Plant Circular RNA Database

Detail information of Os01g0178000_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os01g0178000_circ_g.1
					
						ID in PlantcircBase
						osa_circ_000513
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 4054711-4057292  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0178000						
					
						Parent gene annotation
						
							Pyridoxal phosphate-dependent transferase, major region, subdoma
in 1 domain containing protein. (Os01t0178000-01);Similar to Tra
nsaminase/ transferase, transferring nitrogenous groups. (Os01t0
178000-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0178000_circ_g.2 Os01g0178000_circ_g.3 						
					
						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
						Os01t0178000-01:5

General Information
CircRNA Name	Os01g0178000_circ_g.1
ID in PlantcircBase	osa_circ_000513
Alias	NA
Organism	Oryza sativa
Position	chr1: 4054711-4057292 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0178000
Parent gene annotation	Pyridoxal phosphate-dependent transferase, major region, subdoma in 1 domain containing protein. (Os01t0178000-01);Similar to Tra nsaminase/ transferase, transferring nitrogenous groups. (Os01t0 178000-02)
Parent gene strand	-
Alternative splicing	Os01g0178000_circ_g.2 Os01g0178000_circ_g.3
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	Os01t0178000-01:5

			
						 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  
						
							TGACCGGCGCTTCCGTCTCCACGGCCCTCCTCGCCAGCCTCCCGAAGCTACCCATCTCACCTCC
TCCTCCTCCTCTTCCTCACCCCTCCAAGAACAAGAAcgacatcaggatgaagagtctcaggatt
gcttgcaccaactaatatgtcagtaactcctgtcatctggaatgacatgtaggaattgaagtaa
tatggtgc

									
								

					

						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: 502
Transcript exons: 4054711-4054867,4055110-4055169,4056396-4056524,4057027-
4057074,4057185-4057292
CGACATCAGGATGAAGAGTCTCAGGATTGCTTGCACCAACTAATATGTCAGTAACTCCTGTCAT
CTGGAATGACATGTAGGAATTGAAGTAATATGGTGCAAACATGACAACTGCATCCCCAGCATCA
CAAAGGGTGAGGACCACATTTACAAAGGCCTGATTTGCACCAGAGGTAACCATAATTGACGACT
TGGTTAGCTTATTCTCTCTGCGCAGCTTCTCGAGAAGTGCTTCTCGGAGTTCAGGAAGACCATC
ATCAGAGCCATATTTACTGATTGATGGTTCCCATACAATTTCTTTAATCTTATTCATAGCTGCC
TCAGGAGGCTGCCAATAAACAACTCCCTGCGCAAGCGACATCACATCCTTGTTCCCTCGAAGCA
ATTCCTGCATCTTGACCATGACCGGCGCTTCCGTCTCCACGGCCCTCCTCGCCAGCCTCCCGAA
GCTACCCATCTCACCTCCTCCTCCTCCTCTTCCTCACCCCTCCAAGAACAAGAA
						
					

