Plant Circular RNA Database

Detail information of AT5G42400_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT5G42400_circ_g.6
					
						ID in PlantcircBase
						ath_circ_042053
					
						Alias
						At_ciR5879
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 16959590-16960698  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT5G42400						
					
						Parent gene annotation
						
							SET domain protein 25
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						2
					
						Tissues
						leaf
					
						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
						AT5G42400.4:3
AT5G42400.7:3
AT5G42400.6:3
AT5G42400.5:3
AT5G42400.3:3
AT5G42400.8:3
AT5G42400.1:3
AT5G42400.2:3

General Information
CircRNA Name	AT5G42400_circ_g.6
ID in PlantcircBase	ath_circ_042053
Alias	At_ciR5879
Organism	Arabidpsis thaliana
Position	chr5: 16959590-16960698 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	AT5G42400
Parent gene annotation	SET domain protein 25
Parent gene strand	-
Alternative splicing	NA
Support reads	2
Tissues	leaf
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	AT5G42400.4:3 AT5G42400.7:3 AT5G42400.6:3 AT5G42400.5:3 AT5G42400.3:3 AT5G42400.8:3 AT5G42400.1:3 AT5G42400.2:3

			
						 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  
						
							AAGCAGAAACTTTCTTCCTTCTACTAGAATAAGAGCTACCATGGCTAGGAAAAGTGGAATCAAC
CGCAACCATGACACAGATAAACTCGAGATATCTTCTcagggctgcatctgaaacatatccatgc
tgctgccaactaaaaagctccaatatagaatgtggaccatgatttctaccttcaccatcaacga
gaaaccag

									
								

					

						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: 921
Transcript exons: 16959590-16959706,16959808-16960414,16960502-16960698
CAGGGCTGCATCTGAAACATATCCATGCTGCTGCCAACTAAAAAGCTCCAATATAGAATGTGGA
CCATGATTTCTACCTTCACCATCAACGAGAAACCAGCAAGCATGTTCGTTTCCCAATGAGAGGA
ATGAAGCTAACATATTTGATTCCTCGTGGTTTAGTGTTAGCTGATCTAAAACAGAACCATTAGA
ACTTGTCTGTGGAGGCATCGTCTGATGGGAGATCAAATGAGTAGCAGAAGTTGCATGCTCTGTT
TGAATCTCATCTTGATGGACTGTAGCATTACTACTAGAAGGGGGAAATGAAGTAACAGATGGGG
CTACACTTATTATTCCATTTTGTAGATATGCAAAGCCAGTAGCGACATGATCTGGAAACTGCTT
GAAGTACTTAAGTGGTACAGAATTTGCAGTATAACCATTGATAATTGGATATACAAGAAGATCC
TCCGGTAAGAAGTTAGTTGATAGCCCATCATATAGCTGCTGTTGCGTGTAAGGGCCACACATCT
GACCTTGCTGATTACCATACATCCAACCACTTGCATACATGGTATACCCTGGAACACTCTTGTC
TAGACCTGAAGCTATGCCACTACCAGAAGCCTCTTGACCCGCACGACAGTCTTCATTTGAACGA
CATCCCATCTCCAAGGCTGAATCCAAACCACACAGTTCATCAAAATTGCAACAAGCGGAAGATA
CAGTAGCCAAATCACCACAGCTGTCACAAGAGTAATCTTGAGCTACTTCTCTTGCAGAGATTGA
AACATCATCACTGTAAACTCCCATACACATTGAACCGAAATAATTCGGTTCCAAAGCAGAAACT
TTCTTCCTTCTACTAGAATAAGAGCTACCATGGCTAGGAAAAGTGGAATCAACCGCAACCATGA
CACAGATAAACTCGAGATATCTTCT
						
					

