Plant Circular RNA Database

Detail information of LOC18054994_circ_g.1

			
						 General Information
					
						CircRNA Name
						LOC18054994_circ_g.1
					
						ID in PlantcircBase
						ptr_circ_000047
					
						Alias
						circRNA047
					
						Organism
						
							Poncirus trifoliata						
					
						Position
						
							chrNW_006263303.1: 26549043-26555183  JBrowse»						
					
						Reference genome
						
							Citrus_clementina_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							LOC18054994						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						shoots
					
						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
						XM_006453156.2:17
XM_024177435.1:17
XM_024177438.1:17
XR_002903831.1:17
XM_024177436.1:17
XM_024177437.1:17
XM_024177440.1:17
XM_024177439.1:17
XM_024177441.1:17

General Information
CircRNA Name	LOC18054994_circ_g.1
ID in PlantcircBase	ptr_circ_000047
Alias	circRNA047
Organism	Poncirus trifoliata
Position	chrNW_006263303.1: 26549043-26555183 JBrowse»
Reference genome	Citrus_clementina_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	LOC18054994
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	NA
Support reads	NA
Tissues	shoots
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	XM_006453156.2:17 XM_024177435.1:17 XM_024177438.1:17 XR_002903831.1:17 XM_024177436.1:17 XM_024177437.1:17 XM_024177440.1:17 XM_024177439.1:17 XM_024177441.1:17

			
						 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  
						
							TCGTCGTCGGAATCGCAGCCAAGCTGGCTGCAACCGGCTTCTTCATCAGTATGTCGCCTATAAG
GCGATCCCTTAAAATTGTCTTCCATTGCTTGTTAAActgattcaaggttaatgttccagtctta
tcactacaaattgttgtagctgagcccattgtctcacaggcagatagtctcctgacctgcattt
cagaatat

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						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	TCGTCGTCGGAATCGCAGCCAAGCTGGCTGCAACCGGCTTCTTCATCAGTATGTCGCCTATAAG GCGATCCCTTAAAATTGTCTTCCATTGCTTGTTAAActgattcaaggttaatgttccagtctta tcactacaaattgttgtagctgagcccattgtctcacaggcagatagtctcctgacctgcattt cagaatat
Assembled circRNA sequence	NA 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	NA
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
						
							NA						
					
						PMCS

Conservation Information
Conserved circRNAs	NA
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							26555173-26554157(-)
						
						Potential amino acid sequence
						
							MEDNFKGSPYRRHTDEEAGCSQLGCDSDDEGTFSIPRTKDAPIVRLKRWRQAALVLNASRRFRY
TLDLKKEEEKLQTLRKIRAHAQAIRAAVLFKEAGEQANGAEKLIAVPSGDFAIGQEQLSIMTRD
HNNNALQQFGRVKGLSDMLKTNLEKGIPGDDVDLLKRRSAFGSNTYPRKKGRSFWMFLWEAWQD
LTLIILMIAAAASLALGIKTEGIEEGWYDGGSIAFAVILVIVVTAVSDYRQSLQFQNLNEEKRN
IHLEVIRGGRRVEVSIYDLVVGDVVPLNIGDQVPADGVLISGHSLSIDESSMTGESKIVHKDSK
DPFLMSGCKVADGNGTMLVTSVGINTEWGLLMASISEDSGEETPLQVRLNGVATFIGIVGLTVA
LIVLVVLLARFFTGHTKNADGSIQFRAGKTKVSHAVDGAIKILTVAVTIVVVAVPEGLPLAVTL
TLAYSMRKMMADKALVRRLSACETMGSATTICSDKTGTLTLNQFNKQWKTILRDRLIGDILMKK
PVAASLAAIPTTRELLVFPEPRMLLSFVSNAGGKRH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						playing an important role in the early flowering process

Functional Information
Coding potential	Y
Potential coding position	26555173-26554157(-)
Potential amino acid sequence	MEDNFKGSPYRRHTDEEAGCSQLGCDSDDEGTFSIPRTKDAPIVRLKRWRQAALVLNASRRFRY TLDLKKEEEKLQTLRKIRAHAQAIRAAVLFKEAGEQANGAEKLIAVPSGDFAIGQEQLSIMTRD HNNNALQQFGRVKGLSDMLKTNLEKGIPGDDVDLLKRRSAFGSNTYPRKKGRSFWMFLWEAWQD LTLIILMIAAAASLALGIKTEGIEEGWYDGGSIAFAVILVIVVTAVSDYRQSLQFQNLNEEKRN IHLEVIRGGRRVEVSIYDLVVGDVVPLNIGDQVPADGVLISGHSLSIDESSMTGESKIVHKDSK DPFLMSGCKVADGNGTMLVTSVGINTEWGLLMASISEDSGEETPLQVRLNGVATFIGIVGLTVA LIVLVVLLARFFTGHTKNADGSIQFRAGKTKVSHAVDGAIKILTVAVTIVVVAVPEGLPLAVTL TLAYSMRKMMADKALVRRLSACETMGSATTICSDKTGTLTLNQFNKQWKTILRDRLIGDILMKK PVAASLAAIPTTRELLVFPEPRMLLSFVSNAGGKRH*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	playing an important role in the early flowering process

			
						 Other Information
					
						References
						Zeng et al., 2018

circRNA

Detail information of LOC18054994_circ_g.1

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