Plant Circular RNA Database

Detail information of AT1G10130_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT1G10130_circ_g.5
					
						ID in PlantcircBase
						ath_circ_001809
					
						Alias
						1:3313604-3316039
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 3313604-3316039  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G10130						
					
						Parent gene annotation
						
							Calcium-transporting ATPase 3, endoplasmic reticulum-type
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G10130_circ_g.3 AT1G10130_circ_g.4 AT1G10130_circ_g.6 AT1G10130_circ_g.7 AT1G10130_circ_g.8 AT1G10130_circ_g.9 						
					
						Support reads
						2/1
					
						Tissues
						seedling;flower
					
						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
						AT1G10130.1:8

General Information
CircRNA Name	AT1G10130_circ_g.5
ID in PlantcircBase	ath_circ_001809
Alias	1:3313604-3316039
Organism	Arabidpsis thaliana
Position	chr1: 3313604-3316039 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G10130
Parent gene annotation	Calcium-transporting ATPase 3, endoplasmic reticulum-type
Parent gene strand	+
Alternative splicing	AT1G10130_circ_g.3 AT1G10130_circ_g.4 AT1G10130_circ_g.6 AT1G10130_circ_g.7 AT1G10130_circ_g.8 AT1G10130_circ_g.9
Support reads	2/1
Tissues	seedling;flower
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	AT1G10130.1:8

			
						 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  
						
							TGTACGGTCATTACCATCTGTCGAGACGCTTGGGTGCACTACTGTAATTTGCAGTGACAAGACT
GGAACATTGACAACCAATATGATGTCGGTGTCTAAGggtgcttctctatcctaccagcaacaga
gctggttccaggcgacattgttgaagttactggtatgtttgttctattatacctagatgatatt
ttgtggca

									
								

					

						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: 689
Transcript exons: 3313604-3313663,3313764-3313844,3314106-3314191,3314347-
3314448,3314744-3314797,3315074-3315175,3315546-3315604,
3315895-3316039
GGTGCTTCTCTATCCTACCAGCAACAGAGCTGGTTCCAGGCGACATTGTTGAAGTTACTGTGGG
ATGTAAGATTCCAGCTGACCTGAGGATGATTGAGATGTCTAGCAATACGTTTCGAGTTGATCAA
GCCATTCTAACTGGTGAAAGCTGTTCCGTGGAAAAAGATGTTGACTGTACTTTAACAACAAATG
CTGTCTACCAAGACAAGAAAAATATTTTATTTTCGGGAACTGATGTGGTCGCGGGTAGGGGAAG
GGCTGTTGTCATTGGAGTTGGTTCAAACACCGCAATGGGTAGCATACACGATTCTATGTTGCAG
ACAGATGATGAGGCAACTCCATTGAAAAAGAAGCTGGACGAGTTTGGCAGCTTTTTGGCTAAGG
TAATTGCGGGTATTTGTGTACTTGTGTGGGTTGTCAACATTGGTCACTTCAGTGACCCTTCTCA
TGGTGGATTTTTTAAAGGCGCAATTCACTATTTTAAGATTGCAGTTGCCCTTGCTGTTGCAGCT
ATTCCTGAAGGACTTCCTGCTGTCGTGACAACGTGTTTAGCTCTTGGAACAAAGAAAATGGCTC
GTTTGAATGCTATTGTACGGTCATTACCATCTGTCGAGACGCTTGGGTGCACTACTGTAATTTG
CAGTGACAAGACTGGAACATTGACAACCAATATGATGTCGGTGTCTAAG
						
					

