Plant Circular RNA Database

Detail information of Os09g0394600_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os09g0394600_circ_g.2
					
						ID in PlantcircBase
						osa_circ_039096
					
						Alias
						Os_ciR5038
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 13689215-13690790  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os09g0394600						
					
						Parent gene annotation
						
							Endonuclease/exonuclease/phosphatase domain containing protein. 
(Os09t0394600-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os09g0394600_circ_g.1 Os09g0394600_circ_g.3 Os09g0394600_circ_g.4 Os09g0394600_circ_g.5 Os09g0394600_circ_g.6 Os09g0394600_circ_g.7 						
					
						Support reads
						4/1
					
						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
						Os09t0394600-01:5

General Information
CircRNA Name	Os09g0394600_circ_g.2
ID in PlantcircBase	osa_circ_039096
Alias	Os_ciR5038
Organism	Oryza sativa
Position	chr9: 13689215-13690790 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os09g0394600
Parent gene annotation	Endonuclease/exonuclease/phosphatase domain containing protein. (Os09t0394600-01)
Parent gene strand	-
Alternative splicing	Os09g0394600_circ_g.1 Os09g0394600_circ_g.3 Os09g0394600_circ_g.4 Os09g0394600_circ_g.5 Os09g0394600_circ_g.6 Os09g0394600_circ_g.7
Support reads	4/1
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	Os09t0394600-01:5

			
						 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  
						
							AGGTTTCATCCACTACACCTGAAATCTCAGAAACTGATCGATGACCACACAGCTGCTGGCGGTG
CGATAGCTTACTTGGAACCAATCTTGGCAGGATGATctggtcgttctctaacaggatggaccaa
ttcttgtcttccaccaacaaccttgtctcagcctcttccaaggatatcctataatttaagtcac
cgagcaaa

									
								

					

						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: 116
Transcript exons: 13689215-13689248,13690709-13690790
CTGGTCGTTCTCTAACAGGATGGACCAATTCTTGCTGAAATCTCAGAAACTGATCGATGACCAC
ACAGCTGCTGGCGGTGCGATAGCTTACTTGGAACCAATCTTGGCAGGATGAT
Transcript length: 864
Transcript exons: 13689215-13689323,13689747-13689931,13690023-13690338,13
690447-13690554,13690645-13690790
CTGGTCGTTCTCTAACAGGATGGACCAATTCTTGTCTTCCACCAACAACCTTGTCTCAGCCTCT
TCCAAGGATATCCTATAATTTAAGTCACCGAGCAAAACGACTTGATCGTGGTCAAGGATCTTCT
TTGGCAATTCTTGGGTTGCACCACCAGGAAATCTCGTCCTCACGAGTATATCCGCAGCATCAAA
GTTCCTCAGCAGTACATCCCCTTGTTTGCCGCCTGAAGCCAGGTGACAGCAAACAAAGCAAAAG
CTCGTCTCGTGTAGCACAAATCGAATTGACACCGAGCCCTTGTTCCCTAGGTAGCCCATGATGC
CTGAACCAACACAAGACACATTCAGATGGTGAATGTATGGCCTAAGATTGCTTCTCACCCAGAC
TGACATAAAGATGCCCACCATCTGCTTGTTCATGATGCATCTAAAGTGTTCTTCCTGCGCAGAT
CTCTCCGTTGCACTGCTATTTGTGATTTCTTGATGCAACACTGCTCCTCTTCTCCTCCTTTTGT
TTAGTGCCTCCCCAATCAGTGAGTTCCACTTTGTAGATATACAGCTATTCCTAGGACCAAGCAC
GTTTCTTGCGTTGAGTGGCACTATCTCTTGGAACCCAAGAACGTAGATGTCATAGGAGTTAGCT
GTTGAATCCATCCAATCCTCCAAGTCTAGATCACTGGATGGTGTCATACCACCAACATTCCACG
TACTAGTGAACACCCTGTATCTGAGTATATCATTCTGCCCATCCAGAGGCCTCTTTCCCAAGGT
TTCATCCACTACACCTGAAATCTCAGAAACTGATCGATGACCACACAGCTGCTGGCGGTGCGAT
AGCTTACTTGGAACCAATCTTGGCAGGATGAT
						
