Plant Circular RNA Database

Detail information of Os04g0620000_circ_g.25

			
						 General Information
					
						CircRNA Name
						Os04g0620000_circ_g.25
					
						ID in PlantcircBase
						osa_circ_025336
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 31511623-31512630  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0620000						
					
						Parent gene annotation
						
							C-type ATP-binding cassette (ABC) transporter, Arsenic (As) deto
xification, Reduction of As in grains (Os04t0620000-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0620000_circ_g.7 Os04g0620000_circ_g.8 Os04g0620000_circ_g.9 Os04g0620000_circ_g.10 Os04g0620000_circ_g.11 Os04g0620000_circ_g.12 Os04g0620000_circ_g.13 Os04g0620000_circ_g.14 Os04g0620000_circ_g.15 Os04g0620000_circ_g.16 Os04g0620000_circ_g.17 Os04g0620000_circ_g.18 Os04g0620000_circ_g.19 Os04g0620000_circ_g.20 Os04g0620000_circ_g.21 Os04g0620000_circ_g.22 Os04g0620000_circ_g.23 Os04g0620000_circ_g.24 Os04g0620000_circ_g.26 Os04g0620000_circ_g.27 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os04t0620000-01:4

General Information
CircRNA Name	Os04g0620000_circ_g.25
ID in PlantcircBase	osa_circ_025336
Alias	NA
Organism	Oryza sativa
Position	chr4: 31511623-31512630 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0620000
Parent gene annotation	C-type ATP-binding cassette (ABC) transporter, Arsenic (As) deto xification, Reduction of As in grains (Os04t0620000-01)
Parent gene strand	-
Alternative splicing	Os04g0620000_circ_g.7 Os04g0620000_circ_g.8 Os04g0620000_circ_g.9 Os04g0620000_circ_g.10 Os04g0620000_circ_g.11 Os04g0620000_circ_g.12 Os04g0620000_circ_g.13 Os04g0620000_circ_g.14 Os04g0620000_circ_g.15 Os04g0620000_circ_g.16 Os04g0620000_circ_g.17 Os04g0620000_circ_g.18 Os04g0620000_circ_g.19 Os04g0620000_circ_g.20 Os04g0620000_circ_g.21 Os04g0620000_circ_g.22 Os04g0620000_circ_g.23 Os04g0620000_circ_g.24 Os04g0620000_circ_g.26 Os04g0620000_circ_g.27
Support reads	1
Tissues	shoot
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	Os04t0620000-01:4

			
						 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  
						
							AATGCAATTTTATTGCCATTGGTTCATGAAACTAGAAGCATACCTCCAACAAGAGGTTCAATAT
GAGTGGGCCAACAAACTGAGAAGCATCATTGCCAATctgaagagattctgcgtcagttgaaatc
aaattggttatcctcccagaggcaaacttctttcgactatcattagttagtcgcaaagacttac
ggaaaaca

						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: 306
Transcript exons: 31511623-31511730,31512049-31512123,31512271-31512336,31
512574-31512630
CTGAAGAGATTCTGCGTCAGTTGAAATCAAATTGGTTATCCTCCCAGAGGCAAACTTCTTTCGA
CTATCATTAGTTAGTCGCAAAGACTTACGGAAAACAGCTGCGATCAATGTTGACCTCAACCTGA
AACCCGTTCGCATGACATTCTGAAAGTACTGTGCTTCAGAAAGAACACCCAGTGACACTCCAGC
GAAGATTGAGAAAGCATAGATGTAACCGCTCCAAGATGGATCACCTTTTTGCATAGACTCCAAC
AAGAGGTTCAATATGAGTGGGCCAACAAACTGAGAAGCATCATTGCCAAT
						
						Genomic sequence
						
							CTGAAGAGATTCTGCGTCAGTTGAAATCAAATTGGTTATCCTCCCAGAGGCAAACTTCTTTCGA
CTATCATTAGTTAGTCGCAAAGACTTACGGAAAACAGCTGCGATCTGCGAAACAACAGAATCAT
GGCATAAGCGTGTAACTCAACATATAACAGCAGCTGAGATGGCTATGGTAGTGTTACTTGCAGG
AAAGTCAATTATTACCAGATAATATTATATCATGGTGAACATAAGAAAAATAAAGGTCTAAACT
TAATATAACAATTACACATGTCCTTGATGCATAAATCAGGAAGTTCAATGCTCAAGATAGCCAT
GGGAGTAGAGAAAAAAAAAAGAGTGGTCCAGAAAAATAGTGGAACAAGTGGTTTGCTGGTTGCC
TGTTGACATCATATTAAACCATGCTAAACAAGCAACACCTACCAATGTTGACCTCAACCTGAAA
CCCGTTCGCATGACATTCTGAAAGTACTGTGCTTCAGAAAGAACACCCAGTGACTGCAGAATGG
TAAACAAAAGGTAAGTGATCAAAAGTCTGTCCAGTTTTGGCTCACATGCAGCATAATTGTTGCT
TGGAAGTTCAAATACACTGAATCAACAAGACATATAAGTGTGAAACATGCAATAGAAGAAAATA
ATCCATACCACTCCAGCGAAGATTGAGAAAGCATAGATGTAACCGCTCCAAGATGGATCACCTT
TTTGCATAGACTGCCAAAAGAACATTGACCTTTAGTGGTACAAAGCACCTAACACTAGCATCTC
AACAACATAAGAGAAAAGTTGGATCTATTCTTTCATATATAAATATTAAAATCTGCACAATTAC
CCAGTATGTTTTGAATTACTTCACAAGTTTGTTGATGGTAAAAACAATAGTAGAATAAGGCTTG
TAAAGGTAATGCAATGCAATTTTATTGCCATTGGTTCATGAAACTAGAAGCATACCTCCAACAA
GAGGTTCAATATGAGTGGGCCAACAAACTGAGAAGCATCATTGCCAAT

