Plant Circular RNA Database

Detail information of Os04g0252200_circ_g.16

			
						 General Information
					
						CircRNA Name
						Os04g0252200_circ_g.16
					
						ID in PlantcircBase
						osa_circ_023201
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 9910943-9913088  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0252200						
					
						Parent gene annotation
						
							Similar to CPSF160; nucleic acid binding. (Os04t0252200-01);Simi
lar to CPSF160; nucleic acid binding. (Os04t0252200-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0252200_circ_g.1 Os04g0252200_circ_g.2 Os04g0252200_circ_g.3 Os04g0252200_circ_g.4 Os04g0252200_circ_g.5 Os04g0252200_circ_g.6 Os04g0252200_circ_g.7 Os04g0252200_circ_g.8 Os04g0252200_circ_g.9 Os04g0252200_circ_g.10 Os04g0252200_circ_g.11 Os04g0252200_circ_g.12 Os04g0252200_circ_g.13 Os04g0252200_circ_g.14 Os04g0252200_circ_g.15 Os04g0252200_circ_g.17 Os04g0252200_circ_g.18 						
					
						Support reads
						2
					
						Tissues
						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  
						
							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
						Os04t0252200-01:6
Os04t0252200-02:6

General Information
CircRNA Name	Os04g0252200_circ_g.16
ID in PlantcircBase	osa_circ_023201
Alias	NA
Organism	Oryza sativa
Position	chr4: 9910943-9913088 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0252200
Parent gene annotation	Similar to CPSF160; nucleic acid binding. (Os04t0252200-01);Simi lar to CPSF160; nucleic acid binding. (Os04t0252200-02)
Parent gene strand	-
Alternative splicing	Os04g0252200_circ_g.1 Os04g0252200_circ_g.2 Os04g0252200_circ_g.3 Os04g0252200_circ_g.4 Os04g0252200_circ_g.5 Os04g0252200_circ_g.6 Os04g0252200_circ_g.7 Os04g0252200_circ_g.8 Os04g0252200_circ_g.9 Os04g0252200_circ_g.10 Os04g0252200_circ_g.11 Os04g0252200_circ_g.12 Os04g0252200_circ_g.13 Os04g0252200_circ_g.14 Os04g0252200_circ_g.15 Os04g0252200_circ_g.17 Os04g0252200_circ_g.18
Support reads	2
Tissues	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	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	Os04t0252200-01:6 Os04t0252200-02:6

			
						 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  
						
							CTAAATGCAGATATCATGCATGTATGGTGCTTTGATAAGATACGCCCAGCCCATGTAGGCTCTT
GCTCATGAAGTATGACCAACACAGGCTCAATATAACctcatttgttaaatcttgcaaaacagat
tttgatgcacagtaggaaaattgcacaagaaggctatcccccagacgactaccaaggaagaaga
atgagttt

									
								

					

						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: 596
Transcript exons: 9910943-9911059,9911146-9911197,9911286-9911417,9912195-
9912247,9912343-9912438,9912943-9913088
CTCATTTGTTAAATCTTGCAAAACAGATTTTGATGCACAGTAGGAAAATTGCACAAGAAGGCTA
TCCCCCAGACGACTACCAAGGAAGAAGAATGAGTTTCCAATAGATGTCACAGCCGAACTGAGGA
CAGATGCTTTTGATTTCATAAGATCTAATCTCTGCACAACTCGCCCATCATAAACCACTGTAAG
TAACAGCATCTCTCCAGCCTTTGTCGAGAACATTACAATGTCATTGGACAACCAAGTTGCTTTA
GCTGCATCAAGCTCAACTTGGAAATTTGACTTAGAAATTTCTGGGCTGCCATCAGGGTGTGATG
AGAAATTGTTCAGGTCAAGAGAACACGATGTGGACTGACTATGGTAATGGATGGAATTTGCACA
GATCACAAGAACACCACTAATAGGGGGAGGCACTGCAAGAAGTTGGTATGCATCGTGGGGCAGA
TTAGCTGCAGACCATATCACTGGATGTTGCTTTAGAGTCATGCTGATGCTAAATGCAGATATCA
TGCATGTATGGTGCTTTGATAAGATACGCCCAGCCCATGTAGGCTCTTGCTCATGAAGTATGAC
CAACACAGGCTCAATATAAC
						
