Plant Circular RNA Database

Detail information of AT4G10340_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT4G10340_circ_g.1
					
						ID in PlantcircBase
						ath_circ_030183
					
						Alias
						Chr4:6408172|6409403
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 6408172-6409403  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer; CIRI
					
						Parent gene
						
							AT4G10340						
					
						Parent gene annotation
						
							Chlorophyll a-b binding protein, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G10340_circ_g.2 AT4G10340_circ_g.3 AT4G10340_circ_g.4 AT4G10340_circ_g.5 AT4G10340_circ_g.6 AT4G10340_circ_g.7 AT4G10340_circ_g.8 AT4G10340_circ_g.9 AT4G10340_circ_g.10 AT4G10340_circ_g.11 AT4G10340_circ_g.12 AT4G10340_circ_g.13 AT4G10340_circ_g.14 						
					
						Support reads
						3
					
						Tissues
						seedling
					
						Exon boundary  
						
							No-No							"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-GA							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
						AT4G10340.1:6

General Information
CircRNA Name	AT4G10340_circ_g.1
ID in PlantcircBase	ath_circ_030183
Alias	Chr4:6408172\|6409403
Organism	Arabidpsis thaliana
Position	chr4: 6408172-6409403 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer; CIRI
Parent gene	AT4G10340
Parent gene annotation	Chlorophyll a-b binding protein, chloroplastic
Parent gene strand	+
Alternative splicing	AT4G10340_circ_g.2 AT4G10340_circ_g.3 AT4G10340_circ_g.4 AT4G10340_circ_g.5 AT4G10340_circ_g.6 AT4G10340_circ_g.7 AT4G10340_circ_g.8 AT4G10340_circ_g.9 AT4G10340_circ_g.10 AT4G10340_circ_g.11 AT4G10340_circ_g.12 AT4G10340_circ_g.13 AT4G10340_circ_g.14
Support reads	3
Tissues	seedling
Exon boundary	No-No "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-GA 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	AT4G10340.1:6

			
						 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  
						
							AGGAGCTCTTCTCAAAGTCAAAGAGATCAAGAACGGGAGATTAGCCATGTTTGCGATGCTCGGT
TTCTTTATCCAAGCGTATGTTACCGGAGAAGGTCCTgtaaagcttgaaactttggactaaaaga
atggcgtctttgggtgtgtcggaaatgcttggtactccccttaacttcagggcagtttcaagat
cgtctgct

						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
						
							GTAAAGCTTGAAACTTTGGACTAAAAGAATGGCGTCTTTGGGTGTGTCGGAAATGCTTGGTACT
CCCCTTAACTTCAGGGCAGTTTCAAGATCGTCTGCTCCGTTGGCATCAAGCCCATCCACGTTCA
AGACTGTTGCTCTCTTCTCTAAGAAAAAGCCAGCTCCTGCTAAGTCCAAGGCTGTCTCTGAGAC
TAGCGATGAGCTCGCCAAGTGGTATGGTATGTGTCTTCTAAATCCCTTTTATAATCATTTCTTG
CTCTGTTTCTTTGTGAATGTGTTTGTAATTGTGACTCTTATGCAGGTCCTGACAGGAGAATTTT
CTTGCCTGATGGTCTTTTGGATAGATCAGAGATCCCAGAGTACTTAAACGGTGAAGTTGCTGGA
GAGTAAGACACTTTTTCATGTCTCTCTTTGTATGTATGCCTACTTTTGGATTCTGTGCTTAAGG
TTTATTGGTCTGAATCTGAATTTGCAGTTATGGTTATGACCCATTTGGTCTTGGAAAGAAGCCT
GAGAACTTTGCTAAGTAAGTAGATTCTTTTATCCTAAACCTTTTGTGTTTGCTTTGAGCTATAT
CTATCGAATTTGTCATTAAGATTGGTTCTTTAATGAATGTGGTTGTAGATACCAAGCTTTTGAA
TTGATCCATGCGAGATGGGCTATGTTAGGAGCAGCTGGTTTCATCATTCCTGAAGCTTTAAACA
AATATGGCGCTAACTGTGGCCCTGAAGCTGTCTGGTTTAAGGTTCTTGCCTACGTCTAATCTTT
ATTTACATTCAGACTTAGATTCTTTAGCAAAGCAAGAATGTGTTGATGTGATGAGATGGTTCTT
TTTGGAATACTGATTGCAGACTGGTGCTTTGCTTCTTGATGGAAACACATTGAACTACTTTGGC
AAGAACATCCCTATCAACCTTGTTCTCGCCGTAGTTGCTGAGGTTGTTCTCCTCGGTGGAGCCG
AGTACTACAGAATCACCAACGGATTGGTACATTACTCTCTAGTCTCTACATTTAGCTATTACTC
ATGGGAAAATGACTAAACTTGAAATGCAAATATTTGGTAGGATTTCGAGGACAAGCTACACCCA
GGAGGTCCATTTGATCCTCTAGGCCTTGCTAAGGACCCTGAGCAAGGAGCTCTTCTCAAAGTCA
AAGAGATCAAGAACGGGAGATTAGCCATGTTTGCGATGCTCGGTTTCTTTATCCAAGCGTATGT
TACCGGAGAAGGTCCT

