Plant Circular RNA Database

Detail information of Os10g0390100_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os10g0390100_circ_g.2
					
						ID in PlantcircBase
						osa_circ_006693
					
						Alias
						Os_ciR4257
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 12942936-12943980  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os10g0390100						
					
						Parent gene annotation
						
							Non-protein coding transcript. (Os10t0390100-01);Armadillo-like 
helical domain containing protein. (Os10t0390100-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						6
					
						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
						Os10t0390100-02:3

General Information
CircRNA Name	Os10g0390100_circ_g.2
ID in PlantcircBase	osa_circ_006693
Alias	Os_ciR4257
Organism	Oryza sativa
Position	chr10: 12942936-12943980 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os10g0390100
Parent gene annotation	Non-protein coding transcript. (Os10t0390100-01);Armadillo-like helical domain containing protein. (Os10t0390100-02)
Parent gene strand	-
Alternative splicing	NA
Support reads	6
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	Os10t0390100-02:3

			
						 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  
						
							AGTTACCACAGTGGTGAGATGAGATCGCAAATAGTGCACCCTTAAGAGTACCTGTCAGCATATT
GTTGCGCAGTTCCTCAGGGGCAACCTCCACGATGACatgtgggtattgcagaattgattgcagc
atcaggcaacccaggacactcatctttgcaccaagaggccattcccaagatgatttctggtgga
ggtagttc

									
								

					

						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: 151
Transcript exons: 12942936-12943012,12943907-12943980
ATGTGGGTATTGCAGAATTGATTGCAGCATCAGGCAACCCAGGACACTCATCTTTGCACCAAGA
GGCCATTCCCAAGGCAAATAGTGCACCCTTAAGAGTACCTGTCAGCATATTGTTGCGCAGTTCC
TCAGGGGCAACCTCCACGATGAC
Transcript length: 444
Transcript exons: 12942936-12943115,12943207-12943326,12943837-12943980
ATGTGGGTATTGCAGAATTGATTGCAGCATCAGGCAACCCAGGACACTCATCTTTGCACCAAGA
GGCCATTCCCAAGATGATTTCTGGTGGAGGTAGTTCTCAAGAAAAAGCATATGTGCAACAATGC
TATCAGAAGATTCAGAATTTGAACTTAATGCTGCAGAAAGAACTTGGGAACTCTCAAGGCGTTT
TGTTTCGAGCCTTTGGCATGCCGCTAAGATAGAAGCTACAACCCCCGCTTTCCCTAGTTCAAGC
AACTCATTGATTCTGGAACCAAGTTCATCCCAAATTTGCTCCATCTGGTCTGAGGTTTTAGCTG
ATGCTACCAAGGCTTGCACCACATAGTTACCACAGTGGTGAGATGAGATCGCAAATAGTGCACC
CTTAAGAGTACCTGTCAGCATATTGTTGCGCAGTTCCTCAGGGGCAACCTCCACGATGAC
						
					

						Genomic sequence
						
							ATGTGGGTATTGCAGAATTGATTGCAGCATCAGGCAACCCAGGACACTCATCTTTGCACCAAGA
GGCCATTCCCAAGATGATTTCTGGTGGAGGTAGTTCTCAAGAAAAAGCATATGTGCAACAATGC
TATCAGAAGATTCAGAATTTGAACTTAATGCTGCAGAAAGAACTTGGGAACTCTGCAGTTCAAA
TCATATGAGTTAGATATCATTGAGTCAAAACTAATTATCCATTATCGATGCAGAAATATTTAGT
TGAAAAAGTGAAGACCTCAAGGCGTTTTGTTTCGAGCCTTTGGCATGCCGCTAAGATAGAAGCT
ACAACCCCCGCTTTCCCTAGTTCAAGCAACTCATTGATTCTGGAACCAAGTTCATCCCAAATTT
GCTCCATCTATCAATGAAACAAGAATTACATCATTGAGGATTAGTCGGTTGTTGAACAAGGAAA
ATCTATAACTTAAATTATGTAGTTGACAAGCATTGGAAACAGAATAGGGTGGAATAGAATTATA
ATCACATAGTATGCACTATGCATTTTAGGCATGCACTCACACATGGACACAAGATTATTATCCT
TCCCAAGATTAGCACATAAATTATGGTTCAGGAATCATGCATTGTTTGTCACACAAAAGGTAGT
CTGACGGTGCATGTTGCATTTTGCAAGTTGAATATGACGATAAATTATAATTAATCTAACATAA
GAAAGGAAGATGTGTCAAAAATCAGCATGTCCCTTAATTTGTGATGATGATTTATGGAATGCTC
ACTGACTCGATGCAATATGAATAGAGAGAAGAAAGCATTTATTTTGGTCCGGCCGATCAACTTG
CTGTAAGGACATCTTTTTTAAGTGAAAGAAATTAATAAAATTGCCAATGAACATTTGAATGACA
TATACCTGGTCTGAGGTTTTAGCTGATGCTACCAAGGCTTGCACCACATAGTTACCACAGTGGT
GAGATGAGATCGCAAATAGTGCACCCTTAAGAGTACCTGTCAGCATATTGTTGCGCAGTTCCTC
AGGGGCAACCTCCACGATGAC
						
