Plant Circular RNA Database

Detail information of AT4G12460_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT4G12460_circ_g.2
					
						ID in PlantcircBase
						ath_circ_030556
					
						Alias
						Ath_circ_FC2611
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 7392691-7394557  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						PcircRNA_finder, circRNA_finder
					
						Parent gene
						
							AT4G12460						
					
						Parent gene annotation
						
							OSBP(oxysterol binding protein)-related protein 2B
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G12460_circ_g.1 AT4G12460_circ_g.3 AT4G12460_circ_g.4 						
					
						Support reads
						8
					
						Tissues
						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
						AT4G12460.2:4
AT4G12460.8:4
AT4G12460.3:4
AT4G12460.9:4
AT4G12460.5:4
AT4G12460.6:4
AT4G12460.7:4
AT4G12460.1:4
AT4G12460.4:4

General Information
CircRNA Name	AT4G12460_circ_g.2
ID in PlantcircBase	ath_circ_030556
Alias	Ath_circ_FC2611
Organism	Arabidpsis thaliana
Position	chr4: 7392691-7394557 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	PcircRNA_finder, circRNA_finder
Parent gene	AT4G12460
Parent gene annotation	OSBP(oxysterol binding protein)-related protein 2B
Parent gene strand	+
Alternative splicing	AT4G12460_circ_g.1 AT4G12460_circ_g.3 AT4G12460_circ_g.4
Support reads	8
Tissues	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	AT4G12460.2:4 AT4G12460.8:4 AT4G12460.3:4 AT4G12460.9:4 AT4G12460.5:4 AT4G12460.6:4 AT4G12460.7:4 AT4G12460.1:4 AT4G12460.4:4

			
						 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  
						
							TTCCACCGAAGGACGACACTGTAAACCTTTCAACCCTTTGCTCGGAGAAACATATGAAGCTGAC
TTTCCTGAAAAGGGAATTCGTTTCTTCTCTGAGAAGgtttcatcttaccgagaaagcaagtctg
atcatagaaagttttatatctttactgcaaccaagactctgcatctgaggactgattctagaag
tgatagag

									
								

					

						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: 951
Transcript exons: 7392691-7393053,7393489-7393585,7393842-7394176,7394402-
7394557
GTTTCATCTTACCGAGAAAGCAAGTCTGATCATAGAAAGTTTTATATCTTTACTGCAACCAAGA
CTCTGCATCTGAGGACTGATTCTAGAAGTGATAGAGCAGCATGGTTACAAGCTTTAGCATCTAC
CAGGGGCATAGTTCCTCTCCAGTCAATTAATGGGGATTTCTCCTTCGTATCACCAAAGGATTTA
TCCATATCTACCGAGAGACTAAAGAAACGGTTGTTTGAAGAGGGAATGAACGAGAGTCTTGTAA
AAGAGTGCGAGCAGATCGTGGATTCAGAGTTCTGTGAAGTTCAAGAACAGATTAAACTTCTTCA
CGAAGAGCGGAAAAAGTTGCTTGATGCTTTGAGGCAGCTAGAGATGGCCAACCTTGAAGCTGAA
GCCTCAGGGATCCATGACGATGTCTACCAATTAAGAAATCACAAGTATTCCAGCTTAGGACGTG
GAAAATATAGTGAATGCAGTACAAGTGCTTCATCTGATGATAAGCAAGAGTTTGAGGATATCTC
TGAGGAAGACGAGGCTTCCTTCCATGACACAAAGGAGTCATTTGGTGAACCTGATGTTGGTTCT
GTGCTCACGCATTTTAAGAGACGAACAAAGCTTCCTGATCCAGCAGAGAAAGAGAGAGGTGTCA
GTCTCTGGTCTATGATCAAAGACAATGTTGGAAAGGATCTCACACGAGTTTGTCTTCCTGTTTA
TTTCAATGAACCAATATCTTCCCTCCAAAAGTGTTTTGAAGACTTGGAGTACTCTTATCTCTTG
GACCAAGCATATGAATACGGAAAATCCGGGAAGAGTCTCCTTAGAGCCCTCAATGTCGCTGCTT
TTGCAGTCTCTGGTTATGCTTCCACCGAAGGACGACACTGTAAACCTTTCAACCCTTTGCTCGG
AGAAACATATGAAGCTGACTTTCCTGAAAAGGGAATTCGTTTCTTCTCTGAGAAG
						
