Plant Circular RNA Database

Detail information of Os05g0349200_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os05g0349200_circ_g.1
					
						ID in PlantcircBase
						osa_circ_027491
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 16478099-16478682  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os05g0349200						
					
						Parent gene annotation
						
							Similar to AMP deaminase 1 (EC 3.5.4.6) (Myoadenylate deaminase)
 (AMP deaminase isoform M). (Os05t0349200-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						1
					
						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  
						
							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
						Os05t0349200-01:3

General Information
CircRNA Name	Os05g0349200_circ_g.1
ID in PlantcircBase	osa_circ_027491
Alias	NA
Organism	Oryza sativa
Position	chr5: 16478099-16478682 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os05g0349200
Parent gene annotation	Similar to AMP deaminase 1 (EC 3.5.4.6) (Myoadenylate deaminase) (AMP deaminase isoform M). (Os05t0349200-01)
Parent gene strand	-
Alternative splicing	NA
Support reads	1
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	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	Os05t0349200-01:3

			
						 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  
						
							ACAAAGGTTGTTTACTTGCCTTGAGAGCATGTGAAAACCCTGATTGATAGACAGAGTTTCTAGC
TATTTCACATAAATCACAAGAACTGAGCTTCCAGAGccaaacatgaaatgtaactcccatggca
accgcgccatatacaccaggtacatgttactggtccacctcgtcaggtaagatgacattgttta
ggtataca

						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: 303
Transcript exons: 16478099-16478221,16478322-16478417,16478599-16478682
CCAAACATGAAATGTAACTCCCATGGCAACCGCGCCATATACACCAGGTACATGTTACTGGTCC
ACCTCGTCAGGTAAGATGACATTGTTTAGGTATACAAGACGCATCTCATCTCTCCAAATCAAGT
CCCTAAACTGAACCCTGATGTGAGGCACATTAGTTTTATGAATATCGTTCCCTGTAGGTCCTCT
TTTGTAATAGTTCTTGCCAATCCAGTGTGCCTTGAGAGCATGTGAAAACCCTGATTGATAGACA
GAGTTTCTAGCTATTTCACATAAATCACAAGAACTGAGCTTCCAGAG
						
						Genomic sequence
						
							CCAAACATGAAATGTAACTCCCATGGCAACCGCGCCATATACACCAGGTACATGTTACTGGTCC
ACCTCGTCAGGTAAGATGACATTGTTTAGGTATACAAGACGCATCTCATCTCTCCAAATCTGAA
AATCACGCAATTTTCTGATCAGCTAACGCGGCTAGCAAGGGAACATGAAAATTCAAGTTTTTCG
TCCAACAGAAGTGAAGGAAATTTGTTCGTACCAAGTCCCTAAACTGAACCCTGATGTGAGGCAC
ATTAGTTTTATGAATATCGTTCCCTGTAGGTCCTCTTTTGTAATAGTTCTTGCCAATCCAGTGT
GCCTGCAATAGATGAAATGATGATATGCTTCACGGTGCCATATAATGCATTACTTACAGAGCAT
ATCAAGCAATAAGTTGCTCAACCATAATTTGTGAAAAATGGTTTGTGGCTGAAATGAATGTAAT
AAGGTAAAGATCACCAACGAGCTTTGAAAGTAGTTGACAAAGGTTGTTTACTTGCCTTGAGAGC
ATGTGAAAACCCTGATTGATAGACAGAGTTTCTAGCTATTTCACATAAATCACAAGAACTGAGC
TTCCAGAG

Sequences
Splice junction sequence	ACAAAGGTTGTTTACTTGCCTTGAGAGCATGTGAAAACCCTGATTGATAGACAGAGTTTCTAGC TATTTCACATAAATCACAAGAACTGAGCTTCCAGAGccaaacatgaaatgtaactcccatggca accgcgccatatacaccaggtacatgttactggtccacctcgtcaggtaagatgacattgttta ggtataca
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: 303 Transcript exons: 16478099-16478221,16478322-16478417,16478599-16478682 CCAAACATGAAATGTAACTCCCATGGCAACCGCGCCATATACACCAGGTACATGTTACTGGTCC ACCTCGTCAGGTAAGATGACATTGTTTAGGTATACAAGACGCATCTCATCTCTCCAAATCAAGT CCCTAAACTGAACCCTGATGTGAGGCACATTAGTTTTATGAATATCGTTCCCTGTAGGTCCTCT TTTGTAATAGTTCTTGCCAATCCAGTGTGCCTTGAGAGCATGTGAAAACCCTGATTGATAGACA GAGTTTCTAGCTATTTCACATAAATCACAAGAACTGAGCTTCCAGAG
Genomic sequence	CCAAACATGAAATGTAACTCCCATGGCAACCGCGCCATATACACCAGGTACATGTTACTGGTCC ACCTCGTCAGGTAAGATGACATTGTTTAGGTATACAAGACGCATCTCATCTCTCCAAATCTGAA AATCACGCAATTTTCTGATCAGCTAACGCGGCTAGCAAGGGAACATGAAAATTCAAGTTTTTCG TCCAACAGAAGTGAAGGAAATTTGTTCGTACCAAGTCCCTAAACTGAACCCTGATGTGAGGCAC ATTAGTTTTATGAATATCGTTCCCTGTAGGTCCTCTTTTGTAATAGTTCTTGCCAATCCAGTGT GCCTGCAATAGATGAAATGATGATATGCTTCACGGTGCCATATAATGCATTACTTACAGAGCAT ATCAAGCAATAAGTTGCTCAACCATAATTTGTGAAAAATGGTTTGTGGCTGAAATGAATGTAAT AAGGTAAAGATCACCAACGAGCTTTGAAAGTAGTTGACAAAGGTTGTTTACTTGCCTTGAGAGC ATGTGAAAACCCTGATTGATAGACAGAGTTTCTAGCTATTTCACATAAATCACAAGAACTGAGC TTCCAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_015345 						
					
						PMCS
						0.128710859

Conservation Information
Conserved circRNAs	osi_circ_015345
PMCS	0.128710859

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16478124-16478155(-)
16478186-16478648(-)
						
						Potential amino acid sequence
						
							MGVTFHVWLWKLSSCDLCEIARNSVYQSGFSHALKAHWIGKNYYKRGPTGNDIHKTNVPHIRVQ
FRDLIWRDEMRLVYLNNVILPDEVDQ*(-)
MSSYLTRWTSNMYLVYMARLPWELHFMFGSGSSVLVIYVK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	16478124-16478155(-) 16478186-16478648(-)
Potential amino acid sequence	MGVTFHVWLWKLSSCDLCEIARNSVYQSGFSHALKAHWIGKNYYKRGPTGNDIHKTNVPHIRVQ FRDLIWRDEMRLVYLNNVILPDEVDQ(-) MSSYLTRWTSNMYLVYMARLPWELHFMFGSGSSVLVIYVK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os05g0349200_circ_g.1

Address

Any questions?

Supported by