					

			
		

Sequences
Splice junction sequence	AGTTACCACAGTGGTGAGATGAGATCGCAAATAGTGCACCCTTAAGAGTACCTGTCAGCATATT GTTGCGCAGTTCCTCAGGGGCAACCTCCACGATGACatgtgggtattgcagaattgattgcagc atcaggcaacccaggacactcatctttgcaccaagaggccattcccaagatgatttctggtgga ggtagttc
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: 151 Transcript exons: 12942936-12943012,12943907-12943980 ATGTGGGTATTGCAGAATTGATTGCAGCATCAGGCAACCCAGGACACTCATCTTTGCACCAAGA GGCCATTCCCAAGGCAAATAGTGCACCCTTAAGAGTACCTGTCAGCATATTGTTGCGCAGTTCC TCAGGGGCAACCTCCACGATGAC Transcript length: 444 Transcript exons: 12942936-12943115,12943207-12943326,12943837-12943980 ATGTGGGTATTGCAGAATTGATTGCAGCATCAGGCAACCCAGGACACTCATCTTTGCACCAAGA GGCCATTCCCAAGATGATTTCTGGTGGAGGTAGTTCTCAAGAAAAAGCATATGTGCAACAATGC TATCAGAAGATTCAGAATTTGAACTTAATGCTGCAGAAAGAACTTGGGAACTCTCAAGGCGTTT TGTTTCGAGCCTTTGGCATGCCGCTAAGATAGAAGCTACAACCCCCGCTTTCCCTAGTTCAAGC AACTCATTGATTCTGGAACCAAGTTCATCCCAAATTTGCTCCATCTGGTCTGAGGTTTTAGCTG ATGCTACCAAGGCTTGCACCACATAGTTACCACAGTGGTGAGATGAGATCGCAAATAGTGCACC CTTAAGAGTACCTGTCAGCATATTGTTGCGCAGTTCCTCAGGGGCAACCTCCACGATGAC
Genomic sequence	ATGTGGGTATTGCAGAATTGATTGCAGCATCAGGCAACCCAGGACACTCATCTTTGCACCAAGA GGCCATTCCCAAGATGATTTCTGGTGGAGGTAGTTCTCAAGAAAAAGCATATGTGCAACAATGC TATCAGAAGATTCAGAATTTGAACTTAATGCTGCAGAAAGAACTTGGGAACTCTGCAGTTCAAA TCATATGAGTTAGATATCATTGAGTCAAAACTAATTATCCATTATCGATGCAGAAATATTTAGT TGAAAAAGTGAAGACCTCAAGGCGTTTTGTTTCGAGCCTTTGGCATGCCGCTAAGATAGAAGCT ACAACCCCCGCTTTCCCTAGTTCAAGCAACTCATTGATTCTGGAACCAAGTTCATCCCAAATTT GCTCCATCTATCAATGAAACAAGAATTACATCATTGAGGATTAGTCGGTTGTTGAACAAGGAAA ATCTATAACTTAAATTATGTAGTTGACAAGCATTGGAAACAGAATAGGGTGGAATAGAATTATA ATCACATAGTATGCACTATGCATTTTAGGCATGCACTCACACATGGACACAAGATTATTATCCT TCCCAAGATTAGCACATAAATTATGGTTCAGGAATCATGCATTGTTTGTCACACAAAAGGTAGT CTGACGGTGCATGTTGCATTTTGCAAGTTGAATATGACGATAAATTATAATTAATCTAACATAA GAAAGGAAGATGTGTCAAAAATCAGCATGTCCCTTAATTTGTGATGATGATTTATGGAATGCTC ACTGACTCGATGCAATATGAATAGAGAGAAGAAAGCATTTATTTTGGTCCGGCCGATCAACTTG CTGTAAGGACATCTTTTTTAAGTGAAAGAAATTAATAAAATTGCCAATGAACATTTGAATGACA TATACCTGGTCTGAGGTTTTAGCTGATGCTACCAAGGCTTGCACCACATAGTTACCACAGTGGT GAGATGAGATCGCAAATAGTGCACCCTTAAGAGTACCTGTCAGCATATTGTTGCGCAGTTCCTC AGGGGCAACCTCCACGATGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.23866

