Plant Circular RNA Database

Detail information of AT1G23935_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT1G23935_circ_g.1
					
						ID in PlantcircBase
						ath_circ_004108
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 8464439-8465895  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						circRNA_finder, find_circ
					
						Parent gene
						
							AT1G23935						
					
						Parent gene annotation
						
							unknown protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G23900_circ_g.1 1_circ_ag.2 1_circ_ag.3 AT1G23900_circ_g.4 1_circ_ag.5 1_circ_ag.6 AT1G23900_circ_g.7 AT1G23900_circ_g.8 AT1G23900_circ_g.9 AT1G23900_circ_g.10 AT1G23900_circ_g.11 AT1G23900_circ_g.12 AT1G23900_circ_g.13 1_circ_ag.14 1_circ_ag.15 AT1G23935_circ_g.2 						
					
						Support reads
						2
					
						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
						AT1G23935.1:3
AT1G23935.3:2
AT1G23935.2:2

General Information
CircRNA Name	AT1G23935_circ_g.1
ID in PlantcircBase	ath_circ_004108
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 8464439-8465895 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	circRNA_finder, find_circ
Parent gene	AT1G23935
Parent gene annotation	unknown protein
Parent gene strand	+
Alternative splicing	AT1G23900_circ_g.1 1_circ_ag.2 1_circ_ag.3 AT1G23900_circ_g.4 1_circ_ag.5 1_circ_ag.6 AT1G23900_circ_g.7 AT1G23900_circ_g.8 AT1G23900_circ_g.9 AT1G23900_circ_g.10 AT1G23900_circ_g.11 AT1G23900_circ_g.12 AT1G23900_circ_g.13 1_circ_ag.14 1_circ_ag.15 AT1G23935_circ_g.2
Support reads	2
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	AT1G23935.1:3 AT1G23935.3:2 AT1G23935.2:2

			
						 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  
						
							CTCAGAAAATGAGGAGGAAGAGGATTATATTCCTAAAGCAAAAAGAGGTCTTACTAAAGATCCT
AAACCAAAAAGAAGTCGTACTGAAGATCCAACAATGttattgaagagaaaaaagtctggctttg
tcaaactttcttggaaagaagctaggaaggcattgttaacctcatatacgtataaacccaattt
attgtcaa

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							TTATTGAAGAGAAAAAAGTCTGGCTTTGTCAAACTTTCTTGGAAAGAAGCTAGGAAGGCATTGT
TAACCTCATATACGTATAAACCCAATTTATTGTCAACTAGGTGAAATCTCTTTGTCTTCTCACA
GGACTCATCTACTTCTTTTATCTTCTCAGAGACAGCACATGCCCGATAGCCCCTATAAGGTCTG
ATGCGCTTGAATCCGTTTCAAAGGATTGTAAGCTAAACCTAGATGATACAGGAATATGCGATCT
AACCGACAAGCAAGTTCAAAGTATTCTGGATTATTCAAAATATCATCAAGTTTCTCGTAACAAA
AATGGTGCATGTGTGTTAAATGACAATGATGACATCGCTATGCTCGGTTGGCAAATGAAAAAAT
CGGTAAACATTTTAAAACTCTTATTTTACCGAAATCTTTTACACCGGATATATGTTCCTATATG
GGAGCTTAATCAATAATCAGATATCTTCTCCATTTTACCTAAATCGTTTTTGATTTACAATATA
TAGGACTTAAGTTTCCTAGAGACGGCTGGGGAACAGGGTAGATCGGGTGAGGTTAGAGATCAAC
TTTTTCACCTTCTCTGCTGGGCCTACGCAGGCTCTGATCTAGTTAGTTACCAGAGATTGTTACA
GAAGTGGGAGAGGAAGACACTTCCTCTTTGTCCTTGGTATTTATGTGCCTTTTGCGAGCCAGAA
AAACTTGGAGAAGAGGAAATACTTGATAGAAATGGAGAAAAGAAAATACTTGTTGATAGACATG
GTCGTGTACATCATTGCTATGGAGGTACAATTGAAAAAGCATTATGCCACGTACAGAGCCATGG
AATTCCAAGGGATGTTGTCACCAATTTCCTTTGCACGGATTATCATCCCCCAAGTGCAGATGAA
CCTGATATGGAAAGAAGAAAAATTAAAGGATTTCGAAAAATCAACACTTGGAAGGATGTTGTAG
AGGCGCTTCAAAAGCAGCAGATAGTGGGGGCAGATTTGCTTAATTACAGTCAACTGATGATGAC
TTCAGGAAAGTATATTTACAAAGGTCCCATGTCACGAATGAGTGTTTACGTCGGATATCACGCC
GTAGTAATAGAGCAGATTAAGAAAATGAATGGAGAATGGGTTGCTGTTTGCAAAATGAGCAATG
GCACGTTGGTGGCTGATTATGGATACGCTTATGTTTCCATAGAAGTTCAGTACATGCCTGTTGG
TGCATCTGATCTGAAAAGGAAGAGGATACGAGGTTCAGACCATCCAATGCATCTCCTTACCAAT
TTCATCATCGTAGACATGGTGGAGGCAGATGAGAATGATAGAAAGGATGCAGAAAGTGAAGAAT
CAGAAGAAAAAGACTCAGAAAATGAGGAGGAAGAGGATTATATTCCTAAAGCAAAAAGAGGTCT
TACTAAAGATCCTAAACCAAAAAGAAGTCGTACTGAAGATCCAACAATG

