Plant Circular RNA Database

Detail information of AT1G04170_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G04170_circ_g.3
					
						ID in PlantcircBase
						ath_circ_000578
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 1097800-1098606  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT1G04170						
					
						Parent gene annotation
						
							Eukaryotic translation initiation factor 2 gamma subunit
							
						Parent gene strand
						+
					
						Alternative splicing
						
							1_circ_ag.6 1_circ_ag.7 AT1G04160_circ_g.8 AT1G04160_circ_g.9 AT1G04160_circ_g.10 AT1G04160_circ_g.11 AT1G04160_circ_g.12 AT1G04160_circ_g.13 AT1G04170_circ_g.1 AT1G04170_circ_g.2 AT1G04170_circ_g.4 AT1G04170_circ_g.5 AT1G04170_circ_g.6 AT1G04190_circ_g.1 AT1G04190_circ_g.2 AT1G04190_circ_g.3 AT1G04200_circ_g.1 AT1G04200_circ_g.2 AT1G04200_circ_g.3 AT1G04200_circ_g.4 AT1G04200_circ_g.5 AT1G04210_circ_g.1 AT1G04210_circ_g.2 AT1G04210_circ_g.3 AT1G04210_circ_g.4 AT1G04210_circ_g.5 AT1G04220_circ_g.1 AT1G04230_circ_g.1 AT1G04230_circ_g.2 AT1G04230_circ_g.3 AT1G04230_circ_g.4 AT1G04230_circ_g.5 AT1G04230_circ_g.6 AT1G04250_circ_g.1 AT1G04270_circ_g.1 AT1G04280_circ_g.1 AT1G04280_circ_g.2 AT1G04300_circ_g.1 AT1G04300_circ_g.2 AT1G04300_circ_g.3 AT1G04300_circ_g.4 AT1G04300_circ_g.5 AT1G04300_circ_g.6 AT1G04300_circ_g.7 AT1G04300_circ_g.8 AT1G04300_circ_g.9 AT1G04300_circ_g.10 AT1G04310_circ_g.1 AT1G04340_circ_g.1 AT1G04400_circ_g.1 AT1G04400_circ_g.2 AT1G04400_circ_g.3 AT1G04400_circ_g.4 AT1G04410_circ_g.1 AT1G04410_circ_g.2 AT1G04410_circ_g.3 AT1G04410_circ_g.4 AT1G04410_circ_g.5 AT1G04410_circ_g.6 AT1G04410_circ_g.7 AT1G04410_circ_g.8 AT1G04420_circ_g.1 AT1G04420_circ_g.2 AT1G04420_circ_g.3 AT1G04420_circ_g.4 AT1G04425_circ_g.1 AT1G04430_circ_g.1 AT1G04430_circ_g.2 AT1G04430_circ_g.3 AT1G04430_circ_g.4 AT1G04440_circ_g.1 AT1G04440_circ_g.2 AT1G04440_circ_g.3 AT1G04440_circ_g.4 AT1G04440_circ_g.5 1_circ_ag.6 AT1G04440_circ_g.7 AT1G04440_circ_g.8 AT1G04440_circ_g.9 AT1G04440_circ_g.10 AT1G04440_circ_g.11 AT1G04440_circ_g.12 AT1G04510_circ_g.1 AT1G04510_circ_g.2 AT1G04510_circ_g.3 AT1G04510_circ_g.4 AT1G04510_circ_g.5 AT1G04510_circ_g.6 AT1G04510_circ_g.7 AT1G04510_circ_g.8 AT1G04510_circ_g.9 AT1G04510_circ_g.10 AT1G04530_circ_g.1 AT1G04530_circ_g.2 AT1G04550_circ_g.1 AT1G04590_circ_g.1 AT1G04590_circ_g.2 AT1G04600_circ_g.1 						
					
						Support reads
						1
					
						Tissues
						root
					
						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
						AT1G04170.1:3
AT1G04170.2:3

