Plant Circular RNA Database

Detail information of Os04g0551800_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0551800_circ_g.3
					
						ID in PlantcircBase
						osa_circ_024794
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 27638826-27640909  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							Os04g0551800						
					
						Parent gene annotation
						
							Similar to T-complex protein 1, alpha subunit (TCP-1-alpha) (CCT
-alpha). (Os04t0551800-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0551800_circ_g.2 Os04g0551800_circ_g.4 Os04g0551800_circ_g.5 Os04g0551800_circ_g.6 Os04g0551800_circ_g.7 						
					
						Support reads
						18
					
						Tissues
						seed
					
						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  
						
							GT-AG							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
						Os04t0551800-01:8

General Information
CircRNA Name	Os04g0551800_circ_g.3
ID in PlantcircBase	osa_circ_024794
Alias	NA
Organism	Oryza sativa
Position	chr4: 27638826-27640909 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	Os04g0551800
Parent gene annotation	Similar to T-complex protein 1, alpha subunit (TCP-1-alpha) (CCT -alpha). (Os04t0551800-01)
Parent gene strand	+
Alternative splicing	Os04g0551800_circ_g.2 Os04g0551800_circ_g.4 Os04g0551800_circ_g.5 Os04g0551800_circ_g.6 Os04g0551800_circ_g.7
Support reads	18
Tissues	seed
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	GT-AG 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	Os04t0551800-01:8

			
						 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  
						
							CAGAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTGAAGGCTGGTGCTAATGTTGTA
CTGACCACTAAGGGAATTGATGATATGTCACTGAAGatgcttgtggatgatattggtgatgtta
ccataacaaatgatggagcaaccattttgaggatgttggaagtcgagcatccagcagccaaggt
gatgtcag

									
								

					

						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
						
							ATGCTTGTGGATGATATTGGTGATGTTACCATAACAAATGATGGAGCAACCATTTTGAGGATGT
TGGAAGTCGAGCATCCAGCAGCCAAGGTGATGTCAGGCAGCTTAAAGGTGCCATCTCCTTTTTC
