Plant Circular RNA Database

Detail information of AT1G78960_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G78960_circ_g.3
					
						ID in PlantcircBase
						ath_circ_010887
					
						Alias
						1:29699068-29700022
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 29699068-29700022  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G78960						
					
						Parent gene annotation
						
							Amyrin synthase LUP2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							1_circ_ag.3 AT1G78960_circ_g.1 AT1G78960_circ_g.2 1_circ_ag.4 AT1G78960_circ_g.5 						
					
						Support reads
						2/1
					
						Tissues
						root;flower
					
						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
						AT1G78960.4:5
AT1G78960.2:5
AT1G78960.1:5
AT1G78960.3:5
AT1G78960.5:5

General Information
CircRNA Name	AT1G78960_circ_g.3
ID in PlantcircBase	ath_circ_010887
Alias	1:29699068-29700022
Organism	Arabidpsis thaliana
Position	chr1: 29699068-29700022 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G78960
Parent gene annotation	Amyrin synthase LUP2
Parent gene strand	+
Alternative splicing	1_circ_ag.3 AT1G78960_circ_g.1 AT1G78960_circ_g.2 1_circ_ag.4 AT1G78960_circ_g.5
Support reads	2/1
Tissues	root;flower
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	AT1G78960.4:5 AT1G78960.2:5 AT1G78960.1:5 AT1G78960.3:5 AT1G78960.5:5

			
						 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  
						
							TCAAACAACTTTATCCGGATCACAGGACAAAAGAGATCATCAAGTCGATTGAGAAAGGGGTGCA
ATTCATTGAAAGCAAACAAACGCCTGATGGTTCATGagctttggaagtcaactctgggacacag
tttttgcgattcaagctttacttgcttgtgacctttctgacgaaactgatgatgtactcaggaa
aggacaca

									
								

					

						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: 590
Transcript exons: 29699068-29699187,29699269-29699391,29699480-29699578,29
699661-29699717,29699832-29700022
AGCTTTGGAAGTCAACTCTGGGACACAGTTTTTGCGATTCAAGCTTTACTTGCTTGTGACCTTT
CTGACGAAACTGATGATGTACTCAGGAAAGGACACAGTTTCATCAAAAAATCCCAGGTTAGAGA
AAACCCTTCAGGTGACTTTAAGAGCATGTATCGCCATATTTCCAAAGGAGCCTGGACTCTGTCC
GATCGAGATCATGGATGGCAAGTCTCAGATTGTACAGCTGAAGCTTTGAAGTGTTGCATGCTGC
TCTCCATGATGCCAGCTGAGGTCGTTGGCCAGAAAATAGATCCTGAACAATTATATGATTCTGT
TAATCTCTTGCTATCGTTGCAGGGTGAAAAAGGAGGTTTGACTGCATGGGAGCCTGTCCGTGCA
CAAGAATGGCTGGAATTGCTCAATCCCACAGATTTCTTTACTTGTGTTATGGCTGAACGCGAGT
ATGTAGAATGTACCTCAGCTGTTATACAAGCTTTGGTACTGTTCAAACAACTTTATCCGGATCA
CAGGACAAAAGAGATCATCAAGTCGATTGAGAAAGGGGTGCAATTCATTGAAAGCAAACAAACG
CCTGATGGTTCATG
						
					

						Genomic sequence
						
							AGCTTTGGAAGTCAACTCTGGGACACAGTTTTTGCGATTCAAGCTTTACTTGCTTGTGACCTTT
CTGACGAAACTGATGATGTACTCAGGAAAGGACACAGTTTCATCAAAAAATCCCAGGTTTAATT
GTAGTCTTGTATCTTGAAATGCCTTATGGAACAATTGCATGTGTTCTTTTCCCTAAATTAAAGC
ACTTTGTAGGTTAGAGAAAACCCTTCAGGTGACTTTAAGAGCATGTATCGCCATATTTCCAAAG
GAGCCTGGACTCTGTCCGATCGAGATCATGGATGGCAAGTCTCAGATTGTACAGCTGAAGCTTT
GAAGGTAATCAAATTAGTTGTGGAAGCAGAATTAGTTAAGAGTTTCCACAAGAGTTATGCCCCA
GATTAACCTGTACTTCTGTGTTTTGTAGTGTTGCATGCTGCTCTCCATGATGCCAGCTGAGGTC
GTTGGCCAGAAAATAGATCCTGAACAATTATATGATTCTGTTAATCTCTTGCTATCGTTGCAGG
TGAGATAATATCTATAAGACTAATTTTGGTAAAAGCTCTGTCTCTAATTAATATTCACGAACAC
AACTTTATTTGATGTAGGGTGAAAAAGGAGGTTTGACTGCATGGGAGCCTGTCCGTGCACAAGA
ATGGCTGGAAGTAAGAGTTACAACACATAAGGACACCTTTTGATGTCCTTTTTGCGGATTTGAA
AATCGTTAAGAATATAACCATTCAGGTGATCAGGTCTAACCTTTGTAACTGGTGTTGCAGTTGC
TCAATCCCACAGATTTCTTTACTTGTGTTATGGCTGAACGCGAGTATGTAGAATGTACCTCAGC
TGTTATACAAGCTTTGGTACTGTTCAAACAACTTTATCCGGATCACAGGACAAAAGAGATCATC
AAGTCGATTGAGAAAGGGGTGCAATTCATTGAAAGCAAACAAACGCCTGATGGTTCATG
						
