Plant Circular RNA Database

Detail information of AT3G13460_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT3G13460_circ_g.4
					
						ID in PlantcircBase
						ath_circ_021454
					
						Alias
						3:4385761-4387911
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 4385761-4387911  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G13460						
					
						Parent gene annotation
						
							ECT2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G13460_circ_g.1 AT3G13460_circ_g.2 AT3G13460_circ_g.3 AT3G13460_circ_g.5 AT3G13460_circ_g.6 AT3G13460_circ_g.7 AT3G13460_circ_g.8 AT3G13460_circ_g.9 AT3G13460_circ_g.10 AT3G13460_circ_g.11 AT3G13460_circ_g.12 AT3G13460_circ_g.13 						
					
						Support reads
						2
					
						Tissues
						seedling
					
						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
						AT3G13460.3:6
AT3G13460.4:6
AT3G13460.2:6
AT3G13460.1:6

General Information
CircRNA Name	AT3G13460_circ_g.4
ID in PlantcircBase	ath_circ_021454
Alias	3:4385761-4387911
Organism	Arabidpsis thaliana
Position	chr3: 4385761-4387911 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G13460
Parent gene annotation	ECT2
Parent gene strand	-
Alternative splicing	AT3G13460_circ_g.1 AT3G13460_circ_g.2 AT3G13460_circ_g.3 AT3G13460_circ_g.5 AT3G13460_circ_g.6 AT3G13460_circ_g.7 AT3G13460_circ_g.8 AT3G13460_circ_g.9 AT3G13460_circ_g.10 AT3G13460_circ_g.11 AT3G13460_circ_g.12 AT3G13460_circ_g.13
Support reads	2
Tissues	seedling
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	AT3G13460.3:6 AT3G13460.4:6 AT3G13460.2:6 AT3G13460.1:6

			
						 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  
						
							CCAAAATTCAATCTGCAAATCACCTTCTTGTTAGGCTCAGGGATCTCTGAAGCTTTTGCTGGCG
AGTCCAAGGATAGTTTCTGCAACAGATCTGTAGCTTctcttgtgtgtctctgctgttggtaaca
ggtttgttctcattgttctctaaagtaatatgcttcagtaaactgtttggcacatccttcacaa
tatgccac

									
								

					

