Plant Circular RNA Database

Detail information of AT1G17220_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT1G17220_circ_g.9
					
						ID in PlantcircBase
						ath_circ_003033
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 5887544-5889857  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT1G17220						
					
						Parent gene annotation
						
							Translation initiation factor IF-2, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G17220_circ_g.4 AT1G17220_circ_g.5 AT1G17220_circ_g.6 AT1G17220_circ_g.7 AT1G17220_circ_g.8 AT1G17220_circ_g.10 AT1G17220_circ_g.11 AT1G17220_circ_g.12 AT1G17220_circ_g.13 AT1G17220_circ_g.14 AT1G17220_circ_g.15 AT1G17220_circ_g.16 AT1G17220_circ_g.17 AT1G17220_circ_g.18 						
					
						Support reads
						29
					
						Tissues
						inflorescences
					
						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
						AT1G17220.1:8

General Information
CircRNA Name	AT1G17220_circ_g.9
ID in PlantcircBase	ath_circ_003033
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 5887544-5889857 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, PcircRNA_finder
Parent gene	AT1G17220
Parent gene annotation	Translation initiation factor IF-2, chloroplastic
Parent gene strand	+
Alternative splicing	AT1G17220_circ_g.4 AT1G17220_circ_g.5 AT1G17220_circ_g.6 AT1G17220_circ_g.7 AT1G17220_circ_g.8 AT1G17220_circ_g.10 AT1G17220_circ_g.11 AT1G17220_circ_g.12 AT1G17220_circ_g.13 AT1G17220_circ_g.14 AT1G17220_circ_g.15 AT1G17220_circ_g.16 AT1G17220_circ_g.17 AT1G17220_circ_g.18
Support reads	29
Tissues	inflorescences
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	AT1G17220.1:8

			
						 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  
						
							ATTTGTCAAAGATTGTGGCATCAGGGTGGTCCGGAAGGGTAAAACTGTCCATGTCGGTGTTCTT
GATTCTCTTAAACGGGTTAAAGAAAACGTGAAAGAGgcatttggtgcaatgagagctcgcggag
cacgagtcactgacattgcaatcattgtggttgctgctgatgatggaattcgtcctcaaacaaa
tgaagcaa

									
								

					

