Plant Circular RNA Database

Detail information of AT5G27540_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT5G27540_circ_g.2
					
						ID in PlantcircBase
						ath_circ_040772
					
						Alias
						Ath_circ_FC3542
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 9722810-9725177  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT5G27540						
					
						Parent gene annotation
						
							Mitochondrial Rho GTPase 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G27540_circ_g.1 AT5G27540_circ_g.3 AT5G27540_circ_g.4 AT5G27540_circ_g.5 AT5G27540_circ_g.6 AT5G27540_circ_g.7 AT5G27540_circ_g.8 						
					
						Support reads
						1
					
						Tissues
						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  
						
							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
						AT5G27540.2:8
AT5G27540.1:8

General Information
CircRNA Name	AT5G27540_circ_g.2
ID in PlantcircBase	ath_circ_040772
Alias	Ath_circ_FC3542
Organism	Arabidpsis thaliana
Position	chr5: 9722810-9725177 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	AT5G27540
Parent gene annotation	Mitochondrial Rho GTPase 1
Parent gene strand	+
Alternative splicing	AT5G27540_circ_g.1 AT5G27540_circ_g.3 AT5G27540_circ_g.4 AT5G27540_circ_g.5 AT5G27540_circ_g.6 AT5G27540_circ_g.7 AT5G27540_circ_g.8
Support reads	1
Tissues	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	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	AT5G27540.2:8 AT5G27540.1:8

			
						 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  
						
							CTAAATTGTGAATGGCAGTCCATGGAAGGAAGCTCCTTATGAAGATGCTGCGGAAAAAACTGCC
CTTGGAGGACTATCATTTGACGCTTTCCTGTCAATGtttcagatggcgagatacgctgctggtg
cggttgattgtcctggttctcccaaatctgtgcgaatcgttgtggttggtgataagggcactgg
aaaatcaa

