Plant Circular RNA Database

Detail information of AT5G48600_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT5G48600_circ_g.6
					
						ID in PlantcircBase
						ath_circ_043121
					
						Alias
						5:19704271-19705075
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 19704271-19705075  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G48600						
					
						Parent gene annotation
						
							Structural maintenance of chromosomes protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G48600_circ_g.7 						
					
						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  
						
							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
						AT5G48600.2:3
AT5G48600.1:3

General Information
CircRNA Name	AT5G48600_circ_g.6
ID in PlantcircBase	ath_circ_043121
Alias	5:19704271-19705075
Organism	Arabidpsis thaliana
Position	chr5: 19704271-19705075 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G48600
Parent gene annotation	Structural maintenance of chromosomes protein
Parent gene strand	+
Alternative splicing	AT5G48600_circ_g.7
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	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	AT5G48600.2:3 AT5G48600.1:3

			
						 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  
						
							AAGAGTCAGAATGAGGTTTTGAAGGCAGTTTTAAGAGCGAAGGAGAACAATCAAATTGAAGGAA
TATATGGAAGGATGGGGGACTTAGGTGCCATTGATGttgaaactgaaggttaccggtctgagct
tacaaaaattcgtgctgaattagaaccttgggaaaaagatctaattgtgcacaggggaaagctt
gatgttgc

						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: 474
Transcript exons: 19704271-19704401,19704656-19704808,19704886-19705075
TTGAAACTGAAGGTTACCGGTCTGAGCTTACAAAAATTCGTGCTGAATTAGAACCTTGGGAAAA
AGATCTAATTGTGCACAGGGGAAAGCTTGATGTTGCATCATCCGAAAGTGAACTCTTGAGCAAG
AAGCATGAAGCTGCTCTGAAAGCCTTCACAGATGCTCAGAAACAGCTCTCTGATATATCAACGA
GAAAAAAAGAAAAAGCTGCAGCAACTACCTCTTGGAAAGCTGATATAAAGAAGAAGAAACAGGA
AGCAATCGAAGCTCGGAAAGTGGAAGAGGAATCACTTAAAGAACAAGAAACACTCGTTCCACAA
GAACAGGCAGCCAGAGAAAAAGTTGCTGAGCTCAAATCAGCAATGAATTCTGAGAAGAGTCAGA
ATGAGGTTTTGAAGGCAGTTTTAAGAGCGAAGGAGAACAATCAAATTGAAGGAATATATGGAAG
GATGGGGGACTTAGGTGCCATTGATG
						
						Genomic sequence
						
							TTGAAACTGAAGGTTACCGGTCTGAGCTTACAAAAATTCGTGCTGAATTAGAACCTTGGGAAAA
AGATCTAATTGTGCACAGGGGAAAGCTTGATGTTGCATCATCCGAAAGTGAACTCTTGAGCAAG
AAGGTACATCTCATATAGTTATAACGATTTGCTTGGAGTCAAGAACTTTTGCTTGTCAAAATAA
CTTGGCTCGTCTTCAAAAGAATTTCTAGAGAGGTTTTTAATTAGCTTATCCCACTGCTTCTTTA
AAGAATTCGTTTGCCATAGTCAAATCTTTATATGCTTCCTGGAGCTGCTTTCGCGCTGAATAAT
CCAAAATACTGTTGGACGACTAATTTTTTTGTTTCTGTTTGAACATTACCTCTTTGTTATTCTA
GCATGAAGCTGCTCTGAAAGCCTTCACAGATGCTCAGAAACAGCTCTCTGATATATCAACGAGA
AAAAAAGAAAAAGCTGCAGCAACTACCTCTTGGAAAGCTGATATAAAGAAGAAGAAACAGGAAG
CAATCGAAGCTCGGAAAGTGGAAGAGGTACTTTTATTAAGATATGACTGTAATCTGTGCAGCTT
AGATGGTGAAACTGAGAGTATGCATCTTAACTTCTGCAGGAATCACTTAAAGAACAAGAAACAC
TCGTTCCACAAGAACAGGCAGCCAGAGAAAAAGTTGCTGAGCTCAAATCAGCAATGAATTCTGA
GAAGAGTCAGAATGAGGTTTTGAAGGCAGTTTTAAGAGCGAAGGAGAACAATCAAATTGAAGGA
ATATATGGAAGGATGGGGGACTTAGGTGCCATTGATG

