Plant Circular RNA Database

Detail information of Os03g0259300_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os03g0259300_circ_g.4
					
						ID in PlantcircBase
						osa_circ_018957
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 8403144-8404463  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os03g0259300						
					
						Parent gene annotation
						
							Homologue of yeast Hrd3/mammalian SEL1L, ER-resident type I memb
rane protein, Polyubiquitination of unfolded proteins, Quality c
ontrol of endoplasmic reticulum-derived protein bodies in rice e
ndosperm (Os03t0259300-01);Non-protein coding transcript. (Os03t
0259300-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0259300_circ_g.3 						
					
						Support reads
						1
					
						Tissues
						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
						Os03t0259300-01:2

General Information
CircRNA Name	Os03g0259300_circ_g.4
ID in PlantcircBase	osa_circ_018957
Alias	NA
Organism	Oryza sativa
Position	chr3: 8403144-8404463 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os03g0259300
Parent gene annotation	Homologue of yeast Hrd3/mammalian SEL1L, ER-resident type I memb rane protein, Polyubiquitination of unfolded proteins, Quality c ontrol of endoplasmic reticulum-derived protein bodies in rice e ndosperm (Os03t0259300-01);Non-protein coding transcript. (Os03t 0259300-02)
Parent gene strand	+
Alternative splicing	Os03g0259300_circ_g.3
Support reads	1
Tissues	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	Os03t0259300-01:2

			
						 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  
						
							TTATGATCAGGCTGTTGAGGTGGATCCAGCAGCTAAGCTCCCTGTCATGCTTGCACTAACAAGT
TTATGGATAAGGAAGAACTATGATGGAAGCTTTTTGgcggcagtgatgtacaaatctgttgctg
agaggggcccctggagctcactttctagatgggctctggaatcttatttgaaaggtgacatagg
gaaagcat

									
								

					

						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: 567
Transcript exons: 8403144-8403467,8404221-8404463
GCGGCAGTGATGTACAAATCTGTTGCTGAGAGGGGCCCCTGGAGCTCACTTTCTAGATGGGCTC
TGGAATCTTATTTGAAAGGTGACATAGGGAAAGCATTACTCCTGTATTCTAGAATGGCGGATCT
TGGATATGAGGTTGCACAAAGCAATGCTGCCTGGATTCTTGATAGGTATGGCGATGAAAGTATT
TGCATGGGAGAATCTGGCTTCTGTACAGATATGGAAAGACATCTCCGTGCACATGCTCTGTGGT
GGCAAGCATCCGAGCAGGGTAACGAACATGCTGCCTTGTTAATTGGTGACGCCTACTACTATGG
CCGGGGTGTTGGCAGGGATTACGAGCGTGCAGCCGAGGCATATATGCATGCGCAATCACAATCT
AATGCTCAGGCCATGTTTAACCTTGGTTATATGCATGAGCATGGCCATGGACTTCCCCTTGACT
TGCACCTGGCAAAAAGATATTATGATCAGGCTGTTGAGGTGGATCCAGCAGCTAAGCTCCCTGT
CATGCTTGCACTAACAAGTTTATGGATAAGGAAGAACTATGATGGAAGCTTTTTG
						
					

						Genomic sequence
						
							GCGGCAGTGATGTACAAATCTGTTGCTGAGAGGGGCCCCTGGAGCTCACTTTCTAGATGGGCTC
TGGAATCTTATTTGAAAGGTGACATAGGGAAAGCATTACTCCTGTATTCTAGAATGGCGGATCT
TGGATATGAGGTTGCACAAAGCAATGCTGCCTGGATTCTTGATAGGTATGGCGATGAAAGTATT
TGCATGGGAGAATCTGGCTTCTGTACAGATATGGAAAGACATCTCCGTGCACATGCTCTGTGGT
GGCAAGCATCCGAGCAGGGTAACGAACATGCTGCCTTGTTAATTGGTGACGCCTACTACTATGG
CCGGGTATGTGTTACAATCCATGTTCTTGGTTATGAGAAATTCTGAAATGCTCTTGAATTTGTT
AGAGGACAGAGGACTTTTCCTAAATACCTTCATCAAATTGACACAAACACTATAATATGTAAGA
ATTTCTTGTATAAGATGCATGAGGTGCAGTTCTTTCTTTTGGTTATCCTGTTAGTATTACCATT
ACAAATTACTAAGTAAATATATGATTTGAAAACATGTTTACTATATACATAAGTGCATGCTAAT
AAATTTCATAAAGTATATATTCATATGTTATGTGCCGTAACTACTGCTTGATGACAATCAACAT
AACCATGTTTTTACCTTGAGTTATGTATTAGTATGATTTTTTTTTCTTTTGAGATGAACCATGT
TTCCAAGGGAGAATATTTAAATAACTAATGAAAGGTTACCTCTAATTTTAGCTTTTCCGAGTTT
TTGGTCATCACCATCTAATCACCTTAGTTTAATAGCCTAGTTCGCATTCCAGTTTCTTTCCGTG
TTCCTCTTTTTGGTACTTGGCCAGGCGAATTGGCTTGTCAGCAAATTGGGAAGTGATCTTGTTC
TTTTTTACCGGTTTACTTGTTGTATGCAAAACTTTTCCATAATTATTACAAAAAAACAGTCTGT
TATTATTATAATTTTGAAAAATTGCTTATGCACTTCTTATATACTGGGGGCCTCTGCGTTCTTA
AAGAGACCATTATTGCTGACATTGTGTATTGGATGTGTACTTTTGTATTACAGGGTGTTGGCAG
GGATTACGAGCGTGCAGCCGAGGCATATATGCATGCGCAATCACAATCTAATGCTCAGGCCATG
TTTAACCTTGGTTATATGCATGAGCATGGCCATGGACTTCCCCTTGACTTGCACCTGGCAAAAA
GATATTATGATCAGGCTGTTGAGGTGGATCCAGCAGCTAAGCTCCCTGTCATGCTTGCACTAAC
AAGTTTATGGATAAGGAAGAACTATGATGGAAGCTTTTTG
						
