Plant Circular RNA Database

Detail information of Os11g0639000_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os11g0639000_circ_g.2
					
						ID in PlantcircBase
						osa_circ_009866
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 25258398-25261515  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os11g0639000						
					
						Parent gene annotation
						
							Similar to Phyb1. (Os11t0639000-00)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os11g0639000_circ_g.3 						
					
						Support reads
						1
					
						Tissues
						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
						Os11t0639000-00:7

General Information
CircRNA Name	Os11g0639000_circ_g.2
ID in PlantcircBase	osa_circ_009866
Alias	NA
Organism	Oryza sativa
Position	chr11: 25258398-25261515 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os11g0639000
Parent gene annotation	Similar to Phyb1. (Os11t0639000-00)
Parent gene strand	+
Alternative splicing	Os11g0639000_circ_g.3
Support reads	1
Tissues	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	Os11t0639000-00:7

			
						 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  
						
							CTGCTATAGATAACTCTCCCCCTTGTTTTCAGGTGAACTTTTCTTATATTGAAGCAGGGGAGCA
GAAACAAGCACTAGTGAAACTGGTAGCTTGCCAGAGgcaataccaatcgcacattcgggggctt
aatgcgtatgatcgacacaagaagttcatgaaggattatggtatgattctttgctggcttcttt
tccacctc

									
								

					

