Plant Circular RNA Database

Detail information of AT5G27540_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G27540_circ_g.4
					
						ID in PlantcircBase
						ath_circ_040774
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 9723566-9725177  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-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.2 AT5G27540_circ_g.3 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
						AT5G27540.1:6
AT5G27540.2:6

General Information
CircRNA Name	AT5G27540_circ_g.4
ID in PlantcircBase	ath_circ_040774
Alias	NA
Organism	Arabidpsis thaliana
Position	chr5: 9723566-9725177 JBrowse»
Reference genome	TAIR10.38
Type	e-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.2 AT5G27540_circ_g.3 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	AT5G27540.1:6 AT5G27540.2:6

			
						 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
CTTGGAGGACTATCATTTGACGCTTTCCTGTCAATGgtaaaaattcctattatcgtagcaggat
gtaagcttgacttcagagacgacaataaccaggtcagcctcgaacaagtgatgtcacctataat
gcagcagt

									
								

					

						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: 789
Transcript exons: 9723566-9723715,9723999-9724175,9724319-9724573,9724799-
9724867,9724944-9724999,9725096-9725177
GTAAAAATTCCTATTATCGTAGCAGGATGTAAGCTTGACTTCAGAGACGACAATAACCAGGTCA
GCCTCGAACAAGTGATGTCACCTATAATGCAGCAGTTTCGGGAGATAGAGACTTGTATCGAGTG
TTCTGCCCTGAAGCAACTCCAGGCACAAGAAGTTTTCTATTATGCACAAAAGACTGTCCTTCAC
CCAACAGGACCTCTGTTTGATCAAGATTCCCAGGCACTGAAACCCCGGTGTGTAAGGGCATTGA
AGCGTATCTTTATACTCTGTGATCATGACAGAGATGGTGCTCTTAGCGAGGCTGAGTTAAATGA
TTTTCAGGTCAAGTGTTTCCATGCACCATTGCAGCCTTCTGAAATTGAAGGTGTTAAGAGGGTT
GTGCAAGAAAAGTTGCCAGAAGGTGTGAATGAAAGAGGACTGACAGTCACTGGCTTCCTATTTT
TACATGCACTTTTTATTGAGAAAGGGAGGCTTGAGACTACGTGGACTGTACTCAGGAAGTTTGG
GTATAATAATGATATAAGACTTGCTGAAGAATTGCTTCCATCTGCAATATTCAAGCGAGCTCCT
GATCAGAGCTTTGAGTTGACAAATGCAGCAATCGATTTCCTGAAAGGAATGTATATGTTGTTTG
ATGACGACCAGGATAACAATCTGAGACCTCAAGAGATCGAGGATCTTTTTTCAACTGCACCTGA
AAGTCCATGGAAGGAAGCTCCTTATGAAGATGCTGCGGAAAAAACTGCCCTTGGAGGACTATCA
TTTGACGCTTTCCTGTCAATG
						
					

						Genomic sequence
						
							GTAAAAATTCCTATTATCGTAGCAGGATGTAAGCTTGACTTCAGAGACGACAATAACCAGGTCA
GCCTCGAACAAGTGATGTCACCTATAATGCAGCAGTTTCGGGAGATAGAGACTTGTATCGAGTG
TTCTGCCCTGAAGCAACTCCAGGTTTCATGACTTCTGAATTCCTCTTGATATGTGATATTTTTC
TTTGTTCAAACATGGCACAAATATTGGTCCGAGGTAGCTTAGGCATGTGCTTGTCTTACTAAGA
AATTTCAAGGACTTAAGATGTGCTAAATTTTTGCCTGAAAGTAGATATTGTTGTTATTGGTTTG
GACTTTTATCAGTCATGAACTGGAAATGCCTAGTCAGAAATTAGCATTCGGTGGTAATTACAAA
TTATATTCCAGGTCTAAACTATCATCCTAATGCACAAGCTTTCCTGTAGGCACAAGAAGTTTTC
TATTATGCACAAAAGACTGTCCTTCACCCAACAGGACCTCTGTTTGATCAAGATTCCCAGGCAC
TGAAACCCCGGTGTGTAAGGGCATTGAAGCGTATCTTTATACTCTGTGATCATGACAGAGATGG
TGCTCTTAGCGAGGCTGAGTTAAATGATTTTCAGGTTCTTATATTTCCTCTTTCGTGTTTCATG
TGCTTCGCTGTTCGTCATTGAATTGGCTTAGCCCTATCCTTCAGATTTTAAAAAGAAGCTTGAA
GTTTAATTATGTTATCCCCATGACGCACCTAATAGTTGTTTTACAATAGGTCAAGTGTTTCCAT
GCACCATTGCAGCCTTCTGAAATTGAAGGTGTTAAGAGGGTTGTGCAAGAAAAGTTGCCAGAAG
GTGTGAATGAAAGAGGACTGACAGTCACTGGCTTCCTATTTTTACATGCACTTTTTATTGAGAA
AGGGAGGCTTGAGACTACGTGGACTGTACTCAGGAAGTTTGGGTATAATAATGATATAAGACTT
GCTGAAGAATTGCTTCCATCTGCAATATTCAAGCGAGCTCCTGATCAGGTAAATTTGCAGAAAT
AACATCCATTGTTCTTCATTATTGTATTTGTTGGTGTTTCAATAATCTATTACTGGAAAGAGCT
GTATATCGAGCATTAAATTTTGTAATCTTATCAGAAATAAGAATTTTGGATGCCTACATTACTG
GAAAACGGTTATCTTACAGCTCACATTAACTTGCCTTCCTTGGTATTGTGCAGCTAATGTTTGT
GTTCATTGTTTTTGTAGAGCTTTGAGTTGACAAATGCAGCAATCGATTTCCTGAAAGGAATGTA
TATGTTGTTTGATGACGACCAGGTATGTTTCTTTTCTTATAAATGGCGTAGTGTTGAGTTGACA
AATAAATTTCTCAGACTGAATTTGCACTTTGCAGGATAACAATCTGAGACCTCAAGAGATCGAG
GATCTTTTTTCAACTGCACCTGAAAGGTACCTTTTTTACACCTCCAGAAGGCAAAGAACGTGTA
CTTTTGATTATGGTAATCTCCATTATATTGCCATGCCATACTAAATTGTGAATGGCAGTCCATG
GAAGGAAGCTCCTTATGAAGATGCTGCGGAAAAAACTGCCCTTGGAGGACTATCATTTGACGCT
TTCCTGTCAATG
						
