Plant Circular RNA Database

Detail information of AT4G38760_circ_g.19

			
						 General Information
					
						CircRNA Name
						AT4G38760_circ_g.19
					
						ID in PlantcircBase
						ath_circ_035485
					
						Alias
						At_ciR1857, AT4G38760_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 18095427-18095960  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, MapSplice, PcircRNA_finder, find_circ, CIRI2
					
						Parent gene
						
							AT4G38760						
					
						Parent gene annotation
						
							Protein of unknown function (DUF3414)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G38760_circ_g.20 						
					
						Support reads
						5/2
					
						Tissues
						leaf/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
						AT4G38760.1:2

General Information
CircRNA Name	AT4G38760_circ_g.19
ID in PlantcircBase	ath_circ_035485
Alias	At_ciR1857, AT4G38760_C1
Organism	Arabidpsis thaliana
Position	chr4: 18095427-18095960 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, MapSplice, PcircRNA_finder, find_circ, CIRI2
Parent gene	AT4G38760
Parent gene annotation	Protein of unknown function (DUF3414)
Parent gene strand	-
Alternative splicing	AT4G38760_circ_g.20
Support reads	5/2
Tissues	leaf/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	AT4G38760.1:2

			
						 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  
						
							CTAGATCCGAATTCAAAGCTTCTTTTGATTTCTCACTCGGTGGCTTGAACATCGACAGAGTTCC
AACGAACCACGCGTGATTCTCCTCCAACTTCTTCGCcatgtcaatgaattcttgagttagttct
tgagctaccgagtcagttgttccatattcctgctccatagatctttccacgaggatgtatgatt
ggatttca

									
								

					

						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: 166
Transcript exons: 18095427-18095491,18095860-18095960
CATGTCAATGAATTCTTGAGTTAGTTCTTGAGCTACCGAGTCAGTTGTTCCATATTCCTGCTCC
AACTAGATCCGAATTCAAAGCTTCTTTTGATTTCTCACTCGGTGGCTTGAACATCGACAGAGTT
CCAACGAACCACGCGTGATTCTCCTCCAACTTCTTCGC
Transcript length: 208
Transcript exons: 18095427-18095501,18095828-18095960
CATGTCAATGAATTCTTGAGTTAGTTCTTGAGCTACCGAGTCAGTTGTTCCATATTCCTGCTCC
ATAGATCTTTCGCTTTATCACCAACTGGTGCTCCTTAATTTTGACTAGATCCGAATTCAAAGCT
TCTTTTGATTTCTCACTCGGTGGCTTGAACATCGACAGAGTTCCAACGAACCACGCGTGATTCT
CCTCCAACTTCTTCGC
Transcript length: 282
Transcript exons: 18095427-18095534,18095787-18095960
CATGTCAATGAATTCTTGAGTTAGTTCTTGAGCTACCGAGTCAGTTGTTCCATATTCCTGCTCC
ATAGATCTTTCCACGAGGATGTATGATTGGATTTCATCTAGATTCAGATGAGAGCTGATTCGAA
GCGCTTTATCTTTCAATTGGGGCTTTATCACCAACTGGTGCTCCTTAATTTTGACTAGATCCGA
ATTCAAAGCTTCTTTTGATTTCTCACTCGGTGGCTTGAACATCGACAGAGTTCCAACGAACCAC
GCGTGATTCTCCTCCAACTTCTTCGC
						
					

						Genomic sequence
						
							CATGTCAATGAATTCTTGAGTTAGTTCTTGAGCTACCGAGTCAGTTGTTCCATATTCCTGCTCC
ATAGATCTTTCCACGAGGATGTATGATTGGATTTCATCTAGATTCTGGCCAAGATTTCAAAAAT
TCAGAAAAAAAATTCAGAACCATGTCAGTTTTTTTCTCCACATCCATTCTACTTATATAATCAT
TTTCAGAAAACAAATTCAGAAATCCACATCCATTCTACTTATATAATCATTTTCACTAATACAG
CATATATATGAAGCCTACATGCTTGATTGAAGACTATTTTGAAATAGATGATAAAGTTTTCTTT
CGAGTTCAATTGAAAATTGAAGAGTGGAAAAGAAGCTAACCAGATGAGAGCTGATTCGAAGCGC
TTTATCTTTCAATTGGGGCTTTATCACCAACTGGTGCTCCTTAATTTTGACTAGATCCGAATTC
AAAGCTTCTTTTGATTTCTCACTCGGTGGCTTGAACATCGACAGAGTTCCAACGAACCACGCGT
GATTCTCCTCCAACTTCTTCGC
						
					

			
		

