Plant Circular RNA Database

Detail information of AT1G50200_circ_g.28

			
						 General Information
					
						CircRNA Name
						AT1G50200_circ_g.28
					
						ID in PlantcircBase
						ath_circ_006626
					
						Alias
						1:18596568-18597207
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 18596568-18597207  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G50200						
					
						Parent gene annotation
						
							Alanyl-tRNA synthetase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							1_circ_igg.3 AT1G50200_circ_g.1 AT1G50200_circ_g.2 AT1G50200_circ_g.3 AT1G50200_circ_g.4 AT1G50200_circ_g.5 AT1G50200_circ_g.6 AT1G50200_circ_g.7 AT1G50200_circ_g.8 AT1G50200_circ_g.9 AT1G50200_circ_g.10 AT1G50200_circ_g.11 AT1G50200_circ_g.12 AT1G50200_circ_g.13 AT1G50200_circ_g.14 AT1G50200_circ_g.15 AT1G50200_circ_g.16 AT1G50200_circ_g.17 AT1G50200_circ_g.18 AT1G50200_circ_g.19 AT1G50200_circ_g.20 AT1G50200_circ_g.21 AT1G50200_circ_g.22 AT1G50200_circ_g.23 AT1G50200_circ_g.24 AT1G50200_circ_g.25 AT1G50200_circ_g.26 AT1G50200_circ_g.27 AT1G50200_circ_g.29 						
					
						Support reads
						1/1/1
					
						Tissues
						seedling;root;leaf
					
						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
						AT1G50200.2:2
AT1G50200.1:2

General Information
CircRNA Name	AT1G50200_circ_g.28
ID in PlantcircBase	ath_circ_006626
Alias	1:18596568-18597207
Organism	Arabidpsis thaliana
Position	chr1: 18596568-18597207 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G50200
Parent gene annotation	Alanyl-tRNA synthetase
Parent gene strand	-
Alternative splicing	1_circ_igg.3 AT1G50200_circ_g.1 AT1G50200_circ_g.2 AT1G50200_circ_g.3 AT1G50200_circ_g.4 AT1G50200_circ_g.5 AT1G50200_circ_g.6 AT1G50200_circ_g.7 AT1G50200_circ_g.8 AT1G50200_circ_g.9 AT1G50200_circ_g.10 AT1G50200_circ_g.11 AT1G50200_circ_g.12 AT1G50200_circ_g.13 AT1G50200_circ_g.14 AT1G50200_circ_g.15 AT1G50200_circ_g.16 AT1G50200_circ_g.17 AT1G50200_circ_g.18 AT1G50200_circ_g.19 AT1G50200_circ_g.20 AT1G50200_circ_g.21 AT1G50200_circ_g.22 AT1G50200_circ_g.23 AT1G50200_circ_g.24 AT1G50200_circ_g.25 AT1G50200_circ_g.26 AT1G50200_circ_g.27 AT1G50200_circ_g.29
Support reads	1/1/1
Tissues	seedling;root;leaf
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	AT1G50200.2:2 AT1G50200.1:2

			
						 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  
						
							TCAACCATATATCCCTAGCCTCATTATCAGGTTGAAGGCCAGCTTTCTCATCACCGCCAAAATA
TGTAGCGTAGATTCGATCAGTCGGTAGCCCATAGACctgaataaagacaagattccatatttct
aaacatgttggatcgtcattgttaactaaggatgcagcatcacggttaccaatgcgatcataat
gtatttca

						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: 288
Transcript exons: 18596568-18596714,18597067-18597207
CTGAATAAAGACAAGATTCCATATTTCTAAACATGTTGGATCGTCATTGTTAACTAAGGATGCA
GCATCACGGTTACCAATGCGATCATAATGTATTTCAGTACAAGGTCCACACGGACCTGTGTCGC
CCATTTCCCAGAAATTGTCTTTGCAACCAAATGGCAGCACACGTCCAGATGGAAGAACCTTCAA
CCATATATCCCTAGCCTCATTATCAGGTTGAAGGCCAGCTTTCTCATCACCGCCAAAATATGTA
GCGTAGATTCGATCAGTCGGTAGCCCATAGAC
						
