Plant Circular RNA Database

Detail information of Os03g0711800_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os03g0711800_circ_g.4
					
						ID in PlantcircBase
						osa_circ_021247
					
						Alias
						Os_ciR1710
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 28757484-28758040  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os03g0711800						
					
						Parent gene annotation
						
							Similar to IRE homolog 1 (Fragment). (Os03t0711800-01);Similar t
o predicted protein. (Os03t0711800-02);Similar to predicted prot
ein. (Os03t0711800-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0711800_circ_g.3 						
					
						Support reads
						12/3
					
						Tissues
						root/shoot, 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  
						
							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
						Os03t0711800-01:2
Os03t0711800-02:2
Os03t0711800-03:2

General Information
CircRNA Name	Os03g0711800_circ_g.4
ID in PlantcircBase	osa_circ_021247
Alias	Os_ciR1710
Organism	Oryza sativa
Position	chr3: 28757484-28758040 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os03g0711800
Parent gene annotation	Similar to IRE homolog 1 (Fragment). (Os03t0711800-01);Similar t o predicted protein. (Os03t0711800-02);Similar to predicted prot ein. (Os03t0711800-03)
Parent gene strand	-
Alternative splicing	Os03g0711800_circ_g.3
Support reads	12/3
Tissues	root/shoot, 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	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	Os03t0711800-01:2 Os03t0711800-02:2 Os03t0711800-03:2

			
						 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  
						
							CTTGCAGATCTTCTATGCAGGTAACCAATAGGGAGAGTGCCCTTTCTTCATCTAGAGGAGTAGT
TGCAATGCACCGCGCAATATCAGCAAGTTCAACAATctttatagcaaagaggtctcctgtagtt
cttttcttggccaagaaaacacgtccaaatgctccacggctgataggtttaatgatttcgaagt
catcaatc

						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: 123
Transcript exons: 28757484-28757544,28757979-28758040
CTTTATAGCAAAGAGGTCTCCTGTAGTTCTTTTCTTGGCCAAGAAAACACGTCCAAATGCTGCC
CTTTCTTCATCTAGAGGAGTAGTTGCAATGCACCGCGCAATATCAGCAAGTTCAACAAT
Transcript length: 408
Transcript exons: 28757484-28757718,28757868-28758040
CTTTATAGCAAAGAGGTCTCCTGTAGTTCTTTTCTTGGCCAAGAAAACACGTCCAAATGCTCCA
CGGCTGATAGGTTTAATGATTTCGAAGTCATCAATCGAAGTACGATCCTTGACTGGGTGAACAG
GACTAGCTCGTAAGCTACGGACAACATCATCTTCTTCATCCATTACAGTACTCGCTGAATCAAC
TTTGTCCATATCAACCGAATCACAAAGCAGTAGGTACTTCTCCCGGTGGAGTTTTTCTATACGT
GTGCCAAATGTCTGCACCGTGAGAGCCTCATGCTTCCTACGATTGACAATTTCTTGCAGATCTT
CTATGCAGGTAACCAATAGGGAGAGTGCCCTTTCTTCATCTAGAGGAGTAGTTGCAATGCACCG
CGCAATATCAGCAAGTTCAACAAT
						
						Genomic sequence
						
							CTTTATAGCAAAGAGGTCTCCTGTAGTTCTTTTCTTGGCCAAGAAAACACGTCCAAATGCTCCA
CGGCTGATAGGTTTAATGATTTCGAAGTCATCAATCGAAGTACGATCCTTGACTGGGTGAACAG
GACTAGCTCGTAAGCTACGGACAACATCATCTTCTTCATCCATTACAGTACTCGCTGAATCAAC
TTTGTCCATATCAACCGAATCACAAAGCAGTAGGTACTTCTCCCTAAGAAATTATATAAATGTG
AAGGGAAATTACAAATGGAAACTAATATAAGTGCTAAAAGTGACCTGCAAGAATTATTTTCATG
TGCTTATTTAGTATAATGTCAACTAAGATAAGCCACTTGTGTAGTGAACTCAGCAGAGACTCAC
CGGTGGAGTTTTTCTATACGTGTGCCAAATGTCTGCACCGTGAGAGCCTCATGCTTCCTACGAT
TGACAATTTCTTGCAGATCTTCTATGCAGGTAACCAATAGGGAGAGTGCCCTTTCTTCATCTAG
AGGAGTAGTTGCAATGCACCGCGCAATATCAGCAAGTTCAACAAT

