Plant Circular RNA Database

Detail information of AT5G12840_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G12840_circ_g.3
					
						ID in PlantcircBase
						ath_circ_037828
					
						Alias
						5:4051532-4052963
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 4051532-4052963  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G12840						
					
						Parent gene annotation
						
							Nuclear transcription factor Y subunit A-1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G12840_circ_g.2 AT5G12840_circ_g.4 AT5G12840_circ_g.5 AT5G12840_circ_g.6 						
					
						Support reads
						1/1
					
						Tissues
						root;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  
						
							CT-AC							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
						AT5G12840.1:4
AT5G12840.4:4
AT5G12840.5:4
AT5G12840.3:4
AT5G12840.2:4

General Information
CircRNA Name	AT5G12840_circ_g.3
ID in PlantcircBase	ath_circ_037828
Alias	5:4051532-4052963
Organism	Arabidpsis thaliana
Position	chr5: 4051532-4052963 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G12840
Parent gene annotation	Nuclear transcription factor Y subunit A-1
Parent gene strand	-
Alternative splicing	AT5G12840_circ_g.2 AT5G12840_circ_g.4 AT5G12840_circ_g.5 AT5G12840_circ_g.6
Support reads	1/1
Tissues	root;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	CT-AC 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	AT5G12840.1:4 AT5G12840.4:4 AT5G12840.5:4 AT5G12840.3:4 AT5G12840.2:4

			
						 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  
						
							TTGTTTTTCCACCAGGGCTCTGCATACATCATCGGCTGCTGAACAGCATGGTGATTATTGACTT
CCTCTTCGTTTTCTCTTCCCGGTTTTGATTGCATCTctttctgtcccggatgactttcctctct
agctctgccttggcacgtgcttttcttcgccttagaattccctcgtactgctttgcattcacat
aaacgggc

									
								

					

						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: 614
Transcript exons: 4051532-4051696,4052008-4052079,4052231-4052328,4052685-
4052963
CTTTCTGTCCCGGATGACTTTCCTCTCTAGCTCTGCCTTGGCACGTGCTTTTCTTCGCCTTAGA
ATTCCCTCGTACTGCTTTGCATTCACATAAACGGGCTCTTGTGCCATGTCAAGTGGCAGAGCTG
TTCTTTCACGAGGCATTCCAAGATATGGACGAAAACCCAATTGCTGATGACCATATGCTCCCAT
CAATCCCCCATAATATGGATCCTGATATGGGTTTGGGACACAAGCGATATAGTGTCCAACAAGC
TCTGGTGGTTGTACAAGTGGCTGATCATGCATGTTACGGATAGAGAGCGCTGGGTCATTTCCTT
CCATTCCGTGATTATCTGAACGAGAGGAAGTTGCAGCTTGTGAATCCTTCCAAGTGCCATCGTT
TTCACCATTCAACGCACCGTCTTCAGATGCTGAATGAACATCGTTTGACTCGGAACCATTGGGG
CAATCCAAAGAAGAGGAATTTGATGGAATTCCAGAAGGTCTCGCTTGAGGTACAACACCAAAGG
AGTTGTTTTTCCACCAGGGCTCTGCATACATCATCGGCTGCTGAACAGCATGGTGATTATTGAC
TTCCTCTTCGTTTTCTCTTCCCGGTTTTGATTGCATCT
						
					

