Plant Circular RNA Database

Detail information of Os04g0608100_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0608100_circ_g.3
					
						ID in PlantcircBase
						osa_circ_025134
					
						Alias
						Os04circ13012
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 30766693-30769406  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						SMALT, Segemehl
					
						Parent gene
						
							Os04g0608100						
					
						Parent gene annotation
						
							Ribosomal protein S5 domain 2-type fold domain containing protei
n. (Os04t0608100-01);Similar to OSIGBa0113I13.15 protein. (Os04t
0608100-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0608100_circ_g.2 Os04g0608100_circ_g.4 Os04g0608100_circ_g.5 						
					
						Support reads
						2
					
						Tissues
						leaf
					
						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
						Os04t0608100-01:7
Os04t0608100-02:2

General Information
CircRNA Name	Os04g0608100_circ_g.3
ID in PlantcircBase	osa_circ_025134
Alias	Os04circ13012
Organism	Oryza sativa
Position	chr4: 30766693-30769406 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	SMALT, Segemehl
Parent gene	Os04g0608100
Parent gene annotation	Ribosomal protein S5 domain 2-type fold domain containing protei n. (Os04t0608100-01);Similar to OSIGBa0113I13.15 protein. (Os04t 0608100-02)
Parent gene strand	-
Alternative splicing	Os04g0608100_circ_g.2 Os04g0608100_circ_g.4 Os04g0608100_circ_g.5
Support reads	2
Tissues	leaf
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	Os04t0608100-01:7 Os04t0608100-02:2

			
						 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  
						
							GAGCCCCCAGAGGGCAAATCCTGTAGGGGCAAGCAACCACCCTGACCTCTCCTGCACCCCTTCC
ACTAATCTCCACTACCTTTGCTCGAACAACATCAAGcttgcagtccatgaaggtgagatagcca
taccgtgagagcaaaatagctgatggatccagaataccattttcaagacccaaatatttatttt
cgatggac

									
								

					