						Genomic sequence
						
							GGTGCTTCTCTATCCTACCAGCAACAGAGCTGGTTCCAGGCGACATTGTTGAAGTTACTGGTAT
GTTTGTTCTATTATACCTAGATGATATTTTGTGGCAATGGCTTAGACTTTTACTAGATTCTAAA
TTCTGTTTTTTTGATGTGTTGATGCTAAACAGTGGGATGTAAGATTCCAGCTGACCTGAGGATG
ATTGAGATGTCTAGCAATACGTTTCGAGTTGATCAAGCCATTCTAACTGGTATGTCATCTGTGT
CACCATAAGTCATAACTCTTGATATGCGTTGCCACAAGAACTACCTATGCCTATTGGTACTTAT
TACAACTTCAAGCCAATCATTTTCTCCACCAATTTATCTCTGGAATGAACATGCATTTTCTTAT
TACATTATAGCTTCAACAACAATAGTGGATTCCTTTTATGTAAAAAAATTTAAAGTGAACATTT
ACAGTGGACTATATCCATACTCTCACTACTAATTGTTTTCCCCGGAAATTGCAGGTGAAAGCTG
TTCCGTGGAAAAAGATGTTGACTGTACTTTAACAACAAATGCTGTCTACCAAGACAAGAAAAAT
ATTTTATTTTCGGTAGGAGTTATAACTCGTAGCTGCATTTGCTAAGTCCAAATTTGTGTATAAT
GCTTTTCCTGTTAGGGCTGTATAATACAATTGCCTATTCTTTTGATTATCTAATGCTATTTCCA
TACGTGTTTAAATTTGATAGAATATAATATTATTGCCAGGGAACTGATGTGGTCGCGGGTAGGG
GAAGGGCTGTTGTCATTGGAGTTGGTTCAAACACCGCAATGGGTAGCATACACGATTCTATGTT
GCAGACAGATGATGTAAGCTATCAATATTCTTTCATTTTTATCTGGAAATGCACCATTTGCACT
TTTAGTATCCTTTGTTACTTGTCAGAACTCTCTTATAAACAGAGGTTATAGTGTAACTTTGACT
GGCTTAAATTTCCTGTGATGAATAGTTTGTCAGTTTTGCACTTATGGGACTGTAGACTTGTATC
CTGCTATATAGTATAGTTTCAGTATTCTATTTGGAGATTCTTTTCTATCTATTTTGAAGTGCAT
TATAACTACTAGAATTTTCCTTATTTATTACTTGTATTTGCTGTTGTCATAGGAGGCAACTCCA
TTGAAAAAGAAGCTGGACGAGTTTGGCAGCTTTTTGGCTAAGGTGACAAACTTTTTTGCTTTTC
GAATTTTTAGATTTTTATGTTTCGAAGAGGCACTTTAATTACAAGACTTGGATGTCCAATTGTA
TCAGTAATCAGAATTTTTTAATTGTCTGAAAGTGATGAATTTCATTTAAAAAAAAAGATTTGTC
GAACGACTGGTGTGACAGAGATCTCTTGCAGAAATTCTAGTTAGTTAATTTCATCATTATGTTA
TATGCTACTCAACATAACATTAAGTCCTCTTAAAACGTATTAAATCTATTTTATTTGTATAGGT
AATTGCGGGTATTTGTGTACTTGTGTGGGTTGTCAACATTGGTCACTTCAGTGACCCTTCTCAT
GGTGGATTTTTTAAAGGCGCAATTCACTATTTTAAGGTAAAGAAATTTGATCTTCTCTTATGAC
AGCTTTGAATTCTTAGTTAGGGAGTAGATAATCAGTTTTGTGTGTCCCACTCTTGCTGTAATAT
CAAAAGATAGATTTTACTTCTCCATTGTTTCGGTGACATCCCCAAAAGTGATTGCATACAGGTA
CAAAGAAATTACCAAAGAATTGTTAACTCACTAAATCGACATTCAACATTTGAATATTGAAAGT
CACAAATAAGAAATTTTCGTTCTGCAATGGGTGGATTTTTATCATTTGCTTATTTGACATAACT
GAAGATGGATGTATTGTCCTCTGAGATTGTTGACTAATAAGTTAAAGTTTGGTAACACGGTTGT
TGCTTTCCTTTTATTTTCCCAGATTGCAGTTGCCCTTGCTGTTGCAGCTATTCCTGAAGGACTT
CCTGCTGTCGTGACAACGTAAGTGTTCACTAAGTCCATTGATAGCAAATACAATATTATGAGAA
AGGCTAATGATCGTTGAAACTTAAGATGATTTCTGTGGAACGTTAGTGATACCTTGGAAACAAG
AAGTTTCCCAGAAAGTAGATGGTTCTTGTGATCGTCAAATGACAATTTTGTTTCAAATTCAGCT
CACTCTAATGTTGGTTGAGTCCAAAATGCTATGAAAAAGTAAATTTCCATGTCGGGAGGCTACT
CCCGGTTATTATATTGTTGCTTAAATAGATTATGATGTTTCGGGTATCTAGGTGTTTAGCTCTT
GGAACAAAGAAAATGGCTCGTTTGAATGCTATTGTACGGTCATTACCATCTGTCGAGACGCTTG
GGTGCACTACTGTAATTTGCAGTGACAAGACTGGAACATTGACAACCAATATGATGTCGGTGTC
TAAG
						