CCCTGGTTGTTGTTTTGTGCTTAGTTGTTTTTTGGTCCTGTTATTGTTAGGTTCTTGTTGAGTT
GGCTGAGCTTCAAGACAGAGAGGTGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAA
TTGCTAAAGGTAATGAAATGGAGCTTTCGTGTCAGTCTTTTCTTCCCTATGTATTTGCCTACCA
TTCTAAATATGCATTTATGACACTCTTTTTTTCTTTTTACCAGCGGGGCAATGATCTTGTGAGA
AACAAAATCCATCCGACATCTATTATCAGTGGCTACAGGGTGAGTTTTGCACTTCATAATTCAG
CTGCAGTACAATTTCAGATTTAAAACGAATGTTCCAGCTGCAAACCCACATTGCTTAACATGTT
TTACCATCATTTACTACCAGCTTGCTATGCGTGAAGCTTGCAAATATGTTGAAGAAAAGTTGGC
TGTCAAGGTAAGAGAATACTATCTGCTTAATGAATAGCAGCAGATTACTTCTTGACACCTGACA
CTAGTATCTATCAACATTTTCAGGTTGATAAACTTGGAAAGGATTCTCTTATAAACTGTGCGAA
GACAAGCATGTCCTCGAAGCTGATTAATAGTGACAGTGATTTCTTCGCAAATCTGGTAAGTTCC
TATTGCCATATATATACATTTGTATTTTCAGCTGTAAGTTTGATTTTAGTGATACTTTTTAAAT
TTAAATAAATATTTAGTTGATACTCTATATCTGTATATATAGGCAGTCCAATTTATTTCTTTCC
AATGTCGTAGCATGCTATAATGCTTCACTGTTAAGTCTCTATCTGACAGTTAGGCATATCCGTA
GCCAAATGCTAGTGCTTTAATTCACTTTCTGTAAGCTTTCCTTCAAACTGTGCTGTATAATTAA
CATGGCTGTTGTTTAATAGGTTGTCGATGCAGTCCAAGCTGTGAAGACCACAAACGCTAAGGGA
GAAGTGAAGTATCCTATCAAGGTGAGTTACATGCTTGTGATTCTTGTTATACATCAAAGCAAAA
CTTTGTTGTGTGCAATTGCAATACACTGAATGAGATATATTGAATTGTGCACTTGTGCTTCACT
GATTGTTCTCTTTCTGTAGCCTCTATTATTGTTTGGAAATTGTAGAGTATTACACTTGTTTGTG
AGCTTTGCTACATGTGACCTTTGTTCTTTTCTCCTGGTTATGTATAACATATTGGACACCTTGA
GAGCTAATAAAGTTTAACTTCTACCTTAATTATATGCTGTTATGTCATTGACTTTCTTGTTAAC
CAATAACCATTCATGTATGGACATGGCATTCAAGTTATTTCTCTAAAAGTACTTCGCAATAACC
ATTTTTTGATTTTTATATTAACAAAATCGACAGAAATTTGCTGGTAACTATAGCTCATCTGATC
TGCAGAGCATTAATATTTTGAAAGCCCATGGTAAAAGTGCCAAGGACAGTTACCTGCTGAATGG
GTATGCACTAAACACAGGCCGTGCAGCTCAAGGAATGCCTACTAGAGTAACCCCGGCAAGAATT
GCATGTCTTGATTTTAACCTTCAGAAGACAAAAATGCAATTGGGTGTTCAAGTCCTTGTAACTG
ATCCAAGGGAACTTGAGAAAATTCGTCAGAGGTATGTGCATTTACTTTTTCCAACGCATTCTGA
TTCATTTGTTTTGTATACTTAATGAGTCAACAATTGGGGTGTTCTCTTTTATCTGATTTGCACA
TTTTATTTTTTTTATATTTTTATTGTGTTTTTTTATTTCTATTGTTTTGTGGAATGTGGTTGGA
TCCACACATAATTCTATTATAATTTATGGTCTCCAATTGTAAAACATAATCTTACTTTTCATGG
CAGAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTGAAGGCTGGTGCTAATGTTGTA
CTGACCACTAAGGGAATTGATGATATGTCACTGAAG
						
