Plant Circular RNA Database

Detail information of Os04g0550400_circ_g.12

			
						 General Information
					
						CircRNA Name
						Os04g0550400_circ_g.12
					
						ID in PlantcircBase
						osa_circ_024782
					
						Alias
						Os04circ10936/Os_ciR1523
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 27556411-27557039  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os04g0550400						
					
						Parent gene annotation
						
							E3 ligases of H2Bub1, Transcriptional regulation of anther devel
opment (Os04t0550400-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0550400_circ_g.4 Os04g0550400_circ_g.5 Os04g0550400_circ_g.6 Os04g0550400_circ_g.7 Os04g0550400_circ_g.8 Os04g0550400_circ_g.9 Os04g0550400_circ_g.10 Os04g0550400_circ_g.11 Os04g0550400_circ_g.13 Os04g0550400_circ_g.14 						
					
						Support reads
						2/7/17
					
						Tissues
						leaf/root/shoot, root, seed
					
						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
						Os04t0550400-01:2

General Information
CircRNA Name	Os04g0550400_circ_g.12
ID in PlantcircBase	osa_circ_024782
Alias	Os04circ10936/Os_ciR1523
Organism	Oryza sativa
Position	chr4: 27556411-27557039 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, find_circ
Parent gene	Os04g0550400
Parent gene annotation	E3 ligases of H2Bub1, Transcriptional regulation of anther devel opment (Os04t0550400-01)
Parent gene strand	-
Alternative splicing	Os04g0550400_circ_g.4 Os04g0550400_circ_g.5 Os04g0550400_circ_g.6 Os04g0550400_circ_g.7 Os04g0550400_circ_g.8 Os04g0550400_circ_g.9 Os04g0550400_circ_g.10 Os04g0550400_circ_g.11 Os04g0550400_circ_g.13 Os04g0550400_circ_g.14
Support reads	2/7/17
Tissues	leaf/root/shoot, root, seed
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	Os04t0550400-01:2

			
						 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  
						
							CTTCCCAAGTGGCAACCAGGCAAACAACCTGAACTTTCAGTTGCACCAGATTCCACAAGACTTC
TAAGAGTGTCCCTCTCTATGGGTGCACAAGTACCATcttttagacgtctatgttcagctctttt
tcgggcactggaatctctttgattttgataatcctctgctaactgcttgtgcttcaactgaaga
ttacttaa

						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: 393
Transcript exons: 27556411-27556578,27556815-27557039
CTTTTAGACGTCTATGTTCAGCTCTTTTTCGGGCACTGGAATCTCTTTGATTTTGATAATCCTC
TGCTAACTGCTTGTGCTTCAACTGAAGATTACTTAATGCTTGTACGACATTATTGAGGCTGGAC
AACAGGTTGCTACTAGTACTCTGTAGTTGCTTACTGCGGTCATTTTCTGGTAATTTAGTGAGAG
CAGCCAAAGCACACTCCTCATTTGCTTGCAAAAGATCACTTGATGGAAAAAAGATATCCCCAAG
AGCATTAGCTGTGGATAGATGTAATGGAGGGGCATCACTTCCCAAGTGGCAACCAGGCAAACAA
CCTGAACTTTCAGTTGCACCAGATTCCACAAGACTTCTAAGAGTGTCCCTCTCTATGGGTGCAC
AAGTACCAT
						
