Plant Circular RNA Database

Detail information of Os01g0607400_circ_g.20

			
						 General Information
					
						CircRNA Name
						Os01g0607400_circ_g.20
					
						ID in PlantcircBase
						osa_circ_002544
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 23944937-23946137  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							Os01g0607400						
					
						Parent gene annotation
						
							Similar to STYLOSA protein. (Os01t0607400-01);Similar to STYLOSA
 protein. (Os01t0607400-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0607400_circ_g.11 Os01g0607400_circ_g.12 Os01g0607400_circ_g.13 Os01g0607400_circ_g.14 Os01g0607400_circ_g.15 Os01g0607400_circ_g.16 Os01g0607400_circ_g.17 Os01g0607400_circ_g.18 Os01g0607400_circ_g.19 Os01g0607400_circ_g.21 Os01g0607400_circ_ag.1 						
					
						Support reads
						121
					
						Tissues
						seed
					
						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
						Os01t0607400-01:3

General Information
CircRNA Name	Os01g0607400_circ_g.20
ID in PlantcircBase	osa_circ_002544
Alias	NA
Organism	Oryza sativa
Position	chr1: 23944937-23946137 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	Os01g0607400
Parent gene annotation	Similar to STYLOSA protein. (Os01t0607400-01);Similar to STYLOSA protein. (Os01t0607400-02)
Parent gene strand	-
Alternative splicing	Os01g0607400_circ_g.11 Os01g0607400_circ_g.12 Os01g0607400_circ_g.13 Os01g0607400_circ_g.14 Os01g0607400_circ_g.15 Os01g0607400_circ_g.16 Os01g0607400_circ_g.17 Os01g0607400_circ_g.18 Os01g0607400_circ_g.19 Os01g0607400_circ_g.21 Os01g0607400_circ_ag.1
Support reads	121
Tissues	seed
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	Os01t0607400-01:3

			
						 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  
						
							ACATTTGTTGCATTTGTATATGCTGTGGTTGCTGTTGTCGCTGTTGAGGAGGTTGCTGCTGCTG
CTGCTGTTGTTGCTCCCTGGCTTTCATGTGCTGAGTctgagctggcccaggaatctgtggactc
ctggactgaacttgttgcagactgcctgacagaccaccaacagtaccatgcaaaatttgcctac
aaaggaaa

						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
						
							CTGAGCTGGCCCAGGAATCTGTGGACTCCTGGACTGAACTTGTTGCAGACTGCCTGACAGACCA
CCAACAGTACCATGCAAAATTTGCCTACAAAGGAAAGAAGTAAACTATCTGAGAAAAGTTACCT
CTTGCAGCGCATGTATATTATGGTCAATATAAAACATGGTGATGTTCAATAGGCATCTACATTC
CATTAAATAAGCAATAAAATATGGGAATGAGATGACACTTCAGTATATTTTGTTTTGGACACAT
CATTTTTCAAAACATAACTAAATGATTTATATCTACACAAGTAATTAAGAACCAAAATTAAGAG
CCAAAACAATGCATGCATGTAAAAAAAACAGCAAAATGCAGAAGCAGCAATTCCAAGCATAAAT
AAGAATAACAAATAGAAGTGTGTCTAATTTATCTCCATAACTAACCAAATGACTAAAAAGAAAA
GTTCAAAATAAAATAATATTTTTCGACCAACAGATAGACAACTCTGTGAATTTCGATACCAGAA
GTACTAAGTGTAGTGTGGATTAGATTACAGTGAAGCTGTAACACGAATGGTGAAATATCAGCTA
CAACTGTACACGGTATAAAGCTTGTTAAAGTAATTATATACTTAATTCACAAATTCAGCAGGTA
CCCTGAAGATTGTCCACTTGCAGATGCTTTCAACAACGCTTCGTTTGAATCAAGTAGTTGTCCA
GCATTCTCTCCATATCTTTGCTGAAACCAAAGTTCACGTGTTATGATAATATTAACCACAAAAT
GAACATATTGGTGAGGTGAGGAATCTATAGAAACAACATCAATCAATGATTATAGATAACAGTC
AACCTTAATTGACACCTCGTCCAAACCATCTCTCTGGGAAGGCAACTTTAACCTCTCCTCATAC
ATTTTTGTTGCCATAACATTTGCAGTACTCTGGTTTTGCCGCATTAAAGGATTGTTTCCAGGAA
GTCCACTTGCAGTACCATTAAGAAGATGAGTACCATCTCTGCGCTGTTGTTGTTGCTGCTGCTG
CTGCTGTTGCTGCTGTTGCTGCTGCTGCTGTTGCTGCTGCTGTTGTTGCTGCTGCTGCTGTGCT
GCTCTTTGTAGCAACATTTGTTGCATTTGTATATGCTGTGGTTGCTGTTGTCGCTGTTGAGGAG
GTTGCTGCTGCTGCTGCTGTTGTTGCTCCCTGGCTTTCATGTGCTGAGT

