Plant Circular RNA Database

Detail information of AT1G17220_circ_g.13

			
						 General Information
					
						CircRNA Name
						AT1G17220_circ_g.13
					
						ID in PlantcircBase
						ath_circ_003037
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 5888297-5889857  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						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.9 AT1G17220_circ_g.10 AT1G17220_circ_g.11 AT1G17220_circ_g.12 AT1G17220_circ_g.14 AT1G17220_circ_g.15 AT1G17220_circ_g.16 AT1G17220_circ_g.17 AT1G17220_circ_g.18 						
					
						Support reads
						24
					
						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
						AT1G17220.1:5

General Information
CircRNA Name	AT1G17220_circ_g.13
ID in PlantcircBase	ath_circ_003037
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 5888297-5889857 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	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.9 AT1G17220_circ_g.10 AT1G17220_circ_g.11 AT1G17220_circ_g.12 AT1G17220_circ_g.14 AT1G17220_circ_g.15 AT1G17220_circ_g.16 AT1G17220_circ_g.17 AT1G17220_circ_g.18
Support reads	24
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	AT1G17220.1:5

			
						 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  
						
							ATTTGTCAAAGATTGTGGCATCAGGGTGGTCCGGAAGGGTAAAACTGTCCATGTCGGTGTTCTT
GATTCTCTTAAACGGGTTAAAGAAAACGTGAAAGAGcttcaagagttgaaagcaaatccacaca
gaaatgccaagggcattgtaatcgaggctggacttgataaagcaaaaggaccatttgcgacgtt
cattgttc

									
								

					

						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: 924
Transcript exons: 5888297-5888452,5888553-5888618,5888792-5889028,5889131-
5889406,5889669-5889857
CTTCAAGAGTTGAAAGCAAATCCACACAGAAATGCCAAGGGCATTGTAATCGAGGCTGGACTTG
ATAAAGCAAAAGGACCATTTGCGACGTTCATTGTTCAGAAGGGGACTTTGAAAAGAGGGGATGT
TGTTGTTTGCGGAGAAGCTTTCGGAAAGGTACGAGCTTTATTTGATCACAGTGGGGAACGAGTT
GATGAAGCTGGACCCTCCATACCTGTACAGGTGATTGGTTTAAATAATGTCCCCATTGCTGGTG
ATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCAGAGGCACGTGCGGTATC
ACTACGAGATGAAAGAATATCTGCAAAGGCTGGGGATGGAAAGGTCACGCTTTCCTCCTTAGCT
TCTGCTGTATCAGCGAAAAAGATGTCAGGCTTAGATTTGCATCAGCTTAATATCATCTTGAAGG
TCGATGTACAGGGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAATGT
CACCTTGAAATTCTTGCTACAAGCAACAGGGGATGTGAGCAACAGTGATGTTGATCTAGCATCA
GCGAGTGAAGCTATCGTTTTTGGATTTAATGTCAAAGCGTCTGGTTCTGTTAAGAAAGCTGCAG
AAAACAAAGGTGTTGAAATCCGACTATATAGAGTTATATATGAGCTTATTGACGATGTGCGAAA
CGCAATGGAAGGACTTCTTGAGTCTGTTGAGGAACAAATCCCAATTGGCTCAGCAGAAGTTCGA
GCTACTTTCAGCAGTGGAAGTGGTCGTGTGGCTGGATGCATGGTGAATGAAGGAAAATTTGTCA
AAGATTGTGGCATCAGGGTGGTCCGGAAGGGTAAAACTGTCCATGTCGGTGTTCTTGATTCTCT
TAAACGGGTTAAAGAAAACGTGAAAGAG
						
					

