Plant Circular RNA Database

Detail information of Os04g0650000_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os04g0650000_circ_g.4
					
						ID in PlantcircBase
						osa_circ_025672
					
						Alias
						Os_ciR2426
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 33124967-33125432  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0650000						
					
						Parent gene annotation
						
							Similar to Oryzain alpha chain precursor (EC 3.4.22.-). (Os04t06
50000-01);Similar to Oryzain alpha chain precursor (EC 3.4.22.-)
. (Os04t0650000-02);Similar to cDNA clone:J013002H09, full inser
t sequence. (Os04t0650000-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0650000_circ_g.5 						
					
						Support reads
						4/1
					
						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  
						
							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
						Os04t0650000-03:1
Os04t0650000-02:2
Os04t0650000-01:1

General Information
CircRNA Name	Os04g0650000_circ_g.4
ID in PlantcircBase	osa_circ_025672
Alias	Os_ciR2426
Organism	Oryza sativa
Position	chr4: 33124967-33125432 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0650000
Parent gene annotation	Similar to Oryzain alpha chain precursor (EC 3.4.22.-). (Os04t06 50000-01);Similar to Oryzain alpha chain precursor (EC 3.4.22.-) . (Os04t0650000-02);Similar to cDNA clone:J013002H09, full inser t sequence. (Os04t0650000-03)
Parent gene strand	-
Alternative splicing	Os04g0650000_circ_g.5
Support reads	4/1
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	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	Os04t0650000-03:1 Os04t0650000-02:2 Os04t0650000-01:1

			
						 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  
						
							CAGTCAACTAGCTCCTGCTCAGACAAAGATATCAGGTCGCCAGTAACAATCTGGTTGATGCCTT
CTACAGCTGCTATTGCTGAGAAAGCCCAGCAACTTCcgatgagtagagctggaatgctctgcca
ccggcttcaattgcaacactgacgggctggtttgctaccgccttctgcagactcgtctcactgt
ttggtgtt

						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: 377
Transcript exons: 33124967-33125107,33125197-33125432
CGATGAGTAGAGCTGGAATGCTCTGCCACCGGCTTCAATTGCAACACTGACGGGCTGGTTTGCT
ACCGCCTTCTGCAGACTCGTCTCACTGTTTGGTGTTACATCTTCGTAGCTGTCAATTGTGACAA
CCTTTGCGTTTTTCCTGTTTACGTCACACCGTTCGTCCTTGCCTTTGTAAGGGTAGTCATCCTC
GGTGTCGATTCCACCATTGTTGATGATGAAATCAAATGCATAGTCCATCAGACCTCCATTGCAT
CCCTCGTTATATGAAGTGTCACAGTCAACTAGCTCCTGCTCAGACAAAGATATCAGGTCGCCAG
TAACAATCTGGTTGATGCCTTCTACAGCTGCTATTGCTGAGAAAGCCCAGCAACTTC
						
						Genomic sequence
						
							CGATGAGTAGAGCTGGAATGCTCTGCCACCGGCTTCAATTGCAACACTGACGGGCTGGTTTGCT
ACCGCCTTCTGCAGACTCGTCTCACTGTTTGGTGTTACATCTTCGTAGCTGTCAATTGTGACAA
CCTTTGCGTTTTTCTGTGAGTATAGCAGCACAAGTGAGCAATAGCATATCAAAATTATGCTACT
ACCTGAAAAACCAAGGGAGCAAAGAAGACGAAAGATACCCTGTTTACGTCACACCGTTCGTCCT
TGCCTTTGTAAGGGTAGTCATCCTCGGTGTCGATTCCACCATTGTTGATGATGAAATCAAATGC
ATAGTCCATCAGACCTCCATTGCATCCCTCGTTATATGAAGTGTCACAGTCAACTAGCTCCTGC
TCAGACAAAGATATCAGGTCGCCAGTAACAATCTGGTTGATGCCTTCTACAGCTGCTATTGCTG
AGAAAGCCCAGCAACTTC

Sequences
Splice junction sequence	CAGTCAACTAGCTCCTGCTCAGACAAAGATATCAGGTCGCCAGTAACAATCTGGTTGATGCCTT CTACAGCTGCTATTGCTGAGAAAGCCCAGCAACTTCcgatgagtagagctggaatgctctgcca ccggcttcaattgcaacactgacgggctggtttgctaccgccttctgcagactcgtctcactgt ttggtgtt
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: 377 Transcript exons: 33124967-33125107,33125197-33125432 CGATGAGTAGAGCTGGAATGCTCTGCCACCGGCTTCAATTGCAACACTGACGGGCTGGTTTGCT ACCGCCTTCTGCAGACTCGTCTCACTGTTTGGTGTTACATCTTCGTAGCTGTCAATTGTGACAA CCTTTGCGTTTTTCCTGTTTACGTCACACCGTTCGTCCTTGCCTTTGTAAGGGTAGTCATCCTC GGTGTCGATTCCACCATTGTTGATGATGAAATCAAATGCATAGTCCATCAGACCTCCATTGCAT CCCTCGTTATATGAAGTGTCACAGTCAACTAGCTCCTGCTCAGACAAAGATATCAGGTCGCCAG TAACAATCTGGTTGATGCCTTCTACAGCTGCTATTGCTGAGAAAGCCCAGCAACTTC
Genomic sequence	CGATGAGTAGAGCTGGAATGCTCTGCCACCGGCTTCAATTGCAACACTGACGGGCTGGTTTGCT ACCGCCTTCTGCAGACTCGTCTCACTGTTTGGTGTTACATCTTCGTAGCTGTCAATTGTGACAA CCTTTGCGTTTTTCTGTGAGTATAGCAGCACAAGTGAGCAATAGCATATCAAAATTATGCTACT ACCTGAAAAACCAAGGGAGCAAAGAAGACGAAAGATACCCTGTTTACGTCACACCGTTCGTCCT TGCCTTTGTAAGGGTAGTCATCCTCGGTGTCGATTCCACCATTGTTGATGATGAAATCAAATGC ATAGTCCATCAGACCTCCATTGCATCCCTCGTTATATGAAGTGTCACAGTCAACTAGCTCCTGC TCAGACAAAGATATCAGGTCGCCAGTAACAATCTGGTTGATGCCTTCTACAGCTGCTATTGCTG AGAAAGCCCAGCAACTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005797* osi_circ_014941 zma_circ_010377* 						
					
						PMCS
						0.40915068

Conservation Information
Conserved circRNAs	osi_circ_005797* osi_circ_014941 zma_circ_010377*
PMCS	0.40915068

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							33125391-33125013(+)
33125297-33125408(-)
						
						Potential amino acid sequence
						
							MPSTAAIAEKAQQLPMSRAGMLCHRLQLQH*(+)
MDYAFDFIINNGGIDTEDDYPYKGKDERCDVNRKNAKVVTIDSYEDVTPNSETSLQKAVANQPV
SVAIEAGGRAFQLYSSEVAGLSQQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	33125391-33125013(+) 33125297-33125408(-)
Potential amino acid sequence	MPSTAAIAEKAQQLPMSRAGMLCHRLQLQH(+) MDYAFDFIINNGGIDTEDDYPYKGKDERCDVNRKNAKVVTIDSYEDVTPNSETSLQKAVANQPV SVAIEAGGRAFQLYSSEVAGLSQQ(-)
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 Os04g0650000_circ_g.4

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