Plant Circular RNA Database

Detail information of Os05g0235300_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os05g0235300_circ_g.4
					
						ID in PlantcircBase
						osa_circ_027119
					
						Alias
						Os_ciR10290
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 8282354-8283753  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os05g0235300						
					
						Parent gene annotation
						
							Serine/threonine (Ser/Thr) protein kinase, Modulation of thylako
id membrane lipid biosynthesis, homeostasis (Os05t0235300-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os05g0235300_circ_g.5 						
					
						Support reads
						2
					
						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  
						
							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
						Os05t0235300-01:5

General Information
CircRNA Name	Os05g0235300_circ_g.4
ID in PlantcircBase	osa_circ_027119
Alias	Os_ciR10290
Organism	Oryza sativa
Position	chr5: 8282354-8283753 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os05g0235300
Parent gene annotation	Serine/threonine (Ser/Thr) protein kinase, Modulation of thylako id membrane lipid biosynthesis, homeostasis (Os05t0235300-01)
Parent gene strand	+
Alternative splicing	Os05g0235300_circ_g.5
Support reads	2
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	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	Os05t0235300-01:5

			
						 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  
						
							ACCAGATATTGCAGGAAAATATGTTGTTGCAGCAGTAACTGGGTATTTCTACTCTATTGCTTGC
GCATCCACGACAAAAGGTGTTGATGATAGCTTACAGgtgattgattactgcactcttccaatgg
aaagtccaatagctgacagccggagggaacttatccgtaatatgtggaatgagcgtattaaagg
aacaaaac

									
								

					

						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: 202
Transcript exons: 8282354-8282390,8283583-8283683,8283690-8283753
GTGATTGATTACTGCACTCTTCCAATGGAAAGTCCAATGGGGCAAGGCATGGCACTTATGGGCC
TTGTTCAACACTGAAGTCATGTCCCGCTATACTTTGCGTGGTCGACCAGATATTGCAGGAAAAT
ATGTTGTTGCAACTGGGTATTTCTACTCTATTGCTTGCGCATCCACGACAAAAGGTGTTGATGA
TAGCTTACAG
Transcript length: 762
Transcript exons: 8282354-8282464,8282783-8282923,8283003-8283131,8283229-
8283394,8283539-8283753
GTGATTGATTACTGCACTCTTCCAATGGAAAGTCCAATAGCTGACAGCCGGAGGGAACTTATCC
GTAATATGTGGAATGAGCGTATTAAAGGAACAAAACGGAATGTTGAGGTGTGGCAAGCCTTACT
TGCTGTTAGAGAGTTGGTTCTCCCTCCTAATGAAGACAGAGACACCTGGATAAAATTTGCCAAA
CTTTGCTGGAAGAGTGGCCGCATTAGTCAGGCTAAATCTACCTTAGTCAAACTCTTACAGTTTG
ATCCAGAATCTTCCCCTGAATTGACGCTGTATCATGGACATCCTCAAGTAGTCCTGGCATACCT
GAAGTACCAGTATGCTGTTGGAGATGAGCTTAAACGAAGGGACGCGTTTTGCAGGCTACAGGAT
TTGTCTGTGCAGCTTGCTACCGCAACAAATAGTTATTCTGGAACATTAGCAAGCCAGGTTGCCA
CATCAAATGCTGGAGTACCACTTATTGCTCGCGTCTATTTGACACTTGCTAGCTGGAAGAGAGC
ATTATCACCTGGGTTAGACGATGATTCTATTCAAGAAATATTGGTCTCTTACAAAAATGCCACA
CTTAATGCCAAGGACTGGGGCAAGGCATGGCACTTATGGGCCTTGTTCAACACTGAAGTCATGT
CCCGCTATACTTTGCGTGGTCGACCAGATATTGCAGGAAAATATGTTGTTGCAGCAGTAACTGG
GTATTTCTACTCTATTGCTTGCGCATCCACGACAAAAGGTGTTGATGATAGCTTACAG
						
					

