Plant Circular RNA Database

Detail information of AT1G48240_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT1G48240_circ_g.1
					
						ID in PlantcircBase
						ath_circ_006271
					
						Alias
						1:17809198-17811378
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 17809198-17811378  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G48240						
					
						Parent gene annotation
						
							Novel plant SNARE 12
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G48240_circ_g.2 AT1G48240_circ_g.3 AT1G48240_circ_g.4 AT1G48240_circ_g.5 AT1G48240_circ_g.6 AT1G48240_circ_g.7 AT1G48240_circ_g.8 						
					
						Support reads
						1/2
					
						Tissues
						seedling;root
					
						Exon boundary  
						
							No-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
						AT1G48240.2:9
AT1G48240.1:9

General Information
CircRNA Name	AT1G48240_circ_g.1
ID in PlantcircBase	ath_circ_006271
Alias	1:17809198-17811378
Organism	Arabidpsis thaliana
Position	chr1: 17809198-17811378 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G48240
Parent gene annotation	Novel plant SNARE 12
Parent gene strand	-
Alternative splicing	AT1G48240_circ_g.2 AT1G48240_circ_g.3 AT1G48240_circ_g.4 AT1G48240_circ_g.5 AT1G48240_circ_g.6 AT1G48240_circ_g.7 AT1G48240_circ_g.8
Support reads	1/2
Tissues	seedling;root
Exon boundary	No-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	AT1G48240.2:9 AT1G48240.1:9

			
						 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  
						
							TGAATACCTTTTACAGTCTCTCATCTTCTCAGCAAGTTCTTCGAGTTGCTTGCTTTGTCTACTA
GAATCCTTGATCTTATCCAACCTCTGGAAGCCATTCcttccctctcggccctgccaaaaggcta
ttctctgaagtacaagagctttctcgattgcgctggaggagctagtccagggatgtctctgatg
tctttgtt

									
								

					

