Plant Circular RNA Database

Detail information of orai.005G196700_circ_g.3

			
						 General Information
					
						CircRNA Name
						orai.005G196700_circ_g.3
					
						ID in PlantcircBase
						gra_circ_000518
					
						Alias
						Chr05:57036958|57037760
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr05: 57036958-57037760  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.005G196700						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							orai.005G196700_circ_g.1 orai.005G196700_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						leaf
					
						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  
						
							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
						Gorai.005G196700.5:2
Gorai.005G196700.2:2
Gorai.005G196700.4:2
Gorai.005G196700.3:2
Gorai.005G196700.1:2

General Information
CircRNA Name	orai.005G196700_circ_g.3
ID in PlantcircBase	gra_circ_000518
Alias	Chr05:57036958\|57037760
Organism	Gossypium raimondii
Position	chrChr05: 57036958-57037760 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.005G196700
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	orai.005G196700_circ_g.1 orai.005G196700_circ_g.2
Support reads	2
Tissues	leaf
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	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	Gorai.005G196700.5:2 Gorai.005G196700.2:2 Gorai.005G196700.4:2 Gorai.005G196700.3:2 Gorai.005G196700.1:2

			
						 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  
						
							TACATTAGAAGATATAGACGTACGTGTATTTTCGGCATCCTTTGAAAAACCTTAAGCTTCTCTC
ACGTAACAACTCGGCGCTTTCCTCCATGCATTGTATcaccaaaagcaacgctaatagggtcatt
atgtcctccaccaaacatttcaagggcacttgcaaaagcaatgtccccatcatatccctcgcca
agtccttc

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							CACCAAAAGCAACGCTAATAGGGTCATTATGTCCTCCACCAAACATTTCAAGGGCACTTGCAAA
AGCAATGTCCCCATCATATCCCTCGCCAAGTCCTTCACTGCAATCAAAGAAAAATAATATGCAA
ATAAATATTTCCCCAACTCATGGCCCCAATAGCAGGCGGTAGCAACCCCCTCCCACTTAAGAGG
AAGAAACCAAAAAAGGAAAGAAAAAGTCTATTCCAGTTGAGAGCTACAATTATATGACTGCTTT
TACAGTGATAGTCAGGAAATTTACGAGTACCAGTATCCTGGTGTAAAACCACAAGCATGGAACC
ATGGTCAAGTACCAAAGAAAAGTAACTAACGGATACATAATTATTGAAGTTTTTGTGTTATAAT
GCAAGGTTGCATTCAGTTTTTTTGTCATATGTTTGACCTACAGGTAAGAAAGAATGTTGAAAAA
CATAAGAAACTTCCATAAACTGGCAGAAAGTCGAGAACAAATATGGGCAATGACTACTAATACA
TGGTAACAGAAACCCTTTATGTTCGAGAGGCATAAAGCAACAAACAACAAATACTTTGCCCATT
ATAAAGACATATCGGACTATTTCTTTATTTAATTTAGAATTCAAGTTTGGCCATGTCACATTCT
CATACACTTCTTTCATTCACTAAAAAGGGAACTTGTTTTGATTAAAACAATCAGATTCATAGAT
ACATTAGAAGATATAGACGTACGTGTATTTTCGGCATCCTTTGAAAAACCTTAAGCTTCTCTCA
CGTAACAACTCGGCGCTTTCCTCCATGCATTGTAT

Sequences
Splice junction sequence	TACATTAGAAGATATAGACGTACGTGTATTTTCGGCATCCTTTGAAAAACCTTAAGCTTCTCTC ACGTAACAACTCGGCGCTTTCCTCCATGCATTGTATcaccaaaagcaacgctaatagggtcatt atgtcctccaccaaacatttcaagggcacttgcaaaagcaatgtccccatcatatccctcgcca agtccttc
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CACCAAAAGCAACGCTAATAGGGTCATTATGTCCTCCACCAAACATTTCAAGGGCACTTGCAAA AGCAATGTCCCCATCATATCCCTCGCCAAGTCCTTCACTGCAATCAAAGAAAAATAATATGCAA ATAAATATTTCCCCAACTCATGGCCCCAATAGCAGGCGGTAGCAACCCCCTCCCACTTAAGAGG AAGAAACCAAAAAAGGAAAGAAAAAGTCTATTCCAGTTGAGAGCTACAATTATATGACTGCTTT TACAGTGATAGTCAGGAAATTTACGAGTACCAGTATCCTGGTGTAAAACCACAAGCATGGAACC ATGGTCAAGTACCAAAGAAAAGTAACTAACGGATACATAATTATTGAAGTTTTTGTGTTATAAT GCAAGGTTGCATTCAGTTTTTTTGTCATATGTTTGACCTACAGGTAAGAAAGAATGTTGAAAAA CATAAGAAACTTCCATAAACTGGCAGAAAGTCGAGAACAAATATGGGCAATGACTACTAATACA TGGTAACAGAAACCCTTTATGTTCGAGAGGCATAAAGCAACAAACAACAAATACTTTGCCCATT ATAAAGACATATCGGACTATTTCTTTATTTAATTTAGAATTCAAGTTTGGCCATGTCACATTCT CATACACTTCTTTCATTCACTAAAAAGGGAACTTGTTTTGATTAAAACAATCAGATTCATAGAT ACATTAGAAGATATAGACGTACGTGTATTTTCGGCATCCTTTGAAAAACCTTAAGCTTCTCTCA CGTAACAACTCGGCGCTTTCCTCCATGCATTGTAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.452888989

Conservation Information
Conserved circRNAs	NA
PMCS	0.452888989

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							57037752-57037725(-)
57037039-57037725(-)
57037026-57037712(+)
						
						Potential amino acid sequence
						
							MEESAELLRERSLRFFKGCRKYTEGLGEGYDGDIAFASALEMFGGGHNDPISVAFGDTMHGGKR
RVVT*(-)
MMGTLLLQVPLKCLVEDIMTLLALLLVIQCMEESAELLRERSLRFFKGCRKYTEGLGEGYDGDI
AFASALEMFGGGHNDPISVAFGDTMHGGKRRVVT*(-)
MSPSYPSPSPSVYFRHPLKNLKLLSRNNSALSSMHCITKSNANRVIMSSTKHFKGTCKSNVPII
SLAKSFSVFSASFEKP*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	57037752-57037725(-) 57037039-57037725(-) 57037026-57037712(+)
Potential amino acid sequence	MEESAELLRERSLRFFKGCRKYTEGLGEGYDGDIAFASALEMFGGGHNDPISVAFGDTMHGGKR RVVT(-) MMGTLLLQVPLKCLVEDIMTLLALLLVIQCMEESAELLRERSLRFFKGCRKYTEGLGEGYDGDI AFASALEMFGGGHNDPISVAFGDTMHGGKRRVVT(-) MSPSYPSPSPSVYFRHPLKNLKLLSRNNSALSSMHCITKSNANRVIMSSTKHFKGTCKSNVPII SLAKSFSVFSASFEKP*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.005G196700_circ_g.3

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