Plant Circular RNA Database

Detail information of Os01g0120300_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0120300_circ_g.3
					
						ID in PlantcircBase
						osa_circ_000154
					
						Alias
						Os_ciR5066
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 1147485-1148794  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os01g0120300						
					
						Parent gene annotation
						
							Similar to EMB2369 (EMBRYO DEFECTIVE 2369); ATP binding / aminoa
cyl-tRNA ligase/ leucine-tRNA ligase/ nucleotide binding. (Os01t
0120300-00)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0120300_circ_g.1 Os01g0120300_circ_g.2 Os01g0120300_circ_g.4 Os01g0120300_circ_g.5 						
					
						Support reads
						3/2
					
						Tissues
						root/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
						Os01t0120300-00:5

General Information
CircRNA Name	Os01g0120300_circ_g.3
ID in PlantcircBase	osa_circ_000154
Alias	Os_ciR5066
Organism	Oryza sativa
Position	chr1: 1147485-1148794 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os01g0120300
Parent gene annotation	Similar to EMB2369 (EMBRYO DEFECTIVE 2369); ATP binding / aminoa cyl-tRNA ligase/ leucine-tRNA ligase/ nucleotide binding. (Os01t 0120300-00)
Parent gene strand	-
Alternative splicing	Os01g0120300_circ_g.1 Os01g0120300_circ_g.2 Os01g0120300_circ_g.4 Os01g0120300_circ_g.5
Support reads	3/2
Tissues	root/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	Os01t0120300-00:5

			
						 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  
						
							GGAGGTAATTAGTTTCACCTACTTCTCCTAGAATCAATCCTTGATTTATCAGGCACTTGAAGGG
CTCTTTAGTGGAAACTACGCCAATATCATAAAGAACcttgtatgcagcattcacaaattccatc
attgcagaaattgcagtgttaaatcttgtttcttgaatttcctctgtgacctataaaacataac
aatacatt

									
								

					

						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: 609
Transcript exons: 1147485-1147562,1148022-1148199,1148269-1148441,1148531-
1148632,1148717-1148794
CTTGTATGCAGCATTCACAAATTCCATCATTGCAGAAATTGCAGTGTTAAATCTTGTTTCTTGA
ATTTCCTCTGTGACTCTTGCAATGCATTTGTGAAGAACTCGGAGCTGATCCAAGGTTGGTTCCT
CATCAGTAACCGTAGTTCCAACTCCATATGATCCATCTGGTAATGGTGTACCAACTACGAGTCT
CCATGTCCTTCCTAGAAATCTATGCACACCTTCAATTCCACCAGTGCTCCATGTTTTTGAATCT
CTCAGTGGTCCCATGAACATTTCATATAAGCGGAGAGAATCAGCACCATATTCTGAAACCACGT
CATCTGGGTTGATGACATTTCCTCGACTTTTACTCATTTTATAAGCACGAGCGTTTAGACGTAT
GTTTGCATCATCCTTCAGTACATAATGATCTCCAACTTTTGTGACCTTATCTGCAGGTACTTTT
TCTTGGTAGCAATCAATCAAACTTGAGTTGGAATCTGCAGAAACCCATCTCCCTTTATTGTCTC
TATATGCAGTATATTCAACTTCTCCTAGAATCAATCCTTGATTTATCAGGCACTTGAAGGGCTC
TTTAGTGGAAACTACGCCAATATCATAAAGAAC
						
					