General Information
CircRNA Name	AT1G04170_circ_g.3
ID in PlantcircBase	ath_circ_000578
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 1097800-1098606 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT1G04170
Parent gene annotation	Eukaryotic translation initiation factor 2 gamma subunit
Parent gene strand	+
Alternative splicing	1_circ_ag.6 1_circ_ag.7 AT1G04160_circ_g.8 AT1G04160_circ_g.9 AT1G04160_circ_g.10 AT1G04160_circ_g.11 AT1G04160_circ_g.12 AT1G04160_circ_g.13 AT1G04170_circ_g.1 AT1G04170_circ_g.2 AT1G04170_circ_g.4 AT1G04170_circ_g.5 AT1G04170_circ_g.6 AT1G04190_circ_g.1 AT1G04190_circ_g.2 AT1G04190_circ_g.3 AT1G04200_circ_g.1 AT1G04200_circ_g.2 AT1G04200_circ_g.3 AT1G04200_circ_g.4 AT1G04200_circ_g.5 AT1G04210_circ_g.1 AT1G04210_circ_g.2 AT1G04210_circ_g.3 AT1G04210_circ_g.4 AT1G04210_circ_g.5 AT1G04220_circ_g.1 AT1G04230_circ_g.1 AT1G04230_circ_g.2 AT1G04230_circ_g.3 AT1G04230_circ_g.4 AT1G04230_circ_g.5 AT1G04230_circ_g.6 AT1G04250_circ_g.1 AT1G04270_circ_g.1 AT1G04280_circ_g.1 AT1G04280_circ_g.2 AT1G04300_circ_g.1 AT1G04300_circ_g.2 AT1G04300_circ_g.3 AT1G04300_circ_g.4 AT1G04300_circ_g.5 AT1G04300_circ_g.6 AT1G04300_circ_g.7 AT1G04300_circ_g.8 AT1G04300_circ_g.9 AT1G04300_circ_g.10 AT1G04310_circ_g.1 AT1G04340_circ_g.1 AT1G04400_circ_g.1 AT1G04400_circ_g.2 AT1G04400_circ_g.3 AT1G04400_circ_g.4 AT1G04410_circ_g.1 AT1G04410_circ_g.2 AT1G04410_circ_g.3 AT1G04410_circ_g.4 AT1G04410_circ_g.5 AT1G04410_circ_g.6 AT1G04410_circ_g.7 AT1G04410_circ_g.8 AT1G04420_circ_g.1 AT1G04420_circ_g.2 AT1G04420_circ_g.3 AT1G04420_circ_g.4 AT1G04425_circ_g.1 AT1G04430_circ_g.1 AT1G04430_circ_g.2 AT1G04430_circ_g.3 AT1G04430_circ_g.4 AT1G04440_circ_g.1 AT1G04440_circ_g.2 AT1G04440_circ_g.3 AT1G04440_circ_g.4 AT1G04440_circ_g.5 1_circ_ag.6 AT1G04440_circ_g.7 AT1G04440_circ_g.8 AT1G04440_circ_g.9 AT1G04440_circ_g.10 AT1G04440_circ_g.11 AT1G04440_circ_g.12 AT1G04510_circ_g.1 AT1G04510_circ_g.2 AT1G04510_circ_g.3 AT1G04510_circ_g.4 AT1G04510_circ_g.5 AT1G04510_circ_g.6 AT1G04510_circ_g.7 AT1G04510_circ_g.8 AT1G04510_circ_g.9 AT1G04510_circ_g.10 AT1G04530_circ_g.1 AT1G04530_circ_g.2 AT1G04550_circ_g.1 AT1G04590_circ_g.1 AT1G04590_circ_g.2 AT1G04600_circ_g.1
Support reads	1
Tissues	root
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	AT1G04170.1:3 AT1G04170.2:3

			
						 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  
						
							TATGCAACTTAAGCATATCATCATCCTTCAGAACAAGATTGATCTTATTCAAGAGAATGTTGCC
ATTAATCAGCACGAGGCAATTCAGAAATTTATAATGactgtccgttttaaaaatgaattggagc
gtaacattaccattaagcttggatatgcaaacgccaagatttacaaatgtgaggatgagaaatg
ccctagac

