Plant Circular RNA Database

Detail information of Os04g0492100_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0492100_circ_g.2
					
						ID in PlantcircBase
						osa_circ_024351
					
						Alias
						Os_ciR9419
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 24585318-24586666  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os04g0492100						
					
						Parent gene annotation
						
							Similar to H0425E08.1 protein. (Os04t0492100-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0492100_circ_igg.1 EPlOSAG00000040437_circ_ig.1 Os04g0492100_circ_g.1 Os04g0492100_circ_g.3 Os04g0492100_circ_g.4 Os04g0492100_circ_g.5 Os04g0492100_circ_g.6 						
					
						Support reads
						2
					
						Tissues
						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
						Os04t0492100-01:5

General Information
CircRNA Name	Os04g0492100_circ_g.2
ID in PlantcircBase	osa_circ_024351
Alias	Os_ciR9419
Organism	Oryza sativa
Position	chr4: 24585318-24586666 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os04g0492100
Parent gene annotation	Similar to H0425E08.1 protein. (Os04t0492100-01)
Parent gene strand	+
Alternative splicing	Os04g0492100_circ_igg.1 EPlOSAG00000040437_circ_ig.1 Os04g0492100_circ_g.1 Os04g0492100_circ_g.3 Os04g0492100_circ_g.4 Os04g0492100_circ_g.5 Os04g0492100_circ_g.6
Support reads	2
Tissues	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	Os04t0492100-01:5

			
						 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  
						
							CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACAT
TACATGCACACCTCCATGCAAATTTGAGTTTTGCTGttgacatgtggaatttgtttcgaaaatt
gtcctcgtacgtcaatgagtgctgctgcatgtggccatccgttctgtagtgcatgttggagagg
tttgacaa

									
								

					

						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: 566
Transcript exons: 24585318-24585408,24585499-24585671,24586009-24586113,24
586186-24586274,24586559-24586666
TTGACATGTGGAATTTGTTTCGAAAATTGTCCTCGTACGTCAATGAGTGCTGCTGCATGTGGCC
ATCCGTTCTGTAGTGCATGTTGGAGAGGTTATATTAGCACTTCTATAAATGATGGTCCAGGATG
CTTGATGTTAAGATGTCCTGATCCGTCCTGCACAGCTGCTGTTGGTCAAGATATGATCAATTCA
CTGGCTGATGACGAGGATAGGGAAAAGTATGGGCGATATCTTCGCAGATCTTACATTGAAGATA
ATAGGAAGACAAAATGGTGTCCTGCTCCTGGATGTGAATATGCTGTAGAATTTGTCATGGGCAG
TGGTAGCTATGATGTGAACTGCAACTGTTCATACGGCTTTTGTTGGAACTGCACTGAGGAAGCT
CATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAA
ATATGAACTGGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAA
CCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTG
						
					

						Genomic sequence
						
							TTGACATGTGGAATTTGTTTCGAAAATTGTCCTCGTACGTCAATGAGTGCTGCTGCATGTGGCC
ATCCGTTCTGTAGTGCATGTTGGAGAGGTTTGACAATCTAACCTTGAGATATTTCTCTTTATCA
ACCCCGGATTCTGTTTTGTGTGGGATCACCACTTACATAGTGCACATTGACAGGTTATATTAGC
ACTTCTATAAATGATGGTCCAGGATGCTTGATGTTAAGATGTCCTGATCCGTCCTGCACAGCTG
CTGTTGGTCAAGATATGATCAATTCACTGGCTGATGACGAGGATAGGGAAAAGTATGGGCGATA
TCTTCGCAGATCTTACATTGAAGATAATAGGAAGGTAGGTTGATCATAATACAAATGAATAAAT
GAAAATCTGTATGGCTGCTACTGTGAATTATTATATGTTTTATGTAAACCAGCCATTCTCCTGC
CTTTGCATCTTGTTTTTCCTAAAAATGGAGTGAACTCTCTGTATTTTGAATAAACCTTGATGTT
CTTACAGTTAATGTGGCAATCATAATATATTTTTGAAATGGTGCTGACAGTTTGTAATTAGTGT
GAATGCCTTCATAGGAAATGATCAAGTGCTATATTTGGCCAATTCTCAAGTTTTGGTATTTATG
TATCTATTTTTTTAAGCATATGTTCATTAAGTTCATTCCTATTTGGAACAGACAAAATGGTGTC
CTGCTCCTGGATGTGAATATGCTGTAGAATTTGTCATGGGCAGTGGTAGCTATGATGTGAACTG
CAACTGTTCATACGGCTTTTGTTGGAACGTGAGTACTGGACCTGCCATTTCATTTCATTGTGAT
CAGCAGGGCATAAACCATTTGAAATAAAATTTGCAGTGCACTGAGGAAGCTCATCGTCCGGTAG
ACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTGGTA
TTGTCAGAATAACACAGCTTTCTTTTTCATTACTACTGACATTTTTCTTATTGTAAGTTTTGTT
CCTTTAATTGCATTTGATCTTTCTTCTGAAAACTTTGTCCTAATCTCATTCCTCCTTTTGGTTC
TGAAAACTTTTGCTATTTTATTGTTTGGTGATTTTCTGAAACACCAATATTTTGACTTTATTTT
TTTGTCATATTAGTAGTAGTTCTTATGTTTTTACTGCAAGTTATTTCTTGTGTCAACTATGTTG
AACTTTCTGTTGGTTATGGTTTCAGGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCG
GCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTT
TGCTG
						
