Plant Circular RNA Database

Detail information of Os04g0624600_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0624600_circ_g.3
					
						ID in PlantcircBase
						osa_circ_025395
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 31755239-31756819  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0624600						
					
						Parent gene annotation
						
							Starch synthase, Starch biosynthesis (Os04t0624600-01);Similar t
o H0215F08.14 protein. (Os04t0624600-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0624600_circ_g.1 Os04g0624600_circ_g.2 Os04g0624600_circ_g.4 Os04g0624600_circ_g.5 						
					
						Support reads
						2
					
						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  
						
							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
						Os04t0624600-01:4
Os04t0624600-02:1

General Information
CircRNA Name	Os04g0624600_circ_g.3
ID in PlantcircBase	osa_circ_025395
Alias	NA
Organism	Oryza sativa
Position	chr4: 31755239-31756819 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0624600
Parent gene annotation	Starch synthase, Starch biosynthesis (Os04t0624600-01);Similar t o H0215F08.14 protein. (Os04t0624600-02)
Parent gene strand	-
Alternative splicing	Os04g0624600_circ_g.1 Os04g0624600_circ_g.2 Os04g0624600_circ_g.4 Os04g0624600_circ_g.5
Support reads	2
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	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	Os04t0624600-01:4 Os04t0624600-02:1

			
						 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  
						
							TGGAAATCCTGGCGTCCATTGTTATCATAATTCCTTGCATTCCCAGGTGGCCCATCAGCAAAAA
CCCAGTCTAACACCAATGCCCCTTCAGGTAGAGTAAattgcttaggtttaaacagtcatacttg
ggaagaataacctcaacattgtggcctaaatcttgaacggctcgtgaaagacttgtaacaacat
caccaaga

									
								

					

						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: 770
Transcript exons: 31755239-31755346,31755418-31755593,31756163-31756433,31
756605-31756819
ATTGCTTAGGTTTAAACAGTCATACTTGGGAAGAATAACCTCAACATTGTGGCCTAAATCTTGA
ACGGCTCGTGAAAGACTTGTAACAACATCACCAAGACCCCCAACCTTTGCAATAGGAGCCATTT
CTACTGCAATGTGCACAATATGCATAGGAGGTTCTTTTGCAACGGAATCAGTCACAGGACTATG
ATAGTCCATGCCATTCCTGTTGTCATATATTCCACCTTCTTCCGACTCAGAGAAAACAAAGTCC
ATCATATATGCATCCAAAGGAACCCTAACTGTTGCTCTTAAGTGTGAACCATTCTCCGCATTCA
CCATCTTCTGTGGCGGCAAAGGACCACTTGGATGAGTCCAACGATTAAAGGAACATCTGAACCA
AACCTCTGGCTTTCCGTTCAGCACCGTGTTAGACGGATTGTATAGAACATCCACGGTGGTTCCT
GCACGTACTTCGAGAGGCTCAGTGTACACAATGTGTTTCTGCGAGAGAAGAAAGTCTCTCATAG
TCTTTTCCTTCATCTCAGCTTTCATTTTTGCAGTTATCTCAGACTTTCTTCGATCAGCATCCTC
CCTTTCTTTCCTTTCTTTCTGAAGCCTTTTAAATATCATGTGCTCTTCTTCCACCCAAAACAGG
TCCTCAGATATGTTATTTGGAACAACAGCATGGAAATCCTGGCGTCCATTGTTATCATAATTCC
TTGCATTCCCAGGTGGCCCATCAGCAAAAACCCAGTCTAACACCAATGCCCCTTCAGGTAGAGT
AA
						
					