					

						Genomic sequence
						
							GTTTCATCTTACCGAGAAAGCAAGTCTGATCATAGAAAGTTTTATATCTTTACTGCAACCAAGA
CTCTGCATCTGAGGACTGATTCTAGAAGTGATAGAGCAGCATGGTTACAAGCTTTAGCATCTAC
CAGGGGCATAGTTCCTCTCCAGTCAATTAATGGGGATTTCTCCTTCGTATCACCAAAGGATTTA
TCCATATCTACCGAGAGACTAAAGAAACGGTTGTTTGAAGAGGGAATGAACGAGAGTCTTGTAA
AAGAGTGCGAGCAGATCGTGGATTCAGAGTTCTGTGAAGTTCAAGAACAGATTAAACTTCTTCA
CGAAGAGCGGAAAAAGTTGCTTGATGCTTTGAGGCAGCTAGAGGTAAAGCTGAATTTTTGGTCT
TCTTTTATGATCGTTTTGGTTTGGTTGAGCTGTTTAGTGTGGTCTCGGTCATTGTTTCCTTTCA
TATAATGACTTAGTATTCCACGGGCTTTACAGTGCAGTTGCATTGGTAACAGCGAGTCTATGCA
CAAAGGCATGCTAGTTTATTTGTCATGTAATCACGAACGGGACGGTTATTTTAATATATGTTTT
ACATTCTTTTATCTCCATTCATGTGGATATTTTGTTAATTGAGTTGATAATTTCTGAACTTCAT
ATATCCATGCCTAGGCATAACACAAAAATTATGTATCATGCATTAAAAACTTGAATGTCAAGTT
ATGATTATTATGAATCTTGCGAAAGATCCCTCCCCGCTTTTTATAATTCTGTTATTTGTTGGCT
ATTCTACACTGAGAGTTTCTTTATGTACAGATGGCCAACCTTGAAGCTGAAGCCTCAGGGATCC
ATGACGATGTCTACCAATTAAGAAATCACAAGTATTCCAGCTTAGGACGTGGAAAATATAGTGG
TACACAAAATTTCTATCGCGTAATTGTTCTTTTATTCACTGCATCTCTTTCTCTTTCTCTGTTT
TAGTTTTGCCATTAAATATTGATGAAGCCAGCTGGCGAGGATCTCGTTACTGCATAGTAGAACA
ATAATTTCTGATACGATATTCAATTATTTGTTTCCTAAATTTTCCTCCTTATGCTTCTTTTACA
TAGCTTCAGTGGAGTTGCATTTAGCTTCCTGTGTTGTTTTGCTTGACAATATTTAATTTCTAGA
ATGCAGTACAAGTGCTTCATCTGATGATAAGCAAGAGTTTGAGGATATCTCTGAGGAAGACGAG
GCTTCCTTCCATGACACAAAGGAGTCATTTGGTGAACCTGATGTTGGTTCTGTGCTCACGCATT
TTAAGAGACGAACAAAGCTTCCTGATCCAGCAGAGAAAGAGAGAGGTGTCAGTCTCTGGTCTAT
GATCAAAGACAATGTTGGAAAGGATCTCACACGAGTTTGTCTTCCTGTTTATTTCAATGAACCA
ATATCTTCCCTCCAAAAGTGTTTTGAAGACTTGGAGTACTCTTATCTCTTGGACCAAGCATATG
AATACGGAAAATCCGTAAGTGATTTCAAAAAACTTACTGTTGTATGTAATTCGCTTCCTTCTGG
AAATGCAAACGTTTTCTCTACTCTTAACTTTTATTTAATTCCAATTACTAAAGTAATTTAACTA
CATAGTTTGAGCTTCTATGCTCTTGCATGATATGATATGTGGTCTATACTTATCTTTTTATCTT
AAATTGACCTCTCAGTTTGTTATATTAACAGAGTTTTTCATCATCAGGGGAAGAGTCTCCTTAG
AGCCCTCAATGTCGCTGCTTTTGCAGTCTCTGGTTATGCTTCCACCGAAGGACGACACTGTAAA
CCTTTCAACCCTTTGCTCGGAGAAACATATGAAGCTGACTTTCCTGAAAAGGGAATTCGTTTCT
TCTCTGAGAAG
						
