Plant Circular RNA Database

Detail information of LOC18033640_circ_g.1

			
						 General Information
					
						CircRNA Name
						LOC18033640_circ_g.1
					
						ID in PlantcircBase
						ptr_circ_000487
					
						Alias
						circRNA489
					
						Organism
						
							Poncirus trifoliata						
					
						Position
						
							chrNW_006262022.1: 15050667-15065553  JBrowse»						
					
						Reference genome
						
							Citrus_clementina_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							LOC18033640						
					
						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_024178412.1:6
XM_006423825.2:9
XM_024178406.1:7
XM_024178399.1:9
XM_024178408.1:7
XM_024178401.1:8
XM_024178393.1:9

General Information
CircRNA Name	LOC18033640_circ_g.1
ID in PlantcircBase	ptr_circ_000487
Alias	circRNA489
Organism	Poncirus trifoliata
Position	chrNW_006262022.1: 15050667-15065553 JBrowse»
Reference genome	Citrus_clementina_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	LOC18033640
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_024178412.1:6 XM_006423825.2:9 XM_024178406.1:7 XM_024178399.1:9 XM_024178408.1:7 XM_024178401.1:8 XM_024178393.1:9

			
						 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  
						
							CTCTTTATCTAGTCAAGGAATTGGTGTGTACATGCTGTCTGGGGATAAAAAAAATTCTGCTGAG
TATGTTGCATCCCTTGTTGGTATTCCAAAGGACAAGggttggaaggcattctttgaggaaccaa
ttatgttgatagcatttgttctgttaggaaagaatcttgaacagagagctaaaataaaagccac
cagtgata

						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	CTCTTTATCTAGTCAAGGAATTGGTGTGTACATGCTGTCTGGGGATAAAAAAAATTCTGCTGAG TATGTTGCATCCCTTGTTGGTATTCCAAAGGACAAGggttggaaggcattctttgaggaaccaa ttatgttgatagcatttgttctgttaggaaagaatcttgaacagagagctaaaataaaagccac cagtgata
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
						
							15050697-15065550(+)
15065411-15050700(+)
15050680-15065464(-)
						
					

						Potential amino acid sequence
						
							MLIAFVLLGKNLEQRAKIKATSDMTGLLGILPSKARLLVDNDAKDSIIEVPCNSLHVGDHIVVL
PGDRIPADGVVRAGRSTVDESSFTGEPLPVTKIPESEVAAGSINLNGTLTVEVRRPGGETAMGD
IVRLVEEAQSREAPVQRLADQVSGHFTYGVIALSAATFVFWNLFGAHVLPTAIQYGGPVSLALQ
LSCSVLVVACPCALGLATPTAMLVGTSLGATRGLLLRGGNILEKFAMVNTVVFDKTGTLTIGRP
VVTKVVTSGSLTDPNSKQNPIHPLSETEILKFAAGVESNTVHPIGKAIVEAAEFSNCQNVKVAD
GTFIEEPGSGTVAIIEDRKVSVGTIDWLRSHGVDTSTFQEVEMEDLMNQSLVYVGVDNMLAGLI
YVEDRIRDDAAHVVNSLSSQGIGVYMLSGDKKNSAEYVASLVGIPKDKGWKAFFEEPIMLIAFV
LLGKNLEQRAKIKATSDMTGLLGILPSKARLLVDNDAKDSIIEVPCNSLHVGDHIVVLPGDRIP
ADGVVRAGRSTVDESSFTGEPLPVTKIPESEVAAGSINLNGTLTVEVRRPGGETAMGDIVRLVE
EAQSREAPVQRLADQVSGHFTYGVIALSAATFVFWNLFGAHVLPTAIQYGGPVSLALQLSCSVL
VVACPCALGLATPTAMLVGTSLGATRGLLLRGGNILEKFAMVNTVVFDKTGTLTIGRPVVTKVV
TSGSLTDPNSKQNPIHPLSETEILKFAAGVESNTVHPIGKAIVEAAEFSNCQNVKVADGTFIEE
PGSGTVAIIEDRKVSVGTIDWLRSHGVDTSTFQEVEMEDLMNQSLVYVGVDNMLAGLIYVEDRI
RDDAAHVVNSLSSQGIGVYMLSGDKKNSAEYVASLVGIPKDKGWKAFFEEPIMLIAFVLLGKNL
EQRAKIKATSDMTGLLGILPSKARLLVDNDAKDSIIEVPCNSLHVGDHIVVLPGDRIPADGVVR
AGRSTVDESSFTGEPLPVTKIPESEVAAGSINLNGTLTVEVRRPGGETAMGDIVRLVEEAQSRE
APVQRLADQVSGHFTYGVIALSAATFVFWNLFGAHVLPTAIQYGGPVSLALQLSCSVLVVACPC
ALGLATPTAMLVGTSLGATRGLLLRGGNILEKFAMVNTVVFDKTGTLTIGRPVVTKVVTSGSLT
DPNSKQNPIHPLSETEILKFAAGVESNTVHPIGKAIVEAAEFSNCQNVKVADGTFIEEPGSGTV
AIIEDRKVSVGTIDWLRSHGVDTSTFQEVEMEDLMNQSLVYVGVDNMLAGLIYVEDRIRDDAAH
VVNSLSSQGIGVYMLSGDKKNSAEYVASLVGIPKDKGWKAFFEEPIMLIAFVLLGKNLEQRAKI
KATSDMTGLLGILPSKARLLVDNDAKDSIIEVPCNSLHVGDHIVVLPGDRIPADGVVRAGRSTV
DESSFTGEPLPVTKIPESEVAAGSINLNGTLTVEVRRPGGETAMGDIVRLVEEAQSREAPVQRL
ADQVSGHFTYGVIALSAATFVFWNLFGAHVLPTAIQYGGPVSLALQLSCSVLVVACPCALGLAT
PTAMLVGTSLGATRGLLLRGGNILEKFAMVNTVVFDKTGTLTIGRPVVTKVVTSGSLTDPNSKQ
NPIHPLSETEILKFAAGVESNTVHPIGKAIVEAAEFSNCQNVKVADGTFIEEPGSGTVAIIEDR
KVSVGTIDWLRSHGVDTSTFQEVEMEDLMNQSLVYVGVDNMLAGLIYVEDRIRDDAAHVVNSLS
SQGIGVYMLSGDKKNSAEYVASLVGIPKDK(+)
MLRIGSGMMQHMLLTLYLVKELVCTCCLGIKKILLSMLHPLLVFQRTRVGRHSLRNQLC*(+)
MPSNPCPLEYQQGMQHTQQNFFYPQTACTHQFLD*(-)
						
