Plant Circular RNA Database

Detail information of Os01g0503400_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0503400_circ_g.4
					
						ID in PlantcircBase
						osa_circ_001851
					
						Alias
						Os_ciR4453
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 17457590-17458770  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os01g0503400						
					
						Parent gene annotation
						
							Similar to (Rice Genome Annotation Project) metal transporter Nr
amp6. (Os01t0503400-01);Similar to cDNA clone:J013164K10, full i
nsert sequence. (Os01t0503400-02);Similar to OsNramp1 (Integral 
membrane protein). (Os01t0503400-03);Similar to (Rice Genome Ann
otation Project) metal transporter Nramp6. (Os01t0503400-04);Sim
ilar to cDNA clone:J013164K10, full insert sequence. (Os01t05034
00-05)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0503400_circ_g.1 Os01g0503400_circ_g.2 Os01g0503400_circ_g.3 Os01g0503400_circ_g.5 						
					
						Support reads
						4
					
						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  
						
							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
						Os01t0503400-05:3
Os01t0503400-01:3
Os01t0503400-03:3

General Information
CircRNA Name	Os01g0503400_circ_g.4
ID in PlantcircBase	osa_circ_001851
Alias	Os_ciR4453
Organism	Oryza sativa
Position	chr1: 17457590-17458770 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Os01g0503400
Parent gene annotation	Similar to (Rice Genome Annotation Project) metal transporter Nr amp6. (Os01t0503400-01);Similar to cDNA clone:J013164K10, full i nsert sequence. (Os01t0503400-02);Similar to OsNramp1 (Integral membrane protein). (Os01t0503400-03);Similar to (Rice Genome Ann otation Project) metal transporter Nramp6. (Os01t0503400-04);Sim ilar to cDNA clone:J013164K10, full insert sequence. (Os01t05034 00-05)
Parent gene strand	-
Alternative splicing	Os01g0503400_circ_g.1 Os01g0503400_circ_g.2 Os01g0503400_circ_g.3 Os01g0503400_circ_g.5
Support reads	4
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	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	Os01t0503400-05:3 Os01t0503400-01:3 Os01t0503400-03:3

			
						 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  
						
							TTACCCCACCAGCAGGAGGATTAACTTTGCCAAGTTCCATAAAAAAGCAAGTAGCCATCACCAA
CATAAGAACTGATATAGTGAACTCCATTTTCCGAGCcttgagtagtacataagttgaattcaat
gttagactgctgcacgtgcttgtgtcggcaaatgagagattgttggcacatatagtaccagata
ttgataca

									
								

					

						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: 423
Transcript exons: 17457590-17457760,17458200-17458269,17458589-17458770
CTTGAGTAGTACATAAGTTGAATTCAATGTTAGACTGCTGCACGTGCTTGTGTCGGCAAATGAG
AGATTGTTGGCACATATAGTACCAGATATTGATACAATAGCGACATTTACAAGTAGTGCAATGA
ACAGAGCTAATGCATTCTCAAGCAAGAAGAATGTAGAAGCATCCTTGCGTCCTTTGGAAGTATA
TGGCATTTTTCTCGTTAGCACCAAAGAAGAATGTAGGAAGAGATTATGCGGAACAACAAGAGAA
CCAAACATAGCAACCGCATCTGAAGTAGAATAATCCCCTTTGGGCCTTGGGATAAAAAGCCCCT
CAATTACCCCACCAGCAGGAGGATTAACTTTGCCAAGTTCCATAAAAAAGCAAGTAGCCATCAC
CAACATAAGAACTGATATAGTGAACTCCATTTTCCGAGC
						
					

