Plant Circular RNA Database

Detail information of AT2G20580_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT2G20580_circ_g.9
					
						ID in PlantcircBase
						ath_circ_014045
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 8862180-8863012  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT2G20580						
					
						Parent gene annotation
						
							RPN1A
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G20580_circ_g.7 AT2G20580_circ_g.8 AT2G20580_circ_g.10 AT2G20580_circ_g.11 AT2G20580_circ_g.12 AT2G20580_circ_g.13 						
					
						Support reads
						8
					
						Tissues
						root, 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  
						
							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
						AT2G20580.1:4

General Information
CircRNA Name	AT2G20580_circ_g.9
ID in PlantcircBase	ath_circ_014045
Alias	NA
Organism	Arabidpsis thaliana
Position	chr2: 8862180-8863012 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT2G20580
Parent gene annotation	RPN1A
Parent gene strand	+
Alternative splicing	AT2G20580_circ_g.7 AT2G20580_circ_g.8 AT2G20580_circ_g.10 AT2G20580_circ_g.11 AT2G20580_circ_g.12 AT2G20580_circ_g.13
Support reads	8
Tissues	root, 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	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	AT2G20580.1:4

			
						 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  
						
							TATTATATTTGCTTTGATGGATCGAAGTGAGGCAGAACTGGGTGATGCCCTCACTCGTTTCTTG
CCACTTGGTCTTGGACTTCTATACCTGGGCAAACAGgacaaactaatgacagtaccttcagact
caaccaccggatcttctggaaactggctcttcaaaaataaagaacatggcaagactagtgcagc
tgctagtc

						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: 570
Transcript exons: 8862180-8862281,8862375-8862515,8862604-8862708,8862791-
8863012
GACAAACTAATGACAGTACCTTCAGACTCAACCACCGGATCTTCTGGAAACTGGCTCTTCAAAA
ATAAAGAACATGGCAAGACTAGTGCAGCTGCTAGTCTGGGTATGATTCAACTGTGGGATGTGGA
CTCTGGACTTTCCCAACTCGACAAATATTTCCATAGTAATGATAATCCTATCATTGCTGGAGCA
CTGCTGGGAGTTGGGATTGTAAATTGTGGCATTAAGAACGATTGTGATCCTGCATTGGCACTTC
TTGGAGACTATATAGACAAAGAGGATTCATCTGTCAGAATCGGTGCTATCATGGGTCTTGGAAT
TTCATACGCAGGTTCCCAAAATGACCAGATTCGAAACAAATTGTCCCCGATACTGAATGATGCA
AAAGCGCCTCTTGATGTGATTGCATTTGCTTCACTTTCTTTGGGAATGATATATGTTGGTTCCT
GTAACGAAGAAGTAGCCCAGTCTATTATATTTGCTTTGATGGATCGAAGTGAGGCAGAACTGGG
TGATGCCCTCACTCGTTTCTTGCCACTTGGTCTTGGACTTCTATACCTGGGCAAACAG
						
						Genomic sequence
						
							GACAAACTAATGACAGTACCTTCAGACTCAACCACCGGATCTTCTGGAAACTGGCTCTTCAAAA
ATAAAGAACATGGCAAGACTAGTGCAGCTGCTAGTCTGGTATACTTTTTCTTATTTGATGAATT
TATTTACTGTGCTCAGATCATGGAAGTAAGAATTGTAACCAGATCTTTTTGTTTCCCTATCATA
TAGGGTATGATTCAACTGTGGGATGTGGACTCTGGACTTTCCCAACTCGACAAATATTTCCATA
GTAATGATAATCCTATCATTGCTGGAGCACTGCTGGGAGTTGGGATTGTAAATTGTGGCATTAA
GAACGATTGTGATCCTGTGAGTTGCTGTCGTGTTTGATTTTGCTGGGACCATTTGTGCTAATAT
TTGCAGCCACTCTTCCATCTTACTCAGCCTTATTTCTCAGGCATTGGCACTTCTTGGAGACTAT
ATAGACAAAGAGGATTCATCTGTCAGAATCGGTGCTATCATGGGTCTTGGAATTTCATACGCAG
GTTCCCAAAATGACCAGGTACTTGTTATATTCTTTCCCATATTACTACTTGAATGTTTCGGGTG
TTCACAAAACTTTAACACGTACACTGTTTCAACAGATTCGAAACAAATTGTCCCCGATACTGAA
TGATGCAAAAGCGCCTCTTGATGTGATTGCATTTGCTTCACTTTCTTTGGGAATGATATATGTT
GGTTCCTGTAACGAAGAAGTAGCCCAGTCTATTATATTTGCTTTGATGGATCGAAGTGAGGCAG
AACTGGGTGATGCCCTCACTCGTTTCTTGCCACTTGGTCTTGGACTTCTATACCTGGGCAAACA
G