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							TTTCAGATGGCGAGATACGCTGCTGGTGCGGTTGATTGTCCTGGTTCTCCCAAATCTGTGCGAA
TCGTTGTGGTTGGTGATAAGGGCACTGGAAAATCAAGCTTGATTGTTGCTGCAGCCACTGATTC
TTTCCCTCCCAATGTCCCTCCTGTTTTGCCTGATTACAAGTTGCCTATTGAATTCTTCCCTGAT
GGTATACCCGTCACCATTGTCGACACTTCCTCGAGGTATATATCCTTATATAAGTTCACTGTAT
TGCTGGATAATTACTCTCTTAAATAAAGCTACTTTGAAAGAAAATAATTTCTAGTTTAGAGAAA
AGAGTGTTGCTTTTATATACAATATTGTTGTTGGGATTGCACTGTGCCAACTGTTTGTGGGTTT
AGGATATTTTAAGCTTTGCCAGCTTTGTTGAGGTTCTTGAAGTATGTTTTGATGTTTTTGTTCG
TTGGTTCAGGCCAGAAGATAGGGACATTGTTGCTGAGGAATTGAAGCGCGCAGATGCAGTAGTT
TTGACATATGCCTGTGATCGACCTGAGACTCTCGAACGTTTGAGTGAATACTGGCTTCCAGAGC
TTCGGCGATTAGAGGTTTGATTTTCATCTCTCTGTTTTCAGTTTGGTCATGTCAATCTTGTTGT
GTGTAAAAGGTGTACAATATCTTATCTATTGATCATATCATTGTCATAATGCTAGAAGGTGTGA
CCTAAACCTTTGCTGTTTCTTATTAAGATTGGCTTGTGATGTTTTTGAACAGGTAAAAATTCCT
ATTATCGTAGCAGGATGTAAGCTTGACTTCAGAGACGACAATAACCAGGTCAGCCTCGAACAAG
TGATGTCACCTATAATGCAGCAGTTTCGGGAGATAGAGACTTGTATCGAGTGTTCTGCCCTGAA
GCAACTCCAGGTTTCATGACTTCTGAATTCCTCTTGATATGTGATATTTTTCTTTGTTCAAACA
TGGCACAAATATTGGTCCGAGGTAGCTTAGGCATGTGCTTGTCTTACTAAGAAATTTCAAGGAC
TTAAGATGTGCTAAATTTTTGCCTGAAAGTAGATATTGTTGTTATTGGTTTGGACTTTTATCAG
TCATGAACTGGAAATGCCTAGTCAGAAATTAGCATTCGGTGGTAATTACAAATTATATTCCAGG
TCTAAACTATCATCCTAATGCACAAGCTTTCCTGTAGGCACAAGAAGTTTTCTATTATGCACAA
AAGACTGTCCTTCACCCAACAGGACCTCTGTTTGATCAAGATTCCCAGGCACTGAAACCCCGGT
GTGTAAGGGCATTGAAGCGTATCTTTATACTCTGTGATCATGACAGAGATGGTGCTCTTAGCGA
GGCTGAGTTAAATGATTTTCAGGTTCTTATATTTCCTCTTTCGTGTTTCATGTGCTTCGCTGTT
CGTCATTGAATTGGCTTAGCCCTATCCTTCAGATTTTAAAAAGAAGCTTGAAGTTTAATTATGT
TATCCCCATGACGCACCTAATAGTTGTTTTACAATAGGTCAAGTGTTTCCATGCACCATTGCAG
CCTTCTGAAATTGAAGGTGTTAAGAGGGTTGTGCAAGAAAAGTTGCCAGAAGGTGTGAATGAAA
GAGGACTGACAGTCACTGGCTTCCTATTTTTACATGCACTTTTTATTGAGAAAGGGAGGCTTGA
GACTACGTGGACTGTACTCAGGAAGTTTGGGTATAATAATGATATAAGACTTGCTGAAGAATTG
CTTCCATCTGCAATATTCAAGCGAGCTCCTGATCAGGTAAATTTGCAGAAATAACATCCATTGT
TCTTCATTATTGTATTTGTTGGTGTTTCAATAATCTATTACTGGAAAGAGCTGTATATCGAGCA
TTAAATTTTGTAATCTTATCAGAAATAAGAATTTTGGATGCCTACATTACTGGAAAACGGTTAT
CTTACAGCTCACATTAACTTGCCTTCCTTGGTATTGTGCAGCTAATGTTTGTGTTCATTGTTTT
TGTAGAGCTTTGAGTTGACAAATGCAGCAATCGATTTCCTGAAAGGAATGTATATGTTGTTTGA
TGACGACCAGGTATGTTTCTTTTCTTATAAATGGCGTAGTGTTGAGTTGACAAATAAATTTCTC
AGACTGAATTTGCACTTTGCAGGATAACAATCTGAGACCTCAAGAGATCGAGGATCTTTTTTCA
ACTGCACCTGAAAGGTACCTTTTTTACACCTCCAGAAGGCAAAGAACGTGTACTTTTGATTATG
GTAATCTCCATTATATTGCCATGCCATACTAAATTGTGAATGGCAGTCCATGGAAGGAAGCTCC
TTATGAAGATGCTGCGGAAAAAACTGCCCTTGGAGGACTATCATTTGACGCTTTCCTGTCAATG
						
					

			
		

