Plant Circular RNA Database

Detail information of Os03g0377500_circ_igg.2

			
						 General Information
					
						CircRNA Name
						Os03g0377500_circ_igg.2
					
						ID in PlantcircBase
						osa_circ_020067
					
						Alias
						Os03circ16439/Os_ciR1085
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 14916244-14917271  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							igg-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							Os03g0377300_circ_ag.1 Os03g0377300_circ_ag.2 Os03g0377500_circ_igg.1 Os03g0377500_circ_g.1 						
					
						Support reads
						4/18/5
					
						Tissues
						leaf and panicle/root/shoot, root, seed
					
						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  
						
							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
						NA

General Information
CircRNA Name	Os03g0377500_circ_igg.2
ID in PlantcircBase	osa_circ_020067
Alias	Os03circ16439/Os_ciR1085
Organism	Oryza sativa
Position	chr3: 14916244-14917271 JBrowse»
Reference genome	IRGSP-1.0.38
Type	igg-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	Os03g0377300_circ_ag.1 Os03g0377300_circ_ag.2 Os03g0377500_circ_igg.1 Os03g0377500_circ_g.1
Support reads	4/18/5
Tissues	leaf and panicle/root/shoot, root, seed
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	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	NA

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: TGCTGTTGAGGGACAAACTC
 R: TGTTCCCTCTGCTTTGGACT
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	Yes 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	F: TGCTGTTGAGGGACAAACTC R: TGTTCCCTCTGCTTTGGACT 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  
						
							TGATGTTGAGAGTTCAGAGTGGACAGAGGTGTTATCAGCAAATGCTATAACATTGATCTACCAA
AACCTCCAGAAGTTCGATGATTTTATTTCTGATCAGgattgccggtcagatgcccaaagctttt
gacatcctacaagatgttgcgcaacacactctgtctaatttgcatgatatccagaagagcttaa
tattttgg

									
								

					

						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: 157
Transcript exons: 14916244-14916293,14917165-14917271
GATTGCCGGTCAGATGCCCAAAGCTTTTGACATCCTACAAGATGTTGCGCCAGAAGTTGATGTT
GAGAGTTCAGAGTGGACAGAGGTGTTATCAGCAAATGCTATAACATTGATCTACCAAAACCTCC
AGAAGTTCGATGATTTTATTTCTGATCAG
Transcript length: 227
Transcript exons: 14916244-14916341,14917143-14917271
GATTGCCGGTCAGATGCCCAAAGCTTTTGACATCCTACAAGATGTTGCGCAACACACTCTGTCT
AATTTGCATGATATCCAGAAGAGCTTAATATTTTGAACTTATCTTTGAAAGATTGCCAGAAGTT
GATGTTGAGAGTTCAGAGTGGACAGAGGTGTTATCAGCAAATGCTATAACATTGATCTACCAAA
ACCTCCAGAAGTTCGATGATTTTATTTCTGATCAG
Transcript length: 237
Transcript exons: 14916244-14916313,14917105-14917271
GATTGCCGGTCAGATGCCCAAAGCTTTTGACATCCTACAAGATGTTGCGCAACACACTCTGTCT
AATTTGGACAAACTCTATTATGCACACATGATGGGAAGTCGCCTGAACTTATCTTTGAAAGATT
GCCAGAAGTTGATGTTGAGAGTTCAGAGTGGACAGAGGTGTTATCAGCAAATGCTATAACATTG
ATCTACCAAAACCTCCAGAAGTTCGATGATTTTATTTCTGATCAG
						
					

						Genomic sequence
						
							GATTGCCGGTCAGATGCCCAAAGCTTTTGACATCCTACAAGATGTTGCGCAACACACTCTGTCT
AATTTGCATGATATCCAGAAGAGCTTAATATTTTGGCAGTCCAAAGCAGAGGTATAAAGTTGAT
TCATAAAAATTGAAGTGCTTCTACACTTTTAATATGTAGAGAAGTCCACTACTTACTCATCTTC
CGTTGTCCTATGCTATTTTCTCCAGGGAACAAGTTCACAGAAACTGTATTTTATGATCTTTGAA
AGAGGTCCAAGGGCCTTTGTCGAAGCAGCATGGCAAACACTGACTAGACTCAAGAGCAATGGGA
GTCCAGTCCCGCACCTTTTGCACTCTGCTTCTGATATGGTCTCAACAAAACTTGCTGTCCTGAC
AAGTATGCAACACTGCTTGGCTGCTTTTCTTGCTGAGGTTTGTTTAATCAAATGCGATTATCAA
TATCAAATGCTGATGTCAAGTAGAATAAATTGTTCTTTACAATAGTTTCAATATCAACTTTGAA
GCAGCTCCCCTATCAACTGGTGTACTATGGTGTCCAAATTATTCAAGCTCTTCTTTTTAATACT
TTGGATAAATTTACTTATAGAACATGGCTACTGTTTCTCATACATGAATTCGAATTCTACCTTG
CCTCTTCTATAGGTTTACTTTGAAGTTGATAAGTGCAGAAAAGGACTAACAGAAAGTTCAGATA
AATCGCTACATACTCTATTCATTGTTCTGAATTCTGTCTTCTCCAAATTGGAGGTATCATTTAG
AAATGCTGTTGAGGTATGCAATGTTCTTTTTGCATGTTTTGGATGTTACAAGTATGACATGCTA
GCTATTTCACATAGTTTCATTTCTTCAGGGACAAACTCTATTATGCACACATGATGGGAAGTCG
CCTGAACTTATCTTTGAAAGATTGCCAGAAGTTGATGTTGAGAGTTCAGAGTGGACAGAGGTGT
TATCAGCAAATGCTATAACATTGATCTACCAAAACCTCCAGAAGTTCGATGATTTTATTTCTGA
TCAG
						
