Plant Circular RNA Database

Detail information of Os01g0118100_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0118100_circ_g.4
					
						ID in PlantcircBase
						osa_circ_000144
					
						Alias
						Os_ciR5682
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 1026722-1028228  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os01g0118100						
					
						Parent gene annotation
						
							Similar to Fructose-bisphosphate aldolase. (Os01t0118100-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0118100_circ_g.1 Os01g0118100_circ_g.2 Os01g0118100_circ_g.3 Os01g0118100_circ_g.5 						
					
						Support reads
						2/1
					
						Tissues
						root/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
						Os01t0118100-01:5

General Information
CircRNA Name	Os01g0118100_circ_g.4
ID in PlantcircBase	osa_circ_000144
Alias	Os_ciR5682
Organism	Oryza sativa
Position	chr1: 1026722-1028228 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os01g0118100
Parent gene annotation	Similar to Fructose-bisphosphate aldolase. (Os01t0118100-01)
Parent gene strand	+
Alternative splicing	Os01g0118100_circ_g.1 Os01g0118100_circ_g.2 Os01g0118100_circ_g.3 Os01g0118100_circ_g.5
Support reads	2/1
Tissues	root/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	Os01t0118100-01:5

			
						 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  
						
							ATTCCCTAATCATTGGTTTTGTTGCTCTTGATAATCACAGAACAAGGAGAAATCAATTTCTCTC
AAGACAATGGAGGATGGGCAAGTCATGCTTTACTCGagacgaggaagagctggtcgagtccaac
caggggagtgttaccatctatatccacaatgcgtgtatgaagcatttgctgactatcagttgcc
agaactcc

									
								

					

						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: 792
Transcript exons: 1026722-1026925,1027012-1027081,1027185-1027333,1027551-
1027859,1028169-1028228
AGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGT
ATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCCTGAGAACTCCTCTGCAATCCCTCTGTTT
GCAAATAAAAAGCTTGCGCCTTGGGAGCATCTCTGAATTTTTATCCAGAGCTTTGCAATCACCT
GAGTCTCTATCGGTAGAAAATGCCATTGAATATCTCAAAGTCATTGGAGCGTTTGATCGTAATG
AAGAGTTAACAATTCTAGGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGAT
GCTGATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTCGGGACTTAGT
GTGAGAGATCCATTCTTGACTCCATTTGACAAGAAGGATCTTGCAGAGTCTGCTAAATTGCAGT
TTTCATGCCGGGACTATAGCGATCACCTTGCACTTGTTCGTGCATACGAAGGATGGAGAGAGGC
TGAAAGAGATCGCAATGGCTATGACTACTGCTGGAAAAATTTTCTATCCGTGCAAACCTTGAAA
GCCATAGATTCCCTTCGGAGACAATTTCTCTTTCTTCTCAGGGATACTGGGTTGGTTGATGAAA
ACATGACTGCGTGCAATAAATGGAGCCGTGATGAAAATCTAGTTCGGGCGGTCATTTGTGCAGG
ATTATATCCAGGTGTTTCCTCTGTTGTGAACAAGGAGAAATCAATTTCTCTCAAGACAATGGAG
GATGGGCAAGTCATGCTTTACTCG
						
					

