Plant Circular RNA Database

Detail information of AT1G05940_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT1G05940_circ_g.1
					
						ID in PlantcircBase
						ath_circ_000906
					
						Alias
						At_ciR4302
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 1802024-1802870  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							AT1G05940						
					
						Parent gene annotation
						
							Cationic amino acid transporter 9, chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G05940_circ_g.2 						
					
						Support reads
						3/1/3
					
						Tissues
						leaf/root/seedlings
					
						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
						AT1G05940.2:3
AT1G05940.1:3
AT1G05940.3:3
AT1G05940.4:3

General Information
CircRNA Name	AT1G05940_circ_g.1
ID in PlantcircBase	ath_circ_000906
Alias	At_ciR4302
Organism	Arabidpsis thaliana
Position	chr1: 1802024-1802870 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	AT1G05940
Parent gene annotation	Cationic amino acid transporter 9, chloroplastic
Parent gene strand	-
Alternative splicing	AT1G05940_circ_g.2
Support reads	3/1/3
Tissues	leaf/root/seedlings
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	AT1G05940.2:3 AT1G05940.1:3 AT1G05940.3:3 AT1G05940.4:3

			
						 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  
						
							GGAGGCTAAAAGGGACCATCCCGGTGAGCACCAAACATACGCCAATATACAGCGAGATACAAAC
CAGAAGGCTCCCCATAATTCCGATTGGCAAATCGCGttggcgataatgaagaactgctgaagca
acaactgccacaccaactgagaggagaataaatataactgaagcactgaaacggtaaaatacgc
cagcacca

						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: 639
Transcript exons: 1802024-1802260,1802357-1802533,1802646-1802870
TTGGCGATAATGAAGAACTGCTGAAGCAACAACTGCCACACCAACTGAGAGGAGAATAAATATA
ACTGAAGCACTGAAACGGTAAAATACGCCAGCACCAAAACCACTGCATGCAATTATAACAAGGC
AAATGACGCCTTCCTGCCAACTTGATGTCCATCTATTGGACGACTCTCTATCTTTTTTATCATT
CAGTCTCAATGCCACAACACAAGCCGCAACAACTGAATACCCAGTCAATGTACCAACAGACAGA
ATATGGGAAAGACTATGTACATTAAATATGCCAGCTAAAACGCCAGCTACAATGCCGCACCAGA
TTTGAGAATGAAGAGGTGTATGAAGAGTTGGGTGTATTCTGGAAAAGATTGAAGGCAATAGACC
ATCCCTTCCAAGTCCCAGATATAACCTGGACTGAACATAAAGACCAACAAGCAGAGTAGTTGTG
AGTCCAGCAACAGCACCAATACTGATTAAGATTGAGACGAACTTCATACCCTTTGATGAAAAGG
CTTCAGCTAAAGGAGCATCTTCGCTGAGGAGGCTAAAAGGGACCATCCCGGTGAGCACCAAACA
TACGCCAATATACAGCGAGATACAAACCAGAAGGCTCCCCATAATTCCGATTGGCAAATCGCG
						
						Genomic sequence
						
							TTGGCGATAATGAAGAACTGCTGAAGCAACAACTGCCACACCAACTGAGAGGAGAATAAATATA
ACTGAAGCACTGAAACGGTAAAATACGCCAGCACCAAAACCACTGCATGCAATTATAACAAGGC
AAATGACGCCTTCCTGCCAACTTGATGTCCATCTATTGGACGACTCTCTATCTTTTTTATCATT
CAGTCTCAATGCCACAACACAAGCCGCAACAACTGAATACCCAGTCTGAAGAAATGGAACACCG
AAAATAATGTTAAACTGGAAAGTATAAGTATCAATAAGAAAAGCAAAGAGATATTTAAAATTAA
GACCTTGACGTACCAATGTACCAACAGACAGAATATGGGAAAGACTATGTACATTAAATATGCC
AGCTAAAACGCCAGCTACAATGCCGCACCAGATTTGAGAATGAAGAGGTGTATGAAGAGTTGGG
TGTATTCTGGAAAAGATTGAAGGCAATAGACCATCCCTTCCAAGTCCCAGATATAACCTGGACT
GTTTATCCGAAATATCATATGATTACTCAAGAGTGTTACCTTGGTTTGCATAATATACAAGTAC
ATAATAAAAGAAATTACAAAAGAAATACATATATATATATTATCACCTGAACATAAAGACCAAC
AAGCAGAGTAGTTGTGAGTCCAGCAACAGCACCAATACTGATTAAGATTGAGACGAACTTCATA
CCCTTTGATGAAAAGGCTTCAGCTAAAGGAGCATCTTCGCTGAGGAGGCTAAAAGGGACCATCC
CGGTGAGCACCAAACATACGCCAATATACAGCGAGATACAAACCAGAAGGCTCCCCATAATTCC
GATTGGCAAATCGCG

