Plant Circular RNA Database

Detail information of Os01g0938200_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os01g0938200_circ_g.1
					
						ID in PlantcircBase
						osa_circ_005744
					
						Alias
						Os_ciR6438
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 41194869-41197131  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os01g0938200						
					
						Parent gene annotation
						
							Similar to RNA-binding protein BRUNOL5 (Fragment). (Os01t0938200
-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0938200_circ_g.2 Os01g0938200_circ_g.3 						
					
						Support reads
						2/2
					
						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
						Os01t0938200-01:5

General Information
CircRNA Name	Os01g0938200_circ_g.1
ID in PlantcircBase	osa_circ_005744
Alias	Os_ciR6438
Organism	Oryza sativa
Position	chr1: 41194869-41197131 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os01g0938200
Parent gene annotation	Similar to RNA-binding protein BRUNOL5 (Fragment). (Os01t0938200 -01)
Parent gene strand	+
Alternative splicing	Os01g0938200_circ_g.2 Os01g0938200_circ_g.3
Support reads	2/2
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	Os01t0938200-01:5

			
						 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  
						
							ATCATCTAATATGCCTAGCGCGAGTCCTATGCAACAATCTTCATTATTTGGGGCTTTACAGATG
GGATATATGCCTCAATATAATGGATTTGGCTATCAGggtgctgcttcctcatatgcccctcgag
ggaagaggctgacaaggcagtgaacgcttaccacaataagcacacacttcctggggtacgtgat
cgttggaa

									
								

					

						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: 202
Transcript exons: 41194869-41194912,41196973-41197073,41197075-41197131
GGTGCTGCTTCCTCATATGCCCCTCGAGGGAAGAGGCTGACAAGAAATGGGCCGATACAGAAAA
GGAAAGGCAGGCCCGAAAAGCACAAAAGGCTCAATTGCAATCATCTAATATGCCTAGCGCGAGT
CCTATGCAACAATCTTCTTATTTGGGGCTTTACAGATGGGATATATGCCTCAATATAATGGATT
TGGCTATCAG
Transcript length: 527
Transcript exons: 41194869-41194951,41196237-41196288,41196370-41196495,41
196608-41196690,41196949-41197131
GGTGCTGCTTCCTCATATGCCCCTCGAGGGAAGAGGCTGACAAGGCAGTGAACGCTTACCACAA
TAAGCACACACTTCCTGGGGCATCAAGTCCTTTACAAGTAAAATATGCTGATGGAGAGTTGGAG
AGACTAGAACACAAGCTTTTTATTGGAATGCTTCCAAAAAATGTAACGGACACCGAATTGACTG
ATTTATTTTCCAAATATGGAAATATCAAGGATTTACAGATTTTAAGGGGTTCACAACAAACAAG
TAAAGCTGGCTGTGCATTCCTTAAATATGAAACAAAGGAGCAAGCAGTGGCAGCTATTGAGGCT
CTAAATGGGAAGCACAAAATAGAGGGCTCTAGTGTGCCGTTGGTTGTCAAATGGGCCGATACAG
AAAAGGAAAGGCAGGCCCGAAAAGCACAAAAGGCTCAATTGCAATCATCTAATATGCCTAGCGC
GAGTCCTATGCAACAATCTTCATTATTTGGGGCTTTACAGATGGGATATATGCCTCAATATAAT
GGATTTGGCTATCAG
						
					

