Plant Circular RNA Database

Detail information of AT1G29120_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G29120_circ_g.2
					
						ID in PlantcircBase
						ath_circ_004752
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 10175216-10177042  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT1G29120						
					
						Parent gene annotation
						
							AT1G29120 protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G29120_circ_g.1 AT1G29120_circ_g.3 AT1G29120_circ_g.4 AT1G29120_circ_g.5 						
					
						Support reads
						1
					
						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
						AT1G29120.3:6
AT1G29120.2:6
AT1G29120.6:6
AT1G29120.7:6
AT1G29120.1:6
AT1G29120.5:6
AT1G29120.8:6
AT1G29120.4:6

General Information
CircRNA Name	AT1G29120_circ_g.2
ID in PlantcircBase	ath_circ_004752
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 10175216-10177042 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder
Parent gene	AT1G29120
Parent gene annotation	AT1G29120 protein
Parent gene strand	+
Alternative splicing	AT1G29120_circ_g.1 AT1G29120_circ_g.3 AT1G29120_circ_g.4 AT1G29120_circ_g.5
Support reads	1
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	AT1G29120.3:6 AT1G29120.2:6 AT1G29120.6:6 AT1G29120.7:6 AT1G29120.1:6 AT1G29120.5:6 AT1G29120.8:6 AT1G29120.4:6

			
						 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  
						
							TTAATGACTTATCTGTAATCCTAATGCATTTCATTGTCTGGCAGATCGGCGCTGGGGGCATTTC
GAAGTCGCATTATATATGCAAACGTATCTTATGACCggtcaaacagaagctggaaccaacaggg
acgcagggttcaggcaatgagttccacagcccaacggaaattttcgctatcgaaaggcgactcc
gatgacaa

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							GGTCAAACAGAAGCTGGAACCAACAGGGACGCAGGGTTCAGGCAATGAGTTCCACAGCCCAACG
GAAATTTTCGCTATCGAAAGGCGACTCCGATGACAAAAATGAACCTGATCATCTTCTTGTTCTT
GTACATGGTATTTTGGCCAGGTATTATTTCTAAGTAGTTCATCAATTGAATGGTACTGGGTTTG
CATCTTGGGAAACCCTCATGGTTTTGTTTTAGGTTGGATAGAAACTTGCAAGTATTTGAATTTG
AAAGTTATGTCTATCATTGTCAAAAAAAAGAAAGAAAGTTATGTCTATCATTTCTGCTACTTTG
TTTTCAGATTGAATAATTTATAGACTCCAAATTTACTAAGACACAATTACTTGCAGTCCCAGCG
ACTGGCTCTACGTAGAAGCTGAGCTGAAAAGACGCCTTGGAAGAAGATTCTTGATTTATGGTAT
GCTCATCTTGTTCTAAATTGTTATCATCTATTAGTTTAGTTGAGTAGTTGTTGGATTGTATGTA
TAATAGAAGAGAATTTTTGGGAATGAAATGGTAACGTAAGTTGAATGCATGTGCTGGGCACAAA
ATTGAAAACACTTCAAGGTCTTATATAATCTTTAGCGGCAAGAGGCGAAATATACATTTTCTTG
AAAAATTTAAGATCTTTTCGTCTGGAACCACAACTCTTCTTTAGTTTTGTATTTTATTATAATA
CTCATGTGCTTTTATGCTATGCGTGGAATGGATCACACGTGATGTGTTTTAATTTACTCTGTTT
CTCCTGAACATTCACAGCAAGTTCTTCCAATACCTTCACTAAAACATTTGGCGGGATCGATGGA
GCTGGAAAACGACTAGCAGAAGAGGTGAGTTTTAATATCTTCATTTGCACCTCGTGTATAGGTA
GGTCTTGGTTTTCTAGCCCTTAACTTCAGTACATGAGCTGATTTCTGTTCCCATTCTGGATGTG
AGAGAGGAATAGGTTAGACAAGTTGTCCAAAAGAGCAAGAGCTTAAAGAAGATTTCGTTTTTAG
CCCACTCCCTCGGTGGCTTATTTTCCAGACATGCTGTTGCTGTTCTTTACTCAGCAGCAATGGC
ACAAGTAAGTGATGTTGCTGTCTCTCAATCTGGCAATTCAAATCTTCTGCGAGGTAGGATTGCG
GGGCTAGAACCGATTAATTTCATCACTTTGGCAACACCTCATCTAGGAGTGAGAGGCAGAAAGC
AGGTTCTCTTCTTCTCTACTTATCATAATTGGAATTTTGGAATCAAAGAGTTTCATATATATCT
CGCAGTACCTGTACGTAGATGTGGTGTATGCGTAATTAAGAAAGTAGTTAGTCGTTTTTCACAT
GTAAATTTCATCTACCTTCTCCTTGTGTTCAGACAGATATCATAAGTTTCATCAAAACTGTCTT
GCGTTTTTTGCTATTTGGTCCCCTAAGTGTCTAGACTGATGAGTGATGAATATTAATTGATAAT
CCCTGTAAATTCTATCTCATTCTCTCCTCTTTTTCTGGAACCCCTTGTATCAGCTGCCTTTTCT
GTTGGGAGTTCCTATTCTTGAGAAACTTGCTGCACCAATAGCTCCATTCTTTGTTGGTCGGACT
GGTAGTCAGTTGTTCCTCACTGATGGTAAAGCTGATAAACCACCTCTTCTTTTGAGGATGGCAT
CTGATGGTGAAGATCTGAAATTCTTGTGAGTAATGCTCTTACCAATTTAAATCATTCGACCCCT
TAATGACTTATCTGTAATCCTAATGCATTTCATTGTCTGGCAGATCGGCGCTGGGGGCATTTCG
AAGTCGCATTATATATGCAAACGTATCTTATGACC
						
