Plant Circular RNA Database

Detail information of Os04g0499300_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0499300_circ_g.1
					
						ID in PlantcircBase
						osa_circ_024435
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 24948249-24949326  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0499500						
					
						Parent gene annotation
						
							Hypothetical protein. (Os04t0499500-00)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0499300_circ_g.2 Os04g0499300_circ_g.3 Os04g0499300_circ_g.4 Os04g0499300_circ_g.5 Os04g0499300_circ_g.6 Os04g0499300_circ_g.7 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os04t0499300-02:2
Os04t0499300-01:4
Os04t0499500-00:4
Os04t0499300-02:2
Os04t0499300-01:4

General Information
CircRNA Name	Os04g0499300_circ_g.1
ID in PlantcircBase	osa_circ_024435
Alias	NA
Organism	Oryza sativa
Position	chr4: 24948249-24949326 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0499500
Parent gene annotation	Hypothetical protein. (Os04t0499500-00)
Parent gene strand	+
Alternative splicing	Os04g0499300_circ_g.2 Os04g0499300_circ_g.3 Os04g0499300_circ_g.4 Os04g0499300_circ_g.5 Os04g0499300_circ_g.6 Os04g0499300_circ_g.7
Support reads	1
Tissues	shoot
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	Os04t0499300-02:2 Os04t0499300-01:4 Os04t0499500-00:4 Os04t0499300-02:2 Os04t0499300-01:4

			
						 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  
						
							ACCCTTTCACTGTTTTCAGGACTCTATCTTTCTCTGAGAGATTGCCTCTTCTAGCTGACCAAGG
TACCTCAGCCTTGATAAGAGCAGGAGTCGGGCCAACctcttcacgtcgaggcacccaattgttt
gaacgaagatcaaccacatcacgaaccataaacctcagacgtggtgccaactgaaggtttgttg
ttaactcc

						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
						
							CTCTTCACGTCGAGGCACCCAATTGTTTGAACGAAGATCAACCACATCACGAACCATAAACCTC
AGACGTGGTGCCAACTGAAGGTTTGTTGTTAACTCCTTCATCTGAATGAAGTAGGTATCATTAA
TTCGACGAGATTTTGGGTTCTCGTCAAGCTGTTTACCAATTGTATTGAAGAACTGACAAATAGC
CTCAACGTTTTCCTCTTCAGGGCAAGCCTTTTTATCAGGTCCAGACCCCAAGAGTTCCTGCATA
TAGAACAGATTAGACAAGCTACCCCTGAATAATAATAACTTTATTACCAATTTGCTAATGCATA
CCTGAACAATGTGATGAACTATCTTTTCAGGTACCATCTTTTGCTTAAGTAGCTCACCAATTAG
ACGGATATTTCCAAGTGTTCTTAGTTTGACAATCCTTTCTTTGTCCCTTCTCTCCATCTCTTGG
TCAGGGCCAGTCAATTTTGCTATTTCAGCCCTTAGGCTCTCAGCACCTTCAAATGCTTCCTGAC
AATTGTTCAACAGCACACGCTTGAATGTAATCTCTTTGCCACCTGGTTCTTCCGAAGGGAATGA
TGGTAGCTTCTCATTGAGATCGGAACAAAGTTGAGCATACATCGGACAGAAGGTGGGCTCAAAA
ACAGCCTTCTCAAATATGAGAGAAATAACATCCTGAATCAAAAGCAGAAGATATATTAATCACA
AGGAGGCTAGCAAAAAATAGAAAGCTACAGAAAAGAGATCTAAAATCATCCAACCTTTAGAATA
TCAGCAGTGGTAATTCCAGATTCCATTAGTTGGCCCTTGAGTAGATCAAATTTCTCCGGTGTCA
GTTTGTTTAGTATACTGCATACGCACAAGAAAAACAGGCAGCAAGTCAATGCCAGAAAACTGTG
TTATAAAGAAATAAAGAAATAAAGAAATAAAAGCACTCAAAAAGGAACAAAAACATGAAAAAGA
CTGAACGATAATTATGATACCCTTTCACTGTTTTCAGGACTCTATCTTTCTCTGAGAGATTGCC
TCTTCTAGCTGACCAAGGTACCTCAGCCTTGATAAGAGCAGGAGTCGGGCCAAC

