Plant Circular RNA Database

Detail information of AT3G52180_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G52180_circ_g.1
					
						ID in PlantcircBase
						ath_circ_027122
					
						Alias
						3:19350613-19353327
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 19350613-19353327  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G52180						
					
						Parent gene annotation
						
							SEX4
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G52180_circ_g.2 AT3G52180_circ_g.3 						
					
						Support reads
						1/2
					
						Tissues
						root;leaf
					
						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  
						
							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
						AT3G52180.2:9
AT3G52180.1:9
AT3G52180.4:7
AT3G52180.3:9

General Information
CircRNA Name	AT3G52180_circ_g.1
ID in PlantcircBase	ath_circ_027122
Alias	3:19350613-19353327
Organism	Arabidpsis thaliana
Position	chr3: 19350613-19353327 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G52180
Parent gene annotation	SEX4
Parent gene strand	-
Alternative splicing	AT3G52180_circ_g.2 AT3G52180_circ_g.3
Support reads	1/2
Tissues	root;leaf
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	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	AT3G52180.2:9 AT3G52180.1:9 AT3G52180.4:7 AT3G52180.3:9

			
						 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  
						
							GGCTTTGATCGGAGGCGATATTAGCATCTTCAAAGAAGAAGAAGAAGAAGAATGATCTCTTTGA
ATGCACCCGAATCCCAGCAGAGGTGAGACTGAACATctgtccccatccaatgtcaaggccagaa
atttctactctggagaaccccttatctttcagtgtcagagtaacagtcttcctcttgagtcctg
taagcttt

									
								

					

						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: 814
Transcript exons: 19350613-19350708,19350842-19350898,19351267-19351326,19
351518-19351650,19352298-19352378,19352495-19352571,1935
2666-19352742,19353010-19353112,19353198-19353327
CTGTCCCCATCCAATGTCAAGGCCAGAAATTTCTACTCTGGAGAACCCCTTATCTTTCAGTGTC
AGAGTAACAGTCTTCCTCTTGAGTCCTGTAAGAATATCAATTGTTGCATTTCTGATAGCATCCA
GCTTCGGAAAGCACGACCTTTTGCTCATAAGTAATTTATGAGCTTCCATAAGCTTATAGCCTTG
CACCCAGAACATGTATGTCAACGCAACAGCAGGAGCCCTTCCCATTCCAGCAGTGCAGTGCACA
TATGTAACTCCTCCATTTCGCTTAACAGCTTTGTAAAGAGTACCAACCACGGCTGGAAGACGCA
TTCTCAAATCAAATGCATCAAAGTCTCTAATTTCACAGCGAATATGCTGAATATCACTATATTT
CTTAGCATAGGCTTGGATGCTGCTTATGTCTACTCCAAAATATTCCAGGTCTGGATCTTGTTGC
AAGCAAAATATGGTTTTAACTCCAATTTTACGAAGCTTGTCAACATCTTCAGGGGTCTGTAAGC
AGGATCCAACAATTAGATCTGGACGAATAAAGTTGTAGTTCATTCCTAACTCGTGCCTGTAAGT
TAGAACAGCACCCATAGCTTGAGTCATGTCTTGGCTATATTCATCAGATTTCTCTTCATCCTTT
GCAACACCACTCATCTCTGAGCTGGATTTTGACTCTGATACTGCATGTAAAACAAGTCGAGATT
TTGGATCATTGGCTTTGATCGGAGGCGATATTAGCATCTTCAAAGAAGAAGAAGAAGAAGAATG
ATCTCTTTGAATGCACCCGAATCCCAGCAGAGGTGAGACTGAACAT
						
					

