Plant Circular RNA Database

Detail information of Os04g0624600_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0624600_circ_g.2
					
						ID in PlantcircBase
						osa_circ_025394
					
						Alias
						Os04circ14413
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 31754709-31756819  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						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.3 Os04g0624600_circ_g.4 Os04g0624600_circ_g.5 						
					
						Support reads
						2/1
					
						Tissues
						leaf and panicle/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
						Os04t0624600-02:2
Os04t0624600-01:5

General Information
CircRNA Name	Os04g0624600_circ_g.2
ID in PlantcircBase	osa_circ_025394
Alias	Os04circ14413
Organism	Oryza sativa
Position	chr4: 31754709-31756819 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
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.3 Os04g0624600_circ_g.4 Os04g0624600_circ_g.5
Support reads	2/1
Tissues	leaf and panicle/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	Os04t0624600-02:2 Os04t0624600-01:5

			
						 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
CCCAGTCTAACACCAATGCCCCTTCAGGTAGAGTAAccattctgtggttccaagaagtaaacag
ggacgtcttcaacttttccaaaccatacttttatctctgtattaccccaagtaaaactttgacg
gtaatgta

									
								

					

						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: 880
Transcript exons: 31754709-31754818,31755239-31755346,31755418-31755593,31
756163-31756433,31756605-31756819
CCATTCTGTGGTTCCAAGAAGTAAACAGGGACGTCTTCAACTTTTCCAAACCATACTTTTATCT
CTGTATTACCCCAAGTAAAACTTTGACGGTAATGTAAATCTTTCACATTGCTTAGGTTTAAACA
GTCATACTTGGGAAGAATAACCTCAACATTGTGGCCTAAATCTTGAACGGCTCGTGAAAGACTT
GTAACAACATCACCAAGACCCCCAACCTTTGCAATAGGAGCCATTTCTACTGCAATGTGCACAA
TATGCATAGGAGGTTCTTTTGCAACGGAATCAGTCACAGGACTATGATAGTCCATGCCATTCCT
GTTGTCATATATTCCACCTTCTTCCGACTCAGAGAAAACAAAGTCCATCATATATGCATCCAAA
GGAACCCTAACTGTTGCTCTTAAGTGTGAACCATTCTCCGCATTCACCATCTTCTGTGGCGGCA
AAGGACCACTTGGATGAGTCCAACGATTAAAGGAACATCTGAACCAAACCTCTGGCTTTCCGTT
CAGCACCGTGTTAGACGGATTGTATAGAACATCCACGGTGGTTCCTGCACGTACTTCGAGAGGC
TCAGTGTACACAATGTGTTTCTGCGAGAGAAGAAAGTCTCTCATAGTCTTTTCCTTCATCTCAG
CTTTCATTTTTGCAGTTATCTCAGACTTTCTTCGATCAGCATCCTCCCTTTCTTTCCTTTCTTT
CTGAAGCCTTTTAAATATCATGTGCTCTTCTTCCACCCAAAACAGGTCCTCAGATATGTTATTT
GGAACAACAGCATGGAAATCCTGGCGTCCATTGTTATCATAATTCCTTGCATTCCCAGGTGGCC
CATCAGCAAAAACCCAGTCTAACACCAATGCCCCTTCAGGTAGAGTAA
						
					

