Plant Circular RNA Database

Detail information of Os01g0856500_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0856500_circ_g.4
					
						ID in PlantcircBase
						osa_circ_004868
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 36999956-37000637  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0856500						
					
						Parent gene annotation
						
							Auxin transporter, Primary root and root hair elongation, Cd str
ess response (Os01t0856500-01);Amino acid transporter, transmemb
rane domain containing protein. (Os01t0856500-02);Splicing varia
nt with unknown function (Os01t0856500-03);Similar to auxin tran
sporter-like protein 1. (Os01t0856500-04)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0856500_circ_g.2 Os01g0856500_circ_g.3 Os01g0856500_circ_g.5 Os01g0856500_circ_g.6 						
					
						Support reads
						5
					
						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  
						
							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
						Os01t0856500-01:3
Os01t0856500-03:2
Os01t0856500-04:2
Os01t0856500-02:3

General Information
CircRNA Name	Os01g0856500_circ_g.4
ID in PlantcircBase	osa_circ_004868
Alias	NA
Organism	Oryza sativa
Position	chr1: 36999956-37000637 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0856500
Parent gene annotation	Auxin transporter, Primary root and root hair elongation, Cd str ess response (Os01t0856500-01);Amino acid transporter, transmemb rane domain containing protein. (Os01t0856500-02);Splicing varia nt with unknown function (Os01t0856500-03);Similar to auxin tran sporter-like protein 1. (Os01t0856500-04)
Parent gene strand	+
Alternative splicing	Os01g0856500_circ_g.2 Os01g0856500_circ_g.3 Os01g0856500_circ_g.5 Os01g0856500_circ_g.6
Support reads	5
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	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	Os01t0856500-01:3 Os01t0856500-03:2 Os01t0856500-04:2 Os01t0856500-02:3

			
						 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  
						
							AGGCCGAAGGCATCACCCACACCGGTCCAACCAAGCTGGTGCTGTACTTCACCGGCGCCACCAA
CATCCTCTACACCTTCGGCGGCCACGCCGTCACAGTtggttcgaggtgctggatgggctactgg
gcccgtactggaaggcggccggactcgccttcaactgcacgttcctcctcttcggctccgtcat
ccagctga

						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: 395
Transcript exons: 36999956-37000068,37000245-37000428,37000540-37000637
TGGTTCGAGGTGCTGGATGGGCTACTGGGCCCGTACTGGAAGGCGGCCGGACTCGCCTTCAACT
GCACGTTCCTCCTCTTCGGCTCCGTCATCCAGCTGATCGCCTGCGCGAGTAACATCTACTACAT
CAACGACCGGCTGGACAAGCGGACGTGGACGTACATCTTCGGCGCGTGCTGCGCCACCACGGTG
TTCATCCCGTCGTTCCACAACTACCGGATCTGGTCCTTCCTGGGCCTCGGCATGACCACCTATA
CCGCTTGGTACCTCGCCATCGCCGCCCTCCTCAACGGCCAGGCCGAAGGCATCACCCACACCGG
TCCAACCAAGCTGGTGCTGTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCAC
GCCGTCACAGT
						
						Genomic sequence
						
							TGGTTCGAGGTGCTGGATGGGCTACTGGGCCCGTACTGGAAGGCGGCCGGACTCGCCTTCAACT
GCACGTTCCTCCTCTTCGGCTCCGTCATCCAGCTGATCGCCTGCGCGAGGTCAAATTCCTTTCC
TCCCCAACTCAACCAACCAACCATCACTCTCCCACTGTCACTTCGCAGCGCCAGTGTAAATATG
TAGCCGTGCTGCTGCGCAACAGTGTGTCGTGGTGACAGATTGGGTTTGTGCGGATGGGCTGAAA
ACCTGACCGATAATTTGGTGGTGTTTTCTTCAGTAACATCTACTACATCAACGACCGGCTGGAC
AAGCGGACGTGGACGTACATCTTCGGCGCGTGCTGCGCCACCACGGTGTTCATCCCGTCGTTCC
ACAACTACCGGATCTGGTCCTTCCTGGGCCTCGGCATGACCACCTATACCGCTTGGTACCTCGC
CATCGCCGCCCTCCTCAACGGCCAGGTGAGATAAGAAGAGGGAAACTGTCCTTGTCACTTTCTC
GATCATCCATCGCGTCTACTACATGTCCATTTAGCTTGGGTTTGCAGTGACTGATGATCGTTTG
CGTCGCAGGCCGAAGGCATCACCCACACCGGTCCAACCAAGCTGGTGCTGTACTTCACCGGCGC
CACCAACATCCTCTACACCTTCGGCGGCCACGCCGTCACAGT

Sequences
Splice junction sequence	AGGCCGAAGGCATCACCCACACCGGTCCAACCAAGCTGGTGCTGTACTTCACCGGCGCCACCAA CATCCTCTACACCTTCGGCGGCCACGCCGTCACAGTtggttcgaggtgctggatgggctactgg gcccgtactggaaggcggccggactcgccttcaactgcacgttcctcctcttcggctccgtcat ccagctga
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: 395 Transcript exons: 36999956-37000068,37000245-37000428,37000540