Plant Circular RNA Database

Detail information of Os04g0442000_circ_g.8

			
						 General Information
					
						CircRNA Name
						Os04g0442000_circ_g.8
					
						ID in PlantcircBase
						osa_circ_023939
					
						Alias
						Os_ciR5419
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 22008852-22009859  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0442000						
					
						Parent gene annotation
						
							Similar to Auxin response factor 2 (ARF1-binding protein) (ARF1-
BP). (Os04t0442000-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0442000_circ_g.4 Os04g0442000_circ_g.5 Os04g0442000_circ_g.6 Os04g0442000_circ_g.7 Os04g0442000_circ_g.9 Os04g0442000_circ_g.10 Os04g0442000_circ_g.11 						
					
						Support reads
						3/2
					
						Tissues
						root/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
						Os04t0442000-01:4

General Information
CircRNA Name	Os04g0442000_circ_g.8
ID in PlantcircBase	osa_circ_023939
Alias	Os_ciR5419
Organism	Oryza sativa
Position	chr4: 22008852-22009859 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0442000
Parent gene annotation	Similar to Auxin response factor 2 (ARF1-binding protein) (ARF1- BP). (Os04t0442000-01)
Parent gene strand	+
Alternative splicing	Os04g0442000_circ_g.4 Os04g0442000_circ_g.5 Os04g0442000_circ_g.6 Os04g0442000_circ_g.7 Os04g0442000_circ_g.9 Os04g0442000_circ_g.10 Os04g0442000_circ_g.11
Support reads	3/2
Tissues	root/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	Os04t0442000-01:4

			
						 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  
						
							ATTTCTGTTTCACAGGTTTAGTGGAACAATTATTGGTATTGGGAGTGTGCCAGCAATGTCAAAA
TCTCCATGGGCAGATTCTGACTGGAAATCTCTGAAGgacaacctaggaggcatctgcttacaac
cggttggagtgtctttgttagctcaaaaagattggttgctggcgatgcatttatcttcctgagg
tacacaat

									
								

					

						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: 461
Transcript exons: 22008852-22008942,22009079-22009243,22009568-22009687,22
009775-22009859
GACAACCTAGGAGGCATCTGCTTACAACCGGTTGGAGTGTCTTTGTTAGCTCAAAAAGATTGGT
TGCTGGCGATGCATTTATCTTCCTGAGGGGCGAAAGTGGTGAGCTACGGGTTGGAGTAAGGAGA
CTTATGAGACAAGTAAATAACATGCCATCATCTGTCATATCAAGCCACAGCATGCATCTTGGAG
TCCTTGCAACAGCTTCCCATGCTATCTCCACTGGAACCCTCTTTTCTGTTTTCTACAAACCCAG
AACAAGCCGGTCTGAGTTTGTTGTGAGCGTTAACAAGTACCTTGAAGCTAAGAAGCAGAACTTG
TCTGTTGGAATGAGGTTTAAGATGAGATTTGAAGGTGATGAAGCTCCTGAAAGAAGGTTTAGTG
GAACAATTATTGGTATTGGGAGTGTGCCAGCAATGTCAAAATCTCCATGGGCAGATTCTGACTG
GAAATCTCTGAAG
						
					

						Genomic sequence
						
							GACAACCTAGGAGGCATCTGCTTACAACCGGTTGGAGTGTCTTTGTTAGCTCAAAAAGATTGGT
TGCTGGCGATGCATTTATCTTCCTGAGGTACACAATACTAAGCATGTAACTTGAAGGCATTAGG
TGCACTTGCATCTATCTCATGACTCAATTTAGTTGCGGATGAATCTAGTCTACAGTTATTACTG
GTTTCTTCCGCTAAATATCGTTGAATAACTTTCAGGGGCGAAAGTGGTGAGCTACGGGTTGGAG
TAAGGAGACTTATGAGACAAGTAAATAACATGCCATCATCTGTCATATCAAGCCACAGCATGCA
TCTTGGAGTCCTTGCAACAGCTTCCCATGCTATCTCCACTGGAACCCTCTTTTCTGTTTTCTAC
AAACCCAGGTTCAATAAATTCTCATTTTGGTTATGCCCTTTGTTTCTGGTTCTTTATTGTATTG
AGTTATGGTGCAAATTTTAATAGTAATGGTTGACGTTTAGACCTATATAAAACTGAATTACTGA
AATATGGCATTATTGGAATATTGTTTACTCTGCTGAGTGTATGATCATTATAAAAATAAACTTA
TGTATGATGATTTACCCATCCAGTCATGCATTGTTTTTGATAAAGTGGAGTAATACTTGGGTTA
TCCTAATTAGCATTATGATGTGCAAGTTTACATTATCTTGCAGACTAAACTTAATGTACATCTA
TTATGTTCCCAGAACAAGCCGGTCTGAGTTTGTTGTGAGCGTTAACAAGTACCTTGAAGCTAAG
AAGCAGAACTTGTCTGTTGGAATGAGGTTTAAGATGAGATTTGAAGGTGATGAAGCTCCTGAAA
GAAGGTACAATCTTGAGTTTCTTTCTGCATAATTATGCTAGCTTTACTCCTGTAGTTTACGGTG
CATATCATAAACATTTCTGTTTCACAGGTTTAGTGGAACAATTATTGGTATTGGGAGTGTGCCA
GCAATGTCAAAATCTCCATGGGCAGATTCTGACTGGAAATCTCTGAAG
						
					

			
		

