Plant Circular RNA Database

Detail information of AT3G25610_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT3G25610_circ_g.6
					
						ID in PlantcircBase
						ath_circ_023792
					
						Alias
						Ath_circ_FC2168
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 9312358-9312807  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT3G25610						
					
						Parent gene annotation
						
							Phospholipid-transporting ATPase 10
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G25610_circ_g.5 						
					
						Support reads
						2
					
						Tissues
						root, leaf, whole_plant
					
						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
						AT3G25610.1:1

General Information
CircRNA Name	AT3G25610_circ_g.6
ID in PlantcircBase	ath_circ_023792
Alias	Ath_circ_FC2168
Organism	Arabidpsis thaliana
Position	chr3: 9312358-9312807 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT3G25610
Parent gene annotation	Phospholipid-transporting ATPase 10
Parent gene strand	-
Alternative splicing	AT3G25610_circ_g.5
Support reads	2
Tissues	root, leaf, whole_plant
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	AT3G25610.1:1

			
						 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  
						
							CTCTTACTATGTCTCCTACTCTTAGATTCCTCCATTCTTCTTGCCGGAATATTCCATTTCCGTC
GTGTACTTTCACTTTTCTGTTATTCACCTCAATATCctttgtgtcatgtccggtgaaaacgaca
gctccgtacacatactctgtgtttctaagcttagaatcacggagaagaatctgttgaatcgaca
atggaaat

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 450
Transcript exons: 9312358-9312807
CTTTGTGTCATGTCCGGTGAAAACGACAGCTCCGTACACATACTCTGTGTTTCTAAGCTTAGAA
TCACGGAGAAGAATCTGTTGAATCGACAATGGAAATCTCTCTTCTTCAAGAGCCAAAGTTCCAA
CGAACACATAAAGATTCACATTTGGATCTTCACATCTAACAACGCCTCTAAAATCTTTAAAATC
AGAATCTTGATTTAACAATGAAGAAGTTGCTTCAAGTCCTTGTTTGACTTTCAGATTCGTCTCA
CCGTCGAGATTCATCGTCTCTACATAACAAACCGAATCTTCGTAGCTTGATGACAATAGCAAAA
GATCCGCCGGAAAAAACTCGTCCTTTTCAACTCTTACTATGTCTCCTACTCTTAGATTCCTCCA
TTCTTCTTGCCGGAATATTCCATTTCCGTCGTGTACTTTCACTTTTCTGTTATTCACCTCAATA
TC
						
						Genomic sequence
						
							CTTTGTGTCATGTCCGGTGAAAACGACAGCTCCGTACACATACTCTGTGTTTCTAAGCTTAGAA
TCACGGAGAAGAATCTGTTGAATCGACAATGGAAATCTCTCTTCTTCAAGAGCCAAAGTTCCAA
CGAACACATAAAGATTCACATTTGGATCTTCACATCTAACAACGCCTCTAAAATCTTTAAAATC
AGAATCTTGATTTAACAATGAAGAAGTTGCTTCAAGTCCTTGTTTGACTTTCAGATTCGTCTCA
CCGTCGAGATTCATCGTCTCTACATAACAAACCGAATCTTCGTAGCTTGATGACAATAGCAAAA
GATCCGCCGGAAAAAACTCGTCCTTTTCAACTCTTACTATGTCTCCTACTCTTAGATTCCTCCA
TTCTTCTTGCCGGAATATTCCATTTCCGTCGTGTACTTTCACTTTTCTGTTATTCACCTCAATA
TC

Sequences
Splice junction sequence	CTCTTACTATGTCTCCTACTCTTAGATTCCTCCATTCTTCTTGCCGGAATATTCCATTTCCGTC GTGTACTTTCACTTTTCTGTTATTCACCTCAATATCctttgtgtcatgtccggtgaaaacgaca gctccgtacacatactctgtgtttctaagcttagaatcacggagaagaatctgttgaatcgaca atggaaat
Assembled circRNA sequence	Yes 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	Transcript length: 450 Transcript exons: 9312358-9312807 CTTTGTGTCATGTCCGGTGAAAACGACAGCTCCGTACACATACTCTGTGTTTCTAAGCTTAGAA TCACGGAGAAGAATCTGTTGAATCGACAATGGAAATCTCTCTTCTTCAAGAGCCAAAGTTCCAA CGAACACATAAAGATTCACATTTGGATCTTCACATCTAACAACGCCTCTAAAATCTTTAAAATC AGAATCTTGATTTAACAATGAAGAAGTTGCTTCAAGTCCTTGTTTGACTTTCAGATTCGTCTCA CCGTCGAGATTCATCGTCTCTACATAACAAACCGAATCTTCGTAGCTTGATGACAATAGCAAAA GATCCGCCGGAAAAAACTCGTCCTTTTCAACTCTTACTATGTCTCCTACTCTTAGATTCCTCCA TTCTTCTTGCCGGAATATTCCATTTCCGTCGTGTACTTTCACTTTTCTGTTATTCACCTCAATA TC
Genomic sequence	CTTTGTGTCATGTCCGGTGAAAACGACAGCTCCGTACACATACTCTGTGTTTCTAAGCTTAGAA TCACGGAGAAGAATCTGTTGAATCGACAATGGAAATCTCTCTTCTTCAAGAGCCAAAGTTCCAA CGAACACATAAAGATTCACATTTGGATCTTCACATCTAACAACGCCTCTAAAATCTTTAAAATC AGAATCTTGATTTAACAATGAAGAAGTTGCTTCAAGTCCTTGTTTGACTTTCAGATTCGTCTCA CCGTCGAGATTCATCGTCTCTACATAACAAACCGAATCTTCGTAGCTTGATGACAATAGCAAAA GATCCGCCGGAAAAAACTCGTCCTTTTCAACTCTTACTATGTCTCCTACTCTTAGATTCCTCCA TTCTTCTTGCCGGAATATTCCATTTCCGTCGTGTACTTTCACTTTTCTGTTATTCACCTCAATA TC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.362198877

Conservation Information
Conserved circRNAs	NA
PMCS	0.362198877

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9312628-9312360(-)
						
						Potential amino acid sequence
						
							MNLDGETNLKVKQGLEATSSLLNQDSDFKDFRGVVRCEDPNVNLYVFVGTLALEEERFPLSIQQ
ILLRDSKLRNTEYVYGAVVFTGHDTKDIEVNNRKVKVHDGNGIFRQEEWRNLRVGDIVRVEKDE
FFPADLLLLSSSYEDSVCYVETMNLDGETNLKVKQGLEATSSLLNQDSDFKDFRGVVRCEDPNV
NLYVFVGTLALEEERFPLSIQQILLRDSKLRNTEYVYGAVVFTGHDTKDIEVNNRKVKVHDGNG
IFRQEEWRNLRVGDIVRVEKDEFFPADLLLLSSSYEDSVCYVETMNLDGETNLKVKQGLEATSS
LLNQDSDFKDFRGVVRCEDPNVNLYVFVGTLALEEERFPLSIQQILLRDSKLRNTEYVYGAVVF
TGHDTKDIEVNNRKVKVHDGNGIFRQEEWRNLRVGDIVRVEKDEFFPADLLLLSSSYEDSVCYV
ETMNLDGETNLKVKQGLEATSSLLNQDSDFKDFRGVVRCEDPNVNLYVFVGTLALEEERFPLSI
QQILLRDSKLRNTEYVYGAVVFTGHDTK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9312628-9312360(-)
Potential amino acid sequence	MNLDGETNLKVKQGLEATSSLLNQDSDFKDFRGVVRCEDPNVNLYVFVGTLALEEERFPLSIQQ ILLRDSKLRNTEYVYGAVVFTGHDTKDIEVNNRKVKVHDGNGIFRQEEWRNLRVGDIVRVEKDE FFPADLLLLSSSYEDSVCYVETMNLDGETNLKVKQGLEATSSLLNQDSDFKDFRGVVRCEDPNV NLYVFVGTLALEEERFPLSIQQILLRDSKLRNTEYVYGAVVFTGHDTKDIEVNNRKVKVHDGNG IFRQEEWRNLRVGDIVRVEKDEFFPADLLLLSSSYEDSVCYVETMNLDGETNLKVKQGLEATSS LLNQDSDFKDFRGVVRCEDPNVNLYVFVGTLALEEERFPLSIQQILLRDSKLRNTEYVYGAVVF TGHDTKDIEVNNRKVKVHDGNGIFRQEEWRNLRVGDIVRVEKDEFFPADLLLLSSSYEDSVCYV ETMNLDGETNLKVKQGLEATSSLLNQDSDFKDFRGVVRCEDPNVNLYVFVGTLALEEERFPLSI QQILLRDSKLRNTEYVYGAVVFTGHDTK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT3G25610_circ_g.6

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