Plant Circular RNA Database

Detail information of AT4G13780_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT4G13780_circ_g.1
					
						ID in PlantcircBase
						ath_circ_030767
					
						Alias
						4:7993689-7997567
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 7993689-7997567  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G13780						
					
						Parent gene annotation
						
							Methionine--tRNA ligase, cytoplasmic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G13780_circ_g.2 AT4G13780_circ_g.3 AT4G13780_circ_g.4 AT4G13780_circ_g.5 AT4G13780_circ_g.6 						
					
						Support reads
						2
					
						Tissues
						root
					
						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
						AT4G13780.1:14

General Information
CircRNA Name	AT4G13780_circ_g.1
ID in PlantcircBase	ath_circ_030767
Alias	4:7993689-7997567
Organism	Arabidpsis thaliana
Position	chr4: 7993689-7997567 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G13780
Parent gene annotation	Methionine--tRNA ligase, cytoplasmic
Parent gene strand	-
Alternative splicing	AT4G13780_circ_g.2 AT4G13780_circ_g.3 AT4G13780_circ_g.4 AT4G13780_circ_g.5 AT4G13780_circ_g.6
Support reads	2
Tissues	root
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	AT4G13780.1:14

			
						 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  
						
							TGCTTGGCACACCTCAGTCTGTTCTGGAGTTGAAGTTCGCCCAAACTTGTCAAAACTTATACCA
AACCAGTCATAAACTTCTTTATGAATGGCATGGTACcttgcttccatcactactggaagctgca
agaaccattgcttgtgacacaatatccctcattttcgccggtttcaagttgcaaagaacacaaa
ccatacga

									
								

					