					

						Genomic sequence
						
							CTGGTCGTTCTCTAACAGGATGGACCAATTCTTGTCTTCCACCAACAACCTTGTCTCAGCCTCT
TCCAAGGATATCCTATAATTTAAGTCACCGAGCAAAACGACTTGACTGCACAGATGACAAAGAA
CAAACGATATAAAGACGATAGACAAATTATTGGTACAGTATAAATTGATGAGAGATGATGAACT
GGGTGATGTATGCACGATGGCATTTAATAGCTTGTAGGATTCTTAATTCTTAGATGGGTACCCC
TTATTAGGCAGGGGACGATGTACGATTAGCTAATTAAAAAATGTCATGCCAATGCAAACTAAGC
TGCAAAAGGATGTGATCATTAGCACAAAAGTACAAAAGCTAACCCATGTCTAGGAGTAGGGATC
TATATGGTTGCTGATACTGATGACAAAAGAATATGGAAAATGGCTAGCTAGGGACCAACGATTG
AGAAAAGAGGACCAATTTGGTGGTCCATTGAACAAAACTAAAAACACAGGAGGGCAGTGAGCTG
AGATACTGTTGTGCACCTACTCGTGGTCAAGGATCTTCTTTGGCAATTCTTGGGTTGCACCACC
AGGAAATCTCGTCCTCACGAGTATATCCGCAGCATCAAAGTTCCTCAGCAGTACATCCCCTTGT
TTGCCGCCTGAAGCCAGGTGACAGCAAACAAAGCAAAAGCTCGTCTCGTGTAGCACAAATCGAA
TTGACACCGAGCCCTGCAATCCACATATCCAAATGCATGGTTATGTGATTGCACATACGGAAGG
TATGACCCTCTTACTTCTGATGTTTGCATTTTGTGCATACCTTGTTCCCTAGGTAGCCCATGAT
GCCTGAACCAACACAAGACACATTCAGATGGTGAATGTATGGCCTAAGATTGCTTCTCACCCAG
ACTGACATAAAGATGCCCACCATCTGCTTGTTCATGATGCATCTAAAGTGTTCTTCCTGCGCAG
ATCTCTCCGTTGCACTGCTATTTGTGATTTCTTGATGCAACACTGCTCCTCTTCTCCTCCTTTT
GTTTAGTGCCTCCCCAATCAGTGAGTTCCACTTTGTAGATATACAGCTATTCCTAGGACCAAGC
ACGTTTCTTGCGTTGAGTGGCACTATCTCTTGGAACCTAAAACACCATCAGCACAGAACAAAAC
AGAACCATCAACAATTAGATCAGTTAGCCCCCTCAACGAAAAAGAGAGGATGAGTTAGAAGGTT
GAAGTGAGCTAAGTACCCAAGAACGTAGATGTCATAGGAGTTAGCTGTTGAATCCATCCAATCC
TCCAAGTCTAGATCACTGGATGGTGTCATACCACCAACATTCCACGTACTAGTGAACACCCTTC
GAACGAACAACAAAATATCCAAATCATCAGATATGAAATGCAGTGAGCAAACTTACAGGTGCAA
TGAAAACTACTACAAAAATCACCTGTATCTGAGTATATCATTCTGCCCATCCAGAGGCCTCTTT
CCCAAGGTTTCATCCACTACACCTGAAATCTCAGAAACTGATCGATGACCACACAGCTGCTGGC
GGTGCGATAGCTTACTTGGAACCAATCTTGGCAGGATGAT
						
					

			
		

