Plant Circular RNA Database

Detail information of Os04g0693000_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0693000_circ_g.3
					
						ID in PlantcircBase
						osa_circ_026120
					
						Alias
						Os04circ19076/Os_ciR447
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 35476589-35477345  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ
					
						Parent gene
						
							Os04g0693000						
					
						Parent gene annotation
						
							Similar to Ribophorin I (Fragment). (Os04t0693000-01);Similar to
 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 
67 kDasubunit. (Os04t0693000-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0693000_circ_g.1 Os04g0693000_circ_g.2 Os04g0693000_circ_g.4 						
					
						Support reads
						14/71/8/6
					
						Tissues
						leaf and panicle/root/root/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
						Os04t0693000-02:1
Os04t0693000-01:2

General Information
CircRNA Name	Os04g0693000_circ_g.3
ID in PlantcircBase	osa_circ_026120
Alias	Os04circ19076/Os_ciR447
Organism	Oryza sativa
Position	chr4: 35476589-35477345 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRI, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ
Parent gene	Os04g0693000
Parent gene annotation	Similar to Ribophorin I (Fragment). (Os04t0693000-01);Similar to dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kDasubunit. (Os04t0693000-02)
Parent gene strand	-
Alternative splicing	Os04g0693000_circ_g.1 Os04g0693000_circ_g.2 Os04g0693000_circ_g.4
Support reads	14/71/8/6
Tissues	leaf and panicle/root/root/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	Os04t0693000-02:1 Os04t0693000-01:2

			
						 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   
						
							Yes							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   
						
							F: AGTGCTGTGCTTCTATCTCCG
 R: TCACGGTAGTAAACCAGCTGG
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	Yes 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	F: AGTGCTGTGCTTCTATCTCCG R: TCACGGTAGTAAACCAGCTGG PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							TAGAAATGCAGACCTTGCTGACATGGCAATTGGTTGAATCGATATCAGAATTTACCTTTAGTGT
GAGGAAAACTTTGACTATGGGGCTGGTGAGGTCGATcttgaaaagactcctttgtgctgagcac
caccatgtttcagcttatactgctcagtgatttggacattcccccaatgagaaatctccacctt
gcgcacaa

									
								

					