						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
						
							CTTGCTTCCATCACTACTGGAAGCTGCAAGAACCATTGCTTGTGACACAATATCCCTCATTTTC
GCCGGTTTCAAGTTGCAAAGAACACAAACCATACGATTCTGTCCAGAAACAATATTAGATCAAT
TGGAATGTATATTACATACTGATATCGGGAAGGAAACAAATGACTAGGTTGATTGAACAAACCT
GCATTTCCTCAAGAGGTATATATTTGACCAGTCCACTGACAACAGTGCGAATTTCACCACCCCC
AACATCAATTTCTTCTACATACAATGCATCTGCCTTGGGATGTTTCTCAGCCTTCACAATTTTA
CCAACTCGGATATCAAGTCTTGCCATAGTTATTTCACGATCAGCAGCTGGTTGAGGTTTGGGTT
TTCCTCCGCCTTTTGATGATGCCTTTTGTTTCTTGGCATCTGGGAGAATAAACAGCAGTTCAGT
ACATAATCAAGTTACTAAAAGCCTAAAGAATGTAAAACAGTATTTTGAGAATGATAATAGAGAA
CCTGAAAGTTTTGTTTTATTAAGTTGATCCGCCAAATTTGCTGCTTCATCCCTAGCACGTCTAT
CAGACTGACTTCCAGCAAACTTTTCTCTGTACCGTGCCACTTCGTCGTTTTCCTGTGATCATAT
TGTTTCAATATAAATAAAATGCTACATGGCATTATAACATACAACAAGTCTGGCTTTCTATCGA
TAAAATCAGAGAGCTACGTACCAACTCCTTGAACAAAGGTTGAGGGGTGCCTATCCTGTGGCTA
GGAGGCAGAATATCCCATGGTCTACTTGCTAGTAATACCTCTCCCCTCTCGTCGGAGAGAGAAA
ATTGTGGAGGCAAATTTAGCTGTTTAAATACCTACAAAATGCAATAACAGCAATAATCACGCTT
GGCATTCTACTACAACTAAATAGAAACAAAATTTACCAAACAAACAATCAAACTGACCTCACAA
GAAAAGGATGGCATGAAAGGTTCTAACAATTGAGCAAGAAGGTGTACTAAACCAGCAGCAGTTC
TTATAACAACTGCACACAAAGGTTTATCTTCCTTGTAAAGTTTCCAAAATTGGCTTGCCTACAT
GGACACAAGAAAACAGTATAGTTGGTAATATGCAACAAAGCTAATATCTAGTTTGTTAATGAGA
ATAGAACCTGCAAGTAATAGTTCCCTTCGCTTGAAATCAGCATAGCAGTTTTCAGTCCCTGCTT
GAGCTTAACCTACATCAAATGAACAGGGGATTTATTAAGAACCTAAAAACCCAGGCACAGAAAC
TCAGATAGCCATACCACGCCAAGGTTCATATAACATTCCTCACCTTTTCCATGGCTTCAACATA
CTCTGCCACAAACTTTTCAACCTTTTCCGCCAGTGATTTTGTTAAAGAATGAGATTCAGCATCA
TGAGCATCAGGAATGACAGACCCGTAACCTTCACAAAACATACAATAGTAAGGTATTGAAACAT
CAAAGACAAATAAGAAAAGTCTTGCCCTAGTTGTCAAGAGTATCACAAAGCAGGTATCTCTCAC
TTGCACACCAATAATAGTAAGCCAGATGCACCTTTCTATCATTCTAGAGTTTTTAGACTATCTA
TTTGTCCCGCGATTCAAATATCTCTCACTTGCACACCAACTGGCTGGTTACAGTAGAAGAATAC
AACACATCCTATATTTTCTATTGGATATGCCAGACTAAAAAGCTATCTACAGCTAACACCAAAC
ACTTGAGTATTGAATTTGAAAGAAATATAACCAACCTGCATTATCAGGCTTTGCTATAAAACTC
AGAACTCGATTAACAAAGTTGCCTAGGTTGCTCAGCAACTCGCCATTCAGTTTTGCTTGCAAAT
CAGTCCATGAAAACGATGTGTCAGACACCTAGAAGGCAGAATCCCCAGAATCAATCAGTGTATG
TGATATTTATGCATGCCTATGATGAACGAAGAAACAATGTTTCTATTTTGCAGCAGCAATCAGT
TACCTCAGGCCTGTTGGTCAGCAAGTAGTATCTCCACACTTCGACAGGTATATTTGTATCTTTT
ACATCATTACCAAACACTCCAACACCTTTACTCTTGGAGAACTTTCCTGAAAACCCATACAAAA
CACATGTCCTCATTTTCTATAAATGGCATAAAAAGTAAATCAAACAAAAATAATTTAAAATAAA
ATCACTCAGCTATGGTGAAACATCAACTGACCGTCTTCATAGTTTAAATATTCAGTCACACTGA
TTGTCTTCATGAGTGTCCAATTTTCCTCAGTTCCAAGCTGGGTAGAGGGAAACATCACCTGCAT
AACAAAAAATTTAGCAGTTGAAAACAACCAAATACAAAAGATAAACATTTCTTAAGAAGACCTT
GAGGATAGCTTCAGAAAAGACAAGAACCAAACAAACTTTTGGTGTTCTATTTCAGTATAAAAGA
AAGGTAAAGAAAAAGGAAATAATTAAAACCATTGGCACAAGTCCTTGGTGGTAAACAAATTTCT
GAAATGTTATATACTCACAGTGTGAAATGGCACATTGTCTTTCCCCATAAACTGATAAAGCTCC
ACATTCTCAGGATTCTTCCACCACTTCTCCCATTCAGATGTGTAGCAAGACGTTATTGAGACGT
ATCCAATAGGAGCATCAAACCAAACATAGAAGACCTATAACCATGATTGGAATTAGTAGTTGAT
CTTTAAATTTTTATGAAACTGGCTGGCAGTGAGGTTCCTACTTTGTCCTTGTATTTCTCATGTG
GGACAGGCACTCCCCACTTAAGATCCCTCGTAATGCATCTCTGTCTAAGCCCATCCCTAAGCCA
TGCATTTGTCGTTTGAATAGCATTTTGACTCCAAGATCCAGTAACAGAGGTCTTTTTAATATAC
GCTTCCAACCTATCTTTCAGTAACGGAAGCTCAATAAACAGGTGGTCTGTGTCGCGAATTCGGG
GTGTGTTTTGACAGACCTGTTTGAAAAGATAAATCATTAGTATTCACAGTAATTACAAACATAG
TCTTGCACCTCTGTAGAAAGCTATATCAACAAACACAATGGCCTATACAGTGAACTCTGTGAAC
CAGAAAAACAAAGTATGCTCCAGACAAACAAAATCAGCTAGCCATTACCAGTAATATATTACAA
GCATATGCAATAAATCTGTACGGCCACAACACTAGAACTGCATAATAACTGTCTTCACTTGTTA
ACTAGTGCAATTGCGCCTCATGTTTCCACATTTAAGTTATATTGATATCTCTACAATAGAAGGT
ACCCAAGATCTTTTTTGTGAACGGGAATTTGTACAGGCGTGAAGAAGCATGCAATGTCCCAGAG
AGACTTTACGAATACTGTAATGTATTGCTATAAACAGTATAAAACCACACAAATACAATCCCTT
AATGGGATGATGGCCATGAAGAAGAGAAGCATAGCCCACCTTGCACTTCGGATCTTTAAGTTCA
GTAGGATTCAGGAGCTTTCCACATTTTTCGCACTGATCTCCACGAGCAGAATCATAATTACATC
CTTCGAACGGACAAGAACCCTCAACAAGCCGGTCAGCTAAGAACTTCTTGCATGTATCGCAGTA
AAGCTGAAGATACAATGGGCCACAAAGACATGAGAGTTAAAACCCCGCTAACTGAGTGGTGTAG
ATCTTTTACTTACGAAGAACATATGTATGCACTTGCGATCAAATAAGTCTAACTGGCATTGGAG
TAAAAGCATTCACCTGCTGCATGGTGTTCTCTGAAAGCCACTTGTTGTCCCACAACTTGTTGAA
AATTGCTTGGCACACCTCAGTCTGTTCTGGAGTTGAAGTTCGCCCAAACTTGTCAAAACTTATA
CCAAACCAGTCATAAACTTCTTTATGAATGGCATGGTAC
						
