Plant Circular RNA Database

Detail information of 1_circ_ag.4

			
						 General Information
					
						CircRNA Name
						1_circ_ag.4
					
						ID in PlantcircBase
						ath_circ_004848
					
						Alias
						At_ciR1937
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 10439963-10444363  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							1_circ_ag.2 AT1G29820_circ_g.1 1_circ_ag.2 1_circ_ag.3 						
					
						Support reads
						4/9
					
						Tissues
						leaf/inflorescences, 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
						NA

General Information
CircRNA Name	1_circ_ag.4
ID in PlantcircBase	ath_circ_004848
Alias	At_ciR1937
Organism	Arabidpsis thaliana
Position	chr1: 10439963-10444363 JBrowse»
Reference genome	TAIR10.38
Type	ag-circRNA
Identification method	find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	1_circ_ag.2 AT1G29820_circ_g.1 1_circ_ag.2 1_circ_ag.3
Support reads	4/9
Tissues	leaf/inflorescences, 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	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  
						
							AGTAACAAATACTATGCTTTTTCTTATTAGGAGAAACCATGAGGATTTGAATCTTTTTAGTATC
ATTCTCAACCAAGAGATCAGAAAATTAGCAAGACAGgtcatccgagtgaagtggtcactacacg
cgagagaggagattatctttgagcttctccagcatttgaggggaaacatagctcgacatctctt
agatggtt

									
								

					