						Genomic sequence
						
							GGTGCTGCTTCCTCATATGCCCCTCGAGGGAAGAGGCTGACAAGGCAGTGAACGCTTACCACAA
TAAGCACACACTTCCTGGGGTACGTGATCGTTGGAATATATTACAATGCTAAAGTTGAATTCAT
GCTGTTTTCCTTAGTTGAATTGTTGCAAGCTGATCCCGTGTTTATGGGGTGAAAATTACATGTG
ATTTTGAAATTCCATAATCTGGTTGCCAAGGAACAGCATTGGAAGCTTGTGCATGTATTTGGCT
GTTTGGTGGGACCAAAATGAAATCTGTAGTGGGAGTGCGGGGCACTGGTGAAATTTGACTTGGG
TAGGGGGTCTAGAATTTGGAATGGTCATGCTAAATATCTGTGGTGGGTGGTCTAAAAATCACTG
GACATGGATTATCCTTATTTTTCAGTCAATAAGTAACATCATTATTCTCCACAGTTCTGCTGCA
AGGCTGCTGATATGCATGTATTAGTTTCAGTACGTTTTGTTTCATGGCTAGCATAGTTAACGAG
TAATCTGATTCAAGGATGTATATTTGGTTGGAAAACAAAAACATTACACTTACCCTCAGGCAGG
GCTAAACTTCGAGCCACACCACTATGAACAAGTAGTGGGTGTGCTTGGTCTTTGACAGCAATAA
AGTTGGATCTATAGGAAATTTAACCTGTCAACAGCTGCATGATGGTCTATCTTACTCTCATAGC
GGCACACCTAACAAAAGTTAGATCACCAATCTGGCCATCACACTTTTGTACCCATCCTGTATGG
AAATGAACTGATTGTAGCTTCAGTTTTGTAGCATACCTAACTGAGGTCCCAACTCCCAACTGAC
CAAACAATATGGACTGAGTGTTATGATTAGGATTTGAATAGAACTTTTGAGATAGGGACAAAAT
CTCAAACTAATTCTGGTGCATACTCTGGTGGACCAAATTCTTTCTTCGGAATGAAAAAGCTTCA
TGATTTCACTAGTTTTGGAAACTTTTAAAAAATTATGTAGGTTGATGTTACTTTCACAGTTCAG
GTGTCTTCACCCAGTTAATCACAGAATAAGACTGGACATCTAATCCCACTCCCAATCAGATGAG
TAATGTTGAGACGTGAAACATGGATGATGATAGAAACAAACTATAAAGTCTTGGAAGTTAGGAC
TTTGTCCTAATGTTGGACAAAAGTTGGAGTGCATATGAGTGTGGTAGTTGGTAATCACTGACTT
TGGGAGCCAGCAAGGCACATTTACGTGACATTTTTTTTCTATAGTGTTAATAGCTACTGTTGTG
ACACCTTGTTCATGAATAGCTGCCAAACATTCCCAGTTGCTTCTTTCTTTTATCTGATGACAAT
CTTCGTTTTCTTTCATCAATTCAGGCATCAAGTCCTTTACAAGTAAAATATGCTGATGGAGAGT
TGGAGAGACTAGGTATGATTGCCCTTTACATAGAACTGTTCTTTTTGCCATTGATTTTATTGCA
CTCATGCTTGTACTTGCTATGATCTCCAGAACACAAGCTTTTTATTGGAATGCTTCCAAAAAAT
GTAACGGACACCGAATTGACTGATTTATTTTCCAAATATGGAAATATCAAGGATTTACAGATTT
TAAGGGGTTCACAACAAACAAGTAAAGGTGAGATCTGGTGAATAACCTATTTTCCTAACCATTT
AGAGCTAGAAGCACTGGTTGACTCTGGAACTTTACAATACCTAATGTTTTTGTTAAATTAACTG
TGTTATTGCAGCTGGCTGTGCATTCCTTAAATATGAAACAAAGGAGCAAGCAGTGGCAGCTATT
GAGGCTCTAAATGGGAAGCACAAAATAGAGGTTTGCCAGAAATTAGTTAGAATAGCAGAAAAAT
TCTTAGTGGTTATTGAAATGTACTGCAATTCACACATGAACATGATCCATAGCTCTACTTAGTC
ATGAGTCTGATACACATAAACAGTCAAAGCTAAAGACACTCTCTGCTATTGCATTTATTTGATA
CCTTGTGTCTGCATTATATTATCCAGTTACATCCCTTCTCAAACCCCACGTTATTTTTCATGAA
TATATTATAATCTCTTCTGATTTATTTGTTAGGGCTCTAGTGTGCCGTTGGTTGTCAAATGGGC
CGATACAGAAAAGGAAAGGCAGGCCCGAAAAGCACAAAAGGCTCAATTGCAATCATCTAATATG
CCTAGCGCGAGTCCTATGCAACAATCTTCATTATTTGGGGCTTTACAGATGGGATATATGCCTC
AATATAATGGATTTGGCTATCAG
						