						Genomic sequence
						
							AGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGT
ATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCCTGAGAACTCCTCTGCAATCCCTCTGTTT
GCAAATAAAAAGCTTGCGCCTTGGGAGCATCTCTGAATTTTTATCCAGAGCTTTGCAATCACCT
GAGTCTCTATCGGTACTTGATTTCCGTATTAATCACAAGCCGCAAAAGTCTATCCTGTGTCTTG
GAATGACTTGATAAATTAATTTGAATTTTTTCAGGTAGAAAATGCCATTGAATATCTCAAAGTC
ATTGGAGCGTTTGATCGTAATGAAGAGTTAACAATTCTAGGTATCAGATCCATCCTTCAAATCA
TCCGTTTATCACTGCTTTATTGAATCATCTTGAGCATTTGTAGCATGTGCTAACTATACCCACG
GATTGGCATTACCAGGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGATGCT
GATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTCGGGACTTAGTGTG
AGAGATCCATTCTTGACTCCATTTGACAAGAAGGATGTAAGTAATTCTTTCTTAGAACTCCAGT
TTGAACTGCCTCTTGTAATGCATTCAAAATTTTTTGTGTTCCTAATGCAGTAAAATATGTATAT
TCTGTTATATACTGCGTTTCCCTTTTTGGTAGTGCCCTTTTTTGTTATTTCATTGTACTTGCCC
TTCTCTTTTCTGAAGTCTCTATGTAATAAATTTCATTTCTGTGCCATCTTTCTGCATGCAGCTT
GCAGAGTCTGCTAAATTGCAGTTTTCATGCCGGGACTATAGCGATCACCTTGCACTTGTTCGTG
CATACGAAGGATGGAGAGAGGCTGAAAGAGATCGCAATGGCTATGACTACTGCTGGAAAAATTT
TCTATCCGTGCAAACCTTGAAAGCCATAGATTCCCTTCGGAGACAATTTCTCTTTCTTCTCAGG
GATACTGGGTTGGTTGATGAAAACATGACTGCGTGCAATAAATGGAGCCGTGATGAAAATCTAG
TTCGGGCGGTCATTTGTGCAGGATTATATCCAGGTGTTTCCTCTGTTGTGGTGAGTTACCTATC
ATTTATTAATATTTCTGTTTTTGCATTTTTCGTGCTTGTATTTTTGCTACTGTTGTATACTTTT
GTTTTGCCTGTGAAGCTGTGACAAGAATTGTGCTAGTTCCAGCTATTTATGGTAATGATCAAAA
GAAAAATTAGTATGCAAGTACTGAAACACTATTTTTTTTAAAGGAGGAAAACATATTATATATG
CTTTATGTGGAGGATGACTGATTCCAATATTAACTTCTTATAAGTCAATGTTGAATGCTTTAAA
TTCCCTAATCATTGGTTTTGTTGCTCTTGATAATCACAGAACAAGGAGAAATCAATTTCTCTCA
AGACAATGGAGGATGGGCAAGTCATGCTTTACTCG
						
					

			
		

