Plant Circular RNA Database

Detail information of Os04g0177600_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0177600_circ_g.2
					
						ID in PlantcircBase
						osa_circ_023023
					
						Alias
						Os_ciR3954
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 5294883-5301419  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os04g0177600						
					
						Parent gene annotation
						
							Similar to Actin-related protein 9. (Os04t0177600-01);Actin/acti
n-like family protein. (Os04t0177600-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0177600_circ_g.1 						
					
						Support reads
						2
					
						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
						Os04t0177600-02:13
Os04t0177600-01:13

General Information
CircRNA Name	Os04g0177600_circ_g.2
ID in PlantcircBase	osa_circ_023023
Alias	Os_ciR3954
Organism	Oryza sativa
Position	chr4: 5294883-5301419 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Os04g0177600
Parent gene annotation	Similar to Actin-related protein 9. (Os04t0177600-01);Actin/acti n-like family protein. (Os04t0177600-02)
Parent gene strand	-
Alternative splicing	Os04g0177600_circ_g.1
Support reads	2
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	Os04t0177600-02:13 Os04t0177600-01:13

			
						 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  
						
							CTAGAACAAGAATTGCAGAATACAGATGCCGATCTCTTGGATTTATATGCAATTTTTCTGTCAA
TATCCAGTTCCAAATAGTGCGCAAATCTTCTAAAACctgttatgaattgtagtaacacattgcc
tgtgcctgaagaaaataagaatccctatattttctcccactccctatgtggacaccatttttag
cccaatct

						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: 1134
Transcript exons: 5294883-5295029,5295874-5295924,5296181-5296226,5296301-
5296350,5296436-5296479,5296552-5296727,5296808-5296878,
5297053-5297142,5297784-5297915,5298837-5298887,5299032-
5299121,5300278-5300342,5301299-5301419
CTGTTATGAATTGTAGTAACACATTGCCTGTGCCTGAAGAAAATAAGAATCCCTATATTTTCTC
CCACTCCCTATGTGGACACCATTTTTAGCCCAATCTTCTCTATGTATCCAAGCATCACGACCAA
TATCAAGTACGCCCAAAATCACACCACCTTTCCATGGGACAAATAATGGATAACTCCTCGACTG
TAATACCTCTGCTTTCTCTATCGGTTGATTTGATGGAATAGTATTGAGAACCCTTTGTTCTAGA
ACTGGTGCAAGGCCTGCTGTTGAAGCTGTACCACCAACCAGCTGAATGCTGCAGAATAGCTTCC
TTTGAAGCTCAATACGTCCTGTCGAAAGGATACTACTAACAATGGCTTCTACAAGACCGATGTT
ATCAAACTTTTTTAATCTGGTGGGAAACATCGGATAATTGTCCCACATACCGAACCCACCATTC
CCACTTGAGTAAAGACTGTCACTTGTTTGCCATGTATCTTCTAACATGTCATCATAATCTTGGA
ACCAAGATCGAGGAGGTGGAGGGTATTCTTCTGGGACAAGAACCCTTGGATAAAGTAGCCCCAT
AGGAGGTACATTCAGAGCCGATAGCTTTGTTTTCTGATGACCAACTGATTTTTCATGCTCATAT
GAATGAACAACACTGACAGCATCAAAACTTCCACTTCTTATCTGGCTGTATGACTCTTTTAGTT
TGTTGAGCATTAGCATATCTATAGGCTTGTTCACTGGATCAGTTTGGAAGTTTGGCCATGTGCA
ATGACGACGTTGAACCCAAAGAAGGCATCTAGATATGTCATCTCCACCGTATGGAAGCGCCAGG
GCTGTGTGGGGTAAAGCAACACCATCCTCAACACAAACTACTTGTGTAACTTGCGCGCCAATGT
TGACCACACAAGATGTCGACAAGCCATTTCCAAATGCTGCAGCTAGAGCTTCCTGATGTATCAC
TGCTGTGCTAAAACCCAAATCGCAAAGTACGATTGACAACATTTCCTTGATTTCTCGGTTATCA
AATGTCTCTCCTAGAACAAGAATTGCAGAATACAGATGCCGATCTCTTGGATTTATATGCAATT
TTTCTGTCAATATCCAGTTCCAAATAGTGCGCAAATCTTCTAAAAC
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CTAGAACAAGAATTGCAGAATACAGATGCCGATCTCTTGGATTTATATGCAATTTTTCTGTCAA TATCCAGTTCCAAATAGTGCGCAAATCTTCTAAAACctgttatgaattgtagtaacacattgcc tgtgcctgaagaaaataagaatccctatattttctcccactccctatgtggacaccatttttag cccaatct
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: 1134 Transcript exons: 5294883-5295029,5295874-5295924,5296181-5296226,5296301- 5296350,5296436-5296479,5296552-5296727,5296808-5296878, 5297053-5297142,5297784-5297915,5298837-5298887,5299032- 5299121,5300278-5300342,5301299-5301419 CTGTTATGAATTGTAGTAACACATTGCCTGTGCCTGAAGAAAATAAGAATCCCTATATTTTCTC CCACTCCCTATGTGGACACCATTTTTAGCCCAATCTTCTCTATGTATCCAAGCATCACGACCAA TATCAAGTACGCCCAAAATCACACCACCTTTCCATGGGACAAATAATGGATAACTCCTCGACTG TAATACCTCTGCTTTCTCTATCGGTTGATTTGATGGAATAGTATTGAGAACCCTTTGTTCTAGA ACTGGTGCAAGGCCTGCTGTTGAAGCTGTACCACCAACCAGCTGAATGCTGCAGAATAGCTTCC TTTGAAGCTCAATACGTCCTGTCGAAAGGATACTACTAACAATGGCTTCTACAAGACCGATGTT ATCAAACTTTTTTAATCTGGTGGGAAACATCGGATAATTGTCCCACATACCGAACCCACCATTC CCACTTGAGTAAAGACTGTCACTTGTTTGCCATGTATCTTCTAACATGTCATCATAATCTTGGA ACCAAGATCGAGGAGGTGGAGGGTATTCTTCTGGGACAAGAACCCTTGGATAAAGTAGCCCCAT AGGAGGTACATTCAGAGCCGATAGCTTTGTTTTCTGATGACCAACTGATTTTTCATGCTCATAT GAATGAACAACACTGACAGCATCAAAACTTCCACTTCTTATCTGGCTGTATGACTCTTTTAGTT TGTTGAGCATTAGCATATCTATAGGCTTGTTCACTGGATCAGTTTGGAAGTTTGGCCATGTGCA ATGACGACGTTGAACCCAAAGAAGGCATCTAGATATGTCATCTCCACCGTATGGAAGCGCCAGG GCTGTGTGGGGTAAAGCAACACCATCCTCAACACAAACTACTTGTGTAACTTGCGCGCCAATGT TGACCACACAAGATGTCGACAAGCCATTTCCAAATGCTGCAGCTAGAGCTTCCTGATGTATCAC TGCTGTGCTAAAACCCAAATCGCAAAGTACGATTGACAACATTTCCTTGATTTCTCGGTTATCA AATGTCTCTCCTAGAACAAGAATTGCAGAATACAGATGCCGATCTCTTGGATTTATATGCAATT TTTCTGTCAATATCCAGTTCCAAATAGTGCGCAAATCTTCTAAAAC
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005333 						
					
						PMCS
						0.200535012

Conservation Information
Conserved circRNAs	osi_circ_005333
PMCS	0.200535012

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os04g0177600_circ_g.2

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