					

			
		

Sequences
Splice junction sequence	CTAAATTGTGAATGGCAGTCCATGGAAGGAAGCTCCTTATGAAGATGCTGCGGAAAAAACTGCC CTTGGAGGACTATCATTTGACGCTTTCCTGTCAATGgtaaaaattcctattatcgtagcaggat gtaagcttgacttcagagacgacaataaccaggtcagcctcgaacaagtgatgtcacctataat gcagcagt
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: 789 Transcript exons: 9723566-9723715,9723999-9724175,9724319-9724573,9724799- 9724867,9724944-9724999,9725096-9725177 GTAAAAATTCCTATTATCGTAGCAGGATGTAAGCTTGACTTCAGAGACGACAATAACCAGGTCA GCCTCGAACAAGTGATGTCACCTATAATGCAGCAGTTTCGGGAGATAGAGACTTGTATCGAGTG TTCTGCCCTGAAGCAACTCCAGGCACAAGAAGTTTTCTATTATGCACAAAAGACTGTCCTTCAC CCAACAGGACCTCTGTTTGATCAAGATTCCCAGGCACTGAAACCCCGGTGTGTAAGGGCATTGA AGCGTATCTTTATACTCTGTGATCATGACAGAGATGGTGCTCTTAGCGAGGCTGAGTTAAATGA TTTTCAGGTCAAGTGTTTCCATGCACCATTGCAGCCTTCTGAAATTGAAGGTGTTAAGAGGGTT GTGCAAGAAAAGTTGCCAGAAGGTGTGAATGAAAGAGGACTGACAGTCACTGGCTTCCTATTTT TACATGCACTTTTTATTGAGAAAGGGAGGCTTGAGACTACGTGGACTGTACTCAGGAAGTTTGG GTATAATAATGATATAAGACTTGCTGAAGAATTGCTTCCATCTGCAATATTCAAGCGAGCTCCT GATCAGAGCTTTGAGTTGACAAATGCAGCAATCGATTTCCTGAAAGGAATGTATATGTTGTTTG ATGACGACCAGGATAACAATCTGAGACCTCAAGAGATCGAGGATCTTTTTTCAACTGCACCTGA AAGTCCATGGAAGGAAGCTCCTTATGAAGATGCTGCGGAAAAAACTGCCCTTGGAGGACTATCA TTTGACGCTTTCCTGTCAATG
Genomic sequence	GTAAAAATTCCTATTATCGTAGCAGGATGTAAGCTTGACTTCAGAGACGACAATAACCAGGTCA GCCTCGAACAAGTGATGTCACCTATAATGCAGCAGTTTCGGGAGATAGAGACTTGTATCGAGTG TTCTGCCCTGAAGCAACTCCAGGTTTCATGACTTCTGAATTCCTCTTGATATGTGATATTTTTC TTTGTTCAAACATGGCACAAATATTGGTCCGAGGTAGCTTAGGCATGTGCTTGTCTTACTAAGA AATTTCAAGGACTTAAGATGTGCTAAATTTTTGCCTGAAAGTAGATATTGTTGTTATTGGTTTG GACTTTTATCAGTCATGAACTGGAAATGCCTAGTCAGAAATTAGCATTCGGTGGTAATTACAAA TTATATTCCAGGTCTAAACTATCATCCTAATGCACAAGCTTTCCTGTAGGCACAAGAAGTTTTC TATTATGCACAAAAGACTGTCCTTCACCCAACAGGACCTCTGTTTGATCAAGATTCCCAGGCAC TGAAACCCCGGTGTGTAAGGGCATTGAAGCGTATCTTTATACTCTGTGATCATGACAGAGATGG TGCTCTTAGCGAGGCTGAGTTAAATGATTTTCAGGTTCTTATATTTCCTCTTTCGTGTTTCATG TGCTTCGCTGTTCGTCATTGAATTGGCTTAGCCCTATCCTTCAGATTTTAAAAAGAAGCTTGAA GTTTAATTATGTTATCCCCATGACGCACCTAATAGTTGTTTTACAATAGGTCAAGTGTTTCCAT GCACCATTGCAGCCTTCTGAAATTGAAGGTGTTAAGAGGGTTGTGCAAGAAAAGTTGCCAGAAG GTGTGAATGAAAGAGGACTGACAGTCACTGGCTTCCTATTTTTACATGCACTTTTTATTGAGAA AGGGAGGCTTGAGACTACGTGGACTGTACTCAGGAAGTTTGGGTATAATAATGATATAAGACTT GCTGAAGAATTGCTTCCATCTGCAATATTCAAGCGAGCTCCTGATCAGGTAAATTTGCAGAAAT AACATCCATTGTTCTTCATTATTGTATTTGTTGGTGTTTCAATAATCTATTACTGGAAAGAGCT GTATATCGAGCATTAAATTTTGTAATCTTATCAGAAATAAGAATTTTGGATGCCTACATTACTG GAAAACGGTTATCTTACAGCTCACATTAACTTGCCTTCCTTGGTATTGTGCAGCTAATGTTTGT GTTCATTGTTTTTGTAGAGCTTTGAGTTGACAAATGCAGCAATCGATTTCCTGAAAGGAATGTA TATGTTGTTTGATGACGACCAGGTATGTTTCTTTTCTTATAAATGGCGTAGTGTTGAGTTGACA AATAAATTTCTCAGACTGAATTTGCACTTTGCAGGATAACAATCTGAGACCTCAAGAGATCGAG GATCTTTTTTCAACTGCACCTGAAAGGTACCTTTTTTACACCTCCAGAAGGCAAAGAACGTGTA CTTTTGATTATGGTAATCTCCATTATATTGCCATGCCATACTAAATTGTGAATGGCAGTCCATG GAAGGAAGCTCCTTATGAAGATGCTGCGGAAAAAACTGCCCTTGGAGGACTATCATTTGACGCT TTCCTGTCAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.26839161