						Genomic sequence
						
							GTGATTGATTACTGCACTCTTCCAATGGAAAGTCCAATAGCTGACAGCCGGAGGGAACTTATCC
GTAATATGTGGAATGAGCGTATTAAAGGAACAAAACGGAATGTTGAGGTCATATTATGCTTCTT
TTAACTGCCTTGTGCCTTATACATATACTCCCTCCGTCCCAAAATATAACAACTTCTAGGCTTC
AATATTTGTCCCAAAATACAACTTCTCCACCTACATTCTGTTCTCTTCTCAACCAATCACAACC
TTCCACCATTCAAATTCCCTACCTACCTCCTCTTCTCAACCAATCACAACCTTCTTCTATTTAA
TTCCACCAACTTTCTTAATACTCATGTCTAACCCTCAAACTCCTTATATTTTGGGACGAAGGTA
GTATAATCTTTTTCATATTGGCTATGCTGACTAAAAAAATTGCAGGTGTGGCAAGCCTTACTTG
CTGTTAGAGAGTTGGTTCTCCCTCCTAATGAAGACAGAGACACCTGGATAAAATTTGCCAAACT
TTGCTGGAAGAGTGGCCGCATTAGTCAGGCTAAATCTACCTTAGTCAAACTCTTACAGGTAGGC
TTTAGTCATTCTTCATCAGTGTGTCTGTGCTACTCCCTCCTATAAAATAGTTAATTCCTGTGTC
AAAATGCAGTTTGATCCAGAATCTTCCCCTGAATTGACGCTGTATCATGGACATCCTCAAGTAG
TCCTGGCATACCTGAAGTACCAGTATGCTGTTGGAGATGAGCTTAAACGAAGGGACGCGTTTTG
CAGGCTACAGGTGAGCTTGTTATTGTCCTTCGTCTTTGACCCCAAGTTGCAGAATTATTCTGCA
TTTAAGTGGTTTTTTATACTTCCTTTTTGGTTTTGTGGTATAGGATTTGTCTGTGCAGCTTGCT
ACCGCAACAAATAGTTATTCTGGAACATTAGCAAGCCAGGTTGCCACATCAAATGCTGGAGTAC
CACTTATTGCTCGCGTCTATTTGACACTTGCTAGCTGGAAGAGAGCATTATCACCTGGGTTAGA
CGATGATTCTATTCAAGGTCTGAATAACTTCAGTTTATTTCCCTCTTGAGGGGTGGGTGGGCAA
GATTGCCTACCAAAGTATTGAGACTTGAAAAAATAGTTATTTTACTTTTTGTCTGCCTGCCCGT
TTTGATGTAAATATACTTTTTTTCTTTATCCAGAAATATTGGTCTCTTACAAAAATGCCACACT
TAATGCCAAGGACTGGGGCAAGGCATGGCACTTATGGGCCTTGTTCAACACTGAAGTCATGTCC
CGCTATACTTTGCGTGGTCGACCAGATATTGCAGGAAAATATGTTGTTGCAGCAGTAACTGGGT
ATTTCTACTCTATTGCTTGCGCATCCACGACAAAAGGTGTTGATGATAGCTTACAG
						
					

			
		