						Genomic sequence
						
							CCATTCTGTGGTTCCAAGAAGTAAACAGGGACGTCTTCAACTTTTCCAAACCATACTTTTATCT
CTGTATTACCCCAAGTAAAACTTTGACGGTAATGTAAATCTTTCACCTGAACCAAAAGACAAGT
AAATTAATGAGAAAAAAGCCCCCACAAACAGCGATGTTCACACTCTCACCAGCGAAGGAAGCAA
ATGATCGTAAAAATAAAAGCATGGACTATAGTTGATTTCACGAGAAATGCTTCAGTGCTCTTTC
AAAAGTGAAAAGTGAAAACCACAGAATTTAAAGTGTTTAGAGGGACTAGTTGCAACCATTGAAC
CACCTATTGCTCCAGCACTTACAGTTGATTTGATATTTGCACTTTGTTTTTGCCAGTATCTTTA
AGATTCCACAAAACCCCAGAGCTACATATATTAGATAAAACAAGAAAGAAACCATCTGCACTGT
GCATATACATAGCATTTCCATAGAATTCCATTGAAACACTGAAAAGAATGCAACCGAAAAGGAA
GACGCCAGGATGCCTTACATTGCTTAGGTTTAAACAGTCATACTTGGGAAGAATAACCTCAACA
TTGTGGCCTAAATCTTGAACGGCTCGTGAAAGACTTGTAACAACATCACCAAGACCCCCAACCT
GTGACAGATCATTTTTTAGTACCTCAGCACTTTCTGTGGTCCAAAAGAATTGGTAAAAGGTGTC
TTTACCTTTGCAATAGGAGCCATTTCTACTGCAATGTGCACAATATGCATAGGAGGTTCTTTTG
CAACGGAATCAGTCACAGGACTATGATAGTCCATGCCATTCCTGTTGTCATATATTCCACCTTC
TTCCGACTCAGAGAAAACAAAGTCCATCATATATGCATCCAAAGGAACCCTAACTAGAAAAAAG
AACAGATCACGTCAAGCAAAGGAAATAAAGTCAAACAACATCATCATACAAAAATGTGTGTGTG
CATCTGAGAGAGAGAGAGAGAAAGAGAGACAGAGAGACAGAGAGAGAACCATGACAAAGAAGCC
AAATTTCTTTTCCTACAGCTCCTACCACCTCTTATTAGTAGTACAATATTACTTTTTATATATT
ATCATTATTATCTTCATTTTCTTGTGTGGCTCCACTTGGGTTTCATGTCGATCCTACATTCCTA
CCCAAGGTTGCTTTGGGACTAAAAGTCATTGGGAATATCATTAATATTGACATATTATTCAAAA
AATTTCAAAAGCATGCGGTGAAAACAAGTGGGATTAGATTTTTACACAAATTTAGTATGTTTGA
AAAAAGGTAACTCCTGCTTTATCAGGTTTGCATGCTTATTAGATTCTTTCTGGTAACCATAGTA
AGAGAGGAAGAGTAGTTTGAACTAGTCTCGAAGAAGTCTAATGACCTTTTAATTGAGGTATTAG
TATGAAAAATGCAATCAGAAAAAAGACCCCCAACAAGGACACACACCTGTTGCTCTTAAGTGTG
AACCATTCTCCGCATTCACCATCTTCTGTGGCGGCAAAGGACCACTTGGATGAGTCCAACGATT
AAAGGAACATCTGAACCAAACCTCTGGCTTTCCGTTCAGCACCGTGTTAGACGGATTGTATAGA
ACATCCACGGTGGTTCCTGCACGTACTTCGAGAGGCTCAGTGTACACAATGTGTTTCTGCGAGA
GAAGAAAGTCTCTCATAGTCTTTTCCTTCATCTCAGCTTTCATTTTTGCAGTTATCTCAGACTG
AAACAAACAAAAGGCAAAAGTCAAATGATGCCCTCCTGGATGTGTTATTGAACTTGAACCAGGG
CCATAAATTACCATTTATCAACAAAGAGTAGCAAGTAACCAAGTATATACAGTAATATAGGTTT
AATGCTCCTAATTAATATGCAAACATTCTCTTGAACTGACCTTTCTTCGATCAGCATCCTCCCT
TTCTTTCCTTTCTTTCTGAAGCCTTTTAAATATCATGTGCTCTTCTTCCACCCAAAACAGGTCC
TCAGATATGTTATTTGGAACAACAGCATGGAAATCCTGGCGTCCATTGTTATCATAATTCCTTG
CATTCCCAGGTGGCCCATCAGCAAAAACCCAGTCTAACACCAATGCCCCTTCAGGTAGAGTAA
						
					

			
		