						Genomic sequence
						
							ATTGCTTAGGTTTAAACAGTCATACTTGGGAAGAATAACCTCAACATTGTGGCCTAAATCTTGA
ACGGCTCGTGAAAGACTTGTAACAACATCACCAAGACCCCCAACCTGTGACAGATCATTTTTTA
GTACCTCAGCACTTTCTGTGGTCCAAAAGAATTGGTAAAAGGTGTCTTTACCTTTGCAATAGGA
GCCATTTCTACTGCAATGTGCACAATATGCATAGGAGGTTCTTTTGCAACGGAATCAGTCACAG
GACTATGATAGTCCATGCCATTCCTGTTGTCATATATTCCACCTTCTTCCGACTCAGAGAAAAC
AAAGTCCATCATATATGCATCCAAAGGAACCCTAACTAGAAAAAAGAACAGATCACGTCAAGCA
AAGGAAATAAAGTCAAACAACATCATCATACAAAAATGTGTGTGTGCATCTGAGAGAGAGAGAG
AGAAAGAGAGACAGAGAGACAGAGAGAGAACCATGACAAAGAAGCCAAATTTCTTTTCCTACAG
CTCCTACCACCTCTTATTAGTAGTACAATATTACTTTTTATATATTATCATTATTATCTTCATT
TTCTTGTGTGGCTCCACTTGGGTTTCATGTCGATCCTACATTCCTACCCAAGGTTGCTTTGGGA
CTAAAAGTCATTGGGAATATCATTAATATTGACATATTATTCAAAAAATTTCAAAAGCATGCGG
TGAAAACAAGTGGGATTAGATTTTTACACAAATTTAGTATGTTTGAAAAAAGGTAACTCCTGCT
TTATCAGGTTTGCATGCTTATTAGATTCTTTCTGGTAACCATAGTAAGAGAGGAAGAGTAGTTT
GAACTAGTCTCGAAGAAGTCTAATGACCTTTTAATTGAGGTATTAGTATGAAAAATGCAATCAG
AAAAAAGACCCCCAACAAGGACACACACCTGTTGCTCTTAAGTGTGAACCATTCTCCGCATTCA
CCATCTTCTGTGGCGGCAAAGGACCACTTGGATGAGTCCAACGATTAAAGGAACATCTGAACCA
AACCTCTGGCTTTCCGTTCAGCACCGTGTTAGACGGATTGTATAGAACATCCACGGTGGTTCCT
GCACGTACTTCGAGAGGCTCAGTGTACACAATGTGTTTCTGCGAGAGAAGAAAGTCTCTCATAG
TCTTTTCCTTCATCTCAGCTTTCATTTTTGCAGTTATCTCAGACTGAAACAAACAAAAGGCAAA
AGTCAAATGATGCCCTCCTGGATGTGTTATTGAACTTGAACCAGGGCCATAAATTACCATTTAT
CAACAAAGAGTAGCAAGTAACCAAGTATATACAGTAATATAGGTTTAATGCTCCTAATTAATAT
GCAAACATTCTCTTGAACTGACCTTTCTTCGATCAGCATCCTCCCTTTCTTTCCTTTCTTTCTG
AAGCCTTTTAAATATCATGTGCTCTTCTTCCACCCAAAACAGGTCCTCAGATATGTTATTTGGA
ACAACAGCATGGAAATCCTGGCGTCCATTGTTATCATAATTCCTTGCATTCCCAGGTGGCCCAT
CAGCAAAAACCCAGTCTAACACCAATGCCCCTTCAGGTAGAGTAA
						
					

			
		

