Plant Circular RNA Database

Detail information of Os10g0420900_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os10g0420900_circ_g.1
					
						ID in PlantcircBase
						osa_circ_006838
					
						Alias
						Os10circ03923/Os_ciR139
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 14835324-14836371  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI, SMALT, Segemehl, circRNA_finder, find_circ
					
						Parent gene
						
							Os10g0420900						
					
						Parent gene annotation
						
							Conserved hypothetical protein. (Os10t0420900-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os10g0420900_circ_g.2 Os10g0420900_circ_g.3 Os10g0420900_circ_g.4 						
					
						Support reads
						4/350/6
					
						Tissues
						leaf and panicle/root/seed, pistil
					
						Exon boundary  
						
							No-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
						Os10t0420900-01:4

General Information
CircRNA Name	Os10g0420900_circ_g.1
ID in PlantcircBase	osa_circ_006838
Alias	Os10circ03923/Os_ciR139
Organism	Oryza sativa
Position	chr10: 14835324-14836371 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRI, SMALT, Segemehl, circRNA_finder, find_circ
Parent gene	Os10g0420900
Parent gene annotation	Conserved hypothetical protein. (Os10t0420900-01)
Parent gene strand	-
Alternative splicing	Os10g0420900_circ_g.2 Os10g0420900_circ_g.3 Os10g0420900_circ_g.4
Support reads	4/350/6
Tissues	leaf and panicle/root/seed, pistil
Exon boundary	No-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	Os10t0420900-01:4

			
						 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  
						
							ACTGGAGAGGCATATTGCAACTTTCTCTCAACTTACATATATCACTGGTTTCCTTCGAGGCAAA
TTGTCAACTTTGCTCTTCTTACTGTGCAGCTTATACctcatcatcatcaacttgcccgtggtta
tccaaaatctgagtttgcttcgagtgtatcaggcaccatccctttggatgaacaacaaaaatga
attaaaaa

						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: 126
Transcript exons: 14835324-14835383,14836306-14836371
CTCATCATCATCAACTTGCCCGTGGTTATCCAAAATCTGAGTTTGCTTCGAGTGTATCAGACAT
ATATCACTGGTTTCCTTCGAGGCAAATTGTCAACTTTGCTCTTCTTACTGTGCAGCTTATAC
						
						Genomic sequence
						
							CTCATCATCATCAACTTGCCCGTGGTTATCCAAAATCTGAGTTTGCTTCGAGTGTATCAGGCAC
CATCCCTTTGGATGAACAACAAAAATGAATTAAAAAGGCTCCACGAAGGAATTGACTCTAATCC
CTTCCTAGAAAGTCCTAAAGTGGAATACTTTCACATTACACTTTAATATGAAATATTTTATCCA
TTTTGTTCCTTTTTTAAATTGTGAACCTGGAACCTTTTCTCTACCCTATTTAGGTCAACAAGAC
CCCCGTATCTTAACAGGCATCTGTGATGTCCAACTGTATACCCTCAGGCAAAAGCAAAAAGAGA
TAGGAAAGCTATAGGTTGCAGTTACAAATATAGTGACGCGGCAGACTGATGATACACATACAAA
GAAAGTTCTTACAAAATTTTACAAACGCTGATGTGGCAGACAGTGGTTGAATCATGATTTTGCA
TAACTAATAACTGAGCAAAACTTAATCATCTACTTTAGCAGTGTATTTGCTCCATCTAGGGTCA
AGGGTTTAAATGGTTTGAGAATTCAAAACATTGTCTCAACCATTTAGTCTTGTCAGATAGTGTA
TTATGCCATAGTGCTTTTTAGTTTCTGTTATTTGTTATCCAAAGAATAATTCAATCAATAATCA
ACACATACCTCTGATTGTGGAGCCCTTCTGGATCTTAATATCTCGTTGCACTGTTCCATCAGGC
TTCTCGTTCCAAATGGTCTGGAAGACTTTGTTGGTCCTGTAAAGCATTCTAAAACAGATCTAAT
GAAGATTTTGTACATTCCACCGTTTTTGGTTAGAGACTTTGGATGGTATGTATAACAGACCTTG
GTATATGCAGTTCTTTACCATAAGTTCAGTATCTGTCTCATGTTAATCATTGATCCACCTGTCA
TAGAATTACAAAGAGGTCTTATTTCATTTCTAAAATCCTCAGTATGGAAGTAACTGGAGAGGCA
TATTGCAACTTTCTCTCAACTTACATATATCACTGGTTTCCTTCGAGGCAAATTGTCAACTTTG
CTCTTCTTACTGTGCAGCTTATAC