					

			
		

Sequences
Splice junction sequence	ATCATCTAATATGCCTAGCGCGAGTCCTATGCAACAATCTTCATTATTTGGGGCTTTACAGATG GGATATATGCCTCAATATAATGGATTTGGCTATCAGggtgctgcttcctcatatgcccctcgag ggaagaggctgacaaggcagtgaacgcttaccacaataagcacacacttcctggggtacgtgat cgttggaa
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: 202 Transcript exons: 41194869-41194912,41196973-41197073,41197075-41197131 GGTGCTGCTTCCTCATATGCCCCTCGAGGGAAGAGGCTGACAAGAAATGGGCCGATACAGAAAA GGAAAGGCAGGCCCGAAAAGCACAAAAGGCTCAATTGCAATCATCTAATATGCCTAGCGCGAGT CCTATGCAACAATCTTCTTATTTGGGGCTTTACAGATGGGATATATGCCTCAATATAATGGATT TGGCTATCAG Transcript length: 527 Transcript exons: 41194869-41194951,41196237-41196288,41196370-41196495,41 196608-41196690,41196949-41197131 GGTGCTGCTTCCTCATATGCCCCTCGAGGGAAGAGGCTGACAAGGCAGTGAACGCTTACCACAA TAAGCACACACTTCCTGGGGCATCAAGTCCTTTACAAGTAAAATATGCTGATGGAGAGTTGGAG AGACTAGAACACAAGCTTTTTATTGGAATGCTTCCAAAAAATGTAACGGACACCGAATTGACTG ATTTATTTTCCAAATATGGAAATATCAAGGATTTACAGATTTTAAGGGGTTCACAACAAACAAG TAAAGCTGGCTGTGCATTCCTTAAATATGAAACAAAGGAGCAAGCAGTGGCAGCTATTGAGGCT CTAAATGGGAAGCACAAAATAGAGGGCTCTAGTGTGCCGTTGGTTGTCAAATGGGCCGATACAG AAAAGGAAAGGCAGGCCCGAAAAGCACAAAAGGCTCAATTGCAATCATCTAATATGCCTAGCGC GAGTCCTATGCAACAATCTTCATTATTTGGGGCTTTACAGATGGGATATATGCCTCAATATAAT GGATTTGGCTATCAG
Genomic sequence	GGTGCTGCTTCCTCATATGCCCCTCGAGGGAAGAGGCTGACAAGGCAGTGAACGCTTACCACAA TAAGCACACACTTCCTGGGGTACGTGATCGTTGGAATATATTACAATGCTAAAGTTGAATTCAT GCTGTTTTCCTTAGTTGAATTGTTGCAAGCTGATCCCGTGTTTATGGGGTGAAAATTACATGTG ATTTTGAAATTCCATAATCTGGTTGCCAAGGAACAGCATTGGAAGCTTGTGCATGTATTTGGCT GTTTGGTGGGACCAAAATGAAATCTGTAGTGGGAGTGCGGGGCACTGGTGAAATTTGACTTGGG TAGGGGGTCTAGAATTTGGAATGGTCATGCTAAATATCTGTGGTGGGTGGTCTAAAAATCACTG GACATGGATTATCCTTATTTTTCAGTCAATAAGTAACATCATTATTCTCCACAGTTCTGCTGCA AGGCTGCTGATATGCATGTATTAGTTTCAGTACGTTTTGTTTCATGGCTAGCATAGTTAACGAG TAATCTGATTCAAGGATGTATATTTGGTTGGAAAACAAAAACATTACACTTACCCTCAGGCAGG GCTAAACTTCGAGCCACACCACTATGAACAAGTAGTGGGTGTGCTTGGTCTTTGACAGCAATAA AGTTGGATCTATAGGAAATTTAACCTGTCAACAGCTGCATGATGGTCTATCTTACTCTCATAGC GGCACACCTAACAAAAGTTAGATCACCAATCTGGCCATCACACTTTTGTACCCATCCTGTATGG AAATGAACTGATTGTAGCTTCAGTTTTGTAGCATACCTAACTGAGGTCCCAACTCCCAACTGAC CAAACAATATGGACTGAGTGTTATGATTAGGATTTGAATAGAACTTTTGAGATAGGGACAAAAT CTCAAACTAATTCTGGTGCATACTCTGGTGGACCAAATTCTTTCTTCGGAATGAAAAAGCTTCA