Plant Circular RNA Database

Detail information of AT1G52410_circ_g.21

			
						 General Information
					
						CircRNA Name
						AT1G52410_circ_g.21
					
						ID in PlantcircBase
						ath_circ_007015
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 19522402-19522642  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, CIRI-full, circRNA_finder
					
						Parent gene
						
							AT1G52410						
					
						Parent gene annotation
						
							TSK-associating protein 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G52410_circ_g.5 AT1G52410_circ_g.6 AT1G52410_circ_g.7 AT1G52410_circ_g.8 AT1G52410_circ_g.9 AT1G52410_circ_g.10 AT1G52410_circ_g.11 AT1G52410_circ_g.12 AT1G52410_circ_g.13 AT1G52410_circ_g.14 AT1G52410_circ_g.15 AT1G52410_circ_g.16 AT1G52410_circ_g.17 AT1G52410_circ_g.18 AT1G52410_circ_g.19 AT1G52410_circ_g.20 AT1G52410_circ_g.22 AT1G52410_circ_g.23 AT1G52410_circ_g.24 AT1G52410_circ_g.25 AT1G52410_circ_g.26 AT1G52410_circ_g.27 AT1G52410_circ_g.28 AT1G52410_circ_g.29 AT1G52410_circ_g.30 AT1G52410_circ_g.31 AT1G52410_circ_g.32 AT1G52410_circ_g.33 AT1G52410_circ_g.34 AT1G52410_circ_g.35 AT1G52410_circ_g.36 AT1G52410_circ_g.37 AT1G52410_circ_g.38 AT1G52410_circ_g.39 AT1G52410_circ_g.40 AT1G52410_circ_g.41 AT1G52410_circ_g.42 AT1G52410_circ_g.43 AT1G52410_circ_g.44 AT1G52410_circ_g.45 AT1G52410_circ_g.46 AT1G52410_circ_g.47 AT1G52410_circ_g.48 AT1G52410_circ_g.49 AT1G52410_circ_g.50 						
					
						Support reads
						29
					
						Tissues
						aerial, seed
					
						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
						AT1G52410.2:2
AT1G52410.1:2

General Information
CircRNA Name	AT1G52410_circ_g.21
ID in PlantcircBase	ath_circ_007015
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 19522402-19522642 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, CIRI-full, circRNA_finder
Parent gene	AT1G52410
Parent gene annotation	TSK-associating protein 1
Parent gene strand	+
Alternative splicing	AT1G52410_circ_g.5 AT1G52410_circ_g.6 AT1G52410_circ_g.7 AT1G52410_circ_g.8 AT1G52410_circ_g.9 AT1G52410_circ_g.10 AT1G52410_circ_g.11 AT1G52410_circ_g.12 AT1G52410_circ_g.13 AT1G52410_circ_g.14 AT1G52410_circ_g.15 AT1G52410_circ_g.16 AT1G52410_circ_g.17 AT1G52410_circ_g.18 AT1G52410_circ_g.19 AT1G52410_circ_g.20 AT1G52410_circ_g.22 AT1G52410_circ_g.23 AT1G52410_circ_g.24 AT1G52410_circ_g.25 AT1G52410_circ_g.26 AT1G52410_circ_g.27 AT1G52410_circ_g.28 AT1G52410_circ_g.29 AT1G52410_circ_g.30 AT1G52410_circ_g.31 AT1G52410_circ_g.32 AT1G52410_circ_g.33 AT1G52410_circ_g.34 AT1G52410_circ_g.35 AT1G52410_circ_g.36 AT1G52410_circ_g.37 AT1G52410_circ_g.38 AT1G52410_circ_g.39 AT1G52410_circ_g.40 AT1G52410_circ_g.41 AT1G52410_circ_g.42 AT1G52410_circ_g.43 AT1G52410_circ_g.44 AT1G52410_circ_g.45 AT1G52410_circ_g.46 AT1G52410_circ_g.47 AT1G52410_circ_g.48 AT1G52410_circ_g.49 AT1G52410_circ_g.50
Support reads	29
Tissues	aerial, seed
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	AT1G52410.2:2 AT1G52410.1:2

			
						 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  
						
							GTGATTTTCTATTTCAATCTCCTACTTGCAGCTGCTATGGAAGGCATTGAAGCACTTAAGGTTT
CTGATTCCACAGGAAGCGGAGATGATGAAGAACAATctgcaaagagaaaaagtatgcttgaagc
tattgaacgcgagtttgaaggtatcttgagacaccagtatgtttcaatatgttctaagaagaat
gcagaaac