						Genomic sequence
						
							CGACATCAGGATGAAGAGTCTCAGGATTGCTTGCACCAACTAATATGTCAGTAACTCCTGTCAT
CTGGAATGACATGTAGGAATTGAAGTAATATGGTGCAAACATGACAACTGCATCCCCAGCATCA
CAAAGGGTGAGGACCACATTTACAAAGGCCTGCCAAAATTTGATAGAAGACATCACTTTATTTG
ACTTTTATTTGGCTAACCTAGTTGGTAAACAAGGTTTAGGTGAAGCAGTCATACAGAAAAGTAA
GAAAGCATCTCATAGAACTGAAGAAGAAAAACAAATTGGCATCCTATAGTCTAGCTAAACAAGG
CAAAATACACAGAGGAAAACCGGAATAAGATGACAAAGCTGTAATAAATCAGGTGGAAACTGGA
AAGCATGTGCATTACCTGATTTGCACCAGAGGTAACCATAATTGACGACTTGGTTAGCTTATTC
TCTCTGCGCAGCTGCAAAATGTATGCTAAAAATTTCAGGAAGAAAATAGAGGGAAGGCAACGAA
CATGTTTATAATAATTACCATTCATATTATTAGTTTTTCAATAAAATATTATCGCAGTAAGAGA
AATCAGTGAATATAACACCCATCTCTACATGAGGGGGCATCGGTAGTACCAAGGGCAATGTCTC
AGAACTGTGCTACTGCACTGTTACATGGTAGCATTGAACTATTATAGCTCTCAACAGAGCTTAG
GGCCCCTTTGATTTGGAGGAAAAACATAGGAATTTTGGAGGATTTCAATCCTATAGGAAAATTT
CCTATGAAGTCCTTTGAATCAAAGGATTGAATCCTATCCAATCCTTTAAAATTCCTATGGAATG
AACAATCCTATAGAAATTTTGGAGGAAATTAAGCAAGAGCTTCAACCTCTTAGTAACTTTTCTT
TGAGTCTATCTCTCTCATCCAAATCCTGCGTTTTTCCTGCGGTTCAATCAAACGGTCATTCCTG
TGTTTTTCCTGCGTTTTGTAATCCTCTATTTTACACTTACATTCCTATCAAAATCCTACGTTTT
TTCTATTACTATGTTTTCTCAATCCTACGATTCAAAGGGGCCCTTAGCTTCCCTCCCCCCCAAG
CCCCCACAGAAGCTGAGAGATACTTTCTGAAACTTTCTCGTTGATAAAATTTTGTAAGGATAGC
ATGTGATTCCTGATATTAGGCTATTCCCAACCCAATGACTAGGATAGTGTCCATAGCATTAAAT
AAGCTGTCACATAGGATGAAAACTGATGTGGCAAGTGAATAAATGAGGAAAGAGGAGGAAACTA
TGTCTTGCATGAGACATGGTTTCTACACAACATCCAAGACATTATGTGAGATAAGTAGCATTAA
ATTTAAGTATGAAATAGTAGTGTTTGCATTGGAAGAGTAGTGTCTAGTACTTATTTCTTGATGA
TGTGGAGTTTATGGAAACTATGTCTAATGTTTTGGGTTGGGAATGGCCTTACTCTCACTCTCTC
AGTATCGAGGTAAAAAAAATTCCAGAATCAATTTCTCACATGACAAAGGCTTAGTAGTAGGCAC
ACAGGTTCCTTTGTCTCACATGATAAAGGCTTAGCAGTAGGCAACCAAGTGCATTTGTCTCACA
TGGTAATTGCTTTGTGATAACTGGGAAGGCTTGATAACATGGGCCATGGAAACCATTATCTAAC
AAATCCCAATTGAAAAATTACCTTCTCGAGAAGTGCTTCTCGGAGTTCAGGAAGACCATCATCA
GAGCCATATTTACTGATTGATGGTTCCCATACAATTTCTTTAATCTTATTCATAGCTGCCTCAG
GAGGCTGCCAATAAACAACTCCCTGCATCCAAGATTTACATTAGTTTAAAAGAAAGCAAATAAT
TTCCAGTAAATATCACATGTTCTGTTGGCAGTAATAGGAGGCCAGCACACACACCACTGCCACT
AATATATATATTTGGATATCTTATTTGGCTAGCATAAGCAGTTAAACGCCATTTTCAGGAACTA
AGCAGGAATACAACCATTTTAGTTTCCAAATTCCATGCTTGATAAATAGTTGTGTTATACAAAG
CACAATATGTTATCAGATGTACTAAACTCTCCTGATTCACCTTACAACGTGAACAGTTTACTGA
GACAATTGACCCAAACAGTAAAGGAACAATACAAATGATCATTTCACTAATCCATTTCGAACAC
TCTTCCCAATCAAATGCAAACATCAAAATGCCTGTGACCAAGTACCAACAACAACACAAACTCA
TTGGTACTCTCATGAAAACACACACACACACACACAATCATTGGACAGATAACCGAAAGAAATT
GCGATCCGATACCTGCGCAAGCGACATCACATCCTTGTTCCCTCGAAGCAATTCCTGCATCTGA
AAAAAGAGCACAAGGCACAAGAGAGATAGAACTCATCAATCAAGACCAAAGAAATCAGAAGGGA
AAGATGCGATTTCGACGAGGCAGGGAGCTTCTTCTCCATCACCTTGACCATGACCGGCGCTTCC
GTCTCCACGGCCCTCCTCGCCAGCCTCCCGAAGCTACCCATCTCACCTCCTCCTCCTCCTCTTC
CTCACCCCTCCAAGAACAAGAA
						
