Plant Circular RNA Database

Detail information of Os05g0595300_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os05g0595300_circ_g.3
					
						ID in PlantcircBase
						osa_circ_029240
					
						Alias
						Os_ciR4884
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 29658392-29659572  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os05g0595300						
					
						Parent gene annotation
						
							NRR alternative splicing variant, Regulation of root development
 in response to macronutrient deficiency (Os05t0595300-01);CCT d
omain-containing protein, Regulator of starch synthesis, Regulat
ion of root development in response to macronutrient deficiency 
(Os05t0595300-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os05g0595300_circ_ag.1 Os05g0595300_circ_g.2 Os05g0595300_circ_ag.4 Os05g0595300_circ_g.5 Os05g0595450_circ_g.1 						
					
						Support reads
						4/1
					
						Tissues
						root/shoot, 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
						Os05t0595300-02:2
Os05t0595300-01:1

General Information
CircRNA Name	Os05g0595300_circ_g.3
ID in PlantcircBase	osa_circ_029240
Alias	Os_ciR4884
Organism	Oryza sativa
Position	chr5: 29658392-29659572 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os05g0595300
Parent gene annotation	NRR alternative splicing variant, Regulation of root development in response to macronutrient deficiency (Os05t0595300-01);CCT d omain-containing protein, Regulator of starch synthesis, Regulat ion of root development in response to macronutrient deficiency (Os05t0595300-02)
Parent gene strand	+
Alternative splicing	Os05g0595300_circ_ag.1 Os05g0595300_circ_g.2 Os05g0595300_circ_ag.4 Os05g0595300_circ_g.5 Os05g0595450_circ_g.1
Support reads	4/1
Tissues	root/shoot, 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	Os05t0595300-02:2 Os05t0595300-01:1

			
						 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  
						
							GCTTGTAACCATCAGTGACCTGAAATCTGAAGAAAGGAAGCAGAAGCTATCTAGGTACAGAAAG
AAGAAGGTGAAGAGAAACTTTGGCAGAAAGATCAAGggaaacatggcacaaccatcctttctat
cagagtatgaccttggaggggaaggggacctgttcaaagctcctgaacccatcattgaagaacc
agtgctta

									
								

					

						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: 699
Transcript exons: 29658392-29658925,29659408-29659572
GGAAACATGGCACAACCATCCTTTCTATCAGAGTATGACCTTGGAGGGGAAGGGGACCTGTTCA
AAGCTCCTGAACCCATCATTGAAGAACCAGTGCTTAGCCTTGATCCAGTTGCAGCAGCCATTTC
GATGATGTCTGGCAGTGAGAACGTAATGGATGAAACTATAGAGGTTGCAGATATCAGCGACATT
CAGAATGACTCTCTTTTAAGCGAAGTATTATACGAGTGCGAGAAGGAACTCATGGAGAAGTCCG
CAATCGAAGAGACTATTTCTGAACTGCTGGACGTCAAGATTCCTATGCTGCAAGTGGAAGAGTT
CCCTAGGGAAACCCAAGTACAACTACCGGCCATGGAGAAGGAGAAGCCATCAGTTCCTGAATGT
TGTTCACTCCAGAAAAGTGTCAGTTCTGGGTGCCTCAACTCAGCTGATTGGATCAATGGACCAG
CCAGGCCAAACTTCCTGGACTTCCAAGGATTGGACTTTGAGACAGCGTTTGGGTTGAGGAGGGC
ATACAGCGAAGGAGACATTCAGAATCTTGGAGCTAGCACCCCTCGACCCGGGAACTCAGGAAAC
GCTCAATTAGCATCTTGCGAGAGGCTTGTAACCATCAGTGACCTGAAATCTGAAGAAAGGAAGC
AGAAGCTATCTAGGTACAGAAAGAAGAAGGTGAAGAGAAACTTTGGCAGAAAGATCAAG
						
					