						Genomic sequence
						
							CAGGGCTGCATCTGAAACATATCCATGCTGCTGCCAACTAAAAAGCTCCAATATAGAATGTGGA
CCATGATTTCTACCTTCACCATCAACGAGAAACCAGCAAGCATGTTCGTTTCCCTAACAGAAAA
CCCAAACATTAAAGAAAATTCTTATGTGAACTCGAGCCATCATGTCTGATGAACTTGTGAACTG
AGTTTTCACCGTTGAAAGGAAGTTACCAATGAGAGGAATGAAGCTAACATATTTGATTCCTCGT
GGTTTAGTGTTAGCTGATCTAAAACAGAACCATTAGAACTTGTCTGTGGAGGCATCGTCTGATG
GGAGATCAAATGAGTAGCAGAAGTTGCATGCTCTGTTTGAATCTCATCTTGATGGACTGTAGCA
TTACTACTAGAAGGGGGAAATGAAGTAACAGATGGGGCTACACTTATTATTCCATTTTGTAGAT
ATGCAAAGCCAGTAGCGACATGATCTGGAAACTGCTTGAAGTACTTAAGTGGTACAGAATTTGC
AGTATAACCATTGATAATTGGATATACAAGAAGATCCTCCGGTAAGAAGTTAGTTGATAGCCCA
TCATATAGCTGCTGTTGCGTGTAAGGGCCACACATCTGACCTTGCTGATTACCATACATCCAAC
CACTTGCATACATGGTATACCCTGGAACACTCTTGTCTAGACCTGAAGCTATGCCACTACCAGA
AGCCTCTTGACCCGCACGACAGTCTTCATTTGAACGACATCCCATCTCCAAGGCTGAATCCAAA
CCACACAGTTCATCAAAATTGCAACAAGCGGAAGATACAGTAGCCAAATCACCACAGCTGAAAA
GCAAAAATACAGTTTTTCTTTTAGATTGACAATCCAACTAGTTAATTCACAACTACGAAAAACT
TAACTACAAGTTGCACCTGTCACAAGAGTAATCTTGAGCTACTTCTCTTGCAGAGATTGAAACA
TCATCACTGTAAACTCCCATACACATTGAACCGAAATAATTCGGTTCCAAAGCAGAAACTTTCT
TCCTTCTACTAGAATAAGAGCTACCATGGCTAGGAAAAGTGGAATCAACCGCAACCATGACACA
GATAAACTCGAGATATCTTCT
						
					

			
		

