Plant Circular RNA Database

Detail information of orai.003G041500_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.003G041500_circ_g.1
					
						ID in PlantcircBase
						gra_circ_000239
					
						Alias
						Chr03:5033499|5033872
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr03: 5033499-5033872  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.003G041500						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						3/7
					
						Tissues
						leaf/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.003G041500.3:1
Gorai.003G041500.2:1
Gorai.003G041500.1:1

General Information
CircRNA Name	orai.003G041500_circ_g.1
ID in PlantcircBase	gra_circ_000239
Alias	Chr03:5033499\|5033872
Organism	Gossypium raimondii
Position	chrChr03: 5033499-5033872 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.003G041500
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	NA
Support reads	3/7
Tissues	leaf/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.003G041500.3:1 Gorai.003G041500.2:1 Gorai.003G041500.1:1

			
						 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  
						
							ACATGACCTGATTCTTCTAAACACCCTTCTTCATCTAATCCATCTAACATCGACTGAAACTCCC
TGCTGTAAACATGGTTGTTCCTAGGACTATGTTCATctctttgagaagagcttcattgtcatgt
tgtaaggcttcataattggccttaagagtttcataactggttttaagaaggccataatcccttt
ccaattgc

						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: 374
Transcript exons: 5033499-5033872
CTCTTTGAGAAGAGCTTCATTGTCATGTTGTAAGGCTTCATAATTGGCCTTAAGAGTTTCATAA
CTGGTTTTAAGAAGGCCATAATCCCTTTCCAATTGCTTGGTCTTCCACCTAGCACGTCGGTTTT
GGAACCAGACAGCTACTTGTCTTGGTTGCAAACCAAGCTCTTGAGCCAACTTCACTTTCCTTTC
AGGTTCAAGCTTGTTTTCAACCTCGAAATTCTTTTCCAAGGCCTTAACTTGATCTACACTTAAT
CTTCTCTTCTTCTCAGCAACATGACCTGATTCTTCTAAACACCCTTCTTCATCTAATCCATCTA
ACATCGACTGAAACTCCCTGCTGTAAACATGGTTGTTCCTAGGACTATGTTCAT
						
						Genomic sequence
						
							CTCTTTGAGAAGAGCTTCATTGTCATGTTGTAAGGCTTCATAATTGGCCTTAAGAGTTTCATAA
CTGGTTTTAAGAAGGCCATAATCCCTTTCCAATTGCTTGGTCTTCCACCTAGCACGTCGGTTTT
GGAACCAGACAGCTACTTGTCTTGGTTGCAAACCAAGCTCTTGAGCCAACTTCACTTTCCTTTC
AGGTTCAAGCTTGTTTTCAACCTCGAAATTCTTTTCCAAGGCCTTAACTTGATCTACACTTAAT
CTTCTCTTCTTCTCAGCAACATGACCTGATTCTTCTAAACACCCTTCTTCATCTAATCCATCTA
ACATCGACTGAAACTCCCTGCTGTAAACATGGTTGTTCCTAGGACTATGTTCAT

Sequences
Splice junction sequence	ACATGACCTGATTCTTCTAAACACCCTTCTTCATCTAATCCATCTAACATCGACTGAAACTCCC TGCTGTAAACATGGTTGTTCCTAGGACTATGTTCATctctttgagaagagcttcattgtcatgt tgtaaggcttcataattggccttaagagtttcataactggttttaagaaggccataatcccttt ccaattgc
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: 374 Transcript exons: 5033499-5033872 CTCTTTGAGAAGAGCTTCATTGTCATGTTGTAAGGCTTCATAATTGGCCTTAAGAGTTTCATAA CTGGTTTTAAGAAGGCCATAATCCCTTTCCAATTGCTTGGTCTTCCACCTAGCACGTCGGTTTT GGAACCAGACAGCTACTTGTCTTGGTTGCAAACCAAGCTCTTGAGCCAACTTCACTTTCCTTTC AGGTTCAAGCTTGTTTTCAACCTCGAAATTCTTTTCCAAGGCCTTAACTTGATCTACACTTAAT CTTCTCTTCTTCTCAGCAACATGACCTGATTCTTCTAAACACCCTTCTTCATCTAATCCATCTA ACATCGACTGAAACTCCCTGCTGTAAACATGGTTGTTCCTAGGACTATGTTCAT
Genomic sequence	CTCTTTGAGAAGAGCTTCATTGTCATGTTGTAAGGCTTCATAATTGGCCTTAAGAGTTTCATAA CTGGTTTTAAGAAGGCCATAATCCCTTTCCAATTGCTTGGTCTTCCACCTAGCACGTCGGTTTT GGAACCAGACAGCTACTTGTCTTGGTTGCAAACCAAGCTCTTGAGCCAACTTCACTTTCCTTTC AGGTTCAAGCTTGTTTTCAACCTCGAAATTCTTTTCCAAGGCCTTAACTTGATCTACACTTAAT CTTCTCTTCTTCTCAGCAACATGACCTGATTCTTCTAAACACCCTTCTTCATCTAATCCATCTA ACATCGACTGAAACTCCCTGCTGTAAACATGGTTGTTCCTAGGACTATGTTCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						1.16705

Conservation Information
Conserved circRNAs	NA
PMCS	1.16705

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5033582-5033871(-)
5033823-5033818(-)
5033847-5033538(+)
						
						Potential amino acid sequence
						
							MAFLKPVMKLLRPIMKPYNMTMKLFSKR*(-)
MLDGLDEEGCLEESGHVAEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVW
FQNRRARWKTKQLERDYGLLKTSYETLKANYEALQHDNEALLKEMNIVLGTTMFTAGSFSRC*(
-)
MVVPRTMFISLRRASLSCCKAS*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5033582-5033871(-) 5033823-5033818(-) 5033847-5033538(+)
Potential amino acid sequence	MAFLKPVMKLLRPIMKPYNMTMKLFSKR(-) MLDGLDEEGCLEESGHVAEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVW FQNRRARWKTKQLERDYGLLKTSYETLKANYEALQHDNEALLKEMNIVLGTTMFTAGSFSRC( -) MVVPRTMFISLRRASLSCCKAS*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.003G041500_circ_g.1

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