Sequences
Splice junction sequence	ACTGGAGAGGCATATTGCAACTTTCTCTCAACTTACATATATCACTGGTTTCCTTCGAGGCAAA TTGTCAACTTTGCTCTTCTTACTGTGCAGCTTATACctcatcatcatcaacttgcccgtggtta tccaaaatctgagtttgcttcgagtgtatcaggcaccatccctttggatgaacaacaaaaatga attaaaaa
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: 126 Transcript exons: 14835324-14835383,14836306-14836371 CTCATCATCATCAACTTGCCCGTGGTTATCCAAAATCTGAGTTTGCTTCGAGTGTATCAGACAT ATATCACTGGTTTCCTTCGAGGCAAATTGTCAACTTTGCTCTTCTTACTGTGCAGCTTATAC
Genomic sequence	CTCATCATCATCAACTTGCCCGTGGTTATCCAAAATCTGAGTTTGCTTCGAGTGTATCAGGCAC CATCCCTTTGGATGAACAACAAAAATGAATTAAAAAGGCTCCACGAAGGAATTGACTCTAATCC CTTCCTAGAAAGTCCTAAAGTGGAATACTTTCACATTACACTTTAATATGAAATATTTTATCCA TTTTGTTCCTTTTTTAAATTGTGAACCTGGAACCTTTTCTCTACCCTATTTAGGTCAACAAGAC CCCCGTATCTTAACAGGCATCTGTGATGTCCAACTGTATACCCTCAGGCAAAAGCAAAAAGAGA TAGGAAAGCTATAGGTTGCAGTTACAAATATAGTGACGCGGCAGACTGATGATACACATACAAA GAAAGTTCTTACAAAATTTTACAAACGCTGATGTGGCAGACAGTGGTTGAATCATGATTTTGCA TAACTAATAACTGAGCAAAACTTAATCATCTACTTTAGCAGTGTATTTGCTCCATCTAGGGTCA AGGGTTTAAATGGTTTGAGAATTCAAAACATTGTCTCAACCATTTAGTCTTGTCAGATAGTGTA TTATGCCATAGTGCTTTTTAGTTTCTGTTATTTGTTATCCAAAGAATAATTCAATCAATAATCA ACACATACCTCTGATTGTGGAGCCCTTCTGGATCTTAATATCTCGTTGCACTGTTCCATCAGGC TTCTCGTTCCAAATGGTCTGGAAGACTTTGTTGGTCCTGTAAAGCATTCTAAAACAGATCTAAT GAAGATTTTGTACATTCCACCGTTTTTGGTTAGAGACTTTGGATGGTATGTATAACAGACCTTG GTATATGCAGTTCTTTACCATAAGTTCAGTATCTGTCTCATGTTAATCATTGATCCACCTGTCA TAGAATTACAAAGAGGTCTTATTTCATTTCTAAAATCCTCAGTATGGAAGTAACTGGAGAGGCA TATTGCAACTTTCTCTCAACTTACATATATCACTGGTTTCCTTCGAGGCAAATTGTCAACTTTG CTCTTCTTACTGTGCAGCTTATAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_008418 osi_circ_008419 						
					
						PMCS
						0.342903356

Conservation Information
Conserved circRNAs	osi_circ_008418 osi_circ_008419
PMCS	0.342903356

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to Pi-starvation

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to Pi-starvation

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

circRNA

Detail information of Os10g0420900_circ_g.1

Address

Any questions?

Supported by