Sequences
Splice junction sequence	CTAGATCCGAATTCAAAGCTTCTTTTGATTTCTCACTCGGTGGCTTGAACATCGACAGAGTTCC AACGAACCACGCGTGATTCTCCTCCAACTTCTTCGCcatgtcaatgaattcttgagttagttct tgagctaccgagtcagttgttccatattcctgctccatagatctttccacgaggatgtatgatt ggatttca
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: 166 Transcript exons: 18095427-18095491,18095860-18095960 CATGTCAATGAATTCTTGAGTTAGTTCTTGAGCTACCGAGTCAGTTGTTCCATATTCCTGCTCC AACTAGATCCGAATTCAAAGCTTCTTTTGATTTCTCACTCGGTGGCTTGAACATCGACAGAGTT CCAACGAACCACGCGTGATTCTCCTCCAACTTCTTCGC Transcript length: 208 Transcript exons: 18095427-18095501,18095828-18095960 CATGTCAATGAATTCTTGAGTTAGTTCTTGAGCTACCGAGTCAGTTGTTCCATATTCCTGCTCC ATAGATCTTTCGCTTTATCACCAACTGGTGCTCCTTAATTTTGACTAGATCCGAATTCAAAGCT TCTTTTGATTTCTCACTCGGTGGCTTGAACATCGACAGAGTTCCAACGAACCACGCGTGATTCT CCTCCAACTTCTTCGC Transcript length: 282 Transcript exons: 18095427-18095534,18095787-18095960 CATGTCAATGAATTCTTGAGTTAGTTCTTGAGCTACCGAGTCAGTTGTTCCATATTCCTGCTCC ATAGATCTTTCCACGAGGATGTATGATTGGATTTCATCTAGATTCAGATGAGAGCTGATTCGAA GCGCTTTATCTTTCAATTGGGGCTTTATCACCAACTGGTGCTCCTTAATTTTGACTAGATCCGA ATTCAAAGCTTCTTTTGATTTCTCACTCGGTGGCTTGAACATCGACAGAGTTCCAACGAACCAC GCGTGATTCTCCTCCAACTTCTTCGC
Genomic sequence	CATGTCAATGAATTCTTGAGTTAGTTCTTGAGCTACCGAGTCAGTTGTTCCATATTCCTGCTCC ATAGATCTTTCCACGAGGATGTATGATTGGATTTCATCTAGATTCTGGCCAAGATTTCAAAAAT TCAGAAAAAAAATTCAGAACCATGTCAGTTTTTTTCTCCACATCCATTCTACTTATATAATCAT TTTCAGAAAACAAATTCAGAAATCCACATCCATTCTACTTATATAATCATTTTCACTAATACAG CATATATATGAAGCCTACATGCTTGATTGAAGACTATTTTGAAATAGATGATAAAGTTTTCTTT CGAGTTCAATTGAAAATTGAAGAGTGGAAAAGAAGCTAACCAGATGAGAGCTGATTCGAAGCGC TTTATCTTTCAATTGGGGCTTTATCACCAACTGGTGCTCCTTAATTTTGACTAGATCCGAATTC AAAGCTTCTTTTGATTTCTCACTCGGTGGCTTGAACATCGACAGAGTTCCAACGAACCACGCGT GATTCTCCTCCAACTTCTTCGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.410148996

Conservation Information
Conserved circRNAs	NA
PMCS	0.410148996

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18095913-18095429(-)
						
						Potential amino acid sequence
						
							MFKPPSEKSKEALNSDLVKIKEHQLVIKPQLKDKALRISSHLNLDEIQSYILVERSMEQEYGTT
DSVAQELTQEFIDMAKKLEENHAWFVGTLSMFKPPSEKSKEALNSDLVKIKEHQLVIKPQLKDK
ALRISSHLNLDEIQSYILVERSMEQEYGTTDSVAQELTQEFIDMAKKLEENHAWFVGTLSMFKP
PSEKSKEALNSDLVKIKEHQLVIKPQLKDKALRISSHLNLDEIQSYILVERSMEQEYGTTDSVA
QELTQEFIDMAKKLEENHAWFVGTLSMFKPPSEKSKEALNSDLVKIKEHQLVIKPQLKDKALRI
SSHLNLDEIQSYILVERSMEQEYGTTDSVAQELTQEFIDM(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	18095913-18095429(-)
Potential amino acid sequence	MFKPPSEKSKEALNSDLVKIKEHQLVIKPQLKDKALRISSHLNLDEIQSYILVERSMEQEYGTT DSVAQELTQEFIDMAKKLEENHAWFVGTLSMFKPPSEKSKEALNSDLVKIKEHQLVIKPQLKDK ALRISSHLNLDEIQSYILVERSMEQEYGTTDSVAQELTQEFIDMAKKLEENHAWFVGTLSMFKP PSEKSKEALNSDLVKIKEHQLVIKPQLKDKALRISSHLNLDEIQSYILVERSMEQEYGTTDSVA QELTQEFIDMAKKLEENHAWFVGTLSMFKPPSEKSKEALNSDLVKIKEHQLVIKPQLKDKALRI SSHLNLDEIQSYILVERSMEQEYGTTDSVAQELTQEFIDM(-)
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 AT4G38760_circ_g.19

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