Plant Circular RNA Database

Detail information of Os06g0142900_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os06g0142900_circ_g.3
					
						ID in PlantcircBase
						osa_circ_029647
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 2253589-2255180  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os06g0142900						
					
						Parent gene annotation
						
							Similar to 1-deoxy-D-xylulose 5-phosphate synthase. (Os06t014290
0-01);Similar to predicted protein. (Os06t0142900-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						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  
						
							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
						Os06t0142900-01:3

General Information
CircRNA Name	Os06g0142900_circ_g.3
ID in PlantcircBase	osa_circ_029647
Alias	NA
Organism	Oryza sativa
Position	chr6: 2253589-2255180 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer
Parent gene	Os06g0142900
Parent gene annotation	Similar to 1-deoxy-D-xylulose 5-phosphate synthase. (Os06t014290 0-01);Similar to predicted protein. (Os06t0142900-02)
Parent gene strand	-
Alternative splicing	NA
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	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	Os06t0142900-01:3

			
						 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  
						
							ATTCGCTCTCGAAACGGGATGTGAAACCTGAAAGCCCCTTTCTTTGCTTAATAGTATGAAAGAG
TGAGCGCCTTCCTGTGAGAATCTTGTGTGCATATGTcttcctcgtcgggagtaatctcactatt
aaattctccacctgagtctttttcattctcagtgattacatgcacaagtactgggccggtagaa
tctagagt

									
								

					

						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: 700
Transcript exons: 2253589-2253868,2254217-2254485,2255030-2255180
CTTCCTCGTCGGGAGTAATCTCACTATTAAATTCTCCACCTGAGTCTTTTTCATTCTCAGTGAT
TACATGCACAAGTACTGGGCCGGTAGAATCTAGAGTAGAAACCTCCTTGAGTACACAAATGAGA
TCATCAATGTTATTCCCATCAATAGGCCCAATATAATATAATCCAAGTTCTTCAAAAAGAGTTG
CTCCATGAGGACCTATCATACCACGGGCATACTCATCAATTTTGGCAGCAAATTCATGCATCCC
TTTACCAAACCATTTGGAAAGTCCCTTTGCAGCCTCCCTAAACTTTCTAAATCCTTTGCTGGAT
TGAACCTTGCTCAGAGCACTAGAGAGGGCATTAATAGACATCTTTGATTGGCTATCTGCTTTAG
GAAGCAAGGTGTGCCGGCTGTCATTTAAAATCACTACCATGTTAGAATCAAGGAAACCGGCATG
ACCCATTGCCTCATACACCTGACCAGCCATAGTTGTCCAGTTACTTATAACTGTTACTATTCGG
TTTTTCCTCCCACCTAGATCCCTTGCGACTGCCATCCCAAGGCCTGCGGAGAGACTATTGCATC
CATGTCCTGCACCAAAGGGATCATATTCGCTCTCGAAACGGGATGTGAAACCTGAAAGCCCCTT
TCTTTGCTTAATAGTATGAAAGAGTGAGCGCCTTCCTGTGAGAATCTTGTGTGCATATGT
						
					

						Genomic sequence
						
							CTTCCTCGTCGGGAGTAATCTCACTATTAAATTCTCCACCTGAGTCTTTTTCATTCTCAGTGAT
TACATGCACAAGTACTGGGCCGGTAGAATCTAGAGTAGAAACCTCCTTGAGTACACAAATGAGA
TCATCAATGTTATTCCCATCAATAGGCCCAATATAATATAATCCAAGTTCTTCAAAAAGAGTTG
CTCCATGAGGACCTATCATACCACGGGCATACTCATCAATTTTGGCAGCAAATTCATGCATCCC
TTTACCAAACCATTTGGAAAGTCCCTAGAAAGGAAACAAAATTCGTATCAAAGCAGGAAACTCA
AGGCAGTGCAAGACTGTTGTTATTAAGAAAGTAGAAAGACAACCCATGCCAAAACTTCCTGGAA
ATTTTTCATCATAATATGTACAGCAGCAAGTCAATTAGCAGGCTTTTATAACAATAAGTTGAAA
GTAACAAGTACATTTGTCACTACCAGATAAAAAAGAGAACTGAAAAGAAACAATCAACTAGAAA
CTATATGTCTATACTATAATCATAATCAGGAAATAACAGGACAGTTAAAAAAAACTATGTTTTA
TTAGCAAGTTCAAATCTAGTACATTATGTCATACAGAAGCATAAAGTTTTACCTTTGCAGCCTC
CCTAAACTTTCTAAATCCTTTGCTGGATTGAACCTTGCTCAGAGCACTAGAGAGGGCATTAATA
GACATCTTTGATTGGCTATCTGCTTTAGGAAGCAAGGTGTGCCGGCTGTCATTTAAAATCACTA
CCATGTTAGAATCAAGGAAACCGGCATGACCCATTGCCTCATACACCTGACCAGCCATAGTTGT
CCAGTTACTTATAACTGTTACTATTCGGTTTTTCCTCCCACCTAGATCCCTTGCGACTGCCATC
CCTGACAAGAGATCATTTTCAAGCTATAAACGAATAAAAGGAAATCATTTGACATAAAAGAATA
AAACATCAGGAGATTCATGATTAAATGTAGAAACATACTTAGGATTCTAATAGACTATGCAAAC
TTCTATAATGATTATTAACTCCATTAGCAAAATAAGATAGTTTAAGAATTTCATATCATGACTG
CTGATACCACACCAGAAGGATATGAACTTGAATACATCAGAACTTATATTATATTTCTTGAATT
ATATTTTGAGTCGTACATCCCGGCACTGTATACCTTGGTTTAAAAAGCAAGAAGCACTGTTTTT
CTCTGTTTCAGGTAGCTGAACTATTGATAAAATGCATGGAAGCTAATCGGAGTCGAAGATGAAA
AAAACTATGGAATATTGTACGGATTCCAAACACAATGAAATCAATATCTTAAGGAAATCCATTT
AAATAGAAGGAGAGGTCTAACAACAAAGCAAGCAGTTCTTGAAGTGCAAGGCATGAATTAATGT
ATTAACATTTAACAGAGGCAACACTATATATACCAAGGCCTGCGGAGAGACTATTGCATCCATG
TCCTGCACCAAAGGGATCATATTCGCTCTCGAAACGGGATGTGAAACCTGAAAGCCCCTTTCTT
TGCTTAATAGTATGAAAGAGTGAGCGCCTTCCTGTGAGAATCTTGTGTGCATATGT
						
