Plant Circular RNA Database

Detail information of AT4G09760_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT4G09760_circ_g.4
					
						ID in PlantcircBase
						ath_circ_030107
					
						Alias
						At_ciR1021
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 6149691-6150091  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ, CIRI-full
					
						Parent gene
						
							AT4G09760						
					
						Parent gene annotation
						
							Probable choline kinase 3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G09760_circ_g.3 						
					
						Support reads
						6
					
						Tissues
						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
						AT4G09760.2:2
AT4G09760.3:2
AT4G09760.4:2
AT4G09760.1:2

General Information
CircRNA Name	AT4G09760_circ_g.4
ID in PlantcircBase	ath_circ_030107
Alias	At_ciR1021
Organism	Arabidpsis thaliana
Position	chr4: 6149691-6150091 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ, CIRI-full
Parent gene	AT4G09760
Parent gene annotation	Probable choline kinase 3
Parent gene strand	-
Alternative splicing	AT4G09760_circ_g.3
Support reads	6
Tissues	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	AT4G09760.2:2 AT4G09760.3:2 AT4G09760.4:2 AT4G09760.1:2

			
						 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  
						
							TAATTCTATCTCCAGGAATGTGTATGCTGTGAAATCTTCTTAGCTTAGATGCAACAAGAGCTGA
TATGTTCGGATCACGAAGATCGGTTGCCGATAGTGTaatgatagtaattgcattggtttcttca
tcaatcatgatgttaccatactgcaagtcattgtgacagaagccaatctcttgttcattgttca
cttcttgt

						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: 315
Transcript exons: 6149691-6150091
AATGATAGTAATTGCATTGGTTTCTTCATCAATCATGATGTTACCATACTGCAAGTCATTGTGA
CAGAAGCCAATCTCTTGTTCATTGTTCACTTCTTGTTCCAGCAGGTTGATTTCATCTTCAATGT
CGTCTAGACCAAACTCTGTTGAATGTTCATTTGAACATAGATTCTTGGCTTGTCCTACCCAAGT
CCTCATCCTGTCCCAGATGAGCATAATTCTATCTCCAGGAATGTGTATGCTGTGAAATCTTCTT
AGCTTAGATGCAACAAGAGCTGATATGTTCGGATCACGAAGATCGGTTGCCGATAGTGT
						
						Genomic sequence
						
							AATGATAGTAATTGCATTGGTTTCTTCATCAATCATGATGTTACCATACTGCAAGTCATTGTGA
CAGAAGCCAATCTCTTGTTCATTGTTCACTTCTTGTTCCAGCAGGTTGATTTCATCTTCAATGT
CGTCTAGACCAAACTCTGTTGAATGTTCATTTGAACATAGATTCTTGGCTTGTCCTACCCAAGT
CCTGTCATTTACATGTTCCAATGAATATTACTTTCATATGATCAAAATATTTACTAGGAAAATC
CTTTTAGTATGCAGTTTCTTTACCTCATCCTGTCCCAGATGAGCATAATTCTATCTCCAGGAAT
GTGTATGCTGTGAAATCTTCTTAGCTTAGATGCAACAAGAGCTGATATGTTCGGATCACGAAGA
TCGGTTGCCGATAGTGT

Sequences
Splice junction sequence	TAATTCTATCTCCAGGAATGTGTATGCTGTGAAATCTTCTTAGCTTAGATGCAACAAGAGCTGA TATGTTCGGATCACGAAGATCGGTTGCCGATAGTGTaatgatagtaattgcattggtttcttca tcaatcatgatgttaccatactgcaagtcattgtgacagaagccaatctcttgttcattgttca cttcttgt
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: 315 Transcript exons: 6149691-6150091 AATGATAGTAATTGCATTGGTTTCTTCATCAATCATGATGTTACCATACTGCAAGTCATTGTGA CAGAAGCCAATCTCTTGTTCATTGTTCACTTCTTGTTCCAGCAGGTTGATTTCATCTTCAATGT CGTCTAGACCAAACTCTGTTGAATGTTCATTTGAACATAGATTCTTGGCTTGTCCTACCCAAGT CCTCATCCTGTCCCAGATGAGCATAATTCTATCTCCAGGAATGTGTATGCTGTGAAATCTTCTT AGCTTAGATGCAACAAGAGCTGATATGTTCGGATCACGAAGATCGGTTGCCGATAGTGT
Genomic sequence	AATGATAGTAATTGCATTGGTTTCTTCATCAATCATGATGTTACCATACTGCAAGTCATTGTGA CAGAAGCCAATCTCTTGTTCATTGTTCACTTCTTGTTCCAGCAGGTTGATTTCATCTTCAATGT CGTCTAGACCAAACTCTGTTGAATGTTCATTTGAACATAGATTCTTGGCTTGTCCTACCCAAGT CCTGTCATTTACATGTTCCAATGAATATTACTTTCATATGATCAAAATATTTACTAGGAAAATC CTTTTAGTATGCAGTTTCTTTACCTCATCCTGTCCCAGATGAGCATAATTCTATCTCCAGGAAT GTGTATGCTGTGAAATCTTCTTAGCTTAGATGCAACAAGAGCTGATATGTTCGGATCACGAAGA TCGGTTGCCGATAGTGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.201808728

Conservation Information
Conserved circRNAs	NA
PMCS	0.201808728

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6149993-6149693(-)
						
						Potential amino acid sequence
						
							MLIWDRMRTWVGQAKNLCSNEHSTEFGLDDIEDEINLLEQEVNNEQEIGFCHNDLQYGNIMIDE
ETNAITIITLSATDLRDPNISALVASKLRRFHSIHIPGDRIMLIWDRMRTWVGQAKNLCSNEHS
TEFGLDDIEDEINLLEQEVNNEQEIGFCHNDLQYGNIMIDEETNAITIITLSATDLRDPNISAL
VASKLRRFHSIHIPGDRIMLIWDRMRTWVGQAKNLCSNEHSTEFGLDDIEDEINLLEQEVNNEQ
EIGFCHNDLQYGNIMIDEETNAITIITLSATDLRDPNISALVASKLRRFHSIHIPGDRIMLIWD
RMRTWVGQAKNLCSNEHSTEFGLDDIEDEINLLEQEVNNEQEIGFCHNDLQYGNIMIDEETNAI
TII(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6149993-6149693(-)
Potential amino acid sequence	MLIWDRMRTWVGQAKNLCSNEHSTEFGLDDIEDEINLLEQEVNNEQEIGFCHNDLQYGNIMIDE ETNAITIITLSATDLRDPNISALVASKLRRFHSIHIPGDRIMLIWDRMRTWVGQAKNLCSNEHS TEFGLDDIEDEINLLEQEVNNEQEIGFCHNDLQYGNIMIDEETNAITIITLSATDLRDPNISAL VASKLRRFHSIHIPGDRIMLIWDRMRTWVGQAKNLCSNEHSTEFGLDDIEDEINLLEQEVNNEQ EIGFCHNDLQYGNIMIDEETNAITIITLSATDLRDPNISALVASKLRRFHSIHIPGDRIMLIWD RMRTWVGQAKNLCSNEHSTEFGLDDIEDEINLLEQEVNNEQEIGFCHNDLQYGNIMIDEETNAI TII(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT4G09760_circ_g.4

Address

Any questions?

Supported by