Plant Circular RNA Database

Detail information of Os04g0182650_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0182650_circ_g.2
					
						ID in PlantcircBase
						osa_circ_023035
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 5622253-5623673  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0182650						
					
						Parent gene annotation
						
							Similar to predicted protein. (Os04t0182650-00)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0182650_circ_g.3 						
					
						Support reads
						1
					
						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  
						
							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
						Os04t0182650-00:3

General Information
CircRNA Name	Os04g0182650_circ_g.2
ID in PlantcircBase	osa_circ_023035
Alias	NA
Organism	Oryza sativa
Position	chr4: 5622253-5623673 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0182650
Parent gene annotation	Similar to predicted protein. (Os04t0182650-00)
Parent gene strand	+
Alternative splicing	Os04g0182650_circ_g.3
Support reads	1
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	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	Os04t0182650-00:3

			
						 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  
						
							CAGAGTCAAGATTGGTGAGAGTGACATCACATACCGGTCAACAAATGCAATCCACAATGATGGC
TGTGCTTCTTTCCCCTTTTTGCTTTCATTGGCTGAGtggaggatctggtaatgatgatggacat
tttggagaaactggaacagtaacaggaaaaaagtgtcctgttggactatatggaacattttgca
ccgtatga

						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
						
							TGGAGGATCTGGTAATGATGATGGACATTTTGGAGAAACTGGAACAGTAACAGGAAAAAAGTGT
CCTGTTGGACTATATGGAACATTTTGCACCGTATGAGCACTTCTCTCATTGTGCCTTTATTGCT
TCATGTTCCTGTTATGATAATAACCTAATCCATAGGAAATAATATTATTATTTTAAATGTGTGT
ATTCAAGAAATTTAATCTCTTTATTTCATATAAGGCTTATATGTAAGAGGGAGAATATAGTTGT
GTCCTTCTGTCCTGTTGGTTAACCTCATGCTAGATGTGTGCAATAGGAGCCAAAATTTGGTCTC
TCCATGTGAATAGAGGAAAATTATAGGGGTTATAGAGGAGATTTTATGTCCTCTGATATCACCA
CCACTCGTAGATAAACTATTTTGAACTTGGGTTGCCACACTGGTTTCTCGCCCTTATCCAGAAA
TACCAGGATGGGGTGGTTATTTGTTCCTTATAAATAATGGTTTTTGTGGTGATGCATGGCAGCT
ACTACGTAAACTGTTTGCCCCCCAGAGGGTGCAAAACTGCAAATAACTGTGCCACTGCTATAAT
CTTAAGCAACATTTTGCCAAAATAACTACTGCTTGATGCTCAGAGTTCTTAACCAACAGTTAGT
TGAACACAGACCTCTGTTTATATTATGCTTTTAACAGTTCATAATGGCCAGGTTGATCTGTGTC
ACTTGCAAATTCAGACACGCTTTTAATTTTAACTGAACTATGTAGGATTTCATTGTGTACTCCG
GGTTTTCTATCTGTATCCATGAGCTAATAAAACATCCTATATTGATATGGTCAATACTTTGCAA
CTAGGTAGTTTCTTTTTATGTACTATTGTTTTGGTAACTAGCAAATGCTTTTTATTAGTTTGTT
CGCAACCAGTAATGATTAAATTATATTCCAGGAATGCCCAATCGGTACATACAAAAATGTTGTT
GGGTCCGATTCATCTCTGTGTATGCCTTGTTCTCTGGATAGTCTTCCTAACCGCGCTGACTTCA
TATATGTAAGAGGTAGGTCCTTGGAAAGACATGGTCTTATGTGGAACTATAATTATTTAATTGC
CTTGTAACTCCAAAATTTATGATGTTAAATTGGAGAAACTAACCATTAACTTTTTACATGCTAG
GTGGTGTTACCGAGCCGTCCTGCCCATATAAGTGCATATCTTCTAAGTACAAGATGCCAAACTG
TTACACACCACTTGAGGAACTTATTTATACTTTTGGTGGTCCTTGGTCTTTTGCAATTATCCTA
TCTTTTACCATTATTCTTTTGGCACTTGTCTTAAGTGCTCTCAGAGTCAAGATTGGTGAGAGTG
ACATCACATACCGGTCAACAAATGCAATCCACAATGATGGCTGTGCTTCTTTCCCCTTTTTGCT
TTCATTGGCTGAG