Sequences
Splice junction sequence	TGGAAATCCTGGCGTCCATTGTTATCATAATTCCTTGCATTCCCAGGTGGCCCATCAGCAAAAA CCCAGTCTAACACCAATGCCCCTTCAGGTAGAGTAAccattctgtggttccaagaagtaaacag ggacgtcttcaacttttccaaaccatacttttatctctgtattaccccaagtaaaactttgacg gtaatgta
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: 880 Transcript exons: 31754709-31754818,31755239-31755346,31755418-31755593,31 756163-31756433,31756605-31756819 CCATTCTGTGGTTCCAAGAAGTAAACAGGGACGTCTTCAACTTTTCCAAACCATACTTTTATCT CTGTATTACCCCAAGTAAAACTTTGACGGTAATGTAAATCTTTCACATTGCTTAGGTTTAAACA GTCATACTTGGGAAGAATAACCTCAACATTGTGGCCTAAATCTTGAACGGCTCGTGAAAGACTT GTAACAACATCACCAAGACCCCCAACCTTTGCAATAGGAGCCATTTCTACTGCAATGTGCACAA TATGCATAGGAGGTTCTTTTGCAACGGAATCAGTCACAGGACTATGATAGTCCATGCCATTCCT GTTGTCATATATTCCACCTTCTTCCGACTCAGAGAAAACAAAGTCCATCATATATGCATCCAAA GGAACCCTAACTGTTGCTCTTAAGTGTGAACCATTCTCCGCATTCACCATCTTCTGTGGCGGCA AAGGACCACTTGGATGAGTCCAACGATTAAAGGAACATCTGAACCAAACCTCTGGCTTTCCGTT CAGCACCGTGTTAGACGGATTGTATAGAACATCCACGGTGGTTCCTGCACGTACTTCGAGAGGC TCAGTGTACACAATGTGTTTCTGCGAGAGAAGAAAGTCTCTCATAGTCTTTTCCTTCATCTCAG CTTTCATTTTTGCAGTTATCTCAGACTTTCTTCGATCAGCATCCTCCCTTTCTTTCCTTTCTTT CTGAAGCCTTTTAAATATCATGTGCTCTTCTTCCACCCAAAACAGGTCCTCAGATATGTTATTT GGAACAACAGCATGGAAATCCTGGCGTCCATTGTTATCATAATTCCTTGCATTCCCAGGTGGCC CATCAGCAAAAACCCAGTCTAACACCAATGCCCCTTCAGGTAGAGTAA
Genomic sequence	CCATTCTGTGGTTCCAAGAAGTAAACAGGGACGTCTTCAACTTTTCCAAACCATACTTTTATCT CTGTATTACCCCAAGTAAAACTTTGACGGTAATGTAAATCTTTCACCTGAACCAAAAGACAAGT AAATTAATGAGAAAAAAGCCCCCACAAACAGCGATGTTCACACTCTCACCAGCGAAGGAAGCAA ATGATCGTAAAAATAAAAGCATGGACTATAGTTGATTTCACGAGAAATGCTTCAGTGCTCTTTC AAAAGTGAAAAGTGAAAACCACAGAATTTAAAGTGTTTAGAGGGACTAGTTGCAACCATTGAAC CACCTATTGCTCCAGCACTTACAGTTGATTTGATATTTGCACTTTGTTTTTGCCAGTATCTTTA AGATTCCACAAAACCCCAGAGCTACATATATTAGATAAAACAAGAAAGAAACCATCTGCACTGT GCATATACATAGCATTTCCATAGAATTCCATTGAAACACTGAAAAGAATGCAACCGAAAAGGAA GACGCCAGGATGCCTTACATTGCTTAGGTTTAAACAGTCATACTTGGGAAGAATAACCTCAACA TTGTGGCCTAAATCTTGAACGGCTCGTGAAAGACTTGTAACAACATCACCAAGACCCCCAACCT GTGACAGATCATTTTTTAGTACCTCAGCACTTTCTGTGGTCCAAAAGAATTGGTAAAAGGTGTC TTTACCTTTGCAATAGGAGCCATTTCTACTGCAATGTGCACAATATGCATAGGAGGTTCTTTTG CAACGGAATCAGTCACAGGACTATGATAGTCCATGCCATTCCTGTTGTCATATATTCCACCTTC TTCCGACTCAGAGAAAACAAAGTCCATCATATATGCATCCAAAGGAACCCTAACTAGAAAAAAG AACAGATCACGTCAAGCAAAGGAAATAAAGTCAAACAACATCATCATACAAAAATGTGTGTGTG CATCTGAGAGAGAGAGAGAGAAAGAGAGACAGAGAGACAGAGAGAGAACCATGACAAAGAAGCC AAATTTCTTTTCCTACAGCTCCTACCACCTCTTATTAGTAGTACAATATTACTTTTTATATATT ATCATTATTATCTTCATTTTCTTGTGTGGCTCCACTTGGGTTTCATGTCGATCCTACATTCCTA CCCAAGGTTGCTTTGGGACTAAAAGTCATTGGGAATATCATTAATATTGACATATTATTCAAAA AATTTCAAAAGCATGCGGTGAAAACAAGTGGGATTAGATTTTTACACAAATTTAGTATGTTTGA AAAAAGGTAACTCCTGCTTTATCAGGTTTGCATGCTTATTAGATTCTTTCTGGTAACCATAGTA AGAGAGGAAGAGTAGTTTGAACTAGTCTCGAAGAAGTCTAATGACCTTTTAATTGAGGTATTAG TATGAAAAATGCAATCAGAAAAAAGACCCCCAACAAGGACACACACCTGTTGCTCTTAAGTGTG AACCATTCTCCGCATTCACCATCTTCTGTGGCGGCAAAGGACCACTTGGATGAGTCCAACGATT AAAGGAACATCTGAACCAAACCTCTGGCTTTCCGTTCAGCACCGTGTTAGACGGATTGTATAGA ACATCCACGGTGGTTCCTGCACGTACTTCGAGAGGCTCAGTGTACACAATGTGTTTCTGCGAGA GAAGAAAGTCTCTCATAGTCTTTTCCTTCATCTCAGCTTTCATTTTTGCAGTTATCTCAGACTG AAACAAACAAAAGGCAAAAGTCAAATGATGCCCTCCTGGATGTGTTATTGAACTTGAACCAGGG CCATAAATTACCATTTATCAACAAAGAGTAGCAAGTAACCAAGTATATACAGTAATATAGGTTT AATGCTCCTAATTAATATGCAAACATTCTCTTGAACTGACCTTTCTTCGATCAGCATCCTCCCT TTCTTTCCTTTCTTTCTGAAGCCTTTTAAATATCATGTGCTCTTCTTCCACCCAAAACAGGTCC TCAGATATGTTATTTGGAACAACAGCATGGAAATCCTGGCGTCCATTGTTATCATAATTCCTTG CATTCCCAGGTGGCCCATCAGCAAAAACCCAGTCTAACACCAATGCCCCTTCAGGTAGAGTAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_014896 						
					