						Genomic sequence
						
							GGAAACATGGCACAACCATCCTTTCTATCAGAGTATGACCTTGGAGGGGAAGGGGACCTGTTCA
AAGCTCCTGAACCCATCATTGAAGAACCAGTGCTTAGCCTTGATCCAGTTGCAGCAGCCATTTC
GATGATGTCTGGCAGTGAGAACGTAATGGATGAAACTATAGAGGTTGCAGATATCAGCGACATT
CAGAATGACTCTCTTTTAAGCGAAGTATTATACGAGTGCGAGAAGGAACTCATGGAGAAGTCCG
CAATCGAAGAGACTATTTCTGAACTGCTGGACGTCAAGATTCCTATGCTGCAAGTGGAAGAGTT
CCCTAGGGAAACCCAAGTACAACTACCGGCCATGGAGAAGGAGAAGCCATCAGTTCCTGAATGT
TGTTCACTCCAGAAAAGTGTCAGTTCTGGGTGCCTCAACTCAGCTGATTGGATCAATGGACCAG
CCAGGCCAAACTTCCTGGACTTCCAAGGATTGGACTTTGAGACAGCGTTTGGGTTGAGGAGGGC
ATACAGCGAAGGAGACATTCAGGTTTGATCATTTTTCTCTTGCGGTTATGTTATGTACTTACTA
CTGTATATAGGTAAGGTAGTGATAGATAAGGAATCGTTGTGAGCAAGCAACGGCTGTGTATTGT
AAAGTGTGTTTCCGAAACACAGGTGTCGAGAAAAGAAATCACCTTTGCCCTTGTATGTATATGT
GCGTGGTGCTTCTTTACTCAAATTAAAGGCCATCAAAGCTATGACACTGATTTTACTATTTCTG
CCCAAAGTAGGCCTTTTCCTTGTGGTTTTAATTTTCTTTCAAGATACTTTTACATGCAAGCTCC
TGCATACAAAGTTGGTTTCTAAGAGACTACCTAGGTGCCAAAGCGTACGTGTATATCCTATGGT
TTTTTGTTTTTATATACTGTATTATTTTAGAAAGGCCGTGAGATTGTTCGAGTAAACATTTGCA
GACCCTGCTAGGTTGTTGAAGAATTGTACTTACGATGCTAGTTGTCTTTCCAACAGAATCTTGG
AGCTAGCACCCCTCGACCCGGGAACTCAGGAAACGCTCAATTAGCATCTTGCGAGAGGCTTGTA
ACCATCAGTGACCTGAAATCTGAAGAAAGGAAGCAGAAGCTATCTAGGTACAGAAAGAAGAAGG
TGAAGAGAAACTTTGGCAGAAAGATCAAG
						
					

			
		