					

			
		

Sequences
Splice junction sequence	TGACCGGCGCTTCCGTCTCCACGGCCCTCCTCGCCAGCCTCCCGAAGCTACCCATCTCACCTCC TCCTCCTCCTCTTCCTCACCCCTCCAAGAACAAGAAcgacatcaggatgaagagtctcaggatt gcttgcaccaactaatatgtcagtaactcctgtcatctggaatgacatgtaggaattgaagtaa tatggtgc
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: 502 Transcript exons: 4054711-4054867,4055110-4055169,4056396-4056524,4057027- 4057074,4057185-4057292 CGACATCAGGATGAAGAGTCTCAGGATTGCTTGCACCAACTAATATGTCAGTAACTCCTGTCAT CTGGAATGACATGTAGGAATTGAAGTAATATGGTGCAAACATGACAACTGCATCCCCAGCATCA CAAAGGGTGAGGACCACATTTACAAAGGCCTGATTTGCACCAGAGGTAACCATAATTGACGACT TGGTTAGCTTATTCTCTCTGCGCAGCTTCTCGAGAAGTGCTTCTCGGAGTTCAGGAAGACCATC ATCAGAGCCATATTTACTGATTGATGGTTCCCATACAATTTCTTTAATCTTATTCATAGCTGCC TCAGGAGGCTGCCAATAAACAACTCCCTGCGCAAGCGACATCACATCCTTGTTCCCTCGAAGCA ATTCCTGCATCTTGACCATGACCGGCGCTTCCGTCTCCACGGCCCTCCTCGCCAGCCTCCCGAA GCTACCCATCTCACCTCCTCCTCCTCCTCTTCCTCACCCCTCCAAGAACAAGAA
Genomic sequence	CGACATCAGGATGAAGAGTCTCAGGATTGCTTGCACCAACTAATATGTCAGTAACTCCTGTCAT CTGGAATGACATGTAGGAATTGAAGTAATATGGTGCAAACATGACAACTGCATCCCCAGCATCA CAAAGGGTGAGGACCACATTTACAAAGGCCTGCCAAAATTTGATAGAAGACATCACTTTATTTG ACTTTTATTTGGCTAACCTAGTTGGTAAACAAGGTTTAGGTGAAGCAGTCATACAGAAAAGTAA GAAAGCATCTCATAGAACTGAAGAAGAAAAACAAATTGGCATCCTATAGTCTAGCTAAACAAGG CAAAATACACAGAGGAAAACCGGAATAAGATGACAAAGCTGTAATAAATCAGGTGGAAACTGGA AAGCATGTGCATTACCTGATTTGCACCAGAGGTAACCATAATTGACGACTTGGTTAGCTTATTC TCTCTGCGCAGCTGCAAAATGTATGCTAAAAATTTCAGGAAGAAAATAGAGGGAAGGCAACGAA CATGTTTATAATAATTACCATTCATATTATTAGTTTTTCAATAAAATATTATCGCAGTAAGAGA AATCAGTGAATATAACACCCATCTCTACATGAGGGGGCATCGGTAGTACCAAGGGCAATGTCTC AGAACTGTGCTACTGCACTGTTACATGGTAGCATTGAACTATTATAGCTCTCAACAGAGCTTAG GGCCCCTTTGATTTGGAGGAAAAACATAGGAATTTTGGAGGATTTCAATCCTATAGGAAAATTT CCTATGAAGTCCTTTGAATCAAAGGATTGAATCCTATCCAATCCTTTAAAATTCCTATGGAATG AACAATCCTATAGAAATTTTGGAGGAAATTAAGCAAGAGCTTCAACCTCTTAGTAACTTTTCTT TGAGTCTATCTCTCTCATCCAAATCCTGCGTTTTTCCTGCGGTTCAATCAAACGGTCATTCCTG TGTTTTTCCTGCGTTTTGTAATCCTCTATTTTACACTTACATTCCTATCAAAATCCTACGTTTT TTCTATTACTATGTTTTCTCAATCCTACGATTCAAAGGGGCCCTTAGCTTCCCTCCCCCCCAAG CCCCCACAGAAGCTGAGAGATACTTTCTGAAACTTTCTCGTTGATAAAATTTTGTAAGGATAGC ATGTGATTCCTGATATTAGGCTATTCCCAACCCAATGACTAGGATAGTGTCCATAGCATTAAAT AAGCTGTCACATAGGATGAAAACTGATGTGGCAAGTGAATAAATGAGGAAAGAGGAGGAAACTA TGTCTTGCATGAGACATGGTTTCTACACAACATCCAAGACATTATGTGAGATAAGTAGCATTAA ATTTAAGTATGAAATAGTAGTGTTTGCATTGGAAGAGTAGTGTCTAGTACTTATTTCTTGATGA TGTGGAGTTTATGGAAACTATGTCTAATGTTTTGGGTTGGGAATGGCCTTACTCTCACTCTCTC AGTATCGAGGTAAAAAAAATTCCAGAATCAATTTCTCACATGACAAAGGCTTAGTAGTAGGCAC ACAGGTTCCTTTGTCTCACATGATAAAGGCTTAGCAGTAGGCAACCAAGTGCATTTGTCTCACA TGGTAATTGCTTTGTGATAACTGGGAAGGCTTGATAACATGGGCCATGGAAACCATTATCTAAC AAATCCCAATTGAAAAATTACCTTCTCGAGAAGTGCTTCTCGGAGTTCAGGAAGACCATCATCA GAGCCATATTTACTGATTGATGGTTCCCATACAATTTCTTTAATCTTATTCATAGCTGCCTCAG GAGGCTGCCAATAAACAACTCCCTGCATCCAAGATTTACATTAGTTTAAAAGAAAGCAAATAAT TTCCAGTAAATATCACATGTTCTGTTGGCAGTAATAGGAGGCCAGCACACACACCACTGCCACT AATATATATATTTGGATATCTTATTTGGCTAGCATAAGCAGTTAAACGCCATTTTCAGGAACTA AGCAGGAATACAACCATTTTAGTTTCCAAATTCCATGCTTGATAAATAGTTGTGTTATACAAAG CACAATATGTTATCAGATGTACTAAACTCTCCTGATTCACCTTACAACGTGAACAGTTTACTGA GACAATTGACCCAAACAGTAAAGGAACAATACAAATGATCATTTCACTAATCCATTTCGAACAC TCTTCCCAATCAAATGCAAACATCAAAATGCCTGTGACCAAGTACCAACAACAACACAAACTCA TTGGTACTCTCATGAAAACACACACACACACACACAATCATTGGACAGATAACCGAAAGAAATT GCGATCCGATACCTGCGCAAGCGACATCACATCCTTGTTCCCTCGAAGCAATTCCTGCATCTGA AAAAAGAGCACAAGGCACAAGAGAGATAGAACTCATCAATCAAGACCAAAGAAATCAGAAGGGA AAGATGCGATTTCGACGAGGCAGGGAGCTTCTTCTCCATCACCTTGACCATGACCGGCGCTTCC GTCTCCACGGCCCTCCTCGCCAGCCTCCCGAAGCTACCCATCTCACCTCCTCCTCCTCCTCTTC CTCACCCCTCCAAGAACAAGAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.110620094

