Plant Circular RNA Database

Detail information of AT2G35110_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT2G35110_circ_g.3
					
						ID in PlantcircBase
						ath_circ_016542
					
						Alias
						At_ciR593, AT2G35110_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 14798952-14799462  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI-full, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, find_circ, CIRI2
					
						Parent gene
						
							AT2G35110						
					
						Parent gene annotation
						
							Protein NAP1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT2G35110_circ_g.1 AT2G35110_circ_g.2 AT2G35110_circ_g.4 AT2G35110_circ_g.5 						
					
						Support reads
						5/6
					
						Tissues
						leaf/root, leaf, aerial, whole_plant
					
						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
						AT2G35110.1:3
AT2G35110.2:3

General Information
CircRNA Name	AT2G35110_circ_g.3
ID in PlantcircBase	ath_circ_016542
Alias	At_ciR593, AT2G35110_C1
Organism	Arabidpsis thaliana
Position	chr2: 14798952-14799462 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI-full, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, find_circ, CIRI2
Parent gene	AT2G35110
Parent gene annotation	Protein NAP1
Parent gene strand	-
Alternative splicing	AT2G35110_circ_g.1 AT2G35110_circ_g.2 AT2G35110_circ_g.4 AT2G35110_circ_g.5
Support reads	5/6
Tissues	leaf/root, leaf, aerial, whole_plant
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	AT2G35110.1:3 AT2G35110.2:3

			
						 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  
						
							TCCCAGTAGAGACAGTGGCTTTTTCCAAATGCCTGATGTTTATCGATGATCGAGAAGAAGTGAC
AATCATCAAAATGGACAACCAATCTTTCCGGAAATCctcctcaggaattattagtgaagcacat
tccgggaaactactagccacactgagccatgcacaacaatgctgaggacgtccttctggtccaa
acattgta

									
								

					

						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: 202
Transcript exons: 14798952-14799007,14799317-14799462
CTCCTCAGGAATTATTAGTGAAGCACATTCCGGGAAACTACTAGCCACACTGAGCCCTGGACCA
GTTATATGCAGCATTTCCTTCCGATAGCAAGCCCTCCTTCCCAGTAGAGACAGTGGCTTTTTCC
AAATGCCTGATGTTTATCGATGATCGAGAAGAAGTGACAATCATCAAAATGGACAACCAATCTT
TCCGGAAATC
Transcript length: 209
Transcript exons: 14798952-14799055,14799358-14799462
CTCCTCAGGAATTATTAGTGAAGCACATTCCGGGAAACTACTAGCCACACTGAGCCATGCACAA
CAATGCTGAGGACGTCCTTCTGGTCCAAACATTGTATTTCCTCCTTCCCAGTAGAGACAGTGGC
TTTTTCCAAATGCCTGATGTTTATCGATGATCGAGAAGAAGTGACAATCATCAAAATGGACAAC
CAATCTTTCCGGAAATC
Transcript length: 218
Transcript exons: 14798952-14799038,14799332-14799462
CTCCTCAGGAATTATTAGTGAAGCACATTCCGGGAAACTACTAGCCACACTGAGCCATGCACAA
CAATGCTGAGGACGTCCTTCTGGGCAGCATTTCCTTCCGATAGCAAGCCCTCCTTCCCAGTAGA
GACAGTGGCTTTTTCCAAATGCCTGATGTTTATCGATGATCGAGAAGAAGTGACAATCATCAAA
ATGGACAACCAATCTTTCCGGAAATC
Transcript length: 339
Transcript exons: 14798952-14799062,14799144-14799225,14799317-14799462
CTCCTCAGGAATTATTAGTGAAGCACATTCCGGGAAACTACTAGCCACACTGAGCCATGCACAA
CAATGCTGAGGACGTCCTTCTGGTCCAAACATTGTATTTCTGAAAACAGTTGTGAGGTGTTGAT
GGTAGAAATATAATTTCTTCAGACTTCCATGCTTTGACAATTGAGACTCTAACTCATCAACACA
TCTGGACCAGTTATATGCAGCATTTCCTTCCGATAGCAAGCCCTCCTTCCCAGTAGAGACAGTG
GCTTTTTCCAAATGCCTGATGTTTATCGATGATCGAGAAGAAGTGACAATCATCAAAATGGACA
ACCAATCTTTCCGGAAATC
Transcript length: 249
Transcript exons: 14798952-14799462
CTCCTCAGGAATTATTAGTGAAGCACATTCCGGGAAACTACTAGCCACACTGAGCCATGCACAA
CAATGCTGAGGACGTCCTTCTGGTCCAAACATTGTATTTCTGGACCAGTTATATGCAGCATTTC
CTTCCGATAGCAAGCCCTCCTTCCCAGTAGAGACAGTGGCTTTTTCCAAATGCCTGATGTTTAT
CGATGATCGAGAAGAAGTGACAATCATCAAAATGGACAACCAATCTTTCCGGAAATC
						
