Plant Circular RNA Database

Detail information of AT1G48860_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G48860_circ_g.2
					
						ID in PlantcircBase
						ath_circ_006370
					
						Alias
						Ath_circ_FC5230
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 18069324-18071106  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT1G48860						
					
						Parent gene annotation
						
							3-phosphoshikimate 1-carboxyvinyltransferase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							1_circ_ag.8 AT1G48860_circ_g.1 AT1G48860_circ_g.3 AT1G48860_circ_g.4 						
					
						Support reads
						11
					
						Tissues
						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
						AT1G48860.2:6
AT1G48860.1:6

General Information
CircRNA Name	AT1G48860_circ_g.2
ID in PlantcircBase	ath_circ_006370
Alias	Ath_circ_FC5230
Organism	Arabidpsis thaliana
Position	chr1: 18069324-18071106 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder
Parent gene	AT1G48860
Parent gene annotation	3-phosphoshikimate 1-carboxyvinyltransferase
Parent gene strand	-
Alternative splicing	1_circ_ag.8 AT1G48860_circ_g.1 AT1G48860_circ_g.3 AT1G48860_circ_g.4
Support reads	11
Tissues	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	AT1G48860.2:6 AT1G48860.1:6

			
						 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  
						
							GAAGCTTTCTCCGCCGTGGAAACAGAAGCCCTAACCTTCACAGGACGAATCTCAGAACCATTTA
GCATCAGATCACTCTTCTTCAATCCCCACGACTGCCcatctctaatggtggttggaccatcggc
aaagagagcaacgacggcaagagtcattgctacatcaggcattttgttcatgttgacatcaata
gcccgcaa

									
								

					

						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
						
							CATCTCTAATGGTGGTTGGACCATCGGCAAAGAGAGCAACGACGGCAAGAGTCATTGCTACATC
AGGCATTTTGTTCATGTTGACATCAATAGCCCGCAAGTGTCTCATTCCAAAAGCATCTCTAGAC
GGCCCTGTCACAGTCACACTGTTCTCTGTCCAGGACACTTTACATCCCATTTTCTCAAGAACCT
CGGCAAATTTCACATCTCCCTAGAGATTCATCACAAAAATTGAACTTAGATTCTTGCGAATATG
TTACATACAACTTGTCAAAGCCTTAAAAAGATGAAACTTTGACCTAAACGAATTTCACTATAAA
CTTAACAGCCTCTTTGATGATTCAGTGTACAAATATTACCTGCAAACTGGTCGTTCCACAACCT
TCAACAGTGACAGTTTCACCGGTAATGGCAGCACCAGCCAGGAAATAACTAGCACTAGAAGCAT
CACCTTCTACGTAAGCATTACCCGGCGACCTGAATCATTTCCCATATTAGTCATTATTTTGTCA
ATCTAAGGTATGTGATTTCAGAAAAGGAAGAGAATAATAACTCTTACTTGTATTTTTGCCCACC
CTTAACAAAGAAACGATCCCAGCTTTCACTATGCTCAGCACTTACCCCAAAACGTTCCATCAAC
TTCAATGTCATTTCAACATACGGAACAGAAATCAATTTATCGACAATTTCAATTTCGACGTCTC
CAAGAGCTAAGGGAGCTGCCATGAGCAGAGCGGTCAAGTACTGACTACTAATAGATCCAGAAAG
CTTCACCTGCAAATGCAAAAAATGTTCGATGCGTCAATAAAGAAACCATACAAGGAAAAGGGTA
ATCAAGAGAGAAAACTAATCCCTACTAAAAAAAAACAATTCGTTTTCAGGAACAATACATTGAC
AACAAACAAAAAAAATGAAATCTTGTCAAGTAAGGCTATGATGAACACAAATTGCTGCAAGTGT
TTATAAAGTTATAAATTCACATGCCATTTGCAAGATCTCACCTTTCCACCAGGAAGGCCACCAT
TAGCGTTGACACGAACAGGAGGGCAGTTAGTGCCAAGAGTACATTCAACATCAGCACCAAGCTG
CTTAAGACCAACAACCAAATCCCCTATAGGTCTCTCTCTCATCCGAGGCACCCCATCAAGGACA
TAACTGAAATAAACCGATTGAAAAGCATCAAAACAAGATCGATTCTTAAGAAATCAAAACTATT
CAGCATTTACTCCTTCAATATACCTTGCGTTGCCACCTGCAGCAGTAACTGCGGCGGTAAGTGG
ACGCATTGCTGTTCCTGCATTGCCGAGGTAAAGTTCGATATCACTCTTGGAATCAATGGAAGCT
GGAAATACCCCGCCACATCCTTCAACTACAGCACGATTGTTTTCACTGTGAGTTTCCACATTAA
GTCCCAATATCTTCAACGCATCAAGCATGTAATTGATGTCATCACTGTTCAACAAGTTGTCCAC
TACAGTAGTTCCCTATATAAGCACAGCAAAATGGTAAAGTTTATATCTTTAATAATCTAAATTC
GGAGTACAGAGAAGGAAGAAATGAAGTGATACATTTATATATACCTCAGATAGAGCAGCGAGAA
GCAGAATTCGATTAGAGAGAGACTTGGAGCCAGGAAGCTTAATGAGACCCGAGATTTCTCTAAT
GGGTTGAAGCACAATCTCCGAAGCTTTCTCCGCCGTGGAAACAGAAGCCCTAACCTTCACAGGA
CGAATCTCAGAACCATTTAGCATCAGATCACTCTTCTTCAATCCCCACGACTGCC
						
