Plant Circular RNA Database

Detail information of AT2G39810_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT2G39810_circ_g.3
					
						ID in PlantcircBase
						ath_circ_017535
					
						Alias
						At_ciR369, Ath_circ_FC4769, AT2G39810_C2
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 16613843-16615133  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, find_circ, CIRI2
					
						Parent gene
						
							AT2G39810						
					
						Parent gene annotation
						
							HOS1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G39810_circ_g.1 AT2G39810_circ_g.2 AT2G39810_circ_g.4 AT2G39810_circ_g.5 AT2G39810_circ_g.6 						
					
						Support reads
						9/22/12
					
						Tissues
						leaf/root, inflorescences, whole_plant/seedlings
					
						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
						AT2G39810.1:3
AT2G39810.2:3

General Information
CircRNA Name	AT2G39810_circ_g.3
ID in PlantcircBase	ath_circ_017535
Alias	At_ciR369, Ath_circ_FC4769, AT2G39810_C2
Organism	Arabidpsis thaliana
Position	chr2: 16613843-16615133 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, find_circ, CIRI2
Parent gene	AT2G39810
Parent gene annotation	HOS1
Parent gene strand	+
Alternative splicing	AT2G39810_circ_g.1 AT2G39810_circ_g.2 AT2G39810_circ_g.4 AT2G39810_circ_g.5 AT2G39810_circ_g.6
Support reads	9/22/12
Tissues	leaf/root, inflorescences, whole_plant/seedlings
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	AT2G39810.1:3 AT2G39810.2:3

			
						 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  
						
							GGGAACTTCAGGATCTTATCCATTTGAGAATCTTAGAACTGCTGCTGACATGCTCTTTTTACAT
GGCGGTTCAGATTTGGTTGTTGCGAAGCAAGCAATTatatcaccaatgtctgtatggatgagac
agctgtatctagtgatccggtcattgctttcttgctggatgaagttgttgtcaaggattgggtc
aagcgtac

									
								

					

						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: 308
Transcript exons: 16613843-16613965,16614949-16615133
ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCT
GGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTACATTCCGGAGCACCTTAGCTGAACCAGAA
TACAGTCAGGAAATAGGTGCCGACCTAGAAGTTGGACGTTTACAGAAGGATAAGAGATCATTTC
TTAGGTCCAAAATAGAGGGAACTTCAGGATCTTATCCATTTGAGAATCTTAGAACTGCTGCTGA
CATGCTCTTTTTACATGGCGGTTCAGATTTGGTTGTTGCGAAGCAAGCAATT
Transcript length: 365
Transcript exons: 16613843-16613961,16614068-16614154,16614975-16615133
ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCT
GGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTACATTCCGGAGCACCTTAGCTATAATCTTG
AAACAAAAGAGATGCAAGCGTGGTTAGATAAACTCCTAAGGTGTTCCAAACAGGTGGCTGGCAT
ATGTAGTGTGCTCGGACCTAGAAGTTGGACGTTTACAGAAGGATAAGAGATCATTTCTTAGGTC
CAAAATAGAGGGAACTTCAGGATCTTATCCATTTGAGAATCTTAGAACTGCTGCTGACATGCTC
TTTTTACATGGCGGTTCAGATTTGGTTGTTGCGAAGCAAGCAATT
Transcript length: 405
Transcript exons: 16613843-16613907,16614068-16614244,16614971-16615133
ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCT
GATAATCTTGAAACAAAAGAGATGCAAGCGTGGTTAGATAAACTCCTAAGGTGTTCCAAACAGG
TGGCTGGCATATGTAGTGTGCTCGAAGTTATGGAATCAGCTTTTAAGGGTTCTGTGTCACCTCA
GCTTCAAGATGTGCAGACGCTGAGAGAGAACATTGGTAAAACAAAGCAGGTGCCGACCTAGAAG
TTGGACGTTTACAGAAGGATAAGAGATCATTTCTTAGGTCCAAAATAGAGGGAACTTCAGGATC
TTATCCATTTGAGAATCTTAGAACTGCTGCTGACATGCTCTTTTTACATGGCGGTTCAGATTTG
GTTGTTGCGAAGCAAGCAATT
Transcript length: 466
Transcript exons: 16613843-16613977,16614068-16614130,16614140-16614243,16
614970-16615133
ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCT
GGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTACATTCCGGAGCACCTTAGCTGAACTTCAA
GAAATCTATAATCTTGAAACAAAAGAGATGCAAGCGTGGTTAGATAAACTCCTAAGGTGTTCCA
AACAGGTATGTAGTGTGCTCGAAGTTATGGAATCAGCTTTTAAGGGTTCTGTGTCACCTCAGCT
TCAAGATGTGCAGACGCTGAGAGAGAACATTGGTAAAACAAAGCAGGTGCCGACCTAGAAGTTG
GACGTTTACAGAAGGATAAGAGATCATTTCTTAGGTCCAAAATAGAGGGAACTTCAGGATCTTA
TCCATTTGAGAATCTTAGAACTGCTGCTGACATGCTCTTTTTACATGGCGGTTCAGATTTGGTT
GTTGCGAAGCAAGCAATT
Transcript length: 713
Transcript exons: 16613843-16613977,16614068-16614243,16614732-16615133
ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCT
GGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTACATTCCGGAGCACCTTAGCTGAACTTCAA
GAAATCTATAATCTTGAAACAAAAGAGATGCAAGCGTGGTTAGATAAACTCCTAAGGTGTTCCA
AACAGGTGGCTGGCATATGTAGTGTGCTCGAAGTTATGGAATCAGCTTTTAAGGGTTCTGTGTC
ACCTCAGCTTCAAGATGTGCAGACGCTGAGAGAGAACATTGGTAAAACAAAGCAGCATTTGGAC
ATAATGGTCTGGTGCATCAGACATGGATTTCTGGATGATGTGAGGTCTCGATATTCGAATTTCA
CATCGTGGAATGCACTGGTAGGGGAAAGAAAATCAAATGCAGTTAAGCGTGCATGGCCTGATGC
TGTAGACCAGTCTTCAGATTGCAGTGTACAGAGTGCTTCCCTCTTTATTGAGGATGCTTTAGAA
AATCTTGAGAGAGAGCCAGAATACAGTCAGGAAATAGGTGCCGACCTAGAAGTTGGACGTTTAC
AGAAGGATAAGAGATCATTTCTTAGGTCCAAAATAGAGGGAACTTCAGGATCTTATCCATTTGA
GAATCTTAGAACTGCTGCTGACATGCTCTTTTTACATGGCGGTTCAGATTTGGTTGTTGCGAAG
CAAGCAATT
						
