Plant Circular RNA Database

Detail information of AT5G28540_circ_g.8

			
						 General Information
					
						CircRNA Name
						AT5G28540_circ_g.8
					
						ID in PlantcircBase
						ath_circ_040908
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 10542154-10543049  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT5G28540						
					
						Parent gene annotation
						
							Mediator of RNA polymerase II transcription subunit 37a
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G28540_circ_g.6 AT5G28540_circ_g.7 AT5G28540_circ_g.9 AT5G28540_circ_g.10 AT5G28540_circ_g.11 						
					
						Support reads
						117
					
						Tissues
						seed, 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
						AT5G28540.1:3

General Information
CircRNA Name	AT5G28540_circ_g.8
ID in PlantcircBase	ath_circ_040908
Alias	NA
Organism	Arabidpsis thaliana
Position	chr5: 10542154-10543049 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT5G28540
Parent gene annotation	Mediator of RNA polymerase II transcription subunit 37a
Parent gene strand	-
Alternative splicing	AT5G28540_circ_g.6 AT5G28540_circ_g.7 AT5G28540_circ_g.9 AT5G28540_circ_g.10 AT5G28540_circ_g.11
Support reads	117
Tissues	seed, 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	AT5G28540.1:3

			
						 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  
						
							TAAACACCAACACAAGAGTAAGTAGTACCAAGATCTATCCCTATCACTGATCCTAACTTCGTAG
CCTCTTCTATTGCAGAGGACAACGCAAATAAACATCctcccaagtgagtgtcaccatttgtgga
gagaacctcaaacactccgttatcaatggtcaagacactgacatcaaaagtaccaccaccaaga
tcaaacac

									
								

					

						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: 726
Transcript exons: 10542154-10542396,10542489-10542703,10542782-10543049
CTCCCAAGTGAGTGTCACCATTTGTGGAGAGAACCTCAAACACTCCGTTATCAATGGTCAAGAC
ACTGACATCAAAAGTACCACCACCAAGATCAAACACAAGGATATTCTTCTCGCCACCCTTCTTA
TCAAGACCATAGGCAATAGCAGCAGCAGTAGGTTCATTAATGATTCTAGCAACATTGAGCCCAG
CAATAACACCAGCATCCTTAGTAGCTTGCCTTTGAGCATCATTGAAGTAAGCTGGAACAGTGAC
AACAGCGTCCTTGATTTTCTTTCCAAGGTAGGCTTCAGCTGTCTCCTTCATCTTAGTCAGAATC
ATAGCACTAATCTCCTCAGGACTGAAAACCTTAGTCTCACCATCCTTGATCTTGACTTGAATGT
ATGGCTTACCATCCTTGTTCACAATCTGGTAAGGTACAAGTTTCCTATCCTTTTGAACCTCCTT
ATCCTCAAATTTTCGCCCGATCAATCTCTTAACGTCGAAGACAGTCCTCTCTGGATTAACAGCT
GCTTGATTCTTAGCAGCCTCACCAATGAGTCTTTCAGAGTCAGTAAAACCAACCCATGAAGGTG
TAATACGGTTTCCTTGGTCATTGGCAATAATTTCGACATGACCATTCTTGTAAACACCAACACA
AGAGTAAGTAGTACCAAGATCTATCCCTATCACTGATCCTAACTTCGTAGCCTCTTCTATTGCA
GAGGACAACGCAAATAAACATC
						
					

						Genomic sequence
						
							CTCCCAAGTGAGTGTCACCATTTGTGGAGAGAACCTCAAACACTCCGTTATCAATGGTCAAGAC
ACTGACATCAAAAGTACCACCACCAAGATCAAACACAAGGATATTCTTCTCGCCACCCTTCTTA
TCAAGACCATAGGCAATAGCAGCAGCAGTAGGTTCATTAATGATTCTAGCAACATTGAGCCCAG
CAATAACACCAGCATCCTTAGTAGCTTGCCTTTGAGCATCATTGAAGTAAGCTACGCAAAGTCA
AAAACACCAAATAAACAATCAATCACCAAATACAGATAATAAAGATACCTCTCCACCACATATA
TAACAACAAACTAACCTGGAACAGTGACAACAGCGTCCTTGATTTTCTTTCCAAGGTAGGCTTC
AGCTGTCTCCTTCATCTTAGTCAGAATCATAGCACTAATCTCCTCAGGACTGAAAACCTTAGTC
TCACCATCCTTGATCTTGACTTGAATGTATGGCTTACCATCCTTGTTCACAATCTGGTAAGGTA
CAAGTTTCCTATCCTTTTGAACCTCCTTATCCTCAAATCTGCCAAATACAATAACAAAGACTTA
AACCAACAATATCATCTCCAAGGTGAAACAAACACAGAGAATAAGTAATTACTTTCGCCCGATC
AATCTCTTAACGTCGAAGACAGTCCTCTCTGGATTAACAGCTGCTTGATTCTTAGCAGCCTCAC
CAATGAGTCTTTCAGAGTCAGTAAAACCAACCCATGAAGGTGTAATACGGTTTCCTTGGTCATT
GGCAATAATTTCGACATGACCATTCTTGTAAACACCAACACAAGAGTAAGTAGTACCAAGATCT
ATCCCTATCACTGATCCTAACTTCGTAGCCTCTTCTATTGCAGAGGACAACGCAAATAAACATC
						
