Plant Circular RNA Database

Detail information of AT1G25540_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT1G25540_circ_g.4
					
						ID in PlantcircBase
						ath_circ_004357
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 8972189-8973094  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder, circRNA_finder, find_circ
					
						Parent gene
						
							AT1G25540						
					
						Parent gene annotation
						
							Mediator of RNA polymerase II transcription subunit 25
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G25540_circ_g.5 						
					
						Support reads
						7
					
						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  
						
							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
						AT1G25540.2:4
AT1G25540.1:4

General Information
CircRNA Name	AT1G25540_circ_g.4
ID in PlantcircBase	ath_circ_004357
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 8972189-8973094 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, PcircRNA_finder, circRNA_finder, find_circ
Parent gene	AT1G25540
Parent gene annotation	Mediator of RNA polymerase II transcription subunit 25
Parent gene strand	-
Alternative splicing	AT1G25540_circ_g.5
Support reads	7
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	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	AT1G25540.2:4 AT1G25540.1:4

			
						 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  
						
							CAGGTGTTGGCAATATGTGAGGATTGCTGGCTGTGATTAGGATACAGTGTCTTTTCAGATCGTT
ACTTGGTTGAGCTTGGCCTGAAGGAGGAGAAAACATaactttcacagtagcagttggaactggt
ccaacagaaactggttgccgattctgaataggtccattggctgaaaatcatacaaaaagagatc
ttcatata

									
								

					

						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: 555
Transcript exons: 8972189-8972256,8972373-8972589,8972733-8972798,8972891-
8973094
AACTTTCACAGTAGCAGTTGGAACTGGTCCAACAGAAACTGGTTGCCGATTCTGAATAGGTCCA
TTGGCTGATGACACAGGAGCTGGAGGTTGCCCAGTGACTGGAATAGATGGAGCAACAGTGGCCC
TGTCCACTTTCACAGGGCTCTGAGTCTGTGGCAAATTTGTAGCAGAATGACTTAAGGCAGCACA
TGCCTCCACAAAATTCTCCGAGATCAGGACAAGATAGAATGTGTTCTTAGCCGTGTCAATTGAC
AAGTCCGCACTTTGTTGATTGGGCTTTCCCGCATTGTATAGTGCTCTAATTGTTGGAAGCTGCT
TTGGACATACAACAGACAAAGAAACAGAACACTTAGCAAAATATGAAGCCACTGTCTCAGCATC
TGATAATCGACTCTCAGCTTGCGCATCACCATTCTCATTCCGTTCCACATTTTGCAATCGTGGA
CGATATACAGGTGTTGGCAATATGTGAGGATTGCTGGCTGTGATTAGGATACAGTGTCTTTTCA
GATCGTTACTTGGTTGAGCTTGGCCTGAAGGAGGAGAAAACAT
						
					

						Genomic sequence
						
							AACTTTCACAGTAGCAGTTGGAACTGGTCCAACAGAAACTGGTTGCCGATTCTGAATAGGTCCA
TTGGCTGAAAATCATACAAAAAGAGATCTTCATATAGAGAAGCAGGATAGAATCCAAAGAAGCA
CAAAGAAAAATCAAGATAGTTGGACTAAGAAAAATGGATGTTGTCAGTAGAAGAACCTGATGAC
ACAGGAGCTGGAGGTTGCCCAGTGACTGGAATAGATGGAGCAACAGTGGCCCTGTCCACTTTCA
CAGGGCTCTGAGTCTGTGGCAAATTTGTAGCAGAATGACTTAAGGCAGCACATGCCTCCACAAA
ATTCTCCGAGATCAGGACAAGATAGAATGTGTTCTTAGCCGTGTCAATTGACAAGTCCGCACTT
TGTTGATTGGGCTTTCCCTGCATTTAAAACAGTATAAAACAAAGATTACACCAGTTTATAGCAT
TGAGAATAAAGACAGCCTTTGAAAGAGCTGTCTGACAAAAGAAAGACTTTTGATAGATGTACAT
CTAGTGAATAGCAAATAGACACGCAGTCTCACCGCATTGTATAGTGCTCTAATTGTTGGAAGCT
GCTTTGGACATACAACAGACAAAGAAACAGAACACTGCACACCAATATGGCAGGTTAGTAATTT
CCCATTAAAAGGAGTAATTATAGCTAGTTGTAATACCTGGGGGAATCAGTTAAAAAAAGTACCT
TAGCAAAATATGAAGCCACTGTCTCAGCATCTGATAATCGACTCTCAGCTTGCGCATCACCATT
CTCATTCCGTTCCACATTTTGCAATCGTGGACGATATACAGGTGTTGGCAATATGTGAGGATTG
CTGGCTGTGATTAGGATACAGTGTCTTTTCAGATCGTTACTTGGTTGAGCTTGGCCTGAAGGAG
GAGAAAACAT
						
					

			
		