Sequences
Splice junction sequence	AGGAGCTCTTCTCAAAGTCAAAGAGATCAAGAACGGGAGATTAGCCATGTTTGCGATGCTCGGT TTCTTTATCCAAGCGTATGTTACCGGAGAAGGTCCTgtaaagcttgaaactttggactaaaaga atggcgtctttgggtgtgtcggaaatgcttggtactccccttaacttcagggcagtttcaagat cgtctgct
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	GTAAAGCTTGAAACTTTGGACTAAAAGAATGGCGTCTTTGGGTGTGTCGGAAATGCTTGGTACT CCCCTTAACTTCAGGGCAGTTTCAAGATCGTCTGCTCCGTTGGCATCAAGCCCATCCACGTTCA AGACTGTTGCTCTCTTCTCTAAGAAAAAGCCAGCTCCTGCTAAGTCCAAGGCTGTCTCTGAGAC TAGCGATGAGCTCGCCAAGTGGTATGGTATGTGTCTTCTAAATCCCTTTTATAATCATTTCTTG CTCTGTTTCTTTGTGAATGTGTTTGTAATTGTGACTCTTATGCAGGTCCTGACAGGAGAATTTT CTTGCCTGATGGTCTTTTGGATAGATCAGAGATCCCAGAGTACTTAAACGGTGAAGTTGCTGGA GAGTAAGACACTTTTTCATGTCTCTCTTTGTATGTATGCCTACTTTTGGATTCTGTGCTTAAGG TTTATTGGTCTGAATCTGAATTTGCAGTTATGGTTATGACCCATTTGGTCTTGGAAAGAAGCCT GAGAACTTTGCTAAGTAAGTAGATTCTTTTATCCTAAACCTTTTGTGTTTGCTTTGAGCTATAT CTATCGAATTTGTCATTAAGATTGGTTCTTTAATGAATGTGGTTGTAGATACCAAGCTTTTGAA TTGATCCATGCGAGATGGGCTATGTTAGGAGCAGCTGGTTTCATCATTCCTGAAGCTTTAAACA AATATGGCGCTAACTGTGGCCCTGAAGCTGTCTGGTTTAAGGTTCTTGCCTACGTCTAATCTTT ATTTACATTCAGACTTAGATTCTTTAGCAAAGCAAGAATGTGTTGATGTGATGAGATGGTTCTT TTTGGAATACTGATTGCAGACTGGTGCTTTGCTTCTTGATGGAAACACATTGAACTACTTTGGC AAGAACATCCCTATCAACCTTGTTCTCGCCGTAGTTGCTGAGGTTGTTCTCCTCGGTGGAGCCG AGTACTACAGAATCACCAACGGATTGGTACATTACTCTCTAGTCTCTACATTTAGCTATTACTC ATGGGAAAATGACTAAACTTGAAATGCAAATATTTGGTAGGATTTCGAGGACAAGCTACACCCA GGAGGTCCATTTGATCCTCTAGGCCTTGCTAAGGACCCTGAGCAAGGAGCTCTTCTCAAAGTCA AAGAGATCAAGAACGGGAGATTAGCCATGTTTGCGATGCTCGGTTTCTTTATCCAAGCGTATGT TACCGGAGAAGGTCCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.200309232

Conservation Information
Conserved circRNAs	NA
PMCS	0.200309232

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to methyl jasmonate

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to methyl jasmonate

			
						 Other Information
					
						References
						Zhang et al., 2020

circRNA

Detail information of AT4G10340_circ_g.1

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