Plant Circular RNA Database

Detail information of Os01g0631100_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os01g0631100_circ_g.1
					
						ID in PlantcircBase
						osa_circ_002800
					
						Alias
						Os_ciR2142
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 25228174-25228805  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os01g0631100						
					
						Parent gene annotation
						
							Cas1p-like family protein. (Os01t0631100-01);Similar to predicte
d protein. (Os01t0631100-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0631100_circ_g.2 Os01g0631100_circ_g.3 Os01g0631100_circ_g.4 						
					
						Support reads
						6/1
					
						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
						Os01t0631100-02:4
Os01t0631100-01:4

General Information
CircRNA Name	Os01g0631100_circ_g.1
ID in PlantcircBase	osa_circ_002800
Alias	Os_ciR2142
Organism	Oryza sativa
Position	chr1: 25228174-25228805 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os01g0631100
Parent gene annotation	Cas1p-like family protein. (Os01t0631100-01);Similar to predicte d protein. (Os01t0631100-02)
Parent gene strand	+
Alternative splicing	Os01g0631100_circ_g.2 Os01g0631100_circ_g.3 Os01g0631100_circ_g.4
Support reads	6/1
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	Os01t0631100-02:4 Os01t0631100-01:4

			
						 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  
						
							ATATTTACAAGCGCTATCTTTCTACAGGGCAGAATTTGGCATCGTTCTGGTTTATTTCTACATT
TGTGATCGGACAAACATATTTCCAGAAAGCAAGAAGgtgtcatttttgcttggtctattccctg
ttctcattgcatggatctattcagaagtcctggagtacagaaaatcttcgtctatgaaagtgta
agttagct

						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: 348
Transcript exons: 25228174-25228262,25228385-25228513,25228599-25228655,25
228733-25228805
GTGTCATTTTTGCTTGGTCTATTCCCTGTTCTCATTGCATGGATCTATTCAGAAGTCCTGGAGT
ACAGAAAATCTTCGTCTATGAAAGTTCACTCCGATTCCAATTTGGAGAATGGAACTGTCAAAGA
AGATGATAAAACGGTATTGCTGGAAGGAGGCCTGTCAAAGTCACCATCTACAAAGTTTCGGATC
AATTCTACAAAAGCAAACCTCATAAGGTTTATAACAATGGATGAATCTTTCCTTCTGGAAAATC
GTGCTGTACTGAGAGCAATGGCAGAATTTGGCATCGTTCTGGTTTATTTCTACATTTGTGATCG
GACAAACATATTTCCAGAAAGCAAGAAG
						
						Genomic sequence
						
							GTGTCATTTTTGCTTGGTCTATTCCCTGTTCTCATTGCATGGATCTATTCAGAAGTCCTGGAGT
ACAGAAAATCTTCGTCTATGAAAGTGTAAGTTAGCTATATTGGTCAGTATTAACTCAGTAGTAC
AGCGATGTTTTTACGAATTTTCTAAGCCTTTGAGTAACAAATACTTACCCTGGCTCTATCTGTG
CATTTTTTTGTTTCTATAGTCACTCCGATTCCAATTTGGAGAATGGAACTGTCAAAGAAGATGA
TAAAACGGTATTGCTGGAAGGAGGCCTGTCAAAGTCACCATCTACAAAGTTTCGGATCAATTCT
ACAAAAGCAAACCTCATAAGGTGATTTGGCATAATAGTAGATGTTTGATTCATGATTACAAACG
TGGAATGCTGAGAATTAACATCTCAATGTCGTGAGCTGTAGGTTTATAACAATGGATGAATCTT
TCCTTCTGGAAAATCGTGCTGTACTGAGAGCAATGTAAGACCCTATAGAACTATTTTGCATTTA
CTGAAAATAAATATCCATCGATATTTACAAGCGCTATCTTTCTACAGGGCAGAATTTGGCATCG
TTCTGGTTTATTTCTACATTTGTGATCGGACAAACATATTTCCAGAAAGCAAGAAG

