Plant Circular RNA Database

Detail information of Os04g0462500_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0462500_circ_g.2
					
						ID in PlantcircBase
						osa_circ_024089
					
						Alias
						Os_ciR1978
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 23104814-23105665  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os04g0462500						
					
						Parent gene annotation
						
							Similar to 14-3-3-like protein GF14-6. (Os04t0462500-01);14-3-3 
protein, Florigen receptor, Flowering (Os04t0462500-02);Similar 
to 14-3-3-like protein GF14-6. (Os04t0462500-03);Similar to 14-3
-3-like protein GF14-6. (Os04t0462500-04);Similar to 14-3-3-like
 protein GF14-6. (Os04t0462500-05)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0462500_circ_g.3 Os04g0462550_circ_g.1 Os04g0462550_circ_g.2 						
					
						Support reads
						4/256
					
						Tissues
						root/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  
						
							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
						Os04t0462500-04:3
Os04t0462500-01:3
Os04t0462500-02:3
Os04t0462500-05:3
Os04t0462500-03:3

General Information
CircRNA Name	Os04g0462500_circ_g.2
ID in PlantcircBase	osa_circ_024089
Alias	Os_ciR1978
Organism	Oryza sativa
Position	chr4: 23104814-23105665 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, find_circ
Parent gene	Os04g0462500
Parent gene annotation	Similar to 14-3-3-like protein GF14-6. (Os04t0462500-01);14-3-3 protein, Florigen receptor, Flowering (Os04t0462500-02);Similar to 14-3-3-like protein GF14-6. (Os04t0462500-03);Similar to 14-3 -3-like protein GF14-6. (Os04t0462500-04);Similar to 14-3-3-like protein GF14-6. (Os04t0462500-05)
Parent gene strand	+
Alternative splicing	Os04g0462500_circ_g.3 Os04g0462550_circ_g.1 Os04g0462550_circ_g.2
Support reads	4/256
Tissues	root/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	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	Os04t0462500-04:3 Os04t0462500-01:3 Os04t0462500-02:3 Os04t0462500-05:3 Os04t0462500-03:3

			
						 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  
						
							TCCTACTCATCCAATTAGGCTTGGGCTAGCTCTTAACTTCTCAGTGTTCTACTATGAGATCCTC
AACTCGCCTGATCGTGCTTGCAACCTCGCAAAGCAGacttggcatttgtagagtttttagattt
atagatagcaaagatgtcggcacaggcggagctttcccgtgaggagaatgtgtacatggccaag
ctcgctga

									
								

					

						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: 653
Transcript exons: 23104814-23105264,23105345-23105423,23105543-23105665
ACTTGGCATTTGTAGAGTTTTTAGATTTATAGATAGCAAAGATGTCGGCACAGGCGGAGCTTTC
CCGTGAGGAGAATGTGTACATGGCCAAGCTCGCTGAGCAAGCCGAGAGGTACGAGGAGATGGTC
GAATTCATGGAGAAGGTGGCCAAGACGGTTGACTCTGAGGAGCTCACCGTGGAGGAGCGCAACC
TCCTGTCTGTTGCATACAAGAATGTGATTGGAGCCCGCCGTGCGTCATGGCGCATTATCTCCTC
CATTGAGCAGAAGGAGGAAAGCCGTGGTAACGAGGACCGTGTCACACTCATCAAGGACTACCGT
GGCAAGATCGAGACTGAGCTCACCAAGATTTGCGACGGCATTCTCAAGCTGCTTGAATCCCACC
TTGTCCCCTCTTCCACTGCCCCTGAGTCCAAGGTCTTCTACCTCAAAATGAAGGGTGACTACTA
CAGGTACCTTGCCGAATTTAAGACCGGGGCTGAGAGGAAGGATGCTGCTGAGAATACCATGGTG
GCATACAAGGCTGCTCAGGACATTGCTTTGGCTGAGCTGCCTCCTACTCATCCAATTAGGCTTG
GGCTAGCTCTTAACTTCTCAGTGTTCTACTATGAGATCCTCAACTCGCCTGATCGTGCTTGCAA
CCTCGCAAAGCAG
						
					