Sequences
Splice junction sequence	GCTTGTAACCATCAGTGACCTGAAATCTGAAGAAAGGAAGCAGAAGCTATCTAGGTACAGAAAG AAGAAGGTGAAGAGAAACTTTGGCAGAAAGATCAAGggaaacatggcacaaccatcctttctat cagagtatgaccttggaggggaaggggacctgttcaaagctcctgaacccatcattgaagaacc agtgctta
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: 699 Transcript exons: 29658392-29658925,29659408-29659572 GGAAACATGGCACAACCATCCTTTCTATCAGAGTATGACCTTGGAGGGGAAGGGGACCTGTTCA AAGCTCCTGAACCCATCATTGAAGAACCAGTGCTTAGCCTTGATCCAGTTGCAGCAGCCATTTC GATGATGTCTGGCAGTGAGAACGTAATGGATGAAACTATAGAGGTTGCAGATATCAGCGACATT CAGAATGACTCTCTTTTAAGCGAAGTATTATACGAGTGCGAGAAGGAACTCATGGAGAAGTCCG CAATCGAAGAGACTATTTCTGAACTGCTGGACGTCAAGATTCCTATGCTGCAAGTGGAAGAGTT CCCTAGGGAAACCCAAGTACAACTACCGGCCATGGAGAAGGAGAAGCCATCAGTTCCTGAATGT TGTTCACTCCAGAAAAGTGTCAGTTCTGGGTGCCTCAACTCAGCTGATTGGATCAATGGACCAG CCAGGCCAAACTTCCTGGACTTCCAAGGATTGGACTTTGAGACAGCGTTTGGGTTGAGGAGGGC ATACAGCGAAGGAGACATTCAGAATCTTGGAGCTAGCACCCCTCGACCCGGGAACTCAGGAAAC GCTCAATTAGCATCTTGCGAGAGGCTTGTAACCATCAGTGACCTGAAATCTGAAGAAAGGAAGC AGAAGCTATCTAGGTACAGAAAGAAGAAGGTGAAGAGAAACTTTGGCAGAAAGATCAAG
Genomic sequence	GGAAACATGGCACAACCATCCTTTCTATCAGAGTATGACCTTGGAGGGGAAGGGGACCTGTTCA AAGCTCCTGAACCCATCATTGAAGAACCAGTGCTTAGCCTTGATCCAGTTGCAGCAGCCATTTC GATGATGTCTGGCAGTGAGAACGTAATGGATGAAACTATAGAGGTTGCAGATATCAGCGACATT CAGAATGACTCTCTTTTAAGCGAAGTATTATACGAGTGCGAGAAGGAACTCATGGAGAAGTCCG CAATCGAAGAGACTATTTCTGAACTGCTGGACGTCAAGATTCCTATGCTGCAAGTGGAAGAGTT CCCTAGGGAAACCCAAGTACAACTACCGGCCATGGAGAAGGAGAAGCCATCAGTTCCTGAATGT TGTTCACTCCAGAAAAGTGTCAGTTCTGGGTGCCTCAACTCAGCTGATTGGATCAATGGACCAG CCAGGCCAAACTTCCTGGACTTCCAAGGATTGGACTTTGAGACAGCGTTTGGGTTGAGGAGGGC ATACAGCGAAGGAGACATTCAGGTTTGATCATTTTTCTCTTGCGGTTATGTTATGTACTTACTA CTGTATATAGGTAAGGTAGTGATAGATAAGGAATCGTTGTGAGCAAGCAACGGCTGTGTATTGT AAAGTGTGTTTCCGAAACACAGGTGTCGAGAAAAGAAATCACCTTTGCCCTTGTATGTATATGT GCGTGGTGCTTCTTTACTCAAATTAAAGGCCATCAAAGCTATGACACTGATTTTACTATTTCTG CCCAAAGTAGGCCTTTTCCTTGTGGTTTTAATTTTCTTTCAAGATACTTTTACATGCAAGCTCC TGCATACAAAGTTGGTTTCTAAGAGACTACCTAGGTGCCAAAGCGTACGTGTATATCCTATGGT TTTTTGTTTTTATATACTGTATTATTTTAGAAAGGCCGTGAGATTGTTCGAGTAAACATTTGCA GACCCTGCTAGGTTGTTGAAGAATTGTACTTACGATGCTAGTTGTCTTTCCAACAGAATCTTGG AGCTAGCACCCCTCGACCCGGGAACTCAGGAAACGCTCAATTAGCATCTTGCGAGAGGCTTGTA ACCATCAGTGACCTGAAATCTGAAGAAAGGAAGCAGAAGCTATCTAGGTACAGAAAGAAGAAGG TGAAGAGAAACTTTGGCAGAAAGATCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.475515424

Conservation Information
Conserved circRNAs	NA
PMCS	0.475515424

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							29658399-29659569(+)
29658584-29659454(-)
						
