Plant Circular RNA Database

Detail information of BGIOSGA017716_circ_g.3

			
						 General Information
					
						CircRNA Name
						BGIOSGA017716_circ_g.3
					
						ID in PlantcircBase
						osi_circ_006347
					
						Alias
						5:27232657|27234498
					
						Organism
						
							Oryza sativa ssp. indica						
					
						Position
						
							chr5: 27232657-27234498  JBrowse»						
					
						Reference genome
						
							Oryza_indica.ASM465v1.42						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							BGIOSGA017716						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							BGIOSGA017716_circ_g.1 BGIOSGA017716_circ_g.2 						
					
						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
						BGIOSGA017716-TA:6

General Information
CircRNA Name	BGIOSGA017716_circ_g.3
ID in PlantcircBase	osi_circ_006347
Alias	5:27232657\|27234498
Organism	Oryza sativa ssp. indica
Position	chr5: 27232657-27234498 JBrowse»
Reference genome	Oryza_indica.ASM465v1.42
Type	e-circRNA
Identification method	find_circ
Parent gene	BGIOSGA017716
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	BGIOSGA017716_circ_g.1 BGIOSGA017716_circ_g.2
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	BGIOSGA017716-TA:6

			
						 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  
						
							CTCGTGTCTTCTGGTCATTTTCAGCATCAGCGAACAAATCTCTCACATTCTTCTCAGTTTCTCC
AACAAACTTGCTCAAGACTTCAGGTCCATTTACAATctgcatctttcaaggtcatcagtggaag
caccaaatgcaggggtaatttcatgaagtgcattcacaaaatcatccatagtaaccttaatgct
ttcttcat

									
								

					

						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
						
							CTGCATCTTTCAAGGTCATCAGTGGAAGCACCAAATGCAGGGGTAATTTCATGAAGTGCATTCA
CAAAATCATCCATAGTAACCTTAATGCTTTCTTCATCCAAAGGCTTGGTAAGGTCATCCATGCT
TATCTGCCTGTTCAAAGCATATGAGACTGCACTTTTGACGACACCTTCCAGCTCTGCTCCACTG
TAGTTCTTTGTCCGTGCAGCTTCATTCAGAAGAGCATGTCACAACCATCAATCACATTATTTTT
GTAGATAATCGATTAAAACCCGGCCTCTACAACCAACATGGATGTACACAGCCAAGATCACATG
CAGCACATATCTTTTAGAACAAGAAATTCCCACAGGCAGCTACTCAGTCATACTAAAATGGGTG
TTGAAGTAAGAAGCATTGCTAAGACAGCAATTTTTGGAAATGGGAAACTAAAACCTTTGAAGCT
TGAGTAATAAGACTAGAATGAGCTAATCAGTCCATTTTAAGAGATCATTTACAACATTTGTTAT
AATGAACGAATGCCTGAAAACAAATATGAATTATCAAAGAATATACCTAGCTCCTGAAGATTAA
CATCCGGGGAAAGGAAAGAGCTTTCTTTCATCTTATTCGTATGAATTTGAAGAATCTGCAAACG
GCCATTTTCATCAGGCAGGTTTATCTCAATATGAACTTCCAATCGTCCAGGCCTGTAACAGATG
TGTCAAATGTCAATGGACACGTGCAAATAGTAAAACAAAAATACAAAAAGAAGATTCCCCAATG
GTTTAGGCCTGCAATATCTAAAATAATCAAGGCAAGCATAATTTTCTGAATTACACAGTAAATG
CAGCACAGAGTTATGTTTAGATATTAAAATGTACATAAAATGAAATGGTAACAATTTTAGGAGG
TCTGATGCATTTCATGATCTAGCTTGAGTGCATTTCTAGAGGGTCAGAAGTTACCTCAGTAAAG
CTTCATCAAGTAAATCCTTACGATTGGTCATTCCAATGAGGAGCACATTATTCAATGCCTCAAC
ACCATCTATCTAAAATGCAGAAAGTTTGACGAGAACTTAGTGTATATGCAGAAAGAAAATACGT
GAGTCCAAAGTTCAAATTCTAGGAAAAGATACCTTTGTAAGGAGCTGATTTACAATGCTATCAT
GTACACCCGTACCATCTCTGGTAGATCCTCTAGACTGCACAGCACAATCAGAGTTTAATTAATT
CAGGAGAAGTTAGCAGTTACTATAAATAAAGCTGAAGCATGCTACAACTGATGTAATCAAACAT
AGCACACTGAATATACACTGGACAAAATTGCAAGTTGAACTTCTAGAAGGGGTAAAAGAGTTTG
ATCTGGAGTACTTATGCTCTGTTATTCCCTAAGAACTTATGCATGACTAATCAGTCAAACTATT
TGCTCTCATATTTCCAACTCACTTAATGTAAGGGTACTTCAACCATTCTCTTCGGTGACATTCT
CAAACTAACCTTATGAAATTAACAAAGGAAGAAACACAAAAAAAGATGTTTTACATCTTGAGAG
AAAGATATAGTCAAGTAGAAATATGCATGATGTTTATTTAAGGAAAAAGAACTCCACCTTGCAG
ATAGCATCAATTTCATCGAAAATGATAACGTGGAGGTCACTCTGATCACCTGTATTTGAAAACA
AGGTACCGCGATTAATTGTTAAAAAGGGTCCACTCCACATAAAAATATGGAAAAGCTTTTATCG
ATGAGGAATCATACCTCGTGTCTTCTGGTCATTTTCAGCATCAGCGAACAAATCTCTCACATTC
TTCTCAGTTTCTCCAACAAACTTGCTCAAGACTTCAGGTCCATTTACAAT
						