					

			
		

Sequences
Splice junction sequence	TAAACACCAACACAAGAGTAAGTAGTACCAAGATCTATCCCTATCACTGATCCTAACTTCGTAG CCTCTTCTATTGCAGAGGACAACGCAAATAAACATCctcccaagtgagtgtcaccatttgtgga gagaacctcaaacactccgttatcaatggtcaagacactgacatcaaaagtaccaccaccaaga tcaaacac
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: 726 Transcript exons: 10542154-10542396,10542489-10542703,10542782-10543049 CTCCCAAGTGAGTGTCACCATTTGTGGAGAGAACCTCAAACACTCCGTTATCAATGGTCAAGAC ACTGACATCAAAAGTACCACCACCAAGATCAAACACAAGGATATTCTTCTCGCCACCCTTCTTA TCAAGACCATAGGCAATAGCAGCAGCAGTAGGTTCATTAATGATTCTAGCAACATTGAGCCCAG CAATAACACCAGCATCCTTAGTAGCTTGCCTTTGAGCATCATTGAAGTAAGCTGGAACAGTGAC AACAGCGTCCTTGATTTTCTTTCCAAGGTAGGCTTCAGCTGTCTCCTTCATCTTAGTCAGAATC ATAGCACTAATCTCCTCAGGACTGAAAACCTTAGTCTCACCATCCTTGATCTTGACTTGAATGT ATGGCTTACCATCCTTGTTCACAATCTGGTAAGGTACAAGTTTCCTATCCTTTTGAACCTCCTT ATCCTCAAATTTTCGCCCGATCAATCTCTTAACGTCGAAGACAGTCCTCTCTGGATTAACAGCT GCTTGATTCTTAGCAGCCTCACCAATGAGTCTTTCAGAGTCAGTAAAACCAACCCATGAAGGTG TAATACGGTTTCCTTGGTCATTGGCAATAATTTCGACATGACCATTCTTGTAAACACCAACACA AGAGTAAGTAGTACCAAGATCTATCCCTATCACTGATCCTAACTTCGTAGCCTCTTCTATTGCA GAGGACAACGCAAATAAACATC
Genomic sequence	CTCCCAAGTGAGTGTCACCATTTGTGGAGAGAACCTCAAACACTCCGTTATCAATGGTCAAGAC ACTGACATCAAAAGTACCACCACCAAGATCAAACACAAGGATATTCTTCTCGCCACCCTTCTTA TCAAGACCATAGGCAATAGCAGCAGCAGTAGGTTCATTAATGATTCTAGCAACATTGAGCCCAG CAATAACACCAGCATCCTTAGTAGCTTGCCTTTGAGCATCATTGAAGTAAGCTACGCAAAGTCA AAAACACCAAATAAACAATCAATCACCAAATACAGATAATAAAGATACCTCTCCACCACATATA TAACAACAAACTAACCTGGAACAGTGACAACAGCGTCCTTGATTTTCTTTCCAAGGTAGGCTTC AGCTGTCTCCTTCATCTTAGTCAGAATCATAGCACTAATCTCCTCAGGACTGAAAACCTTAGTC TCACCATCCTTGATCTTGACTTGAATGTATGGCTTACCATCCTTGTTCACAATCTGGTAAGGTA CAAGTTTCCTATCCTTTTGAACCTCCTTATCCTCAAATCTGCCAAATACAATAACAAAGACTTA AACCAACAATATCATCTCCAAGGTGAAACAAACACAGAGAATAAGTAATTACTTTCGCCCGATC AATCTCTTAACGTCGAAGACAGTCCTCTCTGGATTAACAGCTGCTTGATTCTTAGCAGCCTCAC CAATGAGTCTTTCAGAGTCAGTAAAACCAACCCATGAAGGTGTAATACGGTTTCCTTGGTCATT GGCAATAATTTCGACATGACCATTCTTGTAAACACCAACACAAGAGTAAGTAGTACCAAGATCT ATCCCTATCACTGATCCTAACTTCGTAGCCTCTTCTATTGCAGAGGACAACGCAAATAAACATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.885709895