Sequences
Splice junction sequence	AGGTTTCATCCACTACACCTGAAATCTCAGAAACTGATCGATGACCACACAGCTGCTGGCGGTG CGATAGCTTACTTGGAACCAATCTTGGCAGGATGATctggtcgttctctaacaggatggaccaa ttcttgtcttccaccaacaaccttgtctcagcctcttccaaggatatcctataatttaagtcac cgagcaaa
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: 116 Transcript exons: 13689215-13689248,13690709-13690790 CTGGTCGTTCTCTAACAGGATGGACCAATTCTTGCTGAAATCTCAGAAACTGATCGATGACCAC ACAGCTGCTGGCGGTGCGATAGCTTACTTGGAACCAATCTTGGCAGGATGAT Transcript length: 864 Transcript exons: 13689215-13689323,13689747-13689931,13690023-13690338,13 690447-13690554,13690645-13690790 CTGGTCGTTCTCTAACAGGATGGACCAATTCTTGTCTTCCACCAACAACCTTGTCTCAGCCTCT TCCAAGGATATCCTATAATTTAAGTCACCGAGCAAAACGACTTGATCGTGGTCAAGGATCTTCT TTGGCAATTCTTGGGTTGCACCACCAGGAAATCTCGTCCTCACGAGTATATCCGCAGCATCAAA GTTCCTCAGCAGTACATCCCCTTGTTTGCCGCCTGAAGCCAGGTGACAGCAAACAAAGCAAAAG CTCGTCTCGTGTAGCACAAATCGAATTGACACCGAGCCCTTGTTCCCTAGGTAGCCCATGATGC CTGAACCAACACAAGACACATTCAGATGGTGAATGTATGGCCTAAGATTGCTTCTCACCCAGAC TGACATAAAGATGCCCACCATCTGCTTGTTCATGATGCATCTAAAGTGTTCTTCCTGCGCAGAT CTCTCCGTTGCACTGCTATTTGTGATTTCTTGATGCAACACTGCTCCTCTTCTCCTCCTTTTGT TTAGTGCCTCCCCAATCAGTGAGTTCCACTTTGTAGATATACAGCTATTCCTAGGACCAAGCAC GTTTCTTGCGTTGAGTGGCACTATCTCTTGGAACCCAAGAACGTAGATGTCATAGGAGTTAGCT GTTGAATCCATCCAATCCTCCAAGTCTAGATCACTGGATGGTGTCATACCACCAACATTCCACG TACTAGTGAACACCCTGTATCTGAGTATATCATTCTGCCCATCCAGAGGCCTCTTTCCCAAGGT TTCATCCACTACACCTGAAATCTCAGAAACTGATCGATGACCACACAGCTGCTGGCGGTGCGAT AGCTTACTTGGAACCAATCTTGGCAGGATGAT
