Plant Circular RNA Database

Detail information of Os05g0596600_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os05g0596600_circ_g.4
					
						ID in PlantcircBase
						osa_circ_029250
					
						Alias
						Os_ciR2074
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 29734822-29735540  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os05g0596600						
					
						Parent gene annotation
						
							Similar to SMC5 protein. (Os05t0596600-01);Similar to SMC5 prote
in. (Os05t0596600-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os05g0596600_circ_g.3 Os05g0596600_circ_g.5 Os05g0596600_circ_g.6 Os05g0596600_circ_g.7 Os05g0596600_circ_g.8 Os05g0596600_circ_g.9 						
					
						Support reads
						9/1
					
						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
						Os05t0596600-02:3

General Information
CircRNA Name	Os05g0596600_circ_g.4
ID in PlantcircBase	osa_circ_029250
Alias	Os_ciR2074
Organism	Oryza sativa
Position	chr5: 29734822-29735540 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os05g0596600
Parent gene annotation	Similar to SMC5 protein. (Os05t0596600-01);Similar to SMC5 prote in. (Os05t0596600-02)
Parent gene strand	-
Alternative splicing	Os05g0596600_circ_g.3 Os05g0596600_circ_g.5 Os05g0596600_circ_g.6 Os05g0596600_circ_g.7 Os05g0596600_circ_g.8 Os05g0596600_circ_g.9
Support reads	9/1
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	Os05t0596600-02:3

			
						 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  
						
							CGCTGATCATTTAACTTTGCCGCCTGATCAACAAACTTTCTTTTGCTTGACTCCATATCTTCCT
CTTTATATATAGTCTCCAACATTCTTCTTTTAATATagttttcatattctttagcagcttcaat
agcattcttttcaagtttcttcacatccttttccatctcccatatctatcagatgattaatgaa
ggacagat

						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: 112
Transcript exons: 29734822-29734852,29735460-29735540
AGTTTTCATATTCTTTAGCAGCTTCAATAGCCCGCCTGATCAACAAACTTTCTTTTGCTTGACT
CCATATCTTCCTCTTTATATATAGTCTCCAACATTCTTCTTTTAATAT
Transcript length: 276
Transcript exons: 29734822-29734894,29735229-29735306,29735416-29735540
AGTTTTCATATTCTTTAGCAGCTTCAATAGCATTCTTTTCAAGTTTCTTCACATCCTTTTCCAT
CTCCCATATCTTTGTATCGAGCTCAATGGAAGCCATGTTCTTTTGTGTGCAACTCCATTTGAGA
GCAACAGCTTCAATAAGTAAATCCTTGAGTTTTAGCACTAGTTCATATCGCTGATCATTTAACT
TTGCCGCCTGATCAACAAACTTTCTTTTGCTTGACTCCATATCTTCCTCTTTATATATAGTCTC
CAACATTCTTCTTTTAATAT
						
						Genomic sequence
						
							AGTTTTCATATTCTTTAGCAGCTTCAATAGCATTCTTTTCAAGTTTCTTCACATCCTTTTCCAT
CTCCCATATCTATCAGATGATTAATGAAGGACAGATGATTACATGTGCGAATTGTTTCGGTACA
AGGAACGGGATAAGACATAAGCAAATATGGCAATTTTCTGGTGTAACATGTGCAAATTATGTGT
GCTTTAGACCAAACTAGTATTTTAGTAATTTATATATCTTATTGCAAGCAGCCAAACATTTGTA
AAACAGCTGTGATTAATTGGGTGATTAATTGCAAAGTTTCCAAGCGGAGATTAATTGGGTCACT
GCAAGGTAATCAAAATGCAAGAAATATGCACAGTTCAATTCAAGAAGTTTTGTGTTATGAAAGT
AACTAGTTTCTCACAAAGCATACCTTTGTATCGAGCTCAATGGAAGCCATGTTCTTTTGTGTGC
AACTCCATTTGAGAGCAACAGCTTCAATAAGTAAATCCTGAGAGAATTTAAATAAAATTTATGC
AAGCACAAATGTGATGATGATCTTCAAGATAAACAAAATATTGTATCATCGTCAGAAGCTCCAA
GCTCTGTTAAGTGCTAACCTTGAGTTTTAGCACTAGTTCATATCGCTGATCATTTAACTTTGCC
GCCTGATCAACAAACTTTCTTTTGCTTGACTCCATATCTTCCTCTTTATATATAGTCTCCAACA
TTCTTCTTTTAATAT