						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
						
							CTTGCAGTCCATGAAGGTGAGATAGCCATACCGTGAGAGCAAAATAGCTGATGGATCCAGAATA
CCATTTTCAAGACCCAAATATTTATTTTCGATGGACCTGACAAATAGGGATATGAAATTAAGAA
CTCTGCTAGTGACCATGACTCAATGAGCTAATAAATCTTATGTAGCAATATTTGATTGTTGCTT
TAGAACATGGCAATAGTAGATAGTTGTGGGGACTTCAACATAGATACTTGAAATTAGAACTGTT
CTGGATCCCATGTATGAATTCATAATGTTAGTCCACATGGAATGCTTACTAAAAGGAAACAAAC
TCACTTGTCCAACTGAATGTTGTCCACTGGTGATACAACCAGATCATTCACATTTTCTAAAGCC
ATCAAATAGGCAATCCCGACCTGATGAGGAGCATACAGAAATAGGCATTTGATGATCACATAAC
TAACCAAAGTATCAATTATATTAATAATTCTTTTGAGAACCTAGAGTAAGAACTGGAAGTTTCT
GTCCTTGTTATGGTGAGCTGAAGGTTTAGAAGATACTAGTACAAAGTTAGTAGCTTCACAAATT
TGCTTTGAACTCCAAGTCAAATGTGAGCCAAGTATATGTCATGATTATGAAATACTGCATATTC
GATTCACAACTAGGTTGGCACTAAACTCATATTTCCAGTTTTCTACATATTACAGATGATTGTG
CCAGCAATTTTAACTCAAATATACATGACATATCAGTTAGCTTACTGCTGCAGATGAACTGAGC
CCTGAACTGTCAAGTCCTTTCACACCAGAAATATATCCTATAATACCCTACAAGAAGTCATCTG
TCAATATTATTTAAAGCATAAGATATTCTGGACTTTGAATTATTAAATGTAAAAGTCACCTTCT
TGAGATCATATCCAAAATTTTGCAGGGCATAAACAGCACCTCTTGCATAGCTCTCCCAGTTTAT
GTTTTCTGGGTTTTCAATGGGCTTTTGCAAGTCATCAACTCTGTTGAAGTGGTGAAACACGTAA
ACGAGTGTCGTCTAATTTAACAAAGCGAGGATTTAGTGATGGAAACACAGCTATAACAAAAAGG
GTGAACAGAACAATGAGAAATAGGTGAGGCAGCACGTCTATTGGAAAAAAAAAAAAGGCTAACA
GAGATTTGAAAAAAAAAGTGCATTTTGTCAAAGTTGCGCATGGATGAATCAGCTGGCTATGCTA
TTTGATGTTAACCAAGAACACCAAAACATGGTGCAACCGCAAACATACCTGAATCGTATCACAC
CTTCGAATTGACCAGATTGGAGTGAAATCTGTAAAACAAACCAGAGGATTACCAGTGTTATATA
TAAGCATATTTTTTTATGACAGGATGGATAATGTGAGTGAGTCAGCGTGTAGAAATTATCATTT
GAATGGAGACAATATGTTCTGATTGATGTATATTCAGAAAAGGTAGGAGAAAGAAAGGGGAAAA
GGGGCAATTAAGGGAGGATGGTATGTTATTTTGGCACAAAGAACTTAACTTGGAATTTCAGGGG
AGCATACAGATAAAAGTGTTTAAGCACAATAACTCACCTCGGCATCATCAGAGGCCACAAAACC
GAGAAGTACACCATAATTAATGGTCATAGCTGTGACAGTTCCACCCTGCCGTAATGCAGAACAG
AATAGAAGTTAGCCAACCACCATATCCCTTGCAGAGGTTCTTTTGAATTGAAGTCAACCCATGA
TATTTGTAACAATAAGGTGTTCATGGGAACACATTTCCATAAATACCCAACTAATATAGCTCTC
CTTGAAGTGAATTATTTAACATTAGAGGGTATCCAGCAATTTTTGAAATGATAAAACTAATTCA
TTACCTTAGGTAGAGTATAACCTAAGGTAGATACCGCCAACAACAGGTTAAGAACTGGTAAAAA
AAATAGTTACTGCAAGGATGTTTGTGTTGATTCTAGTCAGTTAGAGATGGTGATGATCCAATAT
ACAGAACTTTTCTCTTACTGCTGACTGATTTAATATGTTATGACCTGAAAATTTATTCCCACGA
AACTAAGTAAATTAGCAGTTTATGCAACTTCCACCCTTTTAAAGAATTACTACGTGTGCTGCTC
AGAAATAAAGAGAAATTGAATTCCACCAATATTGATGGATCTGCTTTGTAACTCAAATAAACTC
AGGTTTACAGACTTAATCCAAAGACTCTCCAAATACAAACCCAAGTGGGAGCTTTATTCTATTT
GTAGGAAAAATCACCACCACTATGCTAGTGCTAATATATTTCCAACATTTGCAGAGGAAAATTC
TTATAGCTAGGTTTATTGTCAAGTACTTAACACTCCCCCTGAAAATCATCAAGGTCTCATCAAC
TCATTCCACACATGTATAGAACAGTCCAATTATGTCACATTTATGCGGCGACGATATGACATTA
AAGCACATGCCATTTATGCTACATTGCTGCCTGACTATACACATATACAAATTTAATATAAGAA
CACATTAAAATAATTTGCAAACATACAGTTTATACAACAGTCTTAACAGTGGGTCACTCTTCTG
AAAAATGAAAACATCAAGGACATAATATCTACAAAGTTACCTGATGATCGATGTGAGCCCCCAG
AGGGCAAATCCTGTAGGGGCAAGCAACCACCCTGACCTCTCCTGCACCCCTTCCACTAATCTCC
ACTACCTTTGCTCGAACAACATCAAG
						
					

			
		