						Genomic sequence
						
							CTGTCCCCATCCAATGTCAAGGCCAGAAATTTCTACTCTGGAGAACCCCTTATCTTTCAGTGTC
AGAGTAACAGTCTTCCTCTTGAGTCCTGTAAGCTTTTATCCATATACACCCGGAAACAATAATC
AGGAGTCAAGGAACCAGGTAACTGTTGCGCACTCATGCTAATCAATGGAACTGAGGTTTTTCAA
ACATAGGAAGCATTGTGAAAGTTGAACGCTGACTCACAATATCAATTGTTGCATTTCTGATAGC
ATCCAGCTTCGGAAAGCACGACCTTTTGCTCTGCAAGAAAATTTCAGAAATGTTATATAAACCA
AATTTACGCGTGCCTTTATGTTTCACCAGCCATCTAGAGATATCAAACTAAAAATGTCTAATGC
TAGACTATTTTGGATGAACTAACCCAAGATTTTTGTCTTTTAAAGTGCTATATCTTCAGTGTAT
ATTTACTACAAACCCCTGACCCAATGGTCTATGATTCTAGTTATCATAATTGTCGGTTCATAGG
AGAAGAAGGAAATCCCCAAACATCCTCACATAATATAACAGGCAGTAACACTAGTAAAACATGA
TTAACATGTTGGTTACTTAATATAAGTATAAAGAAACACATATAGAGAACATAAACCACAAGTA
AATTAGTATCTTACCATAAGTAATTTATGAGCTTCCATAAGCTTATAGCCTTGCACCCAGAACA
TGTATGTCAACTGAAAATGAAATTAATATCCCTTCTCAGTATCAGTCAGCAAAATGTGAAAACT
TGTTCATACCTTCATGAGTCAACCAAATAAGCACAAAATTAAGACAACTACTGTTTGCAACAGT
CTTACATTTTTTCAATACTGGAAAGAAAAGGGGGAAAAAGAGAAGAGCTTAGTAACAGGTTTCT
GTAACATACCGCAACAGCAGGAGCCCTTCCCATTCCAGCAGTGCAGTGCACATATGTAACTCCT
CCATTTCGCTTAACAGCTTTGTAAAGAGTACCAACCACGGCTGGAAGACGCATTCTCAAATCAA
ATGCATCAAAGTCTCTGTTACATCAATGATATATAATATGTCAATCCCCTACGTTGTGAGTGGG
TACGTCCATGGTGAATTTTTCTATGCATGTGCTCGTGAACAGTCTCATATATGCCAAAAGGGAT
GATGATGGTTCCAAGTCTTTAGCAGTAAAGAAATTTAGTGAGAATGGGATGATGACTAACTTCT
ACAGTTACTCTAGTTTGTAAACAGACAAAGGTGGACGAACAAAAAAGTTAGTTGATAGCAGTGA
TTTCACACCCGGTAAAAAAAAACTATCACTCACAATTCGTCATAAACCAGTTATTGCTTACACA
AAAGTGTGCTGATTTCCCATTAGCTTAGGAAACGTGATAAAAGTAAAGAGCCCAAAGAAAAAGA
AAGTATAACACTTCACTGACAAAACAATAAGAATTTAAAGATTGCGTGCCTAAAAGATATCTGA
GACTACCCTCCAACAGTGTATATACCTTTGTTCCCTCGCCTATTCAGATAATTCTGGAAAAAAA
ACTACCTCATATGCTTCTTATAAAGTCAAGCAATAAGAAAAATATTGGAAAGGAAACTAAAAAT
CAACTCATGATCTCTCCTTCGATTCATTACGCATCAGCTTTGAATACCAATATATTAAAAAGTC
ACAGCTAGATCGTTGCCTTACCTAATTTCACAGCGAATATGCTGAATATCACTATATTTCTTAG
CATAGGCTTGGATGCTGCTTATGTCTACTCCAAAATATCTGGAAGGATTGGTCAAGGCATTCTG
CACTGCAGATCATTCTTCCTCACTCAATGCGAAGGAAAGTGAAAACAAAATCATAATCATGAAC
AGAAAAAGAGGGCTTTGGAAGGATACTCCAGGTCTGGATCTTGTTGCAAGCAAAATATGGTTTT
AACTCCAATTTTACGAAGCTTGTCAACATCTTCAGGGGTCTAGCAATAAAGGAGAGCATACAGT
AAGAACACGAGGAAAGTACCACATATCCAAAACAAAATCATCATTTGAGAGAAGGATATAAAAG
TGAACCTGTAAGCAGGATCCAACAATTAGATCTGGACGAATAAAGTTGTAGTTCATTCCTAACT
CGTGCCTGTAAGTTAGAACTGAAATGAAAGACACATGAGAATGAATCAGTGACTGAAATACATA
ATTAAGGAGAACAAGAAGATAAGTTTGTCAATAAACAAGCAAAAGATATAAGATTCCTTGGTAG
ACAGATGAACAAAACTAATCAAGATGAAAGATGAAAAACAAGAGTAGAATACAATCCAATGAGC
TAAATCAATATTTCCAATATGAGACAAAAAATGGTGGACATCATTAGAGTTTCCAATCTAAGGA
CATGTATAGGTATGATGAAAACAATTTACCAGCACCCATAGCTTGAGTCATGTCTTGGCTATAT
TCATCAGATTTCTCTTCATCCTTTGCAACACCACTCATCTCTGAGCTGGATTTTGACTCTGATA
CTGCCTACACTCAAAGCATTTACAAAAGTGTCAATAAAAGTTAGAAGAAAAAAACTGATATAAC
AATATATCTTAAAAGAGGTGTATACATGTAAAACAAGTCGAGATTTTGGATCATTGGCTTTGAT
CGGAGGCGATATTAGCATCTTCAAAGAAGAAGAAGAAGAAGAATGATCTCTTTGAATGCACCCG
AATCCCAGCAGAGGTGAGACTGAACAT
						