Sequences
Splice junction sequence	ACCCTTTCACTGTTTTCAGGACTCTATCTTTCTCTGAGAGATTGCCTCTTCTAGCTGACCAAGG TACCTCAGCCTTGATAAGAGCAGGAGTCGGGCCAACctcttcacgtcgaggcacccaattgttt gaacgaagatcaaccacatcacgaaccataaacctcagacgtggtgccaactgaaggtttgttg ttaactcc
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	CTCTTCACGTCGAGGCACCCAATTGTTTGAACGAAGATCAACCACATCACGAACCATAAACCTC AGACGTGGTGCCAACTGAAGGTTTGTTGTTAACTCCTTCATCTGAATGAAGTAGGTATCATTAA TTCGACGAGATTTTGGGTTCTCGTCAAGCTGTTTACCAATTGTATTGAAGAACTGACAAATAGC CTCAACGTTTTCCTCTTCAGGGCAAGCCTTTTTATCAGGTCCAGACCCCAAGAGTTCCTGCATA TAGAACAGATTAGACAAGCTACCCCTGAATAATAATAACTTTATTACCAATTTGCTAATGCATA CCTGAACAATGTGATGAACTATCTTTTCAGGTACCATCTTTTGCTTAAGTAGCTCACCAATTAG ACGGATATTTCCAAGTGTTCTTAGTTTGACAATCCTTTCTTTGTCCCTTCTCTCCATCTCTTGG TCAGGGCCAGTCAATTTTGCTATTTCAGCCCTTAGGCTCTCAGCACCTTCAAATGCTTCCTGAC AATTGTTCAACAGCACACGCTTGAATGTAATCTCTTTGCCACCTGGTTCTTCCGAAGGGAATGA TGGTAGCTTCTCATTGAGATCGGAACAAAGTTGAGCATACATCGGACAGAAGGTGGGCTCAAAA ACAGCCTTCTCAAATATGAGAGAAATAACATCCTGAATCAAAAGCAGAAGATATATTAATCACA AGGAGGCTAGCAAAAAATAGAAAGCTACAGAAAAGAGATCTAAAATCATCCAACCTTTAGAATA TCAGCAGTGGTAATTCCAGATTCCATTAGTTGGCCCTTGAGTAGATCAAATTTCTCCGGTGTCA GTTTGTTTAGTATACTGCATACGCACAAGAAAAACAGGCAGCAAGTCAATGCCAGAAAACTGTG TTATAAAGAAATAAAGAAATAAAGAAATAAAAGCACTCAAAAAGGAACAAAAACATGAAAAAGA CTGAACGATAATTATGATACCCTTTCACTGTTTTCAGGACTCTATCTTTCTCTGAGAGATTGCC TCTTCTAGCTGACCAAGGTACCTCAGCCTTGATAAGAGCAGGAGTCGGGCCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.427014069

Conservation Information
Conserved circRNAs	NA
PMCS	0.427014069

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24948905-24948327(+)
24949044-24948251(-)
24948297-24949244(-)
						
