Plant Circular RNA Database

Detail information of AT4G38760_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT4G38760_circ_g.9
					
						ID in PlantcircBase
						ath_circ_035475
					
						Alias
						4:18091515-18093340
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 18091515-18093340  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G38760						
					
						Parent gene annotation
						
							Protein of unknown function (DUF3414)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G38760_circ_g.7 AT4G38760_circ_g.8 AT4G38760_circ_g.10 AT4G38760_circ_g.11 AT4G38760_circ_g.12 AT4G38760_circ_g.13 AT4G38760_circ_g.14 AT4G38760_circ_g.15 						
					
						Support reads
						3
					
						Tissues
						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
						AT4G38760.1:8

General Information
CircRNA Name	AT4G38760_circ_g.9
ID in PlantcircBase	ath_circ_035475
Alias	4:18091515-18093340
Organism	Arabidpsis thaliana
Position	chr4: 18091515-18093340 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G38760
Parent gene annotation	Protein of unknown function (DUF3414)
Parent gene strand	-
Alternative splicing	AT4G38760_circ_g.7 AT4G38760_circ_g.8 AT4G38760_circ_g.10 AT4G38760_circ_g.11 AT4G38760_circ_g.12 AT4G38760_circ_g.13 AT4G38760_circ_g.14 AT4G38760_circ_g.15
Support reads	3
Tissues	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	AT4G38760.1:8

			
						 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  
						
							TCTCTAGATAATAGAGTTTTACCTGAAGATTGATCTCATAAGATGCAATAAATGCTGAAATAAA
AGTCCTCACGACACTACGATGACCAGAAATTGGTCCctcaatgaaatattatagccactgtcag
ggacgtctgaacatgaagtcatgtcaaatatatttgactttaagaccatgggagcaacacttga
cggggaac

									
								

					

						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
						
							CTCAATGAAATATTATAGCCACTGTCAGGGACGTCTGAACATGAAGTCATGTCAAATATATTTG
ACTTTAAGACCATGGGAGCAACACTTGACGGGGAACTGCTCAAAGAGTAAAATAAAATTAGCTA
TCAATGTTCCAGAGAGAAGTGATACCGAATTCCAAACTATACCATATAACAAGACATTGCACAT
GACATGTAATATTATGACACGCATTTGCTAGAAAAGAAATACTGAAGAAAAAATTGATAACCAA
GACAGCAAAAGAATAAGCATTACAACAAAAATTACCATCGCAGTAGTTTAGCTAAGATATCAAT
AGCCATTGCCATCACAGCGGCACCGCCAGAGTCAAAAGTCAGGCTTCTGACTGAATTACAAATT
ATATCAACCACCCTGGAACAAAAAAATCCCTGTTCAAGTACTCCGGAAGAGAGCATGTAAGAAA
GAAATAAAAATGCAAATACTTCACCTCACATCACTTTCCATCTTCCCATTCACATAAGATTCTT
GAACATAAAAGAAGTGGCTGATATTCAGTAAGGAGAAACATACGGCCTGAAATCAAATTACAGA
ACCTGGTCAGAGAAGTAAAAATACGGATGCATAGCCTTCATTCAAATTTTGAGAACGGTCAGAG
AAGAATTGATTCAAAGGCAGAAAAGCCATAGACTACTTCATGGTGTACAAATACTAAAGCAATC
CCTACTTCATAACCTGGATAAAAATGAAAATGGAGCAATGCAGTTACCTTGTTAAATGTCACCA
TCCGACGAAGTAGCTCCAGAGTCACAAAAGCTTCACGATTGTTACCAATGTAGAGTTTATTGGC
CAAACGGATGATCAACACAATTATGCCGGATAGCGAATACTTGGAAAGGAAAATGTATTTCATG
AATCAGTAAGACCATAAAAAATATAACATTGGAGGAGTCTATGAATAAGGTTTTCAAAGAATGA
TGAGATCACTTACCTCCCACCGTACAAGGACAGTATTTTCACTGATTACTCTCAGAATTCGCCC
ACGAGTATTACTGGGAATAACTAAACCTTCGAGACCTGGAATATGCAACGGCCGGGAAGTTTCA
ACAAGTTGAGAGGCATCATCCGCTGGAGAGTCACTAGTAATATCAAATAAGGTTGATACCCCGA
CTGATTTATCCAGAAAGTTGTATCTGCACAAAAAAAAAGAACAGCAGATTGCAGGAGGGTGATG
GTTTGAAACCAGTAAATAAGAAATTCTGTACTGAGACAAGAAAAGAAGCTTAGATTGATGAATG
CAAAACATTGCTCTCGTCTACATAGAAAAGTTCCATATAAAAGTACATAAACGCAGATAGTATA
TTGTCCAGTTCATACTTACACACATTCAGCAGGCCAACTTCCTTCACTCAGGGACGACAAGAGG
CGAATGAATTCAGCACTTCTGAATGGAAATTCACTCTCCAGATCAAAGAGGAGACACCGGATAG
GGCCATCAACAAAACTTTTTCGATCCCAAAACTGACAACAGAGGGACTCCTGAATAATTAAGCA
CACAATGAGCATTTATGGATGTCTAACATAGAGGAAAAAGCTAGGGACAACATGCATATATGAT
TTTTACCTCTCCTTGATAAACCTTAGAGAGGATGTCCAGTATCAACTCGAGGGTGCCATCTTCC
AGCTACCAAAAATGTAAAGATGACTAAGACTTTTAAACACTTCATAATTATATAATTTATCATC
TCTAGATAATAGAGTTTTACCTGAAGATTGATCTCATAAGATGCAATAAATGCTGAAATAAAAG
TCCTCACGACACTACGATGACCAGAAATTGGTCC
						