						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
						
							GCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTG
CTGATGATGGAATTCGTCCTCAAACAAATGAAGCAATAGCTCACGCAAAGGCTGCTGCTGTACC
AATAGTTATAGCTATAAATAAGGTATTTTGTTATTCTTCTTTACCTTGGGTATATGTAAGTTTC
TCCCAGTCTTATTCATTTCATGTTCCAGATAGATAAAGAAGGAGCTAGTCCAGATAGAGTGATG
CAAGAGCTTTCTTCAATTGGTTTGATGCCTGAAGATTGGGGTGGTGATGTTCCAATGGTTCAGG
TTGGAATACATACTTTCATCACGTATATGTTTTAGGGTCCAAATGTTCCATGGGTTCTCATATC
ATGCTCTATATTTGCCTTTGACAGATCAGTGCTTTGAAAGGGGAAAATGTCGATGATCTGTTGG
AAACTGTCATGCTTGTTGCAGAGGTTAGTTTGTTATTCATCCCATGATAACAGGTTTGCTTGAT
TTTTCCGTTTCTGTTTTCGGTAGATGCATAATGAAGCTCAATTTTGTTCTCTTCATGTAAGCAC
TACATAGTGGCTACGAAATGACTTACATAATTGCTCCAAAGTCGGCCCAAAATCTTGTTTTATG
GAGGGCTAAAGACTAATAACGCTTACATAAATTCATTTTTTTTTTCTCCCACTTTCTGCTTTTG
CTTCTCAATTAGCTTTTGCTTGTGGGCTGACTGTATTTTGCTGTTTCAGCTTCAAGAGTTGAAA
GCAAATCCACACAGAAATGCCAAGGGCATTGTAATCGAGGCTGGACTTGATAAAGCAAAAGGAC
CATTTGCGACGTTCATTGTTCAGAAGGGGACTTTGAAAAGAGGGGATGTTGTTGTTTGCGGAGA
AGCTTTCGGAAAGGTCTATCCCAAATTTGGGTTTTCCTCAAGTCACATTGCGCAGATGATATAT
AATCGCTAAAAACTTACCTACTTTGGTCTTGCTCTGTTTCTGTGTTTAGGTACGAGCTTTATTT
GATCACAGTGGGGAACGAGTTGATGAAGCTGGACCCTCCATACCTGTACAGGTTTGTAGTTTCA
TAATCTACCCTAAGTTAAACGTCATTGCACACAAACGTCATTGCAAACGTCATTGCACACAAAC
GTCATGTTTATTTTCTTGGTGACAGGATTTTGATACTATGTTCTCATGTATAGATGATTTAGAT
ATCTAATTTGAGGATCTAAAATACATTTGCAGGTGATTGGTTTAAATAATGTCCCCATTGCTGG
TGATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCAGAGGCACGTGCGGTA
TCACTACGAGATGAAAGAATATCTGCAAAGGCTGGGGATGGAAAGGTCACGCTTTCCTCCTTAG
CTTCTGCTGTATCAGCGAAAAAGATGTCAGGCTTAGATTTGCATCAGCTTAATATCATCTTGAA
GGTCGATGTACAGGTAAATAGTCACTTTGGATTCATCCACTCATCGCCTTAAACATTTTGGTTT
CCTCTGTCTCTTCTTATTTATGCTGATGCAAATCATCAATGTGACTACTAGGGATCCATTGAAG
CTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAATGTCACCTTGAAATTCTTGCTACAAGC
AACAGGGGATGTGAGCAACAGTGATGTTGATCTAGCATCAGCGAGTGAAGCTATCGTTTTTGGA
TTTAATGTCAAAGCGTCTGGTTCTGTTAAGAAAGCTGCAGAAAACAAAGGTGTTGAAATCCGAC
TATATAGAGTTATATATGAGCTTATTGACGATGTGCGAAACGCAATGGAAGGACTTCTTGAGTC
TGTTGAGGTTAGCATTGATTTCTTTAGCAATTTGAAGCGTTTTGTTATTGCCTAATCTGATCAG
CATTTCTCATCATTGTTTTGTCTTCTTTCCACATGAGTTGGCATAACAACTGTTTTTATTGTTG
GGTTGAATAATTGAATTGCCTGAAAAGGAAACCTCTGTATCATGTCATAGATTATCATAAAAAC
ATAGGTTTTAGTCTCACTTCATGAGCCTTTTTGGAGTTTTGAAACTGAAGATTCATGTGGCTGT
TGATATTTGATAGGAACAAATCCCAATTGGCTCAGCAGAAGTTCGAGCTACTTTCAGCAGTGGA
AGTGGTCGTGTGGCTGGATGCATGGTGAATGAAGGAAAATTTGTCAAAGATTGTGGCATCAGGG
TGGTCCGGAAGGGTAAAACTGTCCATGTCGGTGTTCTTGATTCTCTTAAACGGGTTAAAGAAAA
CGTGAAAGAG
						
					

			
		