Sequences
Splice junction sequence	AATGCAATTTTATTGCCATTGGTTCATGAAACTAGAAGCATACCTCCAACAAGAGGTTCAATAT GAGTGGGCCAACAAACTGAGAAGCATCATTGCCAATctgaagagattctgcgtcagttgaaatc aaattggttatcctcccagaggcaaacttctttcgactatcattagttagtcgcaaagacttac ggaaaaca
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: 306 Transcript exons: 31511623-31511730,31512049-31512123,31512271-31512336,31 512574-31512630 CTGAAGAGATTCTGCGTCAGTTGAAATCAAATTGGTTATCCTCCCAGAGGCAAACTTCTTTCGA CTATCATTAGTTAGTCGCAAAGACTTACGGAAAACAGCTGCGATCAATGTTGACCTCAACCTGA AACCCGTTCGCATGACATTCTGAAAGTACTGTGCTTCAGAAAGAACACCCAGTGACACTCCAGC GAAGATTGAGAAAGCATAGATGTAACCGCTCCAAGATGGATCACCTTTTTGCATAGACTCCAAC AAGAGGTTCAATATGAGTGGGCCAACAAACTGAGAAGCATCATTGCCAAT
Genomic sequence	CTGAAGAGATTCTGCGTCAGTTGAAATCAAATTGGTTATCCTCCCAGAGGCAAACTTCTTTCGA CTATCATTAGTTAGTCGCAAAGACTTACGGAAAACAGCTGCGATCTGCGAAACAACAGAATCAT GGCATAAGCGTGTAACTCAACATATAACAGCAGCTGAGATGGCTATGGTAGTGTTACTTGCAGG AAAGTCAATTATTACCAGATAATATTATATCATGGTGAACATAAGAAAAATAAAGGTCTAAACT TAATATAACAATTACACATGTCCTTGATGCATAAATCAGGAAGTTCAATGCTCAAGATAGCCAT GGGAGTAGAGAAAAAAAAAAGAGTGGTCCAGAAAAATAGTGGAACAAGTGGTTTGCTGGTTGCC TGTTGACATCATATTAAACCATGCTAAACAAGCAACACCTACCAATGTTGACCTCAACCTGAAA CCCGTTCGCATGACATTCTGAAAGTACTGTGCTTCAGAAAGAACACCCAGTGACTGCAGAATGG TAAACAAAAGGTAAGTGATCAAAAGTCTGTCCAGTTTTGGCTCACATGCAGCATAATTGTTGCT TGGAAGTTCAAATACACTGAATCAACAAGACATATAAGTGTGAAACATGCAATAGAAGAAAATA ATCCATACCACTCCAGCGAAGATTGAGAAAGCATAGATGTAACCGCTCCAAGATGGATCACCTT TTTGCATAGACTGCCAAAAGAACATTGACCTTTAGTGGTACAAAGCACCTAACACTAGCATCTC AACAACATAAGAGAAAAGTTGGATCTATTCTTTCATATATAAATATTAAAATCTGCACAATTAC CCAGTATGTTTTGAATTACTTCACAAGTTTGTTGATGGTAAAAACAATAGTAGAATAAGGCTTG TAAAGGTAATGCAATGCAATTTTATTGCCATTGGTTCATGAAACTAGAAGCATACCTCCAACAA GAGGTTCAATATGAGTGGGCCAACAAACTGAGAAGCATCATTGCCAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.241380655

Conservation Information
Conserved circRNAs	NA
PMCS	0.241380655

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							31512335-31511625(-)
						
						Potential amino acid sequence
						
							MQKGDPSWSGYIYAFSIFAGVSLGVLSEAQYFQNVMRTGFRLRSTLIAAVFRKSLRLTNDSRKK
FASGRITNLISTDAESLQIGNDASQFVGPLILNLLLESMQKGDPSWSGYIYAFSIFAGVSLGVL
SEAQYFQNVMRTGFRLRSTLIAAVFRKSLRLTNDSRKKFASGRITNLISTDAESLQIGNDASQF
VGPLILNLLLESMQKGDPSWSGYIYAFSIFAGVSLGVLSEAQYFQNVMRTGFRLRSTLIAAVFR
KSLRLTNDSRKKFASGRITNLISTDAESLQIGNDASQFVGPLILNLLLESMQKGDPSWSGYIYA
FSIFAGVSLGVLSEAQYFQNVMRTGFRLRSTLIAAVFRKSLRLTNDSRKKFASGRITNLISTDA
ESLQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	31512335-31511625(-)
Potential amino acid sequence	MQKGDPSWSGYIYAFSIFAGVSLGVLSEAQYFQNVMRTGFRLRSTLIAAVFRKSLRLTNDSRKK FASGRITNLISTDAESLQIGNDASQFVGPLILNLLLESMQKGDPSWSGYIYAFSIFAGVSLGVL SEAQYFQNVMRTGFRLRSTLIAAVFRKSLRLTNDSRKKFASGRITNLISTDAESLQIGNDASQF VGPLILNLLLESMQKGDPSWSGYIYAFSIFAGVSLGVLSEAQYFQNVMRTGFRLRSTLIAAVFR KSLRLTNDSRKKFASGRITNLISTDAESLQIGNDASQFVGPLILNLLLESMQKGDPSWSGYIYA FSIFAGVSLGVLSEAQYFQNVMRTGFRLRSTLIAAVFRKSLRLTNDSRKKFASGRITNLISTDA ESLQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0620000_circ_g.25

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