Plant Circular RNA Database

Detail information of AT4G17730_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G17730_circ_g.3
					
						ID in PlantcircBase
						ath_circ_031489
					
						Alias
						At_ciR3350, Ath_circ_FC2685, AT4G17730_C2
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 9866028-9866524  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT4G17730						
					
						Parent gene annotation
						
							AT4G17730 protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G17730_circ_g.1 AT4G17730_circ_g.2 						
					
						Support reads
						2/3
					
						Tissues
						leaf/root, aerial, 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
						AT4G17730.2:3
AT4G17730.1:3

General Information
CircRNA Name	AT4G17730_circ_g.3
ID in PlantcircBase	ath_circ_031489
Alias	At_ciR3350, Ath_circ_FC2685, AT4G17730_C2
Organism	Arabidpsis thaliana
Position	chr4: 9866028-9866524 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, find_circ, CIRI-full, CIRI2
Parent gene	AT4G17730
Parent gene annotation	AT4G17730 protein
Parent gene strand	+
Alternative splicing	AT4G17730_circ_g.1 AT4G17730_circ_g.2
Support reads	2/3
Tissues	leaf/root, aerial, 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	AT4G17730.2:3 AT4G17730.1:3

			
						 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  
						
							ATGATATTGGTACTCACATCGATAACTCTTACGCTGCAACTGCCCAAGGAAAATCCCATCTCGT
AAGGCATCAAAGACACAAAGATCAAATTCTTCTCTGctacacatccagtgagatagatgtgaat
ggagataagcatccagagcagcgtgcccttcttgtggaatcaaaaaggttagtttatacagaca
atggtgtc

						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: 333
Transcript exons: 9866028-9866102,9866184-9866341,9866425-9866524
CTACACATCCAGTGAGATAGATGTGAATGGAGATAAGCATCCAGAGCAGCGTGCCCTTCTTGTG
GAATCAAAAAGACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTG
AGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAGGTGCACGAGATCTTCAA
AGACTTGGCAGTGTTGGTGCACGATCAAGGAAACATGATAGATGATATTGGTACTCACATCGAT
AACTCTTACGCTGCAACTGCCCAAGGAAAATCCCATCTCGTAAGGCATCAAAGACACAAAGATC
AAATTCTTCTCTG
Transcript length: 416
Transcript exons: 9866028-9866524
CTACACATCCAGTGAGATAGATGTGAATGGAGATAAGCATCCAGAGCAGCGTGCCCTTCTTGTG
GAATCAAAAAGACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTG
AGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAGGTGCACGAGATCTTCAA
AGACTTGGCAGTGTTGGTGCACGATCAAGGAAACATGATAGGTAAAACTGATTCCAACTCTTGT
TATGCTAAAACTCTCACTTATGTCTTCAAAACCTAAGACGTAAGACCTATTTTTGTGTAGATGA
TATTGGTACTCACATCGATAACTCTTACGCTGCAACTGCCCAAGGAAAATCCCATCTCGTAAGG
CATCAAAGACACAAAGATCAAATTCTTCTCTG
						
						Genomic sequence
						
							CTACACATCCAGTGAGATAGATGTGAATGGAGATAAGCATCCAGAGCAGCGTGCCCTTCTTGTG
GAATCAAAAAGGTTAGTTTATACAGACAATGGTGTCCATCTTTGTTCGGTTGATGAGTTATCTA
TTGATTGGTTTGTTGTTTTTTGTTGCAGACAAGAACTTGTACTGTTGGACAATGAGATTGCGTT
CAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
GTGCACGAGATCTTCAAAGACTTGGCAGTGTTGGTGCACGATCAAGGAAACATGATAGGTAAAA
CTGATTCCAACTCTTGTTATGCTAAAACTCTCACTTATGTCTTCAAAACCTAAGACGTAAGACC
TATTTTTGTGTAGATGATATTGGTACTCACATCGATAACTCTTACGCTGCAACTGCCCAAGGAA
AATCCCATCTCGTAAGGCATCAAAGACACAAAGATCAAATTCTTCTCTG

