Plant Circular RNA Database

Detail information of Os03g0311300_circ_g.10

			
						 General Information
					
						CircRNA Name
						Os03g0311300_circ_g.10
					
						ID in PlantcircBase
						osa_circ_019497
					
						Alias
						Os03circ13282
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 11112767-11113119  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os03g0311300						
					
						Parent gene annotation
						
							Similar to HAD-superfamily hydrolase, subfamily IA, variant 3 co
ntaining protein, expressed. (Os03t0311300-01);Similar to HAD-su
perfamily hydrolase, subfamily IA, variant 3 containing protein,
 expressed. (Os03t0311300-02);NHL repeat domain containing prote
in. (Os03t0311300-03)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0311300_circ_g.4 Os03g0311300_circ_g.5 Os03g0311300_circ_g.6 Os03g0311300_circ_g.7 Os03g0311300_circ_g.8 Os03g0311300_circ_g.9 Os03g0311300_circ_g.11 Os03g0311300_circ_g.12 Os03g0311300_circ_g.13 Os03g0311300_circ_g.14 Os03g0311300_circ_g.15 Os03g0311300_circ_g.16 Os03g0311300_circ_g.17 Os03g0311300_circ_g.18 Os03g0311300_circ_g.19 Os03g0311300_circ_g.20 						
					
						Support reads
						2/1
					
						Tissues
						leaf/shoot
					
						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
						Os03t0311300-02:2
Os03t0311300-03:2

General Information
CircRNA Name	Os03g0311300_circ_g.10
ID in PlantcircBase	osa_circ_019497
Alias	Os03circ13282
Organism	Oryza sativa
Position	chr3: 11112767-11113119 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os03g0311300
Parent gene annotation	Similar to HAD-superfamily hydrolase, subfamily IA, variant 3 co ntaining protein, expressed. (Os03t0311300-01);Similar to HAD-su perfamily hydrolase, subfamily IA, variant 3 containing protein, expressed. (Os03t0311300-02);NHL repeat domain containing prote in. (Os03t0311300-03)
Parent gene strand	+
Alternative splicing	Os03g0311300_circ_g.4 Os03g0311300_circ_g.5 Os03g0311300_circ_g.6 Os03g0311300_circ_g.7 Os03g0311300_circ_g.8 Os03g0311300_circ_g.9 Os03g0311300_circ_g.11 Os03g0311300_circ_g.12 Os03g0311300_circ_g.13 Os03g0311300_circ_g.14 Os03g0311300_circ_g.15 Os03g0311300_circ_g.16 Os03g0311300_circ_g.17 Os03g0311300_circ_g.18 Os03g0311300_circ_g.19 Os03g0311300_circ_g.20
Support reads	2/1
Tissues	leaf/shoot
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	Os03t0311300-02:2 Os03t0311300-03:2

			
						 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  
						
							CTTGTGGAGAGAACTGGGGGTGAACTCTTGGCCTACATTTGTTGTGATTGGGCCCAACGGGAAG
GTTTTAGCACAAATATCAGGTGAAGGTCACAGAAAGttcactgttgtcggtgtgcactctgcca
aatttgataatgaaaaagatcttgaagccatcagaaatgctgttctgcgctacaacattactca
tccggtaa

						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: 219
Transcript exons: 11112767-11112862,11112997-11113119
TTCACTGTTGTCGGTGTGCACTCTGCCAAATTTGATAATGAAAAAGATCTTGAAGCCATCAGAA
ATGCTGTTCTGCGCTACAACATTACTCATCCGGTTGTAAATGATGGGGACATGTACTTGTGGAG
AGAACTGGGGGTGAACTCTTGGCCTACATTTGTTGTGATTGGGCCCAACGGGAAGGTTTTAGCA
CAAATATCAGGTGAAGGTCACAGAAAG
						
