Plant Circular RNA Database

Detail information of AT1G07180_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT1G07180_circ_g.6
					
						ID in PlantcircBase
						ath_circ_001129
					
						Alias
						At_ciR173, Ath_circ_FC4782, AT1G07180_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 2206339-2206518  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ, circseq_cup, CIRI-full, CIRI2
					
						Parent gene
						
							AT1G07180						
					
						Parent gene annotation
						
							Internal alternative NAD(P)H-ubiquinone oxidoreductase A1, mitoc
hondrial
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G07180_circ_g.5 						
					
						Support reads
						81/12
					
						Tissues
						leaf/leaf, aerial, whole_plant
					
						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
						AT1G07180.1:1

General Information
CircRNA Name	AT1G07180_circ_g.6
ID in PlantcircBase	ath_circ_001129
Alias	At_ciR173, Ath_circ_FC4782, AT1G07180_C1
Organism	Arabidpsis thaliana
Position	chr1: 2206339-2206518 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ, circseq_cup, CIRI-full, CIRI2
Parent gene	AT1G07180
Parent gene annotation	Internal alternative NAD(P)H-ubiquinone oxidoreductase A1, mitoc hondrial
Parent gene strand	+
Alternative splicing	AT1G07180_circ_g.5
Support reads	81/12
Tissues	leaf/leaf, aerial, whole_plant
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	AT1G07180.1:1

			
						 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  
						
							GAGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAGTATGGCTACTATTGGGAGATACAAAG
CTCTCGTTGATCTCCGTGAGAGCAAGgtggctgagagagaaggcaaatacttggcgaatctgtt
taacgtgatgggaaaagctggaggaggacgggccaatagcgcaaaggaaatg

									
								

					

						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: 145
Transcript exons: 2206339-2206441,2206477-2206518
GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG
GACGGGCCAATAGCGCAAAGGAAATGGAGCTTGGGGAACATTGGGAGATACAAAGCTCTCGTTG
ATCTCCGTGAGAGCAAG
Transcript length: 156
Transcript exons: 2206339-2206410,2206435-2206518
GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG
GACGGGCCGGGGAACCATTTGTGTATAAACATCTCGGAAGTATGGCTACTATTGGGAGATACAA
AGCTCTCGTTGATCTCCGTGAGAGCAAG
Transcript length: 156
Transcript exons: 2206339-2206432,2206457-2206518
GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG
GACGGGCCAATAGCGCAAAGGAAATGGAGCATCTCGGAAGTATGGCTACTATTGGGAGATACAA
AGCTCTCGTTGATCTCCGTGAGAGCAAG
Transcript length: 157
Transcript exons: 2206339-2206408,2206432-2206518
GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG
GACGGGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAGTATGGCTACTATTGGGAGATACA
AAGCTCTCGTTGATCTCCGTGAGAGCAAG
Transcript length: 169
Transcript exons: 2206339-2206409,2206421-2206518
GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG
GACGGGCAGGAAATGGAGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAGTATGGCTACTA
TTGGGAGATACAAAGCTCTCGTTGATCTCCGTGAGAGCAAG
Transcript length: 172
Transcript exons: 2206339-2206422,2206431-2206518
GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG
GACGGGCCAATAGCGCAAAGGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAGTATGGCTA
CTATTGGGAGATACAAAGCTCTCGTTGATCTCCGTGAGAGCAAG
Transcript length: 180
Transcript exons: 2206339-2206518
GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCCGGAGGAG
GACGGGCCAATAGCGCAAAGGAAATGGAGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAG
TATGGCTACTATTGGGAGATACAAAGCTCTCGTTGATCTCCGTGAGAGCAAG
Transcript length: 180
Transcript exons: 2206339-2206518
GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG
GACGGGCCAATAGCGCAAAGGAAATGGAGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAG
TATGGCTACTATTGGGAGATACAAAGCTCTCGTTGATCTCCGTGAGAGCAAG
						
					

						Genomic sequence
						
							GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG
GACGGGCCAATAGCGCAAAGGAAATGGAGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAG
TATGGCTACTATTGGGAGATACAAAGCTCTCGTTGATCTCCGTGAGAGCAAG
						
					

			
		

