Plant Circular RNA Database

Detail information of AT1G55810_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G55810_circ_g.3
					
						ID in PlantcircBase
						ath_circ_007607
					
						Alias
						Ath_circ_FC0797
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 20862584-20863419  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, circRNA_finder
					
						Parent gene
						
							AT1G55810						
					
						Parent gene annotation
						
							uridine kinase-like 3
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G55810_circ_g.1 AT1G55810_circ_g.2 AT1G55810_circ_g.4 AT1G55810_circ_g.5 AT1G55810_circ_g.6 AT1G55810_circ_g.7 						
					
						Support reads
						20
					
						Tissues
						root, 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  
						
							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
						AT1G55810.3:5
AT1G55810.6:5
AT1G55810.7:5
AT1G55810.4:5
AT1G55810.5:5
AT1G55810.2:5
AT1G55810.1:5

General Information
CircRNA Name	AT1G55810_circ_g.3
ID in PlantcircBase	ath_circ_007607
Alias	Ath_circ_FC0797
Organism	Arabidpsis thaliana
Position	chr1: 20862584-20863419 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, circRNA_finder
Parent gene	AT1G55810
Parent gene annotation	uridine kinase-like 3
Parent gene strand	+
Alternative splicing	AT1G55810_circ_g.1 AT1G55810_circ_g.2 AT1G55810_circ_g.4 AT1G55810_circ_g.5 AT1G55810_circ_g.6 AT1G55810_circ_g.7
Support reads	20
Tissues	root, 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	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	AT1G55810.3:5 AT1G55810.6:5 AT1G55810.7:5 AT1G55810.4:5 AT1G55810.5:5 AT1G55810.2:5 AT1G55810.1:5

			
						 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  
						
							ACATAGCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAG
ATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGtactcaaagtttgtgaagccagcatttg
aggatttcatactcccaacaaagaaatacgcagatataataattccccgaggtggtgataacca
tgttgcta

						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: 495
Transcript exons: 20862584-20862778,20862871-20862954,20863028-20863088,20
863196-20863256,20863326-20863419
TACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATA
TAATAATTCCCCGAGGTGGTGATAACCATGTTGCTATTGATTTGATTGTGCAACACATCCATAC
GAAGCTCGGTCAACATGATCTCTGTAAAATTTATCCAAATCTTTATGTTATTCAATCAACTTTT
CAGATACGTGGTATGCACACTCTAATCCGCGACTCTAAAACAACAAAGCATGACTTTATCTTCT
ACTCCGATCGATTGATACGTTTGGTCGTTGAACATGGCCTCGGACACCTTCCCTTTACAGAAAA
GCAAGTGGTTACTCCAACAGGATCTGTGTATTCGGGTGTGGACTTCTGTAAGAAACTGTGTGGT
GTCTCAGTTATCAGAAGCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCA
AAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
						
						Genomic sequence
						
							TACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATA
TAATAATTCCCCGAGGTGGTGATAACCATGTTGCTATTGATTTGATTGTGCAACACATCCATAC
GAAGCTCGGTCAACATGATCTCTGTAAAATTTATCCAAATCTTTATGTTATTCAATCAACTTTT
CAGGTTTTACTTATTCCCCTTTTCTCGTCTACTCAACAACAATCATTTTCTTGTTTAGTCACCC
AAAAGACTGATCCTTTGGCCGCTGCTTGCAGATACGTGGTATGCACACTCTAATCCGCGACTCT
AAAACAACAAAGCATGACTTTATCTTCTACTCCGATCGATTGATACGTTTGGTGGGTGCAAGAT
TTGATTTCTGTTCGTTTTATTTCACCATGTTTGCTGACTCTAACAATGAGCTCTCGCCAGGTCG
TTGAACATGGCCTCGGACACCTTCCCTTTACAGAAAAGCAAGTGGTTACTCCAACAGGTAAGCT
AATGAAAAAGATTATACCTTACTACAATCTTGGAGAAGAACTCTCCAATCATAGTAATATTATA
AACTCATGTTGAGTTTTTGGATTTCTGTAATTGTAGGATCTGTGTATTCGGGTGTGGACTTCTG
TAAGAAACTGTGTGGTGTCTCAGTTATCAGAAGGTAAAGAAATCAGCTTAAACACTAATAGTTA
ACGTCAATACTATATAATGATTTTGTCTCTGAACATAGCGGTGAGAGTATGGAGAACGCTCTTA
GAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCA
ACAG

Sequences
Splice junction sequence	ACATAGCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAG ATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGtactcaaagtttgtgaagccagcatttg aggatttcatactcccaacaaagaaatacgcagatataataattccccgaggtggtgataacca tgttgcta
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: 495 Transcript exons: 20862584-20862778,20862871-20862954,20863028-20863088,20 863196-20863256,20863326-20863419 TACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATA TAATAATTCCCCGAGGTGGTGATAACCATGTTGCTATTGATTTGATTGTGCAACACATCCATAC GAAGCTCGGTCAACATGATCTCTGTAAAATTTATCCAAATCTTTATGTTATTCAATCAACTTTT CAGATACGTGGTATGCACACTCTAATCCGCGACTCTAAAACAACAAAGCATGACTTTATCTTCT ACTCCGATCGATTGATACGTTTGGTCGTTGAACATGGCCTCGGACACCTTCCCTTTACAGAAAA GCAAGTGGTTACTCCAACAGGATCTGTGTATTCGGGTGTGGACTTCTGTAAGAAACTGTGTGGT GTCTCAGTTATCAGAAGCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCA AAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
Genomic sequence	TACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATA TAATAATTCCCCGAGGTGGTGATAACCATGTTGCTATTGATTTGATTGTGCAACACATCCATAC GAAGCTCGGTCAACATGATCTCTGTAAAATTTATCCAAATCTTTATGTTATTCAATCAACTTTT CAGGTTTTACTTATTCCCCTTTTCTCGTCTACTCAACAACAATCATTTTCTTGTTTAGTCACCC AAAAGACTGATCCTTTGGCCGCTGCTTGCAGATACGTGGTATGCACACTCTAATCCGCGACTCT AAAACAACAAAGCATGACTTTATCTTCTACTCCGATCGATTGATACGTTTGGTGGGTGCAAGAT TTGATTTCTGTTCGTTTTATTTCACCATGTTTGCTGACTCTAACAATGAGCTCTCGCCAGGTCG TTGAACATGGCCTCGGACACCTTCCCTTTACAGAAAAGCAAGTGGTTACTCCAACAGGTAAGCT AATGAAAAAGATTATACCTTACTACAATCTTGGAGAAGAACTCTCCAATCATAGTAATATTATA AACTCATGTTGAGTTTTTGGATTTCTGTAATTGTAGGATCTGTGTATTCGGGTGTGGACTTCTG TAAGAAACTGTGTGGTGTCTCAGTTATCAGAAGGTAAAGAAATCAGCTTAAACACTAATAGTTA ACGTCAATACTATATAATGATTTTGTCTCTGAACATAGCGGTGAGAGTATGGAGAACGCTCTTA GAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCA ACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.357094768

Conservation Information
Conserved circRNAs	NA
PMCS	0.357094768

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20862880-20863416(+)
						
						Potential amino acid sequence
						
							MHTLIRDSKTTKHDFIFYSDRLIRLVVEHGLGHLPFTEKQVVTPTGSVYSGVDFCKKLCGVSVI
RSGESMENALRACCKGIKIGKILIHREGDNGQQYSKFVKPAFEDFILPTKKYADIIIPRGGDNH
VAIDLIVQHIHTKLGQHDLCKIYPNLYVIQSTFQIRGMHTLIRDSKTTKHDFIFYSDRLIRLVV
EHGLGHLPFTEKQVVTPTGSVYSGVDFCKKLCGVSVIRSGESMENALRACCKGIKIGKILIHRE
GDNGQQYSKFVKPAFEDFILPTKKYADIIIPRGGDNHVAIDLIVQHIHTKLGQHDLCKIYPNLY
VIQSTFQIRGMHTLIRDSKTTKHDFIFYSDRLIRLVVEHGLGHLPFTEKQVVTPTGSVYSGVDF
CKKLCGVSVIRSGESMENALRACCKGIKIGKILIHREGDNGQQYSKFVKPAFEDFILPTKKYAD
IIIPRGGDNHVAIDLIVQHIHTKLGQHDLCKIYPNLYVIQSTFQIRGMHTLIRDSKTTKHDFIF
YSDRLIRLVVEHGLGHLPFTEKQVVTPTGSVYSGVDFCKKLCGVSVIRSGESMENALRACCKGI
KIGKILIHREGDNGQQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20862880-20863416(+)
Potential amino acid sequence	MHTLIRDSKTTKHDFIFYSDRLIRLVVEHGLGHLPFTEKQVVTPTGSVYSGVDFCKKLCGVSVI RSGESMENALRACCKGIKIGKILIHREGDNGQQYSKFVKPAFEDFILPTKKYADIIIPRGGDNH VAIDLIVQHIHTKLGQHDLCKIYPNLYVIQSTFQIRGMHTLIRDSKTTKHDFIFYSDRLIRLVV EHGLGHLPFTEKQVVTPTGSVYSGVDFCKKLCGVSVIRSGESMENALRACCKGIKIGKILIHRE GDNGQQYSKFVKPAFEDFILPTKKYADIIIPRGGDNHVAIDLIVQHIHTKLGQHDLCKIYPNLY VIQSTFQIRGMHTLIRDSKTTKHDFIFYSDRLIRLVVEHGLGHLPFTEKQVVTPTGSVYSGVDF CKKLCGVSVIRSGESMENALRACCKGIKIGKILIHREGDNGQQYSKFVKPAFEDFILPTKKYAD IIIPRGGDNHVAIDLIVQHIHTKLGQHDLCKIYPNLYVIQSTFQIRGMHTLIRDSKTTKHDFIF YSDRLIRLVVEHGLGHLPFTEKQVVTPTGSVYSGVDFCKKLCGVSVIRSGESMENALRACCKGI KIGKILIHREGDNGQQ(+)
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 AT1G55810_circ_g.3

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