						Genomic sequence
						
							CTTTCTGTCCCGGATGACTTTCCTCTCTAGCTCTGCCTTGGCACGTGCTTTTCTTCGCCTTAGA
ATTCCCTCGTACTGCTTTGCATTCACATAAACGGGCTCTTGTGCCATGTCAAGTGGCAGAGCTG
TTCTTTCACGAGGCATTCCAAGATATGGACGAAAACCCTGTTTAAACCAATGAACAAAATAAAT
GCAACAAATAGACTCAGATCATCGAAAACTTTACATATAACTTATAAGACCCCAAGAATCCCCA
TTAGTTGTTCTCGATAATTTCAGATATAACTTTGGATTCTCAGTTATTTCAGAAATGAACTTTA
AAAGCATCTCACTGACTATTGCTGAACCCAGACACATTCCAACAGTAAATAAAATCACCACAAA
CGGGTACTTAGTGGCAAAAGCGCACATACATCAAATAAACACTGCACCATATGGAACTATTGTA
GAGATTGAAAGAGGTTTCGACAAGATACCAATTGCTGATGACCATATGCTCCCATCAATCCCCC
ATAATATGGATCCTGATATGGGTTTGGGACACAAGCCTGTAAGGAAGTTTTGAGTTTATCATAC
ATATGAAAAGGGCGTTATACAAGATAAATCCTTTTGAGGGACCAATAAGAAGTCAATTTAACAG
CTCAAGAACTCATAAAGCATATATATATATATATTAAGGAATGAGAGGAAACCACATACGATAT
AGTGTCCAACAAGCTCTGGTGGTTGTACAAGTGGCTGATCATGCATGTTACGGATAGAGAGCGC
TGGGTCATTTCCTTCCATTCCGTGATTATCTACTGAAGTTGAAGAAAGACACCATTACAAACAA
AATAAAGAAATCACAATGCACATATCAACGAGACAGAATCTCCTTGGCATGGATAGAACTATGA
AACCCTACAATTACAATGCAAGTATATTTCAAGGACCAGATTCATGAACTTGACACGCCCTATA
GTGCCGAATCACACAAATGCCCATTTAATTTCCCTGCCTGCTTGAGGAACAACTCTTCACCAAG
TTGCAACATTCCGAACGTGGAACAACATCACTTTCGACAGTGATCACTAGGTCATCCAGTAAAA
CAGTACTGCAGAAATGATGAATATGAACAATACACCAAGTAGGCCTAAAGACCAAGAACTCAAA
CCTGAACGAGAGGAAGTTGCAGCTTGTGAATCCTTCCAAGTGCCATCGTTTTCACCATTCAACG
CACCGTCTTCAGATGCTGAATGAACATCGTTTGACTCGGAACCATTGGGGCAATCCAAAGAAGA
GGAATTTGATGGAATTCCAGAAGGTCTCGCTTGAGGTACAACACCAAAGGAGTTGTTTTTCCAC
CAGGGCTCTGCATACATCATCGGCTGCTGAACAGCATGGTGATTATTGACTTCCTCTTCGTTTT
CTCTTCCCGGTTTTGATTGCATCT
						
					

			
		

