Plant Circular RNA Database

Detail information of orai.009G000300_circ_g.2

			
						 General Information
					
						CircRNA Name
						orai.009G000300_circ_g.2
					
						ID in PlantcircBase
						gra_circ_000904
					
						Alias
						Chr09:103319|104034
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr09: 103319-104034  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.009G000300						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							orai.009G000300_circ_g.1 						
					
						Support reads
						2/10
					
						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  
						
							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.009G000300.1:2
Gorai.009G000300.3:1
Gorai.009G000300.2:2
Gorai.009G000300.4:1
Gorai.009G000300.5:1

General Information
CircRNA Name	orai.009G000300_circ_g.2
ID in PlantcircBase	gra_circ_000904
Alias	Chr09:103319\|104034
Organism	Gossypium raimondii
Position	chrChr09: 103319-104034 JBrowse»
Reference genome	Graimondii_221
Type	ue-circRNA
Identification method	CIRI
Parent gene	Gorai.009G000300
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	orai.009G000300_circ_g.1
Support reads	2/10
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	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.009G000300.1:2 Gorai.009G000300.3:1 Gorai.009G000300.2:2 Gorai.009G000300.4:1 Gorai.009G000300.5:1

			
						 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  
						
							GATAATTGTTGAGCATTATGGACTCCAAGTTGATCAGTCTGCTATAACGGTTTTTGTCTGCCTG
ATTCCGGTTGTTATTGATGCTTGTGTGAAGCTTTGGgtggctttgctgaaatttgcaggttaca
aaataataagtaatatttcagatactggaaaggcatttctcattatactgattacagacatttt
tttagggt

						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: 234
Transcript exons: 103319-103416,103899-104034
GTGGCTTTGCTGAAATTTGCAGGTTACAAAATAATAAGTAATATTTCAGATACTGGAAAGGCAT
TTCTCATTATACTGATTACAGACATTTTTTTAGGGTATCATTCTGAATCGGGTTGGCAGACTTT
GCTTGAGATAATTGTTGAGCATTATGGACTCCAAGTTGATCAGTCTGCTATAACGGTTTTTGTC
TGCCTGATTCCGGTTGTTATTGATGCTTGTGTGAAGCTTTGG
						
						Genomic sequence
						
							GTGGCTTTGCTGAAATTTGCAGGTTACAAAATAATAAGTAATATTTCAGATACTGGAAAGGCAT
TTCTCATTATACTGATTACAGACATTTTTTTAGGGTAATGTGCTTTTATATCGTAGTTTTAAGT
GCTACTTATATATTTATATGTTTATGTACTGAGTTAATATTGAATGTTTTAAACAATAGTAGCT
TCTATGAGAGAGAATATAATTAATGTTTTTTACTGCTTTAGATTAAATTTGTATTTTTTTAAAA
TCTATATGTGTGTAAATATACATTGAGCAGCTTCTTATATCATTTGATAGACACATCCAAGTCT
TAATCAGAAGAAACCAAAGTCATATTACCTGCAGATATGCCAGTTATAAGCTATGCTTTTGGTC
TCTAGTCAAAATGGCCAAATGCCAAGAATTCTATCATGCTAATTAATTTTTCTTATTGAAGGTT
TCTCCTAATTTCATTTTCGTCTTCTTGACCCCAAACTTGCCCTTGTTTACTAAAAAAACATAGT
ATAGAAAAGGTGAGTTTTGCAGTTCCTTTTTATTTCTAAAGTATAGCTTATGACTGGCCCATCT
GCAGGTATCATTCTGAATCGGGTTGGCAGACTTTGCTTGAGATAATTGTTGAGCATTATGGACT
CCAAGTTGATCAGTCTGCTATAACGGTTTTTGTCTGCCTGATTCCGGTTGTTATTGATGCTTGT
GTGAAGCTTTGG

Sequences
Splice junction sequence	GATAATTGTTGAGCATTATGGACTCCAAGTTGATCAGTCTGCTATAACGGTTTTTGTCTGCCTG ATTCCGGTTGTTATTGATGCTTGTGTGAAGCTTTGGgtggctttgctgaaatttgcaggttaca aaataataagtaatatttcagatactggaaaggcatttctcattatactgattacagacatttt tttagggt
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: 234 Transcript exons: 103319-103416,103899-104034 GTGGCTTTGCTGAAATTTGCAGGTTACAAAATAATAAGTAATATTTCAGATACTGGAAAGGCAT TTCTCATTATACTGATTACAGACATTTTTTTAGGGTATCATTCTGAATCGGGTTGGCAGACTTT GCTTGAGATAATTGTTGAGCATTATGGACTCCAAGTTGATCAGTCTGCTATAACGGTTTTTGTC TGCCTGATTCCGGTTGTTATTGATGCTTGTGTGAAGCTTTGG
Genomic sequence	GTGGCTTTGCTGAAATTTGCAGGTTACAAAATAATAAGTAATATTTCAGATACTGGAAAGGCAT TTCTCATTATACTGATTACAGACATTTTTTTAGGGTAATGTGCTTTTATATCGTAGTTTTAAGT GCTACTTATATATTTATATGTTTATGTACTGAGTTAATATTGAATGTTTTAAACAATAGTAGCT TCTATGAGAGAGAATATAATTAATGTTTTTTACTGCTTTAGATTAAATTTGTATTTTTTTAAAA TCTATATGTGTGTAAATATACATTGAGCAGCTTCTTATATCATTTGATAGACACATCCAAGTCT TAATCAGAAGAAACCAAAGTCATATTACCTGCAGATATGCCAGTTATAAGCTATGCTTTTGGTC TCTAGTCAAAATGGCCAAATGCCAAGAATTCTATCATGCTAATTAATTTTTCTTATTGAAGGTT TCTCCTAATTTCATTTTCGTCTTCTTGACCCCAAACTTGCCCTTGTTTACTAAAAAAACATAGT ATAGAAAAGGTGAGTTTTGCAGTTCCTTTTTATTTCTAAAGTATAGCTTATGACTGGCCCATCT GCAGGTATCATTCTGAATCGGGTTGGCAGACTTTGCTTGAGATAATTGTTGAGCATTATGGACT CCAAGTTGATCAGTCTGCTATAACGGTTTTTGTCTGCCTGATTCCGGTTGTTATTGATGCTTGT GTGAAGCTTTGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.874655319

Conservation Information
Conserved circRNAs	NA
PMCS	0.874655319

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							103951-103970(-)
						
						Potential amino acid sequence
						
							MLNNYLKQSLPTRFRMIPANFSKATQSFTQASITTGIRQTKTVIAD*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	103951-103970(-)
Potential amino acid sequence	MLNNYLKQSLPTRFRMIPANFSKATQSFTQASITTGIRQTKTVIAD*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.009G000300_circ_g.2

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