						Potential amino acid sequence
						
							MREITSFRISAVVIPDSISWPLSRSNFSGVSLFSIPFTVFRTLSFSERLPLLADQGTSALIRAG
VGPTSSRRGTQLFERRSTTSRTINLRRGAN*(+)
MESGITTADILKDVISLIFEKAVFEPTFCPMYAQLCSDLNEKLPSFPSEEPGGKEITFKRVLLN
NCQEAFEGAESLRAEIAKLTGPDQEMERRDKERIVKLRTLGNIRLIGELLKQKMVPEKIVHHIV
QELLGSGPDKKACPEEENVEAICQFFNTIGKQLDENPKSRRINDTYFIQMKELTTNLQLAPRLR
FMVRDVVDLRSNNWVPRREEVGPTPALIKAEVPWSARRGNLSEKDRVLKTVKGILNKLTPEKFD
LLKGQLMESGITTADILKDVISLIFEKAVFEPTFCPMYAQLCSDLNEKLPSFPSEEPGGKEITF
KRVLLNNCQEAFEGAESLRAEIAKLTGPDQEMERRDKERIVKLRTLGNIRLIGELLKQKMVPEK
IVHHIVQELLGSGPDKKACPEEENVEAICQFFNTIGKQLDENPKSRRINDTYFIQMKELTTNLQ
LAPRLRFMVRDVVDLRSNNWVPRREEVGPTPALIKAEVPWSARRGNLSEKDRVLKTVKGILNKL
TPEKFDLLKGQLMESGITTADILKDVISLIFEKAVFEPTFCPMYAQLCSDLNEKLPSFPSEEPG
GKEITFKRVLLNNCQEAFEGAESLRAEIAKLTGPDQEMERRDKERIVKLRTLGNIRLIGELLKQ
KMVPEKIVHHIVQELLGSGPDKKACPEEENVEAICQFFNTIGKQLDENPKSRRINDTYFIQMKE
LTTNLQLAPRLRFMVRDVVDLRSNNWVPRREEVGPTPALIKAEVPWSARRGNLSEKDRVLKTVK
GILNKLTPEKFDLLKGQLMESGITTADILKDVISLIFEKAVFEPTFCPMYAQLCSDLNEKLPSF
PSEEPGGKEITFKRVLLNNCQEAFEGAESLRAEIAKLTGPDQEMERRDKERIVKLRTLGNIRLI
GELLKQKMVPEKIVHHIVQELLGSGPDKKACPEEENVEAICQFFNTIGKQLDENPKSRRINDTY
FIQMKELTTNLQLAPRLRFMVRDVVDLRSNNWVPRREE(-)
MWLIFVQTIGCLDVKRLARLLLLSRLRYLGQLEEAISQRKIES*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24948905-24948327(+) 24949044-24948251(-) 24948297-24949244(-)
Potential amino acid sequence	MREITSFRISAVVIPDSISWPLSRSNFSGVSLFSIPFTVFRTLSFSERLPLLADQGTSALIRAG VGPTSSRRGTQLFERRSTTSRTINLRRGAN(+) MESGITTADILKDVISLIFEKAVFEPTFCPMYAQLCSDLNEKLPSFPSEEPGGKEITFKRVLLN NCQEAFEGAESLRAEIAKLTGPDQEMERRDKERIVKLRTLGNIRLIGELLKQKMVPEKIVHHIV QELLGSGPDKKACPEEENVEAICQFFNTIGKQLDENPKSRRINDTYFIQMKELTTNLQLAPRLR FMVRDVVDLRSNNWVPRREEVGPTPALIKAEVPWSARRGNLSEKDRVLKTVKGILNKLTPEKFD LLKGQLMESGITTADILKDVISLIFEKAVFEPTFCPMYAQLCSDLNEKLPSFPSEEPGGKEITF KRVLLNNCQEAFEGAESLRAEIAKLTGPDQEMERRDKERIVKLRTLGNIRLIGELLKQKMVPEK IVHHIVQELLGSGPDKKACPEEENVEAICQFFNTIGKQLDENPKSRRINDTYFIQMKELTTNLQ LAPRLRFMVRDVVDLRSNNWVPRREEVGPTPALIKAEVPWSARRGNLSEKDRVLKTVKGILNKL TPEKFDLLKGQLMESGITTADILKDVISLIFEKAVFEPTFCPMYAQLCSDLNEKLPSFPSEEPG GKEITFKRVLLNNCQEAFEGAESLRAEIAKLTGPDQEMERRDKERIVKLRTLGNIRLIGELLKQ KMVPEKIVHHIVQELLGSGPDKKACPEEENVEAICQFFNTIGKQLDENPKSRRINDTYFIQMKE LTTNLQLAPRLRFMVRDVVDLRSNNWVPRREEVGPTPALIKAEVPWSARRGNLSEKDRVLKTVK GILNKLTPEKFDLLKGQLMESGITTADILKDVISLIFEKAVFEPTFCPMYAQLCSDLNEKLPSF PSEEPGGKEITFKRVLLNNCQEAFEGAESLRAEIAKLTGPDQEMERRDKERIVKLRTLGNIRLI GELLKQKMVPEKIVHHIVQELLGSGPDKKACPEEENVEAICQFFNTIGKQLDENPKSRRINDTY FIQMKELTTNLQLAPRLRFMVRDVVDLRSNNWVPRREE(-) MWLIFVQTIGCLDVKRLARLLLLSRLRYLGQLEEAISQRKIES(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0499300_circ_g.1

Address

Any questions?

Supported by