					

						Genomic sequence
						
							CTCATTTGTTAAATCTTGCAAAACAGATTTTGATGCACAGTAGGAAAATTGCACAAGAAGGCTA
TCCCCCAGACGACTACCAAGGAAGAAGAATGAGTTTCCAATAGATGTCACAGCCTGTCCATAAA
TAGGTTAGTAAACTTAAAAAAGAGCAATATCTAAAAAAGGAAGCATATAAGCACAGAAGTACAT
AGGTAACCAACCGAACTGAGGACAGATGCTTTTGATTTCATAAGATCTAATCTCTGCACAACTC
TGTAAAAAGAATAAAAGAACATGTAATGATCAACTCTGAACAACAGTAGCACAGACAATAGGAC
AATGAACCATAGAATTATCATACCGCCCATCATAAACCACTGTAAGTAACAGCATCTCTCCAGC
CTTTGTCGAGAACATTACAATGTCATTGGACAACCAAGTTGCTTTAGCTGCATCAAGCTCAACT
TGGAAATTTGACTTAGAAATTTCTGGGCTGCAAAGCCAGCAAAAGAACAGAAGGTTACCAGCAT
ACAAATCTACTGAAAAAGAAAGAAGCTAAGCAATATCAATACGGTATAGACTACAGAACTTAAG
AATAATCAACTATTCAATATTGATAGGTATAACACTGCTGCCGGAGTAGTATATGTGCCATATT
TCGCAGGTTTTCTATATCTTTTTGGATCAACCCACTATTTTCATGTAAGATTTGCTCTCAGCAA
GAAAAGCATGCCAGTACAGTAGATTTGACTACCTTTTTACAACCAAATAAGTACAATGAGGTGT
GTTATGCACACCCAATCACCCATAATCAACAGCAAGCACCTTCTAGTAATTTCACCTTACGAAT
TACTCAGTTCACATGTTTACCAGTACATCAAGATGGGCTCAAATGCTGTGCTAATGTCTCAGTT
AACACCTTTAGTAATAATGGATTTAAAAGTATGTAGCTTCAAACATAATCTTCCAAAAAAATTA
AATAATTAGGTTGCTAGGACCTAGGGGAAGTTCAAGATGGTTATTTTAATCTTATTTTCTATGG
ACAACCATATAAGAAGAGACCACACTACACGTCTTGAGCTTATCACTTTTAAATCAGGTATCCA
CATTGGTGATCTTGGTATGTGATTGTGATGGTACTGCACCACTGATATGTGTGTAGCCGTGTAG
TAGTTAAGCAGAAACAGGGCCCATTTGTATGTGATCCGAGAAAAAGAACAAACTATCGTAATCC
AATTAGTACTTTGCATTTAACATATACAAACAGTACCTGCCATCAGGGTGTGATGAGAAATTGT
TCAGGTCAAGAGAACACGATGTGGACTACAATAACAAAGAGAACTTCAAATCAATGATCCACGT
TCAGCAAATCAAAATAAAGTATGTGCCTTCACCACGAGTATTTAAAGGGATCAAACCTGACTAT
GGTAATGGATGGAATTTGCACAGATCACAAGAACACCACTAATAGGGGGAGGCACTGCAAGAAG
TTGGTATGCATCGTGGGGCAGATTCTGAAAGGAACAAACACTTTGTAATGGTAAGTATATTATT
TTGTAATGGCAAGAAGTTATATATAGAGTCAAATAAATCCAGTGCTTAAACGCAATGGAATCCC
TAAAATATGTAATACAATTGAGCAATCAACAAGAAAAAAAAAAAGGATTCGCGATCATAGTATG
TCAACTTTGATCTATGGACAGAAATGATAGCACCACTAAAATCAATACCATTCACCTCAATGCG
GTATTGCTGACCTAAAATGAGGGACTTGAATACTAGGATTAGTCCTGAAATAGAGCAAAATTTG
ATAACTTATCTAAATTCGGAACATTTACCAATCACAGATAAACCTACCGTGTTCTATGCAAAAG
AAATAAGTAATTATTTAGTGAATACCACAAGCCACCTTAGTACATTCTAGTACTCTGAACGCCA
AAATTTATTGCCGAAAGAACATAGGAATAAGCTACCAAAGACAGAAAAGACAATGCTTAGGAGC
AATCTTGTACACTTACAGCTGCAGACCATATCACTGGATGTTGCTTTAGAGTCATGCTGATGCT
AAATGCAGATATCATGCATGTATGGTGCTTTGATAAGATACGCCCAGCCCATGTAGGCTCTTGC
TCATGAAGTATGACCAACACAGGCTCAATATAAC
						