					

			
		

Sequences
Splice junction sequence	ATTCGCTCTCGAAACGGGATGTGAAACCTGAAAGCCCCTTTCTTTGCTTAATAGTATGAAAGAG TGAGCGCCTTCCTGTGAGAATCTTGTGTGCATATGTcttcctcgtcgggagtaatctcactatt aaattctccacctgagtctttttcattctcagtgattacatgcacaagtactgggccggtagaa tctagagt
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: 700 Transcript exons: 2253589-2253868,2254217-2254485,2255030-2255180 CTTCCTCGTCGGGAGTAATCTCACTATTAAATTCTCCACCTGAGTCTTTTTCATTCTCAGTGAT TACATGCACAAGTACTGGGCCGGTAGAATCTAGAGTAGAAACCTCCTTGAGTACACAAATGAGA TCATCAATGTTATTCCCATCAATAGGCCCAATATAATATAATCCAAGTTCTTCAAAAAGAGTTG CTCCATGAGGACCTATCATACCACGGGCATACTCATCAATTTTGGCAGCAAATTCATGCATCCC TTTACCAAACCATTTGGAAAGTCCCTTTGCAGCCTCCCTAAACTTTCTAAATCCTTTGCTGGAT TGAACCTTGCTCAGAGCACTAGAGAGGGCATTAATAGACATCTTTGATTGGCTATCTGCTTTAG GAAGCAAGGTGTGCCGGCTGTCATTTAAAATCACTACCATGTTAGAATCAAGGAAACCGGCATG ACCCATTGCCTCATACACCTGACCAGCCATAGTTGTCCAGTTACTTATAACTGTTACTATTCGG TTTTTCCTCCCACCTAGATCCCTTGCGACTGCCATCCCAAGGCCTGCGGAGAGACTATTGCATC CATGTCCTGCACCAAAGGGATCATATTCGCTCTCGAAACGGGATGTGAAACCTGAAAGCCCCTT TCTTTGCTTAATAGTATGAAAGAGTGAGCGCCTTCCTGTGAGAATCTTGTGTGCATATGT
Genomic sequence	CTTCCTCGTCGGGAGTAATCTCACTATTAAATTCTCCACCTGAGTCTTTTTCATTCTCAGTGAT TACATGCACAAGTACTGGGCCGGTAGAATCTAGAGTAGAAACCTCCTTGAGTACACAAATGAGA TCATCAATGTTATTCCCATCAATAGGCCCAATATAATATAATCCAAGTTCTTCAAAAAGAGTTG CTCCATGAGGACCTATCATACCACGGGCATACTCATCAATTTTGGCAGCAAATTCATGCATCCC TTTACCAAACCATTTGGAAAGTCCCTAGAAAGGAAACAAAATTCGTATCAAAGCAGGAAACTCA AGGCAGTGCAAGACTGTTGTTATTAAGAAAGTAGAAAGACAACCCATGCCAAAACTTCCTGGAA ATTTTTCATCATAATATGTACAGCAGCAAGTCAATTAGCAGGCTTTTATAACAATAAGTTGAAA GTAACAAGTACATTTGTCACTACCAGATAAAAAAGAGAACTGAAAAGAAACAATCAACTAGAAA CTATATGTCTATACTATAATCATAATCAGGAAATAACAGGACAGTTAAAAAAAACTATGTTTTA TTAGCAAGTTCAAATCTAGTACATTATGTCATACAGAAGCATAAAGTTTTACCTTTGCAGCCTC CCTAAACTTTCTAAATCCTTTGCTGGATTGAACCTTGCTCAGAGCACTAGAGAGGGCATTAATA GACATCTTTGATTGGCTATCTGCTTTAGGAAGCAAGGTGTGCCGGCTGTCATTTAAAATCACTA CCATGTTAGAATCAAGGAAACCGGCATGACCCATTGCCTCATACACCTGACCAGCCATAGTTGT CCAGTTACTTATAACTGTTACTATTCGGTTTTTCCTCCCACCTAGATCCCTTGCGACTGCCATC CCTGACAAGAGATCATTTTCAAGCTATAAACGAATAAAAGGAAATCATTTGACATAAAAGAATA AAACATCAGGAGATTCATGATTAAATGTAGAAACATACTTAGGATTCTAATAGACTATGCAAAC TTCTATAATGATTATTAACTCCATTAGCAAAATAAGATAGTTTAAGAATTTCATATCATGACTG CTGATACCACACCAGAAGGATATGAACTTGAATACATCAGAACTTATATTATATTTCTTGAATT ATATTTTGAGTCGTACATCCCGGCACTGTATACCTTGGTTTAAAAAGCAAGAAGCACTGTTTTT CTCTGTTTCAGGTAGCTGAACTATTGATAAAATGCATGGAAGCTAATCGGAGTCGAAGATGAAA AAAACTATGGAATATTGTACGGATTCCAAACACAATGAAATCAATATCTTAAGGAAATCCATTT AAATAGAAGGAGAGGTCTAACAACAAAGCAAGCAGTTCTTGAAGTGCAAGGCATGAATTAATGT ATTAACATTTAACAGAGGCAACACTATATATACCAAGGCCTGCGGAGAGACTATTGCATCCATG TCCTGCACCAAAGGGATCATATTCGCTCTCGAAACGGGATGTGAAACCTGAAAGCCCCTTTCTT TGCTTAATAGTATGAAAGAGTGAGCGCCTTCCTGTGAGAATCTTGTGTGCATATGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.119254031