						Genomic sequence
						
							CTTGTATGCAGCATTCACAAATTCCATCATTGCAGAAATTGCAGTGTTAAATCTTGTTTCTTGA
ATTTCCTCTGTGACCTATAAAACATAACAATACATTATAGTCATCAATCACCAATCACATCAGC
ACAACTACAGGAAAAAAATTATCAGTGCATAATCATGTTTAGCAGTAAGGAGACCCTGAGAATT
GTGTGATGATACAATCTTGAAATAGTCAGTACATAGGCAAAGCTTTTCACAGGGTAACTGATAG
GGGAACAGTTGCAAAGTACCATTACAACTAATCCATCTCAATATTGGAAGCATAAAAGGTACAA
AAATAATTGAAATGGTGGCACAGGCTGTAAAATTAATTAATAGAATTTATATTCCCCAAAGGGC
ATGTCATGTATAGGAATTATGTGCCGGGAACTTGGTAAAACTGTACAAATTTCCAAACCAAACT
GCTAGTAAACCTAAAATTTTGAATGGCTTTCATTTCAGAGTGAATTAGTGAAAAGATGTTATGT
GATCATGCTGTCAACTGTGACGTACTCTTGCAATGCATTTGTGAAGAACTCGGAGCTGATCCAA
GGTTGGTTCCTCATCAGTAACCGTAGTTCCAACTCCATATGATCCATCTGGTAATGGTGTACCA
ACTACGAGTCTCCATGTCCTTCCTAGAAATCTATGCACACCTTCAATTCCACCAGTGCTCCATG
TTTTTGAATCTCTGTGTACATCAGATATTCTGTCAGCTTTCTAAAATGGCTGTAACTTCATCTG
TAATATGGATGCATACCTCAGTGGTCCCATGAACATTTCATATAAGCGGAGAGAATCAGCACCA
TATTCTGAAACCACGTCATCTGGGTTGATGACATTTCCTCGACTTTTACTCATTTTATAAGCAC
GAGCGTTTAGACGTATGTTTGCATCATCCTTCAGTACATAATGATCTCCAACTTTTGTGACCTT
TAAAAACATAGAAGAAAGAAAAAAAATCAAACTAAAAAACTTTTATCATGCCAATTGAATAAAG
TTATAAATGTACCAGAGCCCACCTTATCTGCAGGTACTTTTTCTTGGTAGCAATCAATCAAACT
TGAGTTGGAATCTGCAGAAACCCATCTCCCTTTATTGTCTCTATATGCAGTATATTCAACCTGT
TATGATATTACCTGTTAGGAACACATGCACAAGATAGTAACGAACATGGGCAACTTTTGGAGGT
AATTAGTTTCACCTACTTCTCCTAGAATCAATCCTTGATTTATCAGGCACTTGAAGGGCTCTTT
AGTGGAAACTACGCCAATATCATAAAGAAC
						
					

			
		

Sequences
Splice junction sequence	GGAGGTAATTAGTTTCACCTACTTCTCCTAGAATCAATCCTTGATTTATCAGGCACTTGAAGGG CTCTTTAGTGGAAACTACGCCAATATCATAAAGAACcttgtatgcagcattcacaaattccatc attgcagaaattgcagtgttaaatcttgtttcttgaatttcctctgtgacctataaaacataac aatacatt
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: 609 Transcript exons: 1147485-1147562,1148022-1148199,1148269-1148441,1148531- 1148632,1148717-1148794 CTTGTATGCAGCATTCACAAATTCCATCATTGCAGAAATTGCAGTGTTAAATCTTGTTTCTTGA ATTTCCTCTGTGACTCTTGCAATGCATTTGTGAAGAACTCGGAGCTGATCCAAGGTTGGTTCCT CATCAGTAACCGTAGTTCCAACTCCATATGATCCATCTGGTAATGGTGTACCAACTACGAGTCT CCATGTCCTTCCTAGAAATCTATGCACACCTTCAATTCCACCAGTGCTCCATGTTTTTGAATCT CTCAGTGGTCCCATGAACATTTCATATAAGCGGAGAGAATCAGCACCATATTCTGAAACCACGT CATCTGGGTTGATGACATTTCCTCGACTTTTACTCATTTTATAAGCACGAGCGTTTAGACGTAT GTTTGCATCATCCTTCAGTACATAATGATCTCCAACTTTTGTGACCTTATCTGCAGGTACTTTT TCTTGGTAGCAATCAATCAAACTTGAGTTGGAATCTGCAGAAACCCATCTCCCTTTATTGTCTC TATATGCAGTATATTCAACTTCTCCTAGAATCAATCCTTGATTTATCAGGCACTTGAAGGGCTC TTTAGTGGAAACTACGCCAATATCATAAAGAAC
Genomic sequence	CTTGTATGCAGCATTCACAAATTCCATCATTGCAGAAATTGCAGTGTTAAATCTTGTTTCTTGA ATTTCCTCTGTGACCTATAAAACATAACAATACATTATAGTCATCAATCACCAATCACATCAGC ACAACTACAGGAAAAAAATTATCAGTGCATAATCATGTTTAGCAGTAAGGAGACCCTGAGAATT GTGTGATGATACAATCTTGAAATAGTCAGTACATAGGCAAAGCTTTTCACAGGGTAACTGATAG GGGAACAGTTGCAAAGTACCATTACAACTAATCCATCTCAATATTGGAAGCATAAAAGGTACAA AAATAATTGAAATGGTGGCACAGGCTGTAAAATTAATTAATAGAATTTATATTCCCCAAAGGGC ATGTCATGTATAGGAATTATGTGCCGGGAACTTGGTAAAACTGTACAAATTTCCAAACCAAACT GCTAGTAAACCTAAAATTTTGAATGGCTTTCATTTCAGAGTGAATTAGTGAAAAGATGTTATGT GATCATGCTGTCAACTGTGACGTACTCTTGCAATGCATTTGTGAAGAACTCGGAGCTGATCCAA GGTTGGTTCCTCATCAGTAACCGTAGTTCCAACTCCATATGATCCATCTGGTAATGGTGTACCA ACTACGAGTCTCCATGTCCTTCCTAGAAATCTATGCACACCTTCAATTCCACCAGTGCTCCATG TTTTTGAATCTCTGTGTACATCAGATATTCTGTCAGCTTTCTAAAATGGCTGTAACTTCATCTG TAATATGGATGCATACCTCAGTGGTCCCATGAACATTTCATATAAGCGGAGAGAATCAGCACCA TATTCTGAAACCACGTCATCTGGGTTGATGACATTTCCTCGACTTTTACTCATTTTATAAGCAC GAGCGTTTAGACGTATGTTTGCATCATCCTTCAGTACATAATGATCTCCAACTTTTGTGACCTT TAAAAACATAGAAGAAAGAAAAAAAATCAAACTAAAAAACTTTTATCATGCCAATTGAATAAAG TTATAAATGTACCAGAGCCCACCTTATCTGCAGGTACTTTTTCTTGGTAGCAATCAATCAAACT TGAGTTGGAATCTGCAGAAACCCATCTCCCTTTATTGTCTCTATATGCAGTATATTCAACCTGT TATGATATTACCTGTTAGGAACACATGCACAAGATAGTAACGAACATGGGCAACTTTTGGAGGT AATTAGTTTCACCTACTTCTCCTAGAATCAATCCTTGATTTATCAGGCACTTGAAGGGCTCTTT AGTGGAAACTACGCCAATATCATAAAGAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_001771* 						
					