Sequences
Splice junction sequence	GAGCCCCCAGAGGGCAAATCCTGTAGGGGCAAGCAACCACCCTGACCTCTCCTGCACCCCTTCC ACTAATCTCCACTACCTTTGCTCGAACAACATCAAGcttgcagtccatgaaggtgagatagcca taccgtgagagcaaaatagctgatggatccagaataccattttcaagacccaaatatttatttt cgatggac
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	CTTGCAGTCCATGAAGGTGAGATAGCCATACCGTGAGAGCAAAATAGCTGATGGATCCAGAATA CCATTTTCAAGACCCAAATATTTATTTTCGATGGACCTGACAAATAGGGATATGAAATTAAGAA CTCTGCTAGTGACCATGACTCAATGAGCTAATAAATCTTATGTAGCAATATTTGATTGTTGCTT TAGAACATGGCAATAGTAGATAGTTGTGGGGACTTCAACATAGATACTTGAAATTAGAACTGTT CTGGATCCCATGTATGAATTCATAATGTTAGTCCACATGGAATGCTTACTAAAAGGAAACAAAC TCACTTGTCCAACTGAATGTTGTCCACTGGTGATACAACCAGATCATTCACATTTTCTAAAGCC ATCAAATAGGCAATCCCGACCTGATGAGGAGCATACAGAAATAGGCATTTGATGATCACATAAC TAACCAAAGTATCAATTATATTAATAATTCTTTTGAGAACCTAGAGTAAGAACTGGAAGTTTCT GTCCTTGTTATGGTGAGCTGAAGGTTTAGAAGATACTAGTACAAAGTTAGTAGCTTCACAAATT TGCTTTGAACTCCAAGTCAAATGTGAGCCAAGTATATGTCATGATTATGAAATACTGCATATTC GATTCACAACTAGGTTGGCACTAAACTCATATTTCCAGTTTTCTACATATTACAGATGATTGTG CCAGCAATTTTAACTCAAATATACATGACATATCAGTTAGCTTACTGCTGCAGATGAACTGAGC CCTGAACTGTCAAGTCCTTTCACACCAGAAATATATCCTATAATACCCTACAAGAAGTCATCTG TCAATATTATTTAAAGCATAAGATATTCTGGACTTTGAATTATTAAATGTAAAAGTCACCTTCT TGAGATCATATCCAAAATTTTGCAGGGCATAAACAGCACCTCTTGCATAGCTCTCCCAGTTTAT GTTTTCTGGGTTTTCAATGGGCTTTTGCAAGTCATCAACTCTGTTGAAGTGGTGAAACACGTAA ACGAGTGTCGTCTAATTTAACAAAGCGAGGATTTAGTGATGGAAACACAGCTATAACAAAAAGG GTGAACAGAACAATGAGAAATAGGTGAGGCAGCACGTCTATTGGAAAAAAAAAAAAGGCTAACA GAGATTTGAAAAAAAAAGTGCATTTTGTCAAAGTTGCGCATGGATGAATCAGCTGGCTATGCTA TTTGATGTTAACCAAGAACACCAAAACATGGTGCAACCGCAAACATACCTGAATCGTATCACAC CTTCGAATTGACCAGATTGGAGTGAAATCTGTAAAACAAACCAGAGGATTACCAGTGTTATATA TAAGCATATTTTTTTATGACAGGATGGATAATGTGAGTGAGTCAGCGTGTAGAAATTATCATTT GAATGGAGACAATATGTTCTGATTGATGTATATTCAGAAAAGGTAGGAGAAAGAAAGGGGAAAA GGGGCAATTAAGGGAGGATGGTATGTTATTTTGGCACAAAGAACTTAACTTGGAATTTCAGGGG AGCATACAGATAAAAGTGTTTAAGCACAATAACTCACCTCGGCATCATCAGAGGCCACAAAACC GAGAAGTACACCATAATTAATGGTCATAGCTGTGACAGTTCCACCCTGCCGTAATGCAGAACAG AATAGAAGTTAGCCAACCACCATATCCCTTGCAGAGGTTCTTTTGAATTGAAGTCAACCCATGA TATTTGTAACAATAAGGTGTTCATGGGAACACATTTCCATAAATACCCAACTAATATAGCTCTC CTTGAAGTGAATTATTTAACATTAGAGGGTATCCAGCAATTTTTGAAATGATAAAACTAATTCA TTACCTTAGGTAGAGTATAACCTAAGGTAGATACCGCCAACAACAGGTTAAGAACTGGTAAAAA AAATAGTTACTGCAAGGATGTTTGTGTTGATTCTAGTCAGTTAGAGATGGTGATGATCCAATAT ACAGAACTTTTCTCTTACTGCTGACTGATTTAATATGTTATGACCTGAAAATTTATTCCCACGA AACTAAGTAAATTAGCAGTTTATGCAACTTCCACCCTTTTAAAGAATTACTACGTGTGCTGCTC AGAAATAAAGAGAAATTGAATTCCACCAATATTGATGGATCTGCTTTGTAACTCAAATAAACTC AGGTTTACAGACTTAATCCAAAGACTCTCCAAATACAAACCCAAGTGGGAGCTTTATTCTATTT GTAGGAAAAATCACCACCACTATGCTAGTGCTAATATATTTCCAACATTTGCAGAGGAAAATTC TTATAGCTAGGTTTATTGTCAAGTACTTAACACTCCCCCTGAAAATCATCAAGGTCTCATCAAC TCATTCCACACATGTATAGAACAGTCCAATTATGTCACATTTATGCGGCGACGATATGACATTA AAGCACATGCCATTTATGCTACATTGCTGCCTGACTATACACATATACAAATTTAATATAAGAA CACATTAAAATAATTTGCAAACATACAGTTTATACAACAGTCTTAACAGTGGGTCACTCTTCTG AAAAATGAAAACATCAAGGACATAATATCTACAAAGTTACCTGATGATCGATGTGAGCCCCCAG AGGGCAAATCCTGTAGGGGCAAGCAACCACCCTGACCTCTCCTGCACCCCTTCCACTAATCTCC ACTACCTTTGCTCGAACAACATCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.11054907