Conservation Information
Conserved circRNAs	NA
PMCS	0.26839161

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9723644-9725174(+)
						
						Potential amino acid sequence
						
							MSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDSQALKPRCVRALKRIFI
LCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVNERGLTVTGFLFLHALF
IEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAAIDFLKGMYMLFDDDQD
NNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSMVKIPIIVAGCKLDFRDDNN
QVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDSQALKPRCVR
ALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVNERGLTVTGF
LFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAAIDFLKGMYM
LFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSMVKIPIIVAGCKL
DFRDDNNQVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDSQA
LKPRCVRALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVNER
GLTVTGFLFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAAID
FLKGMYMLFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSMVKIPI
IVAGCKLDFRDDNNQVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPL
FDQDSQALKPRCVRALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKL
PEGVNERGLTVTGFLFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFE
LTNAAIDFLKGMYMLFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFL
SM(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9723644-9725174(+)
Potential amino acid sequence	MSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDSQALKPRCVRALKRIFI LCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVNERGLTVTGFLFLHALF IEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAAIDFLKGMYMLFDDDQD NNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSMVKIPIIVAGCKLDFRDDNN QVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDSQALKPRCVR ALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVNERGLTVTGF LFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAAIDFLKGMYM LFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSMVKIPIIVAGCKL DFRDDNNQVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPLFDQDSQA LKPRCVRALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKLPEGVNER GLTVTGFLFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFELTNAAID FLKGMYMLFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFLSMVKIPI IVAGCKLDFRDDNNQVSLEQVMSPIMQQFREIETCIECSALKQLQAQEVFYYAQKTVLHPTGPL FDQDSQALKPRCVRALKRIFILCDHDRDGALSEAELNDFQVKCFHAPLQPSEIEGVKRVVQEKL PEGVNERGLTVTGFLFLHALFIEKGRLETTWTVLRKFGYNNDIRLAEELLPSAIFKRAPDQSFE LTNAAIDFLKGMYMLFDDDQDNNLRPQEIEDLFSTAPESPWKEAPYEDAAEKTALGGLSFDAFL SM(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT5G27540_circ_g.4

Address

Any questions?

Supported by