Plant Circular RNA Database

Detail information of Os04g0605300_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0605300_circ_g.1
					
						ID in PlantcircBase
						osa_circ_025101
					
						Alias
						Os04circ12857/Os_ciR9540
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 30555858-30556903  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os04g0605300						
					
						Parent gene annotation
						
							Leucine-rich repeat, typical subtype containing protein. (Os04t0
605300-01);Leucine-rich repeat, typical subtype containing prote
in. (Os04t0605300-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0605300_circ_g.2 Os04g0605300_circ_g.3 Os04g0605300_circ_g.4 						
					
						Support reads
						2/2/3
					
						Tissues
						leaf/root/shoot, 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
						Os04t0605300-02:2
Os04t0605300-01:2

General Information
CircRNA Name	Os04g0605300_circ_g.1
ID in PlantcircBase	osa_circ_025101
Alias	Os04circ12857/Os_ciR9540
Organism	Oryza sativa
Position	chr4: 30555858-30556903 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl, find_circ
Parent gene	Os04g0605300
Parent gene annotation	Leucine-rich repeat, typical subtype containing protein. (Os04t0 605300-01);Leucine-rich repeat, typical subtype containing prote in. (Os04t0605300-02)
Parent gene strand	-
Alternative splicing	Os04g0605300_circ_g.2 Os04g0605300_circ_g.3 Os04g0605300_circ_g.4
Support reads	2/2/3
Tissues	leaf/root/shoot, 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	Os04t0605300-02:2 Os04t0605300-01:2

			
						 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  
						
							TGCAACCCTCCTGCAAAACCAGCAGGGTTAAGGTGTCCACGCCTCCTCTTCTCTCCCATTTCCC
TCATGCTTCCAATCTTCTTCTCCACTTCTGATATACcggcactcctcgatggtgttggggaggg
actcgagcaggttgccggagacgttgaggaccttgagcttggagaggcagccgatggagttggg
cagcgatt

						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: 400
Transcript exons: 30555858-30556027,30556674-30556903
CGGCACTCCTCGATGGTGTTGGGGAGGGACTCGAGCAGGTTGCCGGAGACGTTGAGGACCTTGA
GCTTGGAGAGGCAGCCGATGGAGTTGGGCAGCGATTTCAGCTGGTTGGACCGCACGTCCAGCAC
CACCACGTTCAGCAGCCGAGCGATTATTGACTCCGGGATGCTCTCAAGATTGTTGTTAGAGAGA
TCCAAGATGGTGACTTGACCAAGAGACATGGTGAGGTGTGGGAGGGCATCCATGGACATGCCAC
TCATGTCTAGCTTATGCTCCTCGTTCTTCTTCTCCTCATGATCATGCAACCCTCCTGCAAAACC
AGCAGGGTTAAGGTGTCCACGCCTCCTCTTCTCTCCCATTTCCCTCATGCTTCCAATCTTCTTC
TCCACTTCTGATATAC
						
						Genomic sequence
						
							CGGCACTCCTCGATGGTGTTGGGGAGGGACTCGAGCAGGTTGCCGGAGACGTTGAGGACCTTGA
GCTTGGAGAGGCAGCCGATGGAGTTGGGCAGCGATTTCAGCTGGTTGGACCGCACGTCCAGCAC
CACCACGTTCAGCAGCCGAGCGATTATTGACTCCGGGATGCTCTGCGGTTTTCCAAAACGGAAG
GAAATTTAAGTCTCGTATAAAGATCGGATTTTTTTTTACTTTCTCCGAAGTTTTGTCAACTGTA
AAAAAAGGTTAGTACAACCAGAGCATACGCACAATTAATCTGCATGTTCTTTTTTGCCGGTACA
GTACTGCAGGCAGTACCATTTCTCCCACCAAGTCAAACAGATAGAGAGATAAGTTTGCAACTTG
CAGGTATTTTCGTCTTTAATACCGTTCATCCCATAATAAAACTTAAAGTTCATCCTACTGGTAT
ACGTATGCATGGTTTCAGAATATTCTTGGCTCTTACAAAGCCATCACTTATTTGATATTTTTCG
TCCTAGAAAATGACAAAATTAAGGAGGACAAGCCAAACGGCAAAAAAACAAGAGATTGTGAAGA
GGGATGCATGGCTAGTTAGGCTCATGTAGTATTAATAATATAGGCCATGCTTATCTCATACAGC
TCGACTTAACTTATCACCAAGATATAAAACTACCGTACACCGTTTGAAGATAAGTTCTTGCTGG
TTATCCATTACTATAATACTCTGAATAGATAGACAAAGAAGCATGTGATCTAGCTAGCTTCCAG
ATCAAAAGTAGTAGTAATAAAATTAAACCACGTATATATGAAATCTACCTCAAGATTGTTGTTA
GAGAGATCCAAGATGGTGACTTGACCAAGAGACATGGTGAGGTGTGGGAGGGCATCCATGGACA
TGCCACTCATGTCTAGCTTATGCTCCTCGTTCTTCTTCTCCTCATGATCATGCAACCCTCCTGC
AAAACCAGCAGGGTTAAGGTGTCCACGCCTCCTCTTCTCTCCCATTTCCCTCATGCTTCCAATC
TTCTTCTCCACTTCTGATATAC