Sequences
Splice junction sequence	CTCAGAAAATGAGGAGGAAGAGGATTATATTCCTAAAGCAAAAAGAGGTCTTACTAAAGATCCT AAACCAAAAAGAAGTCGTACTGAAGATCCAACAATGttattgaagagaaaaaagtctggctttg tcaaactttcttggaaagaagctaggaaggcattgttaacctcatatacgtataaacccaattt attgtcaa
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TTATTGAAGAGAAAAAAGTCTGGCTTTGTCAAACTTTCTTGGAAAGAAGCTAGGAAGGCATTGT TAACCTCATATACGTATAAACCCAATTTATTGTCAACTAGGTGAAATCTCTTTGTCTTCTCACA GGACTCATCTACTTCTTTTATCTTCTCAGAGACAGCACATGCCCGATAGCCCCTATAAGGTCTG ATGCGCTTGAATCCGTTTCAAAGGATTGTAAGCTAAACCTAGATGATACAGGAATATGCGATCT AACCGACAAGCAAGTTCAAAGTATTCTGGATTATTCAAAATATCATCAAGTTTCTCGTAACAAA AATGGTGCATGTGTGTTAAATGACAATGATGACATCGCTATGCTCGGTTGGCAAATGAAAAAAT CGGTAAACATTTTAAAACTCTTATTTTACCGAAATCTTTTACACCGGATATATGTTCCTATATG GGAGCTTAATCAATAATCAGATATCTTCTCCATTTTACCTAAATCGTTTTTGATTTACAATATA TAGGACTTAAGTTTCCTAGAGACGGCTGGGGAACAGGGTAGATCGGGTGAGGTTAGAGATCAAC TTTTTCACCTTCTCTGCTGGGCCTACGCAGGCTCTGATCTAGTTAGTTACCAGAGATTGTTACA GAAGTGGGAGAGGAAGACACTTCCTCTTTGTCCTTGGTATTTATGTGCCTTTTGCGAGCCAGAA AAACTTGGAGAAGAGGAAATACTTGATAGAAATGGAGAAAAGAAAATACTTGTTGATAGACATG GTCGTGTACATCATTGCTATGGAGGTACAATTGAAAAAGCATTATGCCACGTACAGAGCCATGG AATTCCAAGGGATGTTGTCACCAATTTCCTTTGCACGGATTATCATCCCCCAAGTGCAGATGAA CCTGATATGGAAAGAAGAAAAATTAAAGGATTTCGAAAAATCAACACTTGGAAGGATGTTGTAG AGGCGCTTCAAAAGCAGCAGATAGTGGGGGCAGATTTGCTTAATTACAGTCAACTGATGATGAC TTCAGGAAAGTATATTTACAAAGGTCCCATGTCACGAATGAGTGTTTACGTCGGATATCACGCC GTAGTAATAGAGCAGATTAAGAAAATGAATGGAGAATGGGTTGCTGTTTGCAAAATGAGCAATG GCACGTTGGTGGCTGATTATGGATACGCTTATGTTTCCATAGAAGTTCAGTACATGCCTGTTGG TGCATCTGATCTGAAAAGGAAGAGGATACGAGGTTCAGACCATCCAATGCATCTCCTTACCAAT TTCATCATCGTAGACATGGTGGAGGCAGATGAGAATGATAGAAAGGATGCAGAAAGTGAAGAAT CAGAAGAAAAAGACTCAGAAAATGAGGAGGAAGAGGATTATATTCCTAAAGCAAAAAGAGGTCT TACTAAAGATCCTAAACCAAAAAGAAGTCGTACTGAAGATCCAACAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.097754844