Sequences
Splice junction sequence	CTAAATTGTGAATGGCAGTCCATGGAAGGAAGCTCCTTATGAAGATGCTGCGGAAAAAACTGCC CTTGGAGGACTATCATTTGACGCTTTCCTGTCAATGtttcagatggcgagatacgctgctggtg cggttgattgtcctggttctcccaaatctgtgcgaatcgttgtggttggtgataagggcactgg aaaatcaa
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TTTCAGATGGCGAGATACGCTGCTGGTGCGGTTGATTGTCCTGGTTCTCCCAAATCTGTGCGAA TCGTTGTGGTTGGTGATAAGGGCACTGGAAAATCAAGCTTGATTGTTGCTGCAGCCACTGATTC TTTCCCTCCCAATGTCCCTCCTGTTTTGCCTGATTACAAGTTGCCTATTGAATTCTTCCCTGAT GGTATACCCGTCACCATTGTCGACACTTCCTCGAGGTATATATCCTTATATAAGTTCACTGTAT TGCTGGATAATTACTCTCTTAAATAAAGCTACTTTGAAAGAAAATAATTTCTAGTTTAGAGAAA AGAGTGTTGCTTTTATATACAATATTGTTGTTGGGATTGCACTGTGCCAACTGTTTGTGGGTTT AGGATATTTTAAGCTTTGCCAGCTTTGTTGAGGTTCTTGAAGTATGTTTTGATGTTTTTGTTCG TTGGTTCAGGCCAGAAGATAGGGACATTGTTGCTGAGGAATTGAAGCGCGCAGATGCAGTAGTT TTGACATATGCCTGTGATCGACCTGAGACTCTCGAACGTTTGAGTGAATACTGGCTTCCAGAGC TTCGGCGATTAGAGGTTTGATTTTCATCTCTCTGTTTTCAGTTTGGTCATGTCAATCTTGTTGT GTGTAAAAGGTGTACAATATCTTATCTATTGATCATATCATTGTCATAATGCTAGAAGGTGTGA CCTAAACCTTTGCTGTTTCTTATTAAGATTGGCTTGTGATGTTTTTGAACAGGTAAAAATTCCT ATTATCGTAGCAGGATGTAAGCTTGACTTCAGAGACGACAATAACCAGGTCAGCCTCGAACAAG TGATGTCACCTATAATGCAGCAGTTTCGGGAGATAGAGACTTGTATCGAGTGTTCTGCCCTGAA GCAACTCCAGGTTTCATGACTTCTGAATTCCTCTTGATATGTGATATTTTTCTTTGTTCAAACA TGGCACAAATATTGGTCCGAGGTAGCTTAGGCATGTGCTTGTCTTACTAAGAAATTTCAAGGAC TTAAGATGTGCTAAATTTTTGCCTGAAAGTAGATATTGTTGTTATTGGTTTGGACTTTTATCAG TCATGAACTGGAAATGCCTAGTCAGAAATTAGCATTCGGTGGTAATTACAAATTATATTCCAGG TCTAAACTATCATCCTAATGCACAAGCTTTCCTGTAGGCACAAGAAGTTTTCTATTATGCACAA AAGACTGTCCTTCACCCAACAGGACCTCTGTTTGATCAAGATTCCCAGGCACTGAAACCCCGGT GTGTAAGGGCATTGAAGCGTATCTTTATACTCTGTGATCATGACAGAGATGGTGCTCTTAGCGA GGCTGAGTTAAATGATTTTCAGGTTCTTATATTTCCTCTTTCGTGTTTCATGTGCTTCGCTGTT CGTCATTGAATTGGCTTAGCCCTATCCTTCAGATTTTAAAAAGAAGCTTGAAGTTTAATTATGT TATCCCCATGACGCACCTAATAGTTGTTTTACAATAGGTCAAGTGTTTCCATGCACCATTGCAG CCTTCTGAAATTGAAGGTGTTAAGAGGGTTGTGCAAGAAAAGTTGCCAGAAGGTGTGAATGAAA GAGGACTGACAGTCACTGGCTTCCTATTTTTACATGCACTTTTTATTGAGAAAGGGAGGCTTGA GACTACGTGGACTGTACTCAGGAAGTTTGGGTATAATAATGATATAAGACTTGCTGAAGAATTG CTTCCATCTGCAATATTCAAGCGAGCTCCTGATCAGGTAAATTTGCAGAAATAACATCCATTGT TCTTCATTATTGTATTTGTTGGTGTTTCAATAATCTATTACTGGAAAGAGCTGTATATCGAGCA TTAAATTTTGTAATCTTATCAGAAATAAGAATTTTGGATGCCTACATTACTGGAAAACGGTTAT CTTACAGCTCACATTAACTTGCCTTCCTTGGTATTGTGCAGCTAATGTTTGTGTTCATTGTTTT TGTAGAGCTTTGAGTTGACAAATGCAGCAATCGATTTCCTGAAAGGAATGTATATGTTGTTTGA TGACGACCAGGTATGTTTCTTTTCTTATAAATGGCGTAGTGTTGAGTTGACAAATAAATTTCTC AGACTGAATTTGCACTTTGCAGGATAACAATCTGAGACCTCAAGAGATCGAGGATCTTTTTTCA ACTGCACCTGAAAGGTACCTTTTTTACACCTCCAGAAGGCAAAGAACGTGTACTTTTGATTATG GTAATCTCCATTATATTGCCATGCCATACTAAATTGTGAATGGCAGTCCATGGAAGGAAGCTCC TTATGAAGATGCTGCGGAAAAAACTGCCCTTGGAGGACTATCATTTGACGCTTTCCTGTCAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.142808885