Sequences
Splice junction sequence	AAGAGTCAGAATGAGGTTTTGAAGGCAGTTTTAAGAGCGAAGGAGAACAATCAAATTGAAGGAA TATATGGAAGGATGGGGGACTTAGGTGCCATTGATGttgaaactgaaggttaccggtctgagct tacaaaaattcgtgctgaattagaaccttgggaaaaagatctaattgtgcacaggggaaagctt gatgttgc
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: 474 Transcript exons: 19704271-19704401,19704656-19704808,19704886-19705075 TTGAAACTGAAGGTTACCGGTCTGAGCTTACAAAAATTCGTGCTGAATTAGAACCTTGGGAAAA AGATCTAATTGTGCACAGGGGAAAGCTTGATGTTGCATCATCCGAAAGTGAACTCTTGAGCAAG AAGCATGAAGCTGCTCTGAAAGCCTTCACAGATGCTCAGAAACAGCTCTCTGATATATCAACGA GAAAAAAAGAAAAAGCTGCAGCAACTACCTCTTGGAAAGCTGATATAAAGAAGAAGAAACAGGA AGCAATCGAAGCTCGGAAAGTGGAAGAGGAATCACTTAAAGAACAAGAAACACTCGTTCCACAA GAACAGGCAGCCAGAGAAAAAGTTGCTGAGCTCAAATCAGCAATGAATTCTGAGAAGAGTCAGA ATGAGGTTTTGAAGGCAGTTTTAAGAGCGAAGGAGAACAATCAAATTGAAGGAATATATGGAAG GATGGGGGACTTAGGTGCCATTGATG
Genomic sequence	TTGAAACTGAAGGTTACCGGTCTGAGCTTACAAAAATTCGTGCTGAATTAGAACCTTGGGAAAA AGATCTAATTGTGCACAGGGGAAAGCTTGATGTTGCATCATCCGAAAGTGAACTCTTGAGCAAG AAGGTACATCTCATATAGTTATAACGATTTGCTTGGAGTCAAGAACTTTTGCTTGTCAAAATAA CTTGGCTCGTCTTCAAAAGAATTTCTAGAGAGGTTTTTAATTAGCTTATCCCACTGCTTCTTTA AAGAATTCGTTTGCCATAGTCAAATCTTTATATGCTTCCTGGAGCTGCTTTCGCGCTGAATAAT CCAAAATACTGTTGGACGACTAATTTTTTTGTTTCTGTTTGAACATTACCTCTTTGTTATTCTA GCATGAAGCTGCTCTGAAAGCCTTCACAGATGCTCAGAAACAGCTCTCTGATATATCAACGAGA AAAAAAGAAAAAGCTGCAGCAACTACCTCTTGGAAAGCTGATATAAAGAAGAAGAAACAGGAAG CAATCGAAGCTCGGAAAGTGGAAGAGGTACTTTTATTAAGATATGACTGTAATCTGTGCAGCTT AGATGGTGAAACTGAGAGTATGCATCTTAACTTCTGCAGGAATCACTTAAAGAACAAGAAACAC TCGTTCCACAAGAACAGGCAGCCAGAGAAAAAGTTGCTGAGCTCAAATCAGCAATGAATTCTGA GAAGAGTCAGAATGAGGTTTTGAAGGCAGTTTTAAGAGCGAAGGAGAACAATCAAATTGAAGGA ATATATGGAAGGATGGGGGACTTAGGTGCCATTGATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.206384256

Conservation Information
Conserved circRNAs	NA
PMCS	0.206384256

			
						 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 AT5G48600_circ_g.6

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