Plant Circular RNA Database

Detail information of BGIOSGA002499_circ_g.3

			
						 General Information
					
						CircRNA Name
						BGIOSGA002499_circ_g.3
					
						ID in PlantcircBase
						osi_circ_001772
					
						Alias
						1:1413426|1416232
					
						Organism
						
							Oryza sativa ssp. indica						
					
						Position
						
							chr1: 1413426-1416232  JBrowse»						
					
						Reference genome
						
							Oryza_indica.ASM465v1.42						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							BGIOSGA002499						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							BGIOSGA002499_circ_g.1 BGIOSGA002499_circ_g.2 BGIOSGA002499_circ_g.4 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						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
						BGIOSGA002499-TA:7

General Information
CircRNA Name	BGIOSGA002499_circ_g.3
ID in PlantcircBase	osi_circ_001772
Alias	1:1413426\|1416232
Organism	Oryza sativa ssp. indica
Position	chr1: 1413426-1416232 JBrowse»
Reference genome	Oryza_indica.ASM465v1.42
Type	e-circRNA
Identification method	find_circ
Parent gene	BGIOSGA002499
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	BGIOSGA002499_circ_g.1 BGIOSGA002499_circ_g.2 BGIOSGA002499_circ_g.4
Support reads	NA
Tissues	leaf
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	BGIOSGA002499-TA:7

			
						 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  
						
							TTGTGTCATGAATAAGTTACCAGCATGATCCAGCCCATTGTGGCATGGTGCTTGTTTCCCTTCT
AGCAGGCTTCCCAGACAAAGGTTCTACGGTTTTAACtcttgcaatgcatttgtgaagaactcgg
agctgatccaaggttggttcctcatcagtaaccgtagttccaactccatatgatccatctggta
atggtgta