						Genomic sequence
						
							CTTGAGTAGTACATAAGTTGAATTCAATGTTAGACTGCTGCACGTGCTTGTGTCGGCAAATGAG
AGATTGTTGGCACATATAGTACCAGATATTGATACAATAGCGACATTTACAAGTAGTGCAATGA
ACAGAGCTAATGCATTCTCAAGCAAGAAGAATGTAGAAGCATCCTGCAAGAAAGTGAATTCAAA
TTATATTACGAAGAAATAATGACTGTTTGAACAGAAATATAAAGAGCTAGAAAAAGGGAAAAAA
AAACCTCCTTTTGAGGATTGTCATAGACTTTCTATAGAATACTGAAATACTGAAATTATTAGGT
AGAGTTCATTGTACTTAAAAATAGAGTTTTTCATGTTATATATGCTTATTCATTCATGGTTGAA
ATTCCTCAATAATAACATGAAAGTAAACGAAAACTTTTGTTCAAATATGCTATGTCTCATACGA
AAATGAATAATCTAGAGGTACTGGTATAGAATTATAGCCCATATACTAAGGGGCACTGGACAGA
CAAAATCAACATCAGTTTAGAGAAAAAAGTAAAAAGAAGTAGCCTATTCCAGAGGTTAAAAATT
AATTTTAATTTTAACATAAAAAATATCCTTTTACCTTGCGTCCTTTGGAAGTATATGGCATTTT
TCTCGTTAGCACCAAAGAAGAATGTAGGAAGAGATTATGCCTAATGTTATAAAAGAACAGAGCA
AGTTAGTGAAATATACCTTTTGCTTTACATCTGACGGGGTAGCCACAATAATACCTTTTAAAGA
GTGTGAAAGACCTTTCAAAGGTTTTTTTTTTATATAACAGATATATAACTTTTAAATTAGTAAA
ACCTGAATTATAATCGTTAACTAATTGAAAAAAAAATGAAAATAATGATGTACAACTAAAAAGT
AGTGGCAATGAAAAAGAAAATTCATTTGAATTTTCAGAGACAAAAGTATAATCATAGTTCTAAG
ATAATCATTAAAATCATTTAATGTGGGAGTGATACTTACGGAACAACAAGAGAACCAAACATAG
CAACCGCATCTGAAGTAGAATAATCCCCTTTGGGCCTTGGGATAAAAAGCCCCTCAATTACCCC
ACCAGCAGGAGGATTAACTTTGCCAAGTTCCATAAAAAAGCAAGTAGCCATCACCAACATAAGA
ACTGATATAGTGAACTCCATTTTCCGAGC
						
					

			
		

Sequences
Splice junction sequence	TTACCCCACCAGCAGGAGGATTAACTTTGCCAAGTTCCATAAAAAAGCAAGTAGCCATCACCAA CATAAGAACTGATATAGTGAACTCCATTTTCCGAGCcttgagtagtacataagttgaattcaat gttagactgctgcacgtgcttgtgtcggcaaatgagagattgttggcacatatagtaccagata ttgataca
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: 423 Transcript exons: 17457590-17457760,17458200-17458269,17458589-17458770 CTTGAGTAGTACATAAGTTGAATTCAATGTTAGACTGCTGCACGTGCTTGTGTCGGCAAATGAG AGATTGTTGGCACATATAGTACCAGATATTGATACAATAGCGACATTTACAAGTAGTGCAATGA ACAGAGCTAATGCATTCTCAAGCAAGAAGAATGTAGAAGCATCCTTGCGTCCTTTGGAAGTATA TGGCATTTTTCTCGTTAGCACCAAAGAAGAATGTAGGAAGAGATTATGCGGAACAACAAGAGAA CCAAACATAGCAACCGCATCTGAAGTAGAATAATCCCCTTTGGGCCTTGGGATAAAAAGCCCCT CAATTACCCCACCAGCAGGAGGATTAACTTTGCCAAGTTCCATAAAAAAGCAAGTAGCCATCAC CAACATAAGAACTGATATAGTGAACTCCATTTTCCGAGC
Genomic sequence	CTTGAGTAGTACATAAGTTGAATTCAATGTTAGACTGCTGCACGTGCTTGTGTCGGCAAATGAG AGATTGTTGGCACATATAGTACCAGATATTGATACAATAGCGACATTTACAAGTAGTGCAATGA ACAGAGCTAATGCATTCTCAAGCAAGAAGAATGTAGAAGCATCCTGCAAGAAAGTGAATTCAAA TTATATTACGAAGAAATAATGACTGTTTGAACAGAAATATAAAGAGCTAGAAAAAGGGAAAAAA AAACCTCCTTTTGAGGATTGTCATAGACTTTCTATAGAATACTGAAATACTGAAATTATTAGGT AGAGTTCATTGTACTTAAAAATAGAGTTTTTCATGTTATATATGCTTATTCATTCATGGTTGAA ATTCCTCAATAATAACATGAAAGTAAACGAAAACTTTTGTTCAAATATGCTATGTCTCATACGA AAATGAATAATCTAGAGGTACTGGTATAGAATTATAGCCCATATACTAAGGGGCACTGGACAGA CAAAATCAACATCAGTTTAGAGAAAAAAGTAAAAAGAAGTAGCCTATTCCAGAGGTTAAAAATT AATTTTAATTTTAACATAAAAAATATCCTTTTACCTTGCGTCCTTTGGAAGTATATGGCATTTT TCTCGTTAGCACCAAAGAAGAATGTAGGAAGAGATTATGCCTAATGTTATAAAAGAACAGAGCA AGTTAGTGAAATATACCTTTTGCTTTACATCTGACGGGGTAGCCACAATAATACCTTTTAAAGA GTGTGAAAGACCTTTCAAAGGTTTTTTTTTTATATAACAGATATATAACTTTTAAATTAGTAAA ACCTGAATTATAATCGTTAACTAATTGAAAAAAAAATGAAAATAATGATGTACAACTAAAAAGT AGTGGCAATGAAAAAGAAAATTCATTTGAATTTTCAGAGACAAAAGTATAATCATAGTTCTAAG ATAATCATTAAAATCATTTAATGTGGGAGTGATACTTACGGAACAACAAGAGAACCAAACATAG CAACCGCATCTGAAGTAGAATAATCCCCTTTGGGCCTTGGGATAAAAAGCCCCTCAATTACCCC ACCAGCAGGAGGATTAACTTTGCCAAGTTCCATAAAAAAGCAAGTAGCCATCACCAACATAAGA ACTGATATAGTGAACTCCATTTTCCGAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_009532 						
					
