Plant Circular RNA Database

Detail information of AT1G20970_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G20970_circ_g.2
					
						ID in PlantcircBase
						ath_circ_003698
					
						Alias
						1:7317660-7319202
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 7317660-7319202  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G20970						
					
						Parent gene annotation
						
							BEST Arabidopsis thaliana protein match is: proton pump interact
or 1 (TAIR:AT4G27500.1) /.../30201 Blast hits to 17322 proteins 
in 780 species: Archae - 12
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G20970_circ_g.3 AT1G20970_circ_g.4 AT1G20970_circ_g.5 						
					
						Support reads
						2
					
						Tissues
						flower
					
						Exon boundary  
						
							Yes-No							"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
						AT1G20970.1:4

General Information
CircRNA Name	AT1G20970_circ_g.2
ID in PlantcircBase	ath_circ_003698
Alias	1:7317660-7319202
Organism	Arabidpsis thaliana
Position	chr1: 7317660-7319202 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G20970
Parent gene annotation	BEST Arabidopsis thaliana protein match is: proton pump interact or 1 (TAIR:AT4G27500.1) /.../30201 Blast hits to 17322 proteins in 780 species: Archae - 12
Parent gene strand	+
Alternative splicing	AT1G20970_circ_g.3 AT1G20970_circ_g.4 AT1G20970_circ_g.5
Support reads	2
Tissues	flower
Exon boundary	Yes-No "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	AT1G20970.1:4

			
						 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  
						
							GTTCCTCTGCCTTTAAGAAACCGAGGAAGCAAGAGAAAACTGCGGCAATGGATGTGGATTGGAC
TCATAGTTGTGATCATCATCGCATTGTTCCTTCTCGgtgttgaggaaggaactagacgcactca
gaaacgatctatcaaaagccgaagaaatcacaaaagctgcgaaaaaaaagtgtgatggggaatg
ggaagcac

									
								

					

						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
						
							GTGTTGAGGAAGGAACTAGACGCACTCAGAAACGATCTATCAAAAGCCGAAGAAATCACAAAAG
CTGCGAAAAAAAAGTGTGATGGGGAATGGGAAGCACAGAGTAAACTGCAAGAACAGTTCAGAGC
TGCTGATGCTGTTCGCCAGGAAGCATTTGTGCACCTACAGGATTTGAAGAAACAACAACGAGAA
AAGGTACCCAAAGAGCATCTGAAAGTGGACATAACTTACAAATGTTTGCATCTGAGGTTTTTAT
TAAATCCTTCACTTTTACTATTTTTTCGTATTGCAGAACAAATATTTCTTCAAGTACAGAGATA
ATTCAAGGGCAGCAAGTGAAATGGCTTTGAAGAAAGACAGAGCAGCACTGCAAAGCCTTTGTTC
TGACCAGGTATAAGCAGAAGCCAAATTTCTACTACGTTTTCAATCCCTGTATGTCGGCTTTGTA
CTCATTTCAGTCTTTAAGCAGGTGGAGAATTTCATGAATATGTGGAACAATGACGACGAGTTCC
GTAAATACTATGTAAAAAGCAACACAAGGAGTACCTTTAGAAGACTAGGAACCCTAGATGGACG
ATCTCTTGGCCCTGATGAGGAGCCACCTCGGATCACTTATGCTCCAAGAACGGACAAACTTAGA
ACTTCTAGTGACAGAGCAGAGAAACATGAGGCAGTTCCAGCACAGAAAGAGAAAGTCGTTAAAT
TTGAAGGTTCAAAAGTTGAAAACAACGGTAAGGAGGTTGCTAAACCCACCGAGCAAAAGAGTCA
GACCACTAAATCTAAAAAGGCCGTCAAGCCAGACCAGCCTCCATCAATTGTCACAGAATTGGTT
TCTGGAAAAGAGGAGATAGAGAAGTCAGCAACACCGGAAGAAGAAGAGCCGCCTAAGTTAACAA
AAGAGGAAGAGGAGTTAATTAAGAAAGAAGAAGAGAAGAGAAAACAAAAGGAAGCTGCAAAGAT
GAAGGAGCAACATCGGTTAGAGGAAATAGCAAAAGCGAAAGAGGCAATGGAGAGGAAGAAGAAG
AGAGAGGAGAAGGCAAAAGCAAGAGCTGTTCTCAAGGCTCAGAAGGAAGCCGAAGAAAGGGAGA
AGGTAAAAGCATATTTTTGTCATTCTGTTATCCAAATTGGATTTCGATCAGTCTCTCTAGCTAG
TATGTTTCTGTTGGGACAAAAATTATTTTAAATACTATGCCATGGATCTGTTGAACAACTCTGT
CTATTTTGTAGGAACGAGAGAAGAAGCTAAGGAAGAAGGAGAGAAGAAAGGGGATTTTTACATC
AGAAGAGACAGCAACAGAAAACCCAATTCCGACAGCAGAAACTGTAGTCGAAACCCCAAGGGAG
ATCGAAACTCCAAAGAAACAAACCGTAGAGGAGAGTCAACAAATGAAGAAATCTCACAAACCTT
CATCACAGTTTCTGAAACAAAACAAGTCAAAATCGGTTCCTCTGCCTTTAAGAAACCGAGGAAG
CAAGAGAAAACTGCGGCAATGGATGTGGATTGGACTCATAGTTGTGATCATCATCGCATTGTTC
CTTCTCG
						