					

			
		

Sequences
Splice junction sequence	TGCTTGGCACACCTCAGTCTGTTCTGGAGTTGAAGTTCGCCCAAACTTGTCAAAACTTATACCA AACCAGTCATAAACTTCTTTATGAATGGCATGGTACcttgcttccatcactactggaagctgca agaaccattgcttgtgacacaatatccctcattttcgccggtttcaagttgcaaagaacacaaa ccatacga
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	CTTGCTTCCATCACTACTGGAAGCTGCAAGAACCATTGCTTGTGACACAATATCCCTCATTTTC GCCGGTTTCAAGTTGCAAAGAACACAAACCATACGATTCTGTCCAGAAACAATATTAGATCAAT TGGAATGTATATTACATACTGATATCGGGAAGGAAACAAATGACTAGGTTGATTGAACAAACCT GCATTTCCTCAAGAGGTATATATTTGACCAGTCCACTGACAACAGTGCGAATTTCACCACCCCC AACATCAATTTCTTCTACATACAATGCATCTGCCTTGGGATGTTTCTCAGCCTTCACAATTTTA CCAACTCGGATATCAAGTCTTGCCATAGTTATTTCACGATCAGCAGCTGGTTGAGGTTTGGGTT TTCCTCCGCCTTTTGATGATGCCTTTTGTTTCTTGGCATCTGGGAGAATAAACAGCAGTTCAGT ACATAATCAAGTTACTAAAAGCCTAAAGAATGTAAAACAGTATTTTGAGAATGATAATAGAGAA CCTGAAAGTTTTGTTTTATTAAGTTGATCCGCCAAATTTGCTGCTTCATCCCTAGCACGTCTAT CAGACTGACTTCCAGCAAACTTTTCTCTGTACCGTGCCACTTCGTCGTTTTCCTGTGATCATAT TGTTTCAATATAAATAAAATGCTACATGGCATTATAACATACAACAAGTCTGGCTTTCTATCGA TAAAATCAGAGAGCTACGTACCAACTCCTTGAACAAAGGTTGAGGGGTGCCTATCCTGTGGCTA GGAGGCAGAATATCCCATGGTCTACTTGCTAGTAATACCTCTCCCCTCTCGTCGGAGAGAGAAA ATTGTGGAGGCAAATTTAGCTGTTTAAATACCTACAAAATGCAATAACAGCAATAATCACGCTT GGCATTCTACTACAACTAAATAGAAACAAAATTTACCAAACAAACAATCAAACTGACCTCACAA GAAAAGGATGGCATGAAAGGTTCTAACAATTGAGCAAGAAGGTGTACTAAACCAGCAGCAGTTC TTATAACAACTGCACACAAAGGTTTATCTTCCTTGTAAAGTTTCCAAAATTGGCTTGCCTACAT GGACACAAGAAAACAGTATAGTTGGTAATATGCAACAAAGCTAATATCTAGTTTGTTAATGAGA ATAGAACCTGCAAGTAATAGTTCCCTTCGCTTGAAATCAGCATAGCAGTTTTCAGTCCCTGCTT GAGCTTAACCTACATCAAATGAACAGGGGATTTATTAAGAACCTAAAAACCCAGGCACAGAAAC TCAGATAGCCATACCACGCCAAGGTTCATATAACATTCCTCACCTTTTCCATGGCTTCAACATA CTCTGCCACAAACTTTTCAACCTTTTCCGCCAGTGATTTTGTTAAAGAATGAGATTCAGCATCA TGAGCATCAGGAATGACAGACCCGTAACCTTCACAAAACATACAATAGTAAGGTATTGAAACAT CAAAGACAAATAAGAAAAGTCTTGCCCTAGTTGTCAAGAGTATCACAAAGCAGGTATCTCTCAC TTGCACACCAATAATAGTAAGCCAGATGCACCTTTCTATCATTCTAGAGTTTTTAGACTATCTA TTTGTCCCGCGATTCAAATATCTCTCACTTGCACACCAACTGGCTGGTTACAGTAGAAGAATAC AACACATCCTATATTTTCTATTGGATATGCCAGACTAAAAAGCTATCTACAGCTAACACCAAAC ACTTGAGTATTGAATTTGAAAGAAATATAACCAACCTGCATTATCAGGCTTTGCTATAAAACTC AGAACTCGATTAACAAAGTTGCCTAGGTTGCTCAGCAACTCGCCATTCAGTTTTGCTTGCAAAT CAGTCCATGAAAACGATGTGTCAGACACCTAGAAGGCAGAATCCCCAGAATCAATCAGTGTATG