					

			
		

Sequences
Splice junction sequence	TTATGATCAGGCTGTTGAGGTGGATCCAGCAGCTAAGCTCCCTGTCATGCTTGCACTAACAAGT TTATGGATAAGGAAGAACTATGATGGAAGCTTTTTGgcggcagtgatgtacaaatctgttgctg agaggggcccctggagctcactttctagatgggctctggaatcttatttgaaaggtgacatagg gaaagcat
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: 567 Transcript exons: 8403144-8403467,8404221-8404463 GCGGCAGTGATGTACAAATCTGTTGCTGAGAGGGGCCCCTGGAGCTCACTTTCTAGATGGGCTC TGGAATCTTATTTGAAAGGTGACATAGGGAAAGCATTACTCCTGTATTCTAGAATGGCGGATCT TGGATATGAGGTTGCACAAAGCAATGCTGCCTGGATTCTTGATAGGTATGGCGATGAAAGTATT TGCATGGGAGAATCTGGCTTCTGTACAGATATGGAAAGACATCTCCGTGCACATGCTCTGTGGT GGCAAGCATCCGAGCAGGGTAACGAACATGCTGCCTTGTTAATTGGTGACGCCTACTACTATGG CCGGGGTGTTGGCAGGGATTACGAGCGTGCAGCCGAGGCATATATGCATGCGCAATCACAATCT AATGCTCAGGCCATGTTTAACCTTGGTTATATGCATGAGCATGGCCATGGACTTCCCCTTGACT TGCACCTGGCAAAAAGATATTATGATCAGGCTGTTGAGGTGGATCCAGCAGCTAAGCTCCCTGT CATGCTTGCACTAACAAGTTTATGGATAAGGAAGAACTATGATGGAAGCTTTTTG
Genomic sequence	GCGGCAGTGATGTACAAATCTGTTGCTGAGAGGGGCCCCTGGAGCTCACTTTCTAGATGGGCTC TGGAATCTTATTTGAAAGGTGACATAGGGAAAGCATTACTCCTGTATTCTAGAATGGCGGATCT TGGATATGAGGTTGCACAAAGCAATGCTGCCTGGATTCTTGATAGGTATGGCGATGAAAGTATT TGCATGGGAGAATCTGGCTTCTGTACAGATATGGAAAGACATCTCCGTGCACATGCTCTGTGGT GGCAAGCATCCGAGCAGGGTAACGAACATGCTGCCTTGTTAATTGGTGACGCCTACTACTATGG CCGGGTATGTGTTACAATCCATGTTCTTGGTTATGAGAAATTCTGAAATGCTCTTGAATTTGTT AGAGGACAGAGGACTTTTCCTAAATACCTTCATCAAATTGACACAAACACTATAATATGTAAGA ATTTCTTGTATAAGATGCATGAGGTGCAGTTCTTTCTTTTGGTTATCCTGTTAGTATTACCATT ACAAATTACTAAGTAAATATATGATTTGAAAACATGTTTACTATATACATAAGTGCATGCTAAT AAATTTCATAAAGTATATATTCATATGTTATGTGCCGTAACTACTGCTTGATGACAATCAACAT AACCATGTTTTTACCTTGAGTTATGTATTAGTATGATTTTTTTTTCTTTTGAGATGAACCATGT TTCCAAGGGAGAATATTTAAATAACTAATGAAAGGTTACCTCTAATTTTAGCTTTTCCGAGTTT TTGGTCATCACCATCTAATCACCTTAGTTTAATAGCCTAGTTCGCATTCCAGTTTCTTTCCGTG TTCCTCTTTTTGGTACTTGGCCAGGCGAATTGGCTTGTCAGCAAATTGGGAAGTGATCTTGTTC TTTTTTACCGGTTTACTTGTTGTATGCAAAACTTTTCCATAATTATTACAAAAAAACAGTCTGT TATTATTATAATTTTGAAAAATTGCTTATGCACTTCTTATATACTGGGGGCCTCTGCGTTCTTA AAGAGACCATTATTGCTGACATTGTGTATTGGATGTGTACTTTTGTATTACAGGGTGTTGGCAG GGATTACGAGCGTGCAGCCGAGGCATATATGCATGCGCAATCACAATCTAATGCTCAGGCCATG TTTAACCTTGGTTATATGCATGAGCATGGCCATGGACTTCCCCTTGACTTGCACCTGGCAAAAA GATATTATGATCAGGCTGTTGAGGTGGATCCAGCAGCTAAGCTCCCTGTCATGCTTGCACTAAC AAGTTTATGGATAAGGAAGAACTATGATGGAAGCTTTTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.166620019