					

			
		

Sequences
Splice junction sequence	GAAGCTTTCTCCGCCGTGGAAACAGAAGCCCTAACCTTCACAGGACGAATCTCAGAACCATTTA GCATCAGATCACTCTTCTTCAATCCCCACGACTGCCcatctctaatggtggttggaccatcggc aaagagagcaacgacggcaagagtcattgctacatcaggcattttgttcatgttgacatcaata gcccgcaa
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	CATCTCTAATGGTGGTTGGACCATCGGCAAAGAGAGCAACGACGGCAAGAGTCATTGCTACATC AGGCATTTTGTTCATGTTGACATCAATAGCCCGCAAGTGTCTCATTCCAAAAGCATCTCTAGAC GGCCCTGTCACAGTCACACTGTTCTCTGTCCAGGACACTTTACATCCCATTTTCTCAAGAACCT CGGCAAATTTCACATCTCCCTAGAGATTCATCACAAAAATTGAACTTAGATTCTTGCGAATATG TTACATACAACTTGTCAAAGCCTTAAAAAGATGAAACTTTGACCTAAACGAATTTCACTATAAA CTTAACAGCCTCTTTGATGATTCAGTGTACAAATATTACCTGCAAACTGGTCGTTCCACAACCT TCAACAGTGACAGTTTCACCGGTAATGGCAGCACCAGCCAGGAAATAACTAGCACTAGAAGCAT CACCTTCTACGTAAGCATTACCCGGCGACCTGAATCATTTCCCATATTAGTCATTATTTTGTCA ATCTAAGGTATGTGATTTCAGAAAAGGAAGAGAATAATAACTCTTACTTGTATTTTTGCCCACC CTTAACAAAGAAACGATCCCAGCTTTCACTATGCTCAGCACTTACCCCAAAACGTTCCATCAAC TTCAATGTCATTTCAACATACGGAACAGAAATCAATTTATCGACAATTTCAATTTCGACGTCTC CAAGAGCTAAGGGAGCTGCCATGAGCAGAGCGGTCAAGTACTGACTACTAATAGATCCAGAAAG CTTCACCTGCAAATGCAAAAAATGTTCGATGCGTCAATAAAGAAACCATACAAGGAAAAGGGTA ATCAAGAGAGAAAACTAATCCCTACTAAAAAAAAACAATTCGTTTTCAGGAACAATACATTGAC AACAAACAAAAAAAATGAAATCTTGTCAAGTAAGGCTATGATGAACACAAATTGCTGCAAGTGT TTATAAAGTTATAAATTCACATGCCATTTGCAAGATCTCACCTTTCCACCAGGAAGGCCACCAT TAGCGTTGACACGAACAGGAGGGCAGTTAGTGCCAAGAGTACATTCAACATCAGCACCAAGCTG CTTAAGACCAACAACCAAATCCCCTATAGGTCTCTCTCTCATCCGAGGCACCCCATCAAGGACA TAACTGAAATAAACCGATTGAAAAGCATCAAAACAAGATCGATTCTTAAGAAATCAAAACTATT CAGCATTTACTCCTTCAATATACCTTGCGTTGCCACCTGCAGCAGTAACTGCGGCGGTAAGTGG ACGCATTGCTGTTCCTGCATTGCCGAGGTAAAGTTCGATATCACTCTTGGAATCAATGGAAGCT GGAAATACCCCGCCACATCCTTCAACTACAGCACGATTGTTTTCACTGTGAGTTTCCACATTAA GTCCCAATATCTTCAACGCATCAAGCATGTAATTGATGTCATCACTGTTCAACAAGTTGTCCAC TACAGTAGTTCCCTATATAAGCACAGCAAAATGGTAAAGTTTATATCTTTAATAATCTAAATTC GGAGTACAGAGAAGGAAGAAATGAAGTGATACATTTATATATACCTCAGATAGAGCAGCGAGAA GCAGAATTCGATTAGAGAGAGACTTGGAGCCAGGAAGCTTAATGAGACCCGAGATTTCTCTAAT GGGTTGAAGCACAATCTCCGAAGCTTTCTCCGCCGTGGAAACAGAAGCCCTAACCTTCACAGGA CGAATCTCAGAACCATTTAGCATCAGATCACTCTTCTTCAATCCCCACGACTGCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.168691876