					

			
		

Sequences
Splice junction sequence	GGCTTTGATCGGAGGCGATATTAGCATCTTCAAAGAAGAAGAAGAAGAAGAATGATCTCTTTGA ATGCACCCGAATCCCAGCAGAGGTGAGACTGAACATctgtccccatccaatgtcaaggccagaa atttctactctggagaaccccttatctttcagtgtcagagtaacagtcttcctcttgagtcctg taagcttt
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: 814 Transcript exons: 19350613-19350708,19350842-19350898,19351267-19351326,19 351518-19351650,19352298-19352378,19352495-19352571,1935 2666-19352742,19353010-19353112,19353198-19353327 CTGTCCCCATCCAATGTCAAGGCCAGAAATTTCTACTCTGGAGAACCCCTTATCTTTCAGTGTC AGAGTAACAGTCTTCCTCTTGAGTCCTGTAAGAATATCAATTGTTGCATTTCTGATAGCATCCA GCTTCGGAAAGCACGACCTTTTGCTCATAAGTAATTTATGAGCTTCCATAAGCTTATAGCCTTG CACCCAGAACATGTATGTCAACGCAACAGCAGGAGCCCTTCCCATTCCAGCAGTGCAGTGCACA TATGTAACTCCTCCATTTCGCTTAACAGCTTTGTAAAGAGTACCAACCACGGCTGGAAGACGCA TTCTCAAATCAAATGCATCAAAGTCTCTAATTTCACAGCGAATATGCTGAATATCACTATATTT CTTAGCATAGGCTTGGATGCTGCTTATGTCTACTCCAAAATATTCCAGGTCTGGATCTTGTTGC AAGCAAAATATGGTTTTAACTCCAATTTTACGAAGCTTGTCAACATCTTCAGGGGTCTGTAAGC AGGATCCAACAATTAGATCTGGACGAATAAAGTTGTAGTTCATTCCTAACTCGTGCCTGTAAGT TAGAACAGCACCCATAGCTTGAGTCATGTCTTGGCTATATTCATCAGATTTCTCTTCATCCTTT GCAACACCACTCATCTCTGAGCTGGATTTTGACTCTGATACTGCATGTAAAACAAGTCGAGATT TTGGATCATTGGCTTTGATCGGAGGCGATATTAGCATCTTCAAAGAAGAAGAAGAAGAAGAATG ATCTCTTTGAATGCACCCGAATCCCAGCAGAGGTGAGACTGAACAT
Genomic sequence	CTGTCCCCATCCAATGTCAAGGCCAGAAATTTCTACTCTGGAGAACCCCTTATCTTTCAGTGTC AGAGTAACAGTCTTCCTCTTGAGTCCTGTAAGCTTTTATCCATATACACCCGGAAACAATAATC AGGAGTCAAGGAACCAGGTAACTGTTGCGCACTCATGCTAATCAATGGAACTGAGGTTTTTCAA ACATAGGAAGCATTGTGAAAGTTGAACGCTGACTCACAATATCAATTGTTGCATTTCTGATAGC ATCCAGCTTCGGAAAGCACGACCTTTTGCTCTGCAAGAAAATTTCAGAAATGTTATATAAACCA AATTTACGCGTGCCTTTATGTTTCACCAGCCATCTAGAGATATCAAACTAAAAATGTCTAATGC TAGACTATTTTGGATGAACTAACCCAAGATTTTTGTCTTTTAAAGTGCTATATCTTCAGTGTAT ATTTACTACAAACCCCTGACCCAATGGTCTATGATTCTAGTTATCATAATTGTCGGTTCATAGG AGAAGAAGGAAATCCCCAAACATCCTCACATAATATAACAGGCAGTAACACTAGTAAAACATGA TTAACATGTTGGTTACTTAATATAAGTATAAAGAAACACATATAGAGAACATAAACCACAAGTA AATTAGTATCTTACCATAAGTAATTTATGAGCTTCCATAAGCTTATAGCCTTGCACCCAGAACA TGTATGTCAACTGAAAATGAAATTAATATCCCTTCTCAGTATCAGTCAGCAAAATGTGAAAACT TGTTCATACCTTCATGAGTCAACCAAATAAGCACAAAATTAAGACAACTACTGTTTGCAACAGT