					

						Genomic sequence
						
							ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCT
GGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTACATTCCGGAGCACCTTAGCTGAACTTCAA
GAAATCTGTATCCTTTTAGCTGTTAATATTTTTATGTTTCTTAAGACTGTATATTTGTGCACCG
TAAGGTCTGTCTATCTTTAATATTGGCCCTCAGATAATCTTGAAACAAAAGAGATGCAAGCGTG
GTTAGATAAACTCCTAAGGTGTTCCAAACAGGTGGCTGGCATATGTAGTGTGCTCGAAGTTATG
GAATCAGCTTTTAAGGGTTCTGTGTCACCTCAGCTTCAAGATGTGCAGACGCTGAGAGAGAACA
TTGGTAAAACAAAGCAGGTCAGCCATGATTTCATTTCATTGATATCCAAACAGTTTTGCAAAAG
TATGCTTAAATAACTCTCTTTATCCCCCTTAGAAATATCCGTTGTACATTGAAGTTTCCTACGT
GCATTAATGTTTAGTTTGCCTCTGTCATAGAATGAGTTACTTGTTTTGTATACGGCTTGCAGTA
AAGTTTGTACTGTAAAAGCTTTGCATTTAGATGTATGAAAGGCACGATAATGGTCTTCCATCAT
CAGCTTGGATCTGATTTTCTATCCCTAGCTTTGTGACTTTATTCTTCTTTTCTTTTTTAATGTC
ATTGCATATTAGTGAATGTAGATGGGGTATATGTAACCTATCTTTATATGACATACTGAATAGT
AAATGAGTATAACCTTATGGCTTCTGACCAGAGAGTGTTTTAAATAGATCAGCTCTTTAGCTAT
TGGTGCAAGATCACTGAGCTTACGTGTGCTTACCCTATTCTTTTTATTTTATTTCAGCATTTGG
ACATAATGGTCTGGTGCATCAGACATGGATTTCTGGATGATGTGAGGTCTCGATATTCGAATTT
CACATCGTGGAATGCACTGGTAGGGGAAAGAAAATCAAATGCAGTTAAGCGTGCATGGCCTGAT
GCTGTAGACCAGTCTTCAGATTGCAGTGTACAGAGTGCTTCCCTCTTTATTGAGGATGCTTTAG
AAAATCTTGAGAGAGAGCCAGAATACAGTCAGGAAATAGGTGCCGACCTAGAAGTTGGACGTTT
ACAGAAGGATAAGAGATCATTTCTTAGGTCCAAAATAGAGGGAACTTCAGGATCTTATCCATTT
GAGAATCTTAGAACTGCTGCTGACATGCTCTTTTTACATGGCGGTTCAGATTTGGTTGTTGCGA
AGCAAGCAATT
						