					

			
		

Sequences
Splice junction sequence	TCTCTAGATAATAGAGTTTTACCTGAAGATTGATCTCATAAGATGCAATAAATGCTGAAATAAA AGTCCTCACGACACTACGATGACCAGAAATTGGTCCctcaatgaaatattatagccactgtcag ggacgtctgaacatgaagtcatgtcaaatatatttgactttaagaccatgggagcaacacttga cggggaac
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	CTCAATGAAATATTATAGCCACTGTCAGGGACGTCTGAACATGAAGTCATGTCAAATATATTTG ACTTTAAGACCATGGGAGCAACACTTGACGGGGAACTGCTCAAAGAGTAAAATAAAATTAGCTA TCAATGTTCCAGAGAGAAGTGATACCGAATTCCAAACTATACCATATAACAAGACATTGCACAT GACATGTAATATTATGACACGCATTTGCTAGAAAAGAAATACTGAAGAAAAAATTGATAACCAA GACAGCAAAAGAATAAGCATTACAACAAAAATTACCATCGCAGTAGTTTAGCTAAGATATCAAT AGCCATTGCCATCACAGCGGCACCGCCAGAGTCAAAAGTCAGGCTTCTGACTGAATTACAAATT ATATCAACCACCCTGGAACAAAAAAATCCCTGTTCAAGTACTCCGGAAGAGAGCATGTAAGAAA GAAATAAAAATGCAAATACTTCACCTCACATCACTTTCCATCTTCCCATTCACATAAGATTCTT GAACATAAAAGAAGTGGCTGATATTCAGTAAGGAGAAACATACGGCCTGAAATCAAATTACAGA ACCTGGTCAGAGAAGTAAAAATACGGATGCATAGCCTTCATTCAAATTTTGAGAACGGTCAGAG AAGAATTGATTCAAAGGCAGAAAAGCCATAGACTACTTCATGGTGTACAAATACTAAAGCAATC CCTACTTCATAACCTGGATAAAAATGAAAATGGAGCAATGCAGTTACCTTGTTAAATGTCACCA TCCGACGAAGTAGCTCCAGAGTCACAAAAGCTTCACGATTGTTACCAATGTAGAGTTTATTGGC CAAACGGATGATCAACACAATTATGCCGGATAGCGAATACTTGGAAAGGAAAATGTATTTCATG AATCAGTAAGACCATAAAAAATATAACATTGGAGGAGTCTATGAATAAGGTTTTCAAAGAATGA TGAGATCACTTACCTCCCACCGTACAAGGACAGTATTTTCACTGATTACTCTCAGAATTCGCCC ACGAGTATTACTGGGAATAACTAAACCTTCGAGACCTGGAATATGCAACGGCCGGGAAGTTTCA ACAAGTTGAGAGGCATCATCCGCTGGAGAGTCACTAGTAATATCAAATAAGGTTGATACCCCGA CTGATTTATCCAGAAAGTTGTATCTGCACAAAAAAAAAGAACAGCAGATTGCAGGAGGGTGATG GTTTGAAACCAGTAAATAAGAAATTCTGTACTGAGACAAGAAAAGAAGCTTAGATTGATGAATG CAAAACATTGCTCTCGTCTACATAGAAAAGTTCCATATAAAAGTACATAAACGCAGATAGTATA TTGTCCAGTTCATACTTACACACATTCAGCAGGCCAACTTCCTTCACTCAGGGACGACAAGAGG CGAATGAATTCAGCACTTCTGAATGGAAATTCACTCTCCAGATCAAAGAGGAGACACCGGATAG GGCCATCAACAAAACTTTTTCGATCCCAAAACTGACAACAGAGGGACTCCTGAATAATTAAGCA CACAATGAGCATTTATGGATGTCTAACATAGAGGAAAAAGCTAGGGACAACATGCATATATGAT TTTTACCTCTCCTTGATAAACCTTAGAGAGGATGTCCAGTATCAACTCGAGGGTGCCATCTTCC AGCTACCAAAAATGTAAAGATGACTAAGACTTTTAAACACTTCATAATTATATAATTTATCATC TCTAGATAATAGAGTTTTACCTGAAGATTGATCTCATAAGATGCAATAAATGCTGAAATAAAAG TCCTCACGACACTACGATGACCAGAAATTGGTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.156357986

Conservation Information
Conserved circRNAs	NA
PMCS	0.156357986

			
						 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 AT4G38760_circ_g.9

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