						PMCS
						0.439337382

Conservation Information
Conserved circRNAs	osi_circ_001771*
PMCS	0.439337382

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1148371-1147487(-)
						
						Potential amino acid sequence
						
							MSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTGGIEGVHRFLGRTWRLVVGTPLP
DGSYGVGTTVTDEEPTLDQLRVLHKCIARVTEEIQETRFNTAISAMMEFVNAAYKVLYDIGVVS
TKEPFKCLINQGLILGEVEYTAYRDNKGRWVSADSNSSLIDCYQEKVPADKVTKVGDHYVLKDD
ANIRLNARAYKMSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTGGIEGVHRFLGR
TWRLVVGTPLPDGSYGVGTTVTDEEPTLDQLRVLHKCIARVTEEIQETRFNTAISAMMEFVNAA
YKVLYDIGVVSTKEPFKCLINQGLILGEVEYTAYRDNKGRWVSADSNSSLIDCYQEKVPADKVT
KVGDHYVLKDDANIRLNARAYKMSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTG
GIEGVHRFLGRTWRLVVGTPLPDGSYGVGTTVTDEEPTLDQLRVLHKCIARVTEEIQETRFNTA
ISAMMEFVNAAYKVLYDIGVVSTKEPFKCLINQGLILGEVEYTAYRDNKGRWVSADSNSSLIDC
YQEKVPADKVTKVGDHYVLKDDANIRLNARAYKMSKSRGNVINPDDVVSEYGADSLRLYEMFMG
PLRDSKTWSTGGIEGVHRFLGRTWRLVVGTPLPDGSYGVGTTVTDEEPTLDQLRVLHKCIARVT
EEIQETRFNTAISAMMEFVNAAYK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1148371-1147487(-)
Potential amino acid sequence	MSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTGGIEGVHRFLGRTWRLVVGTPLP DGSYGVGTTVTDEEPTLDQLRVLHKCIARVTEEIQETRFNTAISAMMEFVNAAYKVLYDIGVVS TKEPFKCLINQGLILGEVEYTAYRDNKGRWVSADSNSSLIDCYQEKVPADKVTKVGDHYVLKDD ANIRLNARAYKMSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTGGIEGVHRFLGR TWRLVVGTPLPDGSYGVGTTVTDEEPTLDQLRVLHKCIARVTEEIQETRFNTAISAMMEFVNAA YKVLYDIGVVSTKEPFKCLINQGLILGEVEYTAYRDNKGRWVSADSNSSLIDCYQEKVPADKVT KVGDHYVLKDDANIRLNARAYKMSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTG GIEGVHRFLGRTWRLVVGTPLPDGSYGVGTTVTDEEPTLDQLRVLHKCIARVTEEIQETRFNTA ISAMMEFVNAAYKVLYDIGVVSTKEPFKCLINQGLILGEVEYTAYRDNKGRWVSADSNSSLIDC YQEKVPADKVTKVGDHYVLKDDANIRLNARAYKMSKSRGNVINPDDVVSEYGADSLRLYEMFMG PLRDSKTWSTGGIEGVHRFLGRTWRLVVGTPLPDGSYGVGTTVTDEEPTLDQLRVLHKCIARVT EEIQETRFNTAISAMMEFVNAAYK(-)
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 Os01g0120300_circ_g.3

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