					

						Genomic sequence
						
							CTCCTCAGGAATTATTAGTGAAGCACATTCCGGGAAACTACTAGCCACACTGAGCCATGCACAA
CAATGCTGAGGACGTCCTTCTGGTCCAAACATTGTATTTCTGAAAACCTTTTACAAAACTCAAA
TGTTAGATTATGCATAAGATGACATGGGAAAATAGTAGACAGTGAACAACAACAGGAAGTATAC
AGTTGTGAGGTGTTGATGGTAGAAATATAATTTCTTCAGACTTCCATGCTTTGACAATTGAGAC
TCTAACTCATCAACACATCTGCATTAATGAAATTCTGCAGGATATTAGTTTCGTTGTTTCTCTA
GCTAGAAGTTAACCAAGTAATGGTATATAAGGCCGGGAACAGTACCTGGACCAGTTATATGCAG
CATTTCCTTCCGATAGCAAGCCCTCCTTCCCAGTAGAGACAGTGGCTTTTTCCAAATGCCTGAT
GTTTATCGATGATCGAGAAGAAGTGACAATCATCAAAATGGACAACCAATCTTTCCGGAAATC
						
					

			
		

Sequences
Splice junction sequence	TCCCAGTAGAGACAGTGGCTTTTTCCAAATGCCTGATGTTTATCGATGATCGAGAAGAAGTGAC AATCATCAAAATGGACAACCAATCTTTCCGGAAATCctcctcaggaattattagtgaagcacat tccgggaaactactagccacactgagccatgcacaacaatgctgaggacgtccttctggtccaa acattgta
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: 202 Transcript exons: 14798952-14799007,14799317-14799462 CTCCTCAGGAATTATTAGTGAAGCACATTCCGGGAAACTACTAGCCACACTGAGCCCTGGACCA GTTATATGCAGCATTTCCTTCCGATAGCAAGCCCTCCTTCCCAGTAGAGACAGTGGCTTTTTCC AAATGCCTGATGTTTATCGATGATCGAGAAGAAGTGACAATCATCAAAATGGACAACCAATCTT TCCGGAAATC Transcript length: 209 Transcript exons: 14798952-14799055,14799358-14799462 CTCCTCAGGAATTATTAGTGAAGCACATTCCGGGAAACTACTAGCCACACTGAGCCATGCACAA CAATGCTGAGGACGTCCTTCTGGTCCAAACATTGTATTTCCTCCTTCCCAGTAGAGACAGTGGC TTTTTCCAAATGCCTGATGTTTATCGATGATCGAGAAGAAGTGACAATCATCAAAATGGACAAC CAATCTTTCCGGAAATC Transcript length: 218 Transcript exons: 14798952-14799038,14799332-14799462 CTCCTCAGGAATTATTAGTGAAGCACATTCCGGGAAACTACTAGCCACACTGAGCCATGCACAA CAATGCTGAGGACGTCCTTCTGGGCAGCATTTCCTTCCGATAGCAAGCCCTCCTTCCCAGTAGA GACAGTGGCTTTTTCCAAATGCCTGATGTTTATCGATGATCGAGAAGAAGTGACAATCATCAAA ATGGACAACCAATCTTTCCGGAAATC Transcript length: 339 Transcript exons: 14798952-14799062,14799144-14799225,14799317-14799462 CTCCTCAGGAATTATTAGTGAAGCACATTCCGGGAAACTACTAGCCACACTGAGCCATGCACAA CAATGCTGAGGACGTCCTTCTGGTCCAAACATTGTATTTCTGAAAACAGTTGTGAGGTGTTGAT GGTAGAAATATAATTTCTTCAGACTTCCATGCTTTGACAATTGAGACTCTAACTCATCAACACA TCTGGACCAGTTATATGCAGCATTTCCTTCCGATAGCAAGCCCTCCTTCCCAGTAGAGACAGTG GCTTTTTCCAAATGCCTGATGTTTATCGATGATCGAGAAGAAGTGACAATCATCAAAATGGACA ACCAATCTTTCCGGAAATC Transcript length: 249 Transcript exons: 14798952-14799462 CTCCTCAGGAATTATTAGTGAAGCACATTCCGGGAAACTACTAGCCACACTGAGCCATGCACAA CAATGCTGAGGACGTCCTTCTGGTCCAAACATTGTATTTCTGGACCAGTTATATGCAGCATTTC CTTCCGATAGCAAGCCCTCCTTCCCAGTAGAGACAGTGGCTTTTTCCAAATGCCTGATGTTTAT CGATGATCGAGAAGAAGTGACAATCATCAAAATGGACAACCAATCTTTCCGGAAATC
Genomic sequence	CTCCTCAGGAATTATTAGTGAAGCACATTCCGGGAAACTACTAGCCACACTGAGCCATGCACAA CAATGCTGAGGACGTCCTTCTGGTCCAAACATTGTATTTCTGAAAACCTTTTACAAAACTCAAA TGTTAGATTATGCATAAGATGACATGGGAAAATAGTAGACAGTGAACAACAACAGGAAGTATAC AGTTGTGAGGTGTTGATGGTAGAAATATAATTTCTTCAGACTTCCATGCTTTGACAATTGAGAC TCTAACTCATCAACACATCTGCATTAATGAAATTCTGCAGGATATTAGTTTCGTTGTTTCTCTA GCTAGAAGTTAACCAAGTAATGGTATATAAGGCCGGGAACAGTACCTGGACCAGTTATATGCAG CATTTCCTTCCGATAGCAAGCCCTCCTTCCCAGTAGAGACAGTGGCTTTTTCCAAATGCCTGAT GTTTATCGATGATCGAGAAGAAGTGACAATCATCAAAATGGACAACCAATCTTTCCGGAAATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.730164067