Conservation Information
Conserved circRNAs	NA
PMCS	0.097754844

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							8464798-8465892(+)
						
					

						Potential amino acid sequence
						
							MLGWQMKKSDLSFLETAGEQGRSGEVRDQLFHLLCWAYAGSDLVSYQRLLQKWERKTLPLCPWY
LCAFCEPEKLGEEEILDRNGEKKILVDRHGRVHHCYGGTIEKALCHVQSHGIPRDVVTNFLCTD
YHPPSADEPDMERRKIKGFRKINTWKDVVEALQKQQIVGADLLNYSQLMMTSGKYIYKGPMSRM
SVYVGYHAVVIEQIKKMNGEWVAVCKMSNGTLVADYGYAYVSIEVQYMPVGASDLKRKRIRGSD
HPMHLLTNFIIVDMVEADENDRKDAESEESEEKDSENEEEEDYIPKAKRGLTKDPKPKRSRTED
PTMLLKRKKSGFVKLSWKEARKALLTSYTDSTCPIAPIRSDALESVSKDCKLNLDDTGICDLTD
KQVQSILDYSKYHQVSRNKNGACVLNDNDDIAMLGWQMKKSDLSFLETAGEQGRSGEVRDQLFH
LLCWAYAGSDLVSYQRLLQKWERKTLPLCPWYLCAFCEPEKLGEEEILDRNGEKKILVDRHGRV
HHCYGGTIEKALCHVQSHGIPRDVVTNFLCTDYHPPSADEPDMERRKIKGFRKINTWKDVVEAL
QKQQIVGADLLNYSQLMMTSGKYIYKGPMSRMSVYVGYHAVVIEQIKKMNGEWVAVCKMSNGTL
VADYGYAYVSIEVQYMPVGASDLKRKRIRGSDHPMHLLTNFIIVDMVEADENDRKDAESEESEE
KDSENEEEEDYIPKAKRGLTKDPKPKRSRTEDPTMLLKRKKSGFVKLSWKEARKALLTSYTDST
CPIAPIRSDALESVSKDCKLNLDDTGICDLTDKQVQSILDYSKYHQVSRNKNGACVLNDNDDIA
MLGWQMKKSDLSFLETAGEQGRSGEVRDQLFHLLCWAYAGSDLVSYQRLLQKWERKTLPLCPWY
LCAFCEPEKLGEEEILDRNGEKKILVDRHGRVHHCYGGTIEKALCHVQSHGIPRDVVTNFLCTD
YHPPSADEPDMERRKIKGFRKINTWKDVVEALQKQQIVGADLLNYSQLMMTSGKYIYKGPMSRM
SVYVGYHAVVIEQIKKMNGEWVAVCKMSNGTLVADYGYAYVSIEVQYMPVGASDLKRKRIRGSD
HPMHLLTNFIIVDMVEADENDRKDAESEESEEKDSENEEEEDYIPKAKRGLTKDPKPKRSRTED
PTMLLKRKKSGFVKLSWKEARKALLTSYTDSTCPIAPIRSDALESVSKDCKLNLDDTGICDLTD
KQVQSILDYSKYHQVSRNKNGACVLNDNDDIAMLGWQMKKSDLSFLETAGEQGRSGEVRDQLFH
LLCWAYAGSDLVSYQRLLQKWERKTLPLCPWYLCAFCEPEKLGEEEILDRNGEKKILVDRHGRV
HHCYGGTIEKALCHVQSHGIPRDVVTNFLCTDYHPPSADEPDMERRKIKGFRKINTWKDVVEAL
QKQQIVGADLLNYSQLMMTSGKYIYKGPMSRMSVYVGYHAVVIEQIKKMNGEWVAVCKMSNGTL
VADYGYAYVSIEVQYMPVGASDLKRKRIRGSDHPMHLLTNFIIVDMVEADENDRKDAESEESEE