Conservation Information
Conserved circRNAs	NA
PMCS	0.168691876

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							18071075-18069326(-)
						
					

						Potential amino acid sequence
						
							MLNGSEIRPVKVRASVSTAEKASEIVLQPIREISGLIKLPGSKSLSNRILLLAALSEGTTVVDN
LLNSDDINYMLDALKILGLNVETHSENNRAVVEGCGGVFPASIDSKSDIELYLGNAGTAMRPLT
AAVTAAGGNASYVLDGVPRMRERPIGDLVVGLKQLGADVECTLGTNCPPVRVNANGGLPGGKVK
LSGSISSQYLTALLMAAPLALGDVEIEIVDKLISVPYVEMTLKLMERFGVSAEHSESWDRFFVK
GGQKYKSPGNAYVEGDASSASYFLAGAAITGETVTVEGCGTTSLQGDVKFAEVLEKMGCKVSWT
ENSVTVTGPSRDAFGMRHLRAIDVNMNKMPDVAMTLAVVALFADGPTTIRDGQSWGLKKSDLML
NGSEIRPVKVRASVSTAEKASEIVLQPIREISGLIKLPGSKSLSNRILLLAALSEGTTVVDNLL
NSDDINYMLDALKILGLNVETHSENNRAVVEGCGGVFPASIDSKSDIELYLGNAGTAMRPLTAA
VTAAGGNASYVLDGVPRMRERPIGDLVVGLKQLGADVECTLGTNCPPVRVNANGGLPGGKVKLS
GSISSQYLTALLMAAPLALGDVEIEIVDKLISVPYVEMTLKLMERFGVSAEHSESWDRFFVKGG
QKYKSPGNAYVEGDASSASYFLAGAAITGETVTVEGCGTTSLQGDVKFAEVLEKMGCKVSWTEN
SVTVTGPSRDAFGMRHLRAIDVNMNKMPDVAMTLAVVALFADGPTTIRDGQSWGLKKSDLMLNG
SEIRPVKVRASVSTAEKASEIVLQPIREISGLIKLPGSKSLSNRILLLAALSEGTTVVDNLLNS
DDINYMLDALKILGLNVETHSENNRAVVEGCGGVFPASIDSKSDIELYLGNAGTAMRPLTAAVT
AAGGNASYVLDGVPRMRERPIGDLVVGLKQLGADVECTLGTNCPPVRVNANGGLPGGKVKLSGS
ISSQYLTALLMAAPLALGDVEIEIVDKLISVPYVEMTLKLMERFGVSAEHSESWDRFFVKGGQK
YKSPGNAYVEGDASSASYFLAGAAITGETVTVEGCGTTSLQGDVKFAEVLEKMGCKVSWTENSV
TVTGPSRDAFGMRHLRAIDVNMNKMPDVAMTLAVVALFADGPTTIRDGQSWGLKKSDLMLNGSE
IRPVKVRASVSTAEKASEIVLQPIREISGLIKLPGSKSLSNRILLLAALSEGTTVVDNLLNSDD
INYMLDALKILGLNVETHSENNRAVVEGCGGVFPASIDSKSDIELYLGNAGTAMRPLTAAVTAA
GGNASYVLDGVPRMRERPIGDLVVGLKQLGADVECTLGTNCPPVRVNANGGLPGGKVKLSGSIS
SQYLTALLMAAPLALGDVEIEIVDKLISVPYVEMTLKLMERFGVSAEHSESWDRFFVKGGQKYK
SPGNAYVEGDASSASYFLAGAAITGETVTVEGCGTTSLQGDVKFAEVLEKMGCKVSWTENSVTV