						Genomic sequence
						
							CTGAATAAAGACAAGATTCCATATTTCTAAACATGTTGGATCGTCATTGTTAACTAAGGATGCA
GCATCACGGTTACCAATGCGATCATAATGTATTTCAGTACAAGGTCCACACGGACCTGTGTCGC
CCATTTCCCAGAAATTGTCCTGCAGTTTAATCAAAAGTTAAATGAAAGAAAAACAGCATTTAAA
AACCCTTAAGTTTTACATTTTGTACAAGATTTTGACTGTAAATCATAAACAATGGTTTTTAAAG
CCTGCCAACTACCAAACATGATAGCGTATTCCTAGCCAAAATGCATTCAAGCTTACAGTTGGTT
GTCGTTAGCATTGACAAACAGATGTGTCAATATATACAAGAAACAATGGTGACAATACAAAGGC
AACTTAGCTGAAGTACTTGTGAAGTAACCTCAGGAGAGAGGAAATCAATGAGTAGTGGATTCAA
AAAAATTAGGTAACAGATTAAAAGTTATTATCTTAAATAATCAATACATACTTTGCAACCAAAT
GGCAGCACACGTCCAGATGGAAGAACCTTCAACCATATATCCCTAGCCTCATTATCAGGTTGAA
GGCCAGCTTTCTCATCACCGCCAAAATATGTAGCGTAGATTCGATCAGTCGGTAGCCCATAGAC

Sequences
Splice junction sequence	TCAACCATATATCCCTAGCCTCATTATCAGGTTGAAGGCCAGCTTTCTCATCACCGCCAAAATA TGTAGCGTAGATTCGATCAGTCGGTAGCCCATAGACctgaataaagacaagattccatatttct aaacatgttggatcgtcattgttaactaaggatgcagcatcacggttaccaatgcgatcataat gtatttca
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: 288 Transcript exons: 18596568-18596714,18597067-18597207 CTGAATAAAGACAAGATTCCATATTTCTAAACATGTTGGATCGTCATTGTTAACTAAGGATGCA GCATCACGGTTACCAATGCGATCATAATGTATTTCAGTACAAGGTCCACACGGACCTGTGTCGC CCATTTCCCAGAAATTGTCTTTGCAACCAAATGGCAGCACACGTCCAGATGGAAGAACCTTCAA CCATATATCCCTAGCCTCATTATCAGGTTGAAGGCCAGCTTTCTCATCACCGCCAAAATATGTA GCGTAGATTCGATCAGTCGGTAGCCCATAGAC
Genomic sequence	CTGAATAAAGACAAGATTCCATATTTCTAAACATGTTGGATCGTCATTGTTAACTAAGGATGCA GCATCACGGTTACCAATGCGATCATAATGTATTTCAGTACAAGGTCCACACGGACCTGTGTCGC CCATTTCCCAGAAATTGTCCTGCAGTTTAATCAAAAGTTAAATGAAAGAAAAACAGCATTTAAA AACCCTTAAGTTTTACATTTTGTACAAGATTTTGACTGTAAATCATAAACAATGGTTTTTAAAG CCTGCCAACTACCAAACATGATAGCGTATTCCTAGCCAAAATGCATTCAAGCTTACAGTTGGTT GTCGTTAGCATTGACAAACAGATGTGTCAATATATACAAGAAACAATGGTGACAATACAAAGGC AACTTAGCTGAAGTACTTGTGAAGTAACCTCAGGAGAGAGGAAATCAATGAGTAGTGGATTCAA AAAAATTAGGTAACAGATTAAAAGTTATTATCTTAAATAATCAATACATACTTTGCAACCAAAT GGCAGCACACGTCCAGATGGAAGAACCTTCAACCATATATCCCTAGCCTCATTATCAGGTTGAA GGCCAGCTTTCTCATCACCGCCAAAATATGTAGCGTAGATTCGATCAGTCGGTAGCCCATAGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.25673453

Conservation Information
Conserved circRNAs	NA
PMCS	0.25673453

			
						 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 AT1G50200_circ_g.28

Address

Any questions?

Supported by