						Genomic sequence
						
							ACTTGGCATTTGTAGAGTTTTTAGATTTATAGATAGCAAAGATGTCGGCACAGGCGGAGCTTTC
CCGTGAGGAGAATGTGTACATGGCCAAGCTCGCTGAGCAAGCCGAGAGGTACGAGGAGATGGTC
GAATTCATGGAGAAGGTGGCCAAGACGGTTGACTCTGAGGAGCTCACCGTGGAGGAGCGCAACC
TCCTGTCTGTTGCATACAAGAATGTGATTGGAGCCCGCCGTGCGTCATGGCGCATTATCTCCTC
CATTGAGCAGAAGGAGGAAAGCCGTGGTAACGAGGACCGTGTCACACTCATCAAGGACTACCGT
GGCAAGATCGAGACTGAGCTCACCAAGATTTGCGACGGCATTCTCAAGCTGCTTGAATCCCACC
TTGTCCCCTCTTCCACTGCCCCTGAGTCCAAGGTCTTCTACCTCAAAATGAAGGGTGACTACTA
CAGGTAATATGATGGGTATTGGTATTTTTGCATTTACTAGTTTGTGATTGCTTTTGCTATGCTG
AATCAATTTTAATAAATAGGTACCTTGCCGAATTTAAGACCGGGGCTGAGAGGAAGGATGCTGC
TGAGAATACCATGGTGGCATACAAGGCTGCTCAGGTGAATATTTTTTCATATTCCTTGATCACG
CTATGGGAAAAAAAAAACAGAACTATGTTGGTGCAATATTATACTTTCTTTGTTTTGTGGAAAT
TAACAACAAACTGATTTTGATGTAGGACATTGCTTTGGCTGAGCTGCCTCCTACTCATCCAATT
AGGCTTGGGCTAGCTCTTAACTTCTCAGTGTTCTACTATGAGATCCTCAACTCGCCTGATCGTG
CTTGCAACCTCGCAAAGCAG
						
					

			
		

Sequences
Splice junction sequence	TCCTACTCATCCAATTAGGCTTGGGCTAGCTCTTAACTTCTCAGTGTTCTACTATGAGATCCTC AACTCGCCTGATCGTGCTTGCAACCTCGCAAAGCAGacttggcatttgtagagtttttagattt atagatagcaaagatgtcggcacaggcggagctttcccgtgaggagaatgtgtacatggccaag ctcgctga
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: 653 Transcript exons: 23104814-23105264,23105345-23105423,23105543-23105665 ACTTGGCATTTGTAGAGTTTTTAGATTTATAGATAGCAAAGATGTCGGCACAGGCGGAGCTTTC CCGTGAGGAGAATGTGTACATGGCCAAGCTCGCTGAGCAAGCCGAGAGGTACGAGGAGATGGTC GAATTCATGGAGAAGGTGGCCAAGACGGTTGACTCTGAGGAGCTCACCGTGGAGGAGCGCAACC TCCTGTCTGTTGCATACAAGAATGTGATTGGAGCCCGCCGTGCGTCATGGCGCATTATCTCCTC CATTGAGCAGAAGGAGGAAAGCCGTGGTAACGAGGACCGTGTCACACTCATCAAGGACTACCGT GGCAAGATCGAGACTGAGCTCACCAAGATTTGCGACGGCATTCTCAAGCTGCTTGAATCCCACC TTGTCCCCTCTTCCACTGCCCCTGAGTCCAAGGTCTTCTACCTCAAAATGAAGGGTGACTACTA CAGGTACCTTGCCGAATTTAAGACCGGGGCTGAGAGGAAGGATGCTGCTGAGAATACCATGGTG GCATACAAGGCTGCTCAGGACATTGCTTTGGCTGAGCTGCCTCCTACTCATCCAATTAGGCTTG GGCTAGCTCTTAACTTCTCAGTGTTCTACTATGAGATCCTCAACTCGCCTGATCGTGCTTGCAA CCTCGCAAAGCAG
Genomic sequence	ACTTGGCATTTGTAGAGTTTTTAGATTTATAGATAGCAAAGATGTCGGCACAGGCGGAGCTTTC CCGTGAGGAGAATGTGTACATGGCCAAGCTCGCTGAGCAAGCCGAGAGGTACGAGGAGATGGTC GAATTCATGGAGAAGGTGGCCAAGACGGTTGACTCTGAGGAGCTCACCGTGGAGGAGCGCAACC TCCTGTCTGTTGCATACAAGAATGTGATTGGAGCCCGCCGTGCGTCATGGCGCATTATCTCCTC CATTGAGCAGAAGGAGGAAAGCCGTGGTAACGAGGACCGTGTCACACTCATCAAGGACTACCGT GGCAAGATCGAGACTGAGCTCACCAAGATTTGCGACGGCATTCTCAAGCTGCTTGAATCCCACC TTGTCCCCTCTTCCACTGCCCCTGAGTCCAAGGTCTTCTACCTCAAAATGAAGGGTGACTACTA CAGGTAATATGATGGGTATTGGTATTTTTGCATTTACTAGTTTGTGATTGCTTTTGCTATGCTG AATCAATTTTAATAAATAGGTACCTTGCCGAATTTAAGACCGGGGCTGAGAGGAAGGATGCTGC TGAGAATACCATGGTGGCATACAAGGCTGCTCAGGTGAATATTTTTTCATATTCCTTGATCACG CTATGGGAAAAAAAAAACAGAACTATGTTGGTGCAATATTATACTTTCTTTGTTTTGTGGAAAT TAACAACAAACTGATTTTGATGTAGGACATTGCTTTGGCTGAGCTGCCTCCTACTCATCCAATT AGGCTTGGGCTAGCTCTTAACTTCTCAGTGTTCTACTATGAGATCCTCAACTCGCCTGATCGTG CTTGCAACCTCGCAAAGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005529* zma_circ_007162 zma_circ_001036 						
					