Genomic sequence	CTGGTCGTTCTCTAACAGGATGGACCAATTCTTGTCTTCCACCAACAACCTTGTCTCAGCCTCT TCCAAGGATATCCTATAATTTAAGTCACCGAGCAAAACGACTTGACTGCACAGATGACAAAGAA CAAACGATATAAAGACGATAGACAAATTATTGGTACAGTATAAATTGATGAGAGATGATGAACT GGGTGATGTATGCACGATGGCATTTAATAGCTTGTAGGATTCTTAATTCTTAGATGGGTACCCC TTATTAGGCAGGGGACGATGTACGATTAGCTAATTAAAAAATGTCATGCCAATGCAAACTAAGC TGCAAAAGGATGTGATCATTAGCACAAAAGTACAAAAGCTAACCCATGTCTAGGAGTAGGGATC TATATGGTTGCTGATACTGATGACAAAAGAATATGGAAAATGGCTAGCTAGGGACCAACGATTG AGAAAAGAGGACCAATTTGGTGGTCCATTGAACAAAACTAAAAACACAGGAGGGCAGTGAGCTG AGATACTGTTGTGCACCTACTCGTGGTCAAGGATCTTCTTTGGCAATTCTTGGGTTGCACCACC AGGAAATCTCGTCCTCACGAGTATATCCGCAGCATCAAAGTTCCTCAGCAGTACATCCCCTTGT TTGCCGCCTGAAGCCAGGTGACAGCAAACAAAGCAAAAGCTCGTCTCGTGTAGCACAAATCGAA TTGACACCGAGCCCTGCAATCCACATATCCAAATGCATGGTTATGTGATTGCACATACGGAAGG TATGACCCTCTTACTTCTGATGTTTGCATTTTGTGCATACCTTGTTCCCTAGGTAGCCCATGAT GCCTGAACCAACACAAGACACATTCAGATGGTGAATGTATGGCCTAAGATTGCTTCTCACCCAG ACTGACATAAAGATGCCCACCATCTGCTTGTTCATGATGCATCTAAAGTGTTCTTCCTGCGCAG ATCTCTCCGTTGCACTGCTATTTGTGATTTCTTGATGCAACACTGCTCCTCTTCTCCTCCTTTT GTTTAGTGCCTCCCCAATCAGTGAGTTCCACTTTGTAGATATACAGCTATTCCTAGGACCAAGC ACGTTTCTTGCGTTGAGTGGCACTATCTCTTGGAACCTAAAACACCATCAGCACAGAACAAAAC AGAACCATCAACAATTAGATCAGTTAGCCCCCTCAACGAAAAAGAGAGGATGAGTTAGAAGGTT GAAGTGAGCTAAGTACCCAAGAACGTAGATGTCATAGGAGTTAGCTGTTGAATCCATCCAATCC TCCAAGTCTAGATCACTGGATGGTGTCATACCACCAACATTCCACGTACTAGTGAACACCCTTC GAACGAACAACAAAATATCCAAATCATCAGATATGAAATGCAGTGAGCAAACTTACAGGTGCAA TGAAAACTACTACAAAAATCACCTGTATCTGAGTATATCATTCTGCCCATCCAGAGGCCTCTTT CCCAAGGTTTCATCCACTACACCTGAAATCTCAGAAACTGATCGATGACCACACAGCTGCTGGC GGTGCGATAGCTTACTTGGAACCAATCTTGGCAGGATGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.260019295