					

			
		

Sequences
Splice junction sequence	CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACAT TACATGCACACCTCCATGCAAATTTGAGTTTTGCTGttgacatgtggaatttgtttcgaaaatt gtcctcgtacgtcaatgagtgctgctgcatgtggccatccgttctgtagtgcatgttggagagg tttgacaa
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: 566 Transcript exons: 24585318-24585408,24585499-24585671,24586009-24586113,24 586186-24586274,24586559-24586666 TTGACATGTGGAATTTGTTTCGAAAATTGTCCTCGTACGTCAATGAGTGCTGCTGCATGTGGCC ATCCGTTCTGTAGTGCATGTTGGAGAGGTTATATTAGCACTTCTATAAATGATGGTCCAGGATG CTTGATGTTAAGATGTCCTGATCCGTCCTGCACAGCTGCTGTTGGTCAAGATATGATCAATTCA CTGGCTGATGACGAGGATAGGGAAAAGTATGGGCGATATCTTCGCAGATCTTACATTGAAGATA ATAGGAAGACAAAATGGTGTCCTGCTCCTGGATGTGAATATGCTGTAGAATTTGTCATGGGCAG TGGTAGCTATGATGTGAACTGCAACTGTTCATACGGCTTTTGTTGGAACTGCACTGAGGAAGCT CATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAA ATATGAACTGGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAA CCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTG
Genomic sequence	TTGACATGTGGAATTTGTTTCGAAAATTGTCCTCGTACGTCAATGAGTGCTGCTGCATGTGGCC ATCCGTTCTGTAGTGCATGTTGGAGAGGTTTGACAATCTAACCTTGAGATATTTCTCTTTATCA ACCCCGGATTCTGTTTTGTGTGGGATCACCACTTACATAGTGCACATTGACAGGTTATATTAGC ACTTCTATAAATGATGGTCCAGGATGCTTGATGTTAAGATGTCCTGATCCGTCCTGCACAGCTG CTGTTGGTCAAGATATGATCAATTCACTGGCTGATGACGAGGATAGGGAAAAGTATGGGCGATA TCTTCGCAGATCTTACATTGAAGATAATAGGAAGGTAGGTTGATCATAATACAAATGAATAAAT GAAAATCTGTATGGCTGCTACTGTGAATTATTATATGTTTTATGTAAACCAGCCATTCTCCTGC CTTTGCATCTTGTTTTTCCTAAAAATGGAGTGAACTCTCTGTATTTTGAATAAACCTTGATGTT CTTACAGTTAATGTGGCAATCATAATATATTTTTGAAATGGTGCTGACAGTTTGTAATTAGTGT GAATGCCTTCATAGGAAATGATCAAGTGCTATATTTGGCCAATTCTCAAGTTTTGGTATTTATG TATCTATTTTTTTAAGCATATGTTCATTAAGTTCATTCCTATTTGGAACAGACAAAATGGTGTC CTGCTCCTGGATGTGAATATGCTGTAGAATTTGTCATGGGCAGTGGTAGCTATGATGTGAACTG CAACTGTTCATACGGCTTTTGTTGGAACGTGAGTACTGGACCTGCCATTTCATTTCATTGTGAT CAGCAGGGCATAAACCATTTGAAATAAAATTTGCAGTGCACTGAGGAAGCTCATCGTCCGGTAG ACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTGGTA TTGTCAGAATAACACAGCTTTCTTTTTCATTACTACTGACATTTTTCTTATTGTAAGTTTTGTT CCTTTAATTGCATTTGATCTTTCTTCTGAAAACTTTGTCCTAATCTCATTCCTCCTTTTGGTTC TGAAAACTTTTGCTATTTTATTGTTTGGTGATTTTCTGAAACACCAATATTTTGACTTTATTTT TTTGTCATATTAGTAGTAGTTCTTATGTTTTTACTGCAAGTTATTTCTTGTGTCAACTATGTTG AACTTTCTGTTGGTTATGGTTTCAGGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCG GCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTT TGCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.285754077

Conservation Information
Conserved circRNAs	NA
PMCS	0.285754077

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24585361-24585318(+)
24585401-24586574(-)
						
						Potential amino acid sequence
						
							MSAAACGHPFCSACWRGYISTSINDGPGCLMLRCPDPSCTAAVGQDMINSLADDEDREKYGRYL
RRSYIEDNRKTKWCPAPGCEYAVEFVMGSGSYDVNCNCSYGFCWNCTEEAHRPVDCATVSKWIL
KNSAESENMNWILANSKPCPKCKRPIEKNQGCMHITCTPPCKFEFCC*(+)
MHYRTDGHMQQHSLTYEDNFRNKFHMSTAKLKFAWRCACNVHASLVFFNGPLALRTRL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24585361-24585318(+) 24585401-24586574(-)
Potential amino acid sequence	MSAAACGHPFCSACWRGYISTSINDGPGCLMLRCPDPSCTAAVGQDMINSLADDEDREKYGRYL RRSYIEDNRKTKWCPAPGCEYAVEFVMGSGSYDVNCNCSYGFCWNCTEEAHRPVDCATVSKWIL KNSAESENMNWILANSKPCPKCKRPIEKNQGCMHITCTPPCKFEFCC(+) MHYRTDGHMQQHSLTYEDNFRNKFHMSTAKLKFAWRCACNVHASLVFFNGPLALRTRL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os04g0492100_circ_g.2

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