Sequences
Splice junction sequence	AAGCAGAAACTTTCTTCCTTCTACTAGAATAAGAGCTACCATGGCTAGGAAAAGTGGAATCAAC CGCAACCATGACACAGATAAACTCGAGATATCTTCTcagggctgcatctgaaacatatccatgc tgctgccaactaaaaagctccaatatagaatgtggaccatgatttctaccttcaccatcaacga gaaaccag
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: 921 Transcript exons: 16959590-16959706,16959808-16960414,16960502-16960698 CAGGGCTGCATCTGAAACATATCCATGCTGCTGCCAACTAAAAAGCTCCAATATAGAATGTGGA CCATGATTTCTACCTTCACCATCAACGAGAAACCAGCAAGCATGTTCGTTTCCCAATGAGAGGA ATGAAGCTAACATATTTGATTCCTCGTGGTTTAGTGTTAGCTGATCTAAAACAGAACCATTAGA ACTTGTCTGTGGAGGCATCGTCTGATGGGAGATCAAATGAGTAGCAGAAGTTGCATGCTCTGTT TGAATCTCATCTTGATGGACTGTAGCATTACTACTAGAAGGGGGAAATGAAGTAACAGATGGGG CTACACTTATTATTCCATTTTGTAGATATGCAAAGCCAGTAGCGACATGATCTGGAAACTGCTT GAAGTACTTAAGTGGTACAGAATTTGCAGTATAACCATTGATAATTGGATATACAAGAAGATCC TCCGGTAAGAAGTTAGTTGATAGCCCATCATATAGCTGCTGTTGCGTGTAAGGGCCACACATCT GACCTTGCTGATTACCATACATCCAACCACTTGCATACATGGTATACCCTGGAACACTCTTGTC TAGACCTGAAGCTATGCCACTACCAGAAGCCTCTTGACCCGCACGACAGTCTTCATTTGAACGA CATCCCATCTCCAAGGCTGAATCCAAACCACACAGTTCATCAAAATTGCAACAAGCGGAAGATA CAGTAGCCAAATCACCACAGCTGTCACAAGAGTAATCTTGAGCTACTTCTCTTGCAGAGATTGA AACATCATCACTGTAAACTCCCATACACATTGAACCGAAATAATTCGGTTCCAAAGCAGAAACT TTCTTCCTTCTACTAGAATAAGAGCTACCATGGCTAGGAAAAGTGGAATCAACCGCAACCATGA CACAGATAAACTCGAGATATCTTCT
Genomic sequence	CAGGGCTGCATCTGAAACATATCCATGCTGCTGCCAACTAAAAAGCTCCAATATAGAATGTGGA CCATGATTTCTACCTTCACCATCAACGAGAAACCAGCAAGCATGTTCGTTTCCCTAACAGAAAA CCCAAACATTAAAGAAAATTCTTATGTGAACTCGAGCCATCATGTCTGATGAACTTGTGAACTG AGTTTTCACCGTTGAAAGGAAGTTACCAATGAGAGGAATGAAGCTAACATATTTGATTCCTCGT GGTTTAGTGTTAGCTGATCTAAAACAGAACCATTAGAACTTGTCTGTGGAGGCATCGTCTGATG GGAGATCAAATGAGTAGCAGAAGTTGCATGCTCTGTTTGAATCTCATCTTGATGGACTGTAGCA TTACTACTAGAAGGGGGAAATGAAGTAACAGATGGGGCTACACTTATTATTCCATTTTGTAGAT ATGCAAAGCCAGTAGCGACATGATCTGGAAACTGCTTGAAGTACTTAAGTGGTACAGAATTTGC AGTATAACCATTGATAATTGGATATACAAGAAGATCCTCCGGTAAGAAGTTAGTTGATAGCCCA TCATATAGCTGCTGTTGCGTGTAAGGGCCACACATCTGACCTTGCTGATTACCATACATCCAAC CACTTGCATACATGGTATACCCTGGAACACTCTTGTCTAGACCTGAAGCTATGCCACTACCAGA AGCCTCTTGACCCGCACGACAGTCTTCATTTGAACGACATCCCATCTCCAAGGCTGAATCCAAA CCACACAGTTCATCAAAATTGCAACAAGCGGAAGATACAGTAGCCAAATCACCACAGCTGAAAA GCAAAAATACAGTTTTTCTTTTAGATTGACAATCCAACTAGTTAATTCACAACTACGAAAAACT TAACTACAAGTTGCACCTGTCACAAGAGTAATCTTGAGCTACTTCTCTTGCAGAGATTGAAACA TCATCACTGTAAACTCCCATACACATTGAACCGAAATAATTCGGTTCCAAAGCAGAAACTTTCT TCCTTCTACTAGAATAAGAGCTACCATGGCTAGGAAAAGTGGAATCAACCGCAACCATGACACA GATAAACTCGAGATATCTTCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.203647375

Conservation Information
Conserved circRNAs	NA
PMCS	0.203647375

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16960672-16959592(-)
						
