Plant Circular RNA Database

Detail information of AT2G34630_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT2G34630_circ_g.3
					
						ID in PlantcircBase
						ath_circ_016451
					
						Alias
						At_ciR490
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 14579660-14580509  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							AT2G34630						
					
						Parent gene annotation
						
							Solanesyl diphosphate synthase 3, chloroplastic/mitochondrial
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G34630_circ_g.1 AT2G34630_circ_g.2 AT2G34630_circ_g.4 						
					
						Support reads
						9/1
					
						Tissues
						leaf/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
						AT2G34630.2:5
AT2G34630.1:5

General Information
CircRNA Name	AT2G34630_circ_g.3
ID in PlantcircBase	ath_circ_016451
Alias	At_ciR490
Organism	Arabidpsis thaliana
Position	chr2: 14579660-14580509 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	AT2G34630
Parent gene annotation	Solanesyl diphosphate synthase 3, chloroplastic/mitochondrial
Parent gene strand	+
Alternative splicing	AT2G34630_circ_g.1 AT2G34630_circ_g.2 AT2G34630_circ_g.4
Support reads	9/1
Tissues	leaf/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	AT2G34630.2:5 AT2G34630.1:5

			
						 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  
						
							GAAGATCACCATTGGCTTCATGTTGTAGATGTCGGTATTAGCAGGAGACTTCTTGCTCTCCCGG
GCTTGTGGGGCTCTCGCTGCTTTAAAGAACACAGAGgaggagcttgacccattttcgcttgttg
ccgatgagctgtcacttcttagtaataagttgagagagatggtacttgccgaggtgagtggcct
tttttcat

						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: 14579660-14579740,14579860-14579931,14580028-14580159,14
580251-14580337,14580438-14580509
GAGGAGCTTGACCCATTTTCGCTTGTTGCCGATGAGCTGTCACTTCTTAGTAATAAGTTGAGAG
AGATGGTACTTGCCGAGGTTCCAAAGCTTGCCTCTGCTGCTGAGTACTTCTTCAAAAGGGGTGT
GCAAGGAAAACAGTTTCGTTCAACTATTTTGCTGCTGATGGCGACAGCTCTGAATGTACGAGTT
CCAGAAGCATTGATTGGGGAATCAACAGATATAGTCACATCAGAATTACGCGTAAGGCAACGGG
GTATTGCTGAAATCACTGAAATGATACACGTCGCAAGTCTACTGCACGATGATGTCTTGGATGA
TGCCGATACAAGGCGTGGTGTTGGTTCCTTAAATGTTGTAATGGGTAACAAGATGTCGGTATTA
GCAGGAGACTTCTTGCTCTCCCGGGCTTGTGGGGCTCTCGCTGCTTTAAAGAACACAGAG
						
						Genomic sequence
						
							GAGGAGCTTGACCCATTTTCGCTTGTTGCCGATGAGCTGTCACTTCTTAGTAATAAGTTGAGAG
AGATGGTACTTGCCGAGGTGAGTGGCCTTTTTTCATTCATTAGTACTCATTGTGTGCACAATGG
TGTGGTGAAAGCAAATTTGCTACTGATGTTCTGAAGCTAATCTCTATTTTTTTTCTATATTCTG
CTGTTTAGGTTCCAAAGCTTGCCTCTGCTGCTGAGTACTTCTTCAAAAGGGGTGTGCAAGGAAA
ACAGTTTCGTTCAACTGTAATGACCATAATCTCTTTATGTCACCATATCTTGTTTTCATGTTCT
GGTTCATTCTCTCTTGGTATCATAACCAGTCTGGTATCATGTTTGTAGATTTTGCTGCTGATGG
CGACAGCTCTGAATGTACGAGTTCCAGAAGCATTGATTGGGGAATCAACAGATATAGTCACATC
AGAATTACGCGTAAGGCAACGGGGTATTGCTGAAATCACTGAAATGATACACGTGAGTAACTAT
AGTTTTACTCATAACATTCATTAAAGATCAAGATCCAGTATCCTCCCTTTTAAAATTAGTAATG
CTCGGGTCATTGTAGGTCGCAAGTCTACTGCACGATGATGTCTTGGATGATGCCGATACAAGGC
GTGGTGTTGGTTCCTTAAATGTTGTAATGGGTAACAAGGTACTCACTTGACAGTAGAAGCTAAG
ACATGATTAAATATGCTTTTTGGCGATTGTGCTGCAATTTGGATATGAAGATCACCATTGGCTT
CATGTTGTAGATGTCGGTATTAGCAGGAGACTTCTTGCTCTCCCGGGCTTGTGGGGCTCTCGCT
GCTTTAAAGAACACAGAG