						Genomic sequence
						
							CTTCAAGAGTTGAAAGCAAATCCACACAGAAATGCCAAGGGCATTGTAATCGAGGCTGGACTTG
ATAAAGCAAAAGGACCATTTGCGACGTTCATTGTTCAGAAGGGGACTTTGAAAAGAGGGGATGT
TGTTGTTTGCGGAGAAGCTTTCGGAAAGGTCTATCCCAAATTTGGGTTTTCCTCAAGTCACATT
GCGCAGATGATATATAATCGCTAAAAACTTACCTACTTTGGTCTTGCTCTGTTTCTGTGTTTAG
GTACGAGCTTTATTTGATCACAGTGGGGAACGAGTTGATGAAGCTGGACCCTCCATACCTGTAC
AGGTTTGTAGTTTCATAATCTACCCTAAGTTAAACGTCATTGCACACAAACGTCATTGCAAACG
TCATTGCACACAAACGTCATGTTTATTTTCTTGGTGACAGGATTTTGATACTATGTTCTCATGT
ATAGATGATTTAGATATCTAATTTGAGGATCTAAAATACATTTGCAGGTGATTGGTTTAAATAA
TGTCCCCATTGCTGGTGATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCA
GAGGCACGTGCGGTATCACTACGAGATGAAAGAATATCTGCAAAGGCTGGGGATGGAAAGGTCA
CGCTTTCCTCCTTAGCTTCTGCTGTATCAGCGAAAAAGATGTCAGGCTTAGATTTGCATCAGCT
TAATATCATCTTGAAGGTCGATGTACAGGTAAATAGTCACTTTGGATTCATCCACTCATCGCCT
TAAACATTTTGGTTTCCTCTGTCTCTTCTTATTTATGCTGATGCAAATCATCAATGTGACTACT
AGGGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAATGTCACCTTGAA
ATTCTTGCTACAAGCAACAGGGGATGTGAGCAACAGTGATGTTGATCTAGCATCAGCGAGTGAA
GCTATCGTTTTTGGATTTAATGTCAAAGCGTCTGGTTCTGTTAAGAAAGCTGCAGAAAACAAAG
GTGTTGAAATCCGACTATATAGAGTTATATATGAGCTTATTGACGATGTGCGAAACGCAATGGA
AGGACTTCTTGAGTCTGTTGAGGTTAGCATTGATTTCTTTAGCAATTTGAAGCGTTTTGTTATT
GCCTAATCTGATCAGCATTTCTCATCATTGTTTTGTCTTCTTTCCACATGAGTTGGCATAACAA
CTGTTTTTATTGTTGGGTTGAATAATTGAATTGCCTGAAAAGGAAACCTCTGTATCATGTCATA
GATTATCATAAAAACATAGGTTTTAGTCTCACTTCATGAGCCTTTTTGGAGTTTTGAAACTGAA
GATTCATGTGGCTGTTGATATTTGATAGGAACAAATCCCAATTGGCTCAGCAGAAGTTCGAGCT
ACTTTCAGCAGTGGAAGTGGTCGTGTGGCTGGATGCATGGTGAATGAAGGAAAATTTGTCAAAG
ATTGTGGCATCAGGGTGGTCCGGAAGGGTAAAACTGTCCATGTCGGTGTTCTTGATTCTCTTAA
ACGGGTTAAAGAAAACGTGAAAGAG
						
					

			
		

