Plant Circular RNA Database

Detail information of Os06g0622300_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os06g0622300_circ_g.2
					
						ID in PlantcircBase
						osa_circ_031404
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 25017703-25018993  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							Os06g0622300						
					
						Parent gene annotation
						
							AT-rich interaction domain-containing protein, Shoot apical meri
stem (SAM) development (Os06t0622300-01);Hypothetical conserved 
gene. (Os06t0622300-02);Similar to DNA-binding protein. (Os06t06
22300-03);Similar to DNA-binding protein. (Os06t0622300-04)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						4
					
						Tissues
						root, 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
						Os06t0622300-03:5
Os06t0622300-04:5
Os06t0622300-02:5
Os06t0622300-01:5

General Information
CircRNA Name	Os06g0622300_circ_g.2
ID in PlantcircBase	osa_circ_031404
Alias	NA
Organism	Oryza sativa
Position	chr6: 25017703-25018993 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	Os06g0622300
Parent gene annotation	AT-rich interaction domain-containing protein, Shoot apical meri stem (SAM) development (Os06t0622300-01);Hypothetical conserved gene. (Os06t0622300-02);Similar to DNA-binding protein. (Os06t06 22300-03);Similar to DNA-binding protein. (Os06t0622300-04)
Parent gene strand	+
Alternative splicing	NA
Support reads	4
Tissues	root, 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	Os06t0622300-03:5 Os06t0622300-04:5 Os06t0622300-02:5 Os06t0622300-01:5

			
						 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  
						
							AACTTCGGCAGTTGTCACTCTCCATGGACAGCTATTTGTCCGTGCACCATTCGAGCAGTCAAAG
TAAATGGTGCTCTACAAGATGAAGCGCAACATGCAAgttctgccaagaggaaaaggacaccgac
cttggaagatgacaggattgtaccatataaacctgacaagctacagtaagtcttgcagatgatt
ctctttcc

									
								

					

						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: 419
Transcript exons: 25017703-25017775,25018002-25018068,25018322-25018372,25
018678-25018770,25018859-25018993
GTTCTGCCAAGAGGAAAAGGACACCGACCTTGGAAGATGACAGGATTGTACCATATAAACCTGA
CAAGCTACAAAATGACTCAATGGTTCTTGACCTTGGCCCTCCAGCTGATTGGGTAAAGATAAAC
GTTCGGAGAACCAAAGATTGCTATGAAGTCTATGCATTGGTTCCTGGCCTTCTGCGTGAGGAGG
TACATGTTCAGTCAGATCCTGCTGGCCGTTTGATAGTTACTGGAGAGCCTGAGCAACTAGACAA
TCCTTGGGGTGTTACTCCATTCAAGAAGGTTATTAGTTTGCCCTCCCGCATTGATCCTCATCAA
ACTTCGGCAGTTGTCACTCTCCATGGACAGCTATTTGTCCGTGCACCATTCGAGCAGTCAAAGT
AAATGGTGCTCTACAAGATGAAGCGCAACATGCAA
						
					

						Genomic sequence
						
							GTTCTGCCAAGAGGAAAAGGACACCGACCTTGGAAGATGACAGGATTGTACCATATAAACCTGA
CAAGCTACAGTAAGTCTTGCAGATGATTCTCTTTCCTTTGTCATCGAGCATCCACAGGAATCAT
GTAATATTACTGTAGGCACCAGTCTGTTCTTTTGAATGTCACGATGATATTATAAGGCTCATCC
AGTTAACTATTTGGGTTTTGGCATGCCAATTGATTTTTTCACTCTTCCACCCTCAATTTGTATG
GATGTGAAACTGTGAACTGATTTCAATTATTTCTATTTGGCAGAAATGACTCAATGGTTCTTGA
CCTTGGCCCTCCAGCTGATTGGGTAAAGATAAACGTTCGGAGAACCGTAAGTATCTCATTTGGA
TCATCATATTTTACCTTTTTCATGCTTTTTTGGCCTCTTTTAGCCACTTGCCCATATTTTCCAG
TTCTAGTAGTTCTCCACAGAAGTTCTGAAAAACAATGCTAGCGAAACGCATATTATGTTTGAAA
TCTGTAGAACTATCGTGGAAGTTAGAAACAGCATGTGTTAACCAGAAATCAGGGGAAACATATT
TTTCATGGTCATTTTGTAAAGGAAAATATCTTTTTTCTTGCAGAAAGATTGCTATGAAGTCTAT
GCATTGGTTCCTGGCCTTCTGCGTGAGGAGGTAAATAAATTCTACCATTCAATTAGCAAGCATG
CAGTTAGACGCTTTTGGTTCAGTTATCATTTACCAAGCACTCCTCTGTCATAAGTTGGCAACGT
GTCCTATGCACACAAGTTCCGGTTGCACTAACTGTGCACACCAACTGAGAGATGCCCTAAAAGA
ATCCAAAAGAATTTCTGCGTATACTTGTAATCTTATTCCACCTATCTATGAATTTCAAGTTTAG
ACTCATACTGCAAAAGTTGGAATGACTTTGGTACTTTGGTTCTAGATATTCCTTATTCATATCT
AATACATTGATGCAGGTACATGTTCAGTCAGATCCTGCTGGCCGTTTGATAGTTACTGGAGAGC
CTGAGCAACTAGACAATCCTTGGGGTGTTACTCCATTCAAGAAGGTCTGTCAAGTGTTAACCTT
TTGAATTTATTTGATGTTTCATTTTATAATTGTATTCTTTGGCATTGAAAACGGTACACTTACT
TCAGGTTATTAGTTTGCCCTCCCGCATTGATCCTCATCAAACTTCGGCAGTTGTCACTCTCCAT
GGACAGCTATTTGTCCGTGCACCATTCGAGCAGTCAAAGTAAATGGTGCTCTACAAGATGAAGC
GCAACATGCAA
						
