Plant Circular RNA Database

Detail information of AT1G53730_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT1G53730_circ_g.4
					
						ID in PlantcircBase
						ath_circ_007202
					
						Alias
						At_ciR3128
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 20062464-20063155  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ, CIRI-full
					
						Parent gene
						
							AT1G53730						
					
						Parent gene annotation
						
							STRUBBELIG-receptor family 6
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G53730_circ_g.1 AT1G53730_circ_g.2 AT1G53730_circ_g.3 AT1G53730_circ_g.5 AT1G53730_circ_g.6 AT1G53730_circ_g.7 AT1G53730_circ_g.8 AT1G53730_circ_g.9 AT1G53730_circ_g.10 AT1G53730_circ_g.11 AT1G53730_circ_g.12 AT1G53730_circ_g.13 AT1G53730_circ_g.14 AT1G53730_circ_g.15 AT1G53730_circ_g.16 						
					
						Support reads
						2/6
					
						Tissues
						leaf/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  
						
							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
						AT1G53730.2:5
AT1G53730.1:5

General Information
CircRNA Name	AT1G53730_circ_g.4
ID in PlantcircBase	ath_circ_007202
Alias	At_ciR3128
Organism	Arabidpsis thaliana
Position	chr1: 20062464-20063155 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ, CIRI-full
Parent gene	AT1G53730
Parent gene annotation	STRUBBELIG-receptor family 6
Parent gene strand	+
Alternative splicing	AT1G53730_circ_g.1 AT1G53730_circ_g.2 AT1G53730_circ_g.3 AT1G53730_circ_g.5 AT1G53730_circ_g.6 AT1G53730_circ_g.7 AT1G53730_circ_g.8 AT1G53730_circ_g.9 AT1G53730_circ_g.10 AT1G53730_circ_g.11 AT1G53730_circ_g.12 AT1G53730_circ_g.13 AT1G53730_circ_g.14 AT1G53730_circ_g.15 AT1G53730_circ_g.16
Support reads	2/6
Tissues	leaf/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	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	AT1G53730.2:5 AT1G53730.1:5

			
						 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  
						
							ATATTTGACAAGATTACATGTGTTTCAGGGACTTCTCTTTCAATTCTTTCACGAACTCTTTACC
GGCAACGTTTTCCTCTCTAACAAGTTTAAAATCACTaaagttgtcaggtcttgagctctctgga
actcttggaggatacatgcttgataaattgacttctcttaccgagctgtaagatcaccctctgt
ctaatcct

									
								

					

						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: 357
Transcript exons: 20062464-20062538,20062636-20062701,20062782-20062853,20
062940-20063011,20063084-20063155
AAAGTTGTCAGGTCTTGAGCTCTCTGGAACTCTTGGAGGATACATGCTTGATAAATTGACTTCT
CTTACCGAGCTTGATCTAAGCAGCAATAATCTTGGAGGTGATTTACCATATCAGTTTCCTCCAA
ATCTGCAACGATTGAACCTTGCGAATAATCAATTCACTGGAGCTGCTTCGTACTCACTTTCTCA
GATTACACCACTTAAGTATCTCAATCTTGGTCACAATCAGTTTAAGGGGCAGATAGCTATCGAC
TTCTCCAAGCTCGACTCTCTCACAACCTTGGACTTCTCTTTCAATTCTTTCACGAACTCTTTAC
CGGCAACGTTTTCCTCTCTAACAAGTTTAAAATCACT
Transcript length: 291
Transcript exons: 20062464-20063155
AAAGTTGTCAGGTCTTGAGCTCTCTGGAACTCTTGGAGGATACATGCTTGATAAATTGACTTCT
CTTACCGAGCTGAACCTTGCGAATAATCAATTCACTGGAGCTGCTTCGTACTCACTTTCTCAGA
TTACACCACTTAAGTATCTCAATCTTGGTCACAATCAGTTTAAGGGGCAGATAGCTATCGACTT
CTCCAAGCTCGACTCTCTCACAACCTTGGACTTCTCTTTCAATTCTTTCACGAACTCTTTACCG
GCAACGTTTTCCTCTCTAACAAGTTTAAAATCACT
						