Sequences
Splice junction sequence	ATTTGTCAAAGATTGTGGCATCAGGGTGGTCCGGAAGGGTAAAACTGTCCATGTCGGTGTTCTT GATTCTCTTAAACGGGTTAAAGAAAACGTGAAAGAGcttcaagagttgaaagcaaatccacaca gaaatgccaagggcattgtaatcgaggctggacttgataaagcaaaaggaccatttgcgacgtt cattgttc
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: 924 Transcript exons: 5888297-5888452,5888553-5888618,5888792-5889028,5889131- 5889406,5889669-5889857 CTTCAAGAGTTGAAAGCAAATCCACACAGAAATGCCAAGGGCATTGTAATCGAGGCTGGACTTG ATAAAGCAAAAGGACCATTTGCGACGTTCATTGTTCAGAAGGGGACTTTGAAAAGAGGGGATGT TGTTGTTTGCGGAGAAGCTTTCGGAAAGGTACGAGCTTTATTTGATCACAGTGGGGAACGAGTT GATGAAGCTGGACCCTCCATACCTGTACAGGTGATTGGTTTAAATAATGTCCCCATTGCTGGTG ATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCAGAGGCACGTGCGGTATC ACTACGAGATGAAAGAATATCTGCAAAGGCTGGGGATGGAAAGGTCACGCTTTCCTCCTTAGCT TCTGCTGTATCAGCGAAAAAGATGTCAGGCTTAGATTTGCATCAGCTTAATATCATCTTGAAGG TCGATGTACAGGGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAATGT CACCTTGAAATTCTTGCTACAAGCAACAGGGGATGTGAGCAACAGTGATGTTGATCTAGCATCA GCGAGTGAAGCTATCGTTTTTGGATTTAATGTCAAAGCGTCTGGTTCTGTTAAGAAAGCTGCAG AAAACAAAGGTGTTGAAATCCGACTATATAGAGTTATATATGAGCTTATTGACGATGTGCGAAA CGCAATGGAAGGACTTCTTGAGTCTGTTGAGGAACAAATCCCAATTGGCTCAGCAGAAGTTCGA GCTACTTTCAGCAGTGGAAGTGGTCGTGTGGCTGGATGCATGGTGAATGAAGGAAAATTTGTCA AAGATTGTGGCATCAGGGTGGTCCGGAAGGGTAAAACTGTCCATGTCGGTGTTCTTGATTCTCT TAAACGGGTTAAAGAAAACGTGAAAGAG
Genomic sequence	CTTCAAGAGTTGAAAGCAAATCCACACAGAAATGCCAAGGGCATTGTAATCGAGGCTGGACTTG ATAAAGCAAAAGGACCATTTGCGACGTTCATTGTTCAGAAGGGGACTTTGAAAAGAGGGGATGT TGTTGTTTGCGGAGAAGCTTTCGGAAAGGTCTATCCCAAATTTGGGTTTTCCTCAAGTCACATT GCGCAGATGATATATAATCGCTAAAAACTTACCTACTTTGGTCTTGCTCTGTTTCTGTGTTTAG GTACGAGCTTTATTTGATCACAGTGGGGAACGAGTTGATGAAGCTGGACCCTCCATACCTGTAC AGGTTTGTAGTTTCATAATCTACCCTAAGTTAAACGTCATTGCACACAAACGTCATTGCAAACG TCATTGCACACAAACGTCATGTTTATTTTCTTGGTGACAGGATTTTGATACTATGTTCTCATGT ATAGATGATTTAGATATCTAATTTGAGGATCTAAAATACATTTGCAGGTGATTGGTTTAAATAA TGTCCCCATTGCTGGTGATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCA GAGGCACGTGCGGTATCACTACGAGATGAAAGAATATCTGCAAAGGCTGGGGATGGAAAGGTCA CGCTTTCCTCCTTAGCTTCTGCTGTATCAGCGAAAAAGATGTCAGGCTTAGATTTGCATCAGCT TAATATCATCTTGAAGGTCGATGTACAGGTAAATAGTCACTTTGGATTCATCCACTCATCGCCT TAAACATTTTGGTTTCCTCTGTCTCTTCTTATTTATGCTGATGCAAATCATCAATGTGACTACT AGGGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAATGTCACCTTGAA ATTCTTGCTACAAGCAACAGGGGATGTGAGCAACAGTGATGTTGATCTAGCATCAGCGAGTGAA GCTATCGTTTTTGGATTTAATGTCAAAGCGTCTGGTTCTGTTAAGAAAGCTGCAGAAAACAAAG GTGTTGAAATCCGACTATATAGAGTTATATATGAGCTTATTGACGATGTGCGAAACGCAATGGA AGGACTTCTTGAGTCTGTTGAGGTTAGCATTGATTTCTTTAGCAATTTGAAGCGTTTTGTTATT GCCTAATCTGATCAGCATTTCTCATCATTGTTTTGTCTTCTTTCCACATGAGTTGGCATAACAA CTGTTTTTATTGTTGGGTTGAATAATTGAATTGCCTGAAAAGGAAACCTCTGTATCATGTCATA GATTATCATAAAAACATAGGTTTTAGTCTCACTTCATGAGCCTTTTTGGAGTTTTGAAACTGAA GATTCATGTGGCTGTTGATATTTGATAGGAACAAATCCCAATTGGCTCAGCAGAAGTTCGAGCT ACTTTCAGCAGTGGAAGTGGTCGTGTGGCTGGATGCATGGTGAATGAAGGAAAATTTGTCAAAG ATTGTGGCATCAGGGTGGTCCGGAAGGGTAAAACTGTCCATGTCGGTGTTCTTGATTCTCTTAA ACGGGTTAAAGAAAACGTGAAAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.313532372

Conservation Information
Conserved circRNAs	NA
PMCS	0.313532372

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5888867-5889854(+)
						