					

			
		

Sequences
Splice junction sequence	GGGAACTTCAGGATCTTATCCATTTGAGAATCTTAGAACTGCTGCTGACATGCTCTTTTTACAT GGCGGTTCAGATTTGGTTGTTGCGAAGCAAGCAATTatatcaccaatgtctgtatggatgagac agctgtatctagtgatccggtcattgctttcttgctggatgaagttgttgtcaaggattgggtc aagcgtac
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: 308 Transcript exons: 16613843-16613965,16614949-16615133 ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCT GGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTACATTCCGGAGCACCTTAGCTGAACCAGAA TACAGTCAGGAAATAGGTGCCGACCTAGAAGTTGGACGTTTACAGAAGGATAAGAGATCATTTC TTAGGTCCAAAATAGAGGGAACTTCAGGATCTTATCCATTTGAGAATCTTAGAACTGCTGCTGA CATGCTCTTTTTACATGGCGGTTCAGATTTGGTTGTTGCGAAGCAAGCAATT Transcript length: 365 Transcript exons: 16613843-16613961,16614068-16614154,16614975-16615133 ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCT GGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTACATTCCGGAGCACCTTAGCTATAATCTTG AAACAAAAGAGATGCAAGCGTGGTTAGATAAACTCCTAAGGTGTTCCAAACAGGTGGCTGGCAT ATGTAGTGTGCTCGGACCTAGAAGTTGGACGTTTACAGAAGGATAAGAGATCATTTCTTAGGTC CAAAATAGAGGGAACTTCAGGATCTTATCCATTTGAGAATCTTAGAACTGCTGCTGACATGCTC TTTTTACATGGCGGTTCAGATTTGGTTGTTGCGAAGCAAGCAATT Transcript length: 405 Transcript exons: 16613843-16613907,16614068-16614244,16614971-16615133 ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCT GATAATCTTGAAACAAAAGAGATGCAAGCGTGGTTAGATAAACTCCTAAGGTGTTCCAAACAGG TGGCTGGCATATGTAGTGTGCTCGAAGTTATGGAATCAGCTTTTAAGGGTTCTGTGTCACCTCA GCTTCAAGATGTGCAGACGCTGAGAGAGAACATTGGTAAAACAAAGCAGGTGCCGACCTAGAAG TTGGACGTTTACAGAAGGATAAGAGATCATTTCTTAGGTCCAAAATAGAGGGAACTTCAGGATC TTATCCATTTGAGAATCTTAGAACTGCTGCTGACATGCTCTTTTTACATGGCGGTTCAGATTTG GTTGTTGCGAAGCAAGCAATT Transcript length: 466 Transcript exons: 16613843-16613977,16614068-16614130,16614140-16614243,16 614970-16615133 ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCT GGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTACATTCCGGAGCACCTTAGCTGAACTTCAA GAAATCTATAATCTTGAAACAAAAGAGATGCAAGCGTGGTTAGATAAACTCCTAAGGTGTTCCA AACAGGTATGTAGTGTGCTCGAAGTTATGGAATCAGCTTTTAAGGGTTCTGTGTCACCTCAGCT TCAAGATGTGCAGACGCTGAGAGAGAACATTGGTAAAACAAAGCAGGTGCCGACCTAGAAGTTG GACGTTTACAGAAGGATAAGAGATCATTTCTTAGGTCCAAAATAGAGGGAACTTCAGGATCTTA TCCATTTGAGAATCTTAGAACTGCTGCTGACATGCTCTTTTTACATGGCGGTTCAGATTTGGTT GTTGCGAAGCAAGCAATT Transcript length: 713 Transcript exons: 16613843-16613977,16614068-16614243,16614732-16615133 ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCT GGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTACATTCCGGAGCACCTTAGCTGAACTTCAA GAAATCTATAATCTTGAAACAAAAGAGATGCAAGCGTGGTTAGATAAACTCCTAAGGTGTTCCA AACAGGTGGCTGGCATATGTAGTGTGCTCGAAGTTATGGAATCAGCTTTTAAGGGTTCTGTGTC ACCTCAGCTTCAAGATGTGCAGACGCTGAGAGAGAACATTGGTAAAACAAAGCAGCATTTGGAC ATAATGGTCTGGTGCATCAGACATGGATTTCTGGATGATGTGAGGTCTCGATATTCGAATTTCA CATCGTGGAATGCACTGGTAGGGGAAAGAAAATCAAATGCAGTTAAGCGTGCATGGCCTGATGC TGTAGACCAGTCTTCAGATTGCAGTGTACAGAGTGCTTCCCTCTTTATTGAGGATGCTTTAGAA AATCTTGAGAGAGAGCCAGAATACAGTCAGGAAATAGGTGCCGACCTAGAAGTTGGACGTTTAC AGAAGGATAAGAGATCATTTCTTAGGTCCAAAATAGAGGGAACTTCAGGATCTTATCCATTTGA GAATCTTAGAACTGCTGCTGACATGCTCTTTTTACATGGCGGTTCAGATTTGGTTGTTGCGAAG CAAGCAATT
Genomic sequence	ATATCACCAATGTCTGTATGGATGAGACAGCTGTATCTAGTGATCCGGTCATTGCTTTCTTGCT GGATGAAGTTGTTGTCAAGGATTGGGTCAAGCGTACATTCCGGAGCACCTTAGCTGAACTTCAA GAAATCTGTATCCTTTTAGCTGTTAATATTTTTATGTTTCTTAAGACTGTATATTTGTGCACCG TAAGGTCTGTCTATCTTTAATATTGGCCCTCAGATAATCTTGAAACAAAAGAGATGCAAGCGTG GTTAGATAAACTCCTAAGGTGTTCCAAACAGGTGGCTGGCATATGTAGTGTGCTCGAAGTTATG GAATCAGCTTTTAAGGGTTCTGTGTCACCTCAGCTTCAAGATGTGCAGACGCTGAGAGAGAACA TTGGTAAAACAAAGCAGGTCAGCCATGATTTCATTTCATTGATATCCAAACAGTTTTGCAAAAG TATGCTTAAATAACTCTCTTTATCCCCCTTAGAAATATCCGTTGTACATTGAAGTTTCCTACGT GCATTAATGTTTAGTTTGCCTCTGTCATAGAATGAGTTACTTGTTTTGTATACGGCTTGCAGTA AAGTTTGTACTGTAAAAGCTTTGCATTTAGATGTATGAAAGGCACGATAATGGTCTTCCATCAT CAGCTTGGATCTGATTTTCTATCCCTAGCTTTGTGACTTTATTCTTCTTTTCTTTTTTAATGTC ATTGCATATTAGTGAATGTAGATGGGGTATATGTAACCTATCTTTATATGACATACTGAATAGT AAATGAGTATAACCTTATGGCTTCTGACCAGAGAGTGTTTTAAATAGATCAGCTCTTTAGCTAT TGGTGCAAGATCACTGAGCTTACGTGTGCTTACCCTATTCTTTTTATTTTATTTCAGCATTTGG ACATAATGGTCTGGTGCATCAGACATGGATTTCTGGATGATGTGAGGTCTCGATATTCGAATTT CACATCGTGGAATGCACTGGTAGGGGAAAGAAAATCAAATGCAGTTAAGCGTGCATGGCCTGAT GCTGTAGACCAGTCTTCAGATTGCAGTGTACAGAGTGCTTCCCTCTTTATTGAGGATGCTTTAG AAAATCTTGAGAGAGAGCCAGAATACAGTCAGGAAATAGGTGCCGACCTAGAAGTTGGACGTTT ACAGAAGGATAAGAGATCATTTCTTAGGTCCAAAATAGAGGGAACTTCAGGATCTTATCCATTT GAGAATCTTAGAACTGCTGCTGACATGCTCTTTTTACATGGCGGTTCAGATTTGGTTGTTGCGA AGCAAGCAATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.860668047

Conservation Information
Conserved circRNAs	NA
PMCS	0.860668047

			
						 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;Pan et al., 2017;Chen et al., 2017a;Liu et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT2G39810_circ_g.3

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