Plant Circular RNA Database

Detail information of AT5G03900_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G03900_circ_g.3
					
						ID in PlantcircBase
						ath_circ_036252
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 1048987-1049842  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder, circRNA_finder, find_circ
					
						Parent gene
						
							AT5G03900						
					
						Parent gene annotation
						
							Uncharacterized protein At5g03900, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G03900_circ_g.1 AT5G03900_circ_g.2 AT5G03900_circ_g.4 AT5G03900_circ_g.5 AT5G03900_circ_g.6 AT5G03900_circ_g.7 						
					
						Support reads
						2
					
						Tissues
						inflorescences
					
						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
						AT5G03900.1:5
AT5G03900.2:5

General Information
CircRNA Name	AT5G03900_circ_g.3
ID in PlantcircBase	ath_circ_036252
Alias	NA
Organism	Arabidpsis thaliana
Position	chr5: 1048987-1049842 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, PcircRNA_finder, circRNA_finder, find_circ
Parent gene	AT5G03900
Parent gene annotation	Uncharacterized protein At5g03900, chloroplastic
Parent gene strand	+
Alternative splicing	AT5G03900_circ_g.1 AT5G03900_circ_g.2 AT5G03900_circ_g.4 AT5G03900_circ_g.5 AT5G03900_circ_g.6 AT5G03900_circ_g.7
Support reads	2
Tissues	inflorescences
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	AT5G03900.1:5 AT5G03900.2:5

			
						 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  
						
							TAATGGCTTGAAATAAGTGAGGGTTCATCTCTAGGTTTTCTCGTTTGTATTTGGAGATGGAGAC
CCAAATCAAGGAATCGAAGAAGAGAGATGGCAGATGgtgtcggatgaaggtgatgtgctttatg
ttttcccaagggactatcgaactaagttggctgccaagtcgttaaggatacaaattgaaccatt
ccttgaaa

						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: 435
Transcript exons: 1048987-1049094,1049189-1049289,1049404-1049487,1049595-
1049670,1049777-1049842
GTGTCGGATGAAGGTGATGTGCTTTATGTTTTCCCAAGGGACTATCGAACTAAGTTGGCTGCCA
AGTCGTTAAGGATACAAATTGAACCATTCCTTGAAAAGGCAAAGGGTGCTGTAGATTATTTGGC
TCGTGTTTCCTTTGGCACGGCGCTTATAGCGTCTATCGTTATTGTCTACACGTCAATTATAGCC
CTGCTTTCAAGCAAAAGCGAGGATGATAATCGTCAAAGAAGACGCGGGCGCAGTTATGATTCAG
GATTCAATTTCTATATCAACCCTGTCGATCTGCTTTGGTACTGGGATCCCAATTATTACAACAG
GCGACGAGCTCGAGAAGATGAAGGAAAGGGAATGAATTTCATTGAATCTGTTTTCTCGTTTGTA
TTTGGAGATGGAGACCCAAATCAAGGAATCGAAGAAGAGAGATGGCAGATG
						
						Genomic sequence
						
							GTGTCGGATGAAGGTGATGTGCTTTATGTTTTCCCAAGGGACTATCGAACTAAGTTGGCTGCCA
AGTCGTTAAGGATACAAATTGAACCATTCCTTGAAAAGGCAAAGGTAGTATTTTTTTTCTGTTA
AGATTTATTGATTTCCTTTTAACAGTGAATTGCTTTGAATTTGAATGTTCTGAGCTCTATTATG
TGTCTCGCAGGGTGCTGTAGATTATTTGGCTCGTGTTTCCTTTGGCACGGCGCTTATAGCGTCT
ATCGTTATTGTCTACACGTCAATTATAGCCCTGCTTTCAAGCAAAAGGTATGTGTTTGCCTTGA
CCGCAATTAAGTTGTCTTGTTATCAAGATATATTATCATTCTGATCAATGGACTTGATTTGGAT
TTTGCACTAACCTTTTTTGGATTTTGTTAAAAGCGAGGATGATAATCGTCAAAGAAGACGCGGG
CGCAGTTATGATTCAGGATTCAATTTCTATATCAACCCTGTCGATCTGCTTTGGTAATTTTAAT
TTCATGATGTAAAAGGCTCCTACTCTCAACCAATAGAGAGGATCAGTAATTGATTTAACAGAAC
CTCGTAGTCATATTCTAGTGTTTTTATGTAAGGTACTGGGATCCCAATTATTACAACAGGCGAC
GAGCTCGAGAAGATGAAGGAAAGGGAATGAATTTCATTGAATCTGTAAGTAGAGTTTGAACTTA
AGAGAGTTTTCATGCTTTGCTAAATGTTTCTTCTTTTGCTGCTTATGAGTGATAATGGCTTGAA
ATAAGTGAGGGTTCATCTCTAGGTTTTCTCGTTTGTATTTGGAGATGGAGACCCAAATCAAGGA
ATCGAAGAAGAGAGATGGCAGATG

Sequences
Splice junction sequence	TAATGGCTTGAAATAAGTGAGGGTTCATCTCTAGGTTTTCTCGTTTGTATTTGGAGATGGAGAC CCAAATCAAGGAATCGAAGAAGAGAGATGGCAGATGgtgtcggatgaaggtgatgtgctttatg ttttcccaagggactatcgaactaagttggctgccaagtcgttaaggatacaaattgaaccatt ccttgaaa
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: 435 Transcript exons: 1048987-1049094,1049189-1049289,1049404-1049487,1049595- 1049670,1049777-1049842 GTGTCGGATGAAGGTGATGTGCTTTATGTTTTCCCAAGGGACTATCGAACTAAGTTGGCTGCCA AGTCGTTAAGGATACAAATTGAACCATTCCTTGAAAAGGCAAAGGGTGCTGTAGATTATTTGGC TCGTGTTTCCTTTGGCACGGCGCTTATAGCGTCTATCGTTATTGTCTACACGTCAATTATAGCC CTGCTTTCAAGCAAAAGCGAGGATGATAATCGTCAAAGAAGACGCGGGCGCAGTTATGATTCAG GATTCAATTTCTATATCAACCCTGTCGATCTGCTTTGGTACTGGGATCCCAATTATTACAACAG GCGACGAGCTCGAGAAGATGAAGGAAAGGGAATGAATTTCATTGAATCTGTTTTCTCGTTTGTA TTTGGAGATGGAGACCCAAATCAAGGAATCGAAGAAGAGAGATGGCAGATG
Genomic sequence	GTGTCGGATGAAGGTGATGTGCTTTATGTTTTCCCAAGGGACTATCGAACTAAGTTGGCTGCCA AGTCGTTAAGGATACAAATTGAACCATTCCTTGAAAAGGCAAAGGTAGTATTTTTTTTCTGTTA AGATTTATTGATTTCCTTTTAACAGTGAATTGCTTTGAATTTGAATGTTCTGAGCTCTATTATG TGTCTCGCAGGGTGCTGTAGATTATTTGGCTCGTGTTTCCTTTGGCACGGCGCTTATAGCGTCT ATCGTTATTGTCTACACGTCAATTATAGCCCTGCTTTCAAGCAAAAGGTATGTGTTTGCCTTGA CCGCAATTAAGTTGTCTTGTTATCAAGATATATTATCATTCTGATCAATGGACTTGATTTGGAT TTTGCACTAACCTTTTTTGGATTTTGTTAAAAGCGAGGATGATAATCGTCAAAGAAGACGCGGG CGCAGTTATGATTCAGGATTCAATTTCTATATCAACCCTGTCGATCTGCTTTGGTAATTTTAAT TTCATGATGTAAAAGGCTCCTACTCTCAACCAATAGAGAGGATCAGTAATTGATTTAACAGAAC CTCGTAGTCATATTCTAGTGTTTTTATGTAAGGTACTGGGATCCCAATTATTACAACAGGCGAC GAGCTCGAGAAGATGAAGGAAAGGGAATGAATTTCATTGAATCTGTAAGTAGAGTTTGAACTTA AGAGAGTTTTCATGCTTTGCTAAATGTTTCTTCTTTTGCTGCTTATGAGTGATAATGGCTTGAA ATAAGTGAGGGTTCATCTCTAGGTTTTCTCGTTTGTATTTGGAGATGGAGACCCAAATCAAGGA ATCGAAGAAGAGAGATGGCAGATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.201209008

Conservation Information
Conserved circRNAs	NA
PMCS	0.201209008

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1049653-1049839(+)
						
						Potential amino acid sequence
						
							MNFIESVFSFVFGDGDPNQGIEEERWQMVSDEGDVLYVFPRDYRTKLAAKSLRIQIEPFLEKAK
GAVDYLARVSFGTALIASIVIVYTSIIALLSSKSEDDNRQRRRGRSYDSGFNFYINPVDLLWYW
DPNYYNRRRAREDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMVSDEGDVLYVFPRDYRTKL
AAKSLRIQIEPFLEKAKGAVDYLARVSFGTALIASIVIVYTSIIALLSSKSEDDNRQRRRGRSY
DSGFNFYINPVDLLWYWDPNYYNRRRAREDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMVS
DEGDVLYVFPRDYRTKLAAKSLRIQIEPFLEKAKGAVDYLARVSFGTALIASIVIVYTSIIALL
SSKSEDDNRQRRRGRSYDSGFNFYINPVDLLWYWDPNYYNRRRAREDEGKGMNFIESVFSFVFG
DGDPNQGIEEERWQM(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1049653-1049839(+)
Potential amino acid sequence	MNFIESVFSFVFGDGDPNQGIEEERWQMVSDEGDVLYVFPRDYRTKLAAKSLRIQIEPFLEKAK GAVDYLARVSFGTALIASIVIVYTSIIALLSSKSEDDNRQRRRGRSYDSGFNFYINPVDLLWYW DPNYYNRRRAREDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMVSDEGDVLYVFPRDYRTKL AAKSLRIQIEPFLEKAKGAVDYLARVSFGTALIASIVIVYTSIIALLSSKSEDDNRQRRRGRSY DSGFNFYINPVDLLWYWDPNYYNRRRAREDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMVS DEGDVLYVFPRDYRTKLAAKSLRIQIEPFLEKAKGAVDYLARVSFGTALIASIVIVYTSIIALL SSKSEDDNRQRRRGRSYDSGFNFYINPVDLLWYWDPNYYNRRRAREDEGKGMNFIESVFSFVFG DGDPNQGIEEERWQM(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT5G03900_circ_g.3

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