Sequences
Splice junction sequence	ATTCCCTAATCATTGGTTTTGTTGCTCTTGATAATCACAGAACAAGGAGAAATCAATTTCTCTC AAGACAATGGAGGATGGGCAAGTCATGCTTTACTCGagacgaggaagagctggtcgagtccaac caggggagtgttaccatctatatccacaatgcgtgtatgaagcatttgctgactatcagttgcc agaactcc
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: 792 Transcript exons: 1026722-1026925,1027012-1027081,1027185-1027333,1027551- 1027859,1028169-1028228 AGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGT ATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCCTGAGAACTCCTCTGCAATCCCTCTGTTT GCAAATAAAAAGCTTGCGCCTTGGGAGCATCTCTGAATTTTTATCCAGAGCTTTGCAATCACCT GAGTCTCTATCGGTAGAAAATGCCATTGAATATCTCAAAGTCATTGGAGCGTTTGATCGTAATG AAGAGTTAACAATTCTAGGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGAT GCTGATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTCGGGACTTAGT GTGAGAGATCCATTCTTGACTCCATTTGACAAGAAGGATCTTGCAGAGTCTGCTAAATTGCAGT TTTCATGCCGGGACTATAGCGATCACCTTGCACTTGTTCGTGCATACGAAGGATGGAGAGAGGC TGAAAGAGATCGCAATGGCTATGACTACTGCTGGAAAAATTTTCTATCCGTGCAAACCTTGAAA GCCATAGATTCCCTTCGGAGACAATTTCTCTTTCTTCTCAGGGATACTGGGTTGGTTGATGAAA ACATGACTGCGTGCAATAAATGGAGCCGTGATGAAAATCTAGTTCGGGCGGTCATTTGTGCAGG ATTATATCCAGGTGTTTCCTCTGTTGTGAACAAGGAGAAATCAATTTCTCTCAAGACAATGGAG GATGGGCAAGTCATGCTTTACTCG
Genomic sequence	AGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGT ATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCCTGAGAACTCCTCTGCAATCCCTCTGTTT GCAAATAAAAAGCTTGCGCCTTGGGAGCATCTCTGAATTTTTATCCAGAGCTTTGCAATCACCT GAGTCTCTATCGGTACTTGATTTCCGTATTAATCACAAGCCGCAAAAGTCTATCCTGTGTCTTG GAATGACTTGATAAATTAATTTGAATTTTTTCAGGTAGAAAATGCCATTGAATATCTCAAAGTC ATTGGAGCGTTTGATCGTAATGAAGAGTTAACAATTCTAGGTATCAGATCCATCCTTCAAATCA TCCGTTTATCACTGCTTTATTGAATCATCTTGAGCATTTGTAGCATGTGCTAACTATACCCACG GATTGGCATTACCAGGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGATGCT GATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTCGGGACTTAGTGTG AGAGATCCATTCTTGACTCCATTTGACAAGAAGGATGTAAGTAATTCTTTCTTAGAACTCCAGT TTGAACTGCCTCTTGTAATGCATTCAAAATTTTTTGTGTTCCTAATGCAGTAAAATATGTATAT TCTGTTATATACTGCGTTTCCCTTTTTGGTAGTGCCCTTTTTTGTTATTTCATTGTACTTGCCC TTCTCTTTTCTGAAGTCTCTATGTAATAAATTTCATTTCTGTGCCATCTTTCTGCATGCAGCTT GCAGAGTCTGCTAAATTGCAGTTTTCATGCCGGGACTATAGCGATCACCTTGCACTTGTTCGTG CATACGAAGGATGGAGAGAGGCTGAAAGAGATCGCAATGGCTATGACTACTGCTGGAAAAATTT TCTATCCGTGCAAACCTTGAAAGCCATAGATTCCCTTCGGAGACAATTTCTCTTTCTTCTCAGG GATACTGGGTTGGTTGATGAAAACATGACTGCGTGCAATAAATGGAGCCGTGATGAAAATCTAG TTCGGGCGGTCATTTGTGCAGGATTATATCCAGGTGTTTCCTCTGTTGTGGTGAGTTACCTATC ATTTATTAATATTTCTGTTTTTGCATTTTTCGTGCTTGTATTTTTGCTACTGTTGTATACTTTT GTTTTGCCTGTGAAGCTGTGACAAGAATTGTGCTAGTTCCAGCTATTTATGGTAATGATCAAAA GAAAAATTAGTATGCAAGTACTGAAACACTATTTTTTTTAAAGGAGGAAAACATATTATATATG CTTTATGTGGAGGATGACTGATTCCAATATTAACTTCTTATAAGTCAATGTTGAATGCTTTAAA TTCCCTAATCATTGGTTTTGTTGCTCTTGATAATCACAGAACAAGGAGAAATCAATTTCTCTCA AGACAATGGAGGATGGGCAAGTCATGCTTTACTCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.394839718

Conservation Information
Conserved circRNAs	NA
PMCS	0.394839718

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1027200-1028225(+)
1028207-1026821(+)
1026768-1028183(-)
1026796-1028217(-)
						