					

			
		

Sequences
Splice junction sequence	TTCCACCGAAGGACGACACTGTAAACCTTTCAACCCTTTGCTCGGAGAAACATATGAAGCTGAC TTTCCTGAAAAGGGAATTCGTTTCTTCTCTGAGAAGgtttcatcttaccgagaaagcaagtctg atcatagaaagttttatatctttactgcaaccaagactctgcatctgaggactgattctagaag tgatagag
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: 951 Transcript exons: 7392691-7393053,7393489-7393585,7393842-7394176,7394402- 7394557 GTTTCATCTTACCGAGAAAGCAAGTCTGATCATAGAAAGTTTTATATCTTTACTGCAACCAAGA CTCTGCATCTGAGGACTGATTCTAGAAGTGATAGAGCAGCATGGTTACAAGCTTTAGCATCTAC CAGGGGCATAGTTCCTCTCCAGTCAATTAATGGGGATTTCTCCTTCGTATCACCAAAGGATTTA TCCATATCTACCGAGAGACTAAAGAAACGGTTGTTTGAAGAGGGAATGAACGAGAGTCTTGTAA AAGAGTGCGAGCAGATCGTGGATTCAGAGTTCTGTGAAGTTCAAGAACAGATTAAACTTCTTCA CGAAGAGCGGAAAAAGTTGCTTGATGCTTTGAGGCAGCTAGAGATGGCCAACCTTGAAGCTGAA GCCTCAGGGATCCATGACGATGTCTACCAATTAAGAAATCACAAGTATTCCAGCTTAGGACGTG GAAAATATAGTGAATGCAGTACAAGTGCTTCATCTGATGATAAGCAAGAGTTTGAGGATATCTC TGAGGAAGACGAGGCTTCCTTCCATGACACAAAGGAGTCATTTGGTGAACCTGATGTTGGTTCT GTGCTCACGCATTTTAAGAGACGAACAAAGCTTCCTGATCCAGCAGAGAAAGAGAGAGGTGTCA GTCTCTGGTCTATGATCAAAGACAATGTTGGAAAGGATCTCACACGAGTTTGTCTTCCTGTTTA TTTCAATGAACCAATATCTTCCCTCCAAAAGTGTTTTGAAGACTTGGAGTACTCTTATCTCTTG GACCAAGCATATGAATACGGAAAATCCGGGAAGAGTCTCCTTAGAGCCCTCAATGTCGCTGCTT TTGCAGTCTCTGGTTATGCTTCCACCGAAGGACGACACTGTAAACCTTTCAACCCTTTGCTCGG AGAAACATATGAAGCTGACTTTCCTGAAAAGGGAATTCGTTTCTTCTCTGAGAAG
Genomic sequence	GTTTCATCTTACCGAGAAAGCAAGTCTGATCATAGAAAGTTTTATATCTTTACTGCAACCAAGA CTCTGCATCTGAGGACTGATTCTAGAAGTGATAGAGCAGCATGGTTACAAGCTTTAGCATCTAC CAGGGGCATAGTTCCTCTCCAGTCAATTAATGGGGATTTCTCCTTCGTATCACCAAAGGATTTA TCCATATCTACCGAGAGACTAAAGAAACGGTTGTTTGAAGAGGGAATGAACGAGAGTCTTGTAA