Sequences
Splice junction sequence	GAGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAGTATGGCTACTATTGGGAGATACAAAG CTCTCGTTGATCTCCGTGAGAGCAAGgtggctgagagagaaggcaaatacttggcgaatctgtt taacgtgatgggaaaagctggaggaggacgggccaatagcgcaaaggaaatg
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: 145 Transcript exons: 2206339-2206441,2206477-2206518 GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG GACGGGCCAATAGCGCAAAGGAAATGGAGCTTGGGGAACATTGGGAGATACAAAGCTCTCGTTG ATCTCCGTGAGAGCAAG Transcript length: 156 Transcript exons: 2206339-2206410,2206435-2206518 GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG GACGGGCCGGGGAACCATTTGTGTATAAACATCTCGGAAGTATGGCTACTATTGGGAGATACAA AGCTCTCGTTGATCTCCGTGAGAGCAAG Transcript length: 156 Transcript exons: 2206339-2206432,2206457-2206518 GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG GACGGGCCAATAGCGCAAAGGAAATGGAGCATCTCGGAAGTATGGCTACTATTGGGAGATACAA AGCTCTCGTTGATCTCCGTGAGAGCAAG Transcript length: 157 Transcript exons: 2206339-2206408,2206432-2206518 GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG GACGGGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAGTATGGCTACTATTGGGAGATACA AAGCTCTCGTTGATCTCCGTGAGAGCAAG Transcript length: 169 Transcript exons: 2206339-2206409,2206421-2206518 GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG GACGGGCAGGAAATGGAGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAGTATGGCTACTA TTGGGAGATACAAAGCTCTCGTTGATCTCCGTGAGAGCAAG Transcript length: 172 Transcript exons: 2206339-2206422,2206431-2206518 GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG GACGGGCCAATAGCGCAAAGGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAGTATGGCTA CTATTGGGAGATACAAAGCTCTCGTTGATCTCCGTGAGAGCAAG Transcript length: 180 Transcript exons: 2206339-2206518 GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCCGGAGGAG GACGGGCCAATAGCGCAAAGGAAATGGAGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAG TATGGCTACTATTGGGAGATACAAAGCTCTCGTTGATCTCCGTGAGAGCAAG Transcript length: 180 Transcript exons: 2206339-2206518 GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG GACGGGCCAATAGCGCAAAGGAAATGGAGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAG TATGGCTACTATTGGGAGATACAAAGCTCTCGTTGATCTCCGTGAGAGCAAG
Genomic sequence	GTGGCTGAGAGAGAAGGCAAATACTTGGCGAATCTGTTTAACGTGATGGGAAAAGCTGGAGGAG GACGGGCCAATAGCGCAAAGGAAATGGAGCTTGGGGAACCATTTGTGTATAAACATCTCGGAAG TATGGCTACTATTGGGAGATACAAAGCTCTCGTTGATCTCCGTGAGAGCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.507853566

Conservation Information
Conserved circRNAs	NA
PMCS	0.507853566

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2206384-2206515(+)
2206459-2206341(-)
						
						Potential amino acid sequence
						
							MGKAGGGRANSAKEMELGEPFVYKHLGSMATIGRYKALVDLRESKVAEREGKYLANLFNVMGKA
GGGRANSAKEMELGEPFVYKHLGSMATIGRYKALVDLRESKVAEREGKYLANLFNVMGKAGGGR
ANSAKEMELGEPFVYKHLGSMATIGRYKALVDLRESKVAEREGKYLANLFNVMGKAGGGRANSA
KEMELGEPFVYKHLGSMATIGRYKALVDLRESK(+)
MFIHKWFPKLHFLCAIGPSSSSFSHHVKQIRQVFAFSLSHLALTEINESFVSPNSSHTSEMFIH
KWFPKLHFLCAIGPSSSSFSHHVKQIRQVFAFSLSHLALTEINESFVSPNSSHTSEMFIHKWFP
KLHFLCAIGPSSSSFSHHVKQIRQVFAFSLSHLALTEINESFVSPNSSHTSEMFIHKWFPKLHF
LCAIGPSSSSFSHHVKQIRQVFAFSLSH(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	2206384-2206515(+) 2206459-2206341(-)
Potential amino acid sequence	MGKAGGGRANSAKEMELGEPFVYKHLGSMATIGRYKALVDLRESKVAEREGKYLANLFNVMGKA GGGRANSAKEMELGEPFVYKHLGSMATIGRYKALVDLRESKVAEREGKYLANLFNVMGKAGGGR ANSAKEMELGEPFVYKHLGSMATIGRYKALVDLRESKVAEREGKYLANLFNVMGKAGGGRANSA KEMELGEPFVYKHLGSMATIGRYKALVDLRESK(+) MFIHKWFPKLHFLCAIGPSSSSFSHHVKQIRQVFAFSLSHLALTEINESFVSPNSSHTSEMFIH KWFPKLHFLCAIGPSSSSFSHHVKQIRQVFAFSLSHLALTEINESFVSPNSSHTSEMFIHKWFP KLHFLCAIGPSSSSFSHHVKQIRQVFAFSLSHLALTEINESFVSPNSSHTSEMFIHKWFPKLHF LCAIGPSSSSFSHHVKQIRQVFAFSLSH(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Chen et al., 2017a;Zhang et al., 2019

circRNA

Detail information of AT1G07180_circ_g.6

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