					

						Genomic sequence
						
							AAAGTTGTCAGGTCTTGAGCTCTCTGGAACTCTTGGAGGATACATGCTTGATAAATTGACTTCT
CTTACCGAGCTGTAAGATCACCCTCTGTCTAATCCTCCAAACTATTACTTGAAGTCGTGTTTAG
AGATAATGAGTTTTCTAATTTGTAATCTTTGATGGAACTTGCAGTGATCTAAGCAGCAATAATC
TTGGAGGTGATTTACCATATCAGTTTCCTCCAAATCTGCAACGATTGTACGGTCCATCAATTCT
CCTTTGTTTTGGTTTCTAATGTAATATCTGTGCTCTCGAGTTTATAACCGTCGGTGTTTCAGGA
ACCTTGCGAATAATCAATTCACTGGAGCTGCTTCGTACTCACTTTCTCAGATTACACCACTTAA
GTATCTGTAAGTAATTGCCTTACTTCACATTTCTCTCGAAATCTCTCATAAAGATGTGAATATT
AATGTTTTGTCTTGTGCAAACAATTCAGCAATCTTGGTCACAATCAGTTTAAGGGGCAGATAGC
TATCGACTTCTCCAAGCTCGACTCTCTCACAACCTTGTAAGATCTTAGTAAAGATACTCAAGGG
TTTTTATCACATTAAGATATTTGACAAGATTACATGTGTTTCAGGGACTTCTCTTTCAATTCTT
TCACGAACTCTTTACCGGCAACGTTTTCCTCTCTAACAAGTTTAAAATCACT
						
					

			
		

Sequences
Splice junction sequence	ATATTTGACAAGATTACATGTGTTTCAGGGACTTCTCTTTCAATTCTTTCACGAACTCTTTACC GGCAACGTTTTCCTCTCTAACAAGTTTAAAATCACTaaagttgtcaggtcttgagctctctgga actcttggaggatacatgcttgataaattgacttctcttaccgagctgtaagatcaccctctgt ctaatcct
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: 357 Transcript exons: 20062464-20062538,20062636-20062701,20062782-20062853,20 062940-20063011,20063084-20063155 AAAGTTGTCAGGTCTTGAGCTCTCTGGAACTCTTGGAGGATACATGCTTGATAAATTGACTTCT CTTACCGAGCTTGATCTAAGCAGCAATAATCTTGGAGGTGATTTACCATATCAGTTTCCTCCAA ATCTGCAACGATTGAACCTTGCGAATAATCAATTCACTGGAGCTGCTTCGTACTCACTTTCTCA GATTACACCACTTAAGTATCTCAATCTTGGTCACAATCAGTTTAAGGGGCAGATAGCTATCGAC TTCTCCAAGCTCGACTCTCTCACAACCTTGGACTTCTCTTTCAATTCTTTCACGAACTCTTTAC CGGCAACGTTTTCCTCTCTAACAAGTTTAAAATCACT Transcript length: 291 Transcript exons: 20062464-20063155 AAAGTTGTCAGGTCTTGAGCTCTCTGGAACTCTTGGAGGATACATGCTTGATAAATTGACTTCT CTTACCGAGCTGAACCTTGCGAATAATCAATTCACTGGAGCTGCTTCGTACTCACTTTCTCAGA TTACACCACTTAAGTATCTCAATCTTGGTCACAATCAGTTTAAGGGGCAGATAGCTATCGACTT CTCCAAGCTCGACTCTCTCACAACCTTGGACTTCTCTTTCAATTCTTTCACGAACTCTTTACCG GCAACGTTTTCCTCTCTAACAAGTTTAAAATCACT
Genomic sequence	AAAGTTGTCAGGTCTTGAGCTCTCTGGAACTCTTGGAGGATACATGCTTGATAAATTGACTTCT CTTACCGAGCTGTAAGATCACCCTCTGTCTAATCCTCCAAACTATTACTTGAAGTCGTGTTTAG AGATAATGAGTTTTCTAATTTGTAATCTTTGATGGAACTTGCAGTGATCTAAGCAGCAATAATC TTGGAGGTGATTTACCATATCAGTTTCCTCCAAATCTGCAACGATTGTACGGTCCATCAATTCT CCTTTGTTTTGGTTTCTAATGTAATATCTGTGCTCTCGAGTTTATAACCGTCGGTGTTTCAGGA ACCTTGCGAATAATCAATTCACTGGAGCTGCTTCGTACTCACTTTCTCAGATTACACCACTTAA GTATCTGTAAGTAATTGCCTTACTTCACATTTCTCTCGAAATCTCTCATAAAGATGTGAATATT AATGTTTTGTCTTGTGCAAACAATTCAGCAATCTTGGTCACAATCAGTTTAAGGGGCAGATAGC TATCGACTTCTCCAAGCTCGACTCTCTCACAACCTTGTAAGATCTTAGTAAAGATACTCAAGGG TTTTTATCACATTAAGATATTTGACAAGATTACATGTGTTTCAGGGACTTCTCTTTCAATTCTT TCACGAACTCTTTACCGGCAACGTTTTCCTCTCTAACAAGTTTAAAATCACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.22074889