						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: 1670
Transcript exons: 4385761-4385973,4386062-4386655,4386782-4387348,4387431-
4387501,4387597-4387744,4387835-4387911
CTCTTGTGTGTCTCTGCTGTTGGTAACAGGTTTGTTCTCATTGTTCTCTAAAGTAATATGCTTC
AGTAAACTGTTTGGCACATCCTTCACAATATGCCACTTGAGGGGGAAAGAGCCGGTCCACTTAT
CTTGCTGCCAGTACTCCACATTTGTGTTGAAATCAACTGGTCCTGTCATTTCAGCAAGACCAAC
AAATTGTCCACTTGCATTGACCGAGAAAAACAGAAAGATGGGACAGCCGCCAGCTTTCTGTTGA
GCTTCCTGGTATGCTGCAGCAAGCTTCTTGTTTCCATTTGGTGTGCTAGCCCAAACATTATATT
TAATGCTCTTGTGCACATCATCTTCACTGTATGACTTGATGATAAAGAACATGGCATTTGCATA
ATCCACTGGGAAATCTTCTTTATTGTACTGTTCTCTGTCAGGAACAACACATGTGTTATCCGCC
TCCCCAACCTCAGTTACATTTGATTCTCCAGTCTGCTCCTTAACCTCTAAGCTATCATCTAGAT
TTCCCTTCTGGTTCTTTGTGCCCTTAGCTCTAGGTCCCCTGTTAAGTTCATTCAAACCATCTAC
ATTGTTCTCATTTCCGTAATAGTAACTGTTACCCCTGCCCCAGCTTCTGTATTTGTTGTCTGTG
GCCGCCCATCCTCTTCCATTTGTTCTTGAATCATACCCAGATGAACCATAACCCAAAGCAGATC
TCCCTGTGCTACCATACTGACCATATAACTTGTTCTGATACATCCTGTTGTAGTACCCCTGAGC
TGTACCATAGCCAGTCACTGATGAAGGCTGGTGCACGCTCGTGTAGTGAGAATTTGAGCGGTAG
TTTTGATTCCTCGATGAAGGTACTGTGCTAGACTTAGAATAGGAGGATGCAACTCCACTACCAG
AAACAGGTCTCTGCACATCAGAGTACTTAGAGCCATCGTGCCACGGCACAGGAGCATAATACCC
TTCATAGGCATACCTGGGGTCCTGATAACCAGCAGCCAAACCTCCTCCTGGAGCACCCATACCA
TACAAATTACTTGAGGTGTTAAGGGTAGCCTGGTTAGTTGGTTTCACTGGAGCTGATCCATTAC
TTCCTTTTGTGATACCAGCAGCAGAAGCAACATTATTGCTATCCGCAGGTAGTGTCTTCACACC
AGCAGGTTTGTTTGCAGAGAGATCCGGCTGGGTAGGTGTAGCCACAGATGAAGCATACGGTCCA
CTGTTTGGAAAATAGTTAGGATACTGATACTGCTGAGCACCGTACAACTGCCCTTCCCCGCCAA
GCTGTGGAGCAGGGCTAGTTGCTGGCGAGTAAGGATACGCTGCATACCCATAACCCTGAGGATA
CACAACAGTCCCATTCTCTCCATAAATTCCAGAATTCATGTCAACACCCTCAGGATTTGTGTAA
GCTGGGTAGTCAGTCCACTCTTGACCACTCCCATATACATTGTAATACTGGTAGGGATTGTAAG
GATTAGGAACATAGCAAACTGAAGGGTCAGCAGCATCACTGGGAAGCATTGGTGTCAAAGATCG
ATCATAAGAAGGAACTTGACCATGAACATCAACGCCTCCATACTGGTAGACGGCAGTCTTCTTG
TTAGGCTCAGGGATCTCTGAAGCTTTTGCTGGCGAGTCCAAGGATAGTTTCTGCAACAGATCTG
TAGCTT
						
					