						Potential amino acid sequence
						
							MLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFLTPFDKKDLAESAKLQFSCRDYSDHLA
LVRAYEGWREAERDRNGYDYCWKNFLSVQTLKAIDSLRRQFLFLLRDTGLVDENMTACNKWSRD
ENLVRAVICAGLYPGVSSVVNKEKSISLKTMEDGQVMLYSRRGRAGRVQPGECYHLYPQCVYEA
FADYQLPELLRTPLQSLCLQIKSLRLGSISEFLSRALQSPESLSVENAIEYLKVIGAFDRNEEL
TILGKHLSMLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFLTPFDKKDLAESAKLQFSC
RDYSDHLALVRAYEGWREAERDRNGYDYCWKNFLSVQTLKAIDSLRRQFLFLLRDTGLVDENMT
ACNKWSRDENLVRAVICAGLYPGVSSVVNKEKSISLKTMEDGQVMLYSRRGRAGRVQPGECYHL
YPQCVYEAFADYQLPELLRTPLQSLCLQIKSLRLGSISEFLSRALQSPESLSVENAIEYLKVIG
AFDRNEELTILGKHLSMLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFLTPFDKKDLAE
SAKLQFSCRDYSDHLALVRAYEGWREAERDRNGYDYCWKNFLSVQTLKAIDSLRRQFLFLLRDT
GLVDENMTACNKWSRDENLVRAVICAGLYPGVSSVVNKEKSISLKTMEDGQVMLYSRRGRAGRV
QPGECYHLYPQCVYEAFADYQLPELLRTPLQSLCLQIKSLRLGSISEFLSRALQSPESLSVENA
IEYLKVIGAFDRNEELTILGKHLSMLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFLTP
FDKKDLAESAKLQFSCRDYSDHLALVRAYEGWREAERDRNGYDYCWKNFLSVQTLKAIDSLRRQ
FLFLLRDTGLVDENMTACNKWSRDENLVRAVICAGLYPGVSSVVNKEKSISLKTMEDGQVMLYS
(+)
MGKSCFTRDEEELVESNQGSVTIYIHNACMKHLLTISCQNS*(+)
MVTLPWLDSTSSSSSRVKHDLPILHCLERN*(-)
MLHTRIVDIDGNTPLVGLDQLFLVSSKA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1027200-1028225(+) 1028207-1026821(+) 1026768-1028183(-) 1026796-1028217(-)
Potential amino acid sequence	MLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFLTPFDKKDLAESAKLQFSCRDYSDHLA LVRAYEGWREAERDRNGYDYCWKNFLSVQTLKAIDSLRRQFLFLLRDTGLVDENMTACNKWSRD ENLVRAVICAGLYPGVSSVVNKEKSISLKTMEDGQVMLYSRRGRAGRVQPGECYHLYPQCVYEA FADYQLPELLRTPLQSLCLQIKSLRLGSISEFLSRALQSPESLSVENAIEYLKVIGAFDRNEEL TILGKHLSMLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFLTPFDKKDLAESAKLQFSC RDYSDHLALVRAYEGWREAERDRNGYDYCWKNFLSVQTLKAIDSLRRQFLFLLRDTGLVDENMT ACNKWSRDENLVRAVICAGLYPGVSSVVNKEKSISLKTMEDGQVMLYSRRGRAGRVQPGECYHL YPQCVYEAFADYQLPELLRTPLQSLCLQIKSLRLGSISEFLSRALQSPESLSVENAIEYLKVIG AFDRNEELTILGKHLSMLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFLTPFDKKDLAE SAKLQFSCRDYSDHLALVRAYEGWREAERDRNGYDYCWKNFLSVQTLKAIDSLRRQFLFLLRDT GLVDENMTACNKWSRDENLVRAVICAGLYPGVSSVVNKEKSISLKTMEDGQVMLYSRRGRAGRV QPGECYHLYPQCVYEAFADYQLPELLRTPLQSLCLQIKSLRLGSISEFLSRALQSPESLSVENA IEYLKVIGAFDRNEELTILGKHLSMLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFLTP FDKKDLAESAKLQFSCRDYSDHLALVRAYEGWREAERDRNGYDYCWKNFLSVQTLKAIDSLRRQ FLFLLRDTGLVDENMTACNKWSRDENLVRAVICAGLYPGVSSVVNKEKSISLKTMEDGQVMLYS (+) MGKSCFTRDEEELVESNQGSVTIYIHNACMKHLLTISCQNS(+) MVTLPWLDSTSSSSSRVKHDLPILHCLERN(-) MLHTRIVDIDGNTPLVGLDQLFLVSSKA*(-)
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 Os01g0118100_circ_g.4

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