Sequences
Splice junction sequence	GGAGGCTAAAAGGGACCATCCCGGTGAGCACCAAACATACGCCAATATACAGCGAGATACAAAC CAGAAGGCTCCCCATAATTCCGATTGGCAAATCGCGttggcgataatgaagaactgctgaagca acaactgccacaccaactgagaggagaataaatataactgaagcactgaaacggtaaaatacgc cagcacca
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: 639 Transcript exons: 1802024-1802260,1802357-1802533,1802646-1802870 TTGGCGATAATGAAGAACTGCTGAAGCAACAACTGCCACACCAACTGAGAGGAGAATAAATATA ACTGAAGCACTGAAACGGTAAAATACGCCAGCACCAAAACCACTGCATGCAATTATAACAAGGC AAATGACGCCTTCCTGCCAACTTGATGTCCATCTATTGGACGACTCTCTATCTTTTTTATCATT CAGTCTCAATGCCACAACACAAGCCGCAACAACTGAATACCCAGTCAATGTACCAACAGACAGA ATATGGGAAAGACTATGTACATTAAATATGCCAGCTAAAACGCCAGCTACAATGCCGCACCAGA TTTGAGAATGAAGAGGTGTATGAAGAGTTGGGTGTATTCTGGAAAAGATTGAAGGCAATAGACC ATCCCTTCCAAGTCCCAGATATAACCTGGACTGAACATAAAGACCAACAAGCAGAGTAGTTGTG AGTCCAGCAACAGCACCAATACTGATTAAGATTGAGACGAACTTCATACCCTTTGATGAAAAGG CTTCAGCTAAAGGAGCATCTTCGCTGAGGAGGCTAAAAGGGACCATCCCGGTGAGCACCAAACA TACGCCAATATACAGCGAGATACAAACCAGAAGGCTCCCCATAATTCCGATTGGCAAATCGCG
Genomic sequence	TTGGCGATAATGAAGAACTGCTGAAGCAACAACTGCCACACCAACTGAGAGGAGAATAAATATA ACTGAAGCACTGAAACGGTAAAATACGCCAGCACCAAAACCACTGCATGCAATTATAACAAGGC AAATGACGCCTTCCTGCCAACTTGATGTCCATCTATTGGACGACTCTCTATCTTTTTTATCATT CAGTCTCAATGCCACAACACAAGCCGCAACAACTGAATACCCAGTCTGAAGAAATGGAACACCG AAAATAATGTTAAACTGGAAAGTATAAGTATCAATAAGAAAAGCAAAGAGATATTTAAAATTAA GACCTTGACGTACCAATGTACCAACAGACAGAATATGGGAAAGACTATGTACATTAAATATGCC AGCTAAAACGCCAGCTACAATGCCGCACCAGATTTGAGAATGAAGAGGTGTATGAAGAGTTGGG TGTATTCTGGAAAAGATTGAAGGCAATAGACCATCCCTTCCAAGTCCCAGATATAACCTGGACT GTTTATCCGAAATATCATATGATTACTCAAGAGTGTTACCTTGGTTTGCATAATATACAAGTAC ATAATAAAAGAAATTACAAAAGAAATACATATATATATATTATCACCTGAACATAAAGACCAAC AAGCAGAGTAGTTGTGAGTCCAGCAACAGCACCAATACTGATTAAGATTGAGACGAACTTCATA CCCTTTGATGAAAAGGCTTCAGCTAAAGGAGCATCTTCGCTGAGGAGGCTAAAAGGGACCATCC CGGTGAGCACCAAACATACGCCAATATACAGCGAGATACAAACCAGAAGGCTCCCCATAATTCC GATTGGCAAATCGCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.245576995

Conservation Information
Conserved circRNAs	NA
PMCS	0.245576995

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1802850-1802026(-)
						
