Plant Circular RNA Database

Detail information of AT1G17940_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT1G17940_circ_g.4
					
						ID in PlantcircBase
						ath_circ_003180
					
						Alias
						At_ciR1273
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 6170414-6172056  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							AT1G17940						
					
						Parent gene annotation
						
							At1g17940
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G17940_circ_g.1 AT1G17940_circ_g.2 AT1G17940_circ_g.3 						
					
						Support reads
						4/1
					
						Tissues
						leaf/root
					
						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  
						
							CT-AC							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
						AT1G17940.6:8
AT1G17940.3:8
AT1G17940.4:8
AT1G17940.2:8
AT1G17940.1:8
AT1G17940.5:8

General Information
CircRNA Name	AT1G17940_circ_g.4
ID in PlantcircBase	ath_circ_003180
Alias	At_ciR1273
Organism	Arabidpsis thaliana
Position	chr1: 6170414-6172056 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	AT1G17940
Parent gene annotation	At1g17940
Parent gene strand	-
Alternative splicing	AT1G17940_circ_g.1 AT1G17940_circ_g.2 AT1G17940_circ_g.3
Support reads	4/1
Tissues	leaf/root
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	CT-AC 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	AT1G17940.6:8 AT1G17940.3:8 AT1G17940.4:8 AT1G17940.2:8 AT1G17940.1:8 AT1G17940.5:8

			
						 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  
						
							ATACTGAAACCTCACCGATGCTTGTTGGCTTTCTTCTGTTCCCACCTGAGTCTTTCGGCGTTGA
CGCAAAGCATCCCATTTTTCACAGAACTTAAGAAATcttagcttcaacatacttccacttaaca
aagagtccatgcttttctccccaaccatttgctaacgggagattcattaaattatcttgtgcct
gtttcagc

									
								

					

						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: 894
Transcript exons: 6170414-6170503,6170639-6170737,6170852-6170918,6171022-
6171118,6171258-6171396,6171476-6171534,6171622-6171696,
6171789-6172056
CTTAGCTTCAACATACTTCCACTTAACAAAGAGTCCATGCTTTTCTCCCCAACCATTTGCTAAC
GGGAGATTCATTAAATTATCTTGTGCCTGCTGCCAATATTTCACCATTTCACATGAAAGTCTTC
GTTTTACTGCAAGAGTGGCCTTTGAGCTATCAATCGCCATGCCAAGTTGGATATCAACACCCTG
GCCAAGTGCTTGCAAGCAAAGAGCCCGTAGAGTTCCTTCTGCTAAGTCAACTGGTAAACTTCTC
CTTTGCTCAGCAGAAAACTGGGGGAGAACATGCTTAACGGCACAATCAAGATATCCAGCTGCTT
TTAAGAAGATATCAATCGAAGTTCGTCTGTTTTCTTCGGATACTTTCGGATGATTGTGACCATC
ACTAGAACCTCTAGGAAGAAGCAGTAAATTGGCTTGAGACATTTGTAGCATTGCCATTAGATGC
AAAACAGATAAAACTTCATACCAAACGTTTGACATCTCTGTTTCCTCTTCCTCATCCTCCTGAT
TTACCCAATTAAATTGCACTTTAAACTGTAGATGGCTACCATCTTTAGTTAATCCCAAGACAAC
AGGTAGATAATCTAGCAAAGCTTGATGGAGATCCAAGAGCGTTGAACCTCCATGTTGTGTCTTT
CTCCTAGTTCTCGTAATTGTAGGTCCTTCTTGATTAGCCATCACTACTATACGCGTTCTTAAAG
CTGTCAAGCGTTCCACTAAAGTCTTCGGTAATTGATCACCAAGTGACTGCAAAAAATCCACCGC
TCTGGGTATCCTTAAACCAGGTACATATACTGAAACCTCACCGATGCTTGTTGGCTTTCTTCTG
TTCCCACCTGAGTCTTTCGGCGTTGACGCAAAGCATCCCATTTTTCACAGAACTTAAGAAAT
						
					