					

			
		

Sequences
Splice junction sequence	CAGAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTGAAGGCTGGTGCTAATGTTGTA CTGACCACTAAGGGAATTGATGATATGTCACTGAAGatgcttgtggatgatattggtgatgtta ccataacaaatgatggagcaaccattttgaggatgttggaagtcgagcatccagcagccaaggt gatgtcag
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	ATGCTTGTGGATGATATTGGTGATGTTACCATAACAAATGATGGAGCAACCATTTTGAGGATGT TGGAAGTCGAGCATCCAGCAGCCAAGGTGATGTCAGGCAGCTTAAAGGTGCCATCTCCTTTTTC CCCTGGTTGTTGTTTTGTGCTTAGTTGTTTTTTGGTCCTGTTATTGTTAGGTTCTTGTTGAGTT GGCTGAGCTTCAAGACAGAGAGGTGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAA TTGCTAAAGGTAATGAAATGGAGCTTTCGTGTCAGTCTTTTCTTCCCTATGTATTTGCCTACCA TTCTAAATATGCATTTATGACACTCTTTTTTTCTTTTTACCAGCGGGGCAATGATCTTGTGAGA AACAAAATCCATCCGACATCTATTATCAGTGGCTACAGGGTGAGTTTTGCACTTCATAATTCAG CTGCAGTACAATTTCAGATTTAAAACGAATGTTCCAGCTGCAAACCCACATTGCTTAACATGTT TTACCATCATTTACTACCAGCTTGCTATGCGTGAAGCTTGCAAATATGTTGAAGAAAAGTTGGC TGTCAAGGTAAGAGAATACTATCTGCTTAATGAATAGCAGCAGATTACTTCTTGACACCTGACA CTAGTATCTATCAACATTTTCAGGTTGATAAACTTGGAAAGGATTCTCTTATAAACTGTGCGAA GACAAGCATGTCCTCGAAGCTGATTAATAGTGACAGTGATTTCTTCGCAAATCTGGTAAGTTCC TATTGCCATATATATACATTTGTATTTTCAGCTGTAAGTTTGATTTTAGTGATACTTTTTAAAT TTAAATAAATATTTAGTTGATACTCTATATCTGTATATATAGGCAGTCCAATTTATTTCTTTCC AATGTCGTAGCATGCTATAATGCTTCACTGTTAAGTCTCTATCTGACAGTTAGGCATATCCGTA GCCAAATGCTAGTGCTTTAATTCACTTTCTGTAAGCTTTCCTTCAAACTGTGCTGTATAATTAA CATGGCTGTTGTTTAATAGGTTGTCGATGCAGTCCAAGCTGTGAAGACCACAAACGCTAAGGGA GAAGTGAAGTATCCTATCAAGGTGAGTTACATGCTTGTGATTCTTGTTATACATCAAAGCAAAA CTTTGTTGTGTGCAATTGCAATACACTGAATGAGATATATTGAATTGTGCACTTGTGCTTCACT GATTGTTCTCTTTCTGTAGCCTCTATTATTGTTTGGAAATTGTAGAGTATTACACTTGTTTGTG AGCTTTGCTACATGTGACCTTTGTTCTTTTCTCCTGGTTATGTATAACATATTGGACACCTTGA GAGCTAATAAAGTTTAACTTCTACCTTAATTATATGCTGTTATGTCATTGACTTTCTTGTTAAC CAATAACCATTCATGTATGGACATGGCATTCAAGTTATTTCTCTAAAAGTACTTCGCAATAACC ATTTTTTGATTTTTATATTAACAAAATCGACAGAAATTTGCTGGTAACTATAGCTCATCTGATC TGCAGAGCATTAATATTTTGAAAGCCCATGGTAAAAGTGCCAAGGACAGTTACCTGCTGAATGG GTATGCACTAAACACAGGCCGTGCAGCTCAAGGAATGCCTACTAGAGTAACCCCGGCAAGAATT GCATGTCTTGATTTTAACCTTCAGAAGACAAAAATGCAATTGGGTGTTCAAGTCCTTGTAACTG ATCCAAGGGAACTTGAGAAAATTCGTCAGAGGTATGTGCATTTACTTTTTCCAACGCATTCTGA TTCATTTGTTTTGTATACTTAATGAGTCAACAATTGGGGTGTTCTCTTTTATCTGATTTGCACA TTTTATTTTTTTTATATTTTTATTGTGTTTTTTTATTTCTATTGTTTTGTGGAATGTGGTTGGA TCCACACATAATTCTATTATAATTTATGGTCTCCAATTGTAAAACATAATCTTACTTTTCATGG CAGAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTGAAGGCTGGTGCTAATGTTGTA CTGACCACTAAGGGAATTGATGATATGTCACTGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.156142015

Conservation Information
Conserved circRNAs	NA
PMCS	0.156142015

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							27638827-27640906(+)
27638905-27640903(-)
27638880-27640581(-)
						