Sequences
Splice junction sequence	ACATTTGTTGCATTTGTATATGCTGTGGTTGCTGTTGTCGCTGTTGAGGAGGTTGCTGCTGCTG CTGCTGTTGTTGCTCCCTGGCTTTCATGTGCTGAGTctgagctggcccaggaatctgtggactc ctggactgaacttgttgcagactgcctgacagaccaccaacagtaccatgcaaaatttgcctac aaaggaaa
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	CTGAGCTGGCCCAGGAATCTGTGGACTCCTGGACTGAACTTGTTGCAGACTGCCTGACAGACCA CCAACAGTACCATGCAAAATTTGCCTACAAAGGAAAGAAGTAAACTATCTGAGAAAAGTTACCT CTTGCAGCGCATGTATATTATGGTCAATATAAAACATGGTGATGTTCAATAGGCATCTACATTC CATTAAATAAGCAATAAAATATGGGAATGAGATGACACTTCAGTATATTTTGTTTTGGACACAT CATTTTTCAAAACATAACTAAATGATTTATATCTACACAAGTAATTAAGAACCAAAATTAAGAG CCAAAACAATGCATGCATGTAAAAAAAACAGCAAAATGCAGAAGCAGCAATTCCAAGCATAAAT AAGAATAACAAATAGAAGTGTGTCTAATTTATCTCCATAACTAACCAAATGACTAAAAAGAAAA GTTCAAAATAAAATAATATTTTTCGACCAACAGATAGACAACTCTGTGAATTTCGATACCAGAA GTACTAAGTGTAGTGTGGATTAGATTACAGTGAAGCTGTAACACGAATGGTGAAATATCAGCTA CAACTGTACACGGTATAAAGCTTGTTAAAGTAATTATATACTTAATTCACAAATTCAGCAGGTA CCCTGAAGATTGTCCACTTGCAGATGCTTTCAACAACGCTTCGTTTGAATCAAGTAGTTGTCCA GCATTCTCTCCATATCTTTGCTGAAACCAAAGTTCACGTGTTATGATAATATTAACCACAAAAT GAACATATTGGTGAGGTGAGGAATCTATAGAAACAACATCAATCAATGATTATAGATAACAGTC AACCTTAATTGACACCTCGTCCAAACCATCTCTCTGGGAAGGCAACTTTAACCTCTCCTCATAC ATTTTTGTTGCCATAACATTTGCAGTACTCTGGTTTTGCCGCATTAAAGGATTGTTTCCAGGAA GTCCACTTGCAGTACCATTAAGAAGATGAGTACCATCTCTGCGCTGTTGTTGTTGCTGCTGCTG CTGCTGTTGCTGCTGTTGCTGCTGCTGCTGTTGCTGCTGCTGTTGTTGCTGCTGCTGCTGTGCT GCTCTTTGTAGCAACATTTGTTGCATTTGTATATGCTGTGGTTGCTGTTGTCGCTGTTGAGGAG GTTGCTGCTGCTGCTGCTGTTGTTGCTCCCTGGCTTTCATGTGCTGAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.194250874

Conservation Information
Conserved circRNAs	NA
PMCS	0.194250874

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23946058-23944990(+)
23946130-23944939(-)
23945015-23946127(-)
						