Sequences
Splice junction sequence	GAAGATCACCATTGGCTTCATGTTGTAGATGTCGGTATTAGCAGGAGACTTCTTGCTCTCCCGG GCTTGTGGGGCTCTCGCTGCTTTAAAGAACACAGAGgaggagcttgacccattttcgcttgttg ccgatgagctgtcacttcttagtaataagttgagagagatggtacttgccgaggtgagtggcct tttttcat
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: 14579660-14579740,14579860-14579931,14580028-14580159,14 580251-14580337,14580438-14580509 GAGGAGCTTGACCCATTTTCGCTTGTTGCCGATGAGCTGTCACTTCTTAGTAATAAGTTGAGAG AGATGGTACTTGCCGAGGTTCCAAAGCTTGCCTCTGCTGCTGAGTACTTCTTCAAAAGGGGTGT GCAAGGAAAACAGTTTCGTTCAACTATTTTGCTGCTGATGGCGACAGCTCTGAATGTACGAGTT CCAGAAGCATTGATTGGGGAATCAACAGATATAGTCACATCAGAATTACGCGTAAGGCAACGGG GTATTGCTGAAATCACTGAAATGATACACGTCGCAAGTCTACTGCACGATGATGTCTTGGATGA TGCCGATACAAGGCGTGGTGTTGGTTCCTTAAATGTTGTAATGGGTAACAAGATGTCGGTATTA GCAGGAGACTTCTTGCTCTCCCGGGCTTGTGGGGCTCTCGCTGCTTTAAAGAACACAGAG
Genomic sequence	GAGGAGCTTGACCCATTTTCGCTTGTTGCCGATGAGCTGTCACTTCTTAGTAATAAGTTGAGAG AGATGGTACTTGCCGAGGTGAGTGGCCTTTTTTCATTCATTAGTACTCATTGTGTGCACAATGG TGTGGTGAAAGCAAATTTGCTACTGATGTTCTGAAGCTAATCTCTATTTTTTTTCTATATTCTG CTGTTTAGGTTCCAAAGCTTGCCTCTGCTGCTGAGTACTTCTTCAAAAGGGGTGTGCAAGGAAA ACAGTTTCGTTCAACTGTAATGACCATAATCTCTTTATGTCACCATATCTTGTTTTCATGTTCT GGTTCATTCTCTCTTGGTATCATAACCAGTCTGGTATCATGTTTGTAGATTTTGCTGCTGATGG CGACAGCTCTGAATGTACGAGTTCCAGAAGCATTGATTGGGGAATCAACAGATATAGTCACATC AGAATTACGCGTAAGGCAACGGGGTATTGCTGAAATCACTGAAATGATACACGTGAGTAACTAT AGTTTTACTCATAACATTCATTAAAGATCAAGATCCAGTATCCTCCCTTTTAAAATTAGTAATG CTCGGGTCATTGTAGGTCGCAAGTCTACTGCACGATGATGTCTTGGATGATGCCGATACAAGGC GTGGTGTTGGTTCCTTAAATGTTGTAATGGGTAACAAGGTACTCACTTGACAGTAGAAGCTAAG ACATGATTAAATATGCTTTTTGGCGATTGTGCTGCAATTTGGATATGAAGATCACCATTGGCTT CATGTTGTAGATGTCGGTATTAGCAGGAGACTTCTTGCTCTCCCGGGCTTGTGGGGCTCTCGCT GCTTTAAAGAACACAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.221404675

Conservation Information
Conserved circRNAs	NA
PMCS	0.221404675

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							14579726-14580506(+)
						
						Potential amino acid sequence
						
							MVLAEVPKLASAAEYFFKRGVQGKQFRSTILLLMATALNVRVPEALIGESTDIVTSELRVRQRG
IAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKMSVLAGDFLLSRACGALAALKNTEEE
LDPFSLVADELSLLSNKLREMVLAEVPKLASAAEYFFKRGVQGKQFRSTILLLMATALNVRVPE
ALIGESTDIVTSELRVRQRGIAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKMSVLAG
DFLLSRACGALAALKNTEEELDPFSLVADELSLLSNKLREMVLAEVPKLASAAEYFFKRGVQGK
QFRSTILLLMATALNVRVPEALIGESTDIVTSELRVRQRGIAEITEMIHVASLLHDDVLDDADT
RRGVGSLNVVMGNKMSVLAGDFLLSRACGALAALKNTEEELDPFSLVADELSLLSNKLREMVLA
EVPKLASAAEYFFKRGVQGKQFRSTILLLMATALNVRVPEALIGESTDIVTSELRVRQRGIAEI
TEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKMSVLAGDFLLSRACGALAALKNTE(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	14579726-14580506(+)
Potential amino acid sequence	MVLAEVPKLASAAEYFFKRGVQGKQFRSTILLLMATALNVRVPEALIGESTDIVTSELRVRQRG IAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKMSVLAGDFLLSRACGALAALKNTEEE LDPFSLVADELSLLSNKLREMVLAEVPKLASAAEYFFKRGVQGKQFRSTILLLMATALNVRVPE ALIGESTDIVTSELRVRQRGIAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKMSVLAG DFLLSRACGALAALKNTEEELDPFSLVADELSLLSNKLREMVLAEVPKLASAAEYFFKRGVQGK QFRSTILLLMATALNVRVPEALIGESTDIVTSELRVRQRGIAEITEMIHVASLLHDDVLDDADT RRGVGSLNVVMGNKMSVLAGDFLLSRACGALAALKNTEEELDPFSLVADELSLLSNKLREMVLA EVPKLASAAEYFFKRGVQGKQFRSTILLLMATALNVRVPEALIGESTDIVTSELRVRQRGIAEI TEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKMSVLAGDFLLSRACGALAALKNTE(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of AT2G34630_circ_g.3

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