Plant Circular RNA Database

Detail information of AT3G13300_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT3G13300_circ_g.6
					
						ID in PlantcircBase
						ath_circ_021419
					
						Alias
						Ath_circ_FC1950, Ath_circ_FC1951
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 4307921-4309040  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT3G13300						
					
						Parent gene annotation
						
							Enhancer of mRNA-decapping protein 4
							
						Parent gene strand
						+
					
						Alternative splicing
						
							3_circ_ag.6 3_circ_ag.7 AT3G13290_circ_g.1 3_circ_ag.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 AT3G13300_circ_g.1 AT3G13300_circ_g.2 AT3G13300_circ_g.3 AT3G13300_circ_g.4 AT3G13300_circ_g.5 						
					
						Support reads
						1
					
						Tissues
						root
					
						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
						AT3G13300.3:4
AT3G13300.2:4
AT3G13300.1:4

General Information
CircRNA Name	AT3G13300_circ_g.6
ID in PlantcircBase	ath_circ_021419
Alias	Ath_circ_FC1950, Ath_circ_FC1951
Organism	Arabidpsis thaliana
Position	chr3: 4307921-4309040 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT3G13300
Parent gene annotation	Enhancer of mRNA-decapping protein 4
Parent gene strand	+
Alternative splicing	3_circ_ag.6 3_circ_ag.7 AT3G13290_circ_g.1 3_circ_ag.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 AT3G13300_circ_g.1 AT3G13300_circ_g.2 AT3G13300_circ_g.3 AT3G13300_circ_g.4 AT3G13300_circ_g.5
Support reads	1
Tissues	root
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	AT3G13300.3:4 AT3G13300.2:4 AT3G13300.1:4

			
						 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  
						
							GAATCTCTTAGCTCTCGCAGCTGCTGGAGCAAATTCTGGTGGGTCTAATTCCTTGGTTACTCAA
CTAAGTGGCGGACCTTTGGGTGCTCTTCTTGAAAAGgtgatggcttcgcagaaggagatgcaga
gacaactatcaaatgctgccactggccctatcggaaaagaaagtaaaagactagaagttgcgtt
agggagaa

									
								

					

						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: 816
Transcript exons: 4307921-4308280,4308363-4308482,4308611-4308781,4308876-
4309040
GTGATGGCTTCGCAGAAGGAGATGCAGAGACAACTATCAAATGCTGCCACTGGCCCTATCGGAA
AAGAAAGTAAAAGACTAGAAGTTGCGTTAGGGAGAATGATTGAGAAATCCAGCAAGTCAAATGC
TGATGCTCTATGGGCCCGCATCCAGGAGGAGACTGTTAAGAATGAAAAGGCATTACGTGACCAT
GCCCAGCAAATTGTGAATGCAACGACAAACTTCATGAGCAAGGAGTTAAATGCCATGTTTGAGA
AAACGATAAAGAAAGAATTGGCTGCAATTGGTCCAGCCCTAGCACGTTCAGTAGTACCAGTTAT
TGAAAAAACTGTATCTTCTGCAATCACAGAGTCCTTTCAGAGAGGAATAGGTGACAAAGCAGTT
AATCAGCTTGACAAATCTGTTAATATAAAGCTTGAAGCAACCGTAGCTAGGCAAATTCAAGCCC
AATTTCAGACCTCTGGCAAGCAAGCCCTCCAGGAAGGTCTTAGGTCAAGTGTGGAGTCCTCAGT
CATACCTTCCTTTGAGAAGGCATGCAAGGCCATGTTTGACCAAATAGACTCAGCCTTCCAGAAA
GGTATTGCTGAGCATACAAATGCAGCCCAGCAACGGTTTGACTCTGGACACTCCCAGCTTGCTC
ATACTCTAAAGGAATCAATTACTTCTGCGTCGTCAGTTGCTCAAGCCTTAAGTCGTGAGTTAGC
CGAGACCCAAAGGAATCTCTTAGCTCTCGCAGCTGCTGGAGCAAATTCTGGTGGGTCTAATTCC
TTGGTTACTCAACTAAGTGGCGGACCTTTGGGTGCTCTTCTTGAAAAG
						
					