						PMCS
						0.313320512

Conservation Information
Conserved circRNAs	osi_circ_009532
PMCS	0.313320512

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17458763-17457592(-)
17457670-17458693(-)
						
						Potential amino acid sequence
						
							MEFTISVLMLVMATCFFMELGKVNPPAGGVIEGLFIPRPKGDYSTSDAVAMFGSLVVPHNLFLH
SSLVLTRKMPYTSKGRKDASTFFLLENALALFIALLVNVAIVSISGTICANNLSFADTSTCSSL
TLNSTYVLLKARKMEFTISVLMLVMATCFFMELGKVNPPAGGVIEGLFIPRPKGDYSTSDAVAM
FGSLVVPHNLFLHSSLVLTRKMPYTSKGRKDASTFFLLENALALFIALLVNVAIVSISGTICAN
NLSFADTSTCSSLTLNSTYVLLKARKMEFTISVLMLVMATCFFMELGKVNPPAGGVIEGLFIPR
PKGDYSTSDAVAMFGSLVVPHNLFLHSSLVLTRKMPYTSKGRKDASTFFLLENALALFIALLVN
VAIVSISGTICANNLSFADTSTCSSLTLNSTYVLLKARKMEFTISVLMLVMATCFFMELGKVNP
PAGGVIEGLFIPRPKGDYSTSDAVAMFGSLVVPHNLFLHSSLVLTRKMPYTSKGRKDASTFFLL
ENALALFIALLVNVAIVSISGTICANNLSFADTSTCSSLTLNSTYVLLK(-)
MCQQSLICRHKHVQQSNIEFNLCTTQGSENGVHYISSYVGDGYLLFYGTWQS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17458763-17457592(-) 17457670-17458693(-)
Potential amino acid sequence	MEFTISVLMLVMATCFFMELGKVNPPAGGVIEGLFIPRPKGDYSTSDAVAMFGSLVVPHNLFLH SSLVLTRKMPYTSKGRKDASTFFLLENALALFIALLVNVAIVSISGTICANNLSFADTSTCSSL TLNSTYVLLKARKMEFTISVLMLVMATCFFMELGKVNPPAGGVIEGLFIPRPKGDYSTSDAVAM FGSLVVPHNLFLHSSLVLTRKMPYTSKGRKDASTFFLLENALALFIALLVNVAIVSISGTICAN NLSFADTSTCSSLTLNSTYVLLKARKMEFTISVLMLVMATCFFMELGKVNPPAGGVIEGLFIPR PKGDYSTSDAVAMFGSLVVPHNLFLHSSLVLTRKMPYTSKGRKDASTFFLLENALALFIALLVN VAIVSISGTICANNLSFADTSTCSSLTLNSTYVLLKARKMEFTISVLMLVMATCFFMELGKVNP PAGGVIEGLFIPRPKGDYSTSDAVAMFGSLVVPHNLFLHSSLVLTRKMPYTSKGRKDASTFFLL ENALALFIALLVNVAIVSISGTICANNLSFADTSTCSSLTLNSTYVLLK(-) MCQQSLICRHKHVQQSNIEFNLCTTQGSENGVHYISSYVGDGYLLFYGTWQS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os01g0503400_circ_g.4

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