Conservation Information
Conserved circRNAs	NA
PMCS	0.110620094

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4057193-4054750(+)
4057249-4057251(-)
						
						Potential amino acid sequence
						
							MTGASVSTALLASLPKLPISPPPPPLPHPSKNKNDIRMKSLRIACTN*(+)
MGSFGRLARRAVETEAPVMVKMQELLRGNKDVMSLAQGVVYWQPPEAAMNKIKEIVWEPSISKY
GSDDGLPELREALLEKLRRENKLTKSSIMVTSGANQAFVNVVLTLCDAGDAVVMFAPYYFNSYM
SFQMTGVTDILVGASNPETLHPDVVLVLGGVRKRRRRR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4057193-4054750(+) 4057249-4057251(-)
Potential amino acid sequence	MTGASVSTALLASLPKLPISPPPPPLPHPSKNKNDIRMKSLRIACTN(+) MGSFGRLARRAVETEAPVMVKMQELLRGNKDVMSLAQGVVYWQPPEAAMNKIKEIVWEPSISKY GSDDGLPELREALLEKLRRENKLTKSSIMVTSGANQAFVNVVLTLCDAGDAVVMFAPYYFNSYM SFQMTGVTDILVGASNPETLHPDVVLVLGGVRKRRRRR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0178000_circ_g.1

Address

Any questions?

Supported by