Plant Circular RNA Database

Detail information of Os04g0558400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0558400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_024829
					
						Alias
						Os_ciR4181
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 27986069-27987754  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0558400						
					
						Parent gene annotation
						
							RmlC-like jelly roll fold domain containing protein. (Os04t05584
00-01);Similar to acyl-CoA thioesterase family protein. (Os04t05
58400-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0558400_circ_g.4 Os04g0558400_circ_g.5 Os04g0558400_circ_g.6 Os04g0558400_circ_g.7 						
					
						Support reads
						12/6
					
						Tissues
						root/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
						Os04t0558400-02:4
Os04t0558400-01:4

General Information
CircRNA Name	Os04g0558400_circ_g.3
ID in PlantcircBase	osa_circ_024829
Alias	Os_ciR4181
Organism	Oryza sativa
Position	chr4: 27986069-27987754 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0558400
Parent gene annotation	RmlC-like jelly roll fold domain containing protein. (Os04t05584 00-01);Similar to acyl-CoA thioesterase family protein. (Os04t05 58400-02)
Parent gene strand	+
Alternative splicing	Os04g0558400_circ_g.4 Os04g0558400_circ_g.5 Os04g0558400_circ_g.6 Os04g0558400_circ_g.7
Support reads	12/6
Tissues	root/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	Os04t0558400-02:4 Os04t0558400-01:4

			
						 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  
						
							TCAGGTTCATCGGGCGCGCGATGGAACAAGCTTTGCCACCAGAAAAGTGGAGGCAAAGCAAAAG
GGCCTTGTCATTTTCACCTTGATTGCTTCATTCCAGctgacctgcttcgtattgccaaatcaat
atggacacttgttgcaaccaaagaccatttggagtgcagaagagacacctgagaaccattcttt
gctagaac

									
								

					

						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: 149
Transcript exons: 27986069-27986143,27987681-27987754
CTGACCTGCTTCGTATTGCCAAATCAATATGGACACTTGTTGCAACCAAAGACCATTTGGAGTG
CAGAAGAGACACAAGCTTTGCCACCAGAAAAGTGGAGGCAAAGCAAAAGGGCCTTGTCATTTTC
ACCTTGATTGCTTCATTCCAG
Transcript length: 405
Transcript exons: 27986069-27986194,27986573-27986648,27987157-27987246,27
987642-27987754
CTGACCTGCTTCGTATTGCCAAATCAATATGGACACTTGTTGCAACCAAAGACCATTTGGAGTG
CAGAAGAGACACCTGAGAACCATTCTTTGCTAGAACAAATTTTGCACTTAGAGCCATTGGAGGT
CGATATCTTCCGTGGGTTTACTTTGCCAGGAGCTCCGACTTTTAGGCAAGTTTTTGGAGGACAG
TTGATAGGACAGGCACTAGCAGCAGCATCCAAGACCGTTGACTGCCTAAAAGCGGTGCACAGTT
TGCACGCAATTTTCCTTATCGCAGGAGACAAGAATTTGCCAATAATATATCAGGTTCATCGGGC
GCGCGATGGAACAAGCTTTGCCACCAGAAAAGTGGAGGCAAAGCAAAAGGGCCTTGTCATTTTC
ACCTTGATTGCTTCATTCCAG
						
					