Sequences
Splice junction sequence	ATTTGTCAAAGATTGTGGCATCAGGGTGGTCCGGAAGGGTAAAACTGTCCATGTCGGTGTTCTT GATTCTCTTAAACGGGTTAAAGAAAACGTGAAAGAGgcatttggtgcaatgagagctcgcggag cacgagtcactgacattgcaatcattgtggttgctgctgatgatggaattcgtcctcaaacaaa tgaagcaa
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	GCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTG CTGATGATGGAATTCGTCCTCAAACAAATGAAGCAATAGCTCACGCAAAGGCTGCTGCTGTACC AATAGTTATAGCTATAAATAAGGTATTTTGTTATTCTTCTTTACCTTGGGTATATGTAAGTTTC TCCCAGTCTTATTCATTTCATGTTCCAGATAGATAAAGAAGGAGCTAGTCCAGATAGAGTGATG CAAGAGCTTTCTTCAATTGGTTTGATGCCTGAAGATTGGGGTGGTGATGTTCCAATGGTTCAGG TTGGAATACATACTTTCATCACGTATATGTTTTAGGGTCCAAATGTTCCATGGGTTCTCATATC ATGCTCTATATTTGCCTTTGACAGATCAGTGCTTTGAAAGGGGAAAATGTCGATGATCTGTTGG AAACTGTCATGCTTGTTGCAGAGGTTAGTTTGTTATTCATCCCATGATAACAGGTTTGCTTGAT TTTTCCGTTTCTGTTTTCGGTAGATGCATAATGAAGCTCAATTTTGTTCTCTTCATGTAAGCAC TACATAGTGGCTACGAAATGACTTACATAATTGCTCCAAAGTCGGCCCAAAATCTTGTTTTATG GAGGGCTAAAGACTAATAACGCTTACATAAATTCATTTTTTTTTTCTCCCACTTTCTGCTTTTG CTTCTCAATTAGCTTTTGCTTGTGGGCTGACTGTATTTTGCTGTTTCAGCTTCAAGAGTTGAAA GCAAATCCACACAGAAATGCCAAGGGCATTGTAATCGAGGCTGGACTTGATAAAGCAAAAGGAC CATTTGCGACGTTCATTGTTCAGAAGGGGACTTTGAAAAGAGGGGATGTTGTTGTTTGCGGAGA AGCTTTCGGAAAGGTCTATCCCAAATTTGGGTTTTCCTCAAGTCACATTGCGCAGATGATATAT AATCGCTAAAAACTTACCTACTTTGGTCTTGCTCTGTTTCTGTGTTTAGGTACGAGCTTTATTT GATCACAGTGGGGAACGAGTTGATGAAGCTGGACCCTCCATACCTGTACAGGTTTGTAGTTTCA TAATCTACCCTAAGTTAAACGTCATTGCACACAAACGTCATTGCAAACGTCATTGCACACAAAC GTCATGTTTATTTTCTTGGTGACAGGATTTTGATACTATGTTCTCATGTATAGATGATTTAGAT ATCTAATTTGAGGATCTAAAATACATTTGCAGGTGATTGGTTTAAATAATGTCCCCATTGCTGG TGATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCAGAGGCACGTGCGGTA TCACTACGAGATGAAAGAATATCTGCAAAGGCTGGGGATGGAAAGGTCACGCTTTCCTCCTTAG CTTCTGCTGTATCAGCGAAAAAGATGTCAGGCTTAGATTTGCATCAGCTTAATATCATCTTGAA GGTCGATGTACAGGTAAATAGTCACTTTGGATTCATCCACTCATCGCCTTAAACATTTTGGTTT CCTCTGTCTCTTCTTATTTATGCTGATGCAAATCATCAATGTGACTACTAGGGATCCATTGAAG CTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAATGTCACCTTGAAATTCTTGCTACAAGC AACAGGGGATGTGAGCAACAGTGATGTTGATCTAGCATCAGCGAGTGAAGCTATCGTTTTTGGA TTTAATGTCAAAGCGTCTGGTTCTGTTAAGAAAGCTGCAGAAAACAAAGGTGTTGAAATCCGAC TATATAGAGTTATATATGAGCTTATTGACGATGTGCGAAACGCAATGGAAGGACTTCTTGAGTC TGTTGAGGTTAGCATTGATTTCTTTAGCAATTTGAAGCGTTTTGTTATTGCCTAATCTGATCAG CATTTCTCATCATTGTTTTGTCTTCTTTCCACATGAGTTGGCATAACAACTGTTTTTATTGTTG GGTTGAATAATTGAATTGCCTGAAAAGGAAACCTCTGTATCATGTCATAGATTATCATAAAAAC ATAGGTTTTAGTCTCACTTCATGAGCCTTTTTGGAGTTTTGAAACTGAAGATTCATGTGGCTGT TGATATTTGATAGGAACAAATCCCAATTGGCTCAGCAGAAGTTCGAGCTACTTTCAGCAGTGGA AGTGGTCGTGTGGCTGGATGCATGGTGAATGAAGGAAAATTTGTCAAAGATTGTGGCATCAGGG TGGTCCGGAAGGGTAAAACTGTCCATGTCGGTGTTCTTGATTCTCTTAAACGGGTTAAAGAAAA CGTGAAAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.176643522