Sequences
Splice junction sequence	CAGGTGTTGGCAATATGTGAGGATTGCTGGCTGTGATTAGGATACAGTGTCTTTTCAGATCGTT ACTTGGTTGAGCTTGGCCTGAAGGAGGAGAAAACATaactttcacagtagcagttggaactggt ccaacagaaactggttgccgattctgaataggtccattggctgaaaatcatacaaaaagagatc ttcatata
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: 555 Transcript exons: 8972189-8972256,8972373-8972589,8972733-8972798,8972891- 8973094 AACTTTCACAGTAGCAGTTGGAACTGGTCCAACAGAAACTGGTTGCCGATTCTGAATAGGTCCA TTGGCTGATGACACAGGAGCTGGAGGTTGCCCAGTGACTGGAATAGATGGAGCAACAGTGGCCC TGTCCACTTTCACAGGGCTCTGAGTCTGTGGCAAATTTGTAGCAGAATGACTTAAGGCAGCACA TGCCTCCACAAAATTCTCCGAGATCAGGACAAGATAGAATGTGTTCTTAGCCGTGTCAATTGAC AAGTCCGCACTTTGTTGATTGGGCTTTCCCGCATTGTATAGTGCTCTAATTGTTGGAAGCTGCT TTGGACATACAACAGACAAAGAAACAGAACACTTAGCAAAATATGAAGCCACTGTCTCAGCATC TGATAATCGACTCTCAGCTTGCGCATCACCATTCTCATTCCGTTCCACATTTTGCAATCGTGGA CGATATACAGGTGTTGGCAATATGTGAGGATTGCTGGCTGTGATTAGGATACAGTGTCTTTTCA GATCGTTACTTGGTTGAGCTTGGCCTGAAGGAGGAGAAAACAT
Genomic sequence	AACTTTCACAGTAGCAGTTGGAACTGGTCCAACAGAAACTGGTTGCCGATTCTGAATAGGTCCA TTGGCTGAAAATCATACAAAAAGAGATCTTCATATAGAGAAGCAGGATAGAATCCAAAGAAGCA CAAAGAAAAATCAAGATAGTTGGACTAAGAAAAATGGATGTTGTCAGTAGAAGAACCTGATGAC ACAGGAGCTGGAGGTTGCCCAGTGACTGGAATAGATGGAGCAACAGTGGCCCTGTCCACTTTCA CAGGGCTCTGAGTCTGTGGCAAATTTGTAGCAGAATGACTTAAGGCAGCACATGCCTCCACAAA ATTCTCCGAGATCAGGACAAGATAGAATGTGTTCTTAGCCGTGTCAATTGACAAGTCCGCACTT TGTTGATTGGGCTTTCCCTGCATTTAAAACAGTATAAAACAAAGATTACACCAGTTTATAGCAT TGAGAATAAAGACAGCCTTTGAAAGAGCTGTCTGACAAAAGAAAGACTTTTGATAGATGTACAT CTAGTGAATAGCAAATAGACACGCAGTCTCACCGCATTGTATAGTGCTCTAATTGTTGGAAGCT GCTTTGGACATACAACAGACAAAGAAACAGAACACTGCACACCAATATGGCAGGTTAGTAATTT CCCATTAAAAGGAGTAATTATAGCTAGTTGTAATACCTGGGGGAATCAGTTAAAAAAAGTACCT TAGCAAAATATGAAGCCACTGTCTCAGCATCTGATAATCGACTCTCAGCTTGCGCATCACCATT CTCATTCCGTTCCACATTTTGCAATCGTGGACGATATACAGGTGTTGGCAATATGTGAGGATTG CTGGCTGTGATTAGGATACAGTGTCTTTTCAGATCGTTACTTGGTTGAGCTTGGCCTGAAGGAG GAGAAAACAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.219071303

Conservation Information
Conserved circRNAs	NA
PMCS	0.219071303

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8973095-8972191(-)
						
						Potential amino acid sequence
						
							MFSPPSGQAQPSNDLKRHCILITASNPHILPTPVYRPRLQNVERNENGDAQAESRLSDAETVAS
YFAKCSVSLSVVCPKQLPTIRALYNAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSHS
ATNLPQTQSPVKVDRATVAPSIPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKVMFSPPSG
QAQPSNDLKRHCILITASNPHILPTPVYRPRLQNVERNENGDAQAESRLSDAETVASYFAKCSV
SLSVVCPKQLPTIRALYNAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSHSATNLPQT
QSPVKVDRATVAPSIPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKVMFSPPSGQAQPSND
LKRHCILITASNPHILPTPVYRPRLQNVERNENGDAQAESRLSDAETVASYFAKCSVSLSVVCP
KQLPTIRALYNAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSHSATNLPQTQSPVKVD
RATVAPSIPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKVMFSPPSGQAQPSNDLKRHCIL
ITASNPHILPTPVYRPRLQNVERNENGDAQAESRLSDAETVASYFAKCSVSLSVVCPKQLPTIR
ALYNAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSHSATNLPQTQSPVKVDRATVAPS
IPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKV(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8973095-8972191(-)
Potential amino acid sequence	MFSPPSGQAQPSNDLKRHCILITASNPHILPTPVYRPRLQNVERNENGDAQAESRLSDAETVAS YFAKCSVSLSVVCPKQLPTIRALYNAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSHS ATNLPQTQSPVKVDRATVAPSIPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKVMFSPPSG QAQPSNDLKRHCILITASNPHILPTPVYRPRLQNVERNENGDAQAESRLSDAETVASYFAKCSV SLSVVCPKQLPTIRALYNAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSHSATNLPQT QSPVKVDRATVAPSIPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKVMFSPPSGQAQPSND LKRHCILITASNPHILPTPVYRPRLQNVERNENGDAQAESRLSDAETVASYFAKCSVSLSVVCP KQLPTIRALYNAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSHSATNLPQTQSPVKVD RATVAPSIPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKVMFSPPSGQAQPSNDLKRHCIL ITASNPHILPTPVYRPRLQNVERNENGDAQAESRLSDAETVASYFAKCSVSLSVVCPKQLPTIR ALYNAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSHSATNLPQTQSPVKVDRATVAPS IPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKV(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G25540_circ_g.4

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