Plant Circular RNA Database

Detail information of Os01g0966400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0966400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_005965
					
						Alias
						Os_ciR4250
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 42620708-42621427  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os01g0966400						
					
						Parent gene annotation
						
							Leucine-rich repeat, SDS22 containing protein. (Os01t0966400-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0966400_circ_g.2 						
					
						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
						Os01t0966400-01:3

General Information
CircRNA Name	Os01g0966400_circ_g.3
ID in PlantcircBase	osa_circ_005965
Alias	Os_ciR4250
Organism	Oryza sativa
Position	chr1: 42620708-42621427 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os01g0966400
Parent gene annotation	Leucine-rich repeat, SDS22 containing protein. (Os01t0966400-01)
Parent gene strand	-
Alternative splicing	Os01g0966400_circ_g.2
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	Os01t0966400-01:3

			
						 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  
						
							TTTAACCCGTAGTACATTGACTAGTTACCTCGAGAGTGAGGAGGCAGTTGTAGCCGAGGTCGAG
GCGCTCCAGATTCACGAAGCTGCTCAGGCACGACACcatttagaatcaatgctcccaggcttgt
caaagatttgacctcatccattgttttaagtttattcttgccagcattcaatacctgtacaaca
ggagagga

						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: 118
Transcript exons: 42620708-42620776,42621379-42621427
CATTTAGAATCAATGCTCCCAGGCTTGTCAAAGATTTGACCTCATCCATTGTTTTAAGTTTATT
CTTGCAGCCGAGGTCGAGGCGCTCCAGATTCACGAAGCTGCTCAGGCACGACAC
Transcript length: 247
Transcript exons: 42620708-42620789,42620877-42620969,42621356-42621427
CATTTAGAATCAATGCTCCCAGGCTTGTCAAAGATTTGACCTCATCCATTGTTTTAAGTTTATT
CTTGCCAGCATTCAATACCTGCAGCTTTGAGAGGCCTTCAACACCTTTTAGGCTCACAAGCTTG
TTTTCAATAACCGAAAGCCACTTCAAATTGGCACAGTTTGATAGACCCTCGAGAGTGAGGAGGC
AGTTGTAGCCGAGGTCGAGGCGCTCCAGATTCACGAAGCTGCTCAGGCACGACAC
						
						Genomic sequence
						
							CATTTAGAATCAATGCTCCCAGGCTTGTCAAAGATTTGACCTCATCCATTGTTTTAAGTTTATT
CTTGCCAGCATTCAATACCTGTACAACAGGAGAGGAGCAACTGCCAATCATTGCAAGTGAAGTA
ATCAGGCTAAGATCCTTTTGCGGGGCAGAGAAGTAACTCACCTGCAGCTTTGAGAGGCCTTCAA
CACCTTTTAGGCTCACAAGCTTGTTTTCAATAACCGAAAGCCACTTCAAATTGGCACAGTTTGA
TAGACCCTTCAGCATTCAAAACCACAATGTGAGTGGAAAAAAAAAAGATACTCTGATGAACACA
GCCACAGCAATGATTTAATGGAACGATTAGCCATCAATTCTCTACTTCAATGAACTCAAAGAAT
AATCCAGACCGAATGGGACATCAAATTAGTCCATTATATGACTTTCTAAAAGGTTATTACGGGA
TTCATCCTTTTAACTATTCAATGTTTCAGATGGATTTACCCAGTGCCTATGCTTGTAGAGAACA
CAGTAACACCGACATCGCATATATCCATACAGGTGAAATTCACCAAGAATCTACACCGATGCTA
AATTTGTTGTATAAACATGTGCATTTCTCACTAGAATACTGTGTTTTAACCCGTAGTACATTGA
CTAGTTACCTCGAGAGTGAGGAGGCAGTTGTAGCCGAGGTCGAGGCGCTCCAGATTCACGAAGC
TGCTCAGGCACGACAC