						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: 117
Transcript exons: 19522402-19522642
CTGCAAAGAGAAAAAGTATGCTTGAAGCTATTGAACGCGAGTTTGAAGCTGCTATGGAAGGCAT
TGAAGCACTTAAGGTTTCTGATTCCACAGGAAGCGGAGATGATGAAGAACAAT
						
						Genomic sequence
						
							CTGCAAAGAGAAAAAGTATGCTTGAAGCTATTGAACGCGAGTTTGAAGGTATCTTGAGACACCA
GTATGTTTCAATATGTTCTAAGAAGAATGCAGAAACCATTATAAATCAATCTGAGTATCATCTA
AGAGTTTGTTTGTGTGATTTTCTATTTCAATCTCCTACTTGCAGCTGCTATGGAAGGCATTGAA
GCACTTAAGGTTTCTGATTCCACAGGAAGCGGAGATGATGAAGAACAAT

Sequences
Splice junction sequence	GTGATTTTCTATTTCAATCTCCTACTTGCAGCTGCTATGGAAGGCATTGAAGCACTTAAGGTTT CTGATTCCACAGGAAGCGGAGATGATGAAGAACAATctgcaaagagaaaaagtatgcttgaagc tattgaacgcgagtttgaaggtatcttgagacaccagtatgtttcaatatgttctaagaagaat gcagaaac
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: 117 Transcript exons: 19522402-19522642 CTGCAAAGAGAAAAAGTATGCTTGAAGCTATTGAACGCGAGTTTGAAGCTGCTATGGAAGGCAT TGAAGCACTTAAGGTTTCTGATTCCACAGGAAGCGGAGATGATGAAGAACAAT
Genomic sequence	CTGCAAAGAGAAAAAGTATGCTTGAAGCTATTGAACGCGAGTTTGAAGGTATCTTGAGACACCA GTATGTTTCAATATGTTCTAAGAAGAATGCAGAAACCATTATAAATCAATCTGAGTATCATCTA AGAGTTTGTTTGTGTGATTTTCTATTTCAATCTCCTACTTGCAGCTGCTATGGAAGGCATTGAA GCACTTAAGGTTTCTGATTCCACAGGAAGCGGAGATGATGAAGAACAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.262312425

Conservation Information
Conserved circRNAs	NA
PMCS	0.262312425

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							19522628-19522639(+)
19522419-19522639(+)
19522590-19522404(-)
						
						Potential amino acid sequence
						
							MMKNNLQREKVCLKLLNASLKLLWKALKHLRFLIPQEAEMMKNNLQREKVCLKLLNASLKLLWK
ALKHLRFLIPQEAEMMKNNLQREKVCLKLLNASLKLLWKALKHLRFLIPQEAEMMKNN(+)
MLEAIEREFEAAMEGIEALKVSDSTGSGDDEEQSAKRKSMLEAIEREFEAAMEGIEALKVSDST
GSGDDEEQSAKRKSMLEAIEREFEAAMEGIEALKVSDSTGSGDDEEQSAKRKSMLEAIEREFEA
AMEGIEALKVSDSTGSGDDEEQ(+)
MPSIAASNSRSIASSILFLFADCSSSSPLPVESETLSASMPSIAASNSRSIASSILFLFADCSS
SSPLPVESETLSASMPSIAASNSRSIASSILFLFADCSSSSPLPVESETLSASMPSIAASNSRS
IASSILFLFA(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	19522628-19522639(+) 19522419-19522639(+) 19522590-19522404(-)
Potential amino acid sequence	MMKNNLQREKVCLKLLNASLKLLWKALKHLRFLIPQEAEMMKNNLQREKVCLKLLNASLKLLWK ALKHLRFLIPQEAEMMKNNLQREKVCLKLLNASLKLLWKALKHLRFLIPQEAEMMKNN(+) MLEAIEREFEAAMEGIEALKVSDSTGSGDDEEQSAKRKSMLEAIEREFEAAMEGIEALKVSDST GSGDDEEQSAKRKSMLEAIEREFEAAMEGIEALKVSDSTGSGDDEEQSAKRKSMLEAIEREFEA AMEGIEALKVSDSTGSGDDEEQ(+) MPSIAASNSRSIASSILFLFADCSSSSPLPVESETLSASMPSIAASNSRSIASSILFLFADCSS SSPLPVESETLSASMPSIAASNSRSIASSILFLFADCSSSSPLPVESETLSASMPSIAASNSRS IASSILFLFA(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G52410_circ_g.21

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