					

			
		

Sequences
Splice junction sequence	TTAATGACTTATCTGTAATCCTAATGCATTTCATTGTCTGGCAGATCGGCGCTGGGGGCATTTC GAAGTCGCATTATATATGCAAACGTATCTTATGACCggtcaaacagaagctggaaccaacaggg acgcagggttcaggcaatgagttccacagcccaacggaaattttcgctatcgaaaggcgactcc gatgacaa
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GGTCAAACAGAAGCTGGAACCAACAGGGACGCAGGGTTCAGGCAATGAGTTCCACAGCCCAACG GAAATTTTCGCTATCGAAAGGCGACTCCGATGACAAAAATGAACCTGATCATCTTCTTGTTCTT GTACATGGTATTTTGGCCAGGTATTATTTCTAAGTAGTTCATCAATTGAATGGTACTGGGTTTG CATCTTGGGAAACCCTCATGGTTTTGTTTTAGGTTGGATAGAAACTTGCAAGTATTTGAATTTG AAAGTTATGTCTATCATTGTCAAAAAAAAGAAAGAAAGTTATGTCTATCATTTCTGCTACTTTG TTTTCAGATTGAATAATTTATAGACTCCAAATTTACTAAGACACAATTACTTGCAGTCCCAGCG ACTGGCTCTACGTAGAAGCTGAGCTGAAAAGACGCCTTGGAAGAAGATTCTTGATTTATGGTAT GCTCATCTTGTTCTAAATTGTTATCATCTATTAGTTTAGTTGAGTAGTTGTTGGATTGTATGTA TAATAGAAGAGAATTTTTGGGAATGAAATGGTAACGTAAGTTGAATGCATGTGCTGGGCACAAA ATTGAAAACACTTCAAGGTCTTATATAATCTTTAGCGGCAAGAGGCGAAATATACATTTTCTTG AAAAATTTAAGATCTTTTCGTCTGGAACCACAACTCTTCTTTAGTTTTGTATTTTATTATAATA CTCATGTGCTTTTATGCTATGCGTGGAATGGATCACACGTGATGTGTTTTAATTTACTCTGTTT CTCCTGAACATTCACAGCAAGTTCTTCCAATACCTTCACTAAAACATTTGGCGGGATCGATGGA GCTGGAAAACGACTAGCAGAAGAGGTGAGTTTTAATATCTTCATTTGCACCTCGTGTATAGGTA GGTCTTGGTTTTCTAGCCCTTAACTTCAGTACATGAGCTGATTTCTGTTCCCATTCTGGATGTG AGAGAGGAATAGGTTAGACAAGTTGTCCAAAAGAGCAAGAGCTTAAAGAAGATTTCGTTTTTAG CCCACTCCCTCGGTGGCTTATTTTCCAGACATGCTGTTGCTGTTCTTTACTCAGCAGCAATGGC ACAAGTAAGTGATGTTGCTGTCTCTCAATCTGGCAATTCAAATCTTCTGCGAGGTAGGATTGCG GGGCTAGAACCGATTAATTTCATCACTTTGGCAACACCTCATCTAGGAGTGAGAGGCAGAAAGC AGGTTCTCTTCTTCTCTACTTATCATAATTGGAATTTTGGAATCAAAGAGTTTCATATATATCT CGCAGTACCTGTACGTAGATGTGGTGTATGCGTAATTAAGAAAGTAGTTAGTCGTTTTTCACAT GTAAATTTCATCTACCTTCTCCTTGTGTTCAGACAGATATCATAAGTTTCATCAAAACTGTCTT GCGTTTTTTGCTATTTGGTCCCCTAAGTGTCTAGACTGATGAGTGATGAATATTAATTGATAAT CCCTGTAAATTCTATCTCATTCTCTCCTCTTTTTCTGGAACCCCTTGTATCAGCTGCCTTTTCT GTTGGGAGTTCCTATTCTTGAGAAACTTGCTGCACCAATAGCTCCATTCTTTGTTGGTCGGACT GGTAGTCAGTTGTTCCTCACTGATGGTAAAGCTGATAAACCACCTCTTCTTTTGAGGATGGCAT CTGATGGTGAAGATCTGAAATTCTTGTGAGTAATGCTCTTACCAATTTAAATCATTCGACCCCT TAATGACTTATCTGTAATCCTAATGCATTTCATTGTCTGGCAGATCGGCGCTGGGGGCATTTCG AAGTCGCATTATATATGCAAACGTATCTTATGACC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.125328352