Sequences
Splice junction sequence	TATTATATTTGCTTTGATGGATCGAAGTGAGGCAGAACTGGGTGATGCCCTCACTCGTTTCTTG CCACTTGGTCTTGGACTTCTATACCTGGGCAAACAGgacaaactaatgacagtaccttcagact caaccaccggatcttctggaaactggctcttcaaaaataaagaacatggcaagactagtgcagc tgctagtc
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: 570 Transcript exons: 8862180-8862281,8862375-8862515,8862604-8862708,8862791- 8863012 GACAAACTAATGACAGTACCTTCAGACTCAACCACCGGATCTTCTGGAAACTGGCTCTTCAAAA ATAAAGAACATGGCAAGACTAGTGCAGCTGCTAGTCTGGGTATGATTCAACTGTGGGATGTGGA CTCTGGACTTTCCCAACTCGACAAATATTTCCATAGTAATGATAATCCTATCATTGCTGGAGCA CTGCTGGGAGTTGGGATTGTAAATTGTGGCATTAAGAACGATTGTGATCCTGCATTGGCACTTC TTGGAGACTATATAGACAAAGAGGATTCATCTGTCAGAATCGGTGCTATCATGGGTCTTGGAAT TTCATACGCAGGTTCCCAAAATGACCAGATTCGAAACAAATTGTCCCCGATACTGAATGATGCA AAAGCGCCTCTTGATGTGATTGCATTTGCTTCACTTTCTTTGGGAATGATATATGTTGGTTCCT GTAACGAAGAAGTAGCCCAGTCTATTATATTTGCTTTGATGGATCGAAGTGAGGCAGAACTGGG TGATGCCCTCACTCGTTTCTTGCCACTTGGTCTTGGACTTCTATACCTGGGCAAACAG
Genomic sequence	GACAAACTAATGACAGTACCTTCAGACTCAACCACCGGATCTTCTGGAAACTGGCTCTTCAAAA ATAAAGAACATGGCAAGACTAGTGCAGCTGCTAGTCTGGTATACTTTTTCTTATTTGATGAATT TATTTACTGTGCTCAGATCATGGAAGTAAGAATTGTAACCAGATCTTTTTGTTTCCCTATCATA TAGGGTATGATTCAACTGTGGGATGTGGACTCTGGACTTTCCCAACTCGACAAATATTTCCATA GTAATGATAATCCTATCATTGCTGGAGCACTGCTGGGAGTTGGGATTGTAAATTGTGGCATTAA GAACGATTGTGATCCTGTGAGTTGCTGTCGTGTTTGATTTTGCTGGGACCATTTGTGCTAATAT TTGCAGCCACTCTTCCATCTTACTCAGCCTTATTTCTCAGGCATTGGCACTTCTTGGAGACTAT ATAGACAAAGAGGATTCATCTGTCAGAATCGGTGCTATCATGGGTCTTGGAATTTCATACGCAG GTTCCCAAAATGACCAGGTACTTGTTATATTCTTTCCCATATTACTACTTGAATGTTTCGGGTG TTCACAAAACTTTAACACGTACACTGTTTCAACAGATTCGAAACAAATTGTCCCCGATACTGAA TGATGCAAAAGCGCCTCTTGATGTGATTGCATTTGCTTCACTTTCTTTGGGAATGATATATGTT GGTTCCTGTAACGAAGAAGTAGCCCAGTCTATTATATTTGCTTTGATGGATCGAAGTGAGGCAG AACTGGGTGATGCCCTCACTCGTTTCTTGCCACTTGGTCTTGGACTTCTATACCTGGGCAAACA G