						Genomic sequence
						
							CTGACCTGCTTCGTATTGCCAAATCAATATGGACACTTGTTGCAACCAAAGACCATTTGGAGTG
CAGAAGAGACACCTGAGAACCATTCTTTGCTAGAACAAATTTTGCACTTAGAGCCATTGGAGGT
AAGTCTAAATGTGTTGTGATGTTTCTGTTTTGTAAAGGTATATATCACTTTACAGTATGATTAC
TGTGCTGAAAAATTATCAGGTATCCTAGTTCGTAAGATCTTATGACTTATATACTACATACGCT
AATTTTGTAGCTCTACCATTCTTTTTACCACCAACAGCGTGTTAAGTATCACCCATTAGAGGTT
AACCTGATTTAGATTATTAATAGATCAGGCTTTCATTTACATCATCTAAAAGAGACAATTTAAG
GTGGATTTGCAGTTTCATATTTACACCTCCTATTTATAAGTGGAAAGGGCAAAATATTTTGTCA
CAGCAAGTCAAATTTAAGTCTGTAAACTTTCTCACTGTAATCATTATCTTTTTTAGGTCGATAT
CTTCCGTGGGTTTACTTTGCCAGGAGCTCCGACTTTTAGGCAAGTTTTTGGAGGACAGTTGATA
GGACAGGCATGTTCCAACTAAAATATCTTACTTTCTATTATCAATATCTGCTGGATGTTTGTAT
TTCACCACTTCCTTTTTCTGTTATGTTGCAACATTCATATTTAAGTAGAAGTGCATGAATCCAT
TTGTGAAAAATAAAAGATAAAAAAGGGAGCTTCTTTAACATGCTTCTGAATCATTTTTTTGCTG
CTTTTTGGAAAACTTTTGGACTTTCCTCGTTGATCACAGAGGGCCAGTTTTTGTAATAGCATGG
ATGTAAGTGCCAAAGGAGGAAAAAACATTGTAAAGGCGGTTCACATAGGACAGCATTATTTTGC
TCAAACATGTTTTCTTCAATGGTATATTAATCTTCTGATTAAATTGTTAAATTGTTTGTCCATG
AAAATTGTTTTTCCACTACTCATTCTCATGCACTCCCAAAAGAAAGTTCAAACACTAGAAAGAG
TACACACATCCATGTCAAAGATTTTCACTATGTCTGAACTTTGTTTGTTATTGGACCCTCATGT
AGGCACTAGCAGCAGCATCCAAGACCGTTGACTGCCTAAAAGCGGTGCACAGTTTGCACGCAAT
TTTCCTTATCGCAGGAGACAAGAATTGTAAGTTCTCTAAGCTTGTGTAGTAGTTCTCTTCTCAA
TCAAGTTGAATTTAAACTACTCCAACAAAAAATGCAATTTTGGGAACCACTAGTCTATCATATC
ACGAAGAGGTGACCTAAGAAGAAACCAATGCCAACAAAATGTAACTTTGATAACCACTAGTCTA
TTAGATCAAGAAAGGATGGTTTAAGACAAAGCTTTACTCTGCCTTCCAAATTATGCATTGTCCC
TGACTTAGAAATGAGCAGTGGATTAATTTGTGCAAACTTTTTTATGAGTCTATCTTTTGAGCTG
TCATCTTAGTAAGCTGCAAATAATTATGCAGTGTAATTTTATTTATTTGAAAAAAAGAATAAAT
CTGATCATGTCTGTTTCTGTTTTGTCCTCTGTTGTAGTGCCAATAATATATCAGGTTCATCGGG
CGCGCGATGGAACAAGCTTTGCCACCAGAAAAGTGGAGGCAAAGCAAAAGGGCCTTGTCATTTT
CACCTTGATTGCTTCATTCCAG
						
					

			
		