Conservation Information
Conserved circRNAs	NA
PMCS	0.176643522

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							5887556-5889854(+)
						
					

						Potential amino acid sequence
						
							MRARGARVTDIAIIVVAADDGIRPQTNEAIAHAKAAAVPIVIAINKIDKEGASPDRVMQELSSI
GLMPEDWGGDVPMVQISALKGENVDDLLETVMLVAELQELKANPHRNAKGIVIEAGLDKAKGPF
ATFIVQKGTLKRGDVVVCGEAFGKVRALFDHSGERVDEAGPSIPVQVIGLNNVPIAGDEFEIVS
SLDVAREMAEARAVSLRDERISAKAGDGKVTLSSLASAVSAKKMSGLDLHQLNIILKVDVQGSI
EAVRQALQVLPQENVTLKFLLQATGDVSNSDVDLASASEAIVFGFNVKASGSVKKAAENKGVEI
RLYRVIYELIDDVRNAMEGLLESVEEQIPIGSAEVRATFSSGSGRVAGCMVNEGKFVKDCGIRV
VRKGKTVHVGVLDSLKRVKENVKEAFGAMRARGARVTDIAIIVVAADDGIRPQTNEAIAHAKAA
AVPIVIAINKIDKEGASPDRVMQELSSIGLMPEDWGGDVPMVQISALKGENVDDLLETVMLVAE
LQELKANPHRNAKGIVIEAGLDKAKGPFATFIVQKGTLKRGDVVVCGEAFGKVRALFDHSGERV
DEAGPSIPVQVIGLNNVPIAGDEFEIVSSLDVAREMAEARAVSLRDERISAKAGDGKVTLSSLA
SAVSAKKMSGLDLHQLNIILKVDVQGSIEAVRQALQVLPQENVTLKFLLQATGDVSNSDVDLAS
ASEAIVFGFNVKASGSVKKAAENKGVEIRLYRVIYELIDDVRNAMEGLLESVEEQIPIGSAEVR
ATFSSGSGRVAGCMVNEGKFVKDCGIRVVRKGKTVHVGVLDSLKRVKENVKEAFGAMRARGARV
TDIAIIVVAADDGIRPQTNEAIAHAKAAAVPIVIAINKIDKEGASPDRVMQELSSIGLMPEDWG
GDVPMVQISALKGENVDDLLETVMLVAELQELKANPHRNAKGIVIEAGLDKAKGPFATFIVQKG
TLKRGDVVVCGEAFGKVRALFDHSGERVDEAGPSIPVQVIGLNNVPIAGDEFEIVSSLDVAREM
AEARAVSLRDERISAKAGDGKVTLSSLASAVSAKKMSGLDLHQLNIILKVDVQGSIEAVRQALQ
VLPQENVTLKFLLQATGDVSNSDVDLASASEAIVFGFNVKASGSVKKAAENKGVEIRLYRVIYE
LIDDVRNAMEGLLESVEEQIPIGSAEVRATFSSGSGRVAGCMVNEGKFVKDCGIRVVRKGKTVH
VGVLDSLKRVKENVKEAFGAMRARGARVTDIAIIVVAADDGIRPQTNEAIAHAKAAAVPIVIAI
NKIDKEGASPDRVMQELSSIGLMPEDWGGDVPMVQISALKGENVDDLLETVMLVAELQELKANP
HRNAKGIVIEAGLDKAKGPFATFIVQKGTLKRGDVVVCGEAFGKVRALFDHSGERVDEAGPSIP
VQVIGLNNVPIAGDEFEIVSSLDVAREMAEARAVSLRDERISAKAGDGKVTLSSLASAVSAKKM
SGLDLHQLNIILKVDVQGSIEAVRQALQVLPQENVTLKFLLQATGDVSNSDVDLASASEAIVFG
FNVKASGSVKKAAENKGVEIRLYRVIYELIDDVRNAMEGLLESVEEQIPIGSAEVRATFSSGSG