Sequences
Splice junction sequence	ACCAGATATTGCAGGAAAATATGTTGTTGCAGCAGTAACTGGGTATTTCTACTCTATTGCTTGC GCATCCACGACAAAAGGTGTTGATGATAGCTTACAGgtgattgattactgcactcttccaatgg aaagtccaatagctgacagccggagggaacttatccgtaatatgtggaatgagcgtattaaagg aacaaaac
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: 202 Transcript exons: 8282354-8282390,8283583-8283683,8283690-8283753 GTGATTGATTACTGCACTCTTCCAATGGAAAGTCCAATGGGGCAAGGCATGGCACTTATGGGCC TTGTTCAACACTGAAGTCATGTCCCGCTATACTTTGCGTGGTCGACCAGATATTGCAGGAAAAT ATGTTGTTGCAACTGGGTATTTCTACTCTATTGCTTGCGCATCCACGACAAAAGGTGTTGATGA TAGCTTACAG Transcript length: 762 Transcript exons: 8282354-8282464,8282783-8282923,8283003-8283131,8283229- 8283394,8283539-8283753 GTGATTGATTACTGCACTCTTCCAATGGAAAGTCCAATAGCTGACAGCCGGAGGGAACTTATCC GTAATATGTGGAATGAGCGTATTAAAGGAACAAAACGGAATGTTGAGGTGTGGCAAGCCTTACT TGCTGTTAGAGAGTTGGTTCTCCCTCCTAATGAAGACAGAGACACCTGGATAAAATTTGCCAAA CTTTGCTGGAAGAGTGGCCGCATTAGTCAGGCTAAATCTACCTTAGTCAAACTCTTACAGTTTG ATCCAGAATCTTCCCCTGAATTGACGCTGTATCATGGACATCCTCAAGTAGTCCTGGCATACCT GAAGTACCAGTATGCTGTTGGAGATGAGCTTAAACGAAGGGACGCGTTTTGCAGGCTACAGGAT TTGTCTGTGCAGCTTGCTACCGCAACAAATAGTTATTCTGGAACATTAGCAAGCCAGGTTGCCA CATCAAATGCTGGAGTACCACTTATTGCTCGCGTCTATTTGACACTTGCTAGCTGGAAGAGAGC ATTATCACCTGGGTTAGACGATGATTCTATTCAAGAAATATTGGTCTCTTACAAAAATGCCACA CTTAATGCCAAGGACTGGGGCAAGGCATGGCACTTATGGGCCTTGTTCAACACTGAAGTCATGT CCCGCTATACTTTGCGTGGTCGACCAGATATTGCAGGAAAATATGTTGTTGCAGCAGTAACTGG GTATTTCTACTCTATTGCTTGCGCATCCACGACAAAAGGTGTTGATGATAGCTTACAG
Genomic sequence	GTGATTGATTACTGCACTCTTCCAATGGAAAGTCCAATAGCTGACAGCCGGAGGGAACTTATCC GTAATATGTGGAATGAGCGTATTAAAGGAACAAAACGGAATGTTGAGGTCATATTATGCTTCTT TTAACTGCCTTGTGCCTTATACATATACTCCCTCCGTCCCAAAATATAACAACTTCTAGGCTTC AATATTTGTCCCAAAATACAACTTCTCCACCTACATTCTGTTCTCTTCTCAACCAATCACAACC TTCCACCATTCAAATTCCCTACCTACCTCCTCTTCTCAACCAATCACAACCTTCTTCTATTTAA TTCCACCAACTTTCTTAATACTCATGTCTAACCCTCAAACTCCTTATATTTTGGGACGAAGGTA GTATAATCTTTTTCATATTGGCTATGCTGACTAAAAAAATTGCAGGTGTGGCAAGCCTTACTTG CTGTTAGAGAGTTGGTTCTCCCTCCTAATGAAGACAGAGACACCTGGATAAAATTTGCCAAACT TTGCTGGAAGAGTGGCCGCATTAGTCAGGCTAAATCTACCTTAGTCAAACTCTTACAGGTAGGC TTTAGTCATTCTTCATCAGTGTGTCTGTGCTACTCCCTCCTATAAAATAGTTAATTCCTGTGTC AAAATGCAGTTTGATCCAGAATCTTCCCCTGAATTGACGCTGTATCATGGACATCCTCAAGTAG TCCTGGCATACCTGAAGTACCAGTATGCTGTTGGAGATGAGCTTAAACGAAGGGACGCGTTTTG CAGGCTACAGGTGAGCTTGTTATTGTCCTTCGTCTTTGACCCCAAGTTGCAGAATTATTCTGCA TTTAAGTGGTTTTTTATACTTCCTTTTTGGTTTTGTGGTATAGGATTTGTCTGTGCAGCTTGCT ACCGCAACAAATAGTTATTCTGGAACATTAGCAAGCCAGGTTGCCACATCAAATGCTGGAGTAC CACTTATTGCTCGCGTCTATTTGACACTTGCTAGCTGGAAGAGAGCATTATCACCTGGGTTAGA CGATGATTCTATTCAAGGTCTGAATAACTTCAGTTTATTTCCCTCTTGAGGGGTGGGTGGGCAA GATTGCCTACCAAAGTATTGAGACTTGAAAAAATAGTTATTTTACTTTTTGTCTGCCTGCCCGT TTTGATGTAAATATACTTTTTTTCTTTATCCAGAAATATTGGTCTCTTACAAAAATGCCACACT TAATGCCAAGGACTGGGGCAAGGCATGGCACTTATGGGCCTTGTTCAACACTGAAGTCATGTCC CGCTATACTTTGCGTGGTCGACCAGATATTGCAGGAAAATATGTTGTTGCAGCAGTAACTGGGT ATTTCTACTCTATTGCTTGCGCATCCACGACAAAAGGTGTTGATGATAGCTTACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_016067 						
					
						PMCS
						0.428256821

Conservation Information
Conserved circRNAs	osi_circ_016067
PMCS	0.428256821

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8282379-8283750(+)
						