Conservation Information
Conserved circRNAs	NA
PMCS	0.166620019

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8403154-8404460(+)
						
						Potential amino acid sequence
						
							MYKSVAERGPWSSLSRWALESYLKGDIGKALLLYSRMADLGYEVAQSNAAWILDRYGDESICMG
ESGFCTDMERHLRAHALWWQASEQGNEHAALLIGDAYYYGRGVGRDYERAAEAYMHAQSQSNAQ
AMFNLGYMHEHGHGLPLDLHLAKRYYDQAVEVDPAAKLPVMLALTSLWIRKNYDGSFLAAVMYK
SVAERGPWSSLSRWALESYLKGDIGKALLLYSRMADLGYEVAQSNAAWILDRYGDESICMGESG
FCTDMERHLRAHALWWQASEQGNEHAALLIGDAYYYGRGVGRDYERAAEAYMHAQSQSNAQAMF
NLGYMHEHGHGLPLDLHLAKRYYDQAVEVDPAAKLPVMLALTSLWIRKNYDGSFLAAVMYKSVA
ERGPWSSLSRWALESYLKGDIGKALLLYSRMADLGYEVAQSNAAWILDRYGDESICMGESGFCT
DMERHLRAHALWWQASEQGNEHAALLIGDAYYYGRGVGRDYERAAEAYMHAQSQSNAQAMFNLG
YMHEHGHGLPLDLHLAKRYYDQAVEVDPAAKLPVMLALTSLWIRKNYDGSFLAAVMYKSVAERG
PWSSLSRWALESYLKGDIGKALLLYSRMADLGYEVAQSNAAWILDRYGDESICMGESGFCTDME
RHLRAHALWWQASEQGNEHAALLIGDAYYYGRGVGRDYERAAEAYMHAQSQSNAQAMFNLGYMH
EHGHGLPLDLHLAKRYYDQAVEVDPAAKLPVMLALTSLWIRKNYDGSFL(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8403154-8404460(+)
Potential amino acid sequence	MYKSVAERGPWSSLSRWALESYLKGDIGKALLLYSRMADLGYEVAQSNAAWILDRYGDESICMG ESGFCTDMERHLRAHALWWQASEQGNEHAALLIGDAYYYGRGVGRDYERAAEAYMHAQSQSNAQ AMFNLGYMHEHGHGLPLDLHLAKRYYDQAVEVDPAAKLPVMLALTSLWIRKNYDGSFLAAVMYK SVAERGPWSSLSRWALESYLKGDIGKALLLYSRMADLGYEVAQSNAAWILDRYGDESICMGESG FCTDMERHLRAHALWWQASEQGNEHAALLIGDAYYYGRGVGRDYERAAEAYMHAQSQSNAQAMF NLGYMHEHGHGLPLDLHLAKRYYDQAVEVDPAAKLPVMLALTSLWIRKNYDGSFLAAVMYKSVA ERGPWSSLSRWALESYLKGDIGKALLLYSRMADLGYEVAQSNAAWILDRYGDESICMGESGFCT DMERHLRAHALWWQASEQGNEHAALLIGDAYYYGRGVGRDYERAAEAYMHAQSQSNAQAMFNLG YMHEHGHGLPLDLHLAKRYYDQAVEVDPAAKLPVMLALTSLWIRKNYDGSFLAAVMYKSVAERG PWSSLSRWALESYLKGDIGKALLLYSRMADLGYEVAQSNAAWILDRYGDESICMGESGFCTDME RHLRAHALWWQASEQGNEHAALLIGDAYYYGRGVGRDYERAAEAYMHAQSQSNAQAMFNLGYMH EHGHGLPLDLHLAKRYYDQAVEVDPAAKLPVMLALTSLWIRKNYDGSFL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0259300_circ_g.4

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