Plant Circular RNA Database

Detail information of orai.012G008800_circ_g.4

			
						 General Information
					
						CircRNA Name
						orai.012G008800_circ_g.4
					
						ID in PlantcircBase
						gra_circ_001288
					
						Alias
						Chr12:938190|943562
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr12: 938190-943562  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.012G008800						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							orai.012G008800_circ_g.2 orai.012G008800_circ_g.3 						
					
						Support reads
						6
					
						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  
						
							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.012G008800.1:4
Gorai.012G008800.2:4
Gorai.012G008800.3:4

General Information
CircRNA Name	orai.012G008800_circ_g.4
ID in PlantcircBase	gra_circ_001288
Alias	Chr12:938190\|943562
Organism	Gossypium raimondii
Position	chrChr12: 938190-943562 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.012G008800
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	orai.012G008800_circ_g.2 orai.012G008800_circ_g.3
Support reads	6
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	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.012G008800.1:4 Gorai.012G008800.2:4 Gorai.012G008800.3:4

			
						 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  
						
							TCCCGCTAGATTCATGCCTTGTATATCCACGCACATGCATTTCGTAAATTATGAGATCTCTGCC
TGGATGTCTCAAAGGTAAATCACCTTCCCAATCAAActtaggtgccagcatgtaatagacacag
ttatcaacacctctaaatgacacactgagacctttctcattgccttcagctgtgtgattgaaaa
caacatcc

						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: 495
Transcript exons: 938190-938297,938384-938525,940474-940565,943410-943562
CTTAGGTGCCAGCATGTAATAGACACAGTTATCAACACCTCTAAATGACACACTGAGACCTTTC
TCATTGCCTTCAGCTGTGTGATTGAAAACAACATCCATGATAACCTCAATTCCGCGTTTATGTG
CTTCTTTAACAAGATATTTGAATTCATTAATTGCATCACGACCACAGCTACGAATACCAGAAGA
TGAATACCTTATCATGGGGGAAAAATAATTGATTGTTGAATATCCCCAAAAGTTCAACTTATAG
TCACCCAAAACAGAATTGTAGCTGTAGTACTCCAACTCATTGAATTCATGACATGGCATTAATT
CTATGCAGTTGACTCCAAGTTCCTTTAAGTGGTCAAGCTTTTCCACCACACCACAATACGTGCC
GGGAAATTTTGTCCCGCTAGATTCATGCCTTGTATATCCACGCACATGCATTTCGTAAATTATG
AGATCTCTGCCTGGATGTCTCAAAGGTAAATCACCTTCCCAATCAAA
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	TCCCGCTAGATTCATGCCTTGTATATCCACGCACATGCATTTCGTAAATTATGAGATCTCTGCC TGGATGTCTCAAAGGTAAATCACCTTCCCAATCAAActtaggtgccagcatgtaatagacacag ttatcaacacctctaaatgacacactgagacctttctcattgccttcagctgtgtgattgaaaa caacatcc
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: 495 Transcript exons: 938190-938297,938384-938525,940474-940565,943410-943562 CTTAGGTGCCAGCATGTAATAGACACAGTTATCAACACCTCTAAATGACACACTGAGACCTTTC TCATTGCCTTCAGCTGTGTGATTGAAAACAACATCCATGATAACCTCAATTCCGCGTTTATGTG CTTCTTTAACAAGATATTTGAATTCATTAATTGCATCACGACCACAGCTACGAATACCAGAAGA TGAATACCTTATCATGGGGGAAAAATAATTGATTGTTGAATATCCCCAAAAGTTCAACTTATAG TCACCCAAAACAGAATTGTAGCTGTAGTACTCCAACTCATTGAATTCATGACATGGCATTAATT CTATGCAGTTGACTCCAAGTTCCTTTAAGTGGTCAAGCTTTTCCACCACACCACAATACGTGCC GGGAAATTTTGTCCCGCTAGATTCATGCCTTGTATATCCACGCACATGCATTTCGTAAATTATG AGATCTCTGCCTGGATGTCTCAAAGGTAAATCACCTTCCCAATCAAA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							ghi_circ_000268* 						
					
						PMCS
						0.59672819

Conservation Information
Conserved circRNAs	ghi_circ_000268*
PMCS	0.59672819

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							943503-938192(-)
938440-943537(-)
943513-938205(+)
						
						Potential amino acid sequence
						
							MHVRGYTRHESSGTKFPGTYCGVVEKLDHLKELGVNCIELMPCHEFNELEYYSYNSVLGDYKLN
FWGYSTINYFSPMIRYSSSGIRSCGRDAINEFKYLVKEAHKRGIEVIMDVVFNHTAEGNEKGLS
VSFRGVDNCVYYMLAPKFDWEGDLPLRHPGRDLIIYEMHVRGYTRHESSGTKFPGTYCGVVEKL
DHLKELGVNCIELMPCHEFNELEYYSYNSVLGDYKLNFWGYSTINYFSPMIRYSSSGIRSCGRD
AINEFKYLVKEAHKRGIEVIMDVVFNHTAEGNEKGLSVSFRGVDNCVYYMLAPKFDWEGDLPLR
HPGRDLIIYEMHVRGYTRHESSGTKFPGTYCGVVEKLDHLKELGVNCIELMPCHEFNELEYYSY
NSVLGDYKLNFWGYSTINYFSPMIRYSSSGIRSCGRDAINEFKYLVKEAHKRGIEVIMDVVFNH
TAEGNEKGLSVSFRGVDNCVYYMLAPKFDWEGDLPLRHPGRDLIIYEMHVRGYTRHESSGTKFP
GTYCGVVEKLDHLKELGVNCIELMPCHEFNELEYYSYNSVLGDYKLNFWGYSTINYFSPMIRYS
SSGIRSCGRDAINEFKYLVKEAHKRGIEVIMDVVFNHTAEGNEKGLSVSFRGVDNCVYYMLAPK
(-)
MQLMNSNILLKKHINAELRLSWMLFSITQLKAMRKVSVCHLEVLITVSITCWHLSLIGKVIYL*
(-)
MRSLPGCLKGKSPSQSNLGASM*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	943503-938192(-) 938440-943537(-) 943513-938205(+)
Potential amino acid sequence	MHVRGYTRHESSGTKFPGTYCGVVEKLDHLKELGVNCIELMPCHEFNELEYYSYNSVLGDYKLN FWGYSTINYFSPMIRYSSSGIRSCGRDAINEFKYLVKEAHKRGIEVIMDVVFNHTAEGNEKGLS VSFRGVDNCVYYMLAPKFDWEGDLPLRHPGRDLIIYEMHVRGYTRHESSGTKFPGTYCGVVEKL DHLKELGVNCIELMPCHEFNELEYYSYNSVLGDYKLNFWGYSTINYFSPMIRYSSSGIRSCGRD AINEFKYLVKEAHKRGIEVIMDVVFNHTAEGNEKGLSVSFRGVDNCVYYMLAPKFDWEGDLPLR HPGRDLIIYEMHVRGYTRHESSGTKFPGTYCGVVEKLDHLKELGVNCIELMPCHEFNELEYYSY NSVLGDYKLNFWGYSTINYFSPMIRYSSSGIRSCGRDAINEFKYLVKEAHKRGIEVIMDVVFNH TAEGNEKGLSVSFRGVDNCVYYMLAPKFDWEGDLPLRHPGRDLIIYEMHVRGYTRHESSGTKFP GTYCGVVEKLDHLKELGVNCIELMPCHEFNELEYYSYNSVLGDYKLNFWGYSTINYFSPMIRYS SSGIRSCGRDAINEFKYLVKEAHKRGIEVIMDVVFNHTAEGNEKGLSVSFRGVDNCVYYMLAPK (-) MQLMNSNILLKKHINAELRLSWMLFSITQLKAMRKVSVCHLEVLITVSITCWHLSLIGKVIYL* (-) MRSLPGCLKGKSPSQSNLGASM*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.012G008800_circ_g.4

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