Sequences
Splice junction sequence	TTGTTTTTCCACCAGGGCTCTGCATACATCATCGGCTGCTGAACAGCATGGTGATTATTGACTT CCTCTTCGTTTTCTCTTCCCGGTTTTGATTGCATCTctttctgtcccggatgactttcctctct agctctgccttggcacgtgcttttcttcgccttagaattccctcgtactgctttgcattcacat aaacgggc
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: 614 Transcript exons: 4051532-4051696,4052008-4052079,4052231-4052328,4052685- 4052963 CTTTCTGTCCCGGATGACTTTCCTCTCTAGCTCTGCCTTGGCACGTGCTTTTCTTCGCCTTAGA ATTCCCTCGTACTGCTTTGCATTCACATAAACGGGCTCTTGTGCCATGTCAAGTGGCAGAGCTG TTCTTTCACGAGGCATTCCAAGATATGGACGAAAACCCAATTGCTGATGACCATATGCTCCCAT CAATCCCCCATAATATGGATCCTGATATGGGTTTGGGACACAAGCGATATAGTGTCCAACAAGC TCTGGTGGTTGTACAAGTGGCTGATCATGCATGTTACGGATAGAGAGCGCTGGGTCATTTCCTT CCATTCCGTGATTATCTGAACGAGAGGAAGTTGCAGCTTGTGAATCCTTCCAAGTGCCATCGTT TTCACCATTCAACGCACCGTCTTCAGATGCTGAATGAACATCGTTTGACTCGGAACCATTGGGG CAATCCAAAGAAGAGGAATTTGATGGAATTCCAGAAGGTCTCGCTTGAGGTACAACACCAAAGG AGTTGTTTTTCCACCAGGGCTCTGCATACATCATCGGCTGCTGAACAGCATGGTGATTATTGAC TTCCTCTTCGTTTTCTCTTCCCGGTTTTGATTGCATCT
Genomic sequence	CTTTCTGTCCCGGATGACTTTCCTCTCTAGCTCTGCCTTGGCACGTGCTTTTCTTCGCCTTAGA ATTCCCTCGTACTGCTTTGCATTCACATAAACGGGCTCTTGTGCCATGTCAAGTGGCAGAGCTG TTCTTTCACGAGGCATTCCAAGATATGGACGAAAACCCTGTTTAAACCAATGAACAAAATAAAT GCAACAAATAGACTCAGATCATCGAAAACTTTACATATAACTTATAAGACCCCAAGAATCCCCA TTAGTTGTTCTCGATAATTTCAGATATAACTTTGGATTCTCAGTTATTTCAGAAATGAACTTTA AAAGCATCTCACTGACTATTGCTGAACCCAGACACATTCCAACAGTAAATAAAATCACCACAAA CGGGTACTTAGTGGCAAAAGCGCACATACATCAAATAAACACTGCACCATATGGAACTATTGTA GAGATTGAAAGAGGTTTCGACAAGATACCAATTGCTGATGACCATATGCTCCCATCAATCCCCC ATAATATGGATCCTGATATGGGTTTGGGACACAAGCCTGTAAGGAAGTTTTGAGTTTATCATAC ATATGAAAAGGGCGTTATACAAGATAAATCCTTTTGAGGGACCAATAAGAAGTCAATTTAACAG CTCAAGAACTCATAAAGCATATATATATATATATTAAGGAATGAGAGGAAACCACATACGATAT AGTGTCCAACAAGCTCTGGTGGTTGTACAAGTGGCTGATCATGCATGTTACGGATAGAGAGCGC TGGGTCATTTCCTTCCATTCCGTGATTATCTACTGAAGTTGAAGAAAGACACCATTACAAACAA AATAAAGAAATCACAATGCACATATCAACGAGACAGAATCTCCTTGGCATGGATAGAACTATGA AACCCTACAATTACAATGCAAGTATATTTCAAGGACCAGATTCATGAACTTGACACGCCCTATA GTGCCGAATCACACAAATGCCCATTTAATTTCCCTGCCTGCTTGAGGAACAACTCTTCACCAAG TTGCAACATTCCGAACGTGGAACAACATCACTTTCGACAGTGATCACTAGGTCATCCAGTAAAA CAGTACTGCAGAAATGATGAATATGAACAATACACCAAGTAGGCCTAAAGACCAAGAACTCAAA CCTGAACGAGAGGAAGTTGCAGCTTGTGAATCCTTCCAAGTGCCATCGTTTTCACCATTCAACG CACCGTCTTCAGATGCTGAATGAACATCGTTTGACTCGGAACCATTGGGGCAATCCAAAGAAGA GGAATTTGATGGAATTCCAGAAGGTCTCGCTTGAGGTACAACACCAAAGGAGTTGTTTTTCCAC CAGGGCTCTGCATACATCATCGGCTGCTGAACAGCATGGTGATTATTGACTTCCTCTTCGTTTT CTCTTCCCGGTTTTGATTGCATCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.177801385

Conservation Information
Conserved circRNAs	NA
PMCS	0.177801385

			
						 Functional Information
					
						Coding potential
						NA
					
						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	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT5G12840_circ_g.3

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