Plant Circular RNA Database

Detail information of LOC18048196_circ_g.1

			
						 General Information
					
						CircRNA Name
						LOC18048196_circ_g.1
					
						ID in PlantcircBase
						ptr_circ_000139
					
						Alias
						circRNA139
					
						Organism
						
							Poncirus trifoliata						
					
						Position
						
							chrNW_006262339.1: 5345972-5346980  JBrowse»						
					
						Reference genome
						
							Citrus_clementina_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							LOC18048196						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							LOC18048196_circ_g.2 						
					
						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_006440192.2:3

General Information
CircRNA Name	LOC18048196_circ_g.1
ID in PlantcircBase	ptr_circ_000139
Alias	circRNA139
Organism	Poncirus trifoliata
Position	chrNW_006262339.1: 5345972-5346980 JBrowse»
Reference genome	Citrus_clementina_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	LOC18048196
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	LOC18048196_circ_g.2
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_006440192.2:3

			
						 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  
						
							GGGAGTATCAGGATGCTACCCATTTGAAAATCTTCGAGCTGCTGTTGACATACTCTTTTTGCAT
GGTAGTTCCGATTTGGTGCTTGCAAAGCAGGCAATTatgttagagatgtttgcatggatgaagc
tgctgtgtctagtgatcctgtcgttgctttcctgttggatgaagtggttgtcaaggattggtgc
aagcgggc

						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
						
							ATGTTAGAGATGTTTGCATGGATGAAGCTGCTGTGTCTAGTGATCCTGTCGTTGCTTTCCTGTT
GGATGAAGTGGTTGTCAAGGATTGGTGCAAGCGGGCATTCAAGAACATCATAGCGGAACTCAAG
CTGATATGTATCCATACCAGTCTTGTTAACATTTGGAATTAAAGCTTATTGATTTCTTATCTTG
TGCTCGTGCGTCTCTGCAGTTTTACACACTTCGTATTGCTTGCTTCCTAACTTTTTTCATTAGA
TAATCTGGAAGTGGAGGTGATGAAAACTAGGCTCAGTTTACTTCTGAAGTTTCAAATGAAGCTG
CGCGACATATCTAGTGTGATTGAAGTCCTCGCCTCGTCATTTAAGGATGATCTTTCAGCACAGG
TTCATGACTTGCACCACTTTCAGGAGAGCATATTGAAGACTAAGCAGGTTTATACTTACTTAGA
TACCTAATTTTAATGATGTACATGTCGTATATCTACTTTGTATTGTTTTAGACGTTTTCTCCAA
TATTGGTTGTTCGATTTATGAATTTTGTTGAACAGTTGGCCTTCATAGGAATTGGCATATTTTC
TCTAAGTATTGGTTTCTTATTCCAGCACTTGGAGATTATGATGTGGTGTGCAAAGCACCAATTT
CTGGAGAATGTGAGGTCTCGTCATGCTAGTTTCACATCATGGCATTCTCTAGTCCGTCAAAGGA
AATCAGCTGCAACTGAGCGTGCATGGTATGATCCAGTAAAAAACTGTGCGGAGTCCACCAAACA
GGATGGTTCCCTGTTCATTGAAGATGCACTAGCTAATCTTGAGATAGAGCAGGAATTTACTCAA
GGTAGGGGAGAGGAATTAGATATTACATCTTTGCACAAGGATGATGAAGGCTCGTCCTTTGTTA
GGTCCAAGATAGAGGGAGTATCAGGATGCTACCCATTTGAAAATCTTCGAGCTGCTGTTGACAT
ACTCTTTTTGCATGGTAGTTCCGATTTGGTGCTTGCAAAGCAGGCAATT

Sequences
Splice junction sequence	GGGAGTATCAGGATGCTACCCATTTGAAAATCTTCGAGCTGCTGTTGACATACTCTTTTTGCAT GGTAGTTCCGATTTGGTGCTTGCAAAGCAGGCAATTatgttagagatgtttgcatggatgaagc tgctgtgtctagtgatcctgtcgttgctttcctgttggatgaagtggttgtcaaggattggtgc aagcgggc
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	ATGTTAGAGATGTTTGCATGGATGAAGCTGCTGTGTCTAGTGATCCTGTCGTTGCTTTCCTGTT GGATGAAGTGGTTGTCAAGGATTGGTGCAAGCGGGCATTCAAGAACATCATAGCGGAACTCAAG CTGATATGTATCCATACCAGTCTTGTTAACATTTGGAATTAAAGCTTATTGATTTCTTATCTTG TGCTCGTGCGTCTCTGCAGTTTTACACACTTCGTATTGCTTGCTTCCTAACTTTTTTCATTAGA TAATCTGGAAGTGGAGGTGATGAAAACTAGGCTCAGTTTACTTCTGAAGTTTCAAATGAAGCTG CGCGACATATCTAGTGTGATTGAAGTCCTCGCCTCGTCATTTAAGGATGATCTTTCAGCACAGG TTCATGACTTGCACCACTTTCAGGAGAGCATATTGAAGACTAAGCAGGTTTATACTTACTTAGA TACCTAATTTTAATGATGTACATGTCGTATATCTACTTTGTATTGTTTTAGACGTTTTCTCCAA TATTGGTTGTTCGATTTATGAATTTTGTTGAACAGTTGGCCTTCATAGGAATTGGCATATTTTC TCTAAGTATTGGTTTCTTATTCCAGCACTTGGAGATTATGATGTGGTGTGCAAAGCACCAATTT CTGGAGAATGTGAGGTCTCGTCATGCTAGTTTCACATCATGGCATTCTCTAGTCCGTCAAAGGA AATCAGCTGCAACTGAGCGTGCATGGTATGATCCAGTAAAAAACTGTGCGGAGTCCACCAAACA GGATGGTTCCCTGTTCATTGAAGATGCACTAGCTAATCTTGAGATAGAGCAGGAATTTACTCAA GGTAGGGGAGAGGAATTAGATATTACATCTTTGCACAAGGATGATGAAGGCTCGTCCTTTGTTA GGTCCAAGATAGAGGGAGTATCAGGATGCTACCCATTTGAAAATCTTCGAGCTGCTGTTGACAT ACTCTTTTTGCATGGTAGTTCCGATTTGGTGCTTGCAAAGCAGGCAATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							csi_circ_002966 						
					
						PMCS

Conservation Information
Conserved circRNAs	csi_circ_002966
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5345989-5346085(+)
						
						Potential amino acid sequence
						
							MDEAAVSSDPVVAFLLDEVVVKDWCKRAFKNIIAELKLIYNLEVEVMKTRLSLLLKFQMKLRDI
SSVIEVLASSFKDDLSAQVHDLHHFQESILKTKQHLEIMMWCAKHQFLENVRSRHASFTSWHSL
VRQRKSAATERAWYDPVKNCAESTKQDGSLFIEDALANLEIEQEFTQGRGEELDITSLHKDDEG
SSFVRSKIEGVSGCYPFENLRAAVDILFLHGSSDLVLAKQAIMLEMFAWMKLLCLVILSLLSCW
MKWLSRIGASGHSRTS*(+)
						
						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	5345989-5346085(+)
Potential amino acid sequence	MDEAAVSSDPVVAFLLDEVVVKDWCKRAFKNIIAELKLIYNLEVEVMKTRLSLLLKFQMKLRDI SSVIEVLASSFKDDLSAQVHDLHHFQESILKTKQHLEIMMWCAKHQFLENVRSRHASFTSWHSL VRQRKSAATERAWYDPVKNCAESTKQDGSLFIEDALANLEIEQEFTQGRGEELDITSLHKDDEG SSFVRSKIEGVSGCYPFENLRAAVDILFLHGSSDLVLAKQAIMLEMFAWMKLLCLVILSLLSCW MKWLSRIGASGHSRTS*(+)
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 LOC18048196_circ_g.1

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