Plant Circular RNA Database

Detail information of AT2G39190_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT2G39190_circ_g.4
					
						ID in PlantcircBase
						ath_circ_017349
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 16351238-16352267  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT2G39190						
					
						Parent gene annotation
						
							Protein kinase superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G39190_circ_g.2 AT2G39190_circ_g.3 AT2G39190_circ_g.5 AT2G39190_circ_g.6 AT2G39190_circ_g.7 AT2G39190_circ_g.8 AT2G39190_circ_g.9 AT2G39190_circ_g.10 AT2G39190_circ_g.11 AT2G39190_circ_g.12 AT2G39190_circ_g.13 						
					
						Support reads
						13
					
						Tissues
						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
						AT2G39190.2:5
AT2G39190.1:5

General Information
CircRNA Name	AT2G39190_circ_g.4
ID in PlantcircBase	ath_circ_017349
Alias	NA
Organism	Arabidpsis thaliana
Position	chr2: 16351238-16352267 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT2G39190
Parent gene annotation	Protein kinase superfamily protein
Parent gene strand	+
Alternative splicing	AT2G39190_circ_g.2 AT2G39190_circ_g.3 AT2G39190_circ_g.5 AT2G39190_circ_g.6 AT2G39190_circ_g.7 AT2G39190_circ_g.8 AT2G39190_circ_g.9 AT2G39190_circ_g.10 AT2G39190_circ_g.11 AT2G39190_circ_g.12 AT2G39190_circ_g.13
Support reads	13
Tissues	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	AT2G39190.2:5 AT2G39190.1:5

			
						 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  
						
							GAGAGAAAATGACATTCGTGTATATGCTGATGAGCTTGGAATGGGTTTGGCTGGAGAATTGGAC
TTTACTTTAGAGGCTGCCAATGCCTCTGAATTTCAGgtattttctgcgttcacgattgctgcca
tcagattacgaacatcagcatcagttaagggcaaaagtttagaagcttcagagcagatttttgg
gatggtgt

									
								

					

						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: 570
Transcript exons: 16351238-16351379,16351503-16351555,16351717-16351860,16
351952-16352056,16352142-16352267
GTATTTTCTGCGTTCACGATTGCTGCCATCAGATTACGAACATCAGCATCAGTTAAGGGCAAAA
GTTTAGAAGCTTCAGAGCAGATTTTTGGGATGGTGTTGAAAGAAACCATGCTACATTTGGGCCC
AACTTTTATCAAAGTTGGTCAATCGCTTTCCACGAGGCCAGATATCATTGGGACTGAAATCTCC
AAGGCACTATCTGAACTGCATGACCGAATCCCTCCCTTTCCCTGGCCTGAGGCTGTAAAAATCC
TTGAAGGGGAATTAGGTGGTCCTGTCGAATCATTCTTTAGTCAGTTTTCGCAAGAAACTGTAGC
AGCAGCATCCTTTGGTCAGGTCTACCGAGGAAGGACCCTCGATGGTGCAGATGTTGCAGTGAAA
GTTCAGCGCCCTGATCTGAGACATGCAGTGCTACGCGACATCTACATTCTGCGACTTGGGTTAG
GTGTATTGCGAAAGGTAGCAAAGAGAGAAAATGACATTCGTGTATATGCTGATGAGCTTGGAAT
GGGTTTGGCTGGAGAATTGGACTTTACTTTAGAGGCTGCCAATGCCTCTGAATTTCAG
						
					

