Plant Circular RNA Database

Detail information of orai.004G101500_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.004G101500_circ_g.1
					
						ID in PlantcircBase
						gra_circ_000351
					
						Alias
						Chr04:18623758|18631492
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr04: 18623758-18631492  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.004G101500						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							orai.004G101500_circ_g.2 						
					
						Support reads
						3/19
					
						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.004G101500.1:7
Gorai.004G101500.3:7
Gorai.004G101500.2:7

General Information
CircRNA Name	orai.004G101500_circ_g.1
ID in PlantcircBase	gra_circ_000351
Alias	Chr04:18623758\|18631492
Organism	Gossypium raimondii
Position	chrChr04: 18623758-18631492 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.004G101500
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	orai.004G101500_circ_g.2
Support reads	3/19
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.004G101500.1:7 Gorai.004G101500.3:7 Gorai.004G101500.2:7

			
						 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  
						
							TATCCACATGTTGTATACATTGAGAGGGAAACTACAAGCAAGATCCAAAATAAAGCTTCCTCTA
TTGCTGGGTCCCAAACAAGTACAAGTGATGTTGAAGtgctgctgattggagatttgctgcagaa
aagtttgtggcgaaactacctgacaaagtaatagagcaccgtaagtttcttttgtgcatttttc
ttgtctct

						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: 818
Transcript exons: 18623758-18623825,18624275-18624345,18624496-18624774,18
630812-18630975,18631069-18631124,18631219-18631271,1863
1366-18631492
TGCTGCTGATTGGAGATTTGCTGCAGAAAAGTTTGTGGCGAAACTACCTGACAAAGTAATAGAG
CACCGCAGTGAATGCAACTACTCAAAATTGACATTTGATGGTGTTGATATGATGGGTGAGAGGC
TAGCTCAAGAGGTATTGGATGTTGTCAAACGTAGGCCTGAGGTACGGAAGATTTCTTTTGTGGC
TCACTCTTTAGGTGGTCTTGTTGCAAGATATGCGATAGGGAGGCTCTATGAGAATTCTACAAAG
TTAGGTCAATCAGGTCCTTTTGTGAGCACTTTAACTGGAGAGCACACAAATTCTTCAATGCAAG
ATCTTGAGCAGCATTCTGAAGATAGAATTGCTGGATTGGAACCAATGAATTTTATAACATTTGC
AACACCGCATCTTGGTTCAAGGGGACATAAACAGCTCTCACTTCTTTGTGGTCTTCCTTTTCTT
GAGAAAAGAGCATCTGAGACTGCACACTTTGTTGTTGGAAGATCAGGAAAGCATCTGTTTCTCA
CTGACAATGATGAGGGAAAACCCCCACTTCTCCTTAGAATGGTTGATGATGGTGATGACTTGAA
ATTCATATCTGCTCTACATGCATTCAAGCGACGTGTGGCATATGCAAATGCAAATTATGATCAT
ATGGTTGGCTGGAGAACATCATCAATCCGGCGTCAAAATGAACTTCCAAAGTCAAATCTTCTTG
TTTTAGATGAGAAATATCCACATGTTGTATACATTGAGAGGGAAACTACAAGCAAGATCCAAAA
TAAAGCTTCCTCTATTGCTGGGTCCCAAACAAGTACAAGTGATGTTGAAG
						
						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	TATCCACATGTTGTATACATTGAGAGGGAAACTACAAGCAAGATCCAAAATAAAGCTTCCTCTA TTGCTGGGTCCCAAACAAGTACAAGTGATGTTGAAGtgctgctgattggagatttgctgcagaa aagtttgtggcgaaactacctgacaaagtaatagagcaccgtaagtttcttttgtgcatttttc ttgtctct
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: 818 Transcript exons: 18623758-18623825,18624275-18624345,18624496-18624774,18 630812-18630975,18631069-18631124,18631219-18631271,1863 1366-18631492 TGCTGCTGATTGGAGATTTGCTGCAGAAAAGTTTGTGGCGAAACTACCTGACAAAGTAATAGAG CACCGCAGTGAATGCAACTACTCAAAATTGACATTTGATGGTGTTGATATGATGGGTGAGAGGC TAGCTCAAGAGGTATTGGATGTTGTCAAACGTAGGCCTGAGGTACGGAAGATTTCTTTTGTGGC TCACTCTTTAGGTGGTCTTGTTGCAAGATATGCGATAGGGAGGCTCTATGAGAATTCTACAAAG TTAGGTCAATCAGGTCCTTTTGTGAGCACTTTAACTGGAGAGCACACAAATTCTTCAATGCAAG ATCTTGAGCAGCATTCTGAAGATAGAATTGCTGGATTGGAACCAATGAATTTTATAACATTTGC AACACCGCATCTTGGTTCAAGGGGACATAAACAGCTCTCACTTCTTTGTGGTCTTCCTTTTCTT GAGAAAAGAGCATCTGAGACTGCACACTTTGTTGTTGGAAGATCAGGAAAGCATCTGTTTCTCA CTGACAATGATGAGGGAAAACCCCCACTTCTCCTTAGAATGGTTGATGATGGTGATGACTTGAA ATTCATATCTGCTCTACATGCATTCAAGCGACGTGTGGCATATGCAAATGCAAATTATGATCAT ATGGTTGGCTGGAGAACATCATCAATCCGGCGTCAAAATGAACTTCCAAAGTCAAATCTTCTTG TTTTAGATGAGAAATATCCACATGTTGTATACATTGAGAGGGAAACTACAAGCAAGATCCAAAA TAAAGCTTCCTCTATTGCTGGGTCCCAAACAAGTACAAGTGATGTTGAAG
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_000336* ghi_circ_000116* gar_circ_001033 						
					
						PMCS
						0.508301533

Conservation Information
Conserved circRNAs	ghi_circ_000336* ghi_circ_000116* gar_circ_001033
PMCS	0.508301533

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18624319-18623813(+)
18631385-18623763(+)
18624305-18631383(-)
						
						Potential amino acid sequence
						
							MMGERLAQEVLDVVKRRPEVRKISFVAHSLGGLVARYAIGRLYENSTKLGQSGPFVSTLTGEHT
NSSMQDLEQHSEDRIAGLEPMNFITFATPHLGSRGHKQLSLLCGLPFLEKRASETAHFVVGRSG
KHLFLTDNDEGKPPLLLRMVDDGDDLKFISALHAFKRRVAYANANYDHMVGWRTSSIRRQNELP
KSNLLVLDEKYPHVVYIERETTSKIQNKASSIAGSQTSTSDVEVLLIGDLLQKSLWRNYLTK*(
+)
MRNIHMLYTLRGKLQARSKIKLPLLLGPKQVQVMLKCC*(+)
MSILSSCIHCGALLLCQVVSPQTFLQQISNQQHFNITCTCLGPSNRGSFILDLACSFPLNVYNM
WIFLI*(-)
						
						Sponge-miRNAs
						
							gra-miR8741 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18624319-18623813(+) 18631385-18623763(+) 18624305-18631383(-)
Potential amino acid sequence	MMGERLAQEVLDVVKRRPEVRKISFVAHSLGGLVARYAIGRLYENSTKLGQSGPFVSTLTGEHT NSSMQDLEQHSEDRIAGLEPMNFITFATPHLGSRGHKQLSLLCGLPFLEKRASETAHFVVGRSG KHLFLTDNDEGKPPLLLRMVDDGDDLKFISALHAFKRRVAYANANYDHMVGWRTSSIRRQNELP KSNLLVLDEKYPHVVYIERETTSKIQNKASSIAGSQTSTSDVEVLLIGDLLQKSLWRNYLTK( +) MRNIHMLYTLRGKLQARSKIKLPLLLGPKQVQVMLKCC(+) MSILSSCIHCGALLLCQVVSPQTFLQQISNQQHFNITCTCLGPSNRGSFILDLACSFPLNVYNM WIFLI*(-)
Sponge-miRNAs	gra-miR8741
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.004G101500_circ_g.1

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