AAGAGTGCGAGCAGATCGTGGATTCAGAGTTCTGTGAAGTTCAAGAACAGATTAAACTTCTTCA CGAAGAGCGGAAAAAGTTGCTTGATGCTTTGAGGCAGCTAGAGGTAAAGCTGAATTTTTGGTCT TCTTTTATGATCGTTTTGGTTTGGTTGAGCTGTTTAGTGTGGTCTCGGTCATTGTTTCCTTTCA TATAATGACTTAGTATTCCACGGGCTTTACAGTGCAGTTGCATTGGTAACAGCGAGTCTATGCA CAAAGGCATGCTAGTTTATTTGTCATGTAATCACGAACGGGACGGTTATTTTAATATATGTTTT ACATTCTTTTATCTCCATTCATGTGGATATTTTGTTAATTGAGTTGATAATTTCTGAACTTCAT ATATCCATGCCTAGGCATAACACAAAAATTATGTATCATGCATTAAAAACTTGAATGTCAAGTT ATGATTATTATGAATCTTGCGAAAGATCCCTCCCCGCTTTTTATAATTCTGTTATTTGTTGGCT ATTCTACACTGAGAGTTTCTTTATGTACAGATGGCCAACCTTGAAGCTGAAGCCTCAGGGATCC ATGACGATGTCTACCAATTAAGAAATCACAAGTATTCCAGCTTAGGACGTGGAAAATATAGTGG TACACAAAATTTCTATCGCGTAATTGTTCTTTTATTCACTGCATCTCTTTCTCTTTCTCTGTTT TAGTTTTGCCATTAAATATTGATGAAGCCAGCTGGCGAGGATCTCGTTACTGCATAGTAGAACA ATAATTTCTGATACGATATTCAATTATTTGTTTCCTAAATTTTCCTCCTTATGCTTCTTTTACA TAGCTTCAGTGGAGTTGCATTTAGCTTCCTGTGTTGTTTTGCTTGACAATATTTAATTTCTAGA ATGCAGTACAAGTGCTTCATCTGATGATAAGCAAGAGTTTGAGGATATCTCTGAGGAAGACGAG GCTTCCTTCCATGACACAAAGGAGTCATTTGGTGAACCTGATGTTGGTTCTGTGCTCACGCATT TTAAGAGACGAACAAAGCTTCCTGATCCAGCAGAGAAAGAGAGAGGTGTCAGTCTCTGGTCTAT GATCAAAGACAATGTTGGAAAGGATCTCACACGAGTTTGTCTTCCTGTTTATTTCAATGAACCA ATATCTTCCCTCCAAAAGTGTTTTGAAGACTTGGAGTACTCTTATCTCTTGGACCAAGCATATG AATACGGAAAATCCGTAAGTGATTTCAAAAAACTTACTGTTGTATGTAATTCGCTTCCTTCTGG AAATGCAAACGTTTTCTCTACTCTTAACTTTTATTTAATTCCAATTACTAAAGTAATTTAACTA CATAGTTTGAGCTTCTATGCTCTTGCATGATATGATATGTGGTCTATACTTATCTTTTTATCTT AAATTGACCTCTCAGTTTGTTATATTAACAGAGTTTTTCATCATCAGGGGAAGAGTCTCCTTAG AGCCCTCAATGTCGCTGCTTTTGCAGTCTCTGGTTATGCTTCCACCGAAGGACGACACTGTAAA CCTTTCAACCCTTTGCTCGGAGAAACATATGAAGCTGACTTTCCTGAAAAGGGAATTCGTTTCT TCTCTGAGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.275587962