Conservation Information
Conserved circRNAs	NA
PMCS	0.22074889

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20062507-20063152(+)
						
						Potential amino acid sequence
						
							MLDKLTSLTELDLSSNNLGGDLPYQFPPNLQRLNLANNQFTGAASYSLSQITPLKYLNLGHNQF
KGQIAIDFSKLDSLTTLDFSFNSFTNSLPATFSSLTSLKSLKLSGLELSGTLGGYMLDKLTSLT
ELDLSSNNLGGDLPYQFPPNLQRLNLANNQFTGAASYSLSQITPLKYLNLGHNQFKGQIAIDFS
KLDSLTTLDFSFNSFTNSLPATFSSLTSLKSLKLSGLELSGTLGGYMLDKLTSLTELDLSSNNL
GGDLPYQFPPNLQRLNLANNQFTGAASYSLSQITPLKYLNLGHNQFKGQIAIDFSKLDSLTTLD
FSFNSFTNSLPATFSSLTSLKSLKLSGLELSGTLGGYMLDKLTSLTELDLSSNNLGGDLPYQFP
PNLQRLNLANNQFTGAASYSLSQITPLKYLNLGHNQFKGQIAIDFSKLDSLTTLDFSFNSFTNS
LPATFSSLTSLKS(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to heat stress

Functional Information
Coding potential	Y
Potential coding position	20062507-20063152(+)
Potential amino acid sequence	MLDKLTSLTELDLSSNNLGGDLPYQFPPNLQRLNLANNQFTGAASYSLSQITPLKYLNLGHNQF KGQIAIDFSKLDSLTTLDFSFNSFTNSLPATFSSLTSLKSLKLSGLELSGTLGGYMLDKLTSLT ELDLSSNNLGGDLPYQFPPNLQRLNLANNQFTGAASYSLSQITPLKYLNLGHNQFKGQIAIDFS KLDSLTTLDFSFNSFTNSLPATFSSLTSLKSLKLSGLELSGTLGGYMLDKLTSLTELDLSSNNL GGDLPYQFPPNLQRLNLANNQFTGAASYSLSQITPLKYLNLGHNQFKGQIAIDFSKLDSLTTLD FSFNSFTNSLPATFSSLTSLKSLKLSGLELSGTLGGYMLDKLTSLTELDLSSNNLGGDLPYQFP PNLQRLNLANNQFTGAASYSLSQITPLKYLNLGHNQFKGQIAIDFSKLDSLTTLDFSFNSFTNS LPATFSSLTSLKS(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to heat stress

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

circRNA

Detail information of AT1G53730_circ_g.4

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