TGATTTCACTAGTTTTGGAAACTTTTAAAAAATTATGTAGGTTGATGTTACTTTCACAGTTCAG GTGTCTTCACCCAGTTAATCACAGAATAAGACTGGACATCTAATCCCACTCCCAATCAGATGAG TAATGTTGAGACGTGAAACATGGATGATGATAGAAACAAACTATAAAGTCTTGGAAGTTAGGAC TTTGTCCTAATGTTGGACAAAAGTTGGAGTGCATATGAGTGTGGTAGTTGGTAATCACTGACTT TGGGAGCCAGCAAGGCACATTTACGTGACATTTTTTTTCTATAGTGTTAATAGCTACTGTTGTG ACACCTTGTTCATGAATAGCTGCCAAACATTCCCAGTTGCTTCTTTCTTTTATCTGATGACAAT CTTCGTTTTCTTTCATCAATTCAGGCATCAAGTCCTTTACAAGTAAAATATGCTGATGGAGAGT TGGAGAGACTAGGTATGATTGCCCTTTACATAGAACTGTTCTTTTTGCCATTGATTTTATTGCA CTCATGCTTGTACTTGCTATGATCTCCAGAACACAAGCTTTTTATTGGAATGCTTCCAAAAAAT GTAACGGACACCGAATTGACTGATTTATTTTCCAAATATGGAAATATCAAGGATTTACAGATTT TAAGGGGTTCACAACAAACAAGTAAAGGTGAGATCTGGTGAATAACCTATTTTCCTAACCATTT AGAGCTAGAAGCACTGGTTGACTCTGGAACTTTACAATACCTAATGTTTTTGTTAAATTAACTG TGTTATTGCAGCTGGCTGTGCATTCCTTAAATATGAAACAAAGGAGCAAGCAGTGGCAGCTATT GAGGCTCTAAATGGGAAGCACAAAATAGAGGTTTGCCAGAAATTAGTTAGAATAGCAGAAAAAT TCTTAGTGGTTATTGAAATGTACTGCAATTCACACATGAACATGATCCATAGCTCTACTTAGTC ATGAGTCTGATACACATAAACAGTCAAAGCTAAAGACACTCTCTGCTATTGCATTTATTTGATA CCTTGTGTCTGCATTATATTATCCAGTTACATCCCTTCTCAAACCCCACGTTATTTTTCATGAA TATATTATAATCTCTTCTGATTTATTTGTTAGGGCTCTAGTGTGCCGTTGGTTGTCAAATGGGC CGATACAGAAAAGGAAAGGCAGGCCCGAAAAGCACAAAAGGCTCAATTGCAATCATCTAATATG CCTAGCGCGAGTCCTATGCAACAATCTTCATTATTTGGGGCTTTACAGATGGGATATATGCCTC AATATAATGGATTTGGCTATCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.242055483

Conservation Information
Conserved circRNAs	NA
PMCS	0.242055483

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							41196391-41194916(+)
41194886-41197060(-)
						
						Potential amino acid sequence
						
							MLPKNVTDTELTDLFSKYGNIKDLQILRGSQQTSKAGCAFLKYETKEQAVAAIEALNGKHKIEG
SSVPLVVKWADTEKERQARKAQKAQLQSSNMPSASPMQQSSLFGALQMGYMPQYNGFGYQGAAS
SYAPRGKRLTRQ*(+)
MRKQHPDSQIHYIEAYIPSVKPQIMKIVA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	41196391-41194916(+) 41194886-41197060(-)
Potential amino acid sequence	MLPKNVTDTELTDLFSKYGNIKDLQILRGSQQTSKAGCAFLKYETKEQAVAAIEALNGKHKIEG SSVPLVVKWADTEKERQARKAQKAQLQSSNMPSASPMQQSSLFGALQMGYMPQYNGFGYQGAAS SYAPRGKRLTRQ(+) MRKQHPDSQIHYIEAYIPSVKPQIMKIVA(-)
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 Os01g0938200_circ_g.1

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