						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
						
							GCAATACCAATCGCACATTCGGGGGCTTAATGCGTATGATCGACACAAGAAGTTCATGAAGGAT
TATGGTATGATTCTTTGCTGGCTTCTTTTCCACCTCTTAAGCATTTCTTGATTGTTTTAAAATT
TTATTGGGAGATCTAGGGCTACTTTCAGTTCAGATTTCATTGGAACAAAATATAATGATAGTGG
AATGGTAATGTCATGATAATATATTACAGTTAATAGCACTGTTTTAGGAAAATGGCACATTTTA
AAGTTTTGCTTCTGCCTTTCTTCACAATAGTCAGACAAATGGTGGTTAGCTTGCACTCCGATAT
TCTGGCACAACTCCCGTTATCCCAGTTCAATTTGATTTTTGATTCCTGATGCCAATGCATGGAA
CGGATGGATCAGAAAGTTGTCCTTTCACAGTGTAAAGGAAATTGAGACGCTGGCATATAACGAG
TTAATTATTTGCTCTGTCTCAGTTTCCAAAAGCAACTGGATGACGAACAGTCCCCTCTACTGTA
GAAAGAATTGGGGGCTACCTTCATCCATACATGGGCTATGCTTATTGATATATAACTTCCCACC
TAGCTTTGGATGAAACTTATTCTGGGTATGCATCTTTTCCATATGGGAGTTGATGGTCTGATAT
GCCATACCAGTGACCCAATCTGTTGAACAATGCTGTCATTGACTAGCAGTTCATCTTCCAACTA
TACTATGAATATTATAGATCAGTTTAAAATCATTATAAAAGTCAAGTGACTTGGATTCTATTGC
TTGTGTTAGTAAAGTACAAGGAAGCTTTTGTTTTAGATATGTAAGTGGAAACTACTATGATAAA
TGAAGAACCAGAATGTAGCCTCACCACAGCATCCTTTATCGTGGATGTATAAATAATTGTGGAT
TGGAGATCATGTTCATGTTTACAAAATTATTGTTTCATTGATTGGCTCTGGCATTTTATTGGTA
TCTCCCTCTTTTCTTGATATTATAAGTTCCCACTGAAAAAACAATGTGCTGTGAACAGTTCAGT
TTTATGGCCATGACAAGAATGTGGATAATCGTGCACCCATCAAGACTGATAAAGATACACTGCG
AGAAGGATATAGGTAAGAAACAAGTCCAATACCCTTTGTTATTTATTTATGGTGGAATGTGTGT
CCATGCTTTATGAAATACTCCTAAATCCTTTTCTTTAATTATTTATCCATATAAAGGTTCATAC
TTTCTGAGGAAGACGATGTGGATTCTACTTGGGAGAAGAGGCTGGTCAAACGTTACTATGACAA
GCTTTTTAAAGAGTATCCTTTTTGGTGGTGTGTTCCTTACATTCTTTTCATTAAGGGTACAGTG
TATATTTCTTCAGAAATTTTCTGTAACATGTTCTGATTTGTGGAGCTGAGGTGATTTGGCAAGT
TCATCCCATTTTATTCTGAGCAATACTGCAAATGTATTGAAGACTGAAGAGCTTGATATAATAG
ACTAATTGGGTATGAACTGTAGATATTATCTCACAAACTCATTAGCGTGTCTGAAAAGATAAGA
GTTGCAGTATAAATTGTAAGATACTATGAGTGAAATTTTCTCATCAAAGAGGTAGACATAACGC
ATATGTATATGGTTATTCTCATAGGCATAACTCGTATTTACTGTTGTCCGCTGCATCAGTATAT
GTCTTTGAGAGAATATTGCAAGTTCGTTCCAAACAAATATAGTGCTTAACGGGTTATTTCCTAA
GAGAAACTATTTACATGATATGCATAAAGTTTCTTGTATTTATGCCTTAAATAGTTGGGCCAAT
ATTATCTGTCAGTCAGTCTCCTATAGAAACAGCATGTTTTGAAGTTCTGTAGTACCTATTTTAG
AAGATGGGAACATGAAGGATGAGAGAGAACCAGGATTGCTATGTTTGATTTGAAGCACTTAAGT
TCTGCTCCTATCTTTATAATCTATCTATATTAACCAAGAGATGTAGTCCTTGCACCTTGAACTT
GTTTTGCTGGCTGTTTTACTGTTCTTGTAATGTTCTTGAAACTTAAATTTATTGTGCCTAGGAT
CCTTAATTTGATACAGATACTGCATTGCTGATATGTCCCAGTACAAAAGAGGCAAGGTATGGTG
ATACAATTCTATAGCAATAAGCCAATAGTTGTTACAGTATTTATTTGTGTCATTTACTGGATAC
AATGATCTCTTGAATGATATTCTTGCTGTTTTTTCTCCTCATTGCTATTAATGCAATAGAAAAG
ACGAAAAATGCTCCTAGTATGATTTATATCTGTAACATTGAGGATTTCAATTAAAAGAAAGAAA
AGAATAATACGAATTGTTGATTTCGTATCCGTAATATTAAGTTTGCGTGAGCAGCATCGACAAA
GTGATCATTCTTGTTTTTGGTCATGGAGTTGCATTATAGTATCAATTATTGTTGCACAGAGCAG
CAAAATCACTAGCACAACCATACTTTTATATATGTTAATGTCTGACAGGCACACACTTGATAGT
GGGGACGCTAAGAAATCCTATTTACTTGGTTCGTTACTGAATAATATCTAAGTATCCTTTAGAA
TTTAGAACAGCACTAACAAGGATATGCTGCTCATAGATATTAGAGGTTTTTTTTAATTGATAAA
ACCATCGGTTTTATTCTTGGAAGTTGAGTGCACATTCTAAGGATCTCATTTATTTCAGATTGGA
TTGAGATGGAGAACTGAAAAGGAGGTGATATCTGGAAAAGGTATTTCCCTTTATAATTCCATGT
GTTTTCAGGTGCACTAAACTGTCGCAAAATGCTAAATGTAGTCTATACATTTTTTTTTTCAAAT
GTGTGCTCTGTTTTACTAATTTTCTTATTGGTAGATGTGATATTCATTACATGTTGTCTTTTGC
AGGGCAGTTTCTCTGTGGCAACAGGATTTGTGATGAGAAAAATGGACTTGGTAGTTATGAGGTA
TGCTCTTGGTCCTTTCTATCTTGTCACTGATGCTACAATGCATAGATCCTTTTGTTCATTAAAG
AACTCCTTTTCTGCTATAGATAACTCTCCCCCTTGTTTTCAGGTGAACTTTTCTTATATTGAAG
CAGGGGAGCAGAAACAAGCACTAGTGAAACTGGTAGCTTGCCAGAG
						
					

			
		