					

						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	15050697-15065550(+) 15065411-15050700(+) 15050680-15065464(-)
Potential amino acid sequence	MLIAFVLLGKNLEQRAKIKATSDMTGLLGILPSKARLLVDNDAKDSIIEVPCNSLHVGDHIVVL PGDRIPADGVVRAGRSTVDESSFTGEPLPVTKIPESEVAAGSINLNGTLTVEVRRPGGETAMGD IVRLVEEAQSREAPVQRLADQVSGHFTYGVIALSAATFVFWNLFGAHVLPTAIQYGGPVSLALQ LSCSVLVVACPCALGLATPTAMLVGTSLGATRGLLLRGGNILEKFAMVNTVVFDKTGTLTIGRP VVTKVVTSGSLTDPNSKQNPIHPLSETEILKFAAGVESNTVHPIGKAIVEAAEFSNCQNVKVAD GTFIEEPGSGTVAIIEDRKVSVGTIDWLRSHGVDTSTFQEVEMEDLMNQSLVYVGVDNMLAGLI YVEDRIRDDAAHVVNSLSSQGIGVYMLSGDKKNSAEYVASLVGIPKDKGWKAFFEEPIMLIAFV LLGKNLEQRAKIKATSDMTGLLGILPSKARLLVDNDAKDSIIEVPCNSLHVGDHIVVLPGDRIP ADGVVRAGRSTVDESSFTGEPLPVTKIPESEVAAGSINLNGTLTVEVRRPGGETAMGDIVRLVE EAQSREAPVQRLADQVSGHFTYGVIALSAATFVFWNLFGAHVLPTAIQYGGPVSLALQLSCSVL VVACPCALGLATPTAMLVGTSLGATRGLLLRGGNILEKFAMVNTVVFDKTGTLTIGRPVVTKVV TSGSLTDPNSKQNPIHPLSETEILKFAAGVESNTVHPIGKAIVEAAEFSNCQNVKVADGTFIEE PGSGTVAIIEDRKVSVGTIDWLRSHGVDTSTFQEVEMEDLMNQSLVYVGVDNMLAGLIYVEDRI RDDAAHVVNSLSSQGIGVYMLSGDKKNSAEYVASLVGIPKDKGWKAFFEEPIMLIAFVLLGKNL EQRAKIKATSDMTGLLGILPSKARLLVDNDAKDSIIEVPCNSLHVGDHIVVLPGDRIPADGVVR AGRSTVDESSFTGEPLPVTKIPESEVAAGSINLNGTLTVEVRRPGGETAMGDIVRLVEEAQSRE APVQRLADQVSGHFTYGVIALSAATFVFWNLFGAHVLPTAIQYGGPVSLALQLSCSVLVVACPC ALGLATPTAMLVGTSLGATRGLLLRGGNILEKFAMVNTVVFDKTGTLTIGRPVVTKVVTSGSLT DPNSKQNPIHPLSETEILKFAAGVESNTVHPIGKAIVEAAEFSNCQNVKVADGTFIEEPGSGTV AIIEDRKVSVGTIDWLRSHGVDTSTFQEVEMEDLMNQSLVYVGVDNMLAGLIYVEDRIRDDAAH VVNSLSSQGIGVYMLSGDKKNSAEYVASLVGIPKDKGWKAFFEEPIMLIAFVLLGKNLEQRAKI KATSDMTGLLGILPSKARLLVDNDAKDSIIEVPCNSLHVGDHIVVLPGDRIPADGVVRAGRSTV DESSFTGEPLPVTKIPESEVAAGSINLNGTLTVEVRRPGGETAMGDIVRLVEEAQSREAPVQRL ADQVSGHFTYGVIALSAATFVFWNLFGAHVLPTAIQYGGPVSLALQLSCSVLVVACPCALGLAT PTAMLVGTSLGATRGLLLRGGNILEKFAMVNTVVFDKTGTLTIGRPVVTKVVTSGSLTDPNSKQ NPIHPLSETEILKFAAGVESNTVHPIGKAIVEAAEFSNCQNVKVADGTFIEEPGSGTVAIIEDR KVSVGTIDWLRSHGVDTSTFQEVEMEDLMNQSLVYVGVDNMLAGLIYVEDRIRDDAAHVVNSLS SQGIGVYMLSGDKKNSAEYVASLVGIPKDK(+) MLRIGSGMMQHMLLTLYLVKELVCTCCLGIKKILLSMLHPLLVFQRTRVGRHSLRNQLC(+) MPSNPCPLEYQQGMQHTQQNFFYPQTACTHQFLD(-)
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 LOC18033640_circ_g.1

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