Plant Circular RNA Database

Detail information of AT1G53730_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G53730_circ_g.3
					
						ID in PlantcircBase
						ath_circ_007201
					
						Alias
						At_ciR75, AT1G53730_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 20062464-20063011  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circseq_cup, find_circ, CIRI-full, CIRI2
					
						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.4 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
						102/3/9
					
						Tissues
						leaf/root, aerial, inflorescences, whole_plant/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
						AT1G53730.2:4
AT1G53730.1:4

General Information
CircRNA Name	AT1G53730_circ_g.3
ID in PlantcircBase	ath_circ_007201
Alias	At_ciR75, AT1G53730_C1
Organism	Arabidpsis thaliana
Position	chr1: 20062464-20063011 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circseq_cup, find_circ, CIRI-full, CIRI2
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.4 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	102/3/9
Tissues	leaf/root, aerial, inflorescences, whole_plant/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	AT1G53730.2:4 AT1G53730.1:4

			
						 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  
						
							AATGTTTTGTCTTGTGCAAACAATTCAGCAATCTTGGTCACAATCAGTTTAAGGGGCAGATAGC
TATCGACTTCTCCAAGCTCGACTCTCTCACAACCTTaaagttgtcaggtcttgagctctctgga
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: 285
Transcript exons: 20062464-20062538,20062636-20062701,20062782-20062853,20
062940-20063011
AAAGTTGTCAGGTCTTGAGCTCTCTGGAACTCTTGGAGGATACATGCTTGATAAATTGACTTCT
CTTACCGAGCTTGATCTAAGCAGCAATAATCTTGGAGGTGATTTACCATATCAGTTTCCTCCAA
ATCTGCAACGATTGAACCTTGCGAATAATCAATTCACTGGAGCTGCTTCGTACTCACTTTCTCA
GATTACACCACTTAAGTATCTCAATCTTGGTCACAATCAGTTTAAGGGGCAGATAGCTATCGAC
TTCTCCAAGCTCGACTCTCTCACAACCTT
						
						Genomic sequence
						
							AAAGTTGTCAGGTCTTGAGCTCTCTGGAACTCTTGGAGGATACATGCTTGATAAATTGACTTCT
CTTACCGAGCTGTAAGATCACCCTCTGTCTAATCCTCCAAACTATTACTTGAAGTCGTGTTTAG
AGATAATGAGTTTTCTAATTTGTAATCTTTGATGGAACTTGCAGTGATCTAAGCAGCAATAATC
TTGGAGGTGATTTACCATATCAGTTTCCTCCAAATCTGCAACGATTGTACGGTCCATCAATTCT
CCTTTGTTTTGGTTTCTAATGTAATATCTGTGCTCTCGAGTTTATAACCGTCGGTGTTTCAGGA
ACCTTGCGAATAATCAATTCACTGGAGCTGCTTCGTACTCACTTTCTCAGATTACACCACTTAA
GTATCTGTAAGTAATTGCCTTACTTCACATTTCTCTCGAAATCTCTCATAAAGATGTGAATATT
AATGTTTTGTCTTGTGCAAACAATTCAGCAATCTTGGTCACAATCAGTTTAAGGGGCAGATAGC
TATCGACTTCTCCAAGCTCGACTCTCTCACAACCTT

Sequences
Splice junction sequence	AATGTTTTGTCTTGTGCAAACAATTCAGCAATCTTGGTCACAATCAGTTTAAGGGGCAGATAGC TATCGACTTCTCCAAGCTCGACTCTCTCACAACCTTaaagttgtcaggtcttgagctctctgga 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: 285 Transcript exons: 20062464-20062538,20062636-20062701,20062782-20062853,20 062940-20063011 AAAGTTGTCAGGTCTTGAGCTCTCTGGAACTCTTGGAGGATACATGCTTGATAAATTGACTTCT CTTACCGAGCTTGATCTAAGCAGCAATAATCTTGGAGGTGATTTACCATATCAGTTTCCTCCAA ATCTGCAACGATTGAACCTTGCGAATAATCAATTCACTGGAGCTGCTTCGTACTCACTTTCTCA GATTACACCACTTAAGTATCTCAATCTTGGTCACAATCAGTTTAAGGGGCAGATAGCTATCGAC TTCTCCAAGCTCGACTCTCTCACAACCTT
Genomic sequence	AAAGTTGTCAGGTCTTGAGCTCTCTGGAACTCTTGGAGGATACATGCTTGATAAATTGACTTCT CTTACCGAGCTGTAAGATCACCCTCTGTCTAATCCTCCAAACTATTACTTGAAGTCGTGTTTAG AGATAATGAGTTTTCTAATTTGTAATCTTTGATGGAACTTGCAGTGATCTAAGCAGCAATAATC TTGGAGGTGATTTACCATATCAGTTTCCTCCAAATCTGCAACGATTGTACGGTCCATCAATTCT CCTTTGTTTTGGTTTCTAATGTAATATCTGTGCTCTCGAGTTTATAACCGTCGGTGTTTCAGGA ACCTTGCGAATAATCAATTCACTGGAGCTGCTTCGTACTCACTTTCTCAGATTACACCACTTAA GTATCTGTAAGTAATTGCCTTACTTCACATTTCTCTCGAAATCTCTCATAAAGATGTGAATATT AATGTTTTGTCTTGTGCAAACAATTCAGCAATCTTGGTCACAATCAGTTTAAGGGGCAGATAGC TATCGACTTCTCCAAGCTCGACTCTCTCACAACCTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.284048841

Conservation Information
Conserved circRNAs	NA
PMCS	0.284048841

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20062507-20063008(+)
						
						Potential amino acid sequence
						
							MLDKLTSLTELDLSSNNLGGDLPYQFPPNLQRLNLANNQFTGAASYSLSQITPLKYLNLGHNQF
KGQIAIDFSKLDSLTTLKLSGLELSGTLGGYMLDKLTSLTELDLSSNNLGGDLPYQFPPNLQRL
NLANNQFTGAASYSLSQITPLKYLNLGHNQFKGQIAIDFSKLDSLTTLKLSGLELSGTLGGYML
DKLTSLTELDLSSNNLGGDLPYQFPPNLQRLNLANNQFTGAASYSLSQITPLKYLNLGHNQFKG
QIAIDFSKLDSLTTLKLSGLELSGTLGGYMLDKLTSLTELDLSSNNLGGDLPYQFPPNLQRLNL
ANNQFTGAASYSLSQITPLKYLNLGHNQFKGQIAIDFSKLDSLTT(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	20062507-20063008(+)
Potential amino acid sequence	MLDKLTSLTELDLSSNNLGGDLPYQFPPNLQRLNLANNQFTGAASYSLSQITPLKYLNLGHNQF KGQIAIDFSKLDSLTTLKLSGLELSGTLGGYMLDKLTSLTELDLSSNNLGGDLPYQFPPNLQRL NLANNQFTGAASYSLSQITPLKYLNLGHNQFKGQIAIDFSKLDSLTTLKLSGLELSGTLGGYML DKLTSLTELDLSSNNLGGDLPYQFPPNLQRLNLANNQFTGAASYSLSQITPLKYLNLGHNQFKG QIAIDFSKLDSLTTLKLSGLELSGTLGGYMLDKLTSLTELDLSSNNLGGDLPYQFPPNLQRLNL ANNQFTGAASYSLSQITPLKYLNLGHNQFKGQIAIDFSKLDSLTT(+)
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;Pan et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT1G53730_circ_g.3

Address

Any questions?

Supported by