Conservation Information
Conserved circRNAs	NA
PMCS	0.142808885

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							9722816-9725174(+)
						
					

						Potential amino acid sequence
						
							MARYAAGAVDCPGSPKSVRIVVVGDKGTGKSSLIVAAATDSFPPNVPPVLPDYKLPIEFFPDGI
PVTIVDTSSRPEDRDIVAEELKRADAVVLTYACDRPETLERLSEYWLPELRRLEVKIPIIVAGC
KLDFRDDNNQVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDS
QALKPRCVRALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVN
ERGLTVTGFLFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAA
IDFLKGMYMLFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSMFQM
ARYAAGAVDCPGSPKSVRIVVVGDKGTGKSSLIVAAATDSFPPNVPPVLPDYKLPIEFFPDGIP
VTIVDTSSRPEDRDIVAEELKRADAVVLTYACDRPETLERLSEYWLPELRRLEVKIPIIVAGCK
LDFRDDNNQVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDSQ
ALKPRCVRALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVNE
RGLTVTGFLFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAAI
DFLKGMYMLFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSMFQMA
RYAAGAVDCPGSPKSVRIVVVGDKGTGKSSLIVAAATDSFPPNVPPVLPDYKLPIEFFPDGIPV
TIVDTSSRPEDRDIVAEELKRADAVVLTYACDRPETLERLSEYWLPELRRLEVKIPIIVAGCKL
DFRDDNNQVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDSQA
LKPRCVRALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVNER
GLTVTGFLFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAAID
FLKGMYMLFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSMFQMAR
YAAGAVDCPGSPKSVRIVVVGDKGTGKSSLIVAAATDSFPPNVPPVLPDYKLPIEFFPDGIPVT
IVDTSSRPEDRDIVAEELKRADAVVLTYACDRPETLERLSEYWLPELRRLEVKIPIIVAGCKLD
FRDDNNQVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDSQAL
KPRCVRALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVNERG
LTVTGFLFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAAIDF
LKGMYMLFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSM(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	9722816-9725174(+)
Potential amino acid sequence	MARYAAGAVDCPGSPKSVRIVVVGDKGTGKSSLIVAAATDSFPPNVPPVLPDYKLPIEFFPDGI PVTIVDTSSRPEDRDIVAEELKRADAVVLTYACDRPETLERLSEYWLPELRRLEVKIPIIVAGC KLDFRDDNNQVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDS QALKPRCVRALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVN ERGLTVTGFLFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAA IDFLKGMYMLFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSMFQM ARYAAGAVDCPGSPKSVRIVVVGDKGTGKSSLIVAAATDSFPPNVPPVLPDYKLPIEFFPDGIP VTIVDTSSRPEDRDIVAEELKRADAVVLTYACDRPETLERLSEYWLPELRRLEVKIPIIVAGCK LDFRDDNNQVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDSQ ALKPRCVRALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVNE RGLTVTGFLFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAAI DFLKGMYMLFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSMFQMA RYAAGAVDCPGSPKSVRIVVVGDKGTGKSSLIVAAATDSFPPNVPPVLPDYKLPIEFFPDGIPV TIVDTSSRPEDRDIVAEELKRADAVVLTYACDRPETLERLSEYWLPELRRLEVKIPIIVAGCKL DFRDDNNQVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDSQA LKPRCVRALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVNER GLTVTGFLFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAAID FLKGMYMLFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSMFQMAR YAAGAVDCPGSPKSVRIVVVGDKGTGKSSLIVAAATDSFPPNVPPVLPDYKLPIEFFPDGIPVT IVDTSSRPEDRDIVAEELKRADAVVLTYACDRPETLERLSEYWLPELRRLEVKIPIIVAGCKLD FRDDNNQVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDSQAL KPRCVRALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVNERG LTVTGFLFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAAIDF LKGMYMLFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSM(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT5G27540_circ_g.2

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