						Potential amino acid sequence
						
							MAEARAVSLRDERISAKAGDGKVTLSSLASAVSAKKMSGLDLHQLNIILKVDVQGSIEAVRQAL
QVLPQENVTLKFLLQATGDVSNSDVDLASASEAIVFGFNVKASGSVKKAAENKGVEIRLYRVIY
ELIDDVRNAMEGLLESVEEQIPIGSAEVRATFSSGSGRVAGCMVNEGKFVKDCGIRVVRKGKTV
HVGVLDSLKRVKENVKELQELKANPHRNAKGIVIEAGLDKAKGPFATFIVQKGTLKRGDVVVCG
EAFGKVRALFDHSGERVDEAGPSIPVQVIGLNNVPIAGDEFEIVSSLDVAREMAEARAVSLRDE
RISAKAGDGKVTLSSLASAVSAKKMSGLDLHQLNIILKVDVQGSIEAVRQALQVLPQENVTLKF
LLQATGDVSNSDVDLASASEAIVFGFNVKASGSVKKAAENKGVEIRLYRVIYELIDDVRNAMEG
LLESVEEQIPIGSAEVRATFSSGSGRVAGCMVNEGKFVKDCGIRVVRKGKTVHVGVLDSLKRVK
ENVKELQELKANPHRNAKGIVIEAGLDKAKGPFATFIVQKGTLKRGDVVVCGEAFGKVRALFDH
SGERVDEAGPSIPVQVIGLNNVPIAGDEFEIVSSLDVAREMAEARAVSLRDERISAKAGDGKVT
LSSLASAVSAKKMSGLDLHQLNIILKVDVQGSIEAVRQALQVLPQENVTLKFLLQATGDVSNSD
VDLASASEAIVFGFNVKASGSVKKAAENKGVEIRLYRVIYELIDDVRNAMEGLLESVEEQIPIG
SAEVRATFSSGSGRVAGCMVNEGKFVKDCGIRVVRKGKTVHVGVLDSLKRVKENVKELQELKAN
PHRNAKGIVIEAGLDKAKGPFATFIVQKGTLKRGDVVVCGEAFGKVRALFDHSGERVDEAGPSI
PVQVIGLNNVPIAGDEFEIVSSLDVAREMAEARAVSLRDERISAKAGDGKVTLSSLASAVSAKK
MSGLDLHQLNIILKVDVQGSIEAVRQALQVLPQENVTLKFLLQATGDVSNSDVDLASASEAIVF
GFNVKASGSVKKAAENKGVEIRLYRVIYELIDDVRNAMEGLLESVEEQIPIGSAEVRATFSSGS
GRVAGCMVNEGKFVKDCGIRVVRKGKTVHVGVLDSLKRVKENVKE(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5888867-5889854(+)
Potential amino acid sequence	MAEARAVSLRDERISAKAGDGKVTLSSLASAVSAKKMSGLDLHQLNIILKVDVQGSIEAVRQAL QVLPQENVTLKFLLQATGDVSNSDVDLASASEAIVFGFNVKASGSVKKAAENKGVEIRLYRVIY ELIDDVRNAMEGLLESVEEQIPIGSAEVRATFSSGSGRVAGCMVNEGKFVKDCGIRVVRKGKTV HVGVLDSLKRVKENVKELQELKANPHRNAKGIVIEAGLDKAKGPFATFIVQKGTLKRGDVVVCG EAFGKVRALFDHSGERVDEAGPSIPVQVIGLNNVPIAGDEFEIVSSLDVAREMAEARAVSLRDE RISAKAGDGKVTLSSLASAVSAKKMSGLDLHQLNIILKVDVQGSIEAVRQALQVLPQENVTLKF LLQATGDVSNSDVDLASASEAIVFGFNVKASGSVKKAAENKGVEIRLYRVIYELIDDVRNAMEG LLESVEEQIPIGSAEVRATFSSGSGRVAGCMVNEGKFVKDCGIRVVRKGKTVHVGVLDSLKRVK ENVKELQELKANPHRNAKGIVIEAGLDKAKGPFATFIVQKGTLKRGDVVVCGEAFGKVRALFDH SGERVDEAGPSIPVQVIGLNNVPIAGDEFEIVSSLDVAREMAEARAVSLRDERISAKAGDGKVT LSSLASAVSAKKMSGLDLHQLNIILKVDVQGSIEAVRQALQVLPQENVTLKFLLQATGDVSNSD VDLASASEAIVFGFNVKASGSVKKAAENKGVEIRLYRVIYELIDDVRNAMEGLLESVEEQIPIG SAEVRATFSSGSGRVAGCMVNEGKFVKDCGIRVVRKGKTVHVGVLDSLKRVKENVKELQELKAN PHRNAKGIVIEAGLDKAKGPFATFIVQKGTLKRGDVVVCGEAFGKVRALFDHSGERVDEAGPSI PVQVIGLNNVPIAGDEFEIVSSLDVAREMAEARAVSLRDERISAKAGDGKVTLSSLASAVSAKK MSGLDLHQLNIILKVDVQGSIEAVRQALQVLPQENVTLKFLLQATGDVSNSDVDLASASEAIVF GFNVKASGSVKKAAENKGVEIRLYRVIYELIDDVRNAMEGLLESVEEQIPIGSAEVRATFSSGS GRVAGCMVNEGKFVKDCGIRVVRKGKTVHVGVLDSLKRVKENVKE(+)
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.13

Address

Any questions?

Supported by