Sequences
Splice junction sequence	TGCAACCCTCCTGCAAAACCAGCAGGGTTAAGGTGTCCACGCCTCCTCTTCTCTCCCATTTCCC TCATGCTTCCAATCTTCTTCTCCACTTCTGATATACcggcactcctcgatggtgttggggaggg actcgagcaggttgccggagacgttgaggaccttgagcttggagaggcagccgatggagttggg cagcgatt
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: 400 Transcript exons: 30555858-30556027,30556674-30556903 CGGCACTCCTCGATGGTGTTGGGGAGGGACTCGAGCAGGTTGCCGGAGACGTTGAGGACCTTGA GCTTGGAGAGGCAGCCGATGGAGTTGGGCAGCGATTTCAGCTGGTTGGACCGCACGTCCAGCAC CACCACGTTCAGCAGCCGAGCGATTATTGACTCCGGGATGCTCTCAAGATTGTTGTTAGAGAGA TCCAAGATGGTGACTTGACCAAGAGACATGGTGAGGTGTGGGAGGGCATCCATGGACATGCCAC TCATGTCTAGCTTATGCTCCTCGTTCTTCTTCTCCTCATGATCATGCAACCCTCCTGCAAAACC AGCAGGGTTAAGGTGTCCACGCCTCCTCTTCTCTCCCATTTCCCTCATGCTTCCAATCTTCTTC TCCACTTCTGATATAC
Genomic sequence	CGGCACTCCTCGATGGTGTTGGGGAGGGACTCGAGCAGGTTGCCGGAGACGTTGAGGACCTTGA GCTTGGAGAGGCAGCCGATGGAGTTGGGCAGCGATTTCAGCTGGTTGGACCGCACGTCCAGCAC CACCACGTTCAGCAGCCGAGCGATTATTGACTCCGGGATGCTCTGCGGTTTTCCAAAACGGAAG GAAATTTAAGTCTCGTATAAAGATCGGATTTTTTTTTACTTTCTCCGAAGTTTTGTCAACTGTA AAAAAAGGTTAGTACAACCAGAGCATACGCACAATTAATCTGCATGTTCTTTTTTGCCGGTACA GTACTGCAGGCAGTACCATTTCTCCCACCAAGTCAAACAGATAGAGAGATAAGTTTGCAACTTG CAGGTATTTTCGTCTTTAATACCGTTCATCCCATAATAAAACTTAAAGTTCATCCTACTGGTAT ACGTATGCATGGTTTCAGAATATTCTTGGCTCTTACAAAGCCATCACTTATTTGATATTTTTCG TCCTAGAAAATGACAAAATTAAGGAGGACAAGCCAAACGGCAAAAAAACAAGAGATTGTGAAGA GGGATGCATGGCTAGTTAGGCTCATGTAGTATTAATAATATAGGCCATGCTTATCTCATACAGC TCGACTTAACTTATCACCAAGATATAAAACTACCGTACACCGTTTGAAGATAAGTTCTTGCTGG TTATCCATTACTATAATACTCTGAATAGATAGACAAAGAAGCATGTGATCTAGCTAGCTTCCAG ATCAAAAGTAGTAGTAATAAAATTAAACCACGTATATATGAAATCTACCTCAAGATTGTTGTTA GAGAGATCCAAGATGGTGACTTGACCAAGAGACATGGTGAGGTGTGGGAGGGCATCCATGGACA TGCCACTCATGTCTAGCTTATGCTCCTCGTTCTTCTTCTCCTCATGATCATGCAACCCTCCTGC AAAACCAGCAGGGTTAAGGTGTCCACGCCTCCTCTTCTCTCCCATTTCCCTCATGCTTCCAATC TTCTTCTCCACTTCTGATATAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005700* 						
					
						PMCS
						0.263011608

Conservation Information
Conserved circRNAs	osi_circ_005700*
PMCS	0.263011608

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30556871-30556012(+)
30556873-30556833(-)
						
						Potential amino acid sequence
						
							MLPIFFSTSDIPALLDGVGEGLEQVAGDVEDLELGEAADGVGQRFQLVGPHVQHHHVQQPSDY*
(+)
MREMGEKRRRGHLNPAGFAGGLHDHEEKKNEEHKLDMSGMSMDALPHLTMSLGQVTILDLSNNN
LESIPESIIARLLNVVVLDVRSNQLKSLPNSIGCLSKLKVLNVSGNLLESLPNTIEECRYIRSG
EEDWKHEGNGREEEAWTP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30556871-30556012(+) 30556873-30556833(-)
Potential amino acid sequence	MLPIFFSTSDIPALLDGVGEGLEQVAGDVEDLELGEAADGVGQRFQLVGPHVQHHHVQQPSDY* (+) MREMGEKRRRGHLNPAGFAGGLHDHEEKKNEEHKLDMSGMSMDALPHLTMSLGQVTILDLSNNN LESIPESIIARLLNVVVLDVRSNQLKSLPNSIGCLSKLKVLNVSGNLLESLPNTIEECRYIRSG EEDWKHEGNGREEEAWTP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os04g0605300_circ_g.1

Address

Any questions?

Supported by