Sequences
Splice junction sequence	TTTAACCCGTAGTACATTGACTAGTTACCTCGAGAGTGAGGAGGCAGTTGTAGCCGAGGTCGAG GCGCTCCAGATTCACGAAGCTGCTCAGGCACGACACcatttagaatcaatgctcccaggcttgt caaagatttgacctcatccattgttttaagtttattcttgccagcattcaatacctgtacaaca ggagagga
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: 118 Transcript exons: 42620708-42620776,42621379-42621427 CATTTAGAATCAATGCTCCCAGGCTTGTCAAAGATTTGACCTCATCCATTGTTTTAAGTTTATT CTTGCAGCCGAGGTCGAGGCGCTCCAGATTCACGAAGCTGCTCAGGCACGACAC Transcript length: 247 Transcript exons: 42620708-42620789,42620877-42620969,42621356-42621427 CATTTAGAATCAATGCTCCCAGGCTTGTCAAAGATTTGACCTCATCCATTGTTTTAAGTTTATT CTTGCCAGCATTCAATACCTGCAGCTTTGAGAGGCCTTCAACACCTTTTAGGCTCACAAGCTTG TTTTCAATAACCGAAAGCCACTTCAAATTGGCACAGTTTGATAGACCCTCGAGAGTGAGGAGGC AGTTGTAGCCGAGGTCGAGGCGCTCCAGATTCACGAAGCTGCTCAGGCACGACAC
Genomic sequence	CATTTAGAATCAATGCTCCCAGGCTTGTCAAAGATTTGACCTCATCCATTGTTTTAAGTTTATT CTTGCCAGCATTCAATACCTGTACAACAGGAGAGGAGCAACTGCCAATCATTGCAAGTGAAGTA ATCAGGCTAAGATCCTTTTGCGGGGCAGAGAAGTAACTCACCTGCAGCTTTGAGAGGCCTTCAA CACCTTTTAGGCTCACAAGCTTGTTTTCAATAACCGAAAGCCACTTCAAATTGGCACAGTTTGA TAGACCCTTCAGCATTCAAAACCACAATGTGAGTGGAAAAAAAAAAGATACTCTGATGAACACA GCCACAGCAATGATTTAATGGAACGATTAGCCATCAATTCTCTACTTCAATGAACTCAAAGAAT AATCCAGACCGAATGGGACATCAAATTAGTCCATTATATGACTTTCTAAAAGGTTATTACGGGA TTCATCCTTTTAACTATTCAATGTTTCAGATGGATTTACCCAGTGCCTATGCTTGTAGAGAACA CAGTAACACCGACATCGCATATATCCATACAGGTGAAATTCACCAAGAATCTACACCGATGCTA AATTTGTTGTATAAACATGTGCATTTCTCACTAGAATACTGTGTTTTAACCCGTAGTACATTGA CTAGTTACCTCGAGAGTGAGGAGGCAGTTGTAGCCGAGGTCGAGGCGCTCCAGATTCACGAAGC TGCTCAGGCACGACAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.242341238

Conservation Information
Conserved circRNAs	NA
PMCS	0.242341238

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							42620758-42620928(-)
42620712-42620928(-)
						
						Potential amino acid sequence
						
							MDEVKSLTSLGALILNGVVPEQLRESGAPRPRLQLPPHSRGSIKLCQFEVAFGY*(-)
MVSCLSSFVNLERLDLGYNCLLTLEGLSNCANLKWLSVIENKLVSLKGVEGLSKLQVLNAGKNK
LKTMDEVKSLTSLGALILNGVVPEQLRESGAPRPRLQLPPHSRGSIKLCQFEVAFGY*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	42620758-42620928(-) 42620712-42620928(-)
Potential amino acid sequence	MDEVKSLTSLGALILNGVVPEQLRESGAPRPRLQLPPHSRGSIKLCQFEVAFGY(-) MVSCLSSFVNLERLDLGYNCLLTLEGLSNCANLKWLSVIENKLVSLKGVEGLSKLQVLNAGKNK LKTMDEVKSLTSLGALILNGVVPEQLRESGAPRPRLQLPPHSRGSIKLCQFEVAFGY(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os01g0966400_circ_g.3

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