						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
						
							GTCATCCGAGTGAAGTGGTCACTACACGCGAGAGAGGAGATTATCTTTGAGCTTCTCCAGCATT
TGAGGGGAAACATAGCTCGACATCTCTTAGATGGTTTGAGGAAGAACACAAGGGAAATGTTGGA
AGAACAAGAAGCAGTTCGTGGACGTCTCTTCACAATTCAAGATGTCATGCAAAGCAGTGTCCGC
GCTTGGTTACAGGTTCTTACTCCACCGAACAAAATTAAAATCGTATCTCATAAATCTAGCATAA
TGGATCCATTTGGCTAAAACCCCAGTTTGCATTTTCAGGACAAAAGCTTGAGAGTAAGCCACAA
CTTGGCCGTCTTCGGAGGATGTGGTCTTGTACTTACCATCATCGTAGGGCTGTTTGGGATCAAT
GTGGATGGGATCCCGGGGGCGCAGAACACGCCTTATGCGTTTGGTCTATTCACTTTTCTGATGG
TTCTCCTTGGGGCTATTCTGATTGTGGTTGGTTTGGTATACTTGGGGCTCAAAAAACCCATTAC
AGAAGAACAAGTAGAAGTTAGAAAGCTGGAGCTACAAGACGTGGTTAAGATATTTCAACACGAA
GCGGAGACTCATGCCCAACTCCGTAGAAACAACCTTTCTCCTACTGCTGGAGATGTCTTTGATG
CTGATTATATTCTCATCCAGTAAACAAACTTGGAATCTATTTTCTGTTAAGATACTACTAAATT
CAGAGAGATGTCAATACAATGTTGTTGCATAAAAGATAAAAGTAGTCTGAATCACTGAGAGAAC
AAAGCTATTAAGTCGAGGTCTCTGTTAAATTTTTATGTGCCAGCATCTATTTCGCTAAAATTTC
GACCAAATTATTCGTCTTCCATATTCTTCCAATTGTACATTTCATGTCTGAAATAGTAAAAGAG
TGAGTAACGAAGAATTATTTTGGTTACAATTATTCTTAAACCAAAATGAGGAATGAGTGTAGAA
AAGGTGTTATGAAGCATGAACATTTCCTCAAAGAGATAAGACAAAAAAAAAACTAGTTGTTCTT
CACAACGACTGTCTTAATGAATTACATAACTGTTGTAACTAATTGACTTTGATGTTTGGTATAA
CAATGATCAGCTCCTTCCATAATCTCCAGCTTGTGGTTTGGTATGAGCTTTGCAAACTCCTTGG
CATCTTCCACCGGTATTACCTCGTCAGTCGAGCCATGAACCGTCAAGACCCTGCCATTACAACC
AATCATGGTTTGTTTGTATCCCAAACATGGATATGAGTTAGTTAAAGGGAAATCAGCGAATCTC
ACCTGCATTATTTGTCAATCTTGAGGCAAGCTTCATGCATATCAGTGTTTAACCTTTCCATTAA
GCTCTCCTCGGTAACACGAAACCCGGAGTTTCCTGTAAAAGACCCGCACCTTGATAAAGACACT
ACTACTAGAGTACTGATATGTGACAGTAGATGAAGAACAAAGAGCGATGACCTTCTTTAATATC
GATGAACCCTTGTTTCTTTATTCTTTGGTGTTACATGTCACATTTCATAACTTTACGGTTAACT
ATGTAAAAATGTAAAACAATAAGGAGCAAATTTATGAAAACGTTTACGCGCGTCTCTCAAAGTC
AAAGCTAAACAATTTGCTTGTAAAGTATTCATAATTTGCGAACTCTCGAGTGTTGGATCAGCCA
TCTGGAGAAAGAGAATACTGTACTTCTCCTAAGGTGAGACTTTTTTTTCTCGAAATTAATTTGT
TTCTTTTATTGGATATTTTTGACTAATTTGGAGATCACATTAACTCGAATTCTCTACAAACCAG
TCAAAAACTTGTATGATCTTATAAGTAGGATTTGTGTCTCTCCTTGGCCATGAATTTTATAGGG
GGTTTTAAGTAGTTTTTAGATTATAGATTTGGTTTTTGTTTTTGGATTTTGGCTAAACAAAAAA
ATCACGATGACATCAAAATAAAATACTAACAATATGTAATTTTCTAGTATTTGTTGGTTTGCAG
TTTTTGTGTTGGTGTTAGTTTGGTGCTTTAATTACATACAATGAGTTTTGGTTCTTATAGATTT
GTGTTATATGTGACAGATTCTAAGTGCATCAGTTTAAGTTAGCTTCCTGTTTGATCTTGAAGAG
TTGAGTTTGCGAGAAAGTATATTGAAGCTGATGTGAATTGACTCTCACTGTCTCACACGTGATA