CTTACATTTTTTCAATACTGGAAAGAAAAGGGGGAAAAAGAGAAGAGCTTAGTAACAGGTTTCT GTAACATACCGCAACAGCAGGAGCCCTTCCCATTCCAGCAGTGCAGTGCACATATGTAACTCCT CCATTTCGCTTAACAGCTTTGTAAAGAGTACCAACCACGGCTGGAAGACGCATTCTCAAATCAA ATGCATCAAAGTCTCTGTTACATCAATGATATATAATATGTCAATCCCCTACGTTGTGAGTGGG TACGTCCATGGTGAATTTTTCTATGCATGTGCTCGTGAACAGTCTCATATATGCCAAAAGGGAT GATGATGGTTCCAAGTCTTTAGCAGTAAAGAAATTTAGTGAGAATGGGATGATGACTAACTTCT ACAGTTACTCTAGTTTGTAAACAGACAAAGGTGGACGAACAAAAAAGTTAGTTGATAGCAGTGA TTTCACACCCGGTAAAAAAAAACTATCACTCACAATTCGTCATAAACCAGTTATTGCTTACACA AAAGTGTGCTGATTTCCCATTAGCTTAGGAAACGTGATAAAAGTAAAGAGCCCAAAGAAAAAGA AAGTATAACACTTCACTGACAAAACAATAAGAATTTAAAGATTGCGTGCCTAAAAGATATCTGA GACTACCCTCCAACAGTGTATATACCTTTGTTCCCTCGCCTATTCAGATAATTCTGGAAAAAAA ACTACCTCATATGCTTCTTATAAAGTCAAGCAATAAGAAAAATATTGGAAAGGAAACTAAAAAT CAACTCATGATCTCTCCTTCGATTCATTACGCATCAGCTTTGAATACCAATATATTAAAAAGTC ACAGCTAGATCGTTGCCTTACCTAATTTCACAGCGAATATGCTGAATATCACTATATTTCTTAG CATAGGCTTGGATGCTGCTTATGTCTACTCCAAAATATCTGGAAGGATTGGTCAAGGCATTCTG CACTGCAGATCATTCTTCCTCACTCAATGCGAAGGAAAGTGAAAACAAAATCATAATCATGAAC AGAAAAAGAGGGCTTTGGAAGGATACTCCAGGTCTGGATCTTGTTGCAAGCAAAATATGGTTTT AACTCCAATTTTACGAAGCTTGTCAACATCTTCAGGGGTCTAGCAATAAAGGAGAGCATACAGT AAGAACACGAGGAAAGTACCACATATCCAAAACAAAATCATCATTTGAGAGAAGGATATAAAAG TGAACCTGTAAGCAGGATCCAACAATTAGATCTGGACGAATAAAGTTGTAGTTCATTCCTAACT CGTGCCTGTAAGTTAGAACTGAAATGAAAGACACATGAGAATGAATCAGTGACTGAAATACATA ATTAAGGAGAACAAGAAGATAAGTTTGTCAATAAACAAGCAAAAGATATAAGATTCCTTGGTAG ACAGATGAACAAAACTAATCAAGATGAAAGATGAAAAACAAGAGTAGAATACAATCCAATGAGC TAAATCAATATTTCCAATATGAGACAAAAAATGGTGGACATCATTAGAGTTTCCAATCTAAGGA CATGTATAGGTATGATGAAAACAATTTACCAGCACCCATAGCTTGAGTCATGTCTTGGCTATAT TCATCAGATTTCTCTTCATCCTTTGCAACACCACTCATCTCTGAGCTGGATTTTGACTCTGATA CTGCCTACACTCAAAGCATTTACAAAAGTGTCAATAAAAGTTAGAAGAAAAAAACTGATATAAC AATATATCTTAAAAGAGGTGTATACATGTAAAACAAGTCGAGATTTTGGATCATTGGCTTTGAT CGGAGGCGATATTAGCATCTTCAAAGAAGAAGAAGAAGAAGAATGATCTCTTTGAATGCACCCG AATCCCAGCAGAGGTGAGACTGAACAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.171367509

Conservation Information
Conserved circRNAs	NA
PMCS	0.171367509

			
						 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 AT3G52180_circ_g.1

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