Plant Circular RNA Database

Detail information of Os01g0120800_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os01g0120800_circ_g.1
					
						ID in PlantcircBase
						osa_circ_000162
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 1173214-1174169  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0120800						
					
						Parent gene annotation
						
							Similar to Eukaryotic translation initiation factor 3 subunit 10
 (eIF-3 theta) (Eukaryotic translation initiation factor 3 large
 subunit) (eIF3a). (Os01t0120800-01);Similar to Translation init
iation factor 3. (Os01t0120800-02);Similar to Translation initia
tion factor 3. (Os01t0120800-03);Similar to Translation initiati
on factor 3. (Os01t0120800-04);Similar to Translation initiation
 factor 3. (Os01t0120800-05);Similar to Translation initiation f
actor 3. (Os01t0120800-06)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0120800_circ_g.2 						
					
						Support reads
						1
					
						Tissues
						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  
						
							CT-GC							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
						Os01t0120800-04:1
Os01t0120800-01:3
Os01t0120800-03:3
Os01t0120800-06:3

General Information
CircRNA Name	Os01g0120800_circ_g.1
ID in PlantcircBase	osa_circ_000162
Alias	NA
Organism	Oryza sativa
Position	chr1: 1173214-1174169 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0120800
Parent gene annotation	Similar to Eukaryotic translation initiation factor 3 subunit 10 (eIF-3 theta) (Eukaryotic translation initiation factor 3 large subunit) (eIF3a). (Os01t0120800-01);Similar to Translation init iation factor 3. (Os01t0120800-02);Similar to Translation initia tion factor 3. (Os01t0120800-03);Similar to Translation initiati on factor 3. (Os01t0120800-04);Similar to Translation initiation factor 3. (Os01t0120800-05);Similar to Translation initiation f actor 3. (Os01t0120800-06)
Parent gene strand	-
Alternative splicing	Os01g0120800_circ_g.2
Support reads	1
Tissues	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	CT-GC 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	Os01t0120800-04:1 Os01t0120800-01:3 Os01t0120800-03:3 Os01t0120800-06:3

			
						 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  
						
							CCATTTGCTTACCAGTCTTCTGTAGTTTTTTCTCCATCTCTTGGCGCTCCTTAAACTGCTCATT
CATAGCCAATTCCATCACAGCCTCCTTAGTAACTTCcttcacgttttctagcttcctcttcctc
acggagcctttggaggcgctgctcttctaagttaagatagtacattaacttccgcactgtatcc
ctttcacg

						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: 487
Transcript exons: 1173214-1173415,1173796-1173876,1173966-1174169
CTTCACGTTTTCTAGCTTCCTCTTCCTCACGGAGCCTTTGGAGGCGCTGCTCTTCTAAGTTAAG
ATAGTACATTAACTTCCGCACTGTATCCCTTTCACGCTTCCTTGATGATATCAATTGACTAGTC
CTTTCATCCCTCTCTTTCTTAAGACGACTAAACTCAGCTTCACGACGTTGGACAATTCTTTCCT
GGAAAATGTTCTTATGCTCCAACATTCGAGAAAGTCTGTTCTTCTCCTGCAGGTCACCTGCATG
GTGTTGCTTGCTGAGCTCAATCTCTCTCAGCTGCTCTTGCTCATGAAGGATTTTCTCTACTTCA
AGGCGTTTTTGAAAAGCTTGCTCAATTAGAGGTGCCTCTTCCTGCCTTTTTGCCCTCTCCAAGT
AATCCATTTGCTTACCAGTCTTCTGTAGTTTTTTCTCCATCTCTTGGCGCTCCTTAAACTGCTC
ATTCATAGCCAATTCCATCACAGCCTCCTTAGTAACTTC
						
						Genomic sequence
						
							CTTCACGTTTTCTAGCTTCCTCTTCCTCACGGAGCCTTTGGAGGCGCTGCTCTTCTAAGTTAAG
ATAGTACATTAACTTCCGCACTGTATCCCTTTCACGCTTCCTTGATGATATCAATTGACTAGTC
CTTTCATCCCTCTCTTTCTTAAGACGACTAAACTCAGCTTCACGACGTTGGACAATTCTTTCCT
GGAAAATGTTCTGCAAGCAAAAAGGGCAATTTAAAATATGTGCGAAGGAGAGAAGACAGCTGTC
TATTCCCTGACAGGAACAAATCGCCTGGTGTATTCAAATGTCTAGTGCTCAAATCATGTGAACA
CACACATAGCCAAAGAAGACATGCCAATATTAGATTCTCAGCAAGTATAGCACATATTATATGT
TAAATTAATCTGTATCTAATCAGACCTTTGCACAGATAATATACTAAGTATTTCAACTGTTATG
CTTGGAATTGCAAAACATGGTTTCGGAAAAACACAGGATTAATTACAGTGGGACATTTGGTCCT
TCAATTAACTAAAAAGAAGATGAAATAGTGCAAGAATATCTGGTCTGAATACAGATATGTATTT
GCTTACCTTATGCTCCAACATTCGAGAAAGTCTGTTCTTCTCCTGCAGGTCACCTGCATGGTGT
TGCTTGCTGAGCTCAATCTCTCTCTACAAGAAGAGATTAATAGTGATTTTTGTGAGCTTAAGTA
ATCATATGCTATTGTAATGTGACAATCAAGGAATTGTGAGAAACAAACCAGCTGCTCTTGCTCA
TGAAGGATTTTCTCTACTTCAAGGCGTTTTTGAAAAGCTTGCTCAATTAGAGGTGCCTCTTCCT
GCCTTTTTGCCCTCTCCAAGTAATCCATTTGCTTACCAGTCTTCTGTAGTTTTTTCTCCATCTC
TTGGCGCTCCTTAAACTGCTCATTCATAGCCAATTCCATCACAGCCTCCTTAGTAACTTC