					

			
		

Sequences
Splice junction sequence	CTCGTGTCTTCTGGTCATTTTCAGCATCAGCGAACAAATCTCTCACATTCTTCTCAGTTTCTCC AACAAACTTGCTCAAGACTTCAGGTCCATTTACAATctgcatctttcaaggtcatcagtggaag caccaaatgcaggggtaatttcatgaagtgcattcacaaaatcatccatagtaaccttaatgct ttcttcat
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	CTGCATCTTTCAAGGTCATCAGTGGAAGCACCAAATGCAGGGGTAATTTCATGAAGTGCATTCA CAAAATCATCCATAGTAACCTTAATGCTTTCTTCATCCAAAGGCTTGGTAAGGTCATCCATGCT TATCTGCCTGTTCAAAGCATATGAGACTGCACTTTTGACGACACCTTCCAGCTCTGCTCCACTG TAGTTCTTTGTCCGTGCAGCTTCATTCAGAAGAGCATGTCACAACCATCAATCACATTATTTTT GTAGATAATCGATTAAAACCCGGCCTCTACAACCAACATGGATGTACACAGCCAAGATCACATG CAGCACATATCTTTTAGAACAAGAAATTCCCACAGGCAGCTACTCAGTCATACTAAAATGGGTG TTGAAGTAAGAAGCATTGCTAAGACAGCAATTTTTGGAAATGGGAAACTAAAACCTTTGAAGCT TGAGTAATAAGACTAGAATGAGCTAATCAGTCCATTTTAAGAGATCATTTACAACATTTGTTAT AATGAACGAATGCCTGAAAACAAATATGAATTATCAAAGAATATACCTAGCTCCTGAAGATTAA CATCCGGGGAAAGGAAAGAGCTTTCTTTCATCTTATTCGTATGAATTTGAAGAATCTGCAAACG GCCATTTTCATCAGGCAGGTTTATCTCAATATGAACTTCCAATCGTCCAGGCCTGTAACAGATG TGTCAAATGTCAATGGACACGTGCAAATAGTAAAACAAAAATACAAAAAGAAGATTCCCCAATG GTTTAGGCCTGCAATATCTAAAATAATCAAGGCAAGCATAATTTTCTGAATTACACAGTAAATG CAGCACAGAGTTATGTTTAGATATTAAAATGTACATAAAATGAAATGGTAACAATTTTAGGAGG TCTGATGCATTTCATGATCTAGCTTGAGTGCATTTCTAGAGGGTCAGAAGTTACCTCAGTAAAG CTTCATCAAGTAAATCCTTACGATTGGTCATTCCAATGAGGAGCACATTATTCAATGCCTCAAC ACCATCTATCTAAAATGCAGAAAGTTTGACGAGAACTTAGTGTATATGCAGAAAGAAAATACGT GAGTCCAAAGTTCAAATTCTAGGAAAAGATACCTTTGTAAGGAGCTGATTTACAATGCTATCAT GTACACCCGTACCATCTCTGGTAGATCCTCTAGACTGCACAGCACAATCAGAGTTTAATTAATT CAGGAGAAGTTAGCAGTTACTATAAATAAAGCTGAAGCATGCTACAACTGATGTAATCAAACAT AGCACACTGAATATACACTGGACAAAATTGCAAGTTGAACTTCTAGAAGGGGTAAAAGAGTTTG ATCTGGAGTACTTATGCTCTGTTATTCCCTAAGAACTTATGCATGACTAATCAGTCAAACTATT TGCTCTCATATTTCCAACTCACTTAATGTAAGGGTACTTCAACCATTCTCTTCGGTGACATTCT CAAACTAACCTTATGAAATTAACAAAGGAAGAAACACAAAAAAAGATGTTTTACATCTTGAGAG AAAGATATAGTCAAGTAGAAATATGCATGATGTTTATTTAAGGAAAAAGAACTCCACCTTGCAG ATAGCATCAATTTCATCGAAAATGATAACGTGGAGGTCACTCTGATCACCTGTATTTGAAAACA AGGTACCGCGATTAATTGTTAAAAAGGGTCCACTCCACATAAAAATATGGAAAAGCTTTTATCG ATGAGGAATCATACCTCGTGTCTTCTGGTCATTTTCAGCATCAGCGAACAAATCTCTCACATTC TTCTCAGTTTCTCCAACAAACTTGCTCAAGACTTCAGGTCCATTTACAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_028544* 						
					