						Genomic sequence
						
							GTGATGGCTTCGCAGAAGGAGATGCAGAGACAACTATCAAATGCTGCCACTGGCCCTATCGGAA
AAGAAAGTAAAAGACTAGAAGTTGCGTTAGGGAGAATGATTGAGAAATCCAGCAAGTCAAATGC
TGATGCTCTATGGGCCCGCATCCAGGAGGAGACTGTTAAGAATGAAAAGGCATTACGTGACCAT
GCCCAGCAAATTGTGAATGCAACGACAAACTTCATGAGCAAGGAGTTAAATGCCATGTTTGAGA
AAACGATAAAGAAAGAATTGGCTGCAATTGGTCCAGCCCTAGCACGTTCAGTAGTACCAGTTAT
TGAAAAAACTGTATCTTCTGCAATCACAGAGTCCTTTCAGGTAAGATTTTACGAGAAATTTAGA
GCTAATTTTTGAGAAGGTTCATTGTTCTTAAAAGAAAGCTGCTTTCTCTTTTGTACAGAGAGGA
ATAGGTGACAAAGCAGTTAATCAGCTTGACAAATCTGTTAATATAAAGCTTGAAGCAACCGTAG
CTAGGCAAATTCAAGCCCAATTTCAGACCTCTGGCAAGCAAGCCCTCCAGGTAAACTTGAGGTT
CACCTAGCTTTGTGGTAGTTTATAGAAGTGTCTATAAGTCTCCAACTGCATACATAGTTTAACG
GAAAGGGAGTTTATCTCTTATATATATTTCCTGCCGTTTATAAACTTCAGGAAGGTCTTAGGTC
AAGTGTGGAGTCCTCAGTCATACCTTCCTTTGAGAAGGCATGCAAGGCCATGTTTGACCAAATA
GACTCAGCCTTCCAGAAAGGTATTGCTGAGCATACAAATGCAGCCCAGCAACGGTTTGACTCTG
GACACTCCCAGCTTGCTCATACTCTAAAGGTACGATGGAAAATCATTCTTCTTACAGCTCTGTT
ATGGTTGCAAAATCCAATCATTTCTTTCTTCTCTCTAAAGCTGCTTGCTCGTTTTACAGGAATC
AATTACTTCTGCGTCGTCAGTTGCTCAAGCCTTAAGTCGTGAGTTAGCCGAGACCCAAAGGAAT
CTCTTAGCTCTCGCAGCTGCTGGAGCAAATTCTGGTGGGTCTAATTCCTTGGTTACTCAACTAA
GTGGCGGACCTTTGGGTGCTCTTCTTGAAAAG
						
					

			
		