						Genomic sequence
						
							CTCTTGTGTGTCTCTGCTGTTGGTAACAGGTTTGTTCTCATTGTTCTCTAAAGTAATATGCTTC
AGTAAACTGTTTGGCACATCCTTCACAATATGCCACTTGAGGGGGAAAGAGCCGGTCCACTTAT
CTTGCTGCCAGTACTCCACATTTGTGTTGAAATCAACTGGTCCTGTCATTTCAGCAAGACCAAC
AAATTGTCCACTTGCATTGACCTGAAAGACAAAAACTGGAGTATAAAGAACAATATCATAAAAC
AAAGTAAAAAGAGCACAGTTTTTAATTTCAGGATTATATACACACCGAGAAAAACAGAAAGATG
GGACAGCCGCCAGCTTTCTGTTGAGCTTCCTGGTATGCTGCAGCAAGCTTCTTGTTTCCATTTG
GTGTGCTAGCCCAAACATTATATTTAATGCTCTTGTGCACATCATCTTCACTGTATGACTTGAT
GATAAAGAACATGGCATTTGCATAATCCACTGGGAAATCTTCTTTATTGTACTGTTCTCTGTCA
GGAACAACACATGTGTTATCCGCCTCCCCAACCTCAGTTACATTTGATTCTCCAGTCTGCTCCT
TAACCTCTAAGCTATCATCTAGATTTCCCTTCTGGTTCTTTGTGCCCTTAGCTCTAGGTCCCCT
GTTAAGTTCATTCAAACCATCTACATTGTTCTCATTTCCGTAATAGTAACTGTTACCCCTGCCC
CAGCTTCTGTATTTGTTGTCTGTGGCCGCCCATCCTCTTCCATTTGTTCTTGAATCATACCCAG
ATGAACCATAACCCAAAGCAGATCTCCCTGTGCTACCATACTGACCATATAACTTGTTCTGATA
CATCCTGTTGTAGTACCCCTGAGCTGTACCATAGCCAGTCACTGATGAAGGCTGGTGCACGCTC
TGCAAAGAAAAAAGTTGATTGAAGGTCAGTTAACAAATTTGGAAGACTTGAGCGGCTATATATA
TATGCCAGTAAAGCAGACAATGGTGTTCATTAGCAAAAAGAAGTTTGGAAAGACATCATACCGT
GTAGTGAGAATTTGAGCGGTAGTTTTGATTCCTCGATGAAGGTACTGTGCTAGACTTAGAATAG
GAGGATGCAACTCCACTACCAGAAACAGGTCTCTGCACATCAGAGTACTTAGAGCCATCGTGCC
ACGGCACAGGAGCATAATACCCTTCATAGGCATACCTGGGGTCCTGATAACCAGCAGCCAAACC
TCCTCCTGGAGCACCCATACCATACAAATTACTTGAGGTGTTAAGGGTAGCCTGGTTAGTTGGT
TTCACTGGAGCTGATCCATTACTTCCTTTTGTGATACCAGCAGCAGAAGCAACATTATTGCTAT
CCGCAGGTAGTGTCTTCACACCAGCAGGTTTGTTTGCAGAGAGATCCGGCTGGGTAGGTGTAGC
CACAGATGAAGCATACGGTCCACTGTTTGGAAAATAGTTAGGATACTGATACTGCTGAGCACCG
TACAACTGCCCTTCCCCGCCAAGCTGTGGAGCAGGGCTAGTTGCTGGCGAGTAAGGATACGCTG
CATACCCATAACCCTGAGGATACACAACAGTCCCATTCTCTCCATAAATTCCCTGGTAAAATAT
TGAACCTGTTAAGCAAAGAAAATATAAAGACGATGAAAGGCACTATTATAACTAGTCAGCACAC
ACTTACAGAATTCATGTCAACACCCTCAGGATTTGTGTAAGCTGGGTAGTCAGTCCACTCTTGA
CCACTCCCATATACTGAAAAGTTACAAAACGAAAAACTTGTTAAACCAGTGGTGACAATTTAGT
GAAATAATGTTTCTAGATTGTAAATGATTTGAGGATGAAGCTACCATTGTAATACTGGTAGGGA
TTGTAAGGATTAGGAACATAGCAAACTGAAGGGTCAGCAGCATCACTGGGAAGCATTGGTGTCA
AAGATCGATCATAAGAAGGAACTTGACCATGAACATCAACGCCTCCATACTGGTAGACGGCAGT
CTACACAAGACACAAAACAAAAGCGTTAAAAAAAACTGGAAGAAGCAAAAGTTGTGACAACAGA
AAACCAAAATTCAATCTGCAAATCACCTTCTTGTTAGGCTCAGGGATCTCTGAAGCTTTTGCTG
GCGAGTCCAAGGATAGTTTCTGCAACAGATCTGTAGCTT
						
					

			
		