						Genomic sequence
						
							CTTAGCTTCAACATACTTCCACTTAACAAAGAGTCCATGCTTTTCTCCCCAACCATTTGCTAAC
GGGAGATTCATTAAATTATCTTGTGCCTGTTTCAGCGCACACCGACAAGGAAAAGGAAGCATTA
ACAAAAAATTTCAGATGTTTCCATGGGAAGTAGGAGGCGGTTCATACATAGACAAAGTCTCAAT
GAGAAACAGATTGGATAATAGTAAGGACTTCACCTGCTGCCAATATTTCACCATTTCACATGAA
AGTCTTCGTTTTACTGCAAGAGTGGCCTTTGAGCTATCAATCGCCATGCCAAGTTGGATATCAA
CACCCTATTTTCAGAAACTTGAAAGATGTTAGATTCTAAATGAGAGAAAGAAACTACATGAGGT
ACAGTTAGATGCCATGGGATAGCTTAACTCTATCCATCAAAGGAGAGGTATTACCTGGCCAAGT
GCTTGCAAGCAAAGAGCCCGTAGAGTTCCTTCTGCTAAGTCAACTGGTAAACTTCTCCTGCAGA
AAAATGAAAACAAAGAGAAGGGTTCTGCCATTAGGCTCAACTGATAAAAGTCAACGAGTAGAGT
GAATGACTTTAGAAACTTTGTCACCTACAAACCTTTGCTCAGCAGAAAACTGGGGGAGAACATG
CTTAACGGCACAATCAAGATATCCAGCTGCTTTTAAGAAGATATCAATCGAAGTTCGTCTGTTT
TCTATAATGAAAAACCAAACAACCATAATGTTAAGTCTGAGAAACCTTACCCTTTTTTTAAGAA
AAAAAATCATTGCATAAAAAATGGTCAAGAGACTGTATGAGAAGATGGATGAGAAAGTTTCTCA
GAGAAGCCTAACCTTCGGATACTTTCGGATGATTGTGACCATCACTAGAACCTCTAGGAAGAAG
CAGTAAATTGGCTTGAGACATTTGTAGCATTGCCATTAGATGCAAAACAGATAAAACTTCATAC
CAAACGTTTGACATCTCTGTTTCCTGGTTAGAAGTAAACATGTAAGAGTCTGTACATTATGATG
ACACTTGAAAGACAAACAGCTTTGAAAAATTATTACACCTCTTCCTCATCCTCCTGATTTACCC
AATTAAATTGCACTTTAAACTGTAGATGGCTACCTGAACAACATCACAAATACTGTAGGGTCAG
AATACATCTCTGAAACCAAAGAGATCTTTTTCTAAGAAACACATAATAGTTTATACCATCTTTA
GTTAATCCCAAGACAACAGGTAGATAATCTAGCAAAGCTTGATGGAGATCCAAGAGCGTTGAAC
CTCCTGCCAGAGAACACTAGTAATTAATTAAGAGTTCCAAACCATAGAAAGCAGAAGGAGATAG
AAAACACACAAAGATCTTGACAGACATATACCATGTTGTGTCTTTCTCCTAGTTCTCGTAATTG
TAGGTCCTTCTTGATTAGCCATCACTACTATACGCGTTCTTAAAGCTGTCAAGCGTTCCACTAA
AGTCTTCGGTAATTGATCACCAAGTGACTGCAAAAAATCCACCGCTCTGGGTATCCTTAAACCA
GGTACATATACTGAAACCTCACCGATGCTTGTTGGCTTTCTTCTGTTCCCACCTGAGTCTTTCG
GCGTTGACGCAAAGCATCCCATTTTTCACAGAACTTAAGAAAT
						
					

			
		