Sequences
Splice junction sequence	CTTGCAGATCTTCTATGCAGGTAACCAATAGGGAGAGTGCCCTTTCTTCATCTAGAGGAGTAGT TGCAATGCACCGCGCAATATCAGCAAGTTCAACAATctttatagcaaagaggtctcctgtagtt cttttcttggccaagaaaacacgtccaaatgctccacggctgataggtttaatgatttcgaagt catcaatc
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: 123 Transcript exons: 28757484-28757544,28757979-28758040 CTTTATAGCAAAGAGGTCTCCTGTAGTTCTTTTCTTGGCCAAGAAAACACGTCCAAATGCTGCC CTTTCTTCATCTAGAGGAGTAGTTGCAATGCACCGCGCAATATCAGCAAGTTCAACAAT Transcript length: 408 Transcript exons: 28757484-28757718,28757868-28758040 CTTTATAGCAAAGAGGTCTCCTGTAGTTCTTTTCTTGGCCAAGAAAACACGTCCAAATGCTCCA CGGCTGATAGGTTTAATGATTTCGAAGTCATCAATCGAAGTACGATCCTTGACTGGGTGAACAG GACTAGCTCGTAAGCTACGGACAACATCATCTTCTTCATCCATTACAGTACTCGCTGAATCAAC TTTGTCCATATCAACCGAATCACAAAGCAGTAGGTACTTCTCCCGGTGGAGTTTTTCTATACGT GTGCCAAATGTCTGCACCGTGAGAGCCTCATGCTTCCTACGATTGACAATTTCTTGCAGATCTT CTATGCAGGTAACCAATAGGGAGAGTGCCCTTTCTTCATCTAGAGGAGTAGTTGCAATGCACCG CGCAATATCAGCAAGTTCAACAAT
Genomic sequence	CTTTATAGCAAAGAGGTCTCCTGTAGTTCTTTTCTTGGCCAAGAAAACACGTCCAAATGCTCCA CGGCTGATAGGTTTAATGATTTCGAAGTCATCAATCGAAGTACGATCCTTGACTGGGTGAACAG GACTAGCTCGTAAGCTACGGACAACATCATCTTCTTCATCCATTACAGTACTCGCTGAATCAAC TTTGTCCATATCAACCGAATCACAAAGCAGTAGGTACTTCTCCCTAAGAAATTATATAAATGTG AAGGGAAATTACAAATGGAAACTAATATAAGTGCTAAAAGTGACCTGCAAGAATTATTTTCATG TGCTTATTTAGTATAATGTCAACTAAGATAAGCCACTTGTGTAGTGAACTCAGCAGAGACTCAC CGGTGGAGTTTTTCTATACGTGTGCCAAATGTCTGCACCGTGAGAGCCTCATGCTTCCTACGAT TGACAATTTCTTGCAGATCTTCTATGCAGGTAACCAATAGGGAGAGTGCCCTTTCTTCATCTAG AGGAGTAGTTGCAATGCACCGCGCAATATCAGCAAGTTCAACAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005059* osi_circ_013503 zma_circ_006902 zma_circ_001894 
						
						PMCS
						0.696617283

Conservation Information
Conserved circRNAs	osi_circ_005059* osi_circ_013503 zma_circ_006902 zma_circ_001894
PMCS	0.696617283

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28757956-28757604(+)
28757686-28757486(-)
						
						Potential amino acid sequence
						
							MQVTNRESALSSSRGVVAMHRAISASSTIFIAKRSPVVLFLAKKTRPNAPRLIGLMISKSSIEV
RSLTG*(+)
MDKVDSASTVMDEEDDVVRSLRASPVHPVKDRTSIDDFEIIKPISRGAFGRVFLAKKRTTGDLF
AIKIVELADIARCIATTPLDEERALSLLVTCIEDLQEIVNRRKHEALTVQTFGTRIEKLHREKY
LLLCDSVDMDKVDSASTVMDEEDDVVRSLRASPVHPVKDRTSIDDFEIIKPISRGAFGRVFLAK
KRTTGDLFAIKIVELADIARCIATTPLDEERALSLLVTCIEDLQEIVNRRKHEALTVQTFGTRI
EKLHREKYLLLCDSVDMDKVDSASTVMDEEDDVVRSLRASPVHPVKDRTSIDDFEIIKPISRGA
FGRVFLAKKRTTGDLFAIKIVELADIARCIATTPLDEERALSLLVTCIEDLQEIVNRRKHEALT
VQTFGTRIEKLHREKYLLLCDSVDMDKVDSASTVMDEEDDVVRSLRASPVHPVKDRTSIDDFEI
IKPISRGAFGRVFLAKKRTTGDLFAIK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28757956-28757604(+) 28757686-28757486(-)
Potential amino acid sequence	MQVTNRESALSSSRGVVAMHRAISASSTIFIAKRSPVVLFLAKKTRPNAPRLIGLMISKSSIEV RSLTG*(+) MDKVDSASTVMDEEDDVVRSLRASPVHPVKDRTSIDDFEIIKPISRGAFGRVFLAKKRTTGDLF AIKIVELADIARCIATTPLDEERALSLLVTCIEDLQEIVNRRKHEALTVQTFGTRIEKLHREKY LLLCDSVDMDKVDSASTVMDEEDDVVRSLRASPVHPVKDRTSIDDFEIIKPISRGAFGRVFLAK KRTTGDLFAIKIVELADIARCIATTPLDEERALSLLVTCIEDLQEIVNRRKHEALTVQTFGTRI EKLHREKYLLLCDSVDMDKVDSASTVMDEEDDVVRSLRASPVHPVKDRTSIDDFEIIKPISRGA FGRVFLAKKRTTGDLFAIKIVELADIARCIATTPLDEERALSLLVTCIEDLQEIVNRRKHEALT VQTFGTRIEKLHREKYLLLCDSVDMDKVDSASTVMDEEDDVVRSLRASPVHPVKDRTSIDDFEI IKPISRGAFGRVFLAKKRTTGDLFAIK(-)
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 Os03g0711800_circ_g.4

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