					

			
		

Sequences
Splice junction sequence	TCAAACAACTTTATCCGGATCACAGGACAAAAGAGATCATCAAGTCGATTGAGAAAGGGGTGCA ATTCATTGAAAGCAAACAAACGCCTGATGGTTCATGagctttggaagtcaactctgggacacag tttttgcgattcaagctttacttgcttgtgacctttctgacgaaactgatgatgtactcaggaa aggacaca
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: 590 Transcript exons: 29699068-29699187,29699269-29699391,29699480-29699578,29 699661-29699717,29699832-29700022 AGCTTTGGAAGTCAACTCTGGGACACAGTTTTTGCGATTCAAGCTTTACTTGCTTGTGACCTTT CTGACGAAACTGATGATGTACTCAGGAAAGGACACAGTTTCATCAAAAAATCCCAGGTTAGAGA AAACCCTTCAGGTGACTTTAAGAGCATGTATCGCCATATTTCCAAAGGAGCCTGGACTCTGTCC GATCGAGATCATGGATGGCAAGTCTCAGATTGTACAGCTGAAGCTTTGAAGTGTTGCATGCTGC TCTCCATGATGCCAGCTGAGGTCGTTGGCCAGAAAATAGATCCTGAACAATTATATGATTCTGT TAATCTCTTGCTATCGTTGCAGGGTGAAAAAGGAGGTTTGACTGCATGGGAGCCTGTCCGTGCA CAAGAATGGCTGGAATTGCTCAATCCCACAGATTTCTTTACTTGTGTTATGGCTGAACGCGAGT ATGTAGAATGTACCTCAGCTGTTATACAAGCTTTGGTACTGTTCAAACAACTTTATCCGGATCA CAGGACAAAAGAGATCATCAAGTCGATTGAGAAAGGGGTGCAATTCATTGAAAGCAAACAAACG CCTGATGGTTCATG
Genomic sequence	AGCTTTGGAAGTCAACTCTGGGACACAGTTTTTGCGATTCAAGCTTTACTTGCTTGTGACCTTT CTGACGAAACTGATGATGTACTCAGGAAAGGACACAGTTTCATCAAAAAATCCCAGGTTTAATT GTAGTCTTGTATCTTGAAATGCCTTATGGAACAATTGCATGTGTTCTTTTCCCTAAATTAAAGC ACTTTGTAGGTTAGAGAAAACCCTTCAGGTGACTTTAAGAGCATGTATCGCCATATTTCCAAAG GAGCCTGGACTCTGTCCGATCGAGATCATGGATGGCAAGTCTCAGATTGTACAGCTGAAGCTTT GAAGGTAATCAAATTAGTTGTGGAAGCAGAATTAGTTAAGAGTTTCCACAAGAGTTATGCCCCA GATTAACCTGTACTTCTGTGTTTTGTAGTGTTGCATGCTGCTCTCCATGATGCCAGCTGAGGTC GTTGGCCAGAAAATAGATCCTGAACAATTATATGATTCTGTTAATCTCTTGCTATCGTTGCAGG TGAGATAATATCTATAAGACTAATTTTGGTAAAAGCTCTGTCTCTAATTAATATTCACGAACAC AACTTTATTTGATGTAGGGTGAAAAAGGAGGTTTGACTGCATGGGAGCCTGTCCGTGCACAAGA ATGGCTGGAAGTAAGAGTTACAACACATAAGGACACCTTTTGATGTCCTTTTTGCGGATTTGAA AATCGTTAAGAATATAACCATTCAGGTGATCAGGTCTAACCTTTGTAACTGGTGTTGCAGTTGC TCAATCCCACAGATTTCTTTACTTGTGTTATGGCTGAACGCGAGTATGTAGAATGTACCTCAGC TGTTATACAAGCTTTGGTACTGTTCAAACAACTTTATCCGGATCACAGGACAAAAGAGATCATC AAGTCGATTGAGAAAGGGGTGCAATTCATTGAAAGCAAACAAACGCCTGATGGTTCATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.232394957

Conservation Information
Conserved circRNAs	NA
PMCS	0.232394957

			
						 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 AT1G78960_circ_g.3

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