Plant Circular RNA Database

Detail information of AT3G02560_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G02560_circ_g.3
					
						ID in PlantcircBase
						ath_circ_019348
					
						Alias
						At_ciR1372, Ath_circ_FC1785, AT3G02560_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 542501-542962  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI-full, PcircRNA_finder, circseq_cup, find_circ, CIRI2
					
						Parent gene
						
							AT3G02560						
					
						Parent gene annotation
						
							40S ribosomal protein S7-2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G02560_circ_g.1 AT3G02560_circ_g.2 AT3G02560_circ_g.4 						
					
						Support reads
						3/18
					
						Tissues
						leaf/inflorescences
					
						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
						AT3G02560.1:2
AT3G02560.2:2
AT3G02560.3:2

General Information
CircRNA Name	AT3G02560_circ_g.3
ID in PlantcircBase	ath_circ_019348
Alias	At_ciR1372, Ath_circ_FC1785, AT3G02560_C1
Organism	Arabidpsis thaliana
Position	chr3: 542501-542962 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI-full, PcircRNA_finder, circseq_cup, find_circ, CIRI2
Parent gene	AT3G02560
Parent gene annotation	40S ribosomal protein S7-2
Parent gene strand	+
Alternative splicing	AT3G02560_circ_g.1 AT3G02560_circ_g.2 AT3G02560_circ_g.4
Support reads	3/18
Tissues	leaf/inflorescences
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	AT3G02560.1:2 AT3G02560.2:2 AT3G02560.3:2

			
						 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  
						
							TACTTCTGTCCATGAAGCCATGCTCGAGGATGTCGCTTACCCTGCTGAGATTGTAGGAAAGAGA
ACCAGATACCGTCTTGATGGCACCAAGATCATGAAGgctttgtttgacttggagaacaccaacc
aggagttgaaaagcgagttgaaagatctctacattaaccaagctgtgtatgtactttgttttct
cgcttgga

						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: 381
Transcript exons: 542501-542574,542656-542962
GCTTTGTTTGACTTGGAGAACACCAACCAGGAGTTGAAAAGCGAGTTGAAAGATCTCTACATTA
ACCAAGCTGTTCAGATGGATATTTCTGGCAACCGCAAAGCTGTTGTGATCTACGTTCCATTCAG
GCTGAGGAAAGCTTTCCGCAAGATTCATCTTCGTCTGGTCAGAGAGCTTGAGAAGAAGTTCAGT
GGAAAAGATGTGATCTTTGTTGCTACCAGAAGAATCATGCGCCCACCAAAGAAAGGCTCAGCTG
TTCAGAGACCACGCAACAGAACTCTTACTTCTGTCCATGAAGCCATGCTCGAGGATGTCGCTTA
CCCTGCTGAGATTGTAGGAAAGAGAACCAGATACCGTCTTGATGGCACCAAGATCATGAAG
						
						Genomic sequence
						
							GCTTTGTTTGACTTGGAGAACACCAACCAGGAGTTGAAAAGCGAGTTGAAAGATCTCTACATTA
ACCAAGCTGTGTATGTACTTTGTTTTCTCGCTTGGAAGGATTTTCATTATGGTTCCCTTACTGA
ACTATCTCCTTTTTCTATTCTGTGTAGTCAGATGGATATTTCTGGCAACCGCAAAGCTGTTGTG
ATCTACGTTCCATTCAGGCTGAGGAAAGCTTTCCGCAAGATTCATCTTCGTCTGGTCAGAGAGC
TTGAGAAGAAGTTCAGTGGAAAAGATGTGATCTTTGTTGCTACCAGAAGAATCATGCGCCCACC
AAAGAAAGGCTCAGCTGTTCAGAGACCACGCAACAGAACTCTTACTTCTGTCCATGAAGCCATG
CTCGAGGATGTCGCTTACCCTGCTGAGATTGTAGGAAAGAGAACCAGATACCGTCTTGATGGCA
CCAAGATCATGAAG