						Potential amino acid sequence
						
							MVAVDSTFPSHGSSYSSRRKKVSALEPNYFGSMCMGVYSDDVSISAREVAQDYSCDSCGDLATV
SSACCNFDELCGLDSALEMGCRSNEDCRAGQEASGSGIASGLDKSVPGYTMYASGWMYGNQQGQ
MCGPYTQQQLYDGLSTNFLPEDLLVYPIINGYTANSVPLKYFKQFPDHVATGFAYLQNGIISVA
PSVTSFPPSSSNATVHQDEIQTEHATSATHLISHQTMPPQTSSNGSVLDQLTLNHEESNMLASF
LSLGNEHACWFLVDGEGRNHGPHSILELFSWQQHGYVSDAALRRYLEFICVMVAVDSTFPSHGS
SYSSRRKKVSALEPNYFGSMCMGVYSDDVSISAREVAQDYSCDSCGDLATVSSACCNFDELCGL
DSALEMGCRSNEDCRAGQEASGSGIASGLDKSVPGYTMYASGWMYGNQQGQMCGPYTQQQLYDG
LSTNFLPEDLLVYPIINGYTANSVPLKYFKQFPDHVATGFAYLQNGIISVAPSVTSFPPSSSNA
TVHQDEIQTEHATSATHLISHQTMPPQTSSNGSVLDQLTLNHEESNMLASFLSLGNEHACWFLV
DGEGRNHGPHSILELFSWQQHGYVSDAALRRYLEFICVMVAVDSTFPSHGSSYSSRRKKVSALE
PNYFGSMCMGVYSDDVSISAREVAQDYSCDSCGDLATVSSACCNFDELCGLDSALEMGCRSNED
CRAGQEASGSGIASGLDKSVPGYTMYASGWMYGNQQGQMCGPYTQQQLYDGLSTNFLPEDLLVY
PIINGYTANSVPLKYFKQFPDHVATGFAYLQNGIISVAPSVTSFPPSSSNATVHQDEIQTEHAT
SATHLISHQTMPPQTSSNGSVLDQLTLNHEESNMLASFLSLGNEHACWFLVDGEGRNHGPHSIL
ELFSWQQHGYVSDAALRRYLEFICVMVAVDSTFPSHGSSYSSRRKKVSALEPNYFGSMCMGVYS
DDVSISAREVAQDYSCDSCGDLATVSSACCNFDELCGLDSALEMGCRSNEDCRAGQEASGSGIA
SGLDKSVPGYTMYASGWMYGNQQGQMCGPYTQQQLYDGLSTNFLPEDLLVYPIINGYTANSVPL
KYFKQFPDHVATGFAYLQNGIISVAPSVTSFPPSSSNATVHQDEIQTEHATSATHLISHQTMPP
QTSSNGSVLDQLTLNHEESNMLASFLSLGNEHACWFLVDGEGRNHGPHSILELFSWQQHGYVSD
AAL(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	16960672-16959592(-)
Potential amino acid sequence	MVAVDSTFPSHGSSYSSRRKKVSALEPNYFGSMCMGVYSDDVSISAREVAQDYSCDSCGDLATV SSACCNFDELCGLDSALEMGCRSNEDCRAGQEASGSGIASGLDKSVPGYTMYASGWMYGNQQGQ MCGPYTQQQLYDGLSTNFLPEDLLVYPIINGYTANSVPLKYFKQFPDHVATGFAYLQNGIISVA PSVTSFPPSSSNATVHQDEIQTEHATSATHLISHQTMPPQTSSNGSVLDQLTLNHEESNMLASF LSLGNEHACWFLVDGEGRNHGPHSILELFSWQQHGYVSDAALRRYLEFICVMVAVDSTFPSHGS SYSSRRKKVSALEPNYFGSMCMGVYSDDVSISAREVAQDYSCDSCGDLATVSSACCNFDELCGL DSALEMGCRSNEDCRAGQEASGSGIASGLDKSVPGYTMYASGWMYGNQQGQMCGPYTQQQLYDG LSTNFLPEDLLVYPIINGYTANSVPLKYFKQFPDHVATGFAYLQNGIISVAPSVTSFPPSSSNA TVHQDEIQTEHATSATHLISHQTMPPQTSSNGSVLDQLTLNHEESNMLASFLSLGNEHACWFLV DGEGRNHGPHSILELFSWQQHGYVSDAALRRYLEFICVMVAVDSTFPSHGSSYSSRRKKVSALE PNYFGSMCMGVYSDDVSISAREVAQDYSCDSCGDLATVSSACCNFDELCGLDSALEMGCRSNED CRAGQEASGSGIASGLDKSVPGYTMYASGWMYGNQQGQMCGPYTQQQLYDGLSTNFLPEDLLVY PIINGYTANSVPLKYFKQFPDHVATGFAYLQNGIISVAPSVTSFPPSSSNATVHQDEIQTEHAT SATHLISHQTMPPQTSSNGSVLDQLTLNHEESNMLASFLSLGNEHACWFLVDGEGRNHGPHSIL ELFSWQQHGYVSDAALRRYLEFICVMVAVDSTFPSHGSSYSSRRKKVSALEPNYFGSMCMGVYS DDVSISAREVAQDYSCDSCGDLATVSSACCNFDELCGLDSALEMGCRSNEDCRAGQEASGSGIA SGLDKSVPGYTMYASGWMYGNQQGQMCGPYTQQQLYDGLSTNFLPEDLLVYPIINGYTANSVPL KYFKQFPDHVATGFAYLQNGIISVAPSVTSFPPSSSNATVHQDEIQTEHATSATHLISHQTMPP QTSSNGSVLDQLTLNHEESNMLASFLSLGNEHACWFLVDGEGRNHGPHSILELFSWQQHGYVSD AAL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT5G42400_circ_g.6

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