Sequences
Splice junction sequence	CAGAGTCAAGATTGGTGAGAGTGACATCACATACCGGTCAACAAATGCAATCCACAATGATGGC TGTGCTTCTTTCCCCTTTTTGCTTTCATTGGCTGAGtggaggatctggtaatgatgatggacat tttggagaaactggaacagtaacaggaaaaaagtgtcctgttggactatatggaacattttgca ccgtatga
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	TGGAGGATCTGGTAATGATGATGGACATTTTGGAGAAACTGGAACAGTAACAGGAAAAAAGTGT CCTGTTGGACTATATGGAACATTTTGCACCGTATGAGCACTTCTCTCATTGTGCCTTTATTGCT TCATGTTCCTGTTATGATAATAACCTAATCCATAGGAAATAATATTATTATTTTAAATGTGTGT ATTCAAGAAATTTAATCTCTTTATTTCATATAAGGCTTATATGTAAGAGGGAGAATATAGTTGT GTCCTTCTGTCCTGTTGGTTAACCTCATGCTAGATGTGTGCAATAGGAGCCAAAATTTGGTCTC TCCATGTGAATAGAGGAAAATTATAGGGGTTATAGAGGAGATTTTATGTCCTCTGATATCACCA CCACTCGTAGATAAACTATTTTGAACTTGGGTTGCCACACTGGTTTCTCGCCCTTATCCAGAAA TACCAGGATGGGGTGGTTATTTGTTCCTTATAAATAATGGTTTTTGTGGTGATGCATGGCAGCT ACTACGTAAACTGTTTGCCCCCCAGAGGGTGCAAAACTGCAAATAACTGTGCCACTGCTATAAT CTTAAGCAACATTTTGCCAAAATAACTACTGCTTGATGCTCAGAGTTCTTAACCAACAGTTAGT TGAACACAGACCTCTGTTTATATTATGCTTTTAACAGTTCATAATGGCCAGGTTGATCTGTGTC ACTTGCAAATTCAGACACGCTTTTAATTTTAACTGAACTATGTAGGATTTCATTGTGTACTCCG GGTTTTCTATCTGTATCCATGAGCTAATAAAACATCCTATATTGATATGGTCAATACTTTGCAA CTAGGTAGTTTCTTTTTATGTACTATTGTTTTGGTAACTAGCAAATGCTTTTTATTAGTTTGTT CGCAACCAGTAATGATTAAATTATATTCCAGGAATGCCCAATCGGTACATACAAAAATGTTGTT GGGTCCGATTCATCTCTGTGTATGCCTTGTTCTCTGGATAGTCTTCCTAACCGCGCTGACTTCA TATATGTAAGAGGTAGGTCCTTGGAAAGACATGGTCTTATGTGGAACTATAATTATTTAATTGC CTTGTAACTCCAAAATTTATGATGTTAAATTGGAGAAACTAACCATTAACTTTTTACATGCTAG GTGGTGTTACCGAGCCGTCCTGCCCATATAAGTGCATATCTTCTAAGTACAAGATGCCAAACTG TTACACACCACTTGAGGAACTTATTTATACTTTTGGTGGTCCTTGGTCTTTTGCAATTATCCTA TCTTTTACCATTATTCTTTTGGCACTTGTCTTAAGTGCTCTCAGAGTCAAGATTGGTGAGAGTG ACATCACATACCGGTCAACAAATGCAATCCACAATGATGGCTGTGCTTCTTTCCCCTTTTTGCT TTCATTGGCTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.157015898

Conservation Information
Conserved circRNAs	NA
PMCS	0.157015898

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5623235-5622264(+)
5623619-5622264(+)
5622282-5623602(-)
5623443-5623664(-)
5623227-5623495(-)
						
						Potential amino acid sequence
						
							MPCSLDSLPNRADFIYVRGGVTEPSCPYKCISSKYKMPNCYTPLEELIYTFGGPWSFAIILSFT
IILLALVLSALRVKIGESDITYRSTNAIHNDGCASFPFLLSLAEWRIW*(+)
MQSTMMAVLLSPFCFHWLSGGSGNDDGHFGETGTVTGKKCPVGLYGTFCTECPIGTYKNVVGSD
SSLCMPCSLDSLPNRADFIYVRGGVTEPSCPYKCISSKYKMPNCYTPLEELIYTFGGPWSFAII
LSFTIILLALVLSALRVKIGESDITYRSTNAIHNDGCASFPFLLSLAEWRIW*(+)
MSIIITRSSTQPMKAKRGKKHSHHCGLHLLTGM*(-)
MHLYGQDGSVTPPLTYMKSARLGRLSREQGIHRDESDPTTFLYVPIGHSVQNVPYSPTGHFFPV
TVPVSPKCPSSLPDPPLSQ*(-)
MNRTQQHFCMYRLGIRCKMFHIVQQDTFFLLLFQFLQNVHHHYQILHSANESKKGKEAQPSLWI
AFVDRYVMSLSPILTLRALKTSAKRIMVKDRIIAKDQGPPKV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5623235-5622264(+) 5623619-5622264(+) 5622282-5623602(-) 5623443-5623664(-) 5623227-5623495(-)
Potential amino acid sequence	MPCSLDSLPNRADFIYVRGGVTEPSCPYKCISSKYKMPNCYTPLEELIYTFGGPWSFAIILSFT IILLALVLSALRVKIGESDITYRSTNAIHNDGCASFPFLLSLAEWRIW(+) MQSTMMAVLLSPFCFHWLSGGSGNDDGHFGETGTVTGKKCPVGLYGTFCTECPIGTYKNVVGSD SSLCMPCSLDSLPNRADFIYVRGGVTEPSCPYKCISSKYKMPNCYTPLEELIYTFGGPWSFAII LSFTIILLALVLSALRVKIGESDITYRSTNAIHNDGCASFPFLLSLAEWRIW(+) MSIIITRSSTQPMKAKRGKKHSHHCGLHLLTGM(-) MHLYGQDGSVTPPLTYMKSARLGRLSREQGIHRDESDPTTFLYVPIGHSVQNVPYSPTGHFFPV TVPVSPKCPSSLPDPPLSQ(-) MNRTQQHFCMYRLGIRCKMFHIVQQDTFFLLLFQFLQNVHHHYQILHSANESKKGKEAQPSLWI AFVDRYVMSLSPILTLRALKTSAKRIMVKDRIIAKDQGPPKV*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0182650_circ_g.2

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