						Potential amino acid sequence
						
							MLVDDIGDVTITNDGATILRMLEVEHPAAKVLVELAELQDREVGDGTTSVVIIAAELLKRGNDL
VRNKIHPTSIISGYRLAMREACKYVEEKLAVKVDKLGKDSLINCAKTSMSSKLINSDSDFFANL
VVDAVQAVKTTNAKGEVKYPIKSINILKAHGKSAKDSYLLNGYALNTGRAAQGMPTRVTPARIA
CLDFNLQKTKMQLGVQVLVTDPRELEKIRQRESDITKERIEKILKAGANVVLTTKGIDDMSLKM
LVDDIGDVTITNDGATILRMLEVEHPAAKVLVELAELQDREVGDGTTSVVIIAAELLKRGNDLV
RNKIHPTSIISGYRLAMREACKYVEEKLAVKVDKLGKDSLINCAKTSMSSKLINSDSDFFANLV
VDAVQAVKTTNAKGEVKYPIKSINILKAHGKSAKDSYLLNGYALNTGRAAQGMPTRVTPARIAC
LDFNLQKTKMQLGVQVLVTDPRELEKIRQRESDITKERIEKILKAGANVVLTTKGIDDMSLKML
VDDIGDVTITNDGATILRMLEVEHPAAKVLVELAELQDREVGDGTTSVVIIAAELLKRGNDLVR
NKIHPTSIISGYRLAMREACKYVEEKLAVKVDKLGKDSLINCAKTSMSSKLINSDSDFFANLVV
DAVQAVKTTNAKGEVKYPIKSINILKAHGKSAKDSYLLNGYALNTGRAAQGMPTRVTPARIACL
DFNLQKTKMQLGVQVLVTDPRELEKIRQRESDITKERIEKILKAGANVVLTTKGIDDMSLKMLV
DDIGDVTITNDGATILRMLEVEHPAAKVLVELAELQDREVGDGTTSVVIIAAELLKRGNDLVRN
KIHPTSIISGYRLAMREACKYVEEKLAVKVDKLGKDSLINCAKTSMSSKLINSDSDFFANLVVD
AVQAVKTTNAKGEVKYPIKSINILKAHGKSAKDSYLLNGYALNTGRAAQGMPTRVTPARIACLD
FNLQKTKMQLGVQVLVTDPRELEKIRQRESDITKERIEKILKAGANVVLTTKGIDDMSLK(+)
MLDFQHPQNGCSIICYGNITNIIHKHLQ*(-)
MVAPSFVMVTSPISSTSIFSDISSIPLVVSTTLAPAFRIFSIRSFVMSDSL*(-)
						
						Sponge-miRNAs
						
							osa-miR5837.1 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	27638827-27640906(+) 27638905-27640903(-) 27638880-27640581(-)
Potential amino acid sequence	MLVDDIGDVTITNDGATILRMLEVEHPAAKVLVELAELQDREVGDGTTSVVIIAAELLKRGNDL VRNKIHPTSIISGYRLAMREACKYVEEKLAVKVDKLGKDSLINCAKTSMSSKLINSDSDFFANL VVDAVQAVKTTNAKGEVKYPIKSINILKAHGKSAKDSYLLNGYALNTGRAAQGMPTRVTPARIA CLDFNLQKTKMQLGVQVLVTDPRELEKIRQRESDITKERIEKILKAGANVVLTTKGIDDMSLKM LVDDIGDVTITNDGATILRMLEVEHPAAKVLVELAELQDREVGDGTTSVVIIAAELLKRGNDLV RNKIHPTSIISGYRLAMREACKYVEEKLAVKVDKLGKDSLINCAKTSMSSKLINSDSDFFANLV VDAVQAVKTTNAKGEVKYPIKSINILKAHGKSAKDSYLLNGYALNTGRAAQGMPTRVTPARIAC LDFNLQKTKMQLGVQVLVTDPRELEKIRQRESDITKERIEKILKAGANVVLTTKGIDDMSLKML VDDIGDVTITNDGATILRMLEVEHPAAKVLVELAELQDREVGDGTTSVVIIAAELLKRGNDLVR NKIHPTSIISGYRLAMREACKYVEEKLAVKVDKLGKDSLINCAKTSMSSKLINSDSDFFANLVV DAVQAVKTTNAKGEVKYPIKSINILKAHGKSAKDSYLLNGYALNTGRAAQGMPTRVTPARIACL DFNLQKTKMQLGVQVLVTDPRELEKIRQRESDITKERIEKILKAGANVVLTTKGIDDMSLKMLV DDIGDVTITNDGATILRMLEVEHPAAKVLVELAELQDREVGDGTTSVVIIAAELLKRGNDLVRN KIHPTSIISGYRLAMREACKYVEEKLAVKVDKLGKDSLINCAKTSMSSKLINSDSDFFANLVVD AVQAVKTTNAKGEVKYPIKSINILKAHGKSAKDSYLLNGYALNTGRAAQGMPTRVTPARIACLD FNLQKTKMQLGVQVLVTDPRELEKIRQRESDITKERIEKILKAGANVVLTTKGIDDMSLK(+) MLDFQHPQNGCSIICYGNITNIIHKHLQ(-) MVAPSFVMVTSPISSTSIFSDISSIPLVVSTTLAPAFRIFSIRSFVMSDSL(-)
Sponge-miRNAs	osa-miR5837.1
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0551800_circ_g.3

Address

Any questions?

Supported by