Plant Circular RNA Database

Detail information of AT4G10070_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT4G10070_circ_g.5
					
						ID in PlantcircBase
						ath_circ_030142
					
						Alias
						4:6298227-6299450
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 6298227-6299450  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G10070						
					
						Parent gene annotation
						
							KH domain-containing protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G10070_circ_g.3 AT4G10070_circ_g.4 AT4G10070_circ_g.6 AT4G10070_circ_g.7 						
					
						Support reads
						1/2
					
						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  
						
							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
						AT4G10070.1:5

General Information
CircRNA Name	AT4G10070_circ_g.5
ID in PlantcircBase	ath_circ_030142
Alias	4:6298227-6299450
Organism	Arabidpsis thaliana
Position	chr4: 6298227-6299450 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G10070
Parent gene annotation	KH domain-containing protein
Parent gene strand	-
Alternative splicing	AT4G10070_circ_g.3 AT4G10070_circ_g.4 AT4G10070_circ_g.6 AT4G10070_circ_g.7
Support reads	1/2
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	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	AT4G10070.1:5

			
						 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  
						
							ACAAGTGGTACAGAATCTTGATTCTCTTCCTTAGGTTCCTGAAGCTGTTCTTCCTCTTTTACCT
CCATTGAAGACCCATTTTCTTGTGTATTCCCATAATctggttcataacatcttttatcatgtca
gttgctatatcaatctgcatcttatctccagatatacggacagtcctctccttcaatccatcac
cttctgca

									
								

					

						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: 866
Transcript exons: 6298227-6298340,6298458-6298529,6298594-6298695,6298782-
6298967,6299059-6299450
CTGGTTCATAACATCTTTTATCATGTCAGTTGCTATATCAATCTGCATCTTATCTCCAGATATA
CGGACAGTCCTCTCCTTCAATCCATCACCTTCTGCATGTTGTGGTATTAACTGAGTACGTGCTC
CTGACCTTGTCTGCATATTCTTGATTGTCTCGCCACCTCGGCCAATAATCAGACCAACCTTATC
ATTTGGAACTTTAATCTCTATCTGTTCTGGGATCCCTATCGCATGAGTGGAAGGATGGCCCCTA
GCAACTAGGGCAGGTGAACCTCCTGCTTCAGCCTCTGCTATGACTGCACTGATAAGCTTCTCAG
CACTTTCAATGCATGCAACACTTCCAATTATCTCCACTGGTCTTAACGCTGAGCTCGGATCAGC
TTCTGAATCCCTCAAAATTTGGATTTTGGCACCAGAGTTAAACTGAAGATACCGTATAGTCTCC
CCACCTTTACCAATCAACACACCTACCTTTGAACTTGGGACATCTATCCTACGAGTTGTCGACT
GTGTGCCATCAACCTCCTTCTGAGATTTTTCACCATCCACTTCCTTATTTTCTTCTTTACCATT
CTCTTGAGAACTACCATCATTCACTTCCTTACTATCGTCATCAATCACCTTCTGATGTTCACCA
CCATTGACATCCTCAATACAACCTTGTTGGTTATCCTCAGGCTTAACCTGATCATCTGTTGGCT
GATCTACACTACAAATCTTATTTTCAGACTCATCAGCATGAATAGGATCCTGAACTTCCTCAAC
AAGTGGTACAGAATCTTGATTCTCTTCCTTAGGTTCCTGAAGCTGTTCTTCCTCTTTTACCTCC
ATTGAAGACCCATTTTCTTGTGTATTCCCATAAT
						
					

						Genomic sequence
						
							CTGGTTCATAACATCTTTTATCATGTCAGTTGCTATATCAATCTGCATCTTATCTCCAGATATA
CGGACAGTCCTCTCCTTCAATCCATCACCTTCTGCATGTTGTGGTATTAACTACACAACAAATT
TTAAAATCAGTTGTCACATAGAATGAGACAAGGTAAACACGTTTCCTAAAATTTAAATACTTTC
AGTCAGTTTCTATTTTTAACATCATACACAAGTAACCACCTGAGTACGTGCTCCTGACCTTGTC
TGCATATTCTTGATTGTCTCGCCACCTCGGCCAATAATCAGACCAACCTGTCAGTTGAAGCTGA
ATTAGATATGATTAAATTGTTGCTGGAAAGAATAAACTAGGGAATACCTTATCATTTGGAACTT
TAATCTCTATCTGTTCTGGGATCCCTATCGCATGAGTGGAAGGATGGCCCCTAGCAACTAGGGC
AGGTGAACCTCCTGCTTCAGCCTAATGTAGTACGAGAAGAAATTCTTGTAACCAAATATCTTAC
AGATACAAAGATGCCAAAACTACTGAAAAAAACAACTGTTAACCTCTGCTATGACTGCACTGAT
AAGCTTCTCAGCACTTTCAATGCATGCAACACTTCCAATTATCTCCACTGGTCTTAACGCTGAG
CTCGGATCAGCTTCTGAATCCCTCAAAATTTGGATTTTGGCACCAGAGTTAAACTGAAGATACC
GTATAGTCTCCCCACCTTTACCAATCAACACACCTACCTGCAAAGCATTGTGATAAGCACGTCA
GTGAAAGTATTCCGAAAGAAAAAAACTCACAGAACAGCCAAAAATGAAAACCAAATCATATCAC
CTTTGAACTTGGGACATCTATCCTACGAGTTGTCGACTGTGTGCCATCAACCTCCTTCTGAGAT
TTTTCACCATCCACTTCCTTATTTTCTTCTTTACCATTCTCTTGAGAACTACCATCATTCACTT
CCTTACTATCGTCATCAATCACCTTCTGATGTTCACCACCATTGACATCCTCAATACAACCTTG
TTGGTTATCCTCAGGCTTAACCTGATCATCTGTTGGCTGATCTACACTACAAATCTTATTTTCA
GACTCATCAGCATGAATAGGATCCTGAACTTCCTCAACAAGTGGTACAGAATCTTGATTCTCTT
CCTTAGGTTCCTGAAGCTGTTCTTCCTCTTTTACCTCCATTGAAGACCCATTTTCTTGTGTATT
CCCATAAT
						