Sequences
Splice junction sequence	CTGCTATAGATAACTCTCCCCCTTGTTTTCAGGTGAACTTTTCTTATATTGAAGCAGGGGAGCA GAAACAAGCACTAGTGAAACTGGTAGCTTGCCAGAGgcaataccaatcgcacattcgggggctt aatgcgtatgatcgacacaagaagttcatgaaggattatggtatgattctttgctggcttcttt tccacctc
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	GCAATACCAATCGCACATTCGGGGGCTTAATGCGTATGATCGACACAAGAAGTTCATGAAGGAT TATGGTATGATTCTTTGCTGGCTTCTTTTCCACCTCTTAAGCATTTCTTGATTGTTTTAAAATT TTATTGGGAGATCTAGGGCTACTTTCAGTTCAGATTTCATTGGAACAAAATATAATGATAGTGG AATGGTAATGTCATGATAATATATTACAGTTAATAGCACTGTTTTAGGAAAATGGCACATTTTA AAGTTTTGCTTCTGCCTTTCTTCACAATAGTCAGACAAATGGTGGTTAGCTTGCACTCCGATAT TCTGGCACAACTCCCGTTATCCCAGTTCAATTTGATTTTTGATTCCTGATGCCAATGCATGGAA CGGATGGATCAGAAAGTTGTCCTTTCACAGTGTAAAGGAAATTGAGACGCTGGCATATAACGAG TTAATTATTTGCTCTGTCTCAGTTTCCAAAAGCAACTGGATGACGAACAGTCCCCTCTACTGTA GAAAGAATTGGGGGCTACCTTCATCCATACATGGGCTATGCTTATTGATATATAACTTCCCACC TAGCTTTGGATGAAACTTATTCTGGGTATGCATCTTTTCCATATGGGAGTTGATGGTCTGATAT GCCATACCAGTGACCCAATCTGTTGAACAATGCTGTCATTGACTAGCAGTTCATCTTCCAACTA TACTATGAATATTATAGATCAGTTTAAAATCATTATAAAAGTCAAGTGACTTGGATTCTATTGC TTGTGTTAGTAAAGTACAAGGAAGCTTTTGTTTTAGATATGTAAGTGGAAACTACTATGATAAA TGAAGAACCAGAATGTAGCCTCACCACAGCATCCTTTATCGTGGATGTATAAATAATTGTGGAT TGGAGATCATGTTCATGTTTACAAAATTATTGTTTCATTGATTGGCTCTGGCATTTTATTGGTA TCTCCCTCTTTTCTTGATATTATAAGTTCCCACTGAAAAAACAATGTGCTGTGAACAGTTCAGT TTTATGGCCATGACAAGAATGTGGATAATCGTGCACCCATCAAGACTGATAAAGATACACTGCG AGAAGGATATAGGTAAGAAACAAGTCCAATACCCTTTGTTATTTATTTATGGTGGAATGTGTGT CCATGCTTTATGAAATACTCCTAAATCCTTTTCTTTAATTATTTATCCATATAAAGGTTCATAC TTTCTGAGGAAGACGATGTGGATTCTACTTGGGAGAAGAGGCTGGTCAAACGTTACTATGACAA GCTTTTTAAAGAGTATCCTTTTTGGTGGTGTGTTCCTTACATTCTTTTCATTAAGGGTACAGTG TATATTTCTTCAGAAATTTTCTGTAACATGTTCTGATTTGTGGAGCTGAGGTGATTTGGCAAGT TCATCCCATTTTATTCTGAGCAATACTGCAAATGTATTGAAGACTGAAGAGCTTGATATAATAG ACTAATTGGGTATGAACTGTAGATATTATCTCACAAACTCATTAGCGTGTCTGAAAAGATAAGA GTTGCAGTATAAATTGTAAGATACTATGAGTGAAATTTTCTCATCAAAGAGGTAGACATAACGC ATATGTATATGGTTATTCTCATAGGCATAACTCGTATTTACTGTTGTCCGCTGCATCAGTATAT GTCTTTGAGAGAATATTGCAAGTTCGTTCCAAACAAATATAGTGCTTAACGGGTTATTTCCTAA GAGAAACTATTTACATGATATGCATAAAGTTTCTTGTATTTATGCCTTAAATAGTTGGGCCAAT ATTATCTGTCAGTCAGTCTCCTATAGAAACAGCATGTTTTGAAGTTCTGTAGTACCTATTTTAG AAGATGGGAACATGAAGGATGAGAGAGAACCAGGATTGCTATGTTTGATTTGAAGCACTTAAGT TCTGCTCCTATCTTTATAATCTATCTATATTAACCAAGAGATGTAGTCCTTGCACCTTGAACTT GTTTTGCTGGCTGTTTTACTGTTCTTGTAATGTTCTTGAAACTTAAATTTATTGTGCCTAGGAT CCTTAATTTGATACAGATACTGCATTGCTGATATGTCCCAGTACAAAAGAGGCAAGGTATGGTG ATACAATTCTATAGCAATAAGCCAATAGTTGTTACAGTATTTATTTGTGTCATTTACTGGATAC AATGATCTCTTGAATGATATTCTTGCTGTTTTTTCTCCTCATTGCTATTAATGCAATAGAAAAG ACGAAAAATGCTCCTAGTATGATTTATATCTGTAACATTGAGGATTTCAATTAAAAGAAAGAAA AGAATAATACGAATTGTTGATTTCGTATCCGTAATATTAAGTTTGCGTGAGCAGCATCGACAAA GTGATCATTCTTGTTTTTGGTCATGGAGTTGCATTATAGTATCAATTATTGTTGCACAGAGCAG CAAAATCACTAGCACAACCATACTTTTATATATGTTAATGTCTGACAGGCACACACTTGATAGT GGGGACGCTAAGAAATCCTATTTACTTGGTTCGTTACTGAATAATATCTAAGTATCCTTTAGAA TTTAGAACAGCACTAACAAGGATATGCTGCTCATAGATATTAGAGGTTTTTTTTAATTGATAAA ACCATCGGTTTTATTCTTGGAAGTTGAGTGCACATTCTAAGGATCTCATTTATTTCAGATTGGA TTGAGATGGAGAACTGAAAAGGAGGTGATATCTGGAAAAGGTATTTCCCTTTATAATTCCATGT GTTTTCAGGTGCACTAAACTGTCGCAAAATGCTAAATGTAGTCTATACATTTTTTTTTTCAAAT GTGTGCTCTGTTTTACTAATTTTCTTATTGGTAGATGTGATATTCATTACATGTTGTCTTTTGC AGGGCAGTTTCTCTGTGGCAACAGGATTTGTGATGAGAAAAATGGACTTGGTAGTTATGAGGTA TGCTCTTGGTCCTTTCTATCTTGTCACTGATGCTACAATGCATAGATCCTTTTGTTCATTAAAG AACTCCTTTTCTGCTATAGATAACTCTCCCCCTTGTTTTCAGGTGAACTTTTCTTATATTGAAG CAGGGGAGCAGAAACAAGCACTAGTGAAACTGGTAGCTTGCCAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.110119366