					

			
		

Sequences
Splice junction sequence	CTAAATGCAGATATCATGCATGTATGGTGCTTTGATAAGATACGCCCAGCCCATGTAGGCTCTT GCTCATGAAGTATGACCAACACAGGCTCAATATAACctcatttgttaaatcttgcaaaacagat tttgatgcacagtaggaaaattgcacaagaaggctatcccccagacgactaccaaggaagaaga atgagttt
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: 596 Transcript exons: 9910943-9911059,9911146-9911197,9911286-9911417,9912195- 9912247,9912343-9912438,9912943-9913088 CTCATTTGTTAAATCTTGCAAAACAGATTTTGATGCACAGTAGGAAAATTGCACAAGAAGGCTA TCCCCCAGACGACTACCAAGGAAGAAGAATGAGTTTCCAATAGATGTCACAGCCGAACTGAGGA CAGATGCTTTTGATTTCATAAGATCTAATCTCTGCACAACTCGCCCATCATAAACCACTGTAAG TAACAGCATCTCTCCAGCCTTTGTCGAGAACATTACAATGTCATTGGACAACCAAGTTGCTTTA GCTGCATCAAGCTCAACTTGGAAATTTGACTTAGAAATTTCTGGGCTGCCATCAGGGTGTGATG AGAAATTGTTCAGGTCAAGAGAACACGATGTGGACTGACTATGGTAATGGATGGAATTTGCACA GATCACAAGAACACCACTAATAGGGGGAGGCACTGCAAGAAGTTGGTATGCATCGTGGGGCAGA TTAGCTGCAGACCATATCACTGGATGTTGCTTTAGAGTCATGCTGATGCTAAATGCAGATATCA TGCATGTATGGTGCTTTGATAAGATACGCCCAGCCCATGTAGGCTCTTGCTCATGAAGTATGAC CAACACAGGCTCAATATAAC
Genomic sequence	CTCATTTGTTAAATCTTGCAAAACAGATTTTGATGCACAGTAGGAAAATTGCACAAGAAGGCTA TCCCCCAGACGACTACCAAGGAAGAAGAATGAGTTTCCAATAGATGTCACAGCCTGTCCATAAA TAGGTTAGTAAACTTAAAAAAGAGCAATATCTAAAAAAGGAAGCATATAAGCACAGAAGTACAT AGGTAACCAACCGAACTGAGGACAGATGCTTTTGATTTCATAAGATCTAATCTCTGCACAACTC TGTAAAAAGAATAAAAGAACATGTAATGATCAACTCTGAACAACAGTAGCACAGACAATAGGAC AATGAACCATAGAATTATCATACCGCCCATCATAAACCACTGTAAGTAACAGCATCTCTCCAGC CTTTGTCGAGAACATTACAATGTCATTGGACAACCAAGTTGCTTTAGCTGCATCAAGCTCAACT TGGAAATTTGACTTAGAAATTTCTGGGCTGCAAAGCCAGCAAAAGAACAGAAGGTTACCAGCAT ACAAATCTACTGAAAAAGAAAGAAGCTAAGCAATATCAATACGGTATAGACTACAGAACTTAAG AATAATCAACTATTCAATATTGATAGGTATAACACTGCTGCCGGAGTAGTATATGTGCCATATT TCGCAGGTTTTCTATATCTTTTTGGATCAACCCACTATTTTCATGTAAGATTTGCTCTCAGCAA GAAAAGCATGCCAGTACAGTAGATTTGACTACCTTTTTACAACCAAATAAGTACAATGAGGTGT GTTATGCACACCCAATCACCCATAATCAACAGCAAGCACCTTCTAGTAATTTCACCTTACGAAT TACTCAGTTCACATGTTTACCAGTACATCAAGATGGGCTCAAATGCTGTGCTAATGTCTCAGTT AACACCTTTAGTAATAATGGATTTAAAAGTATGTAGCTTCAAACATAATCTTCCAAAAAAATTA AATAATTAGGTTGCTAGGACCTAGGGGAAGTTCAAGATGGTTATTTTAATCTTATTTTCTATGG ACAACCATATAAGAAGAGACCACACTACACGTCTTGAGCTTATCACTTTTAAATCAGGTATCCA CATTGGTGATCTTGGTATGTGATTGTGATGGTACTGCACCACTGATATGTGTGTAGCCGTGTAG TAGTTAAGCAGAAACAGGGCCCATTTGTATGTGATCCGAGAAAAAGAACAAACTATCGTAATCC AATTAGTACTTTGCATTTAACATATACAAACAGTACCTGCCATCAGGGTGTGATGAGAAATTGT TCAGGTCAAGAGAACACGATGTGGACTACAATAACAAAGAGAACTTCAAATCAATGATCCACGT TCAGCAAATCAAAATAAAGTATGTGCCTTCACCACGAGTATTTAAAGGGATCAAACCTGACTAT GGTAATGGATGGAATTTGCACAGATCACAAGAACACCACTAATAGGGGGAGGCACTGCAAGAAG TTGGTATGCATCGTGGGGCAGATTCTGAAAGGAACAAACACTTTGTAATGGTAAGTATATTATT TTGTAATGGCAAGAAGTTATATATAGAGTCAAATAAATCCAGTGCTTAAACGCAATGGAATCCC TAAAATATGTAATACAATTGAGCAATCAACAAGAAAAAAAAAAAGGATTCGCGATCATAGTATG TCAACTTTGATCTATGGACAGAAATGATAGCACCACTAAAATCAATACCATTCACCTCAATGCG GTATTGCTGACCTAAAATGAGGGACTTGAATACTAGGATTAGTCCTGAAATAGAGCAAAATTTG ATAACTTATCTAAATTCGGAACATTTACCAATCACAGATAAACCTACCGTGTTCTATGCAAAAG AAATAAGTAATTATTTAGTGAATACCACAAGCCACCTTAGTACATTCTAGTACTCTGAACGCCA AAATTTATTGCCGAAAGAACATAGGAATAAGCTACCAAAGACAGAAAAGACAATGCTTAGGAGC AATCTTGTACACTTACAGCTGCAGACCATATCACTGGATGTTGCTTTAGAGTCATGCTGATGCT AAATGCAGATATCATGCATGTATGGTGCTTTGATAAGATACGCCCAGCCCATGTAGGCTCTTGC TCATGAAGTATGACCAACACAGGCTCAATATAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.228098629