						Genomic sequence
						
							GTATTTTCTGCGTTCACGATTGCTGCCATCAGATTACGAACATCAGCATCAGTTAAGGGCAAAA
GTTTAGAAGCTTCAGAGCAGATTTTTGGGATGGTGTTGAAAGAAACCATGCTACATTTGGGCCC
AACTTTTATCAAAGGTCTGTGATTAGCTTATTATTTTTGAAGTGAAACTATCCATCAGTCACCA
TTTACATTTACTGCCATATATTAGATACTTTGATCTGTTGTGAATGATTCTTCCCTCTCTTCTG
CTGGTTCAGTTGGTCAATCGCTTTCCACGAGGCCAGATATCATTGGGACTGAAATCTCCAAGGT
CAGATAGAAGTTATGGTCACATTTGTCTAAATCTCTTAGCTTTTAATAGTGTCTTTCTGGTGCA
TGTTTCCATTGTTCTTTCTCTATTCTGCATGCTACATTTGGTTGTTCTTAGGGATGTAGCTGTC
TGACTATGTTTGTTATGATTTGAAACTGCAGGCACTATCTGAACTGCATGACCGAATCCCTCCC
TTTCCCTGGCCTGAGGCTGTAAAAATCCTTGAAGGGGAATTAGGTGGTCCTGTCGAATCATTCT
TTAGTCAGTTTTCGCAAGAAACTGTAGCAGCAGCATCCTTTGGTCAGGTATTTACTCTGGTTTT
TATCTTACAAGAAGTAAGCATCATATGAATCAACTTGTAGGATGCATGCCTTATACTTGATATG
ATATGTTAAGGTCTACCGAGGAAGGACCCTCGATGGTGCAGATGTTGCAGTGAAAGTTCAGCGC
CCTGATCTGAGACATGCAGTGCTACGCGACATCTACATTCTGCGACTTGGGGTTCGTGTGAAAT
CTACCAAGTTATGACAAATCAATCTGCTTGAATCATGTCATAGTTATATGATATTTCTTTTGAT
TGTTGCAGTTAGGTGTATTGCGAAAGGTAGCAAAGAGAGAAAATGACATTCGTGTATATGCTGA
TGAGCTTGGAATGGGTTTGGCTGGAGAATTGGACTTTACTTTAGAGGCTGCCAATGCCTCTGAA
TTTCAG
						
					

			
		

Sequences
Splice junction sequence	GAGAGAAAATGACATTCGTGTATATGCTGATGAGCTTGGAATGGGTTTGGCTGGAGAATTGGAC TTTACTTTAGAGGCTGCCAATGCCTCTGAATTTCAGgtattttctgcgttcacgattgctgcca tcagattacgaacatcagcatcagttaagggcaaaagtttagaagcttcagagcagatttttgg gatggtgt
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: 570 Transcript exons: 16351238-16351379,16351503-16351555,16351717-16351860,16 351952-16352056,16352142-16352267 GTATTTTCTGCGTTCACGATTGCTGCCATCAGATTACGAACATCAGCATCAGTTAAGGGCAAAA GTTTAGAAGCTTCAGAGCAGATTTTTGGGATGGTGTTGAAAGAAACCATGCTACATTTGGGCCC AACTTTTATCAAAGTTGGTCAATCGCTTTCCACGAGGCCAGATATCATTGGGACTGAAATCTCC AAGGCACTATCTGAACTGCATGACCGAATCCCTCCCTTTCCCTGGCCTGAGGCTGTAAAAATCC TTGAAGGGGAATTAGGTGGTCCTGTCGAATCATTCTTTAGTCAGTTTTCGCAAGAAACTGTAGC AGCAGCATCCTTTGGTCAGGTCTACCGAGGAAGGACCCTCGATGGTGCAGATGTTGCAGTGAAA GTTCAGCGCCCTGATCTGAGACATGCAGTGCTACGCGACATCTACATTCTGCGACTTGGGTTAG GTGTATTGCGAAAGGTAGCAAAGAGAGAAAATGACATTCGTGTATATGCTGATGAGCTTGGAAT GGGTTTGGCTGGAGAATTGGACTTTACTTTAGAGGCTGCCAATGCCTCTGAATTTCAG
Genomic sequence	GTATTTTCTGCGTTCACGATTGCTGCCATCAGATTACGAACATCAGCATCAGTTAAGGGCAAAA GTTTAGAAGCTTCAGAGCAGATTTTTGGGATGGTGTTGAAAGAAACCATGCTACATTTGGGCCC AACTTTTATCAAAGGTCTGTGATTAGCTTATTATTTTTGAAGTGAAACTATCCATCAGTCACCA TTTACATTTACTGCCATATATTAGATACTTTGATCTGTTGTGAATGATTCTTCCCTCTCTTCTG CTGGTTCAGTTGGTCAATCGCTTTCCACGAGGCCAGATATCATTGGGACTGAAATCTCCAAGGT CAGATAGAAGTTATGGTCACATTTGTCTAAATCTCTTAGCTTTTAATAGTGTCTTTCTGGTGCA TGTTTCCATTGTTCTTTCTCTATTCTGCATGCTACATTTGGTTGTTCTTAGGGATGTAGCTGTC TGACTATGTTTGTTATGATTTGAAACTGCAGGCACTATCTGAACTGCATGACCGAATCCCTCCC TTTCCCTGGCCTGAGGCTGTAAAAATCCTTGAAGGGGAATTAGGTGGTCCTGTCGAATCATTCT TTAGTCAGTTTTCGCAAGAAACTGTAGCAGCAGCATCCTTTGGTCAGGTATTTACTCTGGTTTT TATCTTACAAGAAGTAAGCATCATATGAATCAACTTGTAGGATGCATGCCTTATACTTGATATG ATATGTTAAGGTCTACCGAGGAAGGACCCTCGATGGTGCAGATGTTGCAGTGAAAGTTCAGCGC CCTGATCTGAGACATGCAGTGCTACGCGACATCTACATTCTGCGACTTGGGGTTCGTGTGAAAT CTACCAAGTTATGACAAATCAATCTGCTTGAATCATGTCATAGTTATATGATATTTCTTTTGAT TGTTGCAGTTAGGTGTATTGCGAAAGGTAGCAAAGAGAGAAAATGACATTCGTGTATATGCTGA TGAGCTTGGAATGGGTTTGGCTGGAGAATTGGACTTTACTTTAGAGGCTGCCAATGCCTCTGAA TTTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.218777551