Conservation Information
Conserved circRNAs	NA
PMCS	0.11054907

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30769297-30766725(+)
30768321-30766695(-)
30767061-30769384(-)
						
						Potential amino acid sequence
						
							MIDVSPQRANPVGASNHPDLSCTPSTNLHYLCSNNIKLAVHEGEIAIP*(+)
MTINYGVLLGFVASDDAEISLQSGQFEGVIRFRVDDLQKPIENPENINWESYARGAVYALQNFG
YDLKKGIIGYISGVKGLDSSGLSSSAAVGIAYLMALENVNDLVVSPVDNIQLDKSIENKYLGLE
NGILDPSAILLSRYGYLTFMDCKLDVVRAKVVEISGRGAGEVRVVACPYRICPLGAHIDHQGGT
VTAMTINYGVLLGFVASDDAEISLQSGQFEGVIRFRVDDLQKPIENPENINWESYARGAVYALQ
NFGYDLKKGIIGYISGVKGLDSSGLSSSAAVGIAYLMALENVNDLVVSPVDNIQLDKSIENKYL
GLENGILDPSAILLSRYGYLTFMDCKLDVVRAKVVEISGRGAGEVRVVACPYRICPLGAHIDHQ
GGTVTAMTINYGVLLGFVASDDAEISLQSGQFEGVIRFRVDDLQKPIENPENINWESYARGAVY
ALQNFGYDLKKGIIGYISGVKGLDSSGLSSSAAVGIAYLMALENVNDLVVSPVDNIQLDKSIEN
KYLGLENGILDPSAILLSRYGYLTFMDCKLDVVRAKVVEISGRGAGEVRVVACPYRICPLGAHI
DHQGGTVTAMTINYGVLLGFVASDDAEISLQSGQFEGVIRFRVDDLQKPIENPENINWESYARG
AVYALQNFGYDLKKGIIGYISGVKGLDSSGLSSSAAVGIAYLMALENVNDLVVSPVDNIQLDKS
IENKYLGLENGILDPSAILLSRYGYLTFMDCK(-)
MIWLYHQWTTFSWTSPSKINIWVLKMVFWIHQLFCSHGMAISPSWTASLMLFEQR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30769297-30766725(+) 30768321-30766695(-) 30767061-30769384(-)
Potential amino acid sequence	MIDVSPQRANPVGASNHPDLSCTPSTNLHYLCSNNIKLAVHEGEIAIP(+) MTINYGVLLGFVASDDAEISLQSGQFEGVIRFRVDDLQKPIENPENINWESYARGAVYALQNFG YDLKKGIIGYISGVKGLDSSGLSSSAAVGIAYLMALENVNDLVVSPVDNIQLDKSIENKYLGLE NGILDPSAILLSRYGYLTFMDCKLDVVRAKVVEISGRGAGEVRVVACPYRICPLGAHIDHQGGT VTAMTINYGVLLGFVASDDAEISLQSGQFEGVIRFRVDDLQKPIENPENINWESYARGAVYALQ NFGYDLKKGIIGYISGVKGLDSSGLSSSAAVGIAYLMALENVNDLVVSPVDNIQLDKSIENKYL GLENGILDPSAILLSRYGYLTFMDCKLDVVRAKVVEISGRGAGEVRVVACPYRICPLGAHIDHQ GGTVTAMTINYGVLLGFVASDDAEISLQSGQFEGVIRFRVDDLQKPIENPENINWESYARGAVY ALQNFGYDLKKGIIGYISGVKGLDSSGLSSSAAVGIAYLMALENVNDLVVSPVDNIQLDKSIEN KYLGLENGILDPSAILLSRYGYLTFMDCKLDVVRAKVVEISGRGAGEVRVVACPYRICPLGAHI DHQGGTVTAMTINYGVLLGFVASDDAEISLQSGQFEGVIRFRVDDLQKPIENPENINWESYARG AVYALQNFGYDLKKGIIGYISGVKGLDSSGLSSSAAVGIAYLMALENVNDLVVSPVDNIQLDKS IENKYLGLENGILDPSAILLSRYGYLTFMDCK(-) MIWLYHQWTTFSWTSPSKINIWVLKMVFWIHQLFCSHGMAISPSWTASLMLFEQR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015

circRNA

Detail information of Os04g0608100_circ_g.3

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