RVAGCMVNEGKFVKDCGIRVVRKGKTVHVGVLDSLKRVKENVKE(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	5887556-5889854(+)
Potential amino acid sequence	MRARGARVTDIAIIVVAADDGIRPQTNEAIAHAKAAAVPIVIAINKIDKEGASPDRVMQELSSI GLMPEDWGGDVPMVQISALKGENVDDLLETVMLVAELQELKANPHRNAKGIVIEAGLDKAKGPF ATFIVQKGTLKRGDVVVCGEAFGKVRALFDHSGERVDEAGPSIPVQVIGLNNVPIAGDEFEIVS SLDVAREMAEARAVSLRDERISAKAGDGKVTLSSLASAVSAKKMSGLDLHQLNIILKVDVQGSI EAVRQALQVLPQENVTLKFLLQATGDVSNSDVDLASASEAIVFGFNVKASGSVKKAAENKGVEI RLYRVIYELIDDVRNAMEGLLESVEEQIPIGSAEVRATFSSGSGRVAGCMVNEGKFVKDCGIRV VRKGKTVHVGVLDSLKRVKENVKEAFGAMRARGARVTDIAIIVVAADDGIRPQTNEAIAHAKAA AVPIVIAINKIDKEGASPDRVMQELSSIGLMPEDWGGDVPMVQISALKGENVDDLLETVMLVAE LQELKANPHRNAKGIVIEAGLDKAKGPFATFIVQKGTLKRGDVVVCGEAFGKVRALFDHSGERV DEAGPSIPVQVIGLNNVPIAGDEFEIVSSLDVAREMAEARAVSLRDERISAKAGDGKVTLSSLA SAVSAKKMSGLDLHQLNIILKVDVQGSIEAVRQALQVLPQENVTLKFLLQATGDVSNSDVDLAS ASEAIVFGFNVKASGSVKKAAENKGVEIRLYRVIYELIDDVRNAMEGLLESVEEQIPIGSAEVR ATFSSGSGRVAGCMVNEGKFVKDCGIRVVRKGKTVHVGVLDSLKRVKENVKEAFGAMRARGARV TDIAIIVVAADDGIRPQTNEAIAHAKAAAVPIVIAINKIDKEGASPDRVMQELSSIGLMPEDWG GDVPMVQISALKGENVDDLLETVMLVAELQELKANPHRNAKGIVIEAGLDKAKGPFATFIVQKG TLKRGDVVVCGEAFGKVRALFDHSGERVDEAGPSIPVQVIGLNNVPIAGDEFEIVSSLDVAREM AEARAVSLRDERISAKAGDGKVTLSSLASAVSAKKMSGLDLHQLNIILKVDVQGSIEAVRQALQ VLPQENVTLKFLLQATGDVSNSDVDLASASEAIVFGFNVKASGSVKKAAENKGVEIRLYRVIYE LIDDVRNAMEGLLESVEEQIPIGSAEVRATFSSGSGRVAGCMVNEGKFVKDCGIRVVRKGKTVH VGVLDSLKRVKENVKEAFGAMRARGARVTDIAIIVVAADDGIRPQTNEAIAHAKAAAVPIVIAI NKIDKEGASPDRVMQELSSIGLMPEDWGGDVPMVQISALKGENVDDLLETVMLVAELQELKANP HRNAKGIVIEAGLDKAKGPFATFIVQKGTLKRGDVVVCGEAFGKVRALFDHSGERVDEAGPSIP VQVIGLNNVPIAGDEFEIVSSLDVAREMAEARAVSLRDERISAKAGDGKVTLSSLASAVSAKKM SGLDLHQLNIILKVDVQGSIEAVRQALQVLPQENVTLKFLLQATGDVSNSDVDLASASEAIVFG FNVKASGSVKKAAENKGVEIRLYRVIYELIDDVRNAMEGLLESVEEQIPIGSAEVRATFSSGSG RVAGCMVNEGKFVKDCGIRVVRKGKTVHVGVLDSLKRVKENVKE(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G17220_circ_g.9

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