Sequences
Splice junction sequence	ATACTGAAACCTCACCGATGCTTGTTGGCTTTCTTCTGTTCCCACCTGAGTCTTTCGGCGTTGA CGCAAAGCATCCCATTTTTCACAGAACTTAAGAAATcttagcttcaacatacttccacttaaca aagagtccatgcttttctccccaaccatttgctaacgggagattcattaaattatcttgtgcct gtttcagc
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: 894 Transcript exons: 6170414-6170503,6170639-6170737,6170852-6170918,6171022- 6171118,6171258-6171396,6171476-6171534,6171622-6171696, 6171789-6172056 CTTAGCTTCAACATACTTCCACTTAACAAAGAGTCCATGCTTTTCTCCCCAACCATTTGCTAAC GGGAGATTCATTAAATTATCTTGTGCCTGCTGCCAATATTTCACCATTTCACATGAAAGTCTTC GTTTTACTGCAAGAGTGGCCTTTGAGCTATCAATCGCCATGCCAAGTTGGATATCAACACCCTG GCCAAGTGCTTGCAAGCAAAGAGCCCGTAGAGTTCCTTCTGCTAAGTCAACTGGTAAACTTCTC CTTTGCTCAGCAGAAAACTGGGGGAGAACATGCTTAACGGCACAATCAAGATATCCAGCTGCTT TTAAGAAGATATCAATCGAAGTTCGTCTGTTTTCTTCGGATACTTTCGGATGATTGTGACCATC ACTAGAACCTCTAGGAAGAAGCAGTAAATTGGCTTGAGACATTTGTAGCATTGCCATTAGATGC AAAACAGATAAAACTTCATACCAAACGTTTGACATCTCTGTTTCCTCTTCCTCATCCTCCTGAT TTACCCAATTAAATTGCACTTTAAACTGTAGATGGCTACCATCTTTAGTTAATCCCAAGACAAC AGGTAGATAATCTAGCAAAGCTTGATGGAGATCCAAGAGCGTTGAACCTCCATGTTGTGTCTTT CTCCTAGTTCTCGTAATTGTAGGTCCTTCTTGATTAGCCATCACTACTATACGCGTTCTTAAAG CTGTCAAGCGTTCCACTAAAGTCTTCGGTAATTGATCACCAAGTGACTGCAAAAAATCCACCGC TCTGGGTATCCTTAAACCAGGTACATATACTGAAACCTCACCGATGCTTGTTGGCTTTCTTCTG TTCCCACCTGAGTCTTTCGGCGTTGACGCAAAGCATCCCATTTTTCACAGAACTTAAGAAAT
Genomic sequence	CTTAGCTTCAACATACTTCCACTTAACAAAGAGTCCATGCTTTTCTCCCCAACCATTTGCTAAC GGGAGATTCATTAAATTATCTTGTGCCTGTTTCAGCGCACACCGACAAGGAAAAGGAAGCATTA ACAAAAAATTTCAGATGTTTCCATGGGAAGTAGGAGGCGGTTCATACATAGACAAAGTCTCAAT GAGAAACAGATTGGATAATAGTAAGGACTTCACCTGCTGCCAATATTTCACCATTTCACATGAA AGTCTTCGTTTTACTGCAAGAGTGGCCTTTGAGCTATCAATCGCCATGCCAAGTTGGATATCAA CACCCTATTTTCAGAAACTTGAAAGATGTTAGATTCTAAATGAGAGAAAGAAACTACATGAGGT ACAGTTAGATGCCATGGGATAGCTTAACTCTATCCATCAAAGGAGAGGTATTACCTGGCCAAGT GCTTGCAAGCAAAGAGCCCGTAGAGTTCCTTCTGCTAAGTCAACTGGTAAACTTCTCCTGCAGA AAAATGAAAACAAAGAGAAGGGTTCTGCCATTAGGCTCAACTGATAAAAGTCAACGAGTAGAGT GAATGACTTTAGAAACTTTGTCACCTACAAACCTTTGCTCAGCAGAAAACTGGGGGAGAACATG CTTAACGGCACAATCAAGATATCCAGCTGCTTTTAAGAAGATATCAATCGAAGTTCGTCTGTTT TCTATAATGAAAAACCAAACAACCATAATGTTAAGTCTGAGAAACCTTACCCTTTTTTTAAGAA AAAAAATCATTGCATAAAAAATGGTCAAGAGACTGTATGAGAAGATGGATGAGAAAGTTTCTCA GAGAAGCCTAACCTTCGGATACTTTCGGATGATTGTGACCATCACTAGAACCTCTAGGAAGAAG CAGTAAATTGGCTTGAGACATTTGTAGCATTGCCATTAGATGCAAAACAGATAAAACTTCATAC CAAACGTTTGACATCTCTGTTTCCTGGTTAGAAGTAAACATGTAAGAGTCTGTACATTATGATG ACACTTGAAAGACAAACAGCTTTGAAAAATTATTACACCTCTTCCTCATCCTCCTGATTTACCC AATTAAATTGCACTTTAAACTGTAGATGGCTACCTGAACAACATCACAAATACTGTAGGGTCAG AATACATCTCTGAAACCAAAGAGATCTTTTTCTAAGAAACACATAATAGTTTATACCATCTTTA GTTAATCCCAAGACAACAGGTAGATAATCTAGCAAAGCTTGATGGAGATCCAAGAGCGTTGAAC CTCCTGCCAGAGAACACTAGTAATTAATTAAGAGTTCCAAACCATAGAAAGCAGAAGGAGATAG AAAACACACAAAGATCTTGACAGACATATACCATGTTGTGTCTTTCTCCTAGTTCTCGTAATTG TAGGTCCTTCTTGATTAGCCATCACTACTATACGCGTTCTTAAAGCTGTCAAGCGTTCCACTAA AGTCTTCGGTAATTGATCACCAAGTGACTGCAAAAAATCCACCGCTCTGGGTATCCTTAAACCA GGTACATATACTGAAACCTCACCGATGCTTGTTGGCTTTCTTCTGTTCCCACCTGAGTCTTTCG GCGTTGACGCAAAGCATCCCATTTTTCACAGAACTTAAGAAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.199678887

Conservation Information
Conserved circRNAs	NA
PMCS	0.199678887

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of AT1G17940_circ_g.4

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