						Potential amino acid sequence
						
							MGSLLVCISLYIGVCLVLTGMVPFSLLSEDAPLAEAFSSKGMKFVSILISIGAVAGLTTTLLVG
LYVQSRLYLGLGRDGLLPSIFSRIHPTLHTPLHSQIWCGIVAGVLAGIFNVHSLSHILSVGTLT
GYSVVAACVVALRLNDKKDRESSNRWTSSWQEGVICLVIIACSGFGAGVFYRFSASVIFILLSV
GVAVVASAVLHYRQRDLPIGIMGSLLVCISLYIGVCLVLTGMVPFSLLSEDAPLAEAFSSKGMK
FVSILISIGAVAGLTTTLLVGLYVQSRLYLGLGRDGLLPSIFSRIHPTLHTPLHSQIWCGIVAG
VLAGIFNVHSLSHILSVGTLTGYSVVAACVVALRLNDKKDRESSNRWTSSWQEGVICLVIIACS
GFGAGVFYRFSASVIFILLSVGVAVVASAVLHYRQRDLPIGIMGSLLVCISLYIGVCLVLTGMV
PFSLLSEDAPLAEAFSSKGMKFVSILISIGAVAGLTTTLLVGLYVQSRLYLGLGRDGLLPSIFS
RIHPTLHTPLHSQIWCGIVAGVLAGIFNVHSLSHILSVGTLTGYSVVAACVVALRLNDKKDRES
SNRWTSSWQEGVICLVIIACSGFGAGVFYRFSASVIFILLSVGVAVVASAVLHYRQRDLPIGIM
GSLLVCISLYIGVCLVLTGMVPFSLLSEDAPLAEAFSSKGMKFVSILISIGAVAGLTTTLLVGL
YVQSRLYLGLGRDGLLPSIFSRIHPTLHTPLHSQIWCGIVAGVLAGIFNVHSLSHILSVGTLTG
YSVVAACVVALRLNDKKDRESSNRWTSSWQEGVICLVIIACSGFGAGVFYRFSASVIFILLSVG
VAVVASAVLHYRQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1802850-1802026(-)
Potential amino acid sequence	MGSLLVCISLYIGVCLVLTGMVPFSLLSEDAPLAEAFSSKGMKFVSILISIGAVAGLTTTLLVG LYVQSRLYLGLGRDGLLPSIFSRIHPTLHTPLHSQIWCGIVAGVLAGIFNVHSLSHILSVGTLT GYSVVAACVVALRLNDKKDRESSNRWTSSWQEGVICLVIIACSGFGAGVFYRFSASVIFILLSV GVAVVASAVLHYRQRDLPIGIMGSLLVCISLYIGVCLVLTGMVPFSLLSEDAPLAEAFSSKGMK FVSILISIGAVAGLTTTLLVGLYVQSRLYLGLGRDGLLPSIFSRIHPTLHTPLHSQIWCGIVAG VLAGIFNVHSLSHILSVGTLTGYSVVAACVVALRLNDKKDRESSNRWTSSWQEGVICLVIIACS GFGAGVFYRFSASVIFILLSVGVAVVASAVLHYRQRDLPIGIMGSLLVCISLYIGVCLVLTGMV PFSLLSEDAPLAEAFSSKGMKFVSILISIGAVAGLTTTLLVGLYVQSRLYLGLGRDGLLPSIFS RIHPTLHTPLHSQIWCGIVAGVLAGIFNVHSLSHILSVGTLTGYSVVAACVVALRLNDKKDRES SNRWTSSWQEGVICLVIIACSGFGAGVFYRFSASVIFILLSVGVAVVASAVLHYRQRDLPIGIM GSLLVCISLYIGVCLVLTGMVPFSLLSEDAPLAEAFSSKGMKFVSILISIGAVAGLTTTLLVGL YVQSRLYLGLGRDGLLPSIFSRIHPTLHTPLHSQIWCGIVAGVLAGIFNVHSLSHILSVGTLTG YSVVAACVVALRLNDKKDRESSNRWTSSWQEGVICLVIIACSGFGAGVFYRFSASVIFILLSVG VAVVASAVLHYRQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Pan et al., 2017

circRNA

Detail information of AT1G05940_circ_g.1

Address

Any questions?

Supported by