					

			
		

Sequences
Splice junction sequence	TGATGTTGAGAGTTCAGAGTGGACAGAGGTGTTATCAGCAAATGCTATAACATTGATCTACCAA AACCTCCAGAAGTTCGATGATTTTATTTCTGATCAGgattgccggtcagatgcccaaagctttt gacatcctacaagatgttgcgcaacacactctgtctaatttgcatgatatccagaagagcttaa tattttgg
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: 157 Transcript exons: 14916244-14916293,14917165-14917271 GATTGCCGGTCAGATGCCCAAAGCTTTTGACATCCTACAAGATGTTGCGCCAGAAGTTGATGTT GAGAGTTCAGAGTGGACAGAGGTGTTATCAGCAAATGCTATAACATTGATCTACCAAAACCTCC AGAAGTTCGATGATTTTATTTCTGATCAG Transcript length: 227 Transcript exons: 14916244-14916341,14917143-14917271 GATTGCCGGTCAGATGCCCAAAGCTTTTGACATCCTACAAGATGTTGCGCAACACACTCTGTCT AATTTGCATGATATCCAGAAGAGCTTAATATTTTGAACTTATCTTTGAAAGATTGCCAGAAGTT GATGTTGAGAGTTCAGAGTGGACAGAGGTGTTATCAGCAAATGCTATAACATTGATCTACCAAA ACCTCCAGAAGTTCGATGATTTTATTTCTGATCAG Transcript length: 237 Transcript exons: 14916244-14916313,14917105-14917271 GATTGCCGGTCAGATGCCCAAAGCTTTTGACATCCTACAAGATGTTGCGCAACACACTCTGTCT AATTTGGACAAACTCTATTATGCACACATGATGGGAAGTCGCCTGAACTTATCTTTGAAAGATT GCCAGAAGTTGATGTTGAGAGTTCAGAGTGGACAGAGGTGTTATCAGCAAATGCTATAACATTG ATCTACCAAAACCTCCAGAAGTTCGATGATTTTATTTCTGATCAG
Genomic sequence	GATTGCCGGTCAGATGCCCAAAGCTTTTGACATCCTACAAGATGTTGCGCAACACACTCTGTCT AATTTGCATGATATCCAGAAGAGCTTAATATTTTGGCAGTCCAAAGCAGAGGTATAAAGTTGAT TCATAAAAATTGAAGTGCTTCTACACTTTTAATATGTAGAGAAGTCCACTACTTACTCATCTTC CGTTGTCCTATGCTATTTTCTCCAGGGAACAAGTTCACAGAAACTGTATTTTATGATCTTTGAA AGAGGTCCAAGGGCCTTTGTCGAAGCAGCATGGCAAACACTGACTAGACTCAAGAGCAATGGGA GTCCAGTCCCGCACCTTTTGCACTCTGCTTCTGATATGGTCTCAACAAAACTTGCTGTCCTGAC AAGTATGCAACACTGCTTGGCTGCTTTTCTTGCTGAGGTTTGTTTAATCAAATGCGATTATCAA TATCAAATGCTGATGTCAAGTAGAATAAATTGTTCTTTACAATAGTTTCAATATCAACTTTGAA GCAGCTCCCCTATCAACTGGTGTACTATGGTGTCCAAATTATTCAAGCTCTTCTTTTTAATACT TTGGATAAATTTACTTATAGAACATGGCTACTGTTTCTCATACATGAATTCGAATTCTACCTTG CCTCTTCTATAGGTTTACTTTGAAGTTGATAAGTGCAGAAAAGGACTAACAGAAAGTTCAGATA AATCGCTACATACTCTATTCATTGTTCTGAATTCTGTCTTCTCCAAATTGGAGGTATCATTTAG AAATGCTGTTGAGGTATGCAATGTTCTTTTTGCATGTTTTGGATGTTACAAGTATGACATGCTA GCTATTTCACATAGTTTCATTTCTTCAGGGACAAACTCTATTATGCACACATGATGGGAAGTCG CCTGAACTTATCTTTGAAAGATTGCCAGAAGTTGATGTTGAGAGTTCAGAGTGGACAGAGGTGT TATCAGCAAATGCTATAACATTGATCTACCAAAACCTCCAGAAGTTCGATGATTTTATTTCTGA TCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.604756963

Conservation Information
Conserved circRNAs	NA
PMCS	0.604756963

			
						 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 Os03g0377500_circ_igg.2

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