGTCAAAGGAAGAA CTTAAAGAGCTCATTGAGAGTGGTGCTTTTGCAAGAAAGTGAGATTTTTAACTTAGTATTGTTC CTGTTTCTCTAAATTTAGGACTTGTGGAGATTGTGATTGATATTGGTTATAATATATAGCGTGG AAGGTAGTAACGAGGATGAAGAAGAAGAGATTGAAGAAGATGGAGAAGAGATAAGTGAAGTTGA TCATGCCAAGGCTGTAGCTGAAGCTTTGGGTAAATCTTCTAAAAGCAAGGCTGTTTCTTCTTCA ATGGAGGTTGATGAGGTTTCTCAAGGATTGAAAGAACTTGACATGGATAATTATGATGAAGAGG ATGATGGTACGTTTAGTTGGCCTTTTGGTGTTTGTTCTGCAATTCTACAAGTGATCATTTTGAT TAGCAGAGATAGTTTGGTGTGTTCCTTATGTAAACGTTACCTTTTTTTTTGGTTGTGTTTGGAT TCAGAAATTGAACTTTTCAGTTCTGGAATGGGGGATCTTTATTATCCAAGTAATGAGATGGATC CATATCTGAAAGATGTTGATGTAAGCCATTTCACTGTTTCTATTTCACAATGAAACATATCGTG TTTAAATTGTTTTGTATGAAGATGATGTTTGGTCTTTTTAGGATGAAGATGATGAAGAGGATAT TGATGACACGACAGTCAAGCCGACCGATTCGGTGATTATTTGTGCTAGGAATGAAGATGATGTT AGCCATCTAGAGGTATGGTCAGTCCTTCTCGCTGTGTAGGTTACATGTTAAACATTAGGGCTCA TATGAAAGCTATATATATATGAACAGGTTTATTTATACGAGGAATCGTCTGGCTCTCCAAACAT GTATGTTCATCATCACATAATTATACCAGAATTCCCATTGTGTACTGCATGGCTTGATTGTCCT CTTAAAGGAGGGGAAAAAGGTTAGTGTACGCTTTTATTGTTCATATGAGGCAGGTTTTTTCCTT CTTGCTATGGATGAAATCTTATTCTTACTCTGTGGTTTGCCTTGGTACTGTCAGGGAATTTTGT AGCTATTGGTTCAAAGGATACACCGACAATCGAGATATGGGATCTTGACGTTGTATGTAATTAT AACAGACTATGTATTTATCTTTGCCTTTATCGATTATGAGTCTATTGATAAGGTTATTATAATG CTTCAGAGGGACGAGGTGCTACCTTGTATACAACTAGGAGGAATAGAGGAGATGATAGTGAGTA AGAAAAAGAAGAGCAAGAAACAGAAACCGGTGTGTGCATCAAACTCGTCTATCTCTAGTTCGTC TATGGCAAGTTCGTATGTATTTATTTATTTAATTTTGAGGTCTGTCTTTTACTTTACAGAAATT CAAAGAAGGTAGCCATACTGAGTCAGTACTTGGTCTTGCTTGGAACAAGGAGTTTCGGTATGTC TAAGCTTACTAGTGCTCATTAATTTTAAGTTTTTTTTTTCTGGTTTGCTCTTTAGGCGTGTCTG ATTTTCTTTTGATTTGTTTGGATAAAAGGAACATACTTGCTAGTGCTAGTGCCGACAAAAAAGT TAAGGTCTGGGATGTGGCTACTGGGACGTGTAAGATTACTATGGAGCATCACACAAAGGAGGTA AAAACGAGAGTCGTAGAAGGAGAAAATTCTTTATTATATGGCATTCTCATTGTTTATTGTTTGT ATGATCACAGGTTCAAGCGGTTGCTTGGAACCATTATGCTCCAGAAGTGCTTCTCAGTGGGTCG TTTGATCAAACTGTTGTCATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.602041712

Conservation Information
Conserved circRNAs	NA
PMCS	0.602041712

			
						 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
						NA

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	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of 4_circ_ag.3

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