						Genomic sequence
						
							TTCACTGTTGTCGGTGTGCACTCTGCCAAATTTGATAATGAAAAAGATCTTGAAGCCATCAGAA
ATGCTGTTCTGCGCTACAACATTACTCATCCGGTAATACAGCTGTGATAACTTGTGAAATGTTG
AAATGAGAAACATCATTCCTGTGCTCCTCCCTGGCATAGACTTTCATGTCTATTGCTTTTTTGT
GGTGTTCTTAACTTTTTAAAGCTATGGTCTTTCTTAAGGTTGTAAATGATGGGGACATGTACTT
GTGGAGAGAACTGGGGGTGAACTCTTGGCCTACATTTGTTGTGATTGGGCCCAACGGGAAGGTT
TTAGCACAAATATCAGGTGAAGGTCACAGAAAG

Sequences
Splice junction sequence	CTTGTGGAGAGAACTGGGGGTGAACTCTTGGCCTACATTTGTTGTGATTGGGCCCAACGGGAAG GTTTTAGCACAAATATCAGGTGAAGGTCACAGAAAGttcactgttgtcggtgtgcactctgcca aatttgataatgaaaaagatcttgaagccatcagaaatgctgttctgcgctacaacattactca tccggtaa
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: 219 Transcript exons: 11112767-11112862,11112997-11113119 TTCACTGTTGTCGGTGTGCACTCTGCCAAATTTGATAATGAAAAAGATCTTGAAGCCATCAGAA ATGCTGTTCTGCGCTACAACATTACTCATCCGGTTGTAAATGATGGGGACATGTACTTGTGGAG AGAACTGGGGGTGAACTCTTGGCCTACATTTGTTGTGATTGGGCCCAACGGGAAGGTTTTAGCA CAAATATCAGGTGAAGGTCACAGAAAG
Genomic sequence	TTCACTGTTGTCGGTGTGCACTCTGCCAAATTTGATAATGAAAAAGATCTTGAAGCCATCAGAA ATGCTGTTCTGCGCTACAACATTACTCATCCGGTAATACAGCTGTGATAACTTGTGAAATGTTG AAATGAGAAACATCATTCCTGTGCTCCTCCCTGGCATAGACTTTCATGTCTATTGCTTTTTTGT GGTGTTCTTAACTTTTTAAAGCTATGGTCTTTCTTAAGGTTGTAAATGATGGGGACATGTACTT GTGGAGAGAACTGGGGGTGAACTCTTGGCCTACATTTGTTGTGATTGGGCCCAACGGGAAGGTT TTAGCACAAATATCAGGTGAAGGTCACAGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.391768618

Conservation Information
Conserved circRNAs	NA
PMCS	0.391768618

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11113016-11113116(+)
11112861-11113101(-)
11112827-11113112(-)
						
						Potential amino acid sequence
						
							MYLWRELGVNSWPTFVVIGPNGKVLAQISGEGHRKFTVVGVHSAKFDNEKDLEAIRNAVLRYNI
THPVVNDGDMYLWRELGVNSWPTFVVIGPNGKVLAQISGEGHRKFTVVGVHSAKFDNEKDLEAI
RNAVLRYNITHPVVNDGDMYLWRELGVNSWPTFVVIGPNGKVLAQISGEGHRKFTVVGVHSAKF
DNEKDLEAIRNAVLRYNITHPVVNDGDMYLWRELGVNSWPTFVVIGPNGKVLAQISGEGHRK(+
)
MSNVVAQNSISDGFKIFFIIKFGRVHTDNSELSVTFT*(-)
MASRSFSLSNLAECTPTTVNFL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11113016-11113116(+) 11112861-11113101(-) 11112827-11113112(-)
Potential amino acid sequence	MYLWRELGVNSWPTFVVIGPNGKVLAQISGEGHRKFTVVGVHSAKFDNEKDLEAIRNAVLRYNI THPVVNDGDMYLWRELGVNSWPTFVVIGPNGKVLAQISGEGHRKFTVVGVHSAKFDNEKDLEAI RNAVLRYNITHPVVNDGDMYLWRELGVNSWPTFVVIGPNGKVLAQISGEGHRKFTVVGVHSAKF DNEKDLEAIRNAVLRYNITHPVVNDGDMYLWRELGVNSWPTFVVIGPNGKVLAQISGEGHRK(+ ) MSNVVAQNSISDGFKIFFIIKFGRVHTDNSELSVTFT(-) MASRSFSLSNLAECTPTTVNFL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Chu et al., 2017

circRNA

Detail information of Os03g0311300_circ_g.10

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