Plant Circular RNA Database

Detail information of AT2G13360_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT2G13360_circ_g.9
					
						ID in PlantcircBase
						ath_circ_013210
					
						Alias
						At_ciR1087
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 5539963-5540930  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						PcircRNA_finder, find_circ
					
						Parent gene
						
							AT2G13360						
					
						Parent gene annotation
						
							Serine--glyoxylate aminotransferase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT2G13360_circ_g.1 AT2G13360_circ_g.2 AT2G13360_circ_g.3 AT2G13360_circ_g.4 AT2G13360_circ_g.5 AT2G13360_circ_g.6 AT2G13360_circ_g.7 AT2G13360_circ_g.8 AT2G13360_circ_g.10 AT2G13360_circ_g.11 AT2G13360_circ_g.12 						
					
						Support reads
						5/430
					
						Tissues
						leaf/leaf
					
						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
						AT2G13360.1:2
AT2G13360.2:2
AT2G13360.3:2

General Information
CircRNA Name	AT2G13360_circ_g.9
ID in PlantcircBase	ath_circ_013210
Alias	At_ciR1087
Organism	Arabidpsis thaliana
Position	chr2: 5539963-5540930 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	PcircRNA_finder, find_circ
Parent gene	AT2G13360
Parent gene annotation	Serine--glyoxylate aminotransferase
Parent gene strand	-
Alternative splicing	AT2G13360_circ_g.1 AT2G13360_circ_g.2 AT2G13360_circ_g.3 AT2G13360_circ_g.4 AT2G13360_circ_g.5 AT2G13360_circ_g.6 AT2G13360_circ_g.7 AT2G13360_circ_g.8 AT2G13360_circ_g.10 AT2G13360_circ_g.11 AT2G13360_circ_g.12
Support reads	5/430
Tissues	leaf/leaf
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	AT2G13360.1:2 AT2G13360.2:2 AT2G13360.3:2

			
						 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  
						
							TACCGGTTCCGGTATGTTCACTGGTCCTGGTACAAACAGATGGTGTCTCCCTGGTCCATACATA
TAGTCCATTTTTTCCTCTTTTCTTTTGGATCCTCCTctggtggcctttcccaaacgagcatggc
gggcgatgatgttctcaagtccttcctcaaagataagatcaagagcagctctaagaccgtagag
aagttgaa

									
								

					

						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: 885
Transcript exons: 5539963-5540329,5540413-5540930
CTGGTGGCCTTTCCCAAACGAGCATGGCGGGCGATGATGTTCTCAAGTCCTTCCTCAAAGATAA
GATCAAGAGCAGCTCTAAGACCGTAGAGAAGTTGAATGGAAGGTGTGTATGGCCAATAGGTTCC
TAGCTTGTAAAACTTAAGGTAGTCATTCCAGTCAAAGAATACTTTGAGAGATTTAGAAGTTTTG
GTAGCTTCCAAAGCTTTAGGACTGGCGCAGACAATACCAAGTCCTGTTGGAAGAGATAAGGCTT
TCTGAGACCCAGTCAAGGCCACGTCCACTCCCCACTCATCCATTCGGAAATCAAGCGCGCAGAT
GGACGAAACACCGTCCACTAGCAGCAAAGCCGGATGCTTGTAGTGATCGAGGAGTGTGCGGACA
GCAGAGATGTCATTGGTAACTCCGGTCGCGGTCTCGTTGTGGACAATGCAAATGGCTTTGATGG
TATGATTCTCGTCTTGTGAGAGCTTTGAGGCCAAGACTTGGAGATTAGCACCTTGTCCCCAATC
ACTCTCAACCACATCAACATTGAAATTAAGCCTCTTCTGCTGGTCAATCCAGAGCAAGCTAAAT
TGTCCAATCAGAAACGAAACAATCCTGTCTCCAGGAGATAACGTGTTGGTCAAGGCACTCTCCC
AAGCACCAGTCCCGGTCGTGGGAAACAGAAAAGGTGTCCCTGATGTGGTCTTGAATATCTTCTT
AACATCCTCCAACAATGTTTTCGTAAGCGCCGGAATGGCTGGTGACCGGTAATCCTCGTTGTTC
CGGTTCATCGCCCGGATTACCGGTTCCGGTATGTTCACTGGTCCTGGTACAAACAGATGGTGTC
TCCCTGGTCCATACATATAGTCCATTTTTTCCTCTTTTCTTTTGGATCCTCCT
						
					