Conservation Information
Conserved circRNAs	NA
PMCS	0.730164067

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							14799433-14798954(-)
						
						Potential amino acid sequence
						
							MIVTSSRSSINIRHLEKATVSTGKEGLLSEGNAAYNWSRCVDELESQLSKHGSLKKLYFYHQHL
TTVFRNTMFGPEGRPQHCCAWLSVASSFPECASLIIPEEDFRKDWLSILMIVTSSRSSINIRHL
EKATVSTGKEGLLSEGNAAYNWSRCVDELESQLSKHGSLKKLYFYHQHLTTVFRNTMFGPEGRP
QHCCAWLSVASSFPECASLIIPEEDFRKDWLSILMIVTSSRSSINIRHLEKATVSTGKEGLLSE
GNAAYNWSRCVDELESQLSKHGSLKKLYFYHQHLTTVFRNTMFGPEGRPQHCCAWLSVASSFPE
CASLIIPEEDFRKDWLSILMIVTSSRSSINIRHLEKATVSTGKEGLLSEGNAAYNWSRCVDELE
SQLSKHGSLKKLYFYHQHLTTVFRNTMFGPEGRPQHCCAWLSVASSFPECASLIIPEE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	14799433-14798954(-)
Potential amino acid sequence	MIVTSSRSSINIRHLEKATVSTGKEGLLSEGNAAYNWSRCVDELESQLSKHGSLKKLYFYHQHL TTVFRNTMFGPEGRPQHCCAWLSVASSFPECASLIIPEEDFRKDWLSILMIVTSSRSSINIRHL EKATVSTGKEGLLSEGNAAYNWSRCVDELESQLSKHGSLKKLYFYHQHLTTVFRNTMFGPEGRP QHCCAWLSVASSFPECASLIIPEEDFRKDWLSILMIVTSSRSSINIRHLEKATVSTGKEGLLSE GNAAYNWSRCVDELESQLSKHGSLKKLYFYHQHLTTVFRNTMFGPEGRPQHCCAWLSVASSFPE CASLIIPEEDFRKDWLSILMIVTSSRSSINIRHLEKATVSTGKEGLLSEGNAAYNWSRCVDELE SQLSKHGSLKKLYFYHQHLTTVFRNTMFGPEGRPQHCCAWLSVASSFPECASLIIPEE(-)
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;Liu et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT2G35110_circ_g.3

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