Sequences
Splice junction sequence	TACTTCTGTCCATGAAGCCATGCTCGAGGATGTCGCTTACCCTGCTGAGATTGTAGGAAAGAGA ACCAGATACCGTCTTGATGGCACCAAGATCATGAAGgctttgtttgacttggagaacaccaacc aggagttgaaaagcgagttgaaagatctctacattaaccaagctgtgtatgtactttgttttct cgcttgga
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: 381 Transcript exons: 542501-542574,542656-542962 GCTTTGTTTGACTTGGAGAACACCAACCAGGAGTTGAAAAGCGAGTTGAAAGATCTCTACATTA ACCAAGCTGTTCAGATGGATATTTCTGGCAACCGCAAAGCTGTTGTGATCTACGTTCCATTCAG GCTGAGGAAAGCTTTCCGCAAGATTCATCTTCGTCTGGTCAGAGAGCTTGAGAAGAAGTTCAGT GGAAAAGATGTGATCTTTGTTGCTACCAGAAGAATCATGCGCCCACCAAAGAAAGGCTCAGCTG TTCAGAGACCACGCAACAGAACTCTTACTTCTGTCCATGAAGCCATGCTCGAGGATGTCGCTTA CCCTGCTGAGATTGTAGGAAAGAGAACCAGATACCGTCTTGATGGCACCAAGATCATGAAG
Genomic sequence	GCTTTGTTTGACTTGGAGAACACCAACCAGGAGTTGAAAAGCGAGTTGAAAGATCTCTACATTA ACCAAGCTGTGTATGTACTTTGTTTTCTCGCTTGGAAGGATTTTCATTATGGTTCCCTTACTGA ACTATCTCCTTTTTCTATTCTGTGTAGTCAGATGGATATTTCTGGCAACCGCAAAGCTGTTGTG ATCTACGTTCCATTCAGGCTGAGGAAAGCTTTCCGCAAGATTCATCTTCGTCTGGTCAGAGAGC TTGAGAAGAAGTTCAGTGGAAAAGATGTGATCTTTGTTGCTACCAGAAGAATCATGCGCCCACC AAAGAAAGGCTCAGCTGTTCAGAGACCACGCAACAGAACTCTTACTTCTGTCCATGAAGCCATG CTCGAGGATGTCGCTTACCCTGCTGAGATTGTAGGAAAGAGAACCAGATACCGTCTTGATGGCA CCAAGATCATGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.521360554

Conservation Information
Conserved circRNAs	NA
PMCS	0.521360554

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							542660-542959(+)
						
						Potential amino acid sequence
						
							MDISGNRKAVVIYVPFRLRKAFRKIHLRLVRELEKKFSGKDVIFVATRRIMRPPKKGSAVQRPR
NRTLTSVHEAMLEDVAYPAEIVGKRTRYRLDGTKIMKALFDLENTNQELKSELKDLYINQAVQM
DISGNRKAVVIYVPFRLRKAFRKIHLRLVRELEKKFSGKDVIFVATRRIMRPPKKGSAVQRPRN
RTLTSVHEAMLEDVAYPAEIVGKRTRYRLDGTKIMKALFDLENTNQELKSELKDLYINQAVQMD
ISGNRKAVVIYVPFRLRKAFRKIHLRLVRELEKKFSGKDVIFVATRRIMRPPKKGSAVQRPRNR
TLTSVHEAMLEDVAYPAEIVGKRTRYRLDGTKIMKALFDLENTNQELKSELKDLYINQAVQMDI
SGNRKAVVIYVPFRLRKAFRKIHLRLVRELEKKFSGKDVIFVATRRIMRPPKKGSAVQRPRNRT
LTSVHEAMLEDVAYPAEIVGKRTRYRLDGTKIMK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	542660-542959(+)
Potential amino acid sequence	MDISGNRKAVVIYVPFRLRKAFRKIHLRLVRELEKKFSGKDVIFVATRRIMRPPKKGSAVQRPR NRTLTSVHEAMLEDVAYPAEIVGKRTRYRLDGTKIMKALFDLENTNQELKSELKDLYINQAVQM DISGNRKAVVIYVPFRLRKAFRKIHLRLVRELEKKFSGKDVIFVATRRIMRPPKKGSAVQRPRN RTLTSVHEAMLEDVAYPAEIVGKRTRYRLDGTKIMKALFDLENTNQELKSELKDLYINQAVQMD ISGNRKAVVIYVPFRLRKAFRKIHLRLVRELEKKFSGKDVIFVATRRIMRPPKKGSAVQRPRNR TLTSVHEAMLEDVAYPAEIVGKRTRYRLDGTKIMKALFDLENTNQELKSELKDLYINQAVQMDI SGNRKAVVIYVPFRLRKAFRKIHLRLVRELEKKFSGKDVIFVATRRIMRPPKKGSAVQRPRNRT LTSVHEAMLEDVAYPAEIVGKRTRYRLDGTKIMK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Chen et al., 2017a;Zhang et al., 2019

circRNA

Detail information of AT3G02560_circ_g.3

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