						Potential amino acid sequence
						
							MAQPSFLSEYDLGGEGDLFKAPEPIIEEPVLSLDPVAAAISMMSGSENVMDETIEVADISDIQN
DSLLSEVLYECEKELMEKSAIEETISELLDVKIPMLQVEEFPRETQVQLPAMEKEKPSVPECCS
LQKSVSSGCLNSADWINGPARPNFLDFQGLDFETAFGLRRAYSEGDIQNLGASTPRPGNSGNAQ
LASCERLVTISDLKSEERKQKLSRYRKKKVKRNFGRKIKGNMAQPSFLSEYDLGGEGDLFKAPE
PIIEEPVLSLDPVAAAISMMSGSENVMDETIEVADISDIQNDSLLSEVLYECEKELMEKSAIEE
TISELLDVKIPMLQVEEFPRETQVQLPAMEKEKPSVPECCSLQKSVSSGCLNSADWINGPARPN
FLDFQGLDFETAFGLRRAYSEGDIQNLGASTPRPGNSGNAQLASCERLVTISDLKSEERKQKLS
RYRKKKVKRNFGRKIKGNMAQPSFLSEYDLGGEGDLFKAPEPIIEEPVLSLDPVAAAISMMSGS
ENVMDETIEVADISDIQNDSLLSEVLYECEKELMEKSAIEETISELLDVKIPMLQVEEFPRETQ
VQLPAMEKEKPSVPECCSLQKSVSSGCLNSADWINGPARPNFLDFQGLDFETAFGLRRAYSEGD
IQNLGASTPRPGNSGNAQLASCERLVTISDLKSEERKQKLSRYRKKKVKRNFGRKIKGNMAQPS
FLSEYDLGGEGDLFKAPEPIIEEPVLSLDPVAAAISMMSGSENVMDETIEVADISDIQNDSLLS
EVLYECEKELMEKSAIEETISELLDVKIPMLQVEEFPRETQVQLPAMEKEKPSVPECCSLQKSV
SSGCLNSADWINGPARPNFLDFQGLDFETAFGLRRAYSEGDIQNLGASTPRPGNSGNAQLASCE
RLVTISDLKSEERKQKLSRYRKKKVKRNFGRKIK(+)
MSLISATSIVSSITFSLPDIIEMAAATGSRLSTGSSMMGSGALNRSPSPPRSYSDRKDGCAMFP
LIFLPKFLFTFFFLYLDSFCFLSSDFRSLMVTSLSQDAN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	29658399-29659569(+) 29658584-29659454(-)
Potential amino acid sequence	MAQPSFLSEYDLGGEGDLFKAPEPIIEEPVLSLDPVAAAISMMSGSENVMDETIEVADISDIQN DSLLSEVLYECEKELMEKSAIEETISELLDVKIPMLQVEEFPRETQVQLPAMEKEKPSVPECCS LQKSVSSGCLNSADWINGPARPNFLDFQGLDFETAFGLRRAYSEGDIQNLGASTPRPGNSGNAQ LASCERLVTISDLKSEERKQKLSRYRKKKVKRNFGRKIKGNMAQPSFLSEYDLGGEGDLFKAPE PIIEEPVLSLDPVAAAISMMSGSENVMDETIEVADISDIQNDSLLSEVLYECEKELMEKSAIEE TISELLDVKIPMLQVEEFPRETQVQLPAMEKEKPSVPECCSLQKSVSSGCLNSADWINGPARPN FLDFQGLDFETAFGLRRAYSEGDIQNLGASTPRPGNSGNAQLASCERLVTISDLKSEERKQKLS RYRKKKVKRNFGRKIKGNMAQPSFLSEYDLGGEGDLFKAPEPIIEEPVLSLDPVAAAISMMSGS ENVMDETIEVADISDIQNDSLLSEVLYECEKELMEKSAIEETISELLDVKIPMLQVEEFPRETQ VQLPAMEKEKPSVPECCSLQKSVSSGCLNSADWINGPARPNFLDFQGLDFETAFGLRRAYSEGD IQNLGASTPRPGNSGNAQLASCERLVTISDLKSEERKQKLSRYRKKKVKRNFGRKIKGNMAQPS FLSEYDLGGEGDLFKAPEPIIEEPVLSLDPVAAAISMMSGSENVMDETIEVADISDIQNDSLLS EVLYECEKELMEKSAIEETISELLDVKIPMLQVEEFPRETQVQLPAMEKEKPSVPECCSLQKSV SSGCLNSADWINGPARPNFLDFQGLDFETAFGLRRAYSEGDIQNLGASTPRPGNSGNAQLASCE RLVTISDLKSEERKQKLSRYRKKKVKRNFGRKIK(+) MSLISATSIVSSITFSLPDIIEMAAATGSRLSTGSSMMGSGALNRSPSPPRSYSDRKDGCAMFP LIFLPKFLFTFFFLYLDSFCFLSSDFRSLMVTSLSQDAN*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os05g0595300_circ_g.3

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