TGATATTTATGCATGCCTATGATGAACGAAGAAACAATGTTTCTATTTTGCAGCAGCAATCAGT TACCTCAGGCCTGTTGGTCAGCAAGTAGTATCTCCACACTTCGACAGGTATATTTGTATCTTTT ACATCATTACCAAACACTCCAACACCTTTACTCTTGGAGAACTTTCCTGAAAACCCATACAAAA CACATGTCCTCATTTTCTATAAATGGCATAAAAAGTAAATCAAACAAAAATAATTTAAAATAAA ATCACTCAGCTATGGTGAAACATCAACTGACCGTCTTCATAGTTTAAATATTCAGTCACACTGA TTGTCTTCATGAGTGTCCAATTTTCCTCAGTTCCAAGCTGGGTAGAGGGAAACATCACCTGCAT AACAAAAAATTTAGCAGTTGAAAACAACCAAATACAAAAGATAAACATTTCTTAAGAAGACCTT GAGGATAGCTTCAGAAAAGACAAGAACCAAACAAACTTTTGGTGTTCTATTTCAGTATAAAAGA AAGGTAAAGAAAAAGGAAATAATTAAAACCATTGGCACAAGTCCTTGGTGGTAAACAAATTTCT GAAATGTTATATACTCACAGTGTGAAATGGCACATTGTCTTTCCCCATAAACTGATAAAGCTCC ACATTCTCAGGATTCTTCCACCACTTCTCCCATTCAGATGTGTAGCAAGACGTTATTGAGACGT ATCCAATAGGAGCATCAAACCAAACATAGAAGACCTATAACCATGATTGGAATTAGTAGTTGAT CTTTAAATTTTTATGAAACTGGCTGGCAGTGAGGTTCCTACTTTGTCCTTGTATTTCTCATGTG GGACAGGCACTCCCCACTTAAGATCCCTCGTAATGCATCTCTGTCTAAGCCCATCCCTAAGCCA TGCATTTGTCGTTTGAATAGCATTTTGACTCCAAGATCCAGTAACAGAGGTCTTTTTAATATAC GCTTCCAACCTATCTTTCAGTAACGGAAGCTCAATAAACAGGTGGTCTGTGTCGCGAATTCGGG GTGTGTTTTGACAGACCTGTTTGAAAAGATAAATCATTAGTATTCACAGTAATTACAAACATAG TCTTGCACCTCTGTAGAAAGCTATATCAACAAACACAATGGCCTATACAGTGAACTCTGTGAAC CAGAAAAACAAAGTATGCTCCAGACAAACAAAATCAGCTAGCCATTACCAGTAATATATTACAA GCATATGCAATAAATCTGTACGGCCACAACACTAGAACTGCATAATAACTGTCTTCACTTGTTA ACTAGTGCAATTGCGCCTCATGTTTCCACATTTAAGTTATATTGATATCTCTACAATAGAAGGT ACCCAAGATCTTTTTTGTGAACGGGAATTTGTACAGGCGTGAAGAAGCATGCAATGTCCCAGAG AGACTTTACGAATACTGTAATGTATTGCTATAAACAGTATAAAACCACACAAATACAATCCCTT AATGGGATGATGGCCATGAAGAAGAGAAGCATAGCCCACCTTGCACTTCGGATCTTTAAGTTCA GTAGGATTCAGGAGCTTTCCACATTTTTCGCACTGATCTCCACGAGCAGAATCATAATTACATC CTTCGAACGGACAAGAACCCTCAACAAGCCGGTCAGCTAAGAACTTCTTGCATGTATCGCAGTA AAGCTGAAGATACAATGGGCCACAAAGACATGAGAGTTAAAACCCCGCTAACTGAGTGGTGTAG ATCTTTTACTTACGAAGAACATATGTATGCACTTGCGATCAAATAAGTCTAACTGGCATTGGAG TAAAAGCATTCACCTGCTGCATGGTGTTCTCTGAAAGCCACTTGTTGTCCCACAACTTGTTGAA AATTGCTTGGCACACCTCAGTCTGTTCTGGAGTTGAAGTTCGCCCAAACTTGTCAAAACTTATA CCAAACCAGTCATAAACTTCTTTATGAATGGCATGGTAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.140153511

Conservation Information
Conserved circRNAs	NA
PMCS	0.140153511

			
						 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 AT4G13780_circ_g.1

Address

Any questions?

Supported by