TGPSRDAFGMRHLRAIDVNMNKMPDVAMTLAVVALFADGPTTIRD(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	18071075-18069326(-)
Potential amino acid sequence	MLNGSEIRPVKVRASVSTAEKASEIVLQPIREISGLIKLPGSKSLSNRILLLAALSEGTTVVDN LLNSDDINYMLDALKILGLNVETHSENNRAVVEGCGGVFPASIDSKSDIELYLGNAGTAMRPLT AAVTAAGGNASYVLDGVPRMRERPIGDLVVGLKQLGADVECTLGTNCPPVRVNANGGLPGGKVK LSGSISSQYLTALLMAAPLALGDVEIEIVDKLISVPYVEMTLKLMERFGVSAEHSESWDRFFVK GGQKYKSPGNAYVEGDASSASYFLAGAAITGETVTVEGCGTTSLQGDVKFAEVLEKMGCKVSWT ENSVTVTGPSRDAFGMRHLRAIDVNMNKMPDVAMTLAVVALFADGPTTIRDGQSWGLKKSDLML NGSEIRPVKVRASVSTAEKASEIVLQPIREISGLIKLPGSKSLSNRILLLAALSEGTTVVDNLL NSDDINYMLDALKILGLNVETHSENNRAVVEGCGGVFPASIDSKSDIELYLGNAGTAMRPLTAA VTAAGGNASYVLDGVPRMRERPIGDLVVGLKQLGADVECTLGTNCPPVRVNANGGLPGGKVKLS GSISSQYLTALLMAAPLALGDVEIEIVDKLISVPYVEMTLKLMERFGVSAEHSESWDRFFVKGG QKYKSPGNAYVEGDASSASYFLAGAAITGETVTVEGCGTTSLQGDVKFAEVLEKMGCKVSWTEN SVTVTGPSRDAFGMRHLRAIDVNMNKMPDVAMTLAVVALFADGPTTIRDGQSWGLKKSDLMLNG SEIRPVKVRASVSTAEKASEIVLQPIREISGLIKLPGSKSLSNRILLLAALSEGTTVVDNLLNS DDINYMLDALKILGLNVETHSENNRAVVEGCGGVFPASIDSKSDIELYLGNAGTAMRPLTAAVT AAGGNASYVLDGVPRMRERPIGDLVVGLKQLGADVECTLGTNCPPVRVNANGGLPGGKVKLSGS ISSQYLTALLMAAPLALGDVEIEIVDKLISVPYVEMTLKLMERFGVSAEHSESWDRFFVKGGQK YKSPGNAYVEGDASSASYFLAGAAITGETVTVEGCGTTSLQGDVKFAEVLEKMGCKVSWTENSV TVTGPSRDAFGMRHLRAIDVNMNKMPDVAMTLAVVALFADGPTTIRDGQSWGLKKSDLMLNGSE IRPVKVRASVSTAEKASEIVLQPIREISGLIKLPGSKSLSNRILLLAALSEGTTVVDNLLNSDD INYMLDALKILGLNVETHSENNRAVVEGCGGVFPASIDSKSDIELYLGNAGTAMRPLTAAVTAA GGNASYVLDGVPRMRERPIGDLVVGLKQLGADVECTLGTNCPPVRVNANGGLPGGKVKLSGSIS SQYLTALLMAAPLALGDVEIEIVDKLISVPYVEMTLKLMERFGVSAEHSESWDRFFVKGGQKYK SPGNAYVEGDASSASYFLAGAAITGETVTVEGCGTTSLQGDVKFAEVLEKMGCKVSWTENSVTV TGPSRDAFGMRHLRAIDVNMNKMPDVAMTLAVVALFADGPTTIRD(-)
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 AT1G48860_circ_g.2

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