						Genomic sequence
						
							CTGGTGGCCTTTCCCAAACGAGCATGGCGGGCGATGATGTTCTCAAGTCCTTCCTCAAAGATAA
GATCAAGAGCAGCTCTAAGACCGTAGAGAAGTTGAATGGAAGGTGTGTATGGCCAATAGGTTCC
TAGCTTGTAAAACTTAAGGTAGTCATTCCAGTCAAAGAATACTTTGAGAGATTTAGAAGTTTTG
GTAGCTTCCAAAGCTTTAGGACTGGCGCAGACAATACCAAGTCCTGTTGGAAGAGATAAGGCTT
TCTGAGACCCAGTCAAGGCCACGTCCACTCCCCACTCATCCATTCGGAAATCAAGCGCGCAGAT
GGACGAAACACCGTCCACTAGCAGCAAAGCCGGATGCTTGTAGTGATCTGTATGTAAACCCTAA
TGTAAGTGAGATTTAAAACAGAGAAAACACAAAAGAAAAACAGATTATTTGTGAGGAATTAATG
ACCGAGGAGTGTGCGGACAGCAGAGATGTCATTGGTAACTCCGGTCGCGGTCTCGTTGTGGACA
ATGCAAATGGCTTTGATGGTATGATTCTCGTCTTGTGAGAGCTTTGAGGCCAAGACTTGGAGAT
TAGCACCTTGTCCCCAATCACTCTCAACCACATCAACATTGAAATTAAGCCTCTTCTGCTGGTC
AATCCAGAGCAAGCTAAATTGTCCAATCAGAAACGAAACAATCCTGTCTCCAGGAGATAACGTG
TTGGTCAAGGCACTCTCCCAAGCACCAGTCCCGGTCGTGGGAAACAGAAAAGGTGTCCCTGATG
TGGTCTTGAATATCTTCTTAACATCCTCCAACAATGTTTTCGTAAGCGCCGGAATGGCTGGTGA
CCGGTAATCCTCGTTGTTCCGGTTCATCGCCCGGATTACCGGTTCCGGTATGTTCACTGGTCCT
GGTACAAACAGATGGTGTCTCCCTGGTCCATACATATAGTCCATTTTTTCCTCTTTTCTTTTGG
ATCCTCCT
						
					

			
		

Sequences
Splice junction sequence	TACCGGTTCCGGTATGTTCACTGGTCCTGGTACAAACAGATGGTGTCTCCCTGGTCCATACATA TAGTCCATTTTTTCCTCTTTTCTTTTGGATCCTCCTctggtggcctttcccaaacgagcatggc gggcgatgatgttctcaagtccttcctcaaagataagatcaagagcagctctaagaccgtagag aagttgaa
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: 885 Transcript exons: 5539963-5540329,5540413-5540930 CTGGTGGCCTTTCCCAAACGAGCATGGCGGGCGATGATGTTCTCAAGTCCTTCCTCAAAGATAA GATCAAGAGCAGCTCTAAGACCGTAGAGAAGTTGAATGGAAGGTGTGTATGGCCAATAGGTTCC TAGCTTGTAAAACTTAAGGTAGTCATTCCAGTCAAAGAATACTTTGAGAGATTTAGAAGTTTTG GTAGCTTCCAAAGCTTTAGGACTGGCGCAGACAATACCAAGTCCTGTTGGAAGAGATAAGGCTT TCTGAGACCCAGTCAAGGCCACGTCCACTCCCCACTCATCCATTCGGAAATCAAGCGCGCAGAT GGACGAAACACCGTCCACTAGCAGCAAAGCCGGATGCTTGTAGTGATCGAGGAGTGTGCGGACA GCAGAGATGTCATTGGTAACTCCGGTCGCGGTCTCGTTGTGGACAATGCAAATGGCTTTGATGG TATGATTCTCGTCTTGTGAGAGCTTTGAGGCCAAGACTTGGAGATTAGCACCTTGTCCCCAATC ACTCTCAACCACATCAACATTGAAATTAAGCCTCTTCTGCTGGTCAATCCAGAGCAAGCTAAAT TGTCCAATCAGAAACGAAACAATCCTGTCTCCAGGAGATAACGTGTTGGTCAAGGCACTCTCCC AAGCACCAGTCCCGGTCGTGGGAAACAGAAAAGGTGTCCCTGATGTGGTCTTGAATATCTTCTT AACATCCTCCAACAATGTTTTCGTAAGCGCCGGAATGGCTGGTGACCGGTAATCCTCGTTGTTC CGGTTCATCGCCCGGATTACCGGTTCCGGTATGTTCACTGGTCCTGGTACAAACAGATGGTGTC TCCCTGGTCCATACATATAGTCCATTTTTTCCTCTTTTCTTTTGGATCCTCCT
Genomic sequence	CTGGTGGCCTTTCCCAAACGAGCATGGCGGGCGATGATGTTCTCAAGTCCTTCCTCAAAGATAA GATCAAGAGCAGCTCTAAGACCGTAGAGAAGTTGAATGGAAGGTGTGTATGGCCAATAGGTTCC TAGCTTGTAAAACTTAAGGTAGTCATTCCAGTCAAAGAATACTTTGAGAGATTTAGAAGTTTTG GTAGCTTCCAAAGCTTTAGGACTGGCGCAGACAATACCAAGTCCTGTTGGAAGAGATAAGGCTT TCTGAGACCCAGTCAAGGCCACGTCCACTCCCCACTCATCCATTCGGAAATCAAGCGCGCAGAT GGACGAAACACCGTCCACTAGCAGCAAAGCCGGATGCTTGTAGTGATCTGTATGTAAACCCTAA TGTAAGTGAGATTTAAAACAGAGAAAACACAAAAGAAAAACAGATTATTTGTGAGGAATTAATG ACCGAGGAGTGTGCGGACAGCAGAGATGTCATTGGTAACTCCGGTCGCGGTCTCGTTGTGGACA ATGCAAATGGCTTTGATGGTATGATTCTCGTCTTGTGAGAGCTTTGAGGCCAAGACTTGGAGAT TAGCACCTTGTCCCCAATCACTCTCAACCACATCAACATTGAAATTAAGCCTCTTCTGCTGGTC AATCCAGAGCAAGCTAAATTGTCCAATCAGAAACGAAACAATCCTGTCTCCAGGAGATAACGTG TTGGTCAAGGCACTCTCCCAAGCACCAGTCCCGGTCGTGGGAAACAGAAAAGGTGTCCCTGATG TGGTCTTGAATATCTTCTTAACATCCTCCAACAATGTTTTCGTAAGCGCCGGAATGGCTGGTGA CCGGTAATCCTCGTTGTTCCGGTTCATCGCCCGGATTACCGGTTCCGGTATGTTCACTGGTCCT GGTACAAACAGATGGTGTCTCCCTGGTCCATACATATAGTCCATTTTTTCCTCTTTTCTTTTGG ATCCTCCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.349572473