Sequences
Splice junction sequence	ATGATATTGGTACTCACATCGATAACTCTTACGCTGCAACTGCCCAAGGAAAATCCCATCTCGT AAGGCATCAAAGACACAAAGATCAAATTCTTCTCTGctacacatccagtgagatagatgtgaat ggagataagcatccagagcagcgtgcccttcttgtggaatcaaaaaggttagtttatacagaca atggtgtc
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: 333 Transcript exons: 9866028-9866102,9866184-9866341,9866425-9866524 CTACACATCCAGTGAGATAGATGTGAATGGAGATAAGCATCCAGAGCAGCGTGCCCTTCTTGTG GAATCAAAAAGACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTG AGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAGGTGCACGAGATCTTCAA AGACTTGGCAGTGTTGGTGCACGATCAAGGAAACATGATAGATGATATTGGTACTCACATCGAT AACTCTTACGCTGCAACTGCCCAAGGAAAATCCCATCTCGTAAGGCATCAAAGACACAAAGATC AAATTCTTCTCTG Transcript length: 416 Transcript exons: 9866028-9866524 CTACACATCCAGTGAGATAGATGTGAATGGAGATAAGCATCCAGAGCAGCGTGCCCTTCTTGTG GAATCAAAAAGACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTG AGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAGGTGCACGAGATCTTCAA AGACTTGGCAGTGTTGGTGCACGATCAAGGAAACATGATAGGTAAAACTGATTCCAACTCTTGT TATGCTAAAACTCTCACTTATGTCTTCAAAACCTAAGACGTAAGACCTATTTTTGTGTAGATGA TATTGGTACTCACATCGATAACTCTTACGCTGCAACTGCCCAAGGAAAATCCCATCTCGTAAGG CATCAAAGACACAAAGATCAAATTCTTCTCTG
Genomic sequence	CTACACATCCAGTGAGATAGATGTGAATGGAGATAAGCATCCAGAGCAGCGTGCCCTTCTTGTG GAATCAAAAAGGTTAGTTTATACAGACAATGGTGTCCATCTTTGTTCGGTTGATGAGTTATCTA TTGATTGGTTTGTTGTTTTTTGTTGCAGACAAGAACTTGTACTGTTGGACAATGAGATTGCGTT CAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG GTGCACGAGATCTTCAAAGACTTGGCAGTGTTGGTGCACGATCAAGGAAACATGATAGGTAAAA CTGATTCCAACTCTTGTTATGCTAAAACTCTCACTTATGTCTTCAAAACCTAAGACGTAAGACC TATTTTTGTGTAGATGATATTGGTACTCACATCGATAACTCTTACGCTGCAACTGCCCAAGGAA AATCCCATCTCGTAAGGCATCAAAGACACAAAGATCAAATTCTTCTCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.422072918

Conservation Information
Conserved circRNAs	NA
PMCS	0.422072918

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9866335-9866521(+)
						
						Potential amino acid sequence
						
							MIDDIGTHIDNSYAATAQGKSHLVRHQRHKDQILLCYTSSEIDVNGDKHPEQRALLVESKRQEL
VLLDNEIAFNEAVIEEREQGIQEIQQQIGEVHEIFKDLAVLVHDQGNMIDDIGTHIDNSYAATA
QGKSHLVRHQRHKDQILLCYTSSEIDVNGDKHPEQRALLVESKRQELVLLDNEIAFNEAVIEER
EQGIQEIQQQIGEVHEIFKDLAVLVHDQGNMIDDIGTHIDNSYAATAQGKSHLVRHQRHKDQIL
LCYTSSEIDVNGDKHPEQRALLVESKRQELVLLDNEIAFNEAVIEEREQGIQEIQQQIGEVHEI
FKDLAVLVHDQGNMIDDIGTHIDNSYAATAQGKSHLVRHQRHKDQILL(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	9866335-9866521(+)
Potential amino acid sequence	MIDDIGTHIDNSYAATAQGKSHLVRHQRHKDQILLCYTSSEIDVNGDKHPEQRALLVESKRQEL VLLDNEIAFNEAVIEEREQGIQEIQQQIGEVHEIFKDLAVLVHDQGNMIDDIGTHIDNSYAATA QGKSHLVRHQRHKDQILLCYTSSEIDVNGDKHPEQRALLVESKRQELVLLDNEIAFNEAVIEER EQGIQEIQQQIGEVHEIFKDLAVLVHDQGNMIDDIGTHIDNSYAATAQGKSHLVRHQRHKDQIL LCYTSSEIDVNGDKHPEQRALLVESKRQELVLLDNEIAFNEAVIEEREQGIQEIQQQIGEVHEI FKDLAVLVHDQGNMIDDIGTHIDNSYAATAQGKSHLVRHQRHKDQILL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Chen et al., 2017a;Zhang et al., 2019

circRNA

Detail information of AT4G17730_circ_g.3

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