Conservation Information
Conserved circRNAs	NA
PMCS	0.218777551

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16351331-16352264(+)
						
						Potential amino acid sequence
						
							MVLKETMLHLGPTFIKVGQSLSTRPDIIGTEISKALSELHDRIPPFPWPEAVKILEGELGGPVE
SFFSQFSQETVAAASFGQVYRGRTLDGADVAVKVQRPDLRHAVLRDIYILRLGLGVLRKVAKRE
NDIRVYADELGMGLAGELDFTLEAANASEFQVFSAFTIAAIRLRTSASVKGKSLEASEQIFGMV
LKETMLHLGPTFIKVGQSLSTRPDIIGTEISKALSELHDRIPPFPWPEAVKILEGELGGPVESF
FSQFSQETVAAASFGQVYRGRTLDGADVAVKVQRPDLRHAVLRDIYILRLGLGVLRKVAKREND
IRVYADELGMGLAGELDFTLEAANASEFQVFSAFTIAAIRLRTSASVKGKSLEASEQIFGMVLK
ETMLHLGPTFIKVGQSLSTRPDIIGTEISKALSELHDRIPPFPWPEAVKILEGELGGPVESFFS
QFSQETVAAASFGQVYRGRTLDGADVAVKVQRPDLRHAVLRDIYILRLGLGVLRKVAKRENDIR
VYADELGMGLAGELDFTLEAANASEFQVFSAFTIAAIRLRTSASVKGKSLEASEQIFGMVLKET
MLHLGPTFIKVGQSLSTRPDIIGTEISKALSELHDRIPPFPWPEAVKILEGELGGPVESFFSQF
SQETVAAASFGQVYRGRTLDGADVAVKVQRPDLRHAVLRDIYILRLGLGVLRKVAKRENDIRVY
ADELGMGLAGELDFTLEAANASEFQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	16351331-16352264(+)
Potential amino acid sequence	MVLKETMLHLGPTFIKVGQSLSTRPDIIGTEISKALSELHDRIPPFPWPEAVKILEGELGGPVE SFFSQFSQETVAAASFGQVYRGRTLDGADVAVKVQRPDLRHAVLRDIYILRLGLGVLRKVAKRE NDIRVYADELGMGLAGELDFTLEAANASEFQVFSAFTIAAIRLRTSASVKGKSLEASEQIFGMV LKETMLHLGPTFIKVGQSLSTRPDIIGTEISKALSELHDRIPPFPWPEAVKILEGELGGPVESF FSQFSQETVAAASFGQVYRGRTLDGADVAVKVQRPDLRHAVLRDIYILRLGLGVLRKVAKREND IRVYADELGMGLAGELDFTLEAANASEFQVFSAFTIAAIRLRTSASVKGKSLEASEQIFGMVLK ETMLHLGPTFIKVGQSLSTRPDIIGTEISKALSELHDRIPPFPWPEAVKILEGELGGPVESFFS QFSQETVAAASFGQVYRGRTLDGADVAVKVQRPDLRHAVLRDIYILRLGLGVLRKVAKRENDIR VYADELGMGLAGELDFTLEAANASEFQVFSAFTIAAIRLRTSASVKGKSLEASEQIFGMVLKET MLHLGPTFIKVGQSLSTRPDIIGTEISKALSELHDRIPPFPWPEAVKILEGELGGPVESFFSQF SQETVAAASFGQVYRGRTLDGADVAVKVQRPDLRHAVLRDIYILRLGLGVLRKVAKRENDIRVY ADELGMGLAGELDFTLEAANASEFQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT2G39190_circ_g.4

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