AGTTCCGTAGAAGAAGCTGGTAGATTTTCTATTTGACTGACCATGGGTGAAAATGGGGAGAATC
ATTCAGTCTCTCAAGAGAGTAAAAATCATTCAGGTGTTCCGAAGAGTGATCTTTGGACTGATGG
GATTATTTGTGCCTTTGAGTTTATTCGAGGCCCAAAAAAACATGTTGATTCAAAGCAACTTTAT
AAAGGTTACTTGAAGCAAGAAGATGGACCGATCAGACATAGTTTCCCTGGTCATAACCCGTTTA
TTGATTCGCCTGCAGTCGATTATTTAAGGTCAAGGTCTGTATCTTCTTTGGATTTTAAAGAGGC
TCATGTCCTTCCATCAGGACATGTTGAGAGATCTGAGGGAAGTCATTGGGTACCTATTGGTTGG
ACTAGAATAACTAAACTAGTTCAACAGGTTCAAGTAAACGCGGAGTGGCCTAATCTAAAGTTGA
TTGATGATGAAGAAGATGTTCCTGTTACAGATTTAGCAGCTCCGTATTGGGAACGACCAGGTGG
CCCTACATGGTGGTGTCACTTGACTGCTGGAAACTCTTTTGTTGAGGGATGGCTCAGAAGTGCT
ACGTGGTTGCATCCTGCAATTAGTCTTGCATTGAGGGATGAAAGTAAGCTAATAAGTGAACGGA
TGAGACATCTTCTATATGAGGTATGTGCCTTTGTTCTGAGTATCTAAATTCAACAACATTTTAA
ATTGTTGCTGATAATTACTTCAAATTTCCAAAATACTTCCACATGGTTCATCGTTGTTTTGGGT
ATGATTAAAGATGTGTGTAGTCTCTTAGCATAATAAAGTTCTTCATTTATCCTCCGGCAAAATT
ACATTATAGCATAATGGTATAAGTTATAGAATGAAAATTTGCAGAATAAAAAGAATGAAACTAT
TTTTTAAAATATGTTGATTGGATACACTTTGCATAATGACAAAATAAAATCTCATATTTATATA
TATACTTCATAAACAAAATAATGTTTTAAATATATTTTAGTAATATTTGATAATTAAAATTTAT
TGGAAAGTTGTGAATTTTTTTTATATTATTAATTATATAATTTTAGTGTAAACAATGATATTTT
TTCTTTTACAATTGCTAATATTTAGTATGCGTAGAATAATATCATTTTGTTATGCAAAAACCCA
ACTATATATCCACTTTTTGGCATAATGAACTTTTACTTGTAATTAGGCGAAAATGCAATCCTGT
GTTTTTACGTTTTTTAATGCAATTATGCAAATTTTCTTAATTGGCAAATTTCATGCATAATCGC
ATTAGAAAACGTCTAATTATACGTGTTATCAATGAAAAGTGTGTTAAGTTTATTTTTCTTGGAT
GTTGTTGTCTAACTTCTATTGCGGTTTATTTTTTAGGTTCCGGTGAGGGTTGATGGGGGTTTAT
TGTTTGAACTCTTAGGACAATCAATGGGTGATCCAGTAATCGGTGAGGATGATGTACCCGTTGT
TTTCCGCTCTTGGCAAGCAAAAAACTTTTTGGTATCTGTGATGCACATAAAAGGAAATGTATCA
AAGAGCAATGTTCTCGGTATCACTGAAGTAGAGGTTAGTTCAAAAAGTGTCAAAATACTCTACT
TGATAAGATTCTTTATAGATACTTAAATAACACAAGCCTACAATATGGATACTAACTAGCGGTA
AAAAAAAATCCCTCATAGGAGTTGCTTTATGCAGGGAGCTATAATGTACCAAGAACAATTCATG
AAGTCATAGCACACTTGGCTTGCCGTCTTTCTCGATGGGATGATAGGTGACCACAATTTTCTGA
TCTAACTTAATAAACGAGTGACTTGAGTTCTATTCTATTAAATGTTCTTGTTTTAGACCAAGTG
TCGTTAACTCAATTGATAAAGACACTAGGCGAAGTTTAGAGATCGCCTGTTCGAGTGACACTTG
GGACGAAACTAATATTAAAGTTCTTGTTTTAGTCCGGTGTGGAAGGTATCTAACAAAATCTTTT
TGTTGGTCATTGATTGGTGACAGATTATTTCGTAAATCCATATTTGGTGCTGCCGATGAAATCG
AATTGAAGTTTATGAACAGGTTCTTATAAATATGTATGTATTCCCGTTATTTTATCTAATAAAA
CAGTACATGTTTTAGTAACAAATACTATGCTTTTTCTTATTAGGAGAAACCATGAGGATTTGAA
TCTTTTTAGTATCATTCTCAACCAAGAGATCAGAAAATTAGCAAGACAG
						