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							TCTTGCAATGCATTTGTGAAGAACTCGGAGCTGATCCAAGGTTGGTTCCTCATCAGTAACCGTA
GTTCCAACTCCATATGATCCATCTGGTAATGGTGTACCAACTACGAGTCTCCATGTCCTTCCTA
GAAATCTATGCACACCTTCAATTCCACCAGTGCTCCATGTTTTTGAATCTCTGTGTACATCAGA
TATTCTGTCAGCTTTCTAAAATGGCTGTAACTTCATCTGTAATATGGATGCATACCTCAGTGGT
CCCATGAACATTTCATATAAGCGGAGAGAATCAGCACCATATTCTGAAACCACGTCATCTGGGT
TGATGACATTTCCTCGACTTTTACTCATTTTATAAGCACGAGCGTTTAGACGTATGTTTGCATC
ATCCTTCAGTACATAATGATCTCCAACTTTTGTGACCTTTAAAAACATAGAAGAAAGAAAAAAA
ATCAAACTAAAAAACTTTTATCATGCCAATTGAATAAAGTTATAAATGTACCAGAGCCCACCTT
ATCTGCAGGTACTTTTTCTTGGTAGCAATCAATCAAACTTGAGTTGGAATCTGCAGAAACCCAT
CTCCCTTTATTGTCTCTATATGCAGTATATTCAACCTGTTATGATATTACCTGTTAGGAACACA
TGCACAAGATAGTAACGAACATGGGCAACTTTTGGAGGTAATTAGTTTCACCTACTTCTCCTAG
AATCAATCCTTGATTTATCAGGCACTTGAAGGGCTCTTTAGTGGAAACTACGCCAATATCATAA
AGAACCTAACATAGAAATCAGTTAGTTTGAAGATAAGGAATGCCAAAAGGAACCAGTAGATTTG
CATGCTACAGAGTACAGAAATAAAAACAAATTAATGGCATAAGCTGGGAGGAAAAACAAATGCA
AATAAGTTTACTCAAAAGAAAAAAAAACAATGCAAACGAGAAAGTAACCGCCTGTACCCGGATT
TCTTAAGAATAAGTCAGTCCCCTCGGGAAAAAAATCATATTAAAGCAGCAAAATCTAATACAAT
TGAACAAACAGACACGATCAACAAGATAAACTAAATGGTTTGTATATATTTGCACGTCAAAAAC
TTGCTAGTAGCATCCGATAGAATTATCAAAGAGCAGATATTTGTCCATGGAAAAAGAGAAGTCA
GAACCTTATGCCAAAATCTTGCATAAAGCAAATGCAAGACAGAATGTTCAGCACCACCAACATA
GATGTCAACTGGGCCCCAATAACTGCATGATGCCAAAAAAAGGGAAAAGAATAAGTAACAGAAT
ACATGATATCCCTTACTGAGGTCATATGAAAGAAGGAGCACCTCTCTTTTGCCTTGTCAACCAA
CATACTGGCATTTTGAGGATCCATAAATCTCAAATAATACCTGAAAACATTGAAATGTTAGGGT
TTAGAAGCCACTTGTAAATTTAAGAGCATATTTCAACATGGCAATAAAGATTTTCGAGTGCGAT
AGCGTTAGCAATTGATATATCTATAACTAATATAAATATTCGTATTTTTCCGGTCGTCACATCT
AATTTTCGTCCGTTTTTCGTCCATACACAATCCGATTCGGTTAGCAATAGCCATGGAAAAAAAA
TTGCAAAAAAAAAAAAAAAAATCGGCGGCCGCCGACGCCTCCACCGCCGCCGGAGGGAGAAGAG
AGGCGGCGGAGGGAGCGCCGCTGCCAGATCCGCCCGCGGTGGCCGCCACCGCCGACGGATCCAC
CCTCGGACGAAGCCAACGCCATCGACGCCGCCGTTGAGAGGGCGCCGTCGAGGCCGACGGGGAG
AGGGAGAGGGGGAGGGAGGGACGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNCTCGGCTGGGGGGGAGTGGGGCCGCCGGAGGGGAGGGGAGGGGGAGAGCCGGTGT
TGGGGGCGGGGGAGGCGGCCGGCTCGGCTAGGTGGAGGGGGAGGGGGAGGGTTAGGGTTAGGGT
TTCATCCATTTCAAAATTATCTGAGCCGTCCATCAAAATGAACAGCTGAGATCGATCAAGGGTT
TGGGCCGCACCACTTGGGCCACACGCGGGCCAACAGTCTAGCAAGCGAGAGGAAGAGTATAGGG
ATATAAATTAGACTTTGGTCGCTTGTAGGCTGAAGAAGAAAGTGGGCCGAAAAAGGCCCATAGA
GATAAAAGAATTTTTATTTAGATTTTTATTTAAATAAATACTTAAATGATGTTTGTATTATCAA
AATTAGCAATTAAGCTACGTAAATTCCAAGAAAATTTCAATGAGTGTAATTAATGATATAGAAA
ATTTAATAAAAATTAAATCCAACCATAACATTTTATTTCTCACACTTACTTTACTTATAAATTA
ATTTAATTATATACCTACCTACTTAAAAAATACCCAAATATTACAGAAAATTTATATTTCATTT
AATTAGAATTTAATATGTTCTAATTCAATTTTATCTTTTTTTCTTTCACGATGCGAGCTAAGCA
GGAATATTTTTATCCATCTTGATTATCATTAGCGCAATAAATAATTTACCTATCTTGGAACATT
ATTATATACATGTTAACGGTGTACTTTATAGAATTTAACAGTTCCTTTACCCGTAGCGAAGCAC
GGGCATTTTGCTAGTTAAAACAAACATTGATAGACGCAGTCTATTTGGAGTCAATTATGTAAAT
TGTTATAAAATTATTGAAATTGTGTCATGAATAAGTTACCAGCATGATCCAGCCCATTGTGGCA
TGGTGCTTGTTTCCCTTCTAGCAGGCTTCCCAGACAAAGGTTCTACGGTTTTAAC
						
					

			
		