						PMCS

Conservation Information
Conserved circRNAs	osa_circ_028544*
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							27233649-27234494(-)
27232719-27234484(-)
27232664-27234494(-)
27233808-27232707(+)
						
						Potential amino acid sequence
						
							MTNRKDLLDEALLRPGRLEVHIEINLPDENGRLQILQIHTNKMKESSFLSPDVNLQELAARTKN
YSGAELEGVVKSAVSYALNRQISMDDLTKPLDEESIKVTMDDFVNALHEITPAFGASTDDLERC
RL*(-)
MHFMKLPLHLVLPLMTLKDADCKWT*(-)
MQIVNGPEVLSKFVGETEKNVRDLFADAENDQKTRGDQSDLHVIIFDEIDAICKSRGSTRDGTG
VHDSIVNQLLTKIDGVEALNNVLLIGMTNRKDLLDEALLRPGRLEVHIEINLPDENGRLQILQI
HTNKMKESSFLSPDVNLQELAARTKNYSGAELEGVVKSAVSYALNRQISMDDLTKPLDEESIKV
TMDDFVNALHEITPAFGASTDDLERCRL*(-)
MYTRTISGRSSRLADSINFIENDNVEVTLITSCLLVIFSISEQISHILLSFSNKLAQDFRSIYN
LHLSRSSVEAPNAGVIS*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	27233649-27234494(-) 27232719-27234484(-) 27232664-27234494(-) 27233808-27232707(+)
Potential amino acid sequence	MTNRKDLLDEALLRPGRLEVHIEINLPDENGRLQILQIHTNKMKESSFLSPDVNLQELAARTKN YSGAELEGVVKSAVSYALNRQISMDDLTKPLDEESIKVTMDDFVNALHEITPAFGASTDDLERC RL(-) MHFMKLPLHLVLPLMTLKDADCKWT(-) MQIVNGPEVLSKFVGETEKNVRDLFADAENDQKTRGDQSDLHVIIFDEIDAICKSRGSTRDGTG VHDSIVNQLLTKIDGVEALNNVLLIGMTNRKDLLDEALLRPGRLEVHIEINLPDENGRLQILQI HTNKMKESSFLSPDVNLQELAARTKNYSGAELEGVVKSAVSYALNRQISMDDLTKPLDEESIKV TMDDFVNALHEITPAFGASTDDLERCRL(-) MYTRTISGRSSRLADSINFIENDNVEVTLITSCLLVIFSISEQISHILLSFSNKLAQDFRSIYN LHLSRSSVEAPNAGVIS(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Huang et al., 2021

circRNA

Detail information of BGIOSGA017716_circ_g.3

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