Sequences
Splice junction sequence	ATATTTACAAGCGCTATCTTTCTACAGGGCAGAATTTGGCATCGTTCTGGTTTATTTCTACATT TGTGATCGGACAAACATATTTCCAGAAAGCAAGAAGgtgtcatttttgcttggtctattccctg ttctcattgcatggatctattcagaagtcctggagtacagaaaatcttcgtctatgaaagtgta agttagct
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: 348 Transcript exons: 25228174-25228262,25228385-25228513,25228599-25228655,25 228733-25228805 GTGTCATTTTTGCTTGGTCTATTCCCTGTTCTCATTGCATGGATCTATTCAGAAGTCCTGGAGT ACAGAAAATCTTCGTCTATGAAAGTTCACTCCGATTCCAATTTGGAGAATGGAACTGTCAAAGA AGATGATAAAACGGTATTGCTGGAAGGAGGCCTGTCAAAGTCACCATCTACAAAGTTTCGGATC AATTCTACAAAAGCAAACCTCATAAGGTTTATAACAATGGATGAATCTTTCCTTCTGGAAAATC GTGCTGTACTGAGAGCAATGGCAGAATTTGGCATCGTTCTGGTTTATTTCTACATTTGTGATCG GACAAACATATTTCCAGAAAGCAAGAAG
Genomic sequence	GTGTCATTTTTGCTTGGTCTATTCCCTGTTCTCATTGCATGGATCTATTCAGAAGTCCTGGAGT ACAGAAAATCTTCGTCTATGAAAGTGTAAGTTAGCTATATTGGTCAGTATTAACTCAGTAGTAC AGCGATGTTTTTACGAATTTTCTAAGCCTTTGAGTAACAAATACTTACCCTGGCTCTATCTGTG CATTTTTTTGTTTCTATAGTCACTCCGATTCCAATTTGGAGAATGGAACTGTCAAAGAAGATGA TAAAACGGTATTGCTGGAAGGAGGCCTGTCAAAGTCACCATCTACAAAGTTTCGGATCAATTCT ACAAAAGCAAACCTCATAAGGTGATTTGGCATAATAGTAGATGTTTGATTCATGATTACAAACG TGGAATGCTGAGAATTAACATCTCAATGTCGTGAGCTGTAGGTTTATAACAATGGATGAATCTT TCCTTCTGGAAAATCGTGCTGTACTGAGAGCAATGTAAGACCCTATAGAACTATTTTGCATTTA CTGAAAATAAATATCCATCGATATTTACAAGCGCTATCTTTCTACAGGGCAGAATTTGGCATCG TTCTGGTTTATTTCTACATTTGTGATCGGACAAACATATTTCCAGAAAGCAAGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010385 						
					
						PMCS
						0.235584744

Conservation Information
Conserved circRNAs	osi_circ_010385
PMCS	0.235584744

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25228256-25228802(+)
25228210-25228765(-)
25228182-25228603(-)
						
						Potential amino acid sequence
						
							MKVHSDSNLENGTVKEDDKTVLLEGGLSKSPSTKFRINSTKANLIRFITMDESFLLENRAVLRA
MAEFGIVLVYFYICDRTNIFPESKKVSFLLGLFPVLIAWIYSEVLEYRKSSSMKVHSDSNLENG
TVKEDDKTVLLEGGLSKSPSTKFRINSTKANLIRFITMDESFLLENRAVLRAMAEFGIVLVYFY
ICDRTNIFPESKKVSFLLGLFPVLIAWIYSEVLEYRKSSSMKVHSDSNLENGTVKEDDKTVLLE
GGLSKSPSTKFRINSTKANLIRFITMDESFLLENRAVLRAMAEFGIVLVYFYICDRTNIFPESK
KVSFLLGLFPVLIAWIYSEVLEYRKSSSMKVHSDSNLENGTVKEDDKTVLLEGGLSKSPSTKFR
INSTKANLIRFITMDESFLLENRAVLRAMAEFGIVLVYFYICDRTNIFPESKK(+)
MRTGNRPSKNDTFLLSGNMFVRSQM*(-)
MTPSCFLEICLSDHKCRNKPERCQILPLLSVQHDFPEGKIHPLL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25228256-25228802(+) 25228210-25228765(-) 25228182-25228603(-)
Potential amino acid sequence	MKVHSDSNLENGTVKEDDKTVLLEGGLSKSPSTKFRINSTKANLIRFITMDESFLLENRAVLRA MAEFGIVLVYFYICDRTNIFPESKKVSFLLGLFPVLIAWIYSEVLEYRKSSSMKVHSDSNLENG TVKEDDKTVLLEGGLSKSPSTKFRINSTKANLIRFITMDESFLLENRAVLRAMAEFGIVLVYFY ICDRTNIFPESKKVSFLLGLFPVLIAWIYSEVLEYRKSSSMKVHSDSNLENGTVKEDDKTVLLE GGLSKSPSTKFRINSTKANLIRFITMDESFLLENRAVLRAMAEFGIVLVYFYICDRTNIFPESK KVSFLLGLFPVLIAWIYSEVLEYRKSSSMKVHSDSNLENGTVKEDDKTVLLEGGLSKSPSTKFR INSTKANLIRFITMDESFLLENRAVLRAMAEFGIVLVYFYICDRTNIFPESKK(+) MRTGNRPSKNDTFLLSGNMFVRSQM(-) MTPSCFLEICLSDHKCRNKPERCQILPLLSVQHDFPEGKIHPLL(-)
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 Os01g0631100_circ_g.1

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