Sequences
Splice junction sequence	TTGTGTCATGAATAAGTTACCAGCATGATCCAGCCCATTGTGGCATGGTGCTTGTTTCCCTTCT AGCAGGCTTCCCAGACAAAGGTTCTACGGTTTTAACtcttgcaatgcatttgtgaagaactcgg agctgatccaaggttggttcctcatcagtaaccgtagttccaactccatatgatccatctggta atggtgta
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TCTTGCAATGCATTTGTGAAGAACTCGGAGCTGATCCAAGGTTGGTTCCTCATCAGTAACCGTA GTTCCAACTCCATATGATCCATCTGGTAATGGTGTACCAACTACGAGTCTCCATGTCCTTCCTA GAAATCTATGCACACCTTCAATTCCACCAGTGCTCCATGTTTTTGAATCTCTGTGTACATCAGA TATTCTGTCAGCTTTCTAAAATGGCTGTAACTTCATCTGTAATATGGATGCATACCTCAGTGGT CCCATGAACATTTCATATAAGCGGAGAGAATCAGCACCATATTCTGAAACCACGTCATCTGGGT TGATGACATTTCCTCGACTTTTACTCATTTTATAAGCACGAGCGTTTAGACGTATGTTTGCATC ATCCTTCAGTACATAATGATCTCCAACTTTTGTGACCTTTAAAAACATAGAAGAAAGAAAAAAA ATCAAACTAAAAAACTTTTATCATGCCAATTGAATAAAGTTATAAATGTACCAGAGCCCACCTT ATCTGCAGGTACTTTTTCTTGGTAGCAATCAATCAAACTTGAGTTGGAATCTGCAGAAACCCAT CTCCCTTTATTGTCTCTATATGCAGTATATTCAACCTGTTATGATATTACCTGTTAGGAACACA TGCACAAGATAGTAACGAACATGGGCAACTTTTGGAGGTAATTAGTTTCACCTACTTCTCCTAG AATCAATCCTTGATTTATCAGGCACTTGAAGGGCTCTTTAGTGGAAACTACGCCAATATCATAA AGAACCTAACATAGAAATCAGTTAGTTTGAAGATAAGGAATGCCAAAAGGAACCAGTAGATTTG CATGCTACAGAGTACAGAAATAAAAACAAATTAATGGCATAAGCTGGGAGGAAAAACAAATGCA AATAAGTTTACTCAAAAGAAAAAAAAACAATGCAAACGAGAAAGTAACCGCCTGTACCCGGATT TCTTAAGAATAAGTCAGTCCCCTCGGGAAAAAAATCATATTAAAGCAGCAAAATCTAATACAAT TGAACAAACAGACACGATCAACAAGATAAACTAAATGGTTTGTATATATTTGCACGTCAAAAAC TTGCTAGTAGCATCCGATAGAATTATCAAAGAGCAGATATTTGTCCATGGAAAAAGAGAAGTCA GAACCTTATGCCAAAATCTTGCATAAAGCAAATGCAAGACAGAATGTTCAGCACCACCAACATA GATGTCAACTGGGCCCCAATAACTGCATGATGCCAAAAAAAGGGAAAAGAATAAGTAACAGAAT ACATGATATCCCTTACTGAGGTCATATGAAAGAAGGAGCACCTCTCTTTTGCCTTGTCAACCAA CATACTGGCATTTTGAGGATCCATAAATCTCAAATAATACCTGAAAACATTGAAATGTTAGGGT TTAGAAGCCACTTGTAAATTTAAGAGCATATTTCAACATGGCAATAAAGATTTTCGAGTGCGAT AGCGTTAGCAATTGATATATCTATAACTAATATAAATATTCGTATTTTTCCGGTCGTCACATCT AATTTTCGTCCGTTTTTCGTCCATACACAATCCGATTCGGTTAGCAATAGCCATGGAAAAAAAA TTGCAAAAAAAAAAAAAAAAATCGGCGGCCGCCGACGCCTCCACCGCCGCCGGAGGGAGAAGAG AGGCGGCGGAGGGAGCGCCGCTGCCAGATCCGCCCGCGGTGGCCGCCACCGCCGACGGATCCAC CCTCGGACGAAGCCAACGCCATCGACGCCGCCGTTGAGAGGGCGCCGTCGAGGCCGACGGGGAG AGGGAGAGGGGGAGGGAGGGACGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNCTCGGCTGGGGGGGAGTGGGGCCGCCGGAGGGGAGGGGAGGGGGAGAGCCGGTGT TGGGGGCGGGGGAGGCGGCCGGCTCGGCTAGGTGGAGGGGGAGGGGGAGGGTTAGGGTTAGGGT TTCATCCATTTCAAAATTATCTGAGCCGTCCATCAAAATGAACAGCTGAGATCGATCAAGGGTT TGGGCCGCACCACTTGGGCCACACGCGGGCCAACAGTCTAGCAAGCGAGAGGAAGAGTATAGGG ATATAAATTAGACTTTGGTCGCTTGTAGGCTGAAGAAGAAAGTGGGCCGAAAAAGGCCCATAGA GATAAAAGAATTTTTATTTAGATTTTTATTTAAATAAATACTTAAATGATGTTTGTATTATCAA AATTAGCAATTAAGCTACGTAAATTCCAAGAAAATTTCAATGAGTGTAATTAATGATATAGAAA ATTTAATAAAAATTAAATCCAACCATAACATTTTATTTCTCACACTTACTTTACTTATAAATTA ATTTAATTATATACCTACCTACTTAAAAAATACCCAAATATTACAGAAAATTTATATTTCATTT AATTAGAATTTAATATGTTCTAATTCAATTTTATCTTTTTTTCTTTCACGATGCGAGCTAAGCA GGAATATTTTTATCCATCTTGATTATCATTAGCGCAATAAATAATTTACCTATCTTGGAACATT ATTATATACATGTTAACGGTGTACTTTATAGAATTTAACAGTTCCTTTACCCGTAGCGAAGCAC GGGCATTTTGCTAGTTAAAACAAACATTGATAGACGCAGTCTATTTGGAGTCAATTATGTAAAT TGTTATAAAATTATTGAAATTGTGTCATGAATAAGTTACCAGCATGATCCAGCCCATTGTGGCA TGGTGCTTGTTTCCCTTCTAGCAGGCTTCCCAGACAAAGGTTCTACGGTTTTAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS

Conservation Information
Conserved circRNAs	NA
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1416180-1413428(-)
1413513-1416222(-)
1416178-1413441(+)
						
						Potential amino acid sequence
						
							MPQWAGSCWYYLRFMDPQNASMLVDKAKESYWGPVDIYVGGAEHSVLHLLYARFWHKVLYDIGV
VSTKEPFKCLINQGLILGEVEYTAYRDNKGRWVSADSNSSLIDCYQEKVPADKVTKVGDHYVLK
DDANIRLNARAYKMSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTGGIEGVHRFL
GRTWRLVVGTPLPDGSYGVGTTVTDEEPTLDQLRVLHKCIARVKTVEPLSGKPARRETSTMPQW
AGSCWYYLRFMDPQNASMLVDKAKESYWGPVDIYVGGAEHSVLHLLYARFWHKVLYDIGVVSTK
EPFKCLINQGLILGEVEYTAYRDNKGRWVSADSNSSLIDCYQEKVPADKVTKVGDHYVLKDDAN
IRLNARAYKMSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTGGIEGVHRFLGRTW
RLVVGTPLPDGSYGVGTTVTDEEPTLDQLRVLHKCIARVKTVEPLSGKPARRETSTMPQWAGSC
WYYLRFMDPQNASMLVDKAKESYWGPVDIYVGGAEHSVLHLLYARFWHKVLYDIGVVSTKEPFK
CLINQGLILGEVEYTAYRDNKGRWVSADSNSSLIDCYQEKVPADKVTKVGDHYVLKDDANIRLN
ARAYKMSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTGGIEGVHRFLGRTWRLVV
GTPLPDGSYGVGTTVTDEEPTLDQLRVLHKCIARVKTVEPLSGKPARRETSTMPQWAGSCWYYL
RFMDPQNASMLVDKAKESYWGPVDIYVGGAEHSVLHLLYARFWHKVLYDIGVVSTKEPFKCLIN
QGLILGEVEYTAYRDNKGRWVSADSNSSLIDCYQEKVPADKVTKVGDHYVLKDDANIRLNARAY
KMSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTGGIEGVHRFLGRTWRLVVGTPL
PDGSYGVGTTVTDEEPTLDQLRVLHKCIAR(-)
MDHMELELRLLMRNQPWISSEFFTNALQELKP*(-)
MVLVSLLAGFPDKGSTVLTLAMHL*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1416180-1413428(-) 1413513-1416222(-) 1416178-1413441(+)
Potential amino acid sequence	MPQWAGSCWYYLRFMDPQNASMLVDKAKESYWGPVDIYVGGAEHSVLHLLYARFWHKVLYDIGV VSTKEPFKCLINQGLILGEVEYTAYRDNKGRWVSADSNSSLIDCYQEKVPADKVTKVGDHYVLK DDANIRLNARAYKMSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTGGIEGVHRFL GRTWRLVVGTPLPDGSYGVGTTVTDEEPTLDQLRVLHKCIARVKTVEPLSGKPARRETSTMPQW AGSCWYYLRFMDPQNASMLVDKAKESYWGPVDIYVGGAEHSVLHLLYARFWHKVLYDIGVVSTK EPFKCLINQGLILGEVEYTAYRDNKGRWVSADSNSSLIDCYQEKVPADKVTKVGDHYVLKDDAN IRLNARAYKMSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTGGIEGVHRFLGRTW RLVVGTPLPDGSYGVGTTVTDEEPTLDQLRVLHKCIARVKTVEPLSGKPARRETSTMPQWAGSC WYYLRFMDPQNASMLVDKAKESYWGPVDIYVGGAEHSVLHLLYARFWHKVLYDIGVVSTKEPFK CLINQGLILGEVEYTAYRDNKGRWVSADSNSSLIDCYQEKVPADKVTKVGDHYVLKDDANIRLN ARAYKMSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTGGIEGVHRFLGRTWRLVV GTPLPDGSYGVGTTVTDEEPTLDQLRVLHKCIARVKTVEPLSGKPARRETSTMPQWAGSCWYYL RFMDPQNASMLVDKAKESYWGPVDIYVGGAEHSVLHLLYARFWHKVLYDIGVVSTKEPFKCLIN QGLILGEVEYTAYRDNKGRWVSADSNSSLIDCYQEKVPADKVTKVGDHYVLKDDANIRLNARAY KMSKSRGNVINPDDVVSEYGADSLRLYEMFMGPLRDSKTWSTGGIEGVHRFLGRTWRLVVGTPL PDGSYGVGTTVTDEEPTLDQLRVLHKCIAR(-) MDHMELELRLLMRNQPWISSEFFTNALQELKP(-) MVLVSLLAGFPDKGSTVLTLAMHL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Huang et al., 2021

circRNA

Detail information of BGIOSGA002499_circ_g.3

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