						PMCS
						0.477281827

Conservation Information
Conserved circRNAs	osi_circ_005529* zma_circ_007162 zma_circ_001036
PMCS	0.477281827

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23105620-23104880(+)
23104856-23104825(+)
23105122-23105630(-)
23104824-23105608(-)
						
						Potential amino acid sequence
						
							MRSSTRLIVLATSQSRLGICRVFRFIDSKDVGTGGAFP*(+)
MSAQAELSREENVYMAKLAEQAERYEEMVEFMEKVAKTVDSEELTVEERNLLSVAYKNVIGARR
ASWRIISSIEQKEESRGNEDRVTLIKDYRGKIETELTKICDGILKLLESHLVPSSTAPESKVFY
LKMKGDYYRYLAEFKTGAERKDAAENTMVAYKAAQDIALAELPPTHPIRLGLALNFSVFYYEIL
NSPDRACNLAKQTWHL*(+)
MSVTRSSLPRLSSFCSMEEIMRHDARRAPITFLYATDRRLRSSTVSSSESTVLATFSMNSTISS
YLSACSASLAMYTFSSRESSACADIFAIYKSKNSTNAKSALRGCKHDQAS*(-)
MPSLLCEVASTIRRVEDLIVEH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23105620-23104880(+) 23104856-23104825(+) 23105122-23105630(-) 23104824-23105608(-)
Potential amino acid sequence	MRSSTRLIVLATSQSRLGICRVFRFIDSKDVGTGGAFP(+) MSAQAELSREENVYMAKLAEQAERYEEMVEFMEKVAKTVDSEELTVEERNLLSVAYKNVIGARR ASWRIISSIEQKEESRGNEDRVTLIKDYRGKIETELTKICDGILKLLESHLVPSSTAPESKVFY LKMKGDYYRYLAEFKTGAERKDAAENTMVAYKAAQDIALAELPPTHPIRLGLALNFSVFYYEIL NSPDRACNLAKQTWHL(+) MSVTRSSLPRLSSFCSMEEIMRHDARRAPITFLYATDRRLRSSTVSSSESTVLATFSMNSTISS YLSACSASLAMYTFSSRESSACADIFAIYKSKNSTNAKSALRGCKHDQAS(-) MPSLLCEVASTIRRVEDLIVEH(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os04g0462500_circ_g.2

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