Plant Circular RNA Database

Detail information of Os07g0660200_circ_ig.4

			
						 General Information
					
						CircRNA Name
						Os07g0660200_circ_ig.4
					
						ID in PlantcircBase
						osa_circ_035158
					
						Alias
						Os07circ19573/Os_ciR238
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 27834197-27835287  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						CIRI, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							NA						
					
						Support reads
						19/186/14/6
					
						Tissues
						leaf and panicle/root/root/seed
					
						Exon boundary  
						
							No-No							"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
						NA

General Information
CircRNA Name	Os07g0660200_circ_ig.4
ID in PlantcircBase	osa_circ_035158
Alias	Os07circ19573/Os_ciR238
Organism	Oryza sativa
Position	chr7: 27834197-27835287 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ig-circRNA
Identification method	CIRI, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	NA
Support reads	19/186/14/6
Tissues	leaf and panicle/root/root/seed
Exon boundary	No-No "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	NA

			
						 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  
						
							ACAATAAAGTTACATAATATCATATTGATAAAATACACAAGTTCTTACCTTGTACTCATCAATA
GCATCCTGAGCAAATTCAATATCTGTATCTTTTTCCctctctgctagcacgatttcccacataa
accacaacattcatgtcaggtagccatttccgaaattctttcgcccagtttgacaatgttgaca
gtggaaca

									
								

					

						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: 145
Transcript exons: 27834197-27834314,27835261-27835287
CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT
TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGACCAGCAAATTCAA
TATCTGTATCTTTTTCC
Transcript length: 157
Transcript exons: 27834197-27834310,27835245-27835287
CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT
TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGATCAATAGCATCCT
GAGCAAATTCAATATCTGTATCTTTTTCC
Transcript length: 160
Transcript exons: 27834197-27834304,27835236-27835287
CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT
TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGCTTGTACTCATCAATAGCAT
CCTGAGCAAATTCAATATCTGTATCTTTTTCC
Transcript length: 162
Transcript exons: 27834197-27834312,27835242-27835287
CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT
TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGACCTCATCAATAGC
ATCCTGAGCAAATTCAATATCTGTATCTTTTTCC
Transcript length: 164
Transcript exons: 27834197-27834332,27835260-27835287
CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT
TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGACCATTAATTTCTT
GAGCATTCAGCAAATTCAATATCTGTATCTTTTTCC
Transcript length: 185
Transcript exons: 27834197-27834329,27835236-27835287
CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT
TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGACCATTAATTTCTT
GAGCACTTGTACTCATCAATAGCATCCTGAGCAAATTCAATATCTGTATCTTTTTCC
Transcript length: 433
Transcript exons: 27834197-27835287
CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT
TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGACCATTAATTTCTT
GAGCATTATGAAGGAAACCCAGCATGGAGACAGATTGAATAGTTTTTCCCAGACCCATCTCATC
AGCAAGAATAACATTAGTGTCATTTCTCCACCCATTAACAAGGAAGTTTAGGCCTTCAAGCTGG
TAATCACGTAGTTTGCCTCCTTTTAGCCATTCTGGTTGGTCGTCAAGCCTCCGCAAACTAGCTT
TGCTTTTTTTCCTTTGGAAATCAACTGTTTTCCCGAGTATAGATGTTGCAGCTTCACGGGCCTT
GTACTCATCAATAGCATCCTGAGCAAATTCAATATCTGTATCTTTTTCC
						
					

						Genomic sequence
						
							CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT
TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGACCATTAATTTCTT
GAGCATTCTGTAATAACCACACAGGGTGTTAGTGATCAATAGATGAATTCTACTACTGTCACGA
TAATAGAGAAGAGCAGAACTGTGTAGGAGAAGATTACATGAAGGAAACCCAGCATGGAGACAGA
TTGAATAGTTTTTCCCAGACCCATCTCATCAGCAAGAATAACATTAGTGTCATTTCTCCACCTG
TTTTACAAATAAATCAATGAGCTTACAAAGTGGCAACACATGTGCTCTCATTTTCATATAAACA
GATCTTACATACCCATTAACAAGGAAGTTTAGGCCTTCAAGCTGGTAATCACGTAGTTTGCCTC
CTTTTAGCCATTCTGGTTGGTCGTCAAGCCTCCGCAAACTAGCTGAATAATGTAAACTTAGTAT
AAGATTTAACTGAAGAGTAATGATCCTTTGTTGCTAGACAAAGATCTCAAATTATACCATGCAT
GGATTTTCCAATGCTTGACAATATTCACATGTAAAACAGTGACCCTAAATAGAAGTGCAACAAA
TTTGAGGAACAGGCCATTTAAAACAATAGTGGTAATCGATAATTTGCCACTCATGTGTCTACAA
CGTCTAGGGCCAGGACCGCACATGATAGTGACGAGTGGCAAATGAATAGGTGATCACTTGGTGT
CCAGACCATCCAGAAAAGAAACTTGTCCACAAAAAGACCAAATAAAATACCAAAAGTAATAAAG
CAAACAAACAAAAAATATTGTGCGGGGAACTTACCTTTGCTTTTTTTCCTTTGGAAATCAACTG
TTTTCCCGAGTATAGATGTTGCAGCTTCACGGGCCTATAATTAATATAATTAAAGTGCAACCCA
AAATATTATACAATCTTATGCACATATGCTCACAATAAAGTTACATAATATCATATTGATAAAA
TACACAAGTTCTTACCTTGTACTCATCAATAGCATCCTGAGCAAATTCAATATCTGTATCTTTT
TCC
						