Conservation Information
Conserved circRNAs	NA
PMCS	0.23866

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12943977-12943029(+)
12943943-12942938(-)
12943007-12943960(-)
						
						Potential amino acid sequence
						
							MTCGYCRIDCSIRQPRTLIFAPRGHSQDDFWWR*(+)
MLTGTLKGALFAISSHHCGNYVVQALVASAKTSDQMEQIWDELGSRINELLELGKAGVVASILA
ACQRLETKRLESSQVLSAALSSNSESSDSIVAHMLFLENYLHQKSSWEWPLGAKMSVLGCLMLQ
SILQYPHVIVEVAPEELRNNMLTGTLKGALFAISSHHCGNYVVQALVASAKTSDQMEQIWDELG
SRINELLELGKAGVVASILAACQRLETKRLESSQVLSAALSSNSESSDSIVAHMLFLENYLHQK
SSWEWPLGAKMSVLGCLMLQSILQYPHVIVEVAPEELRNNMLTGTLKGALFAISSHHCGNYVVQ
ALVASAKTSDQMEQIWDELGSRINELLELGKAGVVASILAACQRLETKRLESSQVLSAALSSNS
ESSDSIVAHMLFLENYLHQKSSWEWPLGAKMSVLGCLMLQSILQYPHVIVEVAPEELRNNMLTG
TLKGALFAISSHHCGNYVVQALVASAKTSDQMEQIWDELGSRINELLELGKAGVVASILAACQR
LETKRLESSQVLSAALSSNSESSDSIVAHMLFLENYLHQKSSWEWPLGAKMSVLGCLMLQSILQ
YPH(-)
MASWCKDECPGLPDAAINSAIPTCHRGGCP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	12943977-12943029(+) 12943943-12942938(-) 12943007-12943960(-)
Potential amino acid sequence	MTCGYCRIDCSIRQPRTLIFAPRGHSQDDFWWR(+) MLTGTLKGALFAISSHHCGNYVVQALVASAKTSDQMEQIWDELGSRINELLELGKAGVVASILA ACQRLETKRLESSQVLSAALSSNSESSDSIVAHMLFLENYLHQKSSWEWPLGAKMSVLGCLMLQ SILQYPHVIVEVAPEELRNNMLTGTLKGALFAISSHHCGNYVVQALVASAKTSDQMEQIWDELG SRINELLELGKAGVVASILAACQRLETKRLESSQVLSAALSSNSESSDSIVAHMLFLENYLHQK SSWEWPLGAKMSVLGCLMLQSILQYPHVIVEVAPEELRNNMLTGTLKGALFAISSHHCGNYVVQ ALVASAKTSDQMEQIWDELGSRINELLELGKAGVVASILAACQRLETKRLESSQVLSAALSSNS ESSDSIVAHMLFLENYLHQKSSWEWPLGAKMSVLGCLMLQSILQYPHVIVEVAPEELRNNMLTG TLKGALFAISSHHCGNYVVQALVASAKTSDQMEQIWDELGSRINELLELGKAGVVASILAACQR LETKRLESSQVLSAALSSNSESSDSIVAHMLFLENYLHQKSSWEWPLGAKMSVLGCLMLQSILQ YPH(-) MASWCKDECPGLPDAAINSAIPTCHRGGCP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os10g0390100_circ_g.2

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