Sequences
Splice junction sequence	TGGAAATCCTGGCGTCCATTGTTATCATAATTCCTTGCATTCCCAGGTGGCCCATCAGCAAAAA CCCAGTCTAACACCAATGCCCCTTCAGGTAGAGTAAattgcttaggtttaaacagtcatacttg ggaagaataacctcaacattgtggcctaaatcttgaacggctcgtgaaagacttgtaacaacat caccaaga
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: 770 Transcript exons: 31755239-31755346,31755418-31755593,31756163-31756433,31 756605-31756819 ATTGCTTAGGTTTAAACAGTCATACTTGGGAAGAATAACCTCAACATTGTGGCCTAAATCTTGA ACGGCTCGTGAAAGACTTGTAACAACATCACCAAGACCCCCAACCTTTGCAATAGGAGCCATTT CTACTGCAATGTGCACAATATGCATAGGAGGTTCTTTTGCAACGGAATCAGTCACAGGACTATG ATAGTCCATGCCATTCCTGTTGTCATATATTCCACCTTCTTCCGACTCAGAGAAAACAAAGTCC ATCATATATGCATCCAAAGGAACCCTAACTGTTGCTCTTAAGTGTGAACCATTCTCCGCATTCA CCATCTTCTGTGGCGGCAAAGGACCACTTGGATGAGTCCAACGATTAAAGGAACATCTGAACCA AACCTCTGGCTTTCCGTTCAGCACCGTGTTAGACGGATTGTATAGAACATCCACGGTGGTTCCT GCACGTACTTCGAGAGGCTCAGTGTACACAATGTGTTTCTGCGAGAGAAGAAAGTCTCTCATAG TCTTTTCCTTCATCTCAGCTTTCATTTTTGCAGTTATCTCAGACTTTCTTCGATCAGCATCCTC CCTTTCTTTCCTTTCTTTCTGAAGCCTTTTAAATATCATGTGCTCTTCTTCCACCCAAAACAGG TCCTCAGATATGTTATTTGGAACAACAGCATGGAAATCCTGGCGTCCATTGTTATCATAATTCC TTGCATTCCCAGGTGGCCCATCAGCAAAAACCCAGTCTAACACCAATGCCCCTTCAGGTAGAGT AA
Genomic sequence	ATTGCTTAGGTTTAAACAGTCATACTTGGGAAGAATAACCTCAACATTGTGGCCTAAATCTTGA ACGGCTCGTGAAAGACTTGTAACAACATCACCAAGACCCCCAACCTGTGACAGATCATTTTTTA GTACCTCAGCACTTTCTGTGGTCCAAAAGAATTGGTAAAAGGTGTCTTTACCTTTGCAATAGGA GCCATTTCTACTGCAATGTGCACAATATGCATAGGAGGTTCTTTTGCAACGGAATCAGTCACAG GACTATGATAGTCCATGCCATTCCTGTTGTCATATATTCCACCTTCTTCCGACTCAGAGAAAAC AAAGTCCATCATATATGCATCCAAAGGAACCCTAACTAGAAAAAAGAACAGATCACGTCAAGCA AAGGAAATAAAGTCAAACAACATCATCATACAAAAATGTGTGTGTGCATCTGAGAGAGAGAGAG AGAAAGAGAGACAGAGAGACAGAGAGAGAACCATGACAAAGAAGCCAAATTTCTTTTCCTACAG CTCCTACCACCTCTTATTAGTAGTACAATATTACTTTTTATATATTATCATTATTATCTTCATT TTCTTGTGTGGCTCCACTTGGGTTTCATGTCGATCCTACATTCCTACCCAAGGTTGCTTTGGGA CTAAAAGTCATTGGGAATATCATTAATATTGACATATTATTCAAAAAATTTCAAAAGCATGCGG TGAAAACAAGTGGGATTAGATTTTTACACAAATTTAGTATGTTTGAAAAAAGGTAACTCCTGCT TTATCAGGTTTGCATGCTTATTAGATTCTTTCTGGTAACCATAGTAAGAGAGGAAGAGTAGTTT GAACTAGTCTCGAAGAAGTCTAATGACCTTTTAATTGAGGTATTAGTATGAAAAATGCAATCAG AAAAAAGACCCCCAACAAGGACACACACCTGTTGCTCTTAAGTGTGAACCATTCTCCGCATTCA CCATCTTCTGTGGCGGCAAAGGACCACTTGGATGAGTCCAACGATTAAAGGAACATCTGAACCA AACCTCTGGCTTTCCGTTCAGCACCGTGTTAGACGGATTGTATAGAACATCCACGGTGGTTCCT GCACGTACTTCGAGAGGCTCAGTGTACACAATGTGTTTCTGCGAGAGAAGAAAGTCTCTCATAG TCTTTTCCTTCATCTCAGCTTTCATTTTTGCAGTTATCTCAGACTGAAACAAACAAAAGGCAAA AGTCAAATGATGCCCTCCTGGATGTGTTATTGAACTTGAACCAGGGCCATAAATTACCATTTAT CAACAAAGAGTAGCAAGTAACCAAGTATATACAGTAATATAGGTTTAATGCTCCTAATTAATAT GCAAACATTCTCTTGAACTGACCTTTCTTCGATCAGCATCCTCCCTTTCTTTCCTTTCTTTCTG AAGCCTTTTAAATATCATGTGCTCTTCTTCCACCCAAAACAGGTCCTCAGATATGTTATTTGGA ACAACAGCATGGAAATCCTGGCGTCCATTGTTATCATAATTCCTTGCATTCCCAGGTGGCCCAT CAGCAAAAACCCAGTCTAACACCAATGCCCCTTCAGGTAGAGTAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.326782052

Conservation Information
Conserved circRNAs	NA
PMCS	0.326782052

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							31756666-31756792(-)
						
						Potential amino acid sequence
						
							MIFKRLQKERKEREDADRRKSEITAKMKAEMKEKTMRDFLLSQKHIVYTEPLEVRAGTTVDVLY
NPSNTVLNGKPEVWFRCSFNRWTHPSGPLPPQKMVNAENGSHLRATVRVPLDAYMMDFVFSESE
EGGIYDNRNGMDYHSPVTDSVAKEPPMHIVHIAVEMAPIAKVGGLGDVVTSLSRAVQDLGHNVE
VILPKYDCLNLSNLLYLKGHWC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	31756666-31756792(-)
Potential amino acid sequence	MIFKRLQKERKEREDADRRKSEITAKMKAEMKEKTMRDFLLSQKHIVYTEPLEVRAGTTVDVLY NPSNTVLNGKPEVWFRCSFNRWTHPSGPLPPQKMVNAENGSHLRATVRVPLDAYMMDFVFSESE EGGIYDNRNGMDYHSPVTDSVAKEPPMHIVHIAVEMAPIAKVGGLGDVVTSLSRAVQDLGHNVE VILPKYDCLNLSNLLYLKGHWC*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0624600_circ_g.3

Address

Any questions?

Supported by