						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: 129
Transcript exons: 35476589-35476683,35477312-35477345
CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA
CATTCCCCCAATGAGAAATCTCCACCTTGCGGGAAAACTTTGACTATGGGGCTGGTGAGGTCGA
T
Transcript length: 139
Transcript exons: 35476589-35476693,35477312-35477345
CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA
CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATTCCGGAAAACTTTGACTATGGGGCTG
GTGAGGTCGAT
Transcript length: 174
Transcript exons: 35476589-35476690,35477274-35477345
CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA
CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATATTGGTTGAATCGATATCAGAATTTA
CCTTTAGTGTGAGGAAAACTTTGACTATGGGGCTGGTGAGGTCGAT
Transcript length: 192
Transcript exons: 35476589-35476645,35477211-35477345
CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGCATCATT
CTCGAGCTGGAAGAGGTTCAAGTGTGACTAGAAATGCAGACCTTGCTGACATGGCAATTGGTTG
AATCGATATCAGAATTTACCTTTAGTGTGAGGAAAACTTTGACTATGGGGCTGGTGAGGTCGAT
Transcript length: 207
Transcript exons: 35476589-35476762,35477313-35477345
CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA
CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATTCCTCAACAACAGCAAACGGACGATT
ATTTTCATAATGCACAAGTATGGGCACATACGAGTTTGGAAGCTGGGAAAACTTTGACTATGGG
GCTGGTGAGGTCGAT
Transcript length: 216
Transcript exons: 35476589-35476740,35477282-35477345
CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA
CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATTCCTCAACAACAGCAAACGGACGATT
ATTTTCATAATGCACAAGTATGGGAATCGATATCAGAATTTACCTTTAGTGTGAGGAAAACTTT
GACTATGGGGCTGGTGAGGTCGAT
Transcript length: 223
Transcript exons: 35476589-35476777,35477312-35477345
CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA
CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATTCCTCAACAACAGCAAACGGACGATT
ATTTTCATAATGCACAAGTATGGGCACATACGAGTTTGGAAGCTGGTTGTTGTATGCGCCGGGA
AAACTTTGACTATGGGGCTGGTGAGGTCGAT
Transcript length: 332
Transcript exons: 35476589-35476656,35476665-35476765,35477176-35477276,35
477284-35477345
CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA
CATTGAGAAATCTCCACCTTGCGCACAAATTCCTCAACAACAGCAAACGGACGATTATTTTCAT
AATGCACAAGTATGGGCACATACGAGTTTGGAAGCTGGTTGTGCGAGTAGAACTTGAGATGCTT
CAGGGGCAGTGGCATCATTCTCGAGCTGGAAGAGGTTCAAGTGTGACTAGAAATGCAGACCTTG
CTGACATGGCAATTTCGATATCAGAATTTACCTTTAGTGTGAGGAAAACTTTGACTATGGGGCT
GGTGAGGTCGAT
Transcript length: 680
Transcript exons: 35476589-35477223,35477301-35477345
CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA
CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATTCCTCAACAACAGCAAACGGACGATT
ATTTTCATAATGCACAAGTATGGGCACATACGAGTTTGGAAGCTGGTTGTTGTATGCGCCGTAT
TTCACTTCATTACCAGCTCGACTGGTGGGGTCCACCCTTGTAAAGGACTCCACCCTATTGCTCG
GCATTTTGATGTAGGTAACCTGCTCCAGAACATGGTACGGAGATAGAAGCACAGCACTGTCACG
GTAGTAAACCAGCTGGGGATCTGACTGGGTGATCTCTGCTGGGAAGGGCTCCAAAGAGTGTGTC
AAAGCATAAAATACTTCCAGCGTCGTCACCTCAGCAGGTTTCAATGGAGTGCTCAGCAAAATGG
AGTACAGGCGAGCACCATTTGGAGCGGCAGCAAGATCAGAGGCTTTCACAGAGAGAGGCACATA
TATCTTCTTCTTGCGCTTCCCCTCCGCTCTGGTCGCCTTGACAATCGCAAGATGTTCAACCTCT
GTGGGTGTGAATGCGAGTAGAACTTGAGATGCTTCAGGGGCAGTGGCATCATTCTCGAGCTTTA
GTGTGAGGAAAACTTTGACTATGGGGCTGGTGAGGTCGAT
						
					

						Genomic sequence
						
							CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA
CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATTCCTCAACAACAGCAAACGGACGATT
ATTTTCATAATGCACAAGTATGGGCACATACGAGTTTGGAAGCTGGTTGTTGTATGCGCCGTAT
TTCACTTCATTACCAGCTCGACTGGTGGGGTCCACCCTTGTAAAGGACTCCACCCTATTGCTCG
GCATTTTGATGTAGGTAACCTGCTCCAGAACATGGTACGGAGATAGAAGCACAGCACTGTCACG
GTAGTAAACCAGCTGGGGATCTGACTGGGTGATCTCTGCTGGGAAGGGCTCCAAAGAGTGTGTC
AAAGCATAAAATACTTCCAGCGTCGTCACCTCAGCAGGTTTCAATGGAGTGCTCAGCAAAATGG
AGTACAGGCGAGCACCATTTGGAGCGGCAGCAAGATCAGAGGCTTTCACAGAGAGAGGCACATA
TATCTTCTTCTTGCGCTTCCCCTCCGCTCTGGTCGCCTTGACAATCGCAAGATGTTCAACCTCT
GTGGGTGTGAATGCGAGTAGAACTTGAGATGCTTCAGGGGCAGTGGCATCATTCTCGAGCTGGA
AGAGGTTCAAGTGTGACTAGAAATGCAGACCTTGCTGACATGGCAATTGGTTGAATCGATATCA
GAATTTACCTTTAGTGTGAGGAAAACTTTGACTATGGGGCTGGTGAGGTCGAT
						