					

			
		

Sequences
Splice junction sequence	AACTTCGGCAGTTGTCACTCTCCATGGACAGCTATTTGTCCGTGCACCATTCGAGCAGTCAAAG TAAATGGTGCTCTACAAGATGAAGCGCAACATGCAAgttctgccaagaggaaaaggacaccgac cttggaagatgacaggattgtaccatataaacctgacaagctacagtaagtcttgcagatgatt ctctttcc
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: 419 Transcript exons: 25017703-25017775,25018002-25018068,25018322-25018372,25 018678-25018770,25018859-25018993 GTTCTGCCAAGAGGAAAAGGACACCGACCTTGGAAGATGACAGGATTGTACCATATAAACCTGA CAAGCTACAAAATGACTCAATGGTTCTTGACCTTGGCCCTCCAGCTGATTGGGTAAAGATAAAC GTTCGGAGAACCAAAGATTGCTATGAAGTCTATGCATTGGTTCCTGGCCTTCTGCGTGAGGAGG TACATGTTCAGTCAGATCCTGCTGGCCGTTTGATAGTTACTGGAGAGCCTGAGCAACTAGACAA TCCTTGGGGTGTTACTCCATTCAAGAAGGTTATTAGTTTGCCCTCCCGCATTGATCCTCATCAA ACTTCGGCAGTTGTCACTCTCCATGGACAGCTATTTGTCCGTGCACCATTCGAGCAGTCAAAGT AAATGGTGCTCTACAAGATGAAGCGCAACATGCAA
Genomic sequence	GTTCTGCCAAGAGGAAAAGGACACCGACCTTGGAAGATGACAGGATTGTACCATATAAACCTGA CAAGCTACAGTAAGTCTTGCAGATGATTCTCTTTCCTTTGTCATCGAGCATCCACAGGAATCAT GTAATATTACTGTAGGCACCAGTCTGTTCTTTTGAATGTCACGATGATATTATAAGGCTCATCC AGTTAACTATTTGGGTTTTGGCATGCCAATTGATTTTTTCACTCTTCCACCCTCAATTTGTATG GATGTGAAACTGTGAACTGATTTCAATTATTTCTATTTGGCAGAAATGACTCAATGGTTCTTGA CCTTGGCCCTCCAGCTGATTGGGTAAAGATAAACGTTCGGAGAACCGTAAGTATCTCATTTGGA TCATCATATTTTACCTTTTTCATGCTTTTTTGGCCTCTTTTAGCCACTTGCCCATATTTTCCAG TTCTAGTAGTTCTCCACAGAAGTTCTGAAAAACAATGCTAGCGAAACGCATATTATGTTTGAAA TCTGTAGAACTATCGTGGAAGTTAGAAACAGCATGTGTTAACCAGAAATCAGGGGAAACATATT TTTCATGGTCATTTTGTAAAGGAAAATATCTTTTTTCTTGCAGAAAGATTGCTATGAAGTCTAT GCATTGGTTCCTGGCCTTCTGCGTGAGGAGGTAAATAAATTCTACCATTCAATTAGCAAGCATG CAGTTAGACGCTTTTGGTTCAGTTATCATTTACCAAGCACTCCTCTGTCATAAGTTGGCAACGT GTCCTATGCACACAAGTTCCGGTTGCACTAACTGTGCACACCAACTGAGAGATGCCCTAAAAGA ATCCAAAAGAATTTCTGCGTATACTTGTAATCTTATTCCACCTATCTATGAATTTCAAGTTTAG ACTCATACTGCAAAAGTTGGAATGACTTTGGTACTTTGGTTCTAGATATTCCTTATTCATATCT AATACATTGATGCAGGTACATGTTCAGTCAGATCCTGCTGGCCGTTTGATAGTTACTGGAGAGC CTGAGCAACTAGACAATCCTTGGGGTGTTACTCCATTCAAGAAGGTCTGTCAAGTGTTAACCTT TTGAATTTATTTGATGTTTCATTTTATAATTGTATTCTTTGGCATTGAAAACGGTACACTTACT TCAGGTTATTAGTTTGCCCTCCCGCATTGATCCTCATCAAACTTCGGCAGTTGTCACTCTCCAT GGACAGCTATTTGTCCGTGCACCATTCGAGCAGTCAAAGTAAATGGTGCTCTACAAGATGAAGC GCAACATGCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.237537393

Conservation Information
Conserved circRNAs	NA
PMCS	0.237537393

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25018962-25018045(+)
25018348-25018954(-)
						
						Potential amino acid sequence
						
							MVLYKMKRNMQVLPRGKGHRPWKMTGLYHINLTSYKMTQWFLTLALQLIG*(+)
MHRLHSNLWFSERLSLPNQLEGQGQEPLSHFVACQVYMVQSCHLPRSVSFSSWQNLHVALHLVE
HHLL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25018962-25018045(+) 25018348-25018954(-)
Potential amino acid sequence	MVLYKMKRNMQVLPRGKGHRPWKMTGLYHINLTSYKMTQWFLTLALQLIG(+) MHRLHSNLWFSERLSLPNQLEGQGQEPLSHFVACQVYMVQSCHLPRSVSFSSWQNLHVALHLVE HHLL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os06g0622300_circ_g.2

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