					

			
		

Sequences
Splice junction sequence	AGTAACAAATACTATGCTTTTTCTTATTAGGAGAAACCATGAGGATTTGAATCTTTTTAGTATC ATTCTCAACCAAGAGATCAGAAAATTAGCAAGACAGgtcatccgagtgaagtggtcactacacg cgagagaggagattatctttgagcttctccagcatttgaggggaaacatagctcgacatctctt agatggtt
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	GTCATCCGAGTGAAGTGGTCACTACACGCGAGAGAGGAGATTATCTTTGAGCTTCTCCAGCATT TGAGGGGAAACATAGCTCGACATCTCTTAGATGGTTTGAGGAAGAACACAAGGGAAATGTTGGA AGAACAAGAAGCAGTTCGTGGACGTCTCTTCACAATTCAAGATGTCATGCAAAGCAGTGTCCGC GCTTGGTTACAGGTTCTTACTCCACCGAACAAAATTAAAATCGTATCTCATAAATCTAGCATAA TGGATCCATTTGGCTAAAACCCCAGTTTGCATTTTCAGGACAAAAGCTTGAGAGTAAGCCACAA CTTGGCCGTCTTCGGAGGATGTGGTCTTGTACTTACCATCATCGTAGGGCTGTTTGGGATCAAT GTGGATGGGATCCCGGGGGCGCAGAACACGCCTTATGCGTTTGGTCTATTCACTTTTCTGATGG TTCTCCTTGGGGCTATTCTGATTGTGGTTGGTTTGGTATACTTGGGGCTCAAAAAACCCATTAC AGAAGAACAAGTAGAAGTTAGAAAGCTGGAGCTACAAGACGTGGTTAAGATATTTCAACACGAA GCGGAGACTCATGCCCAACTCCGTAGAAACAACCTTTCTCCTACTGCTGGAGATGTCTTTGATG CTGATTATATTCTCATCCAGTAAACAAACTTGGAATCTATTTTCTGTTAAGATACTACTAAATT CAGAGAGATGTCAATACAATGTTGTTGCATAAAAGATAAAAGTAGTCTGAATCACTGAGAGAAC AAAGCTATTAAGTCGAGGTCTCTGTTAAATTTTTATGTGCCAGCATCTATTTCGCTAAAATTTC GACCAAATTATTCGTCTTCCATATTCTTCCAATTGTACATTTCATGTCTGAAATAGTAAAAGAG TGAGTAACGAAGAATTATTTTGGTTACAATTATTCTTAAACCAAAATGAGGAATGAGTGTAGAA AAGGTGTTATGAAGCATGAACATTTCCTCAAAGAGATAAGACAAAAAAAAAACTAGTTGTTCTT CACAACGACTGTCTTAATGAATTACATAACTGTTGTAACTAATTGACTTTGATGTTTGGTATAA CAATGATCAGCTCCTTCCATAATCTCCAGCTTGTGGTTTGGTATGAGCTTTGCAAACTCCTTGG CATCTTCCACCGGTATTACCTCGTCAGTCGAGCCATGAACCGTCAAGACCCTGCCATTACAACC AATCATGGTTTGTTTGTATCCCAAACATGGATATGAGTTAGTTAAAGGGAAATCAGCGAATCTC ACCTGCATTATTTGTCAATCTTGAGGCAAGCTTCATGCATATCAGTGTTTAACCTTTCCATTAA GCTCTCCTCGGTAACACGAAACCCGGAGTTTCCTGTAAAAGACCCGCACCTTGATAAAGACACT ACTACTAGAGTACTGATATGTGACAGTAGATGAAGAACAAAGAGCGATGACCTTCTTTAATATC GATGAACCCTTGTTTCTTTATTCTTTGGTGTTACATGTCACATTTCATAACTTTACGGTTAACT ATGTAAAAATGTAAAACAATAAGGAGCAAATTTATGAAAACGTTTACGCGCGTCTCTCAAAGTC AAAGCTAAACAATTTGCTTGTAAAGTATTCATAATTTGCGAACTCTCGAGTGTTGGATCAGCCA TCTGGAGAAAGAGAATACTGTACTTCTCCTAAGGTGAGACTTTTTTTTCTCGAAATTAATTTGT TTCTTTTATTGGATATTTTTGACTAATTTGGAGATCACATTAACTCGAATTCTCTACAAACCAG TCAAAAACTTGTATGATCTTATAAGTAGGATTTGTGTCTCTCCTTGGCCATGAATTTTATAGGG GGTTTTAAGTAGTTTTTAGATTATAGATTTGGTTTTTGTTTTTGGATTTTGGCTAAACAAAAAA ATCACGATGACATCAAAATAAAATACTAACAATATGTAATTTTCTAGTATTTGTTGGTTTGCAG TTTTTGTGTTGGTGTTAGTTTGGTGCTTTAATTACATACAATGAGTTTTGGTTCTTATAGATTT GTGTTATATGTGACAGATTCTAAGTGCATCAGTTTAAGTTAGCTTCCTGTTTGATCTTGAAGAG TTGAGTTTGCGAGAAAGTATATTGAAGCTGATGTGAATTGACTCTCACTGTCTCACACGTGATA AGTTCCGTAGAAGAAGCTGGTAGATTTTCTATTTGACTGACCATGGGTGAAAATGGGGAGAATC ATTCAGTCTCTCAAGAGAGTAAAAATCATTCAGGTGTTCCGAAGAGTGATCTTTGGACTGATGG GATTATTTGTGCCTTTGAGTTTATTCGAGGCCCAAAAAAACATGTTGATTCAAAGCAACTTTAT AAAGGTTACTTGAAGCAAGAAGATGGACCGATCAGACATAGTTTCCCTGGTCATAACCCGTTTA TTGATTCGCCTGCAGTCGATTATTTAAGGTCAAGGTCTGTATCTTCTTTGGATTTTAAAGAGGC TCATGTCCTTCCATCAGGACATGTTGAGAGATCTGAGGGAAGTCATTGGGTACCTATTGGTTGG ACTAGAATAACTAAACTAGTTCAACAGGTTCAAGTAAACGCGGAGTGGCCTAATCTAAAGTTGA TTGATGATGAAGAAGATGTTCCTGTTACAGATTTAGCAGCTCCGTATTGGGAACGACCAGGTGG CCCTACATGGTGGTGTCACTTGACTGCTGGAAACTCTTTTGTTGAGGGATGGCTCAGAAGTGCT ACGTGGTTGCATCCTGCAATTAGTCTTGCATTGAGGGATGAAAGTAAGCTAATAAGTGAACGGA TGAGACATCTTCTATATGAGGTATGTGCCTTTGTTCTGAGTATCTAAATTCAACAACATTTTAA ATTGTTGCTGATAATTACTTCAAATTTCCAAAATACTTCCACATGGTTCATCGTTGTTTTGGGT ATGATTAAAGATGTGTGTAGTCTCTTAGCATAATAAAGTTCTTCATTTATCCTCCGGCAAAATT ACATTATAGCATAATGGTATAAGTTATAGAATGAAAATTTGCAGAATAAAAAGAATGAAACTAT TTTTTAAAATATGTTGATTGGATACACTTTGCATAATGACAAAATAAAATCTCATATTTATATA TATACTTCATAAACAAAATAATGTTTTAAATATATTTTAGTAATATTTGATAATTAAAATTTAT TGGAAAGTTGTGAATTTTTTTTATATTATTAATTATATAATTTTAGTGTAAACAATGATATTTT TTCTTTTACAATTGCTAATATTTAGTATGCGTAGAATAATATCATTTTGTTATGCAAAAACCCA ACTATATATCCACTTTTTGGCATAATGAACTTTTACTTGTAATTAGGCGAAAATGCAATCCTGT GTTTTTACGTTTTTTAATGCAATTATGCAAATTTTCTTAATTGGCAAATTTCATGCATAATCGC ATTAGAAAACGTCTAATTATACGTGTTATCAATGAAAAGTGTGTTAAGTTTATTTTTCTTGGAT GTTGTTGTCTAACTTCTATTGCGGTTTATTTTTTAGGTTCCGGTGAGGGTTGATGGGGGTTTAT TGTTTGAACTCTTAGGACAATCAATGGGTGATCCAGTAATCGGTGAGGATGATGTACCCGTTGT TTTCCGCTCTTGGCAAGCAAAAAACTTTTTGGTATCTGTGATGCACATAAAAGGAAATGTATCA AAGAGCAATGTTCTCGGTATCACTGAAGTAGAGGTTAGTTCAAAAAGTGTCAAAATACTCTACT TGATAAGATTCTTTATAGATACTTAAATAACACAAGCCTACAATATGGATACTAACTAGCGGTA AAAAAAAATCCCTCATAGGAGTTGCTTTATGCAGGGAGCTATAATGTACCAAGAACAATTCATG AAGTCATAGCACACTTGGCTTGCCGTCTTTCTCGATGGGATGATAGGTGACCACAATTTTCTGA TCTAACTTAATAAACGAGTGACTTGAGTTCTATTCTATTAAATGTTCTTGTTTTAGACCAAGTG TCGTTAACTCAATTGATAAAGACACTAGGCGAAGTTTAGAGATCGCCTGTTCGAGTGACACTTG GGACGAAACTAATATTAAAGTTCTTGTTTTAGTCCGGTGTGGAAGGTATCTAACAAAATCTTTT TGTTGGTCATTGATTGGTGACAGATTATTTCGTAAATCCATATTTGGTGCTGCCGATGAAATCG AATTGAAGTTTATGAACAGGTTCTTATAAATATGTATGTATTCCCGTTATTTTATCTAATAAAA CAGTACATGTTTTAGTAACAAATACTATGCTTTTTCTTATTAGGAGAAACCATGAGGATTTGAA TCTTTTTAGTATCATTCTCAACCAAGAGATCAGAAAATTAGCAAGACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.686507003

Conservation Information
Conserved circRNAs	NA
PMCS	0.686507003

			
						 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
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of 1_circ_ag.4

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