						Potential amino acid sequence
						
							MLWLLLSLLRRLLLLLLLLLPGFHVLSLSWPRNLWTPGLNLLQTA*(+)
MKAREQQQQQQQQPPQQRQQQPQHIQMQQMLLQRAAQQQQQQQQQQQQQQQQQQQQQQQQQQQR
RDGTHLLNGTASGLPGNNPLMRQNQSTANVMATKMYEERLKLPSQRDGLDEVSIKQRYGENAGQ
LLDSNEALLKASASGQSSGQILHGTVGGLSGSLQQVQSRSPQIPGPAQTQHMKAREQQQQQQQQ
PPQQRQQQPQHIQMQQMLLQRAAQQQQQQQQQQQQQQQQQQQQQQQQQQQRRDGTHLLNGTASG
LPGNNPLMRQNQSTANVMATKMYEERLKLPSQRDGLDEVSIKQRYGENAGQLLDSNEALLKASA
SGQSSGQILHGTVGGLSGSLQQVQSRSPQIPGPAQTQHMKAREQQQQQQQQPPQQRQQQPQHIQ
MQQMLLQRAAQQQQQQQQQQQQQQQQQQQQQQQQQQQRRDGTHLLNGTASGLPGNNPLMRQNQS
TANVMATKMYEERLKLPSQRDGLDEVSIKQRYGENAGQLLDSNEALLKASASGQSSGQILHGTV
GGLSGSLQQVQSRSPQIPGPAQTQHMKAREQQQQQQQQPPQQRQQQPQHIQMQQMLLQRAAQQQ
QQQQQQQQQQQQQQQQQQQQQQQQRRDGTHLLNGTASGLPGNNPLMRQNQSTANVMATKMYEER
LKLPSQRDGLDEVSIKQRYGENAGQLLDSNEALLKASASGQSSGQILHGTVGGLSGSLQQVQSR
SPQIPGPAQ(-)
MVLLVVCQAVCNKFSPGVHRFLGQLRLST*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23946058-23944990(+) 23946130-23944939(-) 23945015-23946127(-)
Potential amino acid sequence	MLWLLLSLLRRLLLLLLLLLPGFHVLSLSWPRNLWTPGLNLLQTA(+) MKAREQQQQQQQQPPQQRQQQPQHIQMQQMLLQRAAQQQQQQQQQQQQQQQQQQQQQQQQQQQR RDGTHLLNGTASGLPGNNPLMRQNQSTANVMATKMYEERLKLPSQRDGLDEVSIKQRYGENAGQ LLDSNEALLKASASGQSSGQILHGTVGGLSGSLQQVQSRSPQIPGPAQTQHMKAREQQQQQQQQ PPQQRQQQPQHIQMQQMLLQRAAQQQQQQQQQQQQQQQQQQQQQQQQQQQRRDGTHLLNGTASG LPGNNPLMRQNQSTANVMATKMYEERLKLPSQRDGLDEVSIKQRYGENAGQLLDSNEALLKASA SGQSSGQILHGTVGGLSGSLQQVQSRSPQIPGPAQTQHMKAREQQQQQQQQPPQQRQQQPQHIQ MQQMLLQRAAQQQQQQQQQQQQQQQQQQQQQQQQQQQRRDGTHLLNGTASGLPGNNPLMRQNQS TANVMATKMYEERLKLPSQRDGLDEVSIKQRYGENAGQLLDSNEALLKASASGQSSGQILHGTV GGLSGSLQQVQSRSPQIPGPAQTQHMKAREQQQQQQQQPPQQRQQQPQHIQMQQMLLQRAAQQQ QQQQQQQQQQQQQQQQQQQQQQQQRRDGTHLLNGTASGLPGNNPLMRQNQSTANVMATKMYEER LKLPSQRDGLDEVSIKQRYGENAGQLLDSNEALLKASASGQSSGQILHGTVGGLSGSLQQVQSR SPQIPGPAQ(-) MVLLVVCQAVCNKFSPGVHRFLGQLRLST(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0607400_circ_g.20

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