Sequences
Splice junction sequence	CCAAAATTCAATCTGCAAATCACCTTCTTGTTAGGCTCAGGGATCTCTGAAGCTTTTGCTGGCG AGTCCAAGGATAGTTTCTGCAACAGATCTGTAGCTTctcttgtgtgtctctgctgttggtaaca ggtttgttctcattgttctctaaagtaatatgcttcagtaaactgtttggcacatccttcacaa tatgccac
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: 1670 Transcript exons: 4385761-4385973,4386062-4386655,4386782-4387348,4387431- 4387501,4387597-4387744,4387835-4387911 CTCTTGTGTGTCTCTGCTGTTGGTAACAGGTTTGTTCTCATTGTTCTCTAAAGTAATATGCTTC AGTAAACTGTTTGGCACATCCTTCACAATATGCCACTTGAGGGGGAAAGAGCCGGTCCACTTAT CTTGCTGCCAGTACTCCACATTTGTGTTGAAATCAACTGGTCCTGTCATTTCAGCAAGACCAAC AAATTGTCCACTTGCATTGACCGAGAAAAACAGAAAGATGGGACAGCCGCCAGCTTTCTGTTGA GCTTCCTGGTATGCTGCAGCAAGCTTCTTGTTTCCATTTGGTGTGCTAGCCCAAACATTATATT TAATGCTCTTGTGCACATCATCTTCACTGTATGACTTGATGATAAAGAACATGGCATTTGCATA ATCCACTGGGAAATCTTCTTTATTGTACTGTTCTCTGTCAGGAACAACACATGTGTTATCCGCC TCCCCAACCTCAGTTACATTTGATTCTCCAGTCTGCTCCTTAACCTCTAAGCTATCATCTAGAT TTCCCTTCTGGTTCTTTGTGCCCTTAGCTCTAGGTCCCCTGTTAAGTTCATTCAAACCATCTAC ATTGTTCTCATTTCCGTAATAGTAACTGTTACCCCTGCCCCAGCTTCTGTATTTGTTGTCTGTG GCCGCCCATCCTCTTCCATTTGTTCTTGAATCATACCCAGATGAACCATAACCCAAAGCAGATC TCCCTGTGCTACCATACTGACCATATAACTTGTTCTGATACATCCTGTTGTAGTACCCCTGAGC TGTACCATAGCCAGTCACTGATGAAGGCTGGTGCACGCTCGTGTAGTGAGAATTTGAGCGGTAG TTTTGATTCCTCGATGAAGGTACTGTGCTAGACTTAGAATAGGAGGATGCAACTCCACTACCAG AAACAGGTCTCTGCACATCAGAGTACTTAGAGCCATCGTGCCACGGCACAGGAGCATAATACCC TTCATAGGCATACCTGGGGTCCTGATAACCAGCAGCCAAACCTCCTCCTGGAGCACCCATACCA TACAAATTACTTGAGGTGTTAAGGGTAGCCTGGTTAGTTGGTTTCACTGGAGCTGATCCATTAC TTCCTTTTGTGATACCAGCAGCAGAAGCAACATTATTGCTATCCGCAGGTAGTGTCTTCACACC AGCAGGTTTGTTTGCAGAGAGATCCGGCTGGGTAGGTGTAGCCACAGATGAAGCATACGGTCCA CTGTTTGGAAAATAGTTAGGATACTGATACTGCTGAGCACCGTACAACTGCCCTTCCCCGCCAA GCTGTGGAGCAGGGCTAGTTGCTGGCGAGTAAGGATACGCTGCATACCCATAACCCTGAGGATA CACAACAGTCCCATTCTCTCCATAAATTCCAGAATTCATGTCAACACCCTCAGGATTTGTGTAA GCTGGGTAGTCAGTCCACTCTTGACCACTCCCATATACATTGTAATACTGGTAGGGATTGTAAG GATTAGGAACATAGCAAACTGAAGGGTCAGCAGCATCACTGGGAAGCATTGGTGTCAAAGATCG ATCATAAGAAGGAACTTGACCATGAACATCAACGCCTCCATACTGGTAGACGGCAGTCTTCTTG TTAGGCTCAGGGATCTCTGAAGCTTTTGCTGGCGAGTCCAAGGATAGTTTCTGCAACAGATCTG TAGCTT