Conservation Information
Conserved circRNAs	NA
PMCS	0.110119366

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25258454-25261512(+)
25258456-25261461(-)
25259434-25261492(-)
						
						Potential amino acid sequence
						
							MKDYVQFYGHDKNVDNRAPIKTDKDTLREGYRFILSEEDDVDSTWEKRLVKRYYDKLFKEYCIA
DMSQYKRGKIGLRWRTEKEVISGKGQFLCGNRICDEKNGLGSYEVNFSYIEAGEQKQALVKLVA
CQRQYQSHIRGLNAYDRHKKFMKDYVQFYGHDKNVDNRAPIKTDKDTLREGYRFILSEEDDVDS
TWEKRLVKRYYDKLFKEYCIADMSQYKRGKIGLRWRTEKEVISGKGQFLCGNRICDEKNGLGSY
EVNFSYIEAGEQKQALVKLVACQRQYQSHIRGLNAYDRHKKFMKDYVQFYGHDKNVDNRAPIKT
DKDTLREGYRFILSEEDDVDSTWEKRLVKRYYDKLFKEYCIADMSQYKRGKIGLRWRTEKEVIS
GKGQFLCGNRICDEKNGLGSYEVNFSYIEAGEQKQALVKLVACQRQYQSHIRGLNAYDRHKKFM
KDYVQFYGHDKNVDNRAPIKTDKDTLREGYRFILSEEDDVDSTWEKRLVKRYYDKLFKEYCIAD
MSQYKRGKIGLRWRTEKEVISGKGQFLCGNRICDEKNGLGSYEVNFSYIEAGEQKQALVKLVAC
Q(+)
MNFLCRSYALSPRMCDWYCLWQATSFTSACFCSPASI*(-)
MAIKLNIILHELLVSIIRIKPPNVRLVLPLASYQFH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25258454-25261512(+) 25258456-25261461(-) 25259434-25261492(-)
Potential amino acid sequence	MKDYVQFYGHDKNVDNRAPIKTDKDTLREGYRFILSEEDDVDSTWEKRLVKRYYDKLFKEYCIA DMSQYKRGKIGLRWRTEKEVISGKGQFLCGNRICDEKNGLGSYEVNFSYIEAGEQKQALVKLVA CQRQYQSHIRGLNAYDRHKKFMKDYVQFYGHDKNVDNRAPIKTDKDTLREGYRFILSEEDDVDS TWEKRLVKRYYDKLFKEYCIADMSQYKRGKIGLRWRTEKEVISGKGQFLCGNRICDEKNGLGSY EVNFSYIEAGEQKQALVKLVACQRQYQSHIRGLNAYDRHKKFMKDYVQFYGHDKNVDNRAPIKT DKDTLREGYRFILSEEDDVDSTWEKRLVKRYYDKLFKEYCIADMSQYKRGKIGLRWRTEKEVIS GKGQFLCGNRICDEKNGLGSYEVNFSYIEAGEQKQALVKLVACQRQYQSHIRGLNAYDRHKKFM KDYVQFYGHDKNVDNRAPIKTDKDTLREGYRFILSEEDDVDSTWEKRLVKRYYDKLFKEYCIAD MSQYKRGKIGLRWRTEKEVISGKGQFLCGNRICDEKNGLGSYEVNFSYIEAGEQKQALVKLVAC Q(+) MNFLCRSYALSPRMCDWYCLWQATSFTSACFCSPASI(-) MAIKLNIILHELLVSIIRIKPPNVRLVLPLASYQFH(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os11g0639000_circ_g.2

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