					

			
		

Sequences
Splice junction sequence	TGTACGGTCATTACCATCTGTCGAGACGCTTGGGTGCACTACTGTAATTTGCAGTGACAAGACT GGAACATTGACAACCAATATGATGTCGGTGTCTAAGggtgcttctctatcctaccagcaacaga gctggttccaggcgacattgttgaagttactggtatgtttgttctattatacctagatgatatt ttgtggca
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: 689 Transcript exons: 3313604-3313663,3313764-3313844,3314106-3314191,3314347- 3314448,3314744-3314797,3315074-3315175,3315546-3315604, 3315895-3316039 GGTGCTTCTCTATCCTACCAGCAACAGAGCTGGTTCCAGGCGACATTGTTGAAGTTACTGTGGG ATGTAAGATTCCAGCTGACCTGAGGATGATTGAGATGTCTAGCAATACGTTTCGAGTTGATCAA GCCATTCTAACTGGTGAAAGCTGTTCCGTGGAAAAAGATGTTGACTGTACTTTAACAACAAATG CTGTCTACCAAGACAAGAAAAATATTTTATTTTCGGGAACTGATGTGGTCGCGGGTAGGGGAAG GGCTGTTGTCATTGGAGTTGGTTCAAACACCGCAATGGGTAGCATACACGATTCTATGTTGCAG ACAGATGATGAGGCAACTCCATTGAAAAAGAAGCTGGACGAGTTTGGCAGCTTTTTGGCTAAGG TAATTGCGGGTATTTGTGTACTTGTGTGGGTTGTCAACATTGGTCACTTCAGTGACCCTTCTCA TGGTGGATTTTTTAAAGGCGCAATTCACTATTTTAAGATTGCAGTTGCCCTTGCTGTTGCAGCT ATTCCTGAAGGACTTCCTGCTGTCGTGACAACGTGTTTAGCTCTTGGAACAAAGAAAATGGCTC GTTTGAATGCTATTGTACGGTCATTACCATCTGTCGAGACGCTTGGGTGCACTACTGTAATTTG CAGTGACAAGACTGGAACATTGACAACCAATATGATGTCGGTGTCTAAG
Genomic sequence	GGTGCTTCTCTATCCTACCAGCAACAGAGCTGGTTCCAGGCGACATTGTTGAAGTTACTGGTAT GTTTGTTCTATTATACCTAGATGATATTTTGTGGCAATGGCTTAGACTTTTACTAGATTCTAAA TTCTGTTTTTTTGATGTGTTGATGCTAAACAGTGGGATGTAAGATTCCAGCTGACCTGAGGATG ATTGAGATGTCTAGCAATACGTTTCGAGTTGATCAAGCCATTCTAACTGGTATGTCATCTGTGT CACCATAAGTCATAACTCTTGATATGCGTTGCCACAAGAACTACCTATGCCTATTGGTACTTAT TACAACTTCAAGCCAATCATTTTCTCCACCAATTTATCTCTGGAATGAACATGCATTTTCTTAT TACATTATAGCTTCAACAACAATAGTGGATTCCTTTTATGTAAAAAAATTTAAAGTGAACATTT ACAGTGGACTATATCCATACTCTCACTACTAATTGTTTTCCCCGGAAATTGCAGGTGAAAGCTG TTCCGTGGAAAAAGATGTTGACTGTACTTTAACAACAAATGCTGTCTACCAAGACAAGAAAAAT ATTTTATTTTCGGTAGGAGTTATAACTCGTAGCTGCATTTGCTAAGTCCAAATTTGTGTATAAT GCTTTTCCTGTTAGGGCTGTATAATACAATTGCCTATTCTTTTGATTATCTAATGCTATTTCCA TACGTGTTTAAATTTGATAGAATATAATATTATTGCCAGGGAACTGATGTGGTCGCGGGTAGGG