Genomic sequence	CTCTTGTGTGTCTCTGCTGTTGGTAACAGGTTTGTTCTCATTGTTCTCTAAAGTAATATGCTTC AGTAAACTGTTTGGCACATCCTTCACAATATGCCACTTGAGGGGGAAAGAGCCGGTCCACTTAT CTTGCTGCCAGTACTCCACATTTGTGTTGAAATCAACTGGTCCTGTCATTTCAGCAAGACCAAC AAATTGTCCACTTGCATTGACCTGAAAGACAAAAACTGGAGTATAAAGAACAATATCATAAAAC AAAGTAAAAAGAGCACAGTTTTTAATTTCAGGATTATATACACACCGAGAAAAACAGAAAGATG GGACAGCCGCCAGCTTTCTGTTGAGCTTCCTGGTATGCTGCAGCAAGCTTCTTGTTTCCATTTG GTGTGCTAGCCCAAACATTATATTTAATGCTCTTGTGCACATCATCTTCACTGTATGACTTGAT GATAAAGAACATGGCATTTGCATAATCCACTGGGAAATCTTCTTTATTGTACTGTTCTCTGTCA GGAACAACACATGTGTTATCCGCCTCCCCAACCTCAGTTACATTTGATTCTCCAGTCTGCTCCT TAACCTCTAAGCTATCATCTAGATTTCCCTTCTGGTTCTTTGTGCCCTTAGCTCTAGGTCCCCT GTTAAGTTCATTCAAACCATCTACATTGTTCTCATTTCCGTAATAGTAACTGTTACCCCTGCCC CAGCTTCTGTATTTGTTGTCTGTGGCCGCCCATCCTCTTCCATTTGTTCTTGAATCATACCCAG ATGAACCATAACCCAAAGCAGATCTCCCTGTGCTACCATACTGACCATATAACTTGTTCTGATA CATCCTGTTGTAGTACCCCTGAGCTGTACCATAGCCAGTCACTGATGAAGGCTGGTGCACGCTC TGCAAAGAAAAAAGTTGATTGAAGGTCAGTTAACAAATTTGGAAGACTTGAGCGGCTATATATA TATGCCAGTAAAGCAGACAATGGTGTTCATTAGCAAAAAGAAGTTTGGAAAGACATCATACCGT GTAGTGAGAATTTGAGCGGTAGTTTTGATTCCTCGATGAAGGTACTGTGCTAGACTTAGAATAG GAGGATGCAACTCCACTACCAGAAACAGGTCTCTGCACATCAGAGTACTTAGAGCCATCGTGCC ACGGCACAGGAGCATAATACCCTTCATAGGCATACCTGGGGTCCTGATAACCAGCAGCCAAACC TCCTCCTGGAGCACCCATACCATACAAATTACTTGAGGTGTTAAGGGTAGCCTGGTTAGTTGGT TTCACTGGAGCTGATCCATTACTTCCTTTTGTGATACCAGCAGCAGAAGCAACATTATTGCTAT CCGCAGGTAGTGTCTTCACACCAGCAGGTTTGTTTGCAGAGAGATCCGGCTGGGTAGGTGTAGC CACAGATGAAGCATACGGTCCACTGTTTGGAAAATAGTTAGGATACTGATACTGCTGAGCACCG TACAACTGCCCTTCCCCGCCAAGCTGTGGAGCAGGGCTAGTTGCTGGCGAGTAAGGATACGCTG CATACCCATAACCCTGAGGATACACAACAGTCCCATTCTCTCCATAAATTCCCTGGTAAAATAT TGAACCTGTTAAGCAAAGAAAATATAAAGACGATGAAAGGCACTATTATAACTAGTCAGCACAC ACTTACAGAATTCATGTCAACACCCTCAGGATTTGTGTAAGCTGGGTAGTCAGTCCACTCTTGA CCACTCCCATATACTGAAAAGTTACAAAACGAAAAACTTGTTAAACCAGTGGTGACAATTTAGT GAAATAATGTTTCTAGATTGTAAATGATTTGAGGATGAAGCTACCATTGTAATACTGGTAGGGA TTGTAAGGATTAGGAACATAGCAAACTGAAGGGTCAGCAGCATCACTGGGAAGCATTGGTGTCA AAGATCGATCATAAGAAGGAACTTGACCATGAACATCAACGCCTCCATACTGGTAGACGGCAGT CTACACAAGACACAAAACAAAAGCGTTAAAAAAAACTGGAAGAAGCAAAAGTTGTGACAACAGA AAACCAAAATTCAATCTGCAAATCACCTTCTTGTTAGGCTCAGGGATCTCTGAAGCTTTTGCTG GCGAGTCCAAGGATAGTTTCTGCAACAGATCTGTAGCTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.256499084

Conservation Information
Conserved circRNAs	NA
PMCS	0.256499084

			
						 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 AT3G13460_circ_g.4

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