Plant Circular RNA Database

Detail information of orai.006G243400_circ_g.2

			
						 General Information
					
						CircRNA Name
						orai.006G243400_circ_g.2
					
						ID in PlantcircBase
						gra_circ_000670
					
						Alias
						Chr06:48920379|48920799
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr06: 48920379-48920799  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.006G243400						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							orai.006G243400_circ_g.1 						
					
						Support reads
						8
					
						Tissues
						ovule
					
						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
						Gorai.006G243400.3:1
Gorai.006G243400.1:2
Gorai.006G243400.2:2

General Information
CircRNA Name	orai.006G243400_circ_g.2
ID in PlantcircBase	gra_circ_000670
Alias	Chr06:48920379\|48920799
Organism	Gossypium raimondii
Position	chrChr06: 48920379-48920799 JBrowse»
Reference genome	Graimondii_221
Type	ue-circRNA
Identification method	CIRI
Parent gene	Gorai.006G243400
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	orai.006G243400_circ_g.1
Support reads	8
Tissues	ovule
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	Gorai.006G243400.3:1 Gorai.006G243400.1:2 Gorai.006G243400.2:2

			
						 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  
						
							GTTTCATTTACAGGTTGCCGCGTACGATAAGACCCAAAGCAAAATGGCTTTCTTCGATCCCTCG
AGAGCTCAAGACTTCCTCTTCATATCAGGCACCAAGgtgctcgaggacggtgttctcgatcctg
aaacaacagtggtctctatattcccatctcctatgcactatgctggcccaactgaagtgcagtg
gcatgcta

						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: 348
Transcript exons: 48920379-48920639,48920713-48920799
GTGCTCGAGGACGGTGTTCTCGATCCTGAAACAACAGTGGTCTCTATATTCCCATCTCCTATGC
ACTATGCTGGCCCAACTGAAGTGCAGTGGCATGCTAAAGCTCGGATCAATGCAGGGGCTAATTT
TTATATCGTTGGTAGAGACCCAGCTGGCATGGGCCATCCCATTGAGAAGAGAGACCTGTATGAT
GCCGATCACGGGAAAAAGGTCTTGAGCATGGCGCCTGGACTCGAGCGGCTGAACATCCTTCCGT
TCAGGGTTGCCGCGTACGATAAGACCCAAAGCAAAATGGCTTTCTTCGATCCCTCGAGAGCTCA
AGACTTCCTCTTCATATCAGGCACCAAG
						
						Genomic sequence
						
							GTGCTCGAGGACGGTGTTCTCGATCCTGAAACAACAGTGGTCTCTATATTCCCATCTCCTATGC
ACTATGCTGGCCCAACTGAAGTGCAGTGGCATGCTAAAGCTCGGATCAATGCAGGGGCTAATTT
TTATATCGTTGGTAGAGACCCAGCTGGCATGGGCCATCCCATTGAGAAGAGAGACCTGTATGAT
GCCGATCACGGGAAAAAGGTCTTGAGCATGGCGCCTGGACTCGAGCGGCTGAACATCCTTCCGT
TCAGGGTATATTGAGCATTCAATCCCTTTACTATGATATCGCTTGTGGCATATTCTTATTGGGT
TGTTTCATTTACAGGTTGCCGCGTACGATAAGACCCAAAGCAAAATGGCTTTCTTCGATCCCTC
GAGAGCTCAAGACTTCCTCTTCATATCAGGCACCAAG

Sequences
Splice junction sequence	GTTTCATTTACAGGTTGCCGCGTACGATAAGACCCAAAGCAAAATGGCTTTCTTCGATCCCTCG AGAGCTCAAGACTTCCTCTTCATATCAGGCACCAAGgtgctcgaggacggtgttctcgatcctg aaacaacagtggtctctatattcccatctcctatgcactatgctggcccaactgaagtgcagtg gcatgcta
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: 348 Transcript exons: 48920379-48920639,48920713-48920799 GTGCTCGAGGACGGTGTTCTCGATCCTGAAACAACAGTGGTCTCTATATTCCCATCTCCTATGC ACTATGCTGGCCCAACTGAAGTGCAGTGGCATGCTAAAGCTCGGATCAATGCAGGGGCTAATTT TTATATCGTTGGTAGAGACCCAGCTGGCATGGGCCATCCCATTGAGAAGAGAGACCTGTATGAT GCCGATCACGGGAAAAAGGTCTTGAGCATGGCGCCTGGACTCGAGCGGCTGAACATCCTTCCGT TCAGGGTTGCCGCGTACGATAAGACCCAAAGCAAAATGGCTTTCTTCGATCCCTCGAGAGCTCA AGACTTCCTCTTCATATCAGGCACCAAG
Genomic sequence	GTGCTCGAGGACGGTGTTCTCGATCCTGAAACAACAGTGGTCTCTATATTCCCATCTCCTATGC ACTATGCTGGCCCAACTGAAGTGCAGTGGCATGCTAAAGCTCGGATCAATGCAGGGGCTAATTT TTATATCGTTGGTAGAGACCCAGCTGGCATGGGCCATCCCATTGAGAAGAGAGACCTGTATGAT GCCGATCACGGGAAAAAGGTCTTGAGCATGGCGCCTGGACTCGAGCGGCTGAACATCCTTCCGT TCAGGGTATATTGAGCATTCAATCCCTTTACTATGATATCGCTTGTGGCATATTCTTATTGGGT TGTTTCATTTACAGGTTGCCGCGTACGATAAGACCCAAAGCAAAATGGCTTTCTTCGATCCCTC GAGAGCTCAAGACTTCCTCTTCATATCAGGCACCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.957948476

Conservation Information
Conserved circRNAs	NA
PMCS	0.957948476

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							48920439-48920796(+)
48920544-48920790(-)
						
						Potential amino acid sequence
						
							MHYAGPTEVQWHAKARINAGANFYIVGRDPAGMGHPIEKRDLYDADHGKKVLSMAPGLERLNIL
PFRVAAYDKTQSKMAFFDPSRAQDFLFISGTKVLEDGVLDPETTVVSIFPSPMHYAGPTEVQWH
AKARINAGANFYIVGRDPAGMGHPIEKRDLYDADHGKKVLSMAPGLERLNILPFRVAAYDKTQS
KMAFFDPSRAQDFLFISGTKVLEDGVLDPETTVVSIFPSPMHYAGPTEVQWHAKARINAGANFY
IVGRDPAGMGHPIEKRDLYDADHGKKVLSMAPGLERLNILPFRVAAYDKTQSKMAFFDPSRAQD
FLFISGTKVLEDGVLDPETTVVSIFPSPMHYAGPTEVQWHAKARINAGANFYIVGRDPAGMGHP
IEKRDLYDADHGKKVLSMAPGLERLNILPFRVAAYDKTQSKMAFFDPSRAQDFLFISGTK(+)
MAHASWVSTNDIKISPCIDPSFSMPLHFSWASIVHRRWEYRDHCCFRIENTVLEHLGA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	48920439-48920796(+) 48920544-48920790(-)
Potential amino acid sequence	MHYAGPTEVQWHAKARINAGANFYIVGRDPAGMGHPIEKRDLYDADHGKKVLSMAPGLERLNIL PFRVAAYDKTQSKMAFFDPSRAQDFLFISGTKVLEDGVLDPETTVVSIFPSPMHYAGPTEVQWH AKARINAGANFYIVGRDPAGMGHPIEKRDLYDADHGKKVLSMAPGLERLNILPFRVAAYDKTQS KMAFFDPSRAQDFLFISGTKVLEDGVLDPETTVVSIFPSPMHYAGPTEVQWHAKARINAGANFY IVGRDPAGMGHPIEKRDLYDADHGKKVLSMAPGLERLNILPFRVAAYDKTQSKMAFFDPSRAQD FLFISGTKVLEDGVLDPETTVVSIFPSPMHYAGPTEVQWHAKARINAGANFYIVGRDPAGMGHP IEKRDLYDADHGKKVLSMAPGLERLNILPFRVAAYDKTQSKMAFFDPSRAQDFLFISGTK(+) MAHASWVSTNDIKISPCIDPSFSMPLHFSWASIVHRRWEYRDHCCFRIENTVLEHLGA*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.006G243400_circ_g.2

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