Conservation Information
Conserved circRNAs	NA
PMCS	0.228098629

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9913058-9910982(+)
9913007-9913004(-)
						
						Potential amino acid sequence
						
							MKYDQHRLNITSFVKSCKTDFDAQ*(+)
MISAFSISMTLKQHPVIWSAANLPHDAYQLLAVPPPISGVLVICANSIHYHSQSTSCSLDLNNF
SSHPDGSPEISKSNFQVELDAAKATWLSNDIVMFSTKAGEMLLLTVVYDGRVVQRLDLMKSKAS
VLSSAVTSIGNSFFFLGSRLGDSLLVQFSYCASKSVLQDLTNEVILSLCWSYFMSKSLHGLGVS
YQSTIHA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9913058-9910982(+) 9913007-9913004(-)
Potential amino acid sequence	MKYDQHRLNITSFVKSCKTDFDAQ(+) MISAFSISMTLKQHPVIWSAANLPHDAYQLLAVPPPISGVLVICANSIHYHSQSTSCSLDLNNF SSHPDGSPEISKSNFQVELDAAKATWLSNDIVMFSTKAGEMLLLTVVYDGRVVQRLDLMKSKAS VLSSAVTSIGNSFFFLGSRLGDSLLVQFSYCASKSVLQDLTNEVILSLCWSYFMSKSLHGLGVS YQSTIHA(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0252200_circ_g.16

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