						Genomic sequence
						
							CTTTTAGACGTCTATGTTCAGCTCTTTTTCGGGCACTGGAATCTCTTTGATTTTGATAATCCTC
TGCTAACTGCTTGTGCTTCAACTGAAGATTACTTAATGCTTGTACGACATTATTGAGGCTGGAC
AACAGGTTGCTACTAGTACTCTGTAGTTGCTTACTGCGGTCTACAGAACATGGATGAAATTAGT
ACTTCTTTTGTATTAGTACAACTGAAAGCTATACTCTCTCCGTCCAACAAAAAACGAATCTAGA
CTGGATGTGACACATTCTAGTACAACAAATCTAGACAGAGATATGTCCAAATTCGTTGTACTAG
GATATGTCACATCCAAAACTAGGTTGGTTTTTTATGGGTCGAAGGGAGTACTAGTTAACAGAAT
ATATGAACTAGAAGACGAACCATTTTCTGGTAATTTAGTGAGAGCAGCCAAAGCACACTCCTCA
TTTGCTTGCAAAAGATCACTTGATGGAAAAAAGATATCCCCAAGAGCATTAGCTGTGGATAGAT
GTAATGGAGGGGCATCACTTCCCAAGTGGCAACCAGGCAAACAACCTGAACTTTCAGTTGCACC
AGATTCCACAAGACTTCTAAGAGTGTCCCTCTCTATGGGTGCACAAGTACCAT

Sequences
Splice junction sequence	CTTCCCAAGTGGCAACCAGGCAAACAACCTGAACTTTCAGTTGCACCAGATTCCACAAGACTTC TAAGAGTGTCCCTCTCTATGGGTGCACAAGTACCATcttttagacgtctatgttcagctctttt tcgggcactggaatctctttgattttgataatcctctgctaactgcttgtgcttcaactgaaga ttacttaa
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: 393 Transcript exons: 27556411-27556578,27556815-27557039 CTTTTAGACGTCTATGTTCAGCTCTTTTTCGGGCACTGGAATCTCTTTGATTTTGATAATCCTC TGCTAACTGCTTGTGCTTCAACTGAAGATTACTTAATGCTTGTACGACATTATTGAGGCTGGAC AACAGGTTGCTACTAGTACTCTGTAGTTGCTTACTGCGGTCATTTTCTGGTAATTTAGTGAGAG CAGCCAAAGCACACTCCTCATTTGCTTGCAAAAGATCACTTGATGGAAAAAAGATATCCCCAAG AGCATTAGCTGTGGATAGATGTAATGGAGGGGCATCACTTCCCAAGTGGCAACCAGGCAAACAA CCTGAACTTTCAGTTGCACCAGATTCCACAAGACTTCTAAGAGTGTCCCTCTCTATGGGTGCAC AAGTACCAT
Genomic sequence	CTTTTAGACGTCTATGTTCAGCTCTTTTTCGGGCACTGGAATCTCTTTGATTTTGATAATCCTC TGCTAACTGCTTGTGCTTCAACTGAAGATTACTTAATGCTTGTACGACATTATTGAGGCTGGAC AACAGGTTGCTACTAGTACTCTGTAGTTGCTTACTGCGGTCTACAGAACATGGATGAAATTAGT ACTTCTTTTGTATTAGTACAACTGAAAGCTATACTCTCTCCGTCCAACAAAAAACGAATCTAGA CTGGATGTGACACATTCTAGTACAACAAATCTAGACAGAGATATGTCCAAATTCGTTGTACTAG GATATGTCACATCCAAAACTAGGTTGGTTTTTTATGGGTCGAAGGGAGTACTAGTTAACAGAAT ATATGAACTAGAAGACGAACCATTTTCTGGTAATTTAGTGAGAGCAGCCAAAGCACACTCCTCA TTTGCTTGCAAAAGATCACTTGATGGAAAAAAGATATCCCCAAGAGCATTAGCTGTGGATAGAT GTAATGGAGGGGCATCACTTCCCAAGTGGCAACCAGGCAAACAACCTGAACTTTCAGTTGCACC AGATTCCACAAGACTTCTAAGAGTGTCCCTCTCTATGGGTGCACAAGTACCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005640* osi_circ_014622 						
					
						PMCS
						0.347201775

Conservation Information
Conserved circRNAs	osi_circ_005640* osi_circ_014622
PMCS	0.347201775

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							27557022-27556457(+)
						
						Potential amino acid sequence
						
							MGAQVPSFRRLCSALFRALESL*(+)
						
						Sponge-miRNAs
						
							osa-miR816 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	27557022-27556457(+)
Potential amino acid sequence	MGAQVPSFRRLCSALFRALESL*(+)
Sponge-miRNAs	osa-miR816
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os04g0550400_circ_g.12

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