Sequences
Splice junction sequence	TCAGGTTCATCGGGCGCGCGATGGAACAAGCTTTGCCACCAGAAAAGTGGAGGCAAAGCAAAAG GGCCTTGTCATTTTCACCTTGATTGCTTCATTCCAGctgacctgcttcgtattgccaaatcaat atggacacttgttgcaaccaaagaccatttggagtgcagaagagacacctgagaaccattcttt gctagaac
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: 149 Transcript exons: 27986069-27986143,27987681-27987754 CTGACCTGCTTCGTATTGCCAAATCAATATGGACACTTGTTGCAACCAAAGACCATTTGGAGTG CAGAAGAGACACAAGCTTTGCCACCAGAAAAGTGGAGGCAAAGCAAAAGGGCCTTGTCATTTTC ACCTTGATTGCTTCATTCCAG Transcript length: 405 Transcript exons: 27986069-27986194,27986573-27986648,27987157-27987246,27 987642-27987754 CTGACCTGCTTCGTATTGCCAAATCAATATGGACACTTGTTGCAACCAAAGACCATTTGGAGTG CAGAAGAGACACCTGAGAACCATTCTTTGCTAGAACAAATTTTGCACTTAGAGCCATTGGAGGT CGATATCTTCCGTGGGTTTACTTTGCCAGGAGCTCCGACTTTTAGGCAAGTTTTTGGAGGACAG TTGATAGGACAGGCACTAGCAGCAGCATCCAAGACCGTTGACTGCCTAAAAGCGGTGCACAGTT TGCACGCAATTTTCCTTATCGCAGGAGACAAGAATTTGCCAATAATATATCAGGTTCATCGGGC GCGCGATGGAACAAGCTTTGCCACCAGAAAAGTGGAGGCAAAGCAAAAGGGCCTTGTCATTTTC ACCTTGATTGCTTCATTCCAG
Genomic sequence	CTGACCTGCTTCGTATTGCCAAATCAATATGGACACTTGTTGCAACCAAAGACCATTTGGAGTG CAGAAGAGACACCTGAGAACCATTCTTTGCTAGAACAAATTTTGCACTTAGAGCCATTGGAGGT AAGTCTAAATGTGTTGTGATGTTTCTGTTTTGTAAAGGTATATATCACTTTACAGTATGATTAC TGTGCTGAAAAATTATCAGGTATCCTAGTTCGTAAGATCTTATGACTTATATACTACATACGCT AATTTTGTAGCTCTACCATTCTTTTTACCACCAACAGCGTGTTAAGTATCACCCATTAGAGGTT AACCTGATTTAGATTATTAATAGATCAGGCTTTCATTTACATCATCTAAAAGAGACAATTTAAG GTGGATTTGCAGTTTCATATTTACACCTCCTATTTATAAGTGGAAAGGGCAAAATATTTTGTCA CAGCAAGTCAAATTTAAGTCTGTAAACTTTCTCACTGTAATCATTATCTTTTTTAGGTCGATAT CTTCCGTGGGTTTACTTTGCCAGGAGCTCCGACTTTTAGGCAAGTTTTTGGAGGACAGTTGATA GGACAGGCATGTTCCAACTAAAATATCTTACTTTCTATTATCAATATCTGCTGGATGTTTGTAT TTCACCACTTCCTTTTTCTGTTATGTTGCAACATTCATATTTAAGTAGAAGTGCATGAATCCAT TTGTGAAAAATAAAAGATAAAAAAGGGAGCTTCTTTAACATGCTTCTGAATCATTTTTTTGCTG CTTTTTGGAAAACTTTTGGACTTTCCTCGTTGATCACAGAGGGCCAGTTTTTGTAATAGCATGG ATGTAAGTGCCAAAGGAGGAAAAAACATTGTAAAGGCGGTTCACATAGGACAGCATTATTTTGC TCAAACATGTTTTCTTCAATGGTATATTAATCTTCTGATTAAATTGTTAAATTGTTTGTCCATG AAAATTGTTTTTCCACTACTCATTCTCATGCACTCCCAAAAGAAAGTTCAAACACTAGAAAGAG TACACACATCCATGTCAAAGATTTTCACTATGTCTGAACTTTGTTTGTTATTGGACCCTCATGT AGGCACTAGCAGCAGCATCCAAGACCGTTGACTGCCTAAAAGCGGTGCACAGTTTGCACGCAAT TTTCCTTATCGCAGGAGACAAGAATTGTAAGTTCTCTAAGCTTGTGTAGTAGTTCTCTTCTCAA TCAAGTTGAATTTAAACTACTCCAACAAAAAATGCAATTTTGGGAACCACTAGTCTATCATATC ACGAAGAGGTGACCTAAGAAGAAACCAATGCCAACAAAATGTAACTTTGATAACCACTAGTCTA TTAGATCAAGAAAGGATGGTTTAAGACAAAGCTTTACTCTGCCTTCCAAATTATGCATTGTCCC TGACTTAGAAATGAGCAGTGGATTAATTTGTGCAAACTTTTTTATGAGTCTATCTTTTGAGCTG TCATCTTAGTAAGCTGCAAATAATTATGCAGTGTAATTTTATTTATTTGAAAAAAAGAATAAAT CTGATCATGTCTGTTTCTGTTTTGTCCTCTGTTGTAGTGCCAATAATATATCAGGTTCATCGGG CGCGCGATGGAACAAGCTTTGCCACCAGAAAAGTGGAGGCAAAGCAAAAGGGCCTTGTCATTTT CACCTTGATTGCTTCATTCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.214446634

Conservation Information
Conserved circRNAs	NA
PMCS	0.214446634

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							27986157-27987748(-)
27986191-27987734(-)
						
						Potential amino acid sequence
						
							MVLRCLFCTPNGLWLQQVSILIWQYEAGQLE*(-)
MALSAKFVLAKNGSQVSLLHSKWSLVATSVHIDLAIRSRSAGMKQSR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	27986157-27987748(-) 27986191-27987734(-)
Potential amino acid sequence	MVLRCLFCTPNGLWLQQVSILIWQYEAGQLE(-) MALSAKFVLAKNGSQVSLLHSKWSLVATSVHIDLAIRSRSAGMKQSR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os04g0558400_circ_g.3

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