					

			
		

Sequences
Splice junction sequence	ACAAGTGGTACAGAATCTTGATTCTCTTCCTTAGGTTCCTGAAGCTGTTCTTCCTCTTTTACCT CCATTGAAGACCCATTTTCTTGTGTATTCCCATAATctggttcataacatcttttatcatgtca gttgctatatcaatctgcatcttatctccagatatacggacagtcctctccttcaatccatcac cttctgca
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: 866 Transcript exons: 6298227-6298340,6298458-6298529,6298594-6298695,6298782- 6298967,6299059-6299450 CTGGTTCATAACATCTTTTATCATGTCAGTTGCTATATCAATCTGCATCTTATCTCCAGATATA CGGACAGTCCTCTCCTTCAATCCATCACCTTCTGCATGTTGTGGTATTAACTGAGTACGTGCTC CTGACCTTGTCTGCATATTCTTGATTGTCTCGCCACCTCGGCCAATAATCAGACCAACCTTATC ATTTGGAACTTTAATCTCTATCTGTTCTGGGATCCCTATCGCATGAGTGGAAGGATGGCCCCTA GCAACTAGGGCAGGTGAACCTCCTGCTTCAGCCTCTGCTATGACTGCACTGATAAGCTTCTCAG CACTTTCAATGCATGCAACACTTCCAATTATCTCCACTGGTCTTAACGCTGAGCTCGGATCAGC TTCTGAATCCCTCAAAATTTGGATTTTGGCACCAGAGTTAAACTGAAGATACCGTATAGTCTCC CCACCTTTACCAATCAACACACCTACCTTTGAACTTGGGACATCTATCCTACGAGTTGTCGACT GTGTGCCATCAACCTCCTTCTGAGATTTTTCACCATCCACTTCCTTATTTTCTTCTTTACCATT CTCTTGAGAACTACCATCATTCACTTCCTTACTATCGTCATCAATCACCTTCTGATGTTCACCA CCATTGACATCCTCAATACAACCTTGTTGGTTATCCTCAGGCTTAACCTGATCATCTGTTGGCT GATCTACACTACAAATCTTATTTTCAGACTCATCAGCATGAATAGGATCCTGAACTTCCTCAAC AAGTGGTACAGAATCTTGATTCTCTTCCTTAGGTTCCTGAAGCTGTTCTTCCTCTTTTACCTCC ATTGAAGACCCATTTTCTTGTGTATTCCCATAAT
Genomic sequence	CTGGTTCATAACATCTTTTATCATGTCAGTTGCTATATCAATCTGCATCTTATCTCCAGATATA CGGACAGTCCTCTCCTTCAATCCATCACCTTCTGCATGTTGTGGTATTAACTACACAACAAATT TTAAAATCAGTTGTCACATAGAATGAGACAAGGTAAACACGTTTCCTAAAATTTAAATACTTTC AGTCAGTTTCTATTTTTAACATCATACACAAGTAACCACCTGAGTACGTGCTCCTGACCTTGTC TGCATATTCTTGATTGTCTCGCCACCTCGGCCAATAATCAGACCAACCTGTCAGTTGAAGCTGA ATTAGATATGATTAAATTGTTGCTGGAAAGAATAAACTAGGGAATACCTTATCATTTGGAACTT TAATCTCTATCTGTTCTGGGATCCCTATCGCATGAGTGGAAGGATGGCCCCTAGCAACTAGGGC AGGTGAACCTCCTGCTTCAGCCTAATGTAGTACGAGAAGAAATTCTTGTAACCAAATATCTTAC AGATACAAAGATGCCAAAACTACTGAAAAAAACAACTGTTAACCTCTGCTATGACTGCACTGAT AAGCTTCTCAGCACTTTCAATGCATGCAACACTTCCAATTATCTCCACTGGTCTTAACGCTGAG CTCGGATCAGCTTCTGAATCCCTCAAAATTTGGATTTTGGCACCAGAGTTAAACTGAAGATACC GTATAGTCTCCCCACCTTTACCAATCAACACACCTACCTGCAAAGCATTGTGATAAGCACGTCA GTGAAAGTATTCCGAAAGAAAAAAACTCACAGAACAGCCAAAAATGAAAACCAAATCATATCAC CTTTGAACTTGGGACATCTATCCTACGAGTTGTCGACTGTGTGCCATCAACCTCCTTCTGAGAT TTTTCACCATCCACTTCCTTATTTTCTTCTTTACCATTCTCTTGAGAACTACCATCATTCACTT CCTTACTATCGTCATCAATCACCTTCTGATGTTCACCACCATTGACATCCTCAATACAACCTTG TTGGTTATCCTCAGGCTTAACCTGATCATCTGTTGGCTGATCTACACTACAAATCTTATTTTCA GACTCATCAGCATGAATAGGATCCTGAACTTCCTCAACAAGTGGTACAGAATCTTGATTCTCTT CCTTAGGTTCCTGAAGCTGTTCTTCCTCTTTTACCTCCATTGAAGACCCATTTTCTTGTGTATT CCCATAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.224626097

Conservation Information
Conserved circRNAs	NA
PMCS	0.224626097

			
						 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 AT4G10070_circ_g.5

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