Plant Circular RNA Database

Detail information of LOC18040093_circ_g.2

			
						 General Information
					
						CircRNA Name
						LOC18040093_circ_g.2
					
						ID in PlantcircBase
						ptr_circ_000410
					
						Alias
						circRNA412
					
						Organism
						
							Poncirus trifoliata						
					
						Position
						
							chrNW_006262139.1: 24213222-24214125  JBrowse»						
					
						Reference genome
						
							Citrus_clementina_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							LOC18040093						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							LOC18040093_circ_g.1 						
					
						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  
						
							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
						XM_024182346.1:3
XM_024182349.1:3
XM_024182348.1:3
XM_024182347.1:3
XR_002904929.1:3

General Information
CircRNA Name	LOC18040093_circ_g.2
ID in PlantcircBase	ptr_circ_000410
Alias	circRNA412
Organism	Poncirus trifoliata
Position	chrNW_006262139.1: 24213222-24214125 JBrowse»
Reference genome	Citrus_clementina_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	LOC18040093
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	LOC18040093_circ_g.1
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	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	XM_024182346.1:3 XM_024182349.1:3 XM_024182348.1:3 XM_024182347.1:3 XR_002904929.1:3

			
						 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  
						
							GTCCAGGGAGCTACTTGCAGCAATCAAACTTGAATGCGGGTTGCAAGGACAACAAGAGCAGGAA
GCTCCTTCATAGGCAAAATAGGAGCTTGTGCCAAAGcaagaagtgatggaatataatactattg
ttgatgcggagcagtgttcatctgataatgagccaagagagtcctcaattgaatcagctaaaag
tagatcat

						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
						
							CAAGAAGTGATGGAATATAATACTATTGTTGATGCGGAGCAGTGTTCATCTGATAATGAGCCAA
GAGAGTCCTCAATTGAATCAGCTAAAAGTAGATCATCTGAAAATGAGCCAATAGAGCAATGTTT
TGAATTAGCTAAAGGTAGATCAGGATTATCAACTCCAATTGGGACAGGGAATGTATGGAATGAG
AATAATTCCAGAGCCATACAACTTTCCAACAGAGACAGGCTTCTCTTGCGAAAACAAGCTCTAA
GAATGAAGAAGCGCCCGGTGCTTGCAGTAGGTGATTTCAATTTTCTCTTTCATACTTCCTGTTT
ACACCTCTTGCCTGTATTGTAGCATTGGCTTTTCCTGATTTGTTTCCTGGCAATTGATTGTAGT
CCTGGGAACTTATCATTTCTAATATGTCTGGTACTATAACTTACTAGGGAGGAGCAACATTGTC
ACTGGAGTTGCAAAAGCAATTAAAGCACACTTTGAGAAGTATCCTCTTGCTATAGTGAATGTCA
AAGGCAGAGCCAAAGGGACGTCCGTCCAGGAAGTGGTTGCAAAGCTGGAGGTCTGCATGCCTAA
ATACAACTTTGTTTTCCCTCCATAAAGACCTTAAGAGTAACACGAAATTATTTCCCGTTGATGA
TTACTCATGCAGGAAGCGACTGGTGCAGTTCTAGTCTCTCAAGAGCCTAGTAAAGTCATTCTGT
ACAGGGGCTGGGGTGCAGAAGATGAATCTAGCCCCAGGGGTAGGCAGAATTCGAGAGCCAAACT
ATCAATTGTCCGAGATGTTCGTCCTTGGCCAGCTGTGTCCAGGGAGCTACTTGCAGCAATCAAA
CTTGAATGCGGGTTGCAAGGACAACAAGAGCAGGAAGCTCCTTCATAGGCAAAATAGGAGCTTG
TGCCAAAG

Sequences
Splice junction sequence	GTCCAGGGAGCTACTTGCAGCAATCAAACTTGAATGCGGGTTGCAAGGACAACAAGAGCAGGAA GCTCCTTCATAGGCAAAATAGGAGCTTGTGCCAAAGcaagaagtgatggaatataatactattg ttgatgcggagcagtgttcatctgataatgagccaagagagtcctcaattgaatcagctaaaag tagatcat
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	CAAGAAGTGATGGAATATAATACTATTGTTGATGCGGAGCAGTGTTCATCTGATAATGAGCCAA GAGAGTCCTCAATTGAATCAGCTAAAAGTAGATCATCTGAAAATGAGCCAATAGAGCAATGTTT TGAATTAGCTAAAGGTAGATCAGGATTATCAACTCCAATTGGGACAGGGAATGTATGGAATGAG AATAATTCCAGAGCCATACAACTTTCCAACAGAGACAGGCTTCTCTTGCGAAAACAAGCTCTAA GAATGAAGAAGCGCCCGGTGCTTGCAGTAGGTGATTTCAATTTTCTCTTTCATACTTCCTGTTT ACACCTCTTGCCTGTATTGTAGCATTGGCTTTTCCTGATTTGTTTCCTGGCAATTGATTGTAGT CCTGGGAACTTATCATTTCTAATATGTCTGGTACTATAACTTACTAGGGAGGAGCAACATTGTC ACTGGAGTTGCAAAAGCAATTAAAGCACACTTTGAGAAGTATCCTCTTGCTATAGTGAATGTCA AAGGCAGAGCCAAAGGGACGTCCGTCCAGGAAGTGGTTGCAAAGCTGGAGGTCTGCATGCCTAA ATACAACTTTGTTTTCCCTCCATAAAGACCTTAAGAGTAACACGAAATTATTTCCCGTTGATGA TTACTCATGCAGGAAGCGACTGGTGCAGTTCTAGTCTCTCAAGAGCCTAGTAAAGTCATTCTGT ACAGGGGCTGGGGTGCAGAAGATGAATCTAGCCCCAGGGGTAGGCAGAATTCGAGAGCCAAACT ATCAATTGTCCGAGATGTTCGTCCTTGGCCAGCTGTGTCCAGGGAGCTACTTGCAGCAATCAAA CTTGAATGCGGGTTGCAAGGACAACAAGAGCAGGAAGCTCCTTCATAGGCAAAATAGGAGCTTG TGCCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS

Conservation Information
Conserved circRNAs	NA
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24213947-24213228(+)
24214059-24213238(+)
24213666-24213902(-)
						
						Potential amino acid sequence
						
							MNLAPGVGRIREPNYQLSEMFVLGQLCPGSYLQQSNLNAGCKDNKSRKLLHRQNRSLCQSKK*(
+)
MRVARTTRAGSSFIGKIGACAKARSDGI*(+)
MLLLPTASTGRFFILRACFRKRSLSLLESCMALELFSFHTFPVPIGVDNPDLPLANSKHCSIGS
FSDDLLLADSIEDSLGSLSDEHCSASTIVLYSITSCFGTSSYFAYEGASCSCCPCNPHSSLIAA
SSSLDTAGQGRTSRTIDSLALEFCLPLGLDSSSAPQPLYRMTLLGS*(-)
						
						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	24213947-24213228(+) 24214059-24213238(+) 24213666-24213902(-)
Potential amino acid sequence	MNLAPGVGRIREPNYQLSEMFVLGQLCPGSYLQQSNLNAGCKDNKSRKLLHRQNRSLCQSKK( +) MRVARTTRAGSSFIGKIGACAKARSDGI(+) MLLLPTASTGRFFILRACFRKRSLSLLESCMALELFSFHTFPVPIGVDNPDLPLANSKHCSIGS FSDDLLLADSIEDSLGSLSDEHCSASTIVLYSITSCFGTSSYFAYEGASCSCCPCNPHSSLIAA SSSLDTAGQGRTSRTIDSLALEFCLPLGLDSSSAPQPLYRMTLLGS*(-)
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 LOC18040093_circ_g.2

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