Conservation Information
Conserved circRNAs	NA
PMCS	0.349572473

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5540903-5539965(-)
						
						Potential amino acid sequence
						
							MDYMYGPGRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFL
FPTTGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLAS
KLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRMDEWGV
DVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYWPYTPSIQLL
YGLRAALDLIFEEGLENIIARHARLGKATRGGSKRKEEKMDYMYGPGRHHLFVPGPVNIPEPVI
RAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPTTGTGAWESALTNTLSPGDRIVS
FLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLASKLSQDENHTIKAICIVHNETATGVT
NDISAVRTLLDHYKHPALLLVDGVSSICALDFRMDEWGVDVALTGSQKALSLPTGLGIVCASPK
ALEATKTSKSLKVFFDWNDYLKFYKLGTYWPYTPSIQLLYGLRAALDLIFEEGLENIIARHARL
GKATRGGSKRKEEKMDYMYGPGRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLED
VKKIFKTTSGTPFLFPTTGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVE
SDWGQGANLQVLASKLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVS
SICALDFRMDEWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYK
LGTYWPYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRGGSKRKEEKMDYMYGPGRHH
LFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPTTGTGAWES
ALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLASKLSQDENHTIK
AICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRMDEWGVDVALTGSQKAL
SLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYWPYTPSIQLLYGLRAALDLIF
EEGLENIIARHARLGKAT(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5540903-5539965(-)
Potential amino acid sequence	MDYMYGPGRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFL FPTTGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLAS KLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRMDEWGV DVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYWPYTPSIQLL YGLRAALDLIFEEGLENIIARHARLGKATRGGSKRKEEKMDYMYGPGRHHLFVPGPVNIPEPVI RAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPTTGTGAWESALTNTLSPGDRIVS FLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLASKLSQDENHTIKAICIVHNETATGVT NDISAVRTLLDHYKHPALLLVDGVSSICALDFRMDEWGVDVALTGSQKALSLPTGLGIVCASPK ALEATKTSKSLKVFFDWNDYLKFYKLGTYWPYTPSIQLLYGLRAALDLIFEEGLENIIARHARL GKATRGGSKRKEEKMDYMYGPGRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLED VKKIFKTTSGTPFLFPTTGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVE SDWGQGANLQVLASKLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVS SICALDFRMDEWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYK LGTYWPYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRGGSKRKEEKMDYMYGPGRHH LFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPTTGTGAWES ALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLASKLSQDENHTIK AICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRMDEWGVDVALTGSQKAL SLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYWPYTPSIQLLYGLRAALDLIF EEGLENIIARHARLGKAT(-)
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 AT2G13360_circ_g.9

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