						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
						
							CTTCCCTCTCGGCCCTGCCAAAAGGCTATTCTCTGAAGTACAAGAGCTTTCTCGATTGCGCTGG
AGGAGCTAGTCCAGGGATGTCTCTGATGTCTTTGTTGTTTGGGTTCACGATCTGTGTTTTTATT
TAAGCAGTGTTAAAACTTGCTTAAGGAATCATAGCTTTATTTGGGCCGTAATGAGAAAAGTTGG
AGAGTGCAATGGTTACCTTCACAATGATTATAGCTATAACACCACAGACAATCAGAAACAGGAA
CGCCATTATGCATTTATCTGTAGCTACCTGTGACAAGAAAGAATTGAGGTTGAAAGGAAACGGT
GATAATAGTTAGACACAATTTTAGCTTTTGCAGTGTCTTAGAATCTTATGTCCTGTGAGAGATC
ATACAAACCTGTCTTCCTATCTCTTTCACCAGCTGCGAAGCTTTCTTAAGAGAGAACTGAATTG
TGTCTAGGTCGTTTACAACGCGGCCCATTTGATCCGTCTGAAAATATTTAGGTCAGCATATTTG
GAACTACACCTGATAAGAATATCGAGAAGAGATGGTGAATGCTTTGTGTTACCTGTCCCTTTAA
GTTAGATGCAGTTTGAGTGCCAACTTCGAGTGTCTGATGCACAACCTGGAAAGAAACACTGGAT
GTTACTAGAGACATAGCATCAAAGACTGAGTGAGATATACTTCTTTCTGTAACTTACCTGTTTA
GAACGTTCAATAGCCTGGTCAGTCTCGTCCATCCTTTTCATTCCAGCATCGACAAGCTCTTGGT
TTGACATTGCTACATATATATAAACGATAAAACAAGAGTCAACATAAAGTTCCACACTTTTTCC
ACAGGATAGTTCAAGGACAATTATTCTTGGAACACATGTAGATATTAGAAATCCAGCCACATAT
GATCCTCCACTAGAAATTTACTAACATCAAACCACCAACATAAACACATTAAAAGGTAAAGTAG
GTAAACAGTTACTGTCATATATGTCTCTCCACTAGAAACTTACTGAAACACATCAAATGATACC
AAACCATTAGCCAAAAGTGCAGGACTAACTATCCTACCCATTCTGATATATAGAAAACAGTTTA
AGCTTCCAATGTGTCAAATTTTGGACTTTTTCTGGTTGCAGAAGAAAATCAACTGAATAGATGA
CATATTTAGACAGACTCACTTGAAGCCATTTGGACGTTTTCTTCAGCTGTGGGTTCACCGCTGA
CTCCAGCTCCAGTATCAAAAAGTTCAACTTTCTTGTTGCCGAGTGTATTCAAGTACCTGAAGTC
ACACAACAAATGGGAATGTATTAACACATACCGATCTATATCTCTATATAAAAAAACATACATT
TGCTAAAAGGATTGGTATATGAGAAAATCAAATATAGGGACAGACAATGAAGCTCCTTGGAAGT
AGACGTACTTACGTTTTTCTTAGTGCAACATAAGAGTTGAGTTCCTTAATCTGTCACATAAATC
ACTGGAAATATCAACAAGCAGATTTTGAAAAGACATAACAACCAGATGCTAGCGAGAAATTAAG
GTAGATAAATCGAGAGATTCACACAAAAACACTCAGAATCTACATTGATATACCACTGAATCAA
CATGCTTTTCGATGGTGACCCAAAACTCAAGTGAGGCGAGAAAGCTGAACTTTATATTCCAATA
CTAACTTCAGAAATATCACACTAACACGAAGCTTAAAAAGTATCATGTCCTCCATAGATTTCAT
CAACACACAGATTATTATAAGTAATAAGAAGTAAACTCACCATAGATTGTTTCTCATCATTCAA
TTGCTTATTTACTTGAGGAGAATTTCGAGCTTCCCCATCTTTGAGTTCACGATCAAACTCCTTA
ACCAACCTAACGTGAAGCGCAGAGATTTAAAAATCGTTGATCACCAAAAAAAACTCTTTCCTAC
TCATGATTACACATCTCATCCATCTCAAATAATACATTTTCCCACAATGCAAAAACATAATCAC
CAATAGACTTACAACATTTTAGTTCTCATGAAAAATTCAATCCCTCATCTAACACCGGAAAGTT
CGAGTAGTAAAAAAACTGATATCTTGGAGAAAGTGAATACCTTTTACAGTCTCTCATCTTCTCA
GCAAGTTCTTCGAGTTGCTTGCTTTGTCTACTAGAATCCTTGATCTTATCCAACCTCTGGAAGC
CATTC
						
					

			
		