KDSENEEEEDYIPKAKRGLTKDPKPKRSRTEDPTM(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	8464798-8465892(+)
Potential amino acid sequence	MLGWQMKKSDLSFLETAGEQGRSGEVRDQLFHLLCWAYAGSDLVSYQRLLQKWERKTLPLCPWY LCAFCEPEKLGEEEILDRNGEKKILVDRHGRVHHCYGGTIEKALCHVQSHGIPRDVVTNFLCTD YHPPSADEPDMERRKIKGFRKINTWKDVVEALQKQQIVGADLLNYSQLMMTSGKYIYKGPMSRM SVYVGYHAVVIEQIKKMNGEWVAVCKMSNGTLVADYGYAYVSIEVQYMPVGASDLKRKRIRGSD HPMHLLTNFIIVDMVEADENDRKDAESEESEEKDSENEEEEDYIPKAKRGLTKDPKPKRSRTED PTMLLKRKKSGFVKLSWKEARKALLTSYTDSTCPIAPIRSDALESVSKDCKLNLDDTGICDLTD KQVQSILDYSKYHQVSRNKNGACVLNDNDDIAMLGWQMKKSDLSFLETAGEQGRSGEVRDQLFH LLCWAYAGSDLVSYQRLLQKWERKTLPLCPWYLCAFCEPEKLGEEEILDRNGEKKILVDRHGRV HHCYGGTIEKALCHVQSHGIPRDVVTNFLCTDYHPPSADEPDMERRKIKGFRKINTWKDVVEAL QKQQIVGADLLNYSQLMMTSGKYIYKGPMSRMSVYVGYHAVVIEQIKKMNGEWVAVCKMSNGTL VADYGYAYVSIEVQYMPVGASDLKRKRIRGSDHPMHLLTNFIIVDMVEADENDRKDAESEESEE KDSENEEEEDYIPKAKRGLTKDPKPKRSRTEDPTMLLKRKKSGFVKLSWKEARKALLTSYTDST CPIAPIRSDALESVSKDCKLNLDDTGICDLTDKQVQSILDYSKYHQVSRNKNGACVLNDNDDIA MLGWQMKKSDLSFLETAGEQGRSGEVRDQLFHLLCWAYAGSDLVSYQRLLQKWERKTLPLCPWY LCAFCEPEKLGEEEILDRNGEKKILVDRHGRVHHCYGGTIEKALCHVQSHGIPRDVVTNFLCTD YHPPSADEPDMERRKIKGFRKINTWKDVVEALQKQQIVGADLLNYSQLMMTSGKYIYKGPMSRM SVYVGYHAVVIEQIKKMNGEWVAVCKMSNGTLVADYGYAYVSIEVQYMPVGASDLKRKRIRGSD HPMHLLTNFIIVDMVEADENDRKDAESEESEEKDSENEEEEDYIPKAKRGLTKDPKPKRSRTED PTMLLKRKKSGFVKLSWKEARKALLTSYTDSTCPIAPIRSDALESVSKDCKLNLDDTGICDLTD KQVQSILDYSKYHQVSRNKNGACVLNDNDDIAMLGWQMKKSDLSFLETAGEQGRSGEVRDQLFH LLCWAYAGSDLVSYQRLLQKWERKTLPLCPWYLCAFCEPEKLGEEEILDRNGEKKILVDRHGRV HHCYGGTIEKALCHVQSHGIPRDVVTNFLCTDYHPPSADEPDMERRKIKGFRKINTWKDVVEAL QKQQIVGADLLNYSQLMMTSGKYIYKGPMSRMSVYVGYHAVVIEQIKKMNGEWVAVCKMSNGTL VADYGYAYVSIEVQYMPVGASDLKRKRIRGSDHPMHLLTNFIIVDMVEADENDRKDAESEESEE KDSENEEEEDYIPKAKRGLTKDPKPKRSRTEDPTM(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G23935_circ_g.1

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