						Potential amino acid sequence
						
							MESPIADSRRELIRNMWNERIKGTKRNVEVWQALLAVRELVLPPNEDRDTWIKFAKLCWKSGRI
SQAKSTLVKLLQFDPESSPELTLYHGHPQVVLAYLKYQYAVGDELKRRDAFCRLQDLSVQLATA
TNSYSGTLASQVATSNAGVPLIARVYLTLASWKRALSPGLDDDSIQEILVSYKNATLNAKDWGK
AWHLWALFNTEVMSRYTLRGRPDIAGKYVVAAVTGYFYSIACASTTKGVDDSLQVIDYCTLPME
SPIADSRRELIRNMWNERIKGTKRNVEVWQALLAVRELVLPPNEDRDTWIKFAKLCWKSGRISQ
AKSTLVKLLQFDPESSPELTLYHGHPQVVLAYLKYQYAVGDELKRRDAFCRLQDLSVQLATATN
SYSGTLASQVATSNAGVPLIARVYLTLASWKRALSPGLDDDSIQEILVSYKNATLNAKDWGKAW
HLWALFNTEVMSRYTLRGRPDIAGKYVVAAVTGYFYSIACASTTKGVDDSLQVIDYCTLPMESP
IADSRRELIRNMWNERIKGTKRNVEVWQALLAVRELVLPPNEDRDTWIKFAKLCWKSGRISQAK
STLVKLLQFDPESSPELTLYHGHPQVVLAYLKYQYAVGDELKRRDAFCRLQDLSVQLATATNSY
SGTLASQVATSNAGVPLIARVYLTLASWKRALSPGLDDDSIQEILVSYKNATLNAKDWGKAWHL
WALFNTEVMSRYTLRGRPDIAGKYVVAAVTGYFYSIACASTTKGVDDSLQVIDYCTLPMESPIA
DSRRELIRNMWNERIKGTKRNVEVWQALLAVRELVLPPNEDRDTWIKFAKLCWKSGRISQAKST
LVKLLQFDPESSPELTLYHGHPQVVLAYLKYQYAVGDELKRRDAFCRLQDLSVQLATATNSYSG
TLASQVATSNAGVPLIARVYLTLASWKRALSPGLDDDSIQEILVSYKNATLNAKDWGKAWHLWA
LFNTEVMSRYTLRGRPDIAGKYVVAAVTGYFYSIACASTTKGVDDSLQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8282379-8283750(+)
Potential amino acid sequence	MESPIADSRRELIRNMWNERIKGTKRNVEVWQALLAVRELVLPPNEDRDTWIKFAKLCWKSGRI SQAKSTLVKLLQFDPESSPELTLYHGHPQVVLAYLKYQYAVGDELKRRDAFCRLQDLSVQLATA TNSYSGTLASQVATSNAGVPLIARVYLTLASWKRALSPGLDDDSIQEILVSYKNATLNAKDWGK AWHLWALFNTEVMSRYTLRGRPDIAGKYVVAAVTGYFYSIACASTTKGVDDSLQVIDYCTLPME SPIADSRRELIRNMWNERIKGTKRNVEVWQALLAVRELVLPPNEDRDTWIKFAKLCWKSGRISQ AKSTLVKLLQFDPESSPELTLYHGHPQVVLAYLKYQYAVGDELKRRDAFCRLQDLSVQLATATN SYSGTLASQVATSNAGVPLIARVYLTLASWKRALSPGLDDDSIQEILVSYKNATLNAKDWGKAW HLWALFNTEVMSRYTLRGRPDIAGKYVVAAVTGYFYSIACASTTKGVDDSLQVIDYCTLPMESP IADSRRELIRNMWNERIKGTKRNVEVWQALLAVRELVLPPNEDRDTWIKFAKLCWKSGRISQAK STLVKLLQFDPESSPELTLYHGHPQVVLAYLKYQYAVGDELKRRDAFCRLQDLSVQLATATNSY SGTLASQVATSNAGVPLIARVYLTLASWKRALSPGLDDDSIQEILVSYKNATLNAKDWGKAWHL WALFNTEVMSRYTLRGRPDIAGKYVVAAVTGYFYSIACASTTKGVDDSLQVIDYCTLPMESPIA DSRRELIRNMWNERIKGTKRNVEVWQALLAVRELVLPPNEDRDTWIKFAKLCWKSGRISQAKST LVKLLQFDPESSPELTLYHGHPQVVLAYLKYQYAVGDELKRRDAFCRLQDLSVQLATATNSYSG TLASQVATSNAGVPLIARVYLTLASWKRALSPGLDDDSIQEILVSYKNATLNAKDWGKAWHLWA LFNTEVMSRYTLRGRPDIAGKYVVAAVTGYFYSIACASTTKGVDDSLQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os05g0235300_circ_g.4

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