					

			
		

Sequences
Splice junction sequence	ACAATAAAGTTACATAATATCATATTGATAAAATACACAAGTTCTTACCTTGTACTCATCAATA GCATCCTGAGCAAATTCAATATCTGTATCTTTTTCCctctctgctagcacgatttcccacataa accacaacattcatgtcaggtagccatttccgaaattctttcgcccagtttgacaatgttgaca gtggaaca
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: 145 Transcript exons: 27834197-27834314,27835261-27835287 CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGACCAGCAAATTCAA TATCTGTATCTTTTTCC Transcript length: 157 Transcript exons: 27834197-27834310,27835245-27835287 CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGATCAATAGCATCCT GAGCAAATTCAATATCTGTATCTTTTTCC Transcript length: 160 Transcript exons: 27834197-27834304,27835236-27835287 CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGCTTGTACTCATCAATAGCAT CCTGAGCAAATTCAATATCTGTATCTTTTTCC Transcript length: 162 Transcript exons: 27834197-27834312,27835242-27835287 CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGACCTCATCAATAGC ATCCTGAGCAAATTCAATATCTGTATCTTTTTCC Transcript length: 164 Transcript exons: 27834197-27834332,27835260-27835287 CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGACCATTAATTTCTT GAGCATTCAGCAAATTCAATATCTGTATCTTTTTCC Transcript length: 185 Transcript exons: 27834197-27834329,27835236-27835287 CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGACCATTAATTTCTT GAGCACTTGTACTCATCAATAGCATCCTGAGCAAATTCAATATCTGTATCTTTTTCC Transcript length: 433 Transcript exons: 27834197-27835287 CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGACCATTAATTTCTT GAGCATTATGAAGGAAACCCAGCATGGAGACAGATTGAATAGTTTTTCCCAGACCCATCTCATC AGCAAGAATAACATTAGTGTCATTTCTCCACCCATTAACAAGGAAGTTTAGGCCTTCAAGCTGG TAATCACGTAGTTTGCCTCCTTTTAGCCATTCTGGTTGGTCGTCAAGCCTCCGCAAACTAGCTT TGCTTTTTTTCCTTTGGAAATCAACTGTTTTCCCGAGTATAGATGTTGCAGCTTCACGGGCCTT GTACTCATCAATAGCATCCTGAGCAAATTCAATATCTGTATCTTTTTCC
Genomic sequence	CTCTCTGCTAGCACGATTTCCCACATAAACCACAACATTCATGTCAGGTAGCCATTTCCGAAAT TCTTTCGCCCAGTTTGACAATGTTGACAGTGGAACAACCACAAGAAACGGACCATTAATTTCTT GAGCATTCTGTAATAACCACACAGGGTGTTAGTGATCAATAGATGAATTCTACTACTGTCACGA TAATAGAGAAGAGCAGAACTGTGTAGGAGAAGATTACATGAAGGAAACCCAGCATGGAGACAGA TTGAATAGTTTTTCCCAGACCCATCTCATCAGCAAGAATAACATTAGTGTCATTTCTCCACCTG TTTTACAAATAAATCAATGAGCTTACAAAGTGGCAACACATGTGCTCTCATTTTCATATAAACA GATCTTACATACCCATTAACAAGGAAGTTTAGGCCTTCAAGCTGGTAATCACGTAGTTTGCCTC CTTTTAGCCATTCTGGTTGGTCGTCAAGCCTCCGCAAACTAGCTGAATAATGTAAACTTAGTAT AAGATTTAACTGAAGAGTAATGATCCTTTGTTGCTAGACAAAGATCTCAAATTATACCATGCAT GGATTTTCCAATGCTTGACAATATTCACATGTAAAACAGTGACCCTAAATAGAAGTGCAACAAA TTTGAGGAACAGGCCATTTAAAACAATAGTGGTAATCGATAATTTGCCACTCATGTGTCTACAA CGTCTAGGGCCAGGACCGCACATGATAGTGACGAGTGGCAAATGAATAGGTGATCACTTGGTGT CCAGACCATCCAGAAAAGAAACTTGTCCACAAAAAGACCAAATAAAATACCAAAAGTAATAAAG CAAACAAACAAAAAATATTGTGCGGGGAACTTACCTTTGCTTTTTTTCCTTTGGAAATCAACTG TTTTCCCGAGTATAGATGTTGCAGCTTCACGGGCCTATAATTAATATAATTAAAGTGCAACCCA AAATATTATACAATCTTATGCACATATGCTCACAATAAAGTTACATAATATCATATTGATAAAA TACACAAGTTCTTACCTTGTACTCATCAATAGCATCCTGAGCAAATTCAATATCTGTATCTTTT TCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_017440 						
					
						PMCS
						0.449833387

Conservation Information
Conserved circRNAs	osi_circ_017440
PMCS	0.449833387

			
						 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
						NA

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	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os07g0660200_circ_ig.4

Address

Any questions?

Supported by