Conservation Information
Conserved circRNAs	NA
PMCS	0.125328352

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10175260-10177039(+)
						
						Potential amino acid sequence
						
							MSSTAQRKFSLSKGDSDDKNEPDHLLVLVHGILASPSDWLYVEAELKRRLGRRFLIYASSSNTF
TKTFGGIDGAGKRLAEEVRQVVQKSKSLKKISFLAHSLGGLFSRHAVAVLYSAAMAQVSDVAVS
QSGNSNLLRGRIAGLEPINFITLATPHLGVRGRKQLPFLLGVPILEKLAAPIAPFFVGRTGSQL
FLTDGKADKPPLLLRMASDGEDLKFLSALGAFRSRIIYANVSYDRSNRSWNQQGRRVQAMSSTA
QRKFSLSKGDSDDKNEPDHLLVLVHGILASPSDWLYVEAELKRRLGRRFLIYASSSNTFTKTFG
GIDGAGKRLAEEVRQVVQKSKSLKKISFLAHSLGGLFSRHAVAVLYSAAMAQVSDVAVSQSGNS
NLLRGRIAGLEPINFITLATPHLGVRGRKQLPFLLGVPILEKLAAPIAPFFVGRTGSQLFLTDG
KADKPPLLLRMASDGEDLKFLSALGAFRSRIIYANVSYDRSNRSWNQQGRRVQAMSSTAQRKFS
LSKGDSDDKNEPDHLLVLVHGILASPSDWLYVEAELKRRLGRRFLIYASSSNTFTKTFGGIDGA
GKRLAEEVRQVVQKSKSLKKISFLAHSLGGLFSRHAVAVLYSAAMAQVSDVAVSQSGNSNLLRG
RIAGLEPINFITLATPHLGVRGRKQLPFLLGVPILEKLAAPIAPFFVGRTGSQLFLTDGKADKP
PLLLRMASDGEDLKFLSALGAFRSRIIYANVSYDRSNRSWNQQGRRVQAMSSTAQRKFSLSKGD
SDDKNEPDHLLVLVHGILASPSDWLYVEAELKRRLGRRFLIYASSSNTFTKTFGGIDGAGKRLA
EEVRQVVQKSKSLKKISFLAHSLGGLFSRHAVAVLYSAAMAQVSDVAVSQSGNSNLLRGRIAGL
EPINFITLATPHLGVRGRKQLPFLLGVPILEKLAAPIAPFFVGRTGSQLFLTDGKADKPPLLLR
MASDGEDLKFLSALGAFRSRIIYANVSYD(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	10175260-10177039(+)
Potential amino acid sequence	MSSTAQRKFSLSKGDSDDKNEPDHLLVLVHGILASPSDWLYVEAELKRRLGRRFLIYASSSNTF TKTFGGIDGAGKRLAEEVRQVVQKSKSLKKISFLAHSLGGLFSRHAVAVLYSAAMAQVSDVAVS QSGNSNLLRGRIAGLEPINFITLATPHLGVRGRKQLPFLLGVPILEKLAAPIAPFFVGRTGSQL FLTDGKADKPPLLLRMASDGEDLKFLSALGAFRSRIIYANVSYDRSNRSWNQQGRRVQAMSSTA QRKFSLSKGDSDDKNEPDHLLVLVHGILASPSDWLYVEAELKRRLGRRFLIYASSSNTFTKTFG GIDGAGKRLAEEVRQVVQKSKSLKKISFLAHSLGGLFSRHAVAVLYSAAMAQVSDVAVSQSGNS NLLRGRIAGLEPINFITLATPHLGVRGRKQLPFLLGVPILEKLAAPIAPFFVGRTGSQLFLTDG KADKPPLLLRMASDGEDLKFLSALGAFRSRIIYANVSYDRSNRSWNQQGRRVQAMSSTAQRKFS LSKGDSDDKNEPDHLLVLVHGILASPSDWLYVEAELKRRLGRRFLIYASSSNTFTKTFGGIDGA GKRLAEEVRQVVQKSKSLKKISFLAHSLGGLFSRHAVAVLYSAAMAQVSDVAVSQSGNSNLLRG RIAGLEPINFITLATPHLGVRGRKQLPFLLGVPILEKLAAPIAPFFVGRTGSQLFLTDGKADKP PLLLRMASDGEDLKFLSALGAFRSRIIYANVSYDRSNRSWNQQGRRVQAMSSTAQRKFSLSKGD SDDKNEPDHLLVLVHGILASPSDWLYVEAELKRRLGRRFLIYASSSNTFTKTFGGIDGAGKRLA EEVRQVVQKSKSLKKISFLAHSLGGLFSRHAVAVLYSAAMAQVSDVAVSQSGNSNLLRGRIAGL EPINFITLATPHLGVRGRKQLPFLLGVPILEKLAAPIAPFFVGRTGSQLFLTDGKADKPPLLLR MASDGEDLKFLSALGAFRSRIIYANVSYD(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G29120_circ_g.2

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