GAAGGGCTGTTGTCATTGGAGTTGGTTCAAACACCGCAATGGGTAGCATACACGATTCTATGTT GCAGACAGATGATGTAAGCTATCAATATTCTTTCATTTTTATCTGGAAATGCACCATTTGCACT TTTAGTATCCTTTGTTACTTGTCAGAACTCTCTTATAAACAGAGGTTATAGTGTAACTTTGACT GGCTTAAATTTCCTGTGATGAATAGTTTGTCAGTTTTGCACTTATGGGACTGTAGACTTGTATC CTGCTATATAGTATAGTTTCAGTATTCTATTTGGAGATTCTTTTCTATCTATTTTGAAGTGCAT TATAACTACTAGAATTTTCCTTATTTATTACTTGTATTTGCTGTTGTCATAGGAGGCAACTCCA TTGAAAAAGAAGCTGGACGAGTTTGGCAGCTTTTTGGCTAAGGTGACAAACTTTTTTGCTTTTC GAATTTTTAGATTTTTATGTTTCGAAGAGGCACTTTAATTACAAGACTTGGATGTCCAATTGTA TCAGTAATCAGAATTTTTTAATTGTCTGAAAGTGATGAATTTCATTTAAAAAAAAAGATTTGTC GAACGACTGGTGTGACAGAGATCTCTTGCAGAAATTCTAGTTAGTTAATTTCATCATTATGTTA TATGCTACTCAACATAACATTAAGTCCTCTTAAAACGTATTAAATCTATTTTATTTGTATAGGT AATTGCGGGTATTTGTGTACTTGTGTGGGTTGTCAACATTGGTCACTTCAGTGACCCTTCTCAT GGTGGATTTTTTAAAGGCGCAATTCACTATTTTAAGGTAAAGAAATTTGATCTTCTCTTATGAC AGCTTTGAATTCTTAGTTAGGGAGTAGATAATCAGTTTTGTGTGTCCCACTCTTGCTGTAATAT CAAAAGATAGATTTTACTTCTCCATTGTTTCGGTGACATCCCCAAAAGTGATTGCATACAGGTA CAAAGAAATTACCAAAGAATTGTTAACTCACTAAATCGACATTCAACATTTGAATATTGAAAGT CACAAATAAGAAATTTTCGTTCTGCAATGGGTGGATTTTTATCATTTGCTTATTTGACATAACT GAAGATGGATGTATTGTCCTCTGAGATTGTTGACTAATAAGTTAAAGTTTGGTAACACGGTTGT TGCTTTCCTTTTATTTTCCCAGATTGCAGTTGCCCTTGCTGTTGCAGCTATTCCTGAAGGACTT CCTGCTGTCGTGACAACGTAAGTGTTCACTAAGTCCATTGATAGCAAATACAATATTATGAGAA AGGCTAATGATCGTTGAAACTTAAGATGATTTCTGTGGAACGTTAGTGATACCTTGGAAACAAG AAGTTTCCCAGAAAGTAGATGGTTCTTGTGATCGTCAAATGACAATTTTGTTTCAAATTCAGCT CACTCTAATGTTGGTTGAGTCCAAAATGCTATGAAAAAGTAAATTTCCATGTCGGGAGGCTACT CCCGGTTATTATATTGTTGCTTAAATAGATTATGATGTTTCGGGTATCTAGGTGTTTAGCTCTT GGAACAAAGAAAATGGCTCGTTTGAATGCTATTGTACGGTCATTACCATCTGTCGAGACGCTTG GGTGCACTACTGTAATTTGCAGTGACAAGACTGGAACATTGACAACCAATATGATGTCGGTGTC TAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.185488428

Conservation Information
Conserved circRNAs	NA
PMCS	0.185488428

			
						 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 AT1G10130_circ_g.5

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