Sequences
Splice junction sequence	CCATTTGCTTACCAGTCTTCTGTAGTTTTTTCTCCATCTCTTGGCGCTCCTTAAACTGCTCATT CATAGCCAATTCCATCACAGCCTCCTTAGTAACTTCcttcacgttttctagcttcctcttcctc acggagcctttggaggcgctgctcttctaagttaagatagtacattaacttccgcactgtatcc ctttcacg
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: 487 Transcript exons: 1173214-1173415,1173796-1173876,1173966-1174169 CTTCACGTTTTCTAGCTTCCTCTTCCTCACGGAGCCTTTGGAGGCGCTGCTCTTCTAAGTTAAG ATAGTACATTAACTTCCGCACTGTATCCCTTTCACGCTTCCTTGATGATATCAATTGACTAGTC CTTTCATCCCTCTCTTTCTTAAGACGACTAAACTCAGCTTCACGACGTTGGACAATTCTTTCCT GGAAAATGTTCTTATGCTCCAACATTCGAGAAAGTCTGTTCTTCTCCTGCAGGTCACCTGCATG GTGTTGCTTGCTGAGCTCAATCTCTCTCAGCTGCTCTTGCTCATGAAGGATTTTCTCTACTTCA AGGCGTTTTTGAAAAGCTTGCTCAATTAGAGGTGCCTCTTCCTGCCTTTTTGCCCTCTCCAAGT AATCCATTTGCTTACCAGTCTTCTGTAGTTTTTTCTCCATCTCTTGGCGCTCCTTAAACTGCTC ATTCATAGCCAATTCCATCACAGCCTCCTTAGTAACTTC
Genomic sequence	CTTCACGTTTTCTAGCTTCCTCTTCCTCACGGAGCCTTTGGAGGCGCTGCTCTTCTAAGTTAAG ATAGTACATTAACTTCCGCACTGTATCCCTTTCACGCTTCCTTGATGATATCAATTGACTAGTC CTTTCATCCCTCTCTTTCTTAAGACGACTAAACTCAGCTTCACGACGTTGGACAATTCTTTCCT GGAAAATGTTCTGCAAGCAAAAAGGGCAATTTAAAATATGTGCGAAGGAGAGAAGACAGCTGTC TATTCCCTGACAGGAACAAATCGCCTGGTGTATTCAAATGTCTAGTGCTCAAATCATGTGAACA CACACATAGCCAAAGAAGACATGCCAATATTAGATTCTCAGCAAGTATAGCACATATTATATGT TAAATTAATCTGTATCTAATCAGACCTTTGCACAGATAATATACTAAGTATTTCAACTGTTATG CTTGGAATTGCAAAACATGGTTTCGGAAAAACACAGGATTAATTACAGTGGGACATTTGGTCCT TCAATTAACTAAAAAGAAGATGAAATAGTGCAAGAATATCTGGTCTGAATACAGATATGTATTT GCTTACCTTATGCTCCAACATTCGAGAAAGTCTGTTCTTCTCCTGCAGGTCACCTGCATGGTGT TGCTTGCTGAGCTCAATCTCTCTCTACAAGAAGAGATTAATAGTGATTTTTGTGAGCTTAAGTA ATCATATGCTATTGTAATGTGACAATCAAGGAATTGTGAGAAACAAACCAGCTGCTCTTGCTCA TGAAGGATTTTCTCTACTTCAAGGCGTTTTTGAAAAGCTTGCTCAATTAGAGGTGCCTCTTCCT GCCTTTTTGCCCTCTCCAAGTAATCCATTTGCTTACCAGTCTTCTGTAGTTTTTTCTCCATCTC TTGGCGCTCCTTAAACTGCTCATTCATAGCCAATTCCATCACAGCCTCCTTAGTAACTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_009337 						
					
						PMCS
						0.380117874

Conservation Information
Conserved circRNAs	osi_circ_009337
PMCS	0.380117874

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1174150-1174161(-)
						
						Potential amino acid sequence
						
							MELAMNEQFKERQEMEKKLQKTGKQMDYLERAKRQEEAPLIEQAFQKRLEVEKILHEQEQLREI
ELSKQHHAGDLQEKNRLSRMLEHKNIFQERIVQRREAEFSRLKKERDERTSQLISSRKRERDTV
RKLMYYLNLEEQRLQRLREEEEARKREGSY*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1174150-1174161(-)
Potential amino acid sequence	MELAMNEQFKERQEMEKKLQKTGKQMDYLERAKRQEEAPLIEQAFQKRLEVEKILHEQEQLREI ELSKQHHAGDLQEKNRLSRMLEHKNIFQERIVQRREAEFSRLKKERDERTSQLISSRKRERDTV RKLMYYLNLEEQRLQRLREEEEARKREGSY*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0120800_circ_g.1

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