					

			
		

Sequences
Splice junction sequence	TAGAAATGCAGACCTTGCTGACATGGCAATTGGTTGAATCGATATCAGAATTTACCTTTAGTGT GAGGAAAACTTTGACTATGGGGCTGGTGAGGTCGATcttgaaaagactcctttgtgctgagcac caccatgtttcagcttatactgctcagtgatttggacattcccccaatgagaaatctccacctt gcgcacaa
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: 129 Transcript exons: 35476589-35476683,35477312-35477345 CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA CATTCCCCCAATGAGAAATCTCCACCTTGCGGGAAAACTTTGACTATGGGGCTGGTGAGGTCGA T Transcript length: 139 Transcript exons: 35476589-35476693,35477312-35477345 CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATTCCGGAAAACTTTGACTATGGGGCTG GTGAGGTCGAT Transcript length: 174 Transcript exons: 35476589-35476690,35477274-35477345 CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATATTGGTTGAATCGATATCAGAATTTA CCTTTAGTGTGAGGAAAACTTTGACTATGGGGCTGGTGAGGTCGAT Transcript length: 192 Transcript exons: 35476589-35476645,35477211-35477345 CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGCATCATT CTCGAGCTGGAAGAGGTTCAAGTGTGACTAGAAATGCAGACCTTGCTGACATGGCAATTGGTTG AATCGATATCAGAATTTACCTTTAGTGTGAGGAAAACTTTGACTATGGGGCTGGTGAGGTCGAT Transcript length: 207 Transcript exons: 35476589-35476762,35477313-35477345 CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATTCCTCAACAACAGCAAACGGACGATT ATTTTCATAATGCACAAGTATGGGCACATACGAGTTTGGAAGCTGGGAAAACTTTGACTATGGG GCTGGTGAGGTCGAT Transcript length: 216 Transcript exons: 35476589-35476740,35477282-35477345 CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATTCCTCAACAACAGCAAACGGACGATT ATTTTCATAATGCACAAGTATGGGAATCGATATCAGAATTTACCTTTAGTGTGAGGAAAACTTT GACTATGGGGCTGGTGAGGTCGAT Transcript length: 223 Transcript exons: 35476589-35476777,35477312-35477345 CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATTCCTCAACAACAGCAAACGGACGATT ATTTTCATAATGCACAAGTATGGGCACATACGAGTTTGGAAGCTGGTTGTTGTATGCGCCGGGA AAACTTTGACTATGGGGCTGGTGAGGTCGAT Transcript length: 332 Transcript exons: 35476589-35476656,35476665-35476765,35477176-35477276,35 477284-35477345 CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA CATTGAGAAATCTCCACCTTGCGCACAAATTCCTCAACAACAGCAAACGGACGATTATTTTCAT AATGCACAAGTATGGGCACATACGAGTTTGGAAGCTGGTTGTGCGAGTAGAACTTGAGATGCTT CAGGGGCAGTGGCATCATTCTCGAGCTGGAAGAGGTTCAAGTGTGACTAGAAATGCAGACCTTG CTGACATGGCAATTTCGATATCAGAATTTACCTTTAGTGTGAGGAAAACTTTGACTATGGGGCT GGTGAGGTCGAT Transcript length: 680 Transcript exons: 35476589-35477223,35477301-35477345 CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATTCCTCAACAACAGCAAACGGACGATT ATTTTCATAATGCACAAGTATGGGCACATACGAGTTTGGAAGCTGGTTGTTGTATGCGCCGTAT TTCACTTCATTACCAGCTCGACTGGTGGGGTCCACCCTTGTAAAGGACTCCACCCTATTGCTCG GCATTTTGATGTAGGTAACCTGCTCCAGAACATGGTACGGAGATAGAAGCACAGCACTGTCACG GTAGTAAACCAGCTGGGGATCTGACTGGGTGATCTCTGCTGGGAAGGGCTCCAAAGAGTGTGTC AAAGCATAAAATACTTCCAGCGTCGTCACCTCAGCAGGTTTCAATGGAGTGCTCAGCAAAATGG AGTACAGGCGAGCACCATTTGGAGCGGCAGCAAGATCAGAGGCTTTCACAGAGAGAGGCACATA TATCTTCTTCTTGCGCTTCCCCTCCGCTCTGGTCGCCTTGACAATCGCAAGATGTTCAACCTCT GTGGGTGTGAATGCGAGTAGAACTTGAGATGCTTCAGGGGCAGTGGCATCATTCTCGAGCTTTA GTGTGAGGAAAACTTTGACTATGGGGCTGGTGAGGTCGAT
Genomic sequence	CTTGAAAAGACTCCTTTGTGCTGAGCACCACCATGTTTCAGCTTATACTGCTCAGTGATTTGGA CATTCCCCCAATGAGAAATCTCCACCTTGCGCACAAATTCCTCAACAACAGCAAACGGACGATT ATTTTCATAATGCACAAGTATGGGCACATACGAGTTTGGAAGCTGGTTGTTGTATGCGCCGTAT TTCACTTCATTACCAGCTCGACTGGTGGGGTCCACCCTTGTAAAGGACTCCACCCTATTGCTCG GCATTTTGATGTAGGTAACCTGCTCCAGAACATGGTACGGAGATAGAAGCACAGCACTGTCACG GTAGTAAACCAGCTGGGGATCTGACTGGGTGATCTCTGCTGGGAAGGGCTCCAAAGAGTGTGTC AAAGCATAAAATACTTCCAGCGTCGTCACCTCAGCAGGTTTCAATGGAGTGCTCAGCAAAATGG AGTACAGGCGAGCACCATTTGGAGCGGCAGCAAGATCAGAGGCTTTCACAGAGAGAGGCACATA TATCTTCTTCTTGCGCTTCCCCTCCGCTCTGGTCGCCTTGACAATCGCAAGATGTTCAACCTCT GTGGGTGTGAATGCGAGTAGAACTTGAGATGCTTCAGGGGCAGTGGCATCATTCTCGAGCTGGA AGAGGTTCAAGTGTGACTAGAAATGCAGACCTTGCTGACATGGCAATTGGTTGAATCGATATCA GAATTTACCTTTAGTGTGAGGAAAACTTTGACTATGGGGCTGGTGAGGTCGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005879 osi_circ_015069 						
					
						PMCS
						0.489029679

Conservation Information
Conserved circRNAs	osi_circ_005879 osi_circ_015069
PMCS	0.489029679

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							35477327-35476643(+)
35476850-35477326(-)
35476624-35477215(-)
						
						Potential amino acid sequence
						
							MGLVRSILKRLLCAEHHHVSAYTAQ*(+)
MPSNRVESFTRVDPTSRAGNEVKYGAYNNQLPNSYVPILVHYENNRPFAVVEEFVRKVEISHWG
NVQITEQYKLKHGGAQHKGVFSRSTSPAP*(-)
MVVLSTKESFQDRPHQPHSQSFPHTKARE*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	35477327-35476643(+) 35476850-35477326(-) 35476624-35477215(-)
Potential amino acid sequence	MGLVRSILKRLLCAEHHHVSAYTAQ(+) MPSNRVESFTRVDPTSRAGNEVKYGAYNNQLPNSYVPILVHYENNRPFAVVEEFVRKVEISHWG NVQITEQYKLKHGGAQHKGVFSRSTSPAP(-) MVVLSTKESFQDRPHQPHSQSFPHTKARE*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os04g0693000_circ_g.3

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