Conservation Information
Conserved circRNAs	NA
PMCS	0.885709895

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10542568-10542156(-)
						
						Potential amino acid sequence
						
							MILTKMKETAEAYLGKKIKDAVVTVPAYFNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGL
DKKGGEKNILVFDLGGGTFDVSVLTIDNGVFEVLSTNGDTHLGGCLFALSSAIEEATKLGSVIG
IDLGTTYSCVGVYKNGHVEIIANDQGNRITPSWVGFTDSERLIGEAAKNQAAVNPERTVFDVKR
LIGRKFEDKEVQKDRKLVPYQIVNKDGKPYIQVKIKDGETKVFSPEEISAMILTKMKETAEAYL
GKKIKDAVVTVPAYFNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGLDKKGGEKNILVFDL
GGGTFDVSVLTIDNGVFEVLSTNGDTHLGGCLFALSSAIEEATKLGSVIGIDLGTTYSCVGVYK
NGHVEIIANDQGNRITPSWVGFTDSERLIGEAAKNQAAVNPERTVFDVKRLIGRKFEDKEVQKD
RKLVPYQIVNKDGKPYIQVKIKDGETKVFSPEEISAMILTKMKETAEAYLGKKIKDAVVTVPAY
FNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGLDKKGGEKNILVFDLGGGTFDVSVLTIDN
GVFEVLSTNGDTHLGGCLFALSSAIEEATKLGSVIGIDLGTTYSCVGVYKNGHVEIIANDQGNR
ITPSWVGFTDSERLIGEAAKNQAAVNPERTVFDVKRLIGRKFEDKEVQKDRKLVPYQIVNKDGK
PYIQVKIKDGETKVFSPEEISAMILTKMKETAEAYLGKKIKDAVVTVPAYFNDAQRQATKDAGV
IAGLNVARIINEPTAAAIAYGLDKKGGEKNILVFDLGGGTFDVSVLTIDNGVFEVLSTNGDTHL
G(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	10542568-10542156(-)
Potential amino acid sequence	MILTKMKETAEAYLGKKIKDAVVTVPAYFNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGL DKKGGEKNILVFDLGGGTFDVSVLTIDNGVFEVLSTNGDTHLGGCLFALSSAIEEATKLGSVIG IDLGTTYSCVGVYKNGHVEIIANDQGNRITPSWVGFTDSERLIGEAAKNQAAVNPERTVFDVKR LIGRKFEDKEVQKDRKLVPYQIVNKDGKPYIQVKIKDGETKVFSPEEISAMILTKMKETAEAYL GKKIKDAVVTVPAYFNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGLDKKGGEKNILVFDL GGGTFDVSVLTIDNGVFEVLSTNGDTHLGGCLFALSSAIEEATKLGSVIGIDLGTTYSCVGVYK NGHVEIIANDQGNRITPSWVGFTDSERLIGEAAKNQAAVNPERTVFDVKRLIGRKFEDKEVQKD RKLVPYQIVNKDGKPYIQVKIKDGETKVFSPEEISAMILTKMKETAEAYLGKKIKDAVVTVPAY FNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGLDKKGGEKNILVFDLGGGTFDVSVLTIDN GVFEVLSTNGDTHLGGCLFALSSAIEEATKLGSVIGIDLGTTYSCVGVYKNGHVEIIANDQGNR ITPSWVGFTDSERLIGEAAKNQAAVNPERTVFDVKRLIGRKFEDKEVQKDRKLVPYQIVNKDGK PYIQVKIKDGETKVFSPEEISAMILTKMKETAEAYLGKKIKDAVVTVPAYFNDAQRQATKDAGV IAGLNVARIINEPTAAAIAYGLDKKGGEKNILVFDLGGGTFDVSVLTIDNGVFEVLSTNGDTHL G(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT5G28540_circ_g.8

Address

Any questions?

Supported by