						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: 444
Transcript exons: 1097800-1097912,1097999-1098101,1098379-1098606
ACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCA
AGATTTACAAATGTGAGGATGAGAAATGCCCTAGACCAATGTGCTACAAGGCCTACGGAAGTGG
AAAGGAAGACACTCCCAATTGTGATGTCCCCGGATTTGAAAACTCCAAGATGAAACTATTGAGG
CATGTCTCATTCGTTGATTGCCCGGGTCACGATATTCTCATGGCAACAATGCTTAATGGAGCAG
CCATCATGGATGGTGCACTACTTTTAATCGCTGCAAATGAAACTTGTCCACAACCACAAACGTC
TGAACATCTTGCTGCCGTTGAGATTATGCAACTTAAGCATATCATCATCCTTCAGAACAAGATT
GATCTTATTCAAGAGAATGTTGCCATTAATCAGCACGAGGCAATTCAGAAATTTATAATG
						
						Genomic sequence
						
							ACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCA
AGATTTACAAATGTGAGGATGAGAAATGCCCTAGACCAATGTGCTACAAGTGAGTCCTTCTTAC
AACAGTGTTTTTATCTTCTACTTCTACTATAAGGTTTGAGTCAAGGTCTAACAACTTATCTGTT
GTATTAGGGCCTACGGAAGTGGAAAGGAAGACACTCCCAATTGTGATGTCCCCGGATTTGAAAA
CTCCAAGATGAAACTATTGAGGCATGTCTCATTCGTTGATTGCCCGGTATGATGAGTTTTACCG
TTATCTTTATTCTTCATTAATTACCATTTTCATTTGATAGTATAAGTGTATAACCATTTCATGT
GTCAATGAGCTGTTCGTTTATTGTGTATTATCGATGTTGTTGTGCTCCACCTGCATGATTTTGG
GTCTCTCATTTAATTGGGTGAAGGGCTTAAAGAGTGAGGGTTGATGGAGAAGTATTCATTGATG
TTTCCATCTTTTGCTTTTCTTATCTCTACTTCATTCTTGTTGAATGTATTCTTGTTCTATTCTT
CAGGGTCACGATATTCTCATGGCAACAATGCTTAATGGAGCAGCCATCATGGATGGTGCACTAC
TTTTAATCGCTGCAAATGAAACTTGTCCACAACCACAAACGTCTGAACATCTTGCTGCCGTTGA
GATTATGCAACTTAAGCATATCATCATCCTTCAGAACAAGATTGATCTTATTCAAGAGAATGTT
GCCATTAATCAGCACGAGGCAATTCAGAAATTTATAATG

Sequences
Splice junction sequence	TATGCAACTTAAGCATATCATCATCCTTCAGAACAAGATTGATCTTATTCAAGAGAATGTTGCC ATTAATCAGCACGAGGCAATTCAGAAATTTATAATGactgtccgttttaaaaatgaattggagc gtaacattaccattaagcttggatatgcaaacgccaagatttacaaatgtgaggatgagaaatg ccctagac
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: 444 Transcript exons: 1097800-1097912,1097999-1098101,1098379-1098606 ACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCA AGATTTACAAATGTGAGGATGAGAAATGCCCTAGACCAATGTGCTACAAGGCCTACGGAAGTGG AAAGGAAGACACTCCCAATTGTGATGTCCCCGGATTTGAAAACTCCAAGATGAAACTATTGAGG CATGTCTCATTCGTTGATTGCCCGGGTCACGATATTCTCATGGCAACAATGCTTAATGGAGCAG CCATCATGGATGGTGCACTACTTTTAATCGCTGCAAATGAAACTTGTCCACAACCACAAACGTC TGAACATCTTGCTGCCGTTGAGATTATGCAACTTAAGCATATCATCATCCTTCAGAACAAGATT GATCTTATTCAAGAGAATGTTGCCATTAATCAGCACGAGGCAATTCAGAAATTTATAATG
Genomic sequence	ACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCA AGATTTACAAATGTGAGGATGAGAAATGCCCTAGACCAATGTGCTACAAGTGAGTCCTTCTTAC AACAGTGTTTTTATCTTCTACTTCTACTATAAGGTTTGAGTCAAGGTCTAACAACTTATCTGTT GTATTAGGGCCTACGGAAGTGGAAAGGAAGACACTCCCAATTGTGATGTCCCCGGATTTGAAAA CTCCAAGATGAAACTATTGAGGCATGTCTCATTCGTTGATTGCCCGGTATGATGAGTTTTACCG TTATCTTTATTCTTCATTAATTACCATTTTCATTTGATAGTATAAGTGTATAACCATTTCATGT GTCAATGAGCTGTTCGTTTATTGTGTATTATCGATGTTGTTGTGCTCCACCTGCATGATTTTGG GTCTCTCATTTAATTGGGTGAAGGGCTTAAAGAGTGAGGGTTGATGGAGAAGTATTCATTGATG TTTCCATCTTTTGCTTTTCTTATCTCTACTTCATTCTTGTTGAATGTATTCTTGTTCTATTCTT CAGGGTCACGATATTCTCATGGCAACAATGCTTAATGGAGCAGCCATCATGGATGGTGCACTAC TTTTAATCGCTGCAAATGAAACTTGTCCACAACCACAAACGTCTGAACATCTTGCTGCCGTTGA GATTATGCAACTTAAGCATATCATCATCCTTCAGAACAAGATTGATCTTATTCAAGAGAATGTT GCCATTAATCAGCACGAGGCAATTCAGAAATTTATAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.422319631