Conservation Information
Conserved circRNAs	NA
PMCS	0.260019295

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13690787-13689293(+)
13690525-13689217(-)
						
						Potential amino acid sequence
						
							MIWSFSNRMDQFLSSTNNLVSASSKDIL*(+)
MTPSSDLDLEDWMDSTANSYDIYVLGFQEIVPLNARNVLGPRNSCISTKWNSLIGEALNKRRRR
GAVLHQEITNSSATERSAQEEHFRCIMNKQMVGIFMSVWVRSNLRPYIHHLNVSCVGSGIMGYL
GNKGSVSIRFVLHETSFCFVCCHLASGGKQGDVLLRNFDAADILVRTRFPGGATQELPKKILDH
DQVVLLGDLNYRISLEEAETRLLVEDKNWSILLENDQIILPRLVPSKLSHRQQLCGHRSVSEIS
GVVDETLGKRPLDGQNDILRYRVFTSTWNVGGMTPSSDLDLEDWMDSTANSYDIYVLGFQEIVP
LNARNVLGPRNSCISTKWNSLIGEALNKRRRRGAVLHQEITNSSATERSAQEEHFRCIMNKQMV
GIFMSVWVRSNLRPYIHHLNVSCVGSGIMGYLGNKGSVSIRFVLHETSFCFVCCHLASGGKQGD
VLLRNFDAADILVRTRFPGGATQELPKKILDHDQVVLLGDLNYRISLEEAETRLLVEDKNWSIL
LENDQIILPRLVPSKLSHRQQLCGHRSVSEISGVVDETLGKRPLDGQNDILRYRVFTSTWNVGG
MTPSSDLDLEDWMDSTANSYDIYVLGFQEIVPLNARNVLGPRNSCISTKWNSLIGEALNKRRRR
GAVLHQEITNSSATERSAQEEHFRCIMNKQMVGIFMSVWVRSNLRPYIHHLNVSCVGSGIMGYL
GNKGSVSIRFVLHETSFCFVCCHLASGGKQGDVLLRNFDAADILVRTRFPGGATQELPKKILDH
DQVVLLGDLNYRISLEEAETRLLVEDKNWSILLENDQIILPRLVPSKLSHRQQLCGHRSVSEIS
GVVDETLGKRPLDGQNDILRYRVFTSTWNVGGMTPSSDLDLEDWMDSTANSYDIYVLGFQEIVP
LNARNVLGPRNSCISTKWNSLIGEALNKRRRRGAVLHQEITNSSATERSAQEEHFRCIMNKQMV
GIFMSVWVRSNLRPYIHHLNVSCVGSGIMGYLGNKGSVSIRFVLHETSFCFVCCHLASGGKQGD
VLLRNFDAADILVRTRFPGGATQELPKKILDHDQVVLLGDLNYRISLEEAETRLLVEDKNWSIL
LENDQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13690787-13689293(+) 13690525-13689217(-)
Potential amino acid sequence	MIWSFSNRMDQFLSSTNNLVSASSKDIL*(+) MTPSSDLDLEDWMDSTANSYDIYVLGFQEIVPLNARNVLGPRNSCISTKWNSLIGEALNKRRRR GAVLHQEITNSSATERSAQEEHFRCIMNKQMVGIFMSVWVRSNLRPYIHHLNVSCVGSGIMGYL GNKGSVSIRFVLHETSFCFVCCHLASGGKQGDVLLRNFDAADILVRTRFPGGATQELPKKILDH DQVVLLGDLNYRISLEEAETRLLVEDKNWSILLENDQIILPRLVPSKLSHRQQLCGHRSVSEIS GVVDETLGKRPLDGQNDILRYRVFTSTWNVGGMTPSSDLDLEDWMDSTANSYDIYVLGFQEIVP LNARNVLGPRNSCISTKWNSLIGEALNKRRRRGAVLHQEITNSSATERSAQEEHFRCIMNKQMV GIFMSVWVRSNLRPYIHHLNVSCVGSGIMGYLGNKGSVSIRFVLHETSFCFVCCHLASGGKQGD VLLRNFDAADILVRTRFPGGATQELPKKILDHDQVVLLGDLNYRISLEEAETRLLVEDKNWSIL LENDQIILPRLVPSKLSHRQQLCGHRSVSEISGVVDETLGKRPLDGQNDILRYRVFTSTWNVGG MTPSSDLDLEDWMDSTANSYDIYVLGFQEIVPLNARNVLGPRNSCISTKWNSLIGEALNKRRRR GAVLHQEITNSSATERSAQEEHFRCIMNKQMVGIFMSVWVRSNLRPYIHHLNVSCVGSGIMGYL GNKGSVSIRFVLHETSFCFVCCHLASGGKQGDVLLRNFDAADILVRTRFPGGATQELPKKILDH DQVVLLGDLNYRISLEEAETRLLVEDKNWSILLENDQIILPRLVPSKLSHRQQLCGHRSVSEIS GVVDETLGKRPLDGQNDILRYRVFTSTWNVGGMTPSSDLDLEDWMDSTANSYDIYVLGFQEIVP LNARNVLGPRNSCISTKWNSLIGEALNKRRRRGAVLHQEITNSSATERSAQEEHFRCIMNKQMV GIFMSVWVRSNLRPYIHHLNVSCVGSGIMGYLGNKGSVSIRFVLHETSFCFVCCHLASGGKQGD VLLRNFDAADILVRTRFPGGATQELPKKILDHDQVVLLGDLNYRISLEEAETRLLVEDKNWSIL LENDQ(-)
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 Os09g0394600_circ_g.2

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