Conservation Information
Conserved circRNAs	NA
PMCS	0.119254031

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2255178-2253749(+)
2254485-2255130(-)
2253644-2255130(-)
						
						Potential amino acid sequence
						
							MSSSSGVISLLNSPPESFSFSVITCTSTGPVESRVETSLSTQMRSSMLFPSIGPI*(+)
MAVARDLGGRKNRIVTVISNWTTMAGQVYEAMGHAGFLDSNMVVILNDSRHTLLPKADSQSKMS
INALSSALSKVQSSKGFRKFREAAKGLSKWFGKGMHEFAAKIDEYARGMIGPHGATLFEELGLY
YIGPIDGNNIDDLICVLKEVSTLDSTGPVLVHVITENEKDSGGEFNSEITPDEEDICTQDSHRK
ALTLSYY*(-)
MKKTQVENLIVRLLPTRKTYAHKILTGRRSLFHTIKQRKGLSGFTSRFESEYDPFGAGHGCNSL
SAGLGMAVARDLGGRKNRIVTVISNWTTMAGQVYEAMGHAGFLDSNMVVILNDSRHTLLPKADS
QSKMSINALSSALSKVQSSKGFRKFREAAKGLSKWFGKGMHEFAAKIDEYARGMIGPHGATLFE
ELGLYYIGPIDGNNIDDLICVLKEVSTLDSTGPVLVHVITENEKDSGGEFNSEITPDEEDICTQ
DSHRKALTLSYY*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2255178-2253749(+) 2254485-2255130(-) 2253644-2255130(-)
Potential amino acid sequence	MSSSSGVISLLNSPPESFSFSVITCTSTGPVESRVETSLSTQMRSSMLFPSIGPI(+) MAVARDLGGRKNRIVTVISNWTTMAGQVYEAMGHAGFLDSNMVVILNDSRHTLLPKADSQSKMS INALSSALSKVQSSKGFRKFREAAKGLSKWFGKGMHEFAAKIDEYARGMIGPHGATLFEELGLY YIGPIDGNNIDDLICVLKEVSTLDSTGPVLVHVITENEKDSGGEFNSEITPDEEDICTQDSHRK ALTLSYY(-) MKKTQVENLIVRLLPTRKTYAHKILTGRRSLFHTIKQRKGLSGFTSRFESEYDPFGAGHGCNSL SAGLGMAVARDLGGRKNRIVTVISNWTTMAGQVYEAMGHAGFLDSNMVVILNDSRHTLLPKADS QSKMSINALSSALSKVQSSKGFRKFREAAKGLSKWFGKGMHEFAAKIDEYARGMIGPHGATLFE ELGLYYIGPIDGNNIDDLICVLKEVSTLDSTGPVLVHVITENEKDSGGEFNSEITPDEEDICTQ DSHRKALTLSYY*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os06g0142900_circ_g.3

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