Conservation Information
Conserved circRNAs	NA
PMCS	0.422319631

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1097902-1098603(+)
						
						Potential amino acid sequence
						
							MCYKAYGSGKEDTPNCDVPGFENSKMKLLRHVSFVDCPGHDILMATMLNGAAIMDGALLLIAAN
ETCPQPQTSEHLAAVEIMQLKHIIILQNKIDLIQENVAINQHEAIQKFIMTVRFKNELERNITI
KLGYANAKIYKCEDEKCPRPMCYKAYGSGKEDTPNCDVPGFENSKMKLLRHVSFVDCPGHDILM
ATMLNGAAIMDGALLLIAANETCPQPQTSEHLAAVEIMQLKHIIILQNKIDLIQENVAINQHEA
IQKFIMTVRFKNELERNITIKLGYANAKIYKCEDEKCPRPMCYKAYGSGKEDTPNCDVPGFENS
KMKLLRHVSFVDCPGHDILMATMLNGAAIMDGALLLIAANETCPQPQTSEHLAAVEIMQLKHII
ILQNKIDLIQENVAINQHEAIQKFIMTVRFKNELERNITIKLGYANAKIYKCEDEKCPRPMCYK
AYGSGKEDTPNCDVPGFENSKMKLLRHVSFVDCPGHDILMATMLNGAAIMDGALLLIAANETCP
QPQTSEHLAAVEIMQLKHIIILQNKIDLIQENVAINQHEAIQKFIM(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1097902-1098603(+)
Potential amino acid sequence	MCYKAYGSGKEDTPNCDVPGFENSKMKLLRHVSFVDCPGHDILMATMLNGAAIMDGALLLIAAN ETCPQPQTSEHLAAVEIMQLKHIIILQNKIDLIQENVAINQHEAIQKFIMTVRFKNELERNITI KLGYANAKIYKCEDEKCPRPMCYKAYGSGKEDTPNCDVPGFENSKMKLLRHVSFVDCPGHDILM ATMLNGAAIMDGALLLIAANETCPQPQTSEHLAAVEIMQLKHIIILQNKIDLIQENVAINQHEA IQKFIMTVRFKNELERNITIKLGYANAKIYKCEDEKCPRPMCYKAYGSGKEDTPNCDVPGFENS KMKLLRHVSFVDCPGHDILMATMLNGAAIMDGALLLIAANETCPQPQTSEHLAAVEIMQLKHII ILQNKIDLIQENVAINQHEAIQKFIMTVRFKNELERNITIKLGYANAKIYKCEDEKCPRPMCYK AYGSGKEDTPNCDVPGFENSKMKLLRHVSFVDCPGHDILMATMLNGAAIMDGALLLIAANETCP QPQTSEHLAAVEIMQLKHIIILQNKIDLIQENVAINQHEAIQKFIM(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G04170_circ_g.3

Address

Any questions?

Supported by