Sequences
Splice junction sequence	TGAATACCTTTTACAGTCTCTCATCTTCTCAGCAAGTTCTTCGAGTTGCTTGCTTTGTCTACTA GAATCCTTGATCTTATCCAACCTCTGGAAGCCATTCcttccctctcggccctgccaaaaggcta ttctctgaagtacaagagctttctcgattgcgctggaggagctagtccagggatgtctctgatg tctttgtt
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	CTTCCCTCTCGGCCCTGCCAAAAGGCTATTCTCTGAAGTACAAGAGCTTTCTCGATTGCGCTGG AGGAGCTAGTCCAGGGATGTCTCTGATGTCTTTGTTGTTTGGGTTCACGATCTGTGTTTTTATT TAAGCAGTGTTAAAACTTGCTTAAGGAATCATAGCTTTATTTGGGCCGTAATGAGAAAAGTTGG AGAGTGCAATGGTTACCTTCACAATGATTATAGCTATAACACCACAGACAATCAGAAACAGGAA CGCCATTATGCATTTATCTGTAGCTACCTGTGACAAGAAAGAATTGAGGTTGAAAGGAAACGGT GATAATAGTTAGACACAATTTTAGCTTTTGCAGTGTCTTAGAATCTTATGTCCTGTGAGAGATC ATACAAACCTGTCTTCCTATCTCTTTCACCAGCTGCGAAGCTTTCTTAAGAGAGAACTGAATTG TGTCTAGGTCGTTTACAACGCGGCCCATTTGATCCGTCTGAAAATATTTAGGTCAGCATATTTG GAACTACACCTGATAAGAATATCGAGAAGAGATGGTGAATGCTTTGTGTTACCTGTCCCTTTAA GTTAGATGCAGTTTGAGTGCCAACTTCGAGTGTCTGATGCACAACCTGGAAAGAAACACTGGAT GTTACTAGAGACATAGCATCAAAGACTGAGTGAGATATACTTCTTTCTGTAACTTACCTGTTTA GAACGTTCAATAGCCTGGTCAGTCTCGTCCATCCTTTTCATTCCAGCATCGACAAGCTCTTGGT TTGACATTGCTACATATATATAAACGATAAAACAAGAGTCAACATAAAGTTCCACACTTTTTCC ACAGGATAGTTCAAGGACAATTATTCTTGGAACACATGTAGATATTAGAAATCCAGCCACATAT GATCCTCCACTAGAAATTTACTAACATCAAACCACCAACATAAACACATTAAAAGGTAAAGTAG GTAAACAGTTACTGTCATATATGTCTCTCCACTAGAAACTTACTGAAACACATCAAATGATACC AAACCATTAGCCAAAAGTGCAGGACTAACTATCCTACCCATTCTGATATATAGAAAACAGTTTA AGCTTCCAATGTGTCAAATTTTGGACTTTTTCTGGTTGCAGAAGAAAATCAACTGAATAGATGA CATATTTAGACAGACTCACTTGAAGCCATTTGGACGTTTTCTTCAGCTGTGGGTTCACCGCTGA CTCCAGCTCCAGTATCAAAAAGTTCAACTTTCTTGTTGCCGAGTGTATTCAAGTACCTGAAGTC ACACAACAAATGGGAATGTATTAACACATACCGATCTATATCTCTATATAAAAAAACATACATT TGCTAAAAGGATTGGTATATGAGAAAATCAAATATAGGGACAGACAATGAAGCTCCTTGGAAGT AGACGTACTTACGTTTTTCTTAGTGCAACATAAGAGTTGAGTTCCTTAATCTGTCACATAAATC ACTGGAAATATCAACAAGCAGATTTTGAAAAGACATAACAACCAGATGCTAGCGAGAAATTAAG GTAGATAAATCGAGAGATTCACACAAAAACACTCAGAATCTACATTGATATACCACTGAATCAA CATGCTTTTCGATGGTGACCCAAAACTCAAGTGAGGCGAGAAAGCTGAACTTTATATTCCAATA CTAACTTCAGAAATATCACACTAACACGAAGCTTAAAAAGTATCATGTCCTCCATAGATTTCAT CAACACACAGATTATTATAAGTAATAAGAAGTAAACTCACCATAGATTGTTTCTCATCATTCAA TTGCTTATTTACTTGAGGAGAATTTCGAGCTTCCCCATCTTTGAGTTCACGATCAAACTCCTTA ACCAACCTAACGTGAAGCGCAGAGATTTAAAAATCGTTGATCACCAAAAAAAACTCTTTCCTAC TCATGATTACACATCTCATCCATCTCAAATAATACATTTTCCCACAATGCAAAAACATAATCAC CAATAGACTTACAACATTTTAGTTCTCATGAAAAATTCAATCCCTCATCTAACACCGGAAAGTT CGAGTAGTAAAAAAACTGATATCTTGGAGAAAGTGAATACCTTTTACAGTCTCTCATCTTCTCA GCAAGTTCTTCGAGTTGCTTGCTTTGTCTACTAGAATCCTTGATCTTATCCAACCTCTGGAAGC CATTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.112866418

Conservation Information
Conserved circRNAs	NA
PMCS	0.112866418

			
						 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
						NA

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	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT1G48240_circ_g.1

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