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.300298028

Conservation Information
Conserved circRNAs	NA
PMCS	0.300298028

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8862189-8863009(+)
						
						Potential amino acid sequence
						
							MTVPSDSTTGSSGNWLFKNKEHGKTSAAASLGMIQLWDVDSGLSQLDKYFHSNDNPIIAGALLG
VGIVNCGIKNDCDPALALLGDYIDKEDSSVRIGAIMGLGISYAGSQNDQIRNKLSPILNDAKAP
LDVIAFASLSLGMIYVGSCNEEVAQSIIFALMDRSEAELGDALTRFLPLGLGLLYLGKQDKLMT
VPSDSTTGSSGNWLFKNKEHGKTSAAASLGMIQLWDVDSGLSQLDKYFHSNDNPIIAGALLGVG
IVNCGIKNDCDPALALLGDYIDKEDSSVRIGAIMGLGISYAGSQNDQIRNKLSPILNDAKAPLD
VIAFASLSLGMIYVGSCNEEVAQSIIFALMDRSEAELGDALTRFLPLGLGLLYLGKQDKLMTVP
SDSTTGSSGNWLFKNKEHGKTSAAASLGMIQLWDVDSGLSQLDKYFHSNDNPIIAGALLGVGIV
NCGIKNDCDPALALLGDYIDKEDSSVRIGAIMGLGISYAGSQNDQIRNKLSPILNDAKAPLDVI
AFASLSLGMIYVGSCNEEVAQSIIFALMDRSEAELGDALTRFLPLGLGLLYLGKQDKLMTVPSD
STTGSSGNWLFKNKEHGKTSAAASLGMIQLWDVDSGLSQLDKYFHSNDNPIIAGALLGVGIVNC
GIKNDCDPALALLGDYIDKEDSSVRIGAIMGLGISYAGSQNDQIRNKLSPILNDAKAPLDVIAF
ASLSLGMIYVGSCNEEVAQSIIFALMDRSEAELGDALTRFLPLGLGLLYLGKQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8862189-8863009(+)
Potential amino acid sequence	MTVPSDSTTGSSGNWLFKNKEHGKTSAAASLGMIQLWDVDSGLSQLDKYFHSNDNPIIAGALLG VGIVNCGIKNDCDPALALLGDYIDKEDSSVRIGAIMGLGISYAGSQNDQIRNKLSPILNDAKAP LDVIAFASLSLGMIYVGSCNEEVAQSIIFALMDRSEAELGDALTRFLPLGLGLLYLGKQDKLMT VPSDSTTGSSGNWLFKNKEHGKTSAAASLGMIQLWDVDSGLSQLDKYFHSNDNPIIAGALLGVG IVNCGIKNDCDPALALLGDYIDKEDSSVRIGAIMGLGISYAGSQNDQIRNKLSPILNDAKAPLD VIAFASLSLGMIYVGSCNEEVAQSIIFALMDRSEAELGDALTRFLPLGLGLLYLGKQDKLMTVP SDSTTGSSGNWLFKNKEHGKTSAAASLGMIQLWDVDSGLSQLDKYFHSNDNPIIAGALLGVGIV NCGIKNDCDPALALLGDYIDKEDSSVRIGAIMGLGISYAGSQNDQIRNKLSPILNDAKAPLDVI AFASLSLGMIYVGSCNEEVAQSIIFALMDRSEAELGDALTRFLPLGLGLLYLGKQDKLMTVPSD STTGSSGNWLFKNKEHGKTSAAASLGMIQLWDVDSGLSQLDKYFHSNDNPIIAGALLGVGIVNC GIKNDCDPALALLGDYIDKEDSSVRIGAIMGLGISYAGSQNDQIRNKLSPILNDAKAPLDVIAF ASLSLGMIYVGSCNEEVAQSIIFALMDRSEAELGDALTRFLPLGLGLLYLGKQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT2G20580_circ_g.9

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