Sequences
Splice junction sequence	CGCTGATCATTTAACTTTGCCGCCTGATCAACAAACTTTCTTTTGCTTGACTCCATATCTTCCT CTTTATATATAGTCTCCAACATTCTTCTTTTAATATagttttcatattctttagcagcttcaat agcattcttttcaagtttcttcacatccttttccatctcccatatctatcagatgattaatgaa ggacagat
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: 112 Transcript exons: 29734822-29734852,29735460-29735540 AGTTTTCATATTCTTTAGCAGCTTCAATAGCCCGCCTGATCAACAAACTTTCTTTTGCTTGACT CCATATCTTCCTCTTTATATATAGTCTCCAACATTCTTCTTTTAATAT Transcript length: 276 Transcript exons: 29734822-29734894,29735229-29735306,29735416-29735540 AGTTTTCATATTCTTTAGCAGCTTCAATAGCATTCTTTTCAAGTTTCTTCACATCCTTTTCCAT CTCCCATATCTTTGTATCGAGCTCAATGGAAGCCATGTTCTTTTGTGTGCAACTCCATTTGAGA GCAACAGCTTCAATAAGTAAATCCTTGAGTTTTAGCACTAGTTCATATCGCTGATCATTTAACT TTGCCGCCTGATCAACAAACTTTCTTTTGCTTGACTCCATATCTTCCTCTTTATATATAGTCTC CAACATTCTTCTTTTAATAT
Genomic sequence	AGTTTTCATATTCTTTAGCAGCTTCAATAGCATTCTTTTCAAGTTTCTTCACATCCTTTTCCAT CTCCCATATCTATCAGATGATTAATGAAGGACAGATGATTACATGTGCGAATTGTTTCGGTACA AGGAACGGGATAAGACATAAGCAAATATGGCAATTTTCTGGTGTAACATGTGCAAATTATGTGT GCTTTAGACCAAACTAGTATTTTAGTAATTTATATATCTTATTGCAAGCAGCCAAACATTTGTA AAACAGCTGTGATTAATTGGGTGATTAATTGCAAAGTTTCCAAGCGGAGATTAATTGGGTCACT GCAAGGTAATCAAAATGCAAGAAATATGCACAGTTCAATTCAAGAAGTTTTGTGTTATGAAAGT AACTAGTTTCTCACAAAGCATACCTTTGTATCGAGCTCAATGGAAGCCATGTTCTTTTGTGTGC AACTCCATTTGAGAGCAACAGCTTCAATAAGTAAATCCTGAGAGAATTTAAATAAAATTTATGC AAGCACAAATGTGATGATGATCTTCAAGATAAACAAAATATTGTATCATCGTCAGAAGCTCCAA GCTCTGTTAAGTGCTAACCTTGAGTTTTAGCACTAGTTCATATCGCTGATCATTTAACTTTGCC GCCTGATCAACAAACTTTCTTTTGCTTGACTCCATATCTTCCTCTTTATATATAGTCTCCAACA TTCTTCTTTTAATAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_006446* osi_circ_015887 						
					
						PMCS
						0.260553129

Conservation Information
Conserved circRNAs	osi_circ_006446* osi_circ_015887
PMCS	0.260553129

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							29734856-29735453(-)
29735528-29734824(-)
						
						Potential amino acid sequence
						
							MLLKLLKNMKTILKEECWRLYIKRKIWSQAKESLLIRRQS*(-)
MLETIYKEEDMESSKRKFVDQAAKLNDQRYELVLKLKDLLIEAVALKWSCTQKNMASIELDTKI
WEMEKDVKKLEKNAIEAAKEYENYIKRRMLETIYKEEDMESSKRKFVDQAAKLNDQRYELVLKL
KDLLIEAVALKWSCTQKNMASIELDTKIWEMEKDVKKLEKNAIEAAKEYENYIKRRMLETIYKE
EDMESSKRKFVDQAAKLNDQRYELVLKLKDLLIEAVALKWSCTQKNMASIELDTKIWEMEKDVK
KLEKNAIEAAKEYENYIKRRMLETIYKEEDMESSKRKFVDQAAKLNDQRYELVLKLKDLLIEAV
ALKWSCTQKNMASIELDTKIWEMEKDVKKLEKNAIEAAKEYEN(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	29734856-29735453(-) 29735528-29734824(-)
Potential amino acid sequence	MLLKLLKNMKTILKEECWRLYIKRKIWSQAKESLLIRRQS*(-) MLETIYKEEDMESSKRKFVDQAAKLNDQRYELVLKLKDLLIEAVALKWSCTQKNMASIELDTKI WEMEKDVKKLEKNAIEAAKEYENYIKRRMLETIYKEEDMESSKRKFVDQAAKLNDQRYELVLKL KDLLIEAVALKWSCTQKNMASIELDTKIWEMEKDVKKLEKNAIEAAKEYENYIKRRMLETIYKE EDMESSKRKFVDQAAKLNDQRYELVLKLKDLLIEAVALKWSCTQKNMASIELDTKIWEMEKDVK KLEKNAIEAAKEYENYIKRRMLETIYKEEDMESSKRKFVDQAAKLNDQRYELVLKLKDLLIEAV ALKWSCTQKNMASIELDTKIWEMEKDVKKLEKNAIEAAKEYEN(-)
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 Os05g0596600_circ_g.4

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