						PMCS
						0.265984964

Conservation Information
Conserved circRNAs	osi_circ_014896
PMCS	0.265984964

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							31754714-31756809(-)
31756666-31756809(-)
						
						Potential amino acid sequence
						
							MVTLPEGALVLDWVFADGPPGNARNYDNNGRQDFHAVVPNNISEDLFWVEEEHMIFKRLQKERK
EREDADRRKSEITAKMKAEMKEKTMRDFLLSQKHIVYTEPLEVRAGTTVDVLYNPSNTVLNGKP
EVWFRCSFNRWTHPSGPLPPQKMVNAENGSHLRATVRVPLDAYMMDFVFSESEEGGIYDNRNGM
DYHSPVTDSVAKEPPMHIVHIAVEMAPIAKVGGLGDVVTSLSRAVQDLGHNVEVILPKYDCLNL
SNVKDLHYRQSFTWGNTEIKVWFGKVEDVPVYFLEPQNGYST*(-)
MIFKRLQKERKEREDADRRKSEITAKMKAEMKEKTMRDFLLSQKHIVYTEPLEVRAGTTVDVLY
NPSNTVLNGKPEVWFRCSFNRWTHPSGPLPPQKMVNAENGSHLRATVRVPLDAYMMDFVFSESE
EGGIYDNRNGMDYHSPVTDSVAKEPPMHIVHIAVEMAPIAKVGGLGDVVTSLSRAVQDLGHNVE
VILPKYDCLNLSNVKDLHYRQSFTWGNTEIKVWFGKVEDVPVYFLEPQNGYST*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	31754714-31756809(-) 31756666-31756809(-)
Potential amino acid sequence	MVTLPEGALVLDWVFADGPPGNARNYDNNGRQDFHAVVPNNISEDLFWVEEEHMIFKRLQKERK EREDADRRKSEITAKMKAEMKEKTMRDFLLSQKHIVYTEPLEVRAGTTVDVLYNPSNTVLNGKP EVWFRCSFNRWTHPSGPLPPQKMVNAENGSHLRATVRVPLDAYMMDFVFSESEEGGIYDNRNGM DYHSPVTDSVAKEPPMHIVHIAVEMAPIAKVGGLGDVVTSLSRAVQDLGHNVEVILPKYDCLNL SNVKDLHYRQSFTWGNTEIKVWFGKVEDVPVYFLEPQNGYST(-) MIFKRLQKERKEREDADRRKSEITAKMKAEMKEKTMRDFLLSQKHIVYTEPLEVRAGTTVDVLY NPSNTVLNGKPEVWFRCSFNRWTHPSGPLPPQKMVNAENGSHLRATVRVPLDAYMMDFVFSESE EGGIYDNRNGMDYHSPVTDSVAKEPPMHIVHIAVEMAPIAKVGGLGDVVTSLSRAVQDLGHNVE VILPKYDCLNLSNVKDLHYRQSFTWGNTEIKVWFGKVEDVPVYFLEPQNGYST(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os04g0624600_circ_g.2

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