Conservation Information
Conserved circRNAs	NA
PMCS	0.275587962

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7392928-7394554(+)
						
						Potential amino acid sequence
						
							MNESLVKECEQIVDSEFCEVQEQIKLLHEERKKLLDALRQLEMANLEAEASGIHDDVYQLRNHK
YSSLGRGKYSECSTSASSDDKQEFEDISEEDEASFHDTKESFGEPDVGSVLTHFKRRTKLPDPA
EKERGVSLWSMIKDNVGKDLTRVCLPVYFNEPISSLQKCFEDLEYSYLLDQAYEYGKSGKSLLR
ALNVAAFAVSGYASTEGRHCKPFNPLLGETYEADFPEKGIRFFSEKVSSYRESKSDHRKFYIFT
ATKTLHLRTDSRSDRAAWLQALASTRGIVPLQSINGDFSFVSPKDLSISTERLKKRLFEEGMNE
SLVKECEQIVDSEFCEVQEQIKLLHEERKKLLDALRQLEMANLEAEASGIHDDVYQLRNHKYSS
LGRGKYSECSTSASSDDKQEFEDISEEDEASFHDTKESFGEPDVGSVLTHFKRRTKLPDPAEKE
RGVSLWSMIKDNVGKDLTRVCLPVYFNEPISSLQKCFEDLEYSYLLDQAYEYGKSGKSLLRALN
VAAFAVSGYASTEGRHCKPFNPLLGETYEADFPEKGIRFFSEKVSSYRESKSDHRKFYIFTATK
TLHLRTDSRSDRAAWLQALASTRGIVPLQSINGDFSFVSPKDLSISTERLKKRLFEEGMNESLV
KECEQIVDSEFCEVQEQIKLLHEERKKLLDALRQLEMANLEAEASGIHDDVYQLRNHKYSSLGR
GKYSECSTSASSDDKQEFEDISEEDEASFHDTKESFGEPDVGSVLTHFKRRTKLPDPAEKERGV
SLWSMIKDNVGKDLTRVCLPVYFNEPISSLQKCFEDLEYSYLLDQAYEYGKSGKSLLRALNVAA
FAVSGYASTEGRHCKPFNPLLGETYEADFPEKGIRFFSEKVSSYRESKSDHRKFYIFTATKTLH
LRTDSRSDRAAWLQALASTRGIVPLQSINGDFSFVSPKDLSISTERLKKRLFEEGMNESLVKEC
EQIVDSEFCEVQEQIKLLHEERKKLLDALRQLEMANLEAEASGIHDDVYQLRNHKYSSLGRGKY
SECSTSASSDDKQEFEDISEEDEASFHDTKESFGEPDVGSVLTHFKRRTKLPDPAEKERGVSLW
SMIKDNVGKDLTRVCLPVYFNEPISSLQKCFEDLEYSYLLDQAYEYGKSGKSLLRALNVAAFAV
SGYASTEGRHCKPFNPLLGETYEADFPEKGIRFFSEK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7392928-7394554(+)
Potential amino acid sequence	MNESLVKECEQIVDSEFCEVQEQIKLLHEERKKLLDALRQLEMANLEAEASGIHDDVYQLRNHK YSSLGRGKYSECSTSASSDDKQEFEDISEEDEASFHDTKESFGEPDVGSVLTHFKRRTKLPDPA EKERGVSLWSMIKDNVGKDLTRVCLPVYFNEPISSLQKCFEDLEYSYLLDQAYEYGKSGKSLLR ALNVAAFAVSGYASTEGRHCKPFNPLLGETYEADFPEKGIRFFSEKVSSYRESKSDHRKFYIFT ATKTLHLRTDSRSDRAAWLQALASTRGIVPLQSINGDFSFVSPKDLSISTERLKKRLFEEGMNE SLVKECEQIVDSEFCEVQEQIKLLHEERKKLLDALRQLEMANLEAEASGIHDDVYQLRNHKYSS LGRGKYSECSTSASSDDKQEFEDISEEDEASFHDTKESFGEPDVGSVLTHFKRRTKLPDPAEKE RGVSLWSMIKDNVGKDLTRVCLPVYFNEPISSLQKCFEDLEYSYLLDQAYEYGKSGKSLLRALN VAAFAVSGYASTEGRHCKPFNPLLGETYEADFPEKGIRFFSEKVSSYRESKSDHRKFYIFTATK TLHLRTDSRSDRAAWLQALASTRGIVPLQSINGDFSFVSPKDLSISTERLKKRLFEEGMNESLV KECEQIVDSEFCEVQEQIKLLHEERKKLLDALRQLEMANLEAEASGIHDDVYQLRNHKYSSLGR GKYSECSTSASSDDKQEFEDISEEDEASFHDTKESFGEPDVGSVLTHFKRRTKLPDPAEKERGV SLWSMIKDNVGKDLTRVCLPVYFNEPISSLQKCFEDLEYSYLLDQAYEYGKSGKSLLRALNVAA FAVSGYASTEGRHCKPFNPLLGETYEADFPEKGIRFFSEKVSSYRESKSDHRKFYIFTATKTLH LRTDSRSDRAAWLQALASTRGIVPLQSINGDFSFVSPKDLSISTERLKKRLFEEGMNESLVKEC EQIVDSEFCEVQEQIKLLHEERKKLLDALRQLEMANLEAEASGIHDDVYQLRNHKYSSLGRGKY SECSTSASSDDKQEFEDISEEDEASFHDTKESFGEPDVGSVLTHFKRRTKLPDPAEKERGVSLW SMIKDNVGKDLTRVCLPVYFNEPISSLQKCFEDLEYSYLLDQAYEYGKSGKSLLRALNVAAFAV SGYASTEGRHCKPFNPLLGETYEADFPEKGIRFFSEK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT4G12460_circ_g.2

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