					

			
		

Sequences
Splice junction sequence	GTTCCTCTGCCTTTAAGAAACCGAGGAAGCAAGAGAAAACTGCGGCAATGGATGTGGATTGGAC TCATAGTTGTGATCATCATCGCATTGTTCCTTCTCGgtgttgaggaaggaactagacgcactca gaaacgatctatcaaaagccgaagaaatcacaaaagctgcgaaaaaaaagtgtgatggggaatg ggaagcac
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	GTGTTGAGGAAGGAACTAGACGCACTCAGAAACGATCTATCAAAAGCCGAAGAAATCACAAAAG CTGCGAAAAAAAAGTGTGATGGGGAATGGGAAGCACAGAGTAAACTGCAAGAACAGTTCAGAGC TGCTGATGCTGTTCGCCAGGAAGCATTTGTGCACCTACAGGATTTGAAGAAACAACAACGAGAA AAGGTACCCAAAGAGCATCTGAAAGTGGACATAACTTACAAATGTTTGCATCTGAGGTTTTTAT TAAATCCTTCACTTTTACTATTTTTTCGTATTGCAGAACAAATATTTCTTCAAGTACAGAGATA ATTCAAGGGCAGCAAGTGAAATGGCTTTGAAGAAAGACAGAGCAGCACTGCAAAGCCTTTGTTC TGACCAGGTATAAGCAGAAGCCAAATTTCTACTACGTTTTCAATCCCTGTATGTCGGCTTTGTA CTCATTTCAGTCTTTAAGCAGGTGGAGAATTTCATGAATATGTGGAACAATGACGACGAGTTCC GTAAATACTATGTAAAAAGCAACACAAGGAGTACCTTTAGAAGACTAGGAACCCTAGATGGACG ATCTCTTGGCCCTGATGAGGAGCCACCTCGGATCACTTATGCTCCAAGAACGGACAAACTTAGA ACTTCTAGTGACAGAGCAGAGAAACATGAGGCAGTTCCAGCACAGAAAGAGAAAGTCGTTAAAT TTGAAGGTTCAAAAGTTGAAAACAACGGTAAGGAGGTTGCTAAACCCACCGAGCAAAAGAGTCA GACCACTAAATCTAAAAAGGCCGTCAAGCCAGACCAGCCTCCATCAATTGTCACAGAATTGGTT TCTGGAAAAGAGGAGATAGAGAAGTCAGCAACACCGGAAGAAGAAGAGCCGCCTAAGTTAACAA AAGAGGAAGAGGAGTTAATTAAGAAAGAAGAAGAGAAGAGAAAACAAAAGGAAGCTGCAAAGAT GAAGGAGCAACATCGGTTAGAGGAAATAGCAAAAGCGAAAGAGGCAATGGAGAGGAAGAAGAAG AGAGAGGAGAAGGCAAAAGCAAGAGCTGTTCTCAAGGCTCAGAAGGAAGCCGAAGAAAGGGAGA AGGTAAAAGCATATTTTTGTCATTCTGTTATCCAAATTGGATTTCGATCAGTCTCTCTAGCTAG TATGTTTCTGTTGGGACAAAAATTATTTTAAATACTATGCCATGGATCTGTTGAACAACTCTGT CTATTTTGTAGGAACGAGAGAAGAAGCTAAGGAAGAAGGAGAGAAGAAAGGGGATTTTTACATC AGAAGAGACAGCAACAGAAAACCCAATTCCGACAGCAGAAACTGTAGTCGAAACCCCAAGGGAG ATCGAAACTCCAAAGAAACAAACCGTAGAGGAGAGTCAACAAATGAAGAAATCTCACAAACCTT CATCACAGTTTCTGAAACAAAACAAGTCAAAATCGGTTCCTCTGCCTTTAAGAAACCGAGGAAG CAAGAGAAAACTGCGGCAATGGATGTGGATTGGACTCATAGTTGTGATCATCATCGCATTGTTC CTTCTCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.171492509

Conservation Information
Conserved circRNAs	NA
PMCS	0.171492509

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR8170-5p 						
					
						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	ath-miR8170-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT1G20970_circ_g.2

Address

Any questions?

Supported by