Sequences
Splice junction sequence	ATTTCTGTTTCACAGGTTTAGTGGAACAATTATTGGTATTGGGAGTGTGCCAGCAATGTCAAAA TCTCCATGGGCAGATTCTGACTGGAAATCTCTGAAGgacaacctaggaggcatctgcttacaac cggttggagtgtctttgttagctcaaaaagattggttgctggcgatgcatttatcttcctgagg tacacaat
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: 461 Transcript exons: 22008852-22008942,22009079-22009243,22009568-22009687,22 009775-22009859 GACAACCTAGGAGGCATCTGCTTACAACCGGTTGGAGTGTCTTTGTTAGCTCAAAAAGATTGGT TGCTGGCGATGCATTTATCTTCCTGAGGGGCGAAAGTGGTGAGCTACGGGTTGGAGTAAGGAGA CTTATGAGACAAGTAAATAACATGCCATCATCTGTCATATCAAGCCACAGCATGCATCTTGGAG TCCTTGCAACAGCTTCCCATGCTATCTCCACTGGAACCCTCTTTTCTGTTTTCTACAAACCCAG AACAAGCCGGTCTGAGTTTGTTGTGAGCGTTAACAAGTACCTTGAAGCTAAGAAGCAGAACTTG TCTGTTGGAATGAGGTTTAAGATGAGATTTGAAGGTGATGAAGCTCCTGAAAGAAGGTTTAGTG GAACAATTATTGGTATTGGGAGTGTGCCAGCAATGTCAAAATCTCCATGGGCAGATTCTGACTG GAAATCTCTGAAG
Genomic sequence	GACAACCTAGGAGGCATCTGCTTACAACCGGTTGGAGTGTCTTTGTTAGCTCAAAAAGATTGGT TGCTGGCGATGCATTTATCTTCCTGAGGTACACAATACTAAGCATGTAACTTGAAGGCATTAGG TGCACTTGCATCTATCTCATGACTCAATTTAGTTGCGGATGAATCTAGTCTACAGTTATTACTG GTTTCTTCCGCTAAATATCGTTGAATAACTTTCAGGGGCGAAAGTGGTGAGCTACGGGTTGGAG TAAGGAGACTTATGAGACAAGTAAATAACATGCCATCATCTGTCATATCAAGCCACAGCATGCA TCTTGGAGTCCTTGCAACAGCTTCCCATGCTATCTCCACTGGAACCCTCTTTTCTGTTTTCTAC AAACCCAGGTTCAATAAATTCTCATTTTGGTTATGCCCTTTGTTTCTGGTTCTTTATTGTATTG AGTTATGGTGCAAATTTTAATAGTAATGGTTGACGTTTAGACCTATATAAAACTGAATTACTGA AATATGGCATTATTGGAATATTGTTTACTCTGCTGAGTGTATGATCATTATAAAAATAAACTTA TGTATGATGATTTACCCATCCAGTCATGCATTGTTTTTGATAAAGTGGAGTAATACTTGGGTTA TCCTAATTAGCATTATGATGTGCAAGTTTACATTATCTTGCAGACTAAACTTAATGTACATCTA TTATGTTCCCAGAACAAGCCGGTCTGAGTTTGTTGTGAGCGTTAACAAGTACCTTGAAGCTAAG AAGCAGAACTTGTCTGTTGGAATGAGGTTTAAGATGAGATTTGAAGGTGATGAAGCTCCTGAAA GAAGGTACAATCTTGAGTTTCTTTCTGCATAATTATGCTAGCTTTACTCCTGTAGTTTACGGTG CATATCATAAACATTTCTGTTTCACAGGTTTAGTGGAACAATTATTGGTATTGGGAGTGTGCCA GCAATGTCAAAATCTCCATGGGCAGATTCTGACTGGAAATCTCTGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005483* osi_circ_014397 						
					
						PMCS
						0.290455498

Conservation Information
Conserved circRNAs	osi_circ_005483* osi_circ_014397
PMCS	0.290455498

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22009120-22008938(+)
22008870-22009234(-)
22009170-22009791(-)
						
						Potential amino acid sequence
						
							MRQVNNMPSSVISSHSMHLGVLATASHAISTGTLFSVFYKPRTSRSEFVVSVNKYLEAKKQNLS
VGMRFKMRFEGDEAPERRFSGTIIGIGSVPAMSKSPWADSDWKSLKDNLGGICLQPVGVSLLAQ
KDWLLAMHLSS*(+)
MPPRLSFRDFQSESAHGDFDIAGTLPIPIIVPLNLLSGASSPSNLILNLIPTDKFCFLASRYLL
TLTTNSDRLVLGL*(-)
MLWLDMTDDGMLFTCLISLLTPTRSSPLSPLRKINASPATNLFELTKTLQPVVSRCLLGCPSEI
SSQNLPMEILTLLAHSQYQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22009120-22008938(+) 22008870-22009234(-) 22009170-22009791(-)
Potential amino acid sequence	MRQVNNMPSSVISSHSMHLGVLATASHAISTGTLFSVFYKPRTSRSEFVVSVNKYLEAKKQNLS VGMRFKMRFEGDEAPERRFSGTIIGIGSVPAMSKSPWADSDWKSLKDNLGGICLQPVGVSLLAQ KDWLLAMHLSS(+) MPPRLSFRDFQSESAHGDFDIAGTLPIPIIVPLNLLSGASSPSNLILNLIPTDKFCFLASRYLL TLTTNSDRLVLGL(-) MLWLDMTDDGMLFTCLISLLTPTRSSPLSPLRKINASPATNLFELTKTLQPVVSRCLLGCPSEI SSQNLPMEILTLLAHSQYQ*(-)
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 Os04g0442000_circ_g.8

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