Plant Circular RNA Database

Detail information of Os11g0708000_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os11g0708000_circ_g.4
					
						ID in PlantcircBase
						osa_circ_010246
					
						Alias
						Os11circ11985/Os_ciR4599
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 28973569-28976848  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os11g0708000						
					
						Parent gene annotation
						
							Hypothetical protein. (Os11t0708000-01);Hypothetical gene. (Os11
t0708000-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os11g0708000_circ_g.1 Os11g0708000_circ_g.2 Os11g0708000_circ_g.3 Os11g0708000_circ_g.5 						
					
						Support reads
						2/4
					
						Tissues
						leaf/root
					
						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
						Os11t0708000-03:3
Os11t0708000-01:3

General Information
CircRNA Name	Os11g0708000_circ_g.4
ID in PlantcircBase	osa_circ_010246
Alias	Os11circ11985/Os_ciR4599
Organism	Oryza sativa
Position	chr11: 28973569-28976848 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	SMALT, Segemehl, find_circ
Parent gene	Os11g0708000
Parent gene annotation	Hypothetical protein. (Os11t0708000-01);Hypothetical gene. (Os11 t0708000-03)
Parent gene strand	-
Alternative splicing	Os11g0708000_circ_g.1 Os11g0708000_circ_g.2 Os11g0708000_circ_g.3 Os11g0708000_circ_g.5
Support reads	2/4
Tissues	leaf/root
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	Os11t0708000-03:3 Os11t0708000-01:3

			
						 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  
						
							TTGGTAAATGTTAGGAACAGGCATTGAATATACCTTACAATGTGCCAACACGGCATCTGATGCA
TGTGGTACTCCCCAGCAACTGAATTATTGAGATATGcagctcttagttctccttcccctgccgc
tggtcacgcagcaaacatggccgtcctgccggagtcacgccggctctccctgctcctcatggcc
gcctgctt

									
								

					

						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: 104
Transcript exons: 28973569-28973646,28976823-28976848
CAGCTCTTAGTTCTCCTTCCCCTGCCGCTGGTCACGCAGCAAACATGGCCGTCCTGCCGGAGTC
ACGCCGGCTCTCCCCCCAGCAACTGAATTATTGAGATATG
						
					

						Genomic sequence
						
							CAGCTCTTAGTTCTCCTTCCCCTGCCGCTGGTCACGCAGCAAACATGGCCGTCCTGCCGGAGTC
ACGCCGGCTCTCCCTGCTCCTCATGGCCGCCTGCTTCCTGCTTCAGGCTCTCAGCGCCCACGCC
ATCACCCGGCATTACAAGTTCAATGTGAGGATATATCGTCATCAAACTTTGCCGCATGATAACT
GCAAGCATGCATCGCAATTGTCACATACATATACAGGTTGCAGCAGAAATGGCAAGATGGTTTA
TTACCACGGTTTTGTCTGTCTTTTCTGTGTCTTGTGCAGGTGGTCATGCGGAACATGACACGGC
TTTGCTCAACCAAGCCTATCCTCACTGTCAATGGCAAGTTCCCGGGGCCAACCCTGTATGCAAG
AGAAGGCGATAATGTCCTAGTCAAGGTCGTCAATCATGTAGCTCACAATGTTACCATCCACTGG
TAAGCAGCTTAGCTAGCTAGCCCATGGCTACTCCATGCATATGCTTCAACTCCACGTGTAATTT
GCACCACAATTTGAATCACCACCTCAAGGCTCCTTTGCTCTCTGTAAGTACCCAAAAAGAAAAG
GAGAATATCATGCTGTGTTAGTTAAAAGGTAAAAAGTATGTATAGCTTGCATTAGATCCTCTCT
GTTGAACAGAAAACAGAAATGTGCTAGTTATTGTTCCCATTTATGCAACAAAAATACACTTGGT
GAATAACTTGATAAACAAGCATGTCATACTAATCAGGCACGGGGTAAGGCAGATCCGGACAGGG
TGGTACGATGGGCCAGCTTACATAACACAGTGCCCAATACAGCCAGGAAGCAGCTTTCTCTATA
ATTTCACTATAACAGGGCAACGAGGCACACTCCTCTGGCATGCTCACATCAATTGGCTAAGGGC
TACCGTCCATGGTGCTATCGTCATCCTTCCAAAGCTTGGCGTGCCCTACCCCTTCCCTGCACCT
CACAAGGAGGCTGTTATCGTGTTAGGTATATATATACACACACATATATATAGCTGCTTCTCTA
CATCTTGATGCATCCAGCACTTAATTTATCAAGTGCTGCATGCAGGAGAATGGTGGAAAGAGGA
CACAGAAACTGTAATTAACCAGGCCATGCAGCTAGGAGTGGGACCCAATATTTCTGATTCACAC
ACCATCAATGGTCATCCTGGTCCGCTGTCTGAGTGTGCTTCTTCACAAGGTAATACTCTTACTC
TACATGAACACGAGACAGACAGTGCATGTTATGGCTAACTATGTGCTAGTCCTACAACTGAGCC
AAAGACCTAACGATTTCCTGATGTATGCTTGCAATACAATGCACAGATGGGTTCAAGCTCAGCG
TCGAAAATGGCAAAACATACATGCTCCGGATCATCAACGCTGCACTGAATGATGACCTATTTTT
CAAGGTTGCTGGGCACGAATTAACTGTGGTTGAGGTTGATGCAGTCTATACCAAGCCATTTAAG
ACCGATACCCTGCTCATCACTCCAGGCCAGACCACCAACGTCCTTGTTAGAGCTAACCAAGGCG
CTGGCCGTTACCTTCTCTCAGTCTCCCCCTTCATGGATGCGCCCGTGCAGGTTGACAACAAAAC
AGGCACCGCTACTTTGCACTACGCCAACACAGTCTCGTCAAGCATGGCATCCCTCACTCTCGTC
AAGCCACCACCACAAAATGCCACCCATATCGTATCAAAATTTACTGATTCACTCCATAGTCTCA
ATTCCAAGGAGTACCCAGCCAATGTGCCACAGACAGTAGACCACTCCCTTCTCCTTACCGTTGG
CGTAGGTGTCAATCCATGTCCAAGCTGCATCAATGGGACAAGGGTGGTGGGCACAATCAACAAC
GTGACGTTCATCATGCCATCAACCCCAATTCTTCAAGCCCACTATTACAACATTCCAGGAGTGT
TCACAGAAGACTTCCCAGCAACCCCACTGCACAAGTTCAACTATACAGGAAGTGGTCCCAAAAA
CCTTCAAACCATGAATGGAACCAGGGTTTACAGGCTGCCATACAATGCTTCAGTGCAGGTTGTA
CTCCAGGATACGGGAATCATATCACCAGAAAGCCACCCAATCCATTTACATGGCTTTAATTTTT
TTGTGGTTGGGAAAGGGGTCGGGAACTACAACCCCAGGACCTCCCCTTCTACATTCAACCTCAT
CGACCCCATCGAGAGGAACACCATTGGAGTTCCTACTGGTGGTTGGACGGCAATCAGATTTAGG
TCAGACAACCCAGGTATTGATTTTAAAACCTATGTTTTTTTAAGATAAATAACCCCTTCTGTTT
CCAGACACATTGATTGAGCTGTTATATTGCAGGTGTTTGGTTTATGCATTGTCATTTCGAGGTG
CACACATCATGGGGACTCAAGATGGCCTTTGTGGTGGATAATGGAAAGAGACCTAGTGAGACTC
TGATTCCACCACCCAAAGATCTTCCGCAGTGTTAACAACATGGGATTCAAAACTGCCCCCACGG
AGAGGAGCCTATTACAAGAAGGGTAATTGGCTTTGGTCCGATGTACGGAAAGAATCAACGGTGA
TTTCTACCATGTGCTACTACTTGACTCTTGCCACACATTTTTTTCTCCTTTTTGATTTTTTTGG
GCTTGTTTACCAAAGATAGTGCATACAGGGCATTCAGGTTGTAATTAGCTCTTGCCATGACCAA
CTTGTTCCCCCTTTTTCAATTAATGAAAATGTATATGTTGGCATGCCTCATGAATTGAATGTTT
GTTGAGAATTAGAGAAAGATGAATCCGCCTTAAAGTATCTCAGTCACCAAATTTTAGAAATATG
TCGCCGCTATCTCCTCCTTTCTAACACCTATCCAGTACTCCCTATCTTCTCTGGCTGGACCCAC
CCCTGTATAGTCTATTTAGTACTAGATCCAGCTTAGTACTTTAAGTTACTGTAAACCTGTTCAC
CGACAGCTCAATCCAAAAAATACCAGGCCAGCCTCGCCATGCCTCTCGGGCCAGGCTTGACCCA
GCTTGAGCCTCCACACGACCCCTATATTAAGCAGCCCTAGTTTCTAGATTTTCTTAGAAAAACC
TTCCAAGAAACAAGTGATGGATATCTATTATCTTCTAACTTGTAGTATTATGTCCAACACAAAT
AGTAATCACGTACTAGCCATAATACCAAAGTAGTCACTAATGAATTGGTAAATGTTAGGAACAG
GCATTGAATATACCTTACAATGTGCCAACACGGCATCTGATGCATGTGGTACTCCCCAGCAACT
GAATTATTGAGATATG
						
					

			
		

Sequences
Splice junction sequence	TTGGTAAATGTTAGGAACAGGCATTGAATATACCTTACAATGTGCCAACACGGCATCTGATGCA TGTGGTACTCCCCAGCAACTGAATTATTGAGATATGcagctcttagttctccttcccctgccgc tggtcacgcagcaaacatggccgtcctgccggagtcacgccggctctccctgctcctcatggcc gcctgctt
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: 104 Transcript exons: 28973569-28973646,28976823-28976848 CAGCTCTTAGTTCTCCTTCCCCTGCCGCTGGTCACGCAGCAAACATGGCCGTCCTGCCGGAGTC ACGCCGGCTCTCCCCCCAGCAACTGAATTATTGAGATATG
Genomic sequence	CAGCTCTTAGTTCTCCTTCCCCTGCCGCTGGTCACGCAGCAAACATGGCCGTCCTGCCGGAGTC ACGCCGGCTCTCCCTGCTCCTCATGGCCGCCTGCTTCCTGCTTCAGGCTCTCAGCGCCCACGCC ATCACCCGGCATTACAAGTTCAATGTGAGGATATATCGTCATCAAACTTTGCCGCATGATAACT GCAAGCATGCATCGCAATTGTCACATACATATACAGGTTGCAGCAGAAATGGCAAGATGGTTTA TTACCACGGTTTTGTCTGTCTTTTCTGTGTCTTGTGCAGGTGGTCATGCGGAACATGACACGGC TTTGCTCAACCAAGCCTATCCTCACTGTCAATGGCAAGTTCCCGGGGCCAACCCTGTATGCAAG AGAAGGCGATAATGTCCTAGTCAAGGTCGTCAATCATGTAGCTCACAATGTTACCATCCACTGG TAAGCAGCTTAGCTAGCTAGCCCATGGCTACTCCATGCATATGCTTCAACTCCACGTGTAATTT GCACCACAATTTGAATCACCACCTCAAGGCTCCTTTGCTCTCTGTAAGTACCCAAAAAGAAAAG GAGAATATCATGCTGTGTTAGTTAAAAGGTAAAAAGTATGTATAGCTTGCATTAGATCCTCTCT GTTGAACAGAAAACAGAAATGTGCTAGTTATTGTTCCCATTTATGCAACAAAAATACACTTGGT GAATAACTTGATAAACAAGCATGTCATACTAATCAGGCACGGGGTAAGGCAGATCCGGACAGGG TGGTACGATGGGCCAGCTTACATAACACAGTGCCCAATACAGCCAGGAAGCAGCTTTCTCTATA ATTTCACTATAACAGGGCAACGAGGCACACTCCTCTGGCATGCTCACATCAATTGGCTAAGGGC TACCGTCCATGGTGCTATCGTCATCCTTCCAAAGCTTGGCGTGCCCTACCCCTTCCCTGCACCT CACAAGGAGGCTGTTATCGTGTTAGGTATATATATACACACACATATATATAGCTGCTTCTCTA CATCTTGATGCATCCAGCACTTAATTTATCAAGTGCTGCATGCAGGAGAATGGTGGAAAGAGGA CACAGAAACTGTAATTAACCAGGCCATGCAGCTAGGAGTGGGACCCAATATTTCTGATTCACAC ACCATCAATGGTCATCCTGGTCCGCTGTCTGAGTGTGCTTCTTCACAAGGTAATACTCTTACTC TACATGAACACGAGACAGACAGTGCATGTTATGGCTAACTATGTGCTAGTCCTACAACTGAGCC AAAGACCTAACGATTTCCTGATGTATGCTTGCAATACAATGCACAGATGGGTTCAAGCTCAGCG TCGAAAATGGCAAAACATACATGCTCCGGATCATCAACGCTGCACTGAATGATGACCTATTTTT CAAGGTTGCTGGGCACGAATTAACTGTGGTTGAGGTTGATGCAGTCTATACCAAGCCATTTAAG ACCGATACCCTGCTCATCACTCCAGGCCAGACCACCAACGTCCTTGTTAGAGCTAACCAAGGCG CTGGCCGTTACCTTCTCTCAGTCTCCCCCTTCATGGATGCGCCCGTGCAGGTTGACAACAAAAC AGGCACCGCTACTTTGCACTACGCCAACACAGTCTCGTCAAGCATGGCATCCCTCACTCTCGTC AAGCCACCACCACAAAATGCCACCCATATCGTATCAAAATTTACTGATTCACTCCATAGTCTCA ATTCCAAGGAGTACCCAGCCAATGTGCCACAGACAGTAGACCACTCCCTTCTCCTTACCGTTGG CGTAGGTGTCAATCCATGTCCAAGCTGCATCAATGGGACAAGGGTGGTGGGCACAATCAACAAC GTGACGTTCATCATGCCATCAACCCCAATTCTTCAAGCCCACTATTACAACATTCCAGGAGTGT TCACAGAAGACTTCCCAGCAACCCCACTGCACAAGTTCAACTATACAGGAAGTGGTCCCAAAAA CCTTCAAACCATGAATGGAACCAGGGTTTACAGGCTGCCATACAATGCTTCAGTGCAGGTTGTA CTCCAGGATACGGGAATCATATCACCAGAAAGCCACCCAATCCATTTACATGGCTTTAATTTTT TTGTGGTTGGGAAAGGGGTCGGGAACTACAACCCCAGGACCTCCCCTTCTACATTCAACCTCAT CGACCCCATCGAGAGGAACACCATTGGAGTTCCTACTGGTGGTTGGACGGCAATCAGATTTAGG TCAGACAACCCAGGTATTGATTTTAAAACCTATGTTTTTTTAAGATAAATAACCCCTTCTGTTT CCAGACACATTGATTGAGCTGTTATATTGCAGGTGTTTGGTTTATGCATTGTCATTTCGAGGTG CACACATCATGGGGACTCAAGATGGCCTTTGTGGTGGATAATGGAAAGAGACCTAGTGAGACTC TGATTCCACCACCCAAAGATCTTCCGCAGTGTTAACAACATGGGATTCAAAACTGCCCCCACGG AGAGGAGCCTATTACAAGAAGGGTAATTGGCTTTGGTCCGATGTACGGAAAGAATCAACGGTGA TTTCTACCATGTGCTACTACTTGACTCTTGCCACACATTTTTTTCTCCTTTTTGATTTTTTTGG GCTTGTTTACCAAAGATAGTGCATACAGGGCATTCAGGTTGTAATTAGCTCTTGCCATGACCAA CTTGTTCCCCCTTTTTCAATTAATGAAAATGTATATGTTGGCATGCCTCATGAATTGAATGTTT GTTGAGAATTAGAGAAAGATGAATCCGCCTTAAAGTATCTCAGTCACCAAATTTTAGAAATATG TCGCCGCTATCTCCTCCTTTCTAACACCTATCCAGTACTCCCTATCTTCTCTGGCTGGACCCAC CCCTGTATAGTCTATTTAGTACTAGATCCAGCTTAGTACTTTAAGTTACTGTAAACCTGTTCAC CGACAGCTCAATCCAAAAAATACCAGGCCAGCCTCGCCATGCCTCTCGGGCCAGGCTTGACCCA GCTTGAGCCTCCACACGACCCCTATATTAAGCAGCCCTAGTTTCTAGATTTTCTTAGAAAAACC TTCCAAGAAACAAGTGATGGATATCTATTATCTTCTAACTTGTAGTATTATGTCCAACACAAAT AGTAATCACGTACTAGCCATAATACCAAAGTAGTCACTAATGAATTGGTAAATGTTAGGAACAG GCATTGAATATACCTTACAATGTGCCAACACGGCATCTGATGCATGTGGTACTCCCCAGCAACT GAATTATTGAGATATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.570888303

Conservation Information
Conserved circRNAs	NA
PMCS	0.570888303

			
						 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

circRNA

Detail information of Os11g0708000_circ_g.4

Address

Any questions?

Supported by