Sequences
Splice junction sequence	GAATCTCTTAGCTCTCGCAGCTGCTGGAGCAAATTCTGGTGGGTCTAATTCCTTGGTTACTCAA CTAAGTGGCGGACCTTTGGGTGCTCTTCTTGAAAAGgtgatggcttcgcagaaggagatgcaga gacaactatcaaatgctgccactggccctatcggaaaagaaagtaaaagactagaagttgcgtt agggagaa
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: 816 Transcript exons: 4307921-4308280,4308363-4308482,4308611-4308781,4308876- 4309040 GTGATGGCTTCGCAGAAGGAGATGCAGAGACAACTATCAAATGCTGCCACTGGCCCTATCGGAA AAGAAAGTAAAAGACTAGAAGTTGCGTTAGGGAGAATGATTGAGAAATCCAGCAAGTCAAATGC TGATGCTCTATGGGCCCGCATCCAGGAGGAGACTGTTAAGAATGAAAAGGCATTACGTGACCAT GCCCAGCAAATTGTGAATGCAACGACAAACTTCATGAGCAAGGAGTTAAATGCCATGTTTGAGA AAACGATAAAGAAAGAATTGGCTGCAATTGGTCCAGCCCTAGCACGTTCAGTAGTACCAGTTAT TGAAAAAACTGTATCTTCTGCAATCACAGAGTCCTTTCAGAGAGGAATAGGTGACAAAGCAGTT AATCAGCTTGACAAATCTGTTAATATAAAGCTTGAAGCAACCGTAGCTAGGCAAATTCAAGCCC AATTTCAGACCTCTGGCAAGCAAGCCCTCCAGGAAGGTCTTAGGTCAAGTGTGGAGTCCTCAGT CATACCTTCCTTTGAGAAGGCATGCAAGGCCATGTTTGACCAAATAGACTCAGCCTTCCAGAAA GGTATTGCTGAGCATACAAATGCAGCCCAGCAACGGTTTGACTCTGGACACTCCCAGCTTGCTC ATACTCTAAAGGAATCAATTACTTCTGCGTCGTCAGTTGCTCAAGCCTTAAGTCGTGAGTTAGC CGAGACCCAAAGGAATCTCTTAGCTCTCGCAGCTGCTGGAGCAAATTCTGGTGGGTCTAATTCC TTGGTTACTCAACTAAGTGGCGGACCTTTGGGTGCTCTTCTTGAAAAG
Genomic sequence	GTGATGGCTTCGCAGAAGGAGATGCAGAGACAACTATCAAATGCTGCCACTGGCCCTATCGGAA AAGAAAGTAAAAGACTAGAAGTTGCGTTAGGGAGAATGATTGAGAAATCCAGCAAGTCAAATGC TGATGCTCTATGGGCCCGCATCCAGGAGGAGACTGTTAAGAATGAAAAGGCATTACGTGACCAT GCCCAGCAAATTGTGAATGCAACGACAAACTTCATGAGCAAGGAGTTAAATGCCATGTTTGAGA AAACGATAAAGAAAGAATTGGCTGCAATTGGTCCAGCCCTAGCACGTTCAGTAGTACCAGTTAT TGAAAAAACTGTATCTTCTGCAATCACAGAGTCCTTTCAGGTAAGATTTTACGAGAAATTTAGA GCTAATTTTTGAGAAGGTTCATTGTTCTTAAAAGAAAGCTGCTTTCTCTTTTGTACAGAGAGGA ATAGGTGACAAAGCAGTTAATCAGCTTGACAAATCTGTTAATATAAAGCTTGAAGCAACCGTAG CTAGGCAAATTCAAGCCCAATTTCAGACCTCTGGCAAGCAAGCCCTCCAGGTAAACTTGAGGTT CACCTAGCTTTGTGGTAGTTTATAGAAGTGTCTATAAGTCTCCAACTGCATACATAGTTTAACG GAAAGGGAGTTTATCTCTTATATATATTTCCTGCCGTTTATAAACTTCAGGAAGGTCTTAGGTC AAGTGTGGAGTCCTCAGTCATACCTTCCTTTGAGAAGGCATGCAAGGCCATGTTTGACCAAATA GACTCAGCCTTCCAGAAAGGTATTGCTGAGCATACAAATGCAGCCCAGCAACGGTTTGACTCTG GACACTCCCAGCTTGCTCATACTCTAAAGGTACGATGGAAAATCATTCTTCTTACAGCTCTGTT ATGGTTGCAAAATCCAATCATTTCTTTCTTCTCTCTAAAGCTGCTTGCTCGTTTTACAGGAATC AATTACTTCTGCGTCGTCAGTTGCTCAAGCCTTAAGTCGTGAGTTAGCCGAGACCCAAAGGAAT CTCTTAGCTCTCGCAGCTGCTGGAGCAAATTCTGGTGGGTCTAATTCCTTGGTTACTCAACTAA GTGGCGGACCTTTGGGTGCTCTTCTTGAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.229080084

Conservation Information
Conserved circRNAs	NA
PMCS	0.229080084

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4307924-4309037(+)
						
						Potential amino acid sequence
						
							MASQKEMQRQLSNAATGPIGKESKRLEVALGRMIEKSSKSNADALWARIQEETVKNEKALRDHA
QQIVNATTNFMSKELNAMFEKTIKKELAAIGPALARSVVPVIEKTVSSAITESFQRGIGDKAVN
QLDKSVNIKLEATVARQIQAQFQTSGKQALQEGLRSSVESSVIPSFEKACKAMFDQIDSAFQKG
IAEHTNAAQQRFDSGHSQLAHTLKESITSASSVAQALSRELAETQRNLLALAAAGANSGGSNSL
VTQLSGGPLGALLEKVMASQKEMQRQLSNAATGPIGKESKRLEVALGRMIEKSSKSNADALWAR
IQEETVKNEKALRDHAQQIVNATTNFMSKELNAMFEKTIKKELAAIGPALARSVVPVIEKTVSS
AITESFQRGIGDKAVNQLDKSVNIKLEATVARQIQAQFQTSGKQALQEGLRSSVESSVIPSFEK
ACKAMFDQIDSAFQKGIAEHTNAAQQRFDSGHSQLAHTLKESITSASSVAQALSRELAETQRNL
LALAAAGANSGGSNSLVTQLSGGPLGALLEKVMASQKEMQRQLSNAATGPIGKESKRLEVALGR
MIEKSSKSNADALWARIQEETVKNEKALRDHAQQIVNATTNFMSKELNAMFEKTIKKELAAIGP
ALARSVVPVIEKTVSSAITESFQRGIGDKAVNQLDKSVNIKLEATVARQIQAQFQTSGKQALQE
GLRSSVESSVIPSFEKACKAMFDQIDSAFQKGIAEHTNAAQQRFDSGHSQLAHTLKESITSASS
VAQALSRELAETQRNLLALAAAGANSGGSNSLVTQLSGGPLGALLEKVMASQKEMQRQLSNAAT
GPIGKESKRLEVALGRMIEKSSKSNADALWARIQEETVKNEKALRDHAQQIVNATTNFMSKELN
AMFEKTIKKELAAIGPALARSVVPVIEKTVSSAITESFQRGIGDKAVNQLDKSVNIKLEATVAR
QIQAQFQTSGKQALQEGLRSSVESSVIPSFEKACKAMFDQIDSAFQKGIAEHTNAAQQRFDSGH
SQLAHTLKESITSASSVAQALSRELAETQRNLLALAAAGANSGGSNSLVTQLSGGPLGALLEK(
+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4307924-4309037(+)
Potential amino acid sequence	MASQKEMQRQLSNAATGPIGKESKRLEVALGRMIEKSSKSNADALWARIQEETVKNEKALRDHA QQIVNATTNFMSKELNAMFEKTIKKELAAIGPALARSVVPVIEKTVSSAITESFQRGIGDKAVN QLDKSVNIKLEATVARQIQAQFQTSGKQALQEGLRSSVESSVIPSFEKACKAMFDQIDSAFQKG IAEHTNAAQQRFDSGHSQLAHTLKESITSASSVAQALSRELAETQRNLLALAAAGANSGGSNSL VTQLSGGPLGALLEKVMASQKEMQRQLSNAATGPIGKESKRLEVALGRMIEKSSKSNADALWAR IQEETVKNEKALRDHAQQIVNATTNFMSKELNAMFEKTIKKELAAIGPALARSVVPVIEKTVSS AITESFQRGIGDKAVNQLDKSVNIKLEATVARQIQAQFQTSGKQALQEGLRSSVESSVIPSFEK ACKAMFDQIDSAFQKGIAEHTNAAQQRFDSGHSQLAHTLKESITSASSVAQALSRELAETQRNL LALAAAGANSGGSNSLVTQLSGGPLGALLEKVMASQKEMQRQLSNAATGPIGKESKRLEVALGR MIEKSSKSNADALWARIQEETVKNEKALRDHAQQIVNATTNFMSKELNAMFEKTIKKELAAIGP ALARSVVPVIEKTVSSAITESFQRGIGDKAVNQLDKSVNIKLEATVARQIQAQFQTSGKQALQE GLRSSVESSVIPSFEKACKAMFDQIDSAFQKGIAEHTNAAQQRFDSGHSQLAHTLKESITSASS VAQALSRELAETQRNLLALAAAGANSGGSNSLVTQLSGGPLGALLEKVMASQKEMQRQLSNAAT GPIGKESKRLEVALGRMIEKSSKSNADALWARIQEETVKNEKALRDHAQQIVNATTNFMSKELN AMFEKTIKKELAAIGPALARSVVPVIEKTVSSAITESFQRGIGDKAVNQLDKSVNIKLEATVAR QIQAQFQTSGKQALQEGLRSSVESSVIPSFEKACKAMFDQIDSAFQKGIAEHTNAAQQRFDSGH SQLAHTLKESITSASSVAQALSRELAETQRNLLALAAAGANSGGSNSLVTQLSGGPLGALLEK( +)
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 AT3G13300_circ_g.6

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