Plant Circular RNA Database

Detail information of Os04g0280200_circ_g.25

			
						 General Information
					
						CircRNA Name
						Os04g0280200_circ_g.25
					
						ID in PlantcircBase
						osa_circ_023306
					
						Alias
						Os_ciR3380
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 11881204-11882171  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0280251						
					
						Parent gene annotation
						
							Hypothetical protein. (Os04t0280251-00)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0280200_circ_g.2 Os04g0280200_circ_g.3 Os04g0280200_circ_g.4 Os04g0280200_circ_g.5 Os04g0280200_circ_g.6 Os04g0280200_circ_g.7 Os04g0280200_circ_g.8 Os04g0280200_circ_g.9 Os04g0280200_circ_g.10 Os04g0280200_circ_g.11 Os04g0280200_circ_g.12 Os04g0280200_circ_g.13 Os04g0280200_circ_g.14 Os04g0280200_circ_g.15 Os04g0280200_circ_g.16 Os04g0280200_circ_g.17 Os04g0280200_circ_g.18 Os04g0280200_circ_g.19 Os04g0280200_circ_g.20 Os04g0280200_circ_g.21 Os04g0280200_circ_g.22 Os04g0280200_circ_g.23 Os04g0280200_circ_g.24 Os04g0280200_circ_g.26 Os04g0280200_circ_g.27 Os04g0280200_circ_g.28 Os04g0280200_circ_g.29 						
					
						Support reads
						3/1
					
						Tissues
						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  
						
							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
						Os04t0280200-01:5
Os04t0280251-00:5
Os04t0280200-01:5

General Information
CircRNA Name	Os04g0280200_circ_g.25
ID in PlantcircBase	osa_circ_023306
Alias	Os_ciR3380
Organism	Oryza sativa
Position	chr4: 11881204-11882171 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ui-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0280251
Parent gene annotation	Hypothetical protein. (Os04t0280251-00)
Parent gene strand	-
Alternative splicing	Os04g0280200_circ_g.2 Os04g0280200_circ_g.3 Os04g0280200_circ_g.4 Os04g0280200_circ_g.5 Os04g0280200_circ_g.6 Os04g0280200_circ_g.7 Os04g0280200_circ_g.8 Os04g0280200_circ_g.9 Os04g0280200_circ_g.10 Os04g0280200_circ_g.11 Os04g0280200_circ_g.12 Os04g0280200_circ_g.13 Os04g0280200_circ_g.14 Os04g0280200_circ_g.15 Os04g0280200_circ_g.16 Os04g0280200_circ_g.17 Os04g0280200_circ_g.18 Os04g0280200_circ_g.19 Os04g0280200_circ_g.20 Os04g0280200_circ_g.21 Os04g0280200_circ_g.22 Os04g0280200_circ_g.23 Os04g0280200_circ_g.24 Os04g0280200_circ_g.26 Os04g0280200_circ_g.27 Os04g0280200_circ_g.28 Os04g0280200_circ_g.29
Support reads	3/1
Tissues	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	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	Os04t0280200-01:5 Os04t0280251-00:5 Os04t0280200-01:5

			
						 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  
						
							TCATTTAATGGTAGCCTATAAGGGAAGGAAATTTTATTATCCAGCCAAAGGTTGATTTTGACAT
TAGTGCCAGCACTGTCGCAGGACTTCTTAAGCTTGGgtaatcttcgaaggtgtctatgctttgc
atcctgctataaggaaatcactggatttatggattgcagttgtaagattttttaccctcaaaaa
aaagttgt

									
								

					

						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: 551
Transcript exons: 11881204-11881272,11881402-11881545,11881669-11881743,11
881818-11881994,11882086-11882171
GTAATCTTCGAAGGTGTCTATGCTTTGCATCCTGCTATAAGGAAATCACTGGATTTATGGATTG
CAGTTGTTGGTGGAGTACATTCTCATCTTATTGCAAGAATACAGAGAGACAAGAATCGTGCAGG
CTTTTCTATTTCTCAGAGTGAAATTATGACTACCGTGTTTCCGCTATTTCAGCAATACATAGAA
CCACATCTTATCGATGCTCATCTTAAGATTCAAAATGACTTTGACCCTGTGCTCTCTCCTGAAA
GCTCACTTTTCGTACTAAAAAGTAAAAAACAGGTATCTTATCAAGACATATTGAAAGTACTCGA
TGCTAGTAAAGCCTGCAGCTGTGTCCAGAATTTTACTGATGTGTATCTAAGACTTCCTGGCATA
CCGTTGAGTGGACAGCTGACAGAAGGCGAGTGTATTAGGGTCCGAATATGTGAAGGAAGATTTG
CACTGTTAATACGAGAGCCTATAAGGGAAGGAAATTTTATTATCCAGCCAAAGGTTGATTTTGA
CATTAGTGCCAGCACTGTCGCAGGACTTCTTAAGCTTGG
						
					

						Genomic sequence
						
							GTAATCTTCGAAGGTGTCTATGCTTTGCATCCTGCTATAAGGAAATCACTGGATTTATGGATTG
CAGTTGTAAGATTTTTTACCCTCAAAAAAAAGTTGTAAGATTTTATTCAAATCTTGAAAAAACT
GTTTATCTAGTTTGATTTTTTTTTACATCATAAATATCTCCCTGGAAATTTACTGCATTCTGTC
TAGTAGGTTGGTGGAGTACATTCTCATCTTATTGCAAGAATACAGAGAGACAAGAATCGTGCAG
GCTTTTCTATTTCTCAGAGTGAAATTATGACTACCGTGTTTCCGCTATTTCAGCAATACATAGA
ACCACATCTTATCGATGCTCATGTTGGTACAAGAAACATGAATTTGACCTATTTGATATATATT
TATCATTTATGGCTTTCCATTATCATGTATTTAGTAACTTGTTTGGACTCACGCAATGTTCCTT
CTCCACGTGCTTTGCAGCTTAAGATTCAAAATGACTTTGACCCTGTGCTCTCTCCTGAAAGCTC
ACTTTTCGTACTAAAAAGTAAAAAACAGGTAAGTTTGAGCTTTATATTGTTCATCTTATTATTA
CGTTGGTGATTATTTATCTATTTTTGTTTCATGAATAGGTATCTTATCAAGACATATTGAAAGT
ACTCGATGCTAGTAAAGCCTGCAGCTGTGTCCAGAATTTTACTGATGTGTATCTAAGACTTCCT
GGCATACCGTTGAGTGGACAGCTGACAGAAGGCGAGTGTATTAGGGTCCGAATATGTGAAGGAA
GATTTGCACTGTTAATACGAGAGGTTAGTTTACCTTTTGCATACCATTTATCTTTGTGTTTTCA
TGAGACAGTCAATGACAGGCTACGTTTTTCCTTTGTTCATTTAATGGTAGCCTATAAGGGAAGG
AAATTTTATTATCCAGCCAAAGGTTGATTTTGACATTAGTGCCAGCACTGTCGCAGGACTTCTT
AAGCTTGG
						
					

			
		

Sequences
Splice junction sequence	TCATTTAATGGTAGCCTATAAGGGAAGGAAATTTTATTATCCAGCCAAAGGTTGATTTTGACAT TAGTGCCAGCACTGTCGCAGGACTTCTTAAGCTTGGgtaatcttcgaaggtgtctatgctttgc atcctgctataaggaaatcactggatttatggattgcagttgtaagattttttaccctcaaaaa aaagttgt
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: 551 Transcript exons: 11881204-11881272,11881402-11881545,11881669-11881743,11 881818-11881994,11882086-11882171 GTAATCTTCGAAGGTGTCTATGCTTTGCATCCTGCTATAAGGAAATCACTGGATTTATGGATTG CAGTTGTTGGTGGAGTACATTCTCATCTTATTGCAAGAATACAGAGAGACAAGAATCGTGCAGG CTTTTCTATTTCTCAGAGTGAAATTATGACTACCGTGTTTCCGCTATTTCAGCAATACATAGAA CCACATCTTATCGATGCTCATCTTAAGATTCAAAATGACTTTGACCCTGTGCTCTCTCCTGAAA GCTCACTTTTCGTACTAAAAAGTAAAAAACAGGTATCTTATCAAGACATATTGAAAGTACTCGA TGCTAGTAAAGCCTGCAGCTGTGTCCAGAATTTTACTGATGTGTATCTAAGACTTCCTGGCATA CCGTTGAGTGGACAGCTGACAGAAGGCGAGTGTATTAGGGTCCGAATATGTGAAGGAAGATTTG CACTGTTAATACGAGAGCCTATAAGGGAAGGAAATTTTATTATCCAGCCAAAGGTTGATTTTGA CATTAGTGCCAGCACTGTCGCAGGACTTCTTAAGCTTGG
Genomic sequence	GTAATCTTCGAAGGTGTCTATGCTTTGCATCCTGCTATAAGGAAATCACTGGATTTATGGATTG CAGTTGTAAGATTTTTTACCCTCAAAAAAAAGTTGTAAGATTTTATTCAAATCTTGAAAAAACT GTTTATCTAGTTTGATTTTTTTTTACATCATAAATATCTCCCTGGAAATTTACTGCATTCTGTC TAGTAGGTTGGTGGAGTACATTCTCATCTTATTGCAAGAATACAGAGAGACAAGAATCGTGCAG GCTTTTCTATTTCTCAGAGTGAAATTATGACTACCGTGTTTCCGCTATTTCAGCAATACATAGA ACCACATCTTATCGATGCTCATGTTGGTACAAGAAACATGAATTTGACCTATTTGATATATATT TATCATTTATGGCTTTCCATTATCATGTATTTAGTAACTTGTTTGGACTCACGCAATGTTCCTT CTCCACGTGCTTTGCAGCTTAAGATTCAAAATGACTTTGACCCTGTGCTCTCTCCTGAAAGCTC ACTTTTCGTACTAAAAAGTAAAAAACAGGTAAGTTTGAGCTTTATATTGTTCATCTTATTATTA CGTTGGTGATTATTTATCTATTTTTGTTTCATGAATAGGTATCTTATCAAGACATATTGAAAGT ACTCGATGCTAGTAAAGCCTGCAGCTGTGTCCAGAATTTTACTGATGTGTATCTAAGACTTCCT GGCATACCGTTGAGTGGACAGCTGACAGAAGGCGAGTGTATTAGGGTCCGAATATGTGAAGGAA GATTTGCACTGTTAATACGAGAGGTTAGTTTACCTTTTGCATACCATTTATCTTTGTGTTTTCA TGAGACAGTCAATGACAGGCTACGTTTTTCCTTTGTTCATTTAATGGTAGCCTATAAGGGAAGG AAATTTTATTATCCAGCCAAAGGTTGATTTTGACATTAGTGCCAGCACTGTCGCAGGACTTCTT AAGCTTGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_015184 						
					
						PMCS
						0.337229795

Conservation Information
Conserved circRNAs	osi_circ_015184
PMCS	0.337229795

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11881487-11881204(+)
11881235-11881828(-)
						
						Potential amino acid sequence
						
							MTTVFPLFQQYIEPHLIDAHLKIQNDFDPVLSPESSLFVLKSKKQVSYQDILKVLDASKACSCV
QNFTDVYLRLPGIPLSGQLTEGECIRVRICEGRFALLIREPIREGNFIIQPKVDFDISASTVAG
LLKLG*(+)
MQSIDTFEDYPSLRSPATVLALMSKSTFGWIIKFPSLIGSRINSANLPSHIRTLIHSPSVSCPL
NGMPGSLRYTSVKFWTQLQALLASSTFNMS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11881487-11881204(+) 11881235-11881828(-)
Potential amino acid sequence	MTTVFPLFQQYIEPHLIDAHLKIQNDFDPVLSPESSLFVLKSKKQVSYQDILKVLDASKACSCV QNFTDVYLRLPGIPLSGQLTEGECIRVRICEGRFALLIREPIREGNFIIQPKVDFDISASTVAG LLKLG(+) MQSIDTFEDYPSLRSPATVLALMSKSTFGWIIKFPSLIGSRINSANLPSHIRTLIHSPSVSCPL NGMPGSLRYTSVKFWTQLQALLASSTFNMS(-)
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 Os04g0280200_circ_g.25

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