Plant Circular RNA Database

Detail information of AT4G16990_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT4G16990_circ_g.1
					
						ID in PlantcircBase
						ath_circ_031350
					
						Alias
						At_ciR1274
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 9561097-9562348  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT4G16990						
					
						Parent gene annotation
						
							disease resistance protein (TIR-NBS class), putative
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G16990_circ_g.2 AT4G16990_circ_g.3 AT4G16990_circ_g.4 AT4G16990_circ_g.5 AT4G16990_circ_g.6 						
					
						Support reads
						4
					
						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
						AT4G16990.2:3
AT4G16990.10:3
AT4G16990.17:3
AT4G16990.19:3
AT4G16990.8:3
AT4G16990.3:3
AT4G16990.13:3
AT4G16990.18:3
AT4G16990.6:3
AT4G16990.12:3
AT4G16990.16:3
AT4G16990.5:3
AT4G16990.1:3
AT4G16990.14:3
AT4G16990.7:3
AT4G16990.4:3
AT4G16990.11:3
AT4G16990.9:3
AT4G16990.15:3

General Information
CircRNA Name	AT4G16990_circ_g.1
ID in PlantcircBase	ath_circ_031350
Alias	At_ciR1274
Organism	Arabidpsis thaliana
Position	chr4: 9561097-9562348 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	AT4G16990
Parent gene annotation	disease resistance protein (TIR-NBS class), putative
Parent gene strand	+
Alternative splicing	AT4G16990_circ_g.2 AT4G16990_circ_g.3 AT4G16990_circ_g.4 AT4G16990_circ_g.5 AT4G16990_circ_g.6
Support reads	4
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	AT4G16990.2:3 AT4G16990.10:3 AT4G16990.17:3 AT4G16990.19:3 AT4G16990.8:3 AT4G16990.3:3 AT4G16990.13:3 AT4G16990.18:3 AT4G16990.6:3 AT4G16990.12:3 AT4G16990.16:3 AT4G16990.5:3 AT4G16990.1:3 AT4G16990.14:3 AT4G16990.7:3 AT4G16990.4:3 AT4G16990.11:3 AT4G16990.9:3 AT4G16990.15:3

			
						 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  
						
							AGCATGGCGCAACAAGCAAAAATATGGTGGTATGAAAATTTGGAAAGAGTGTGCAAGAAGTACA
ATATATGTGGCATAGATAGCTCAACTGATGGTGGTGgcgtagcgaagcagaaatgcttgaaaat
atcgccaaggatgtttcaaacaaactcttccccccatcaaataatttcagtgacttcgtcggga
ttgaagct

									
								

					

						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: 1034
Transcript exons: 9561097-9561917,9562015-9562123,9562245-9562348
GCGTAGCGAAGCAGAAATGCTTGAAAATATCGCCAAGGATGTTTCAAACAAACTCTTCCCCCCA
TCAAATAATTTCAGTGACTTCGTCGGGATTGAAGCTCATATAGAGGCATTGATATCAATGTTGC
GCTTCGACTCCAAGAAAGCGCGAATGATAGGGATTTGTGGGCCTTCTGAAACTGGTAAGACTAC
TATAGGAAGAGCTTTATACAGCAGACTCAAAAGCGACTTCCACCATCGGGCTTTCGTAGCATAT
AAGAGAAAAATACGGAGCGACTATGACCAGAAGCTGTATTGGGAAGAACAATTTCTATCAGAAA
TTCTTTGTCAGAAGGATATAAAGATAGAGGAATGTGGTGCGGTGGAACAACGACTAAAGCACAC
GAAAGTTCTTATTGTTCTTGATGATGTTGATGATATAGAGCTACTAAAAACGTTGGTAGGACGT
ATCAGATGGTTTGGATCTGAGAGCAAAATTGTTGTGATTACTCAAAAAAGGGAACTTCTCAAGG
CTCACAACATTGCACATGTTTATGAAGTGGGATTCCCATCAGAAGAACTGGCTCATCAAATGTT
TTGTCGATATGCTTTTGGGAAAAACTCTCCACCTCATGGTTTCAACGAGCTTGCAGATGAAGCT
GCAAAGATTGCCGGTAATCGTCCTAAAGCTCTCAAGTACGTTGGTTCGTCTTTTAGAAGACTAG
ACAAGGAACAATGGGTGAAGATGCTATCGGAGTTCCGTAGTAATGGGAATAAACTAAAAATCAG
CTATGATGAGTTAGATGGTAAAGGTCAAGATTACGTTGCGTGTTTAACCAATGGTTCAAATTCC
CAGGTGAAGGCAGAGTGGATCCACTTGGCACTAGGCGTGTCTATATTACTTAACATCCGCAGTG
ACGGAACGACAATTCTCAAACATTTGAGCTACAATCGAAGCATGGCGCAACAAGCAAAAATATG
GTGGTATGAAAATTTGGAAAGAGTGTGCAAGAAGTACAATATATGTGGCATAGATAGCTCAACT
GATGGTGGTG
						
					

						Genomic sequence
						
							GCGTAGCGAAGCAGAAATGCTTGAAAATATCGCCAAGGATGTTTCAAACAAACTCTTCCCCCCA
TCAAATAATTTCAGTGACTTCGTCGGGATTGAAGCTCATATAGAGGCATTGATATCAATGTTGC
GCTTCGACTCCAAGAAAGCGCGAATGATAGGGATTTGTGGGCCTTCTGAAACTGGTAAGACTAC
TATAGGAAGAGCTTTATACAGCAGACTCAAAAGCGACTTCCACCATCGGGCTTTCGTAGCATAT
AAGAGAAAAATACGGAGCGACTATGACCAGAAGCTGTATTGGGAAGAACAATTTCTATCAGAAA
TTCTTTGTCAGAAGGATATAAAGATAGAGGAATGTGGTGCGGTGGAACAACGACTAAAGCACAC
GAAAGTTCTTATTGTTCTTGATGATGTTGATGATATAGAGCTACTAAAAACGTTGGTAGGACGT
ATCAGATGGTTTGGATCTGAGAGCAAAATTGTTGTGATTACTCAAAAAAGGGAACTTCTCAAGG
CTCACAACATTGCACATGTTTATGAAGTGGGATTCCCATCAGAAGAACTGGCTCATCAAATGTT
TTGTCGATATGCTTTTGGGAAAAACTCTCCACCTCATGGTTTCAACGAGCTTGCAGATGAAGCT
GCAAAGATTGCCGGTAATCGTCCTAAAGCTCTCAAGTACGTTGGTTCGTCTTTTAGAAGACTAG
ACAAGGAACAATGGGTGAAGATGCTATCGGAGTTCCGTAGTAATGGGAATAAACTAAAAATCAG
CTATGATGAGTTAGATGGTAAAGGTCAAGATTACGTTGCGTGTTTAACCAATGGTGAGAAAAAA
TCAATATTAAAAATTATTGCATGGAGATAGTGTTAACACTGAAATTACCATTATTGCTGATAAT
TCCCTCAAACACATGCATGCAGGTTCAAATTCCCAGGTGAAGGCAGAGTGGATCCACTTGGCAC
TAGGCGTGTCTATATTACTTAACATCCGCAGTGACGGAACGACAATTCTCAAACATTTGAGCTA
CAAGTAATGTGGGCTCTAAGCTTATACAATGCTACACTTTCTTTTTGCATAGTAATCTGTTGGG
ATCATAAGTAATAATCTAGGATTTGTATCAATCAATCTAACAATAAGTGGTTGTTTACAGTCGA
AGCATGGCGCAACAAGCAAAAATATGGTGGTATGAAAATTTGGAAAGAGTGTGCAAGAAGTACA
ATATATGTGGCATAGATAGCTCAACTGATGGTGGTG
						
					

			
		

Sequences
Splice junction sequence	AGCATGGCGCAACAAGCAAAAATATGGTGGTATGAAAATTTGGAAAGAGTGTGCAAGAAGTACA ATATATGTGGCATAGATAGCTCAACTGATGGTGGTGgcgtagcgaagcagaaatgcttgaaaat atcgccaaggatgtttcaaacaaactcttccccccatcaaataatttcagtgacttcgtcggga ttgaagct
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: 1034 Transcript exons: 9561097-9561917,9562015-9562123,9562245-9562348 GCGTAGCGAAGCAGAAATGCTTGAAAATATCGCCAAGGATGTTTCAAACAAACTCTTCCCCCCA TCAAATAATTTCAGTGACTTCGTCGGGATTGAAGCTCATATAGAGGCATTGATATCAATGTTGC GCTTCGACTCCAAGAAAGCGCGAATGATAGGGATTTGTGGGCCTTCTGAAACTGGTAAGACTAC TATAGGAAGAGCTTTATACAGCAGACTCAAAAGCGACTTCCACCATCGGGCTTTCGTAGCATAT AAGAGAAAAATACGGAGCGACTATGACCAGAAGCTGTATTGGGAAGAACAATTTCTATCAGAAA TTCTTTGTCAGAAGGATATAAAGATAGAGGAATGTGGTGCGGTGGAACAACGACTAAAGCACAC GAAAGTTCTTATTGTTCTTGATGATGTTGATGATATAGAGCTACTAAAAACGTTGGTAGGACGT ATCAGATGGTTTGGATCTGAGAGCAAAATTGTTGTGATTACTCAAAAAAGGGAACTTCTCAAGG CTCACAACATTGCACATGTTTATGAAGTGGGATTCCCATCAGAAGAACTGGCTCATCAAATGTT TTGTCGATATGCTTTTGGGAAAAACTCTCCACCTCATGGTTTCAACGAGCTTGCAGATGAAGCT GCAAAGATTGCCGGTAATCGTCCTAAAGCTCTCAAGTACGTTGGTTCGTCTTTTAGAAGACTAG ACAAGGAACAATGGGTGAAGATGCTATCGGAGTTCCGTAGTAATGGGAATAAACTAAAAATCAG CTATGATGAGTTAGATGGTAAAGGTCAAGATTACGTTGCGTGTTTAACCAATGGTTCAAATTCC CAGGTGAAGGCAGAGTGGATCCACTTGGCACTAGGCGTGTCTATATTACTTAACATCCGCAGTG ACGGAACGACAATTCTCAAACATTTGAGCTACAATCGAAGCATGGCGCAACAAGCAAAAATATG GTGGTATGAAAATTTGGAAAGAGTGTGCAAGAAGTACAATATATGTGGCATAGATAGCTCAACT GATGGTGGTG
Genomic sequence	GCGTAGCGAAGCAGAAATGCTTGAAAATATCGCCAAGGATGTTTCAAACAAACTCTTCCCCCCA TCAAATAATTTCAGTGACTTCGTCGGGATTGAAGCTCATATAGAGGCATTGATATCAATGTTGC GCTTCGACTCCAAGAAAGCGCGAATGATAGGGATTTGTGGGCCTTCTGAAACTGGTAAGACTAC TATAGGAAGAGCTTTATACAGCAGACTCAAAAGCGACTTCCACCATCGGGCTTTCGTAGCATAT AAGAGAAAAATACGGAGCGACTATGACCAGAAGCTGTATTGGGAAGAACAATTTCTATCAGAAA TTCTTTGTCAGAAGGATATAAAGATAGAGGAATGTGGTGCGGTGGAACAACGACTAAAGCACAC GAAAGTTCTTATTGTTCTTGATGATGTTGATGATATAGAGCTACTAAAAACGTTGGTAGGACGT ATCAGATGGTTTGGATCTGAGAGCAAAATTGTTGTGATTACTCAAAAAAGGGAACTTCTCAAGG CTCACAACATTGCACATGTTTATGAAGTGGGATTCCCATCAGAAGAACTGGCTCATCAAATGTT TTGTCGATATGCTTTTGGGAAAAACTCTCCACCTCATGGTTTCAACGAGCTTGCAGATGAAGCT GCAAAGATTGCCGGTAATCGTCCTAAAGCTCTCAAGTACGTTGGTTCGTCTTTTAGAAGACTAG ACAAGGAACAATGGGTGAAGATGCTATCGGAGTTCCGTAGTAATGGGAATAAACTAAAAATCAG CTATGATGAGTTAGATGGTAAAGGTCAAGATTACGTTGCGTGTTTAACCAATGGTGAGAAAAAA TCAATATTAAAAATTATTGCATGGAGATAGTGTTAACACTGAAATTACCATTATTGCTGATAAT TCCCTCAAACACATGCATGCAGGTTCAAATTCCCAGGTGAAGGCAGAGTGGATCCACTTGGCAC TAGGCGTGTCTATATTACTTAACATCCGCAGTGACGGAACGACAATTCTCAAACATTTGAGCTA CAAGTAATGTGGGCTCTAAGCTTATACAATGCTACACTTTCTTTTTGCATAGTAATCTGTTGGG ATCATAAGTAATAATCTAGGATTTGTATCAATCAATCTAACAATAAGTGGTTGTTTACAGTCGA AGCATGGCGCAACAAGCAAAAATATGGTGGTATGAAAATTTGGAAAGAGTGTGCAAGAAGTACA ATATATGTGGCATAGATAGCTCAACTGATGGTGGTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.160630473

Conservation Information
Conserved circRNAs	NA
PMCS	0.160630473

			
						 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

circRNA

Detail information of AT4G16990_circ_g.1

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