Plant Circular RNA Database

Detail information of LOC18051308_circ_g.1

			
						 General Information
					
						CircRNA Name
						LOC18051308_circ_g.1
					
						ID in PlantcircBase
						ptr_circ_000055
					
						Alias
						circRNA055
					
						Organism
						
							Poncirus trifoliata						
					
						Position
						
							chrNW_006262688.1: 2960142-2962880  JBrowse»						
					
						Reference genome
						
							Citrus_clementina_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							LOC18051308						
					
						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  
						
							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_024190274.1:6
XM_024190275.1:6
XM_024190277.1:6
XM_024190276.1:6

General Information
CircRNA Name	LOC18051308_circ_g.1
ID in PlantcircBase	ptr_circ_000055
Alias	circRNA055
Organism	Poncirus trifoliata
Position	chrNW_006262688.1: 2960142-2962880 JBrowse»
Reference genome	Citrus_clementina_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	LOC18051308
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	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_024190274.1:6 XM_024190275.1:6 XM_024190277.1:6 XM_024190276.1:6

			
						 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  
						
							ATTTTCTAGCTGCTTTTTGAGGATCAAAATGATGTTATTTTGCAGCGGCCTCGAGCAGGTTGCA
ATGGACAGACTTGTTGAGTTGGCAAGCAAGAAGATGatcttgcctgttctggtccattttggaa
gaaaattgaaacggtttttgcttcccccagcatagaggatgtatccttcctgaagcaacaggta
ggaactgg

									
								

					

						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
						
							ATCTTGCCTGTTCTGGTCCATTTTGGAAGAAAATTGAAACGGTTTTTGCTTCCCCCAGCATAGA
GGATGTATCCTTCCTGAAGCAACAGGTAGGAACTGGAATTTATGTCTAGACAAATAATTTTGGC
CACTGTGAGTTAATTTTTTGTCATGCGCAACTGATCACTCCCTTTCTTTTCTTCTTTGCTGTCT
TTTGACACCAGTTGAAATCTACAGATGAGCATCGTGAAAGCCTATCTCAGGTGTGTAGCCTTGA
GTCAACATTTTGGAAGCCAAAAGAAAAAATTCATTATGTTGGTCAAACATGTCAAAAGTTTATG
ATTGTGGTTTTGCCACCTTGATTAGTGTAATTTTTTCTTAATGTAAAGCAAACTCTCATAGTTT
AGTTTGGGTTTGGAGCCCAGCTCCAACTACTTCTTCGTAAGTGAGGTGAGGTACTTCTTTCGGT
TTGAATAGGGGTCGGCCCTATTTTGGTTGAAGCAGCTACGACTTCGGTCGTAGTCAGTTTAAAC
ACATAAACCCAGTGCACTTGCAGTCATGTTGATCAAAATGACTAAGTGATTGAATTAGTTTTCC
GTTTATGATTTTTCTGAAAGTAGAGTCTATCTTCTGAGGTAAACTTGATATATAAAAGTGGGTG
CTTCATAAAAATGGTGGATTAAGCTTGAAATAATGTCATTTTATTTTTTTTGTCAAGTCCTTGA
AATTATTGCCAACATGCTATGATAAAACTCTAGCTTCAAATTAGCGTTGTGGGAAAAACTAGAA
TAATTTGATTTAACCATGATACTGTAATTGATTCATGTTACTTCCCAAGGCTCGGGTGATGCCG
ACTAATATTCACTATCATGTTGCAAAACCATTATACCAATCTATCCATTCCTTTTACTGCAATT
GTCTCCTTTTTGGACACCCTGAACCTGCAGTGCCTCTGTGATTCTGTTCCTATATGCACTTTGC
TGTATCTCCTGTTACTTCTCATATCTTTTCCAAAAGTTCTGTTCACACTCCAATATGTTAGTGA
AAAAATGGAAGCACTTACAAAGAACAGTTCTAAATTTTTGTATGGATTTTAATTCTTGTGTGGT
TGTTCTAAAGTTGTATATTCTTCATAGGGCGACCTTGTCCATGGACAGGATTTTCGGTCTCAGA
CTCTTGTTGCTGGTGAAAAAGAAAGATGCCTGGAAGAGAAAATTCATTCAAAAGAGCCAACTAG
GATTCTCAAGCTTGGTGATCAGGTTAATGATGATGGTGACTTCTGTAGAACATTGGACTCAGAA
GGAATGAAAGAGGAGACCCCACTGTATCAAAGAGTGCTGTCAGCTCTAATTGTGGAAGATGAAA
CTGAAGGACTTGAAGAGAACAGTGGAGGGAGAAATATGCCTTTCCAATATAGTAGGGATCATTC
TCCTGGTGCTACCAGTTTCCTTGTTGATTCGGATTCCAGAAAGAGGGACAGAGTTGAATTTGAA
TACAACTCCATGGCGGTTCATCAAGATCATAGGCAATTGGCTGTTGACAGACCATCCTGCAATG
GGAGCACTATCATTAATGGGGGTGCAAACATTCAAAATCAATTATATCACAGCAATTTTTCCAA
TGGAGGGGGTGGACACATGCATACAGAGAACAGAATTTTCCCTGGTTTTTCTGAAAATGGCACA
AAAGGAGCACAAGCTCTACATGCAAATGCTTTGGGCATTTGTTCCTCTGAATGGAAATATGAGC
AAATTTGTTTAGGGGACAAACTTATGCTGGAGCTGCAGAGTATTGGGCTATGTCTAGATGCAGT
GGTAAGCTTGATATATAAAAATATTATGTGCATGGAATTACTTGTTCTCTTTCTCAATCATGTC
AAAAGATTTGTAATTAGTTCTCTTATTATTGTTTTATATTTCTTTTTTAGATTCTGGTCTGAAA
ATGCAGTTAAGTTTCCAAGGTTTACTGCTGTTTTTATAGTTTATCTTTGTTTCTTATCAAAAAA
GGAAAGGAAAAACTAGAAGAGGGAAAAAAATGCAGTTAAAGTTAATTTAGCTAGATATCTGCAT
GTAAATTGAGTGGCATAATATTAGAAAATTCAAACAAAAGGTCTCTTTTAATCTATCCGTACAC
AAATAACTGGTCGTTTTTTTAAAACATATTTTAATTTCCCATCATTTATGGTTGCTATTTACAG
CCTGATCTAGCAGATGGAGAGGATGAAACTGTTAATCAAGAGATTATTGAACTACAAAAGGGAC
TTTGTCAACAGGTTATTTTTCTTTCTATGTAGAATTTTTGAAAATATATTTATTTTTCAGCACT
GGTGTAACTTAAAATGTTCAGTTTTCCAATTACTCTGCTACTGGAAGAAACTTTTATTTTATTT
TATTTTTTTGCTATCTGGTTTGAGCAATCCCAGTTCACAAGTCATTTTCACTTAAAAATATTTC
TAAATGCATTTAAAAAAAAATTACGCACACACATACCTATTTTCTTATTGTTGATTTTGTAGAT
TGGTAAAAAGAAGGAACATATAAGCAACATACTTAAAGCAATCAAGGAAGCCAAGGAAACGGAA
GAGCGGTAGGGTATTCAGTATTTAATGAAAATTTTCTTGTATTTAGCATTTTATCCTTTCAAGT
TGAAAATTAGCGAAAATTTTCTAGCTGCTTTTTGAGGATCAAAATGATGTTATTTTGCAGCGGC
CTCGAGCAGGTTGCAATGGACAGACTTGTTGAGTTGGCAAGCAAGAAGATG
						
					

			
		

Sequences
Splice junction sequence	ATTTTCTAGCTGCTTTTTGAGGATCAAAATGATGTTATTTTGCAGCGGCCTCGAGCAGGTTGCA ATGGACAGACTTGTTGAGTTGGCAAGCAAGAAGATGatcttgcctgttctggtccattttggaa gaaaattgaaacggtttttgcttcccccagcatagaggatgtatccttcctgaagcaacaggta ggaactgg
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	ATCTTGCCTGTTCTGGTCCATTTTGGAAGAAAATTGAAACGGTTTTTGCTTCCCCCAGCATAGA GGATGTATCCTTCCTGAAGCAACAGGTAGGAACTGGAATTTATGTCTAGACAAATAATTTTGGC CACTGTGAGTTAATTTTTTGTCATGCGCAACTGATCACTCCCTTTCTTTTCTTCTTTGCTGTCT TTTGACACCAGTTGAAATCTACAGATGAGCATCGTGAAAGCCTATCTCAGGTGTGTAGCCTTGA GTCAACATTTTGGAAGCCAAAAGAAAAAATTCATTATGTTGGTCAAACATGTCAAAAGTTTATG ATTGTGGTTTTGCCACCTTGATTAGTGTAATTTTTTCTTAATGTAAAGCAAACTCTCATAGTTT AGTTTGGGTTTGGAGCCCAGCTCCAACTACTTCTTCGTAAGTGAGGTGAGGTACTTCTTTCGGT TTGAATAGGGGTCGGCCCTATTTTGGTTGAAGCAGCTACGACTTCGGTCGTAGTCAGTTTAAAC ACATAAACCCAGTGCACTTGCAGTCATGTTGATCAAAATGACTAAGTGATTGAATTAGTTTTCC GTTTATGATTTTTCTGAAAGTAGAGTCTATCTTCTGAGGTAAACTTGATATATAAAAGTGGGTG CTTCATAAAAATGGTGGATTAAGCTTGAAATAATGTCATTTTATTTTTTTTGTCAAGTCCTTGA AATTATTGCCAACATGCTATGATAAAACTCTAGCTTCAAATTAGCGTTGTGGGAAAAACTAGAA TAATTTGATTTAACCATGATACTGTAATTGATTCATGTTACTTCCCAAGGCTCGGGTGATGCCG ACTAATATTCACTATCATGTTGCAAAACCATTATACCAATCTATCCATTCCTTTTACTGCAATT GTCTCCTTTTTGGACACCCTGAACCTGCAGTGCCTCTGTGATTCTGTTCCTATATGCACTTTGC TGTATCTCCTGTTACTTCTCATATCTTTTCCAAAAGTTCTGTTCACACTCCAATATGTTAGTGA AAAAATGGAAGCACTTACAAAGAACAGTTCTAAATTTTTGTATGGATTTTAATTCTTGTGTGGT TGTTCTAAAGTTGTATATTCTTCATAGGGCGACCTTGTCCATGGACAGGATTTTCGGTCTCAGA CTCTTGTTGCTGGTGAAAAAGAAAGATGCCTGGAAGAGAAAATTCATTCAAAAGAGCCAACTAG GATTCTCAAGCTTGGTGATCAGGTTAATGATGATGGTGACTTCTGTAGAACATTGGACTCAGAA GGAATGAAAGAGGAGACCCCACTGTATCAAAGAGTGCTGTCAGCTCTAATTGTGGAAGATGAAA CTGAAGGACTTGAAGAGAACAGTGGAGGGAGAAATATGCCTTTCCAATATAGTAGGGATCATTC TCCTGGTGCTACCAGTTTCCTTGTTGATTCGGATTCCAGAAAGAGGGACAGAGTTGAATTTGAA TACAACTCCATGGCGGTTCATCAAGATCATAGGCAATTGGCTGTTGACAGACCATCCTGCAATG GGAGCACTATCATTAATGGGGGTGCAAACATTCAAAATCAATTATATCACAGCAATTTTTCCAA TGGAGGGGGTGGACACATGCATACAGAGAACAGAATTTTCCCTGGTTTTTCTGAAAATGGCACA AAAGGAGCACAAGCTCTACATGCAAATGCTTTGGGCATTTGTTCCTCTGAATGGAAATATGAGC AAATTTGTTTAGGGGACAAACTTATGCTGGAGCTGCAGAGTATTGGGCTATGTCTAGATGCAGT GGTAAGCTTGATATATAAAAATATTATGTGCATGGAATTACTTGTTCTCTTTCTCAATCATGTC AAAAGATTTGTAATTAGTTCTCTTATTATTGTTTTATATTTCTTTTTTAGATTCTGGTCTGAAA ATGCAGTTAAGTTTCCAAGGTTTACTGCTGTTTTTATAGTTTATCTTTGTTTCTTATCAAAAAA GGAAAGGAAAAACTAGAAGAGGGAAAAAAATGCAGTTAAAGTTAATTTAGCTAGATATCTGCAT GTAAATTGAGTGGCATAATATTAGAAAATTCAAACAAAAGGTCTCTTTTAATCTATCCGTACAC AAATAACTGGTCGTTTTTTTAAAACATATTTTAATTTCCCATCATTTATGGTTGCTATTTACAG CCTGATCTAGCAGATGGAGAGGATGAAACTGTTAATCAAGAGATTATTGAACTACAAAAGGGAC TTTGTCAACAGGTTATTTTTCTTTCTATGTAGAATTTTTGAAAATATATTTATTTTTCAGCACT GGTGTAACTTAAAATGTTCAGTTTTCCAATTACTCTGCTACTGGAAGAAACTTTTATTTTATTT TATTTTTTTGCTATCTGGTTTGAGCAATCCCAGTTCACAAGTCATTTTCACTTAAAAATATTTC TAAATGCATTTAAAAAAAAATTACGCACACACATACCTATTTTCTTATTGTTGATTTTGTAGAT TGGTAAAAAGAAGGAACATATAAGCAACATACTTAAAGCAATCAAGGAAGCCAAGGAAACGGAA GAGCGGTAGGGTATTCAGTATTTAATGAAAATTTTCTTGTATTTAGCATTTTATCCTTTCAAGT TGAAAATTAGCGAAAATTTTCTAGCTGCTTTTTGAGGATCAAAATGATGTTATTTTGCAGCGGC CTCGAGCAGGTTGCAATGGACAGACTTGTTGAGTTGGCAAGCAAGAAGATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS

Conservation Information
Conserved circRNAs	NA
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2961425-2960201(+)
2960366-2962388(-)
2960203-2962681(-)
2960163-2962371(-)
						
						Potential amino acid sequence
						
							MKEETPLYQRVLSALIVEDETEGLEENSGGRNMPFQYSRDHSPGATSFLVDSDSRKRDRVEFEY
NSMAVHQDHRQLAVDRPSCNGSTIINGGANIQNQLYHSNFSNGGGGHMHTENRIFPGFSENGTK
GAQALHANALGICSSEWKYEQICLGDKLMLELQSIGLCLDAVPDLADGEDETVNQEIIELQKGL
CQQIGKKKEHISNILKAIKEAKETEERGLEQVAMDRLVELASKKMILPVLVHFGRKLKRFLLPP
A*(+)
MLICRFQLLLQEGYILYAGGSKNRFNFLPKWTRTGKIIFLLANSTSLSIATCSRPRSSVSLASL
IALSMLLICSFFLPIC*(-)
MLGEAKTVSIFFQNGPEQARSSSCLPTQQVCPLQPARGRALPFPWLP*(-)
MDQNRQDHLLACQLNKSVHCNLLEAALFRFLGFLDCFKYVAYMFLLFTNLLTKSLL*(-)
						
						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	2961425-2960201(+) 2960366-2962388(-) 2960203-2962681(-) 2960163-2962371(-)
Potential amino acid sequence	MKEETPLYQRVLSALIVEDETEGLEENSGGRNMPFQYSRDHSPGATSFLVDSDSRKRDRVEFEY NSMAVHQDHRQLAVDRPSCNGSTIINGGANIQNQLYHSNFSNGGGGHMHTENRIFPGFSENGTK GAQALHANALGICSSEWKYEQICLGDKLMLELQSIGLCLDAVPDLADGEDETVNQEIIELQKGL CQQIGKKKEHISNILKAIKEAKETEERGLEQVAMDRLVELASKKMILPVLVHFGRKLKRFLLPP A(+) MLICRFQLLLQEGYILYAGGSKNRFNFLPKWTRTGKIIFLLANSTSLSIATCSRPRSSVSLASL IALSMLLICSFFLPIC(-) MLGEAKTVSIFFQNGPEQARSSSCLPTQQVCPLQPARGRALPFPWLP(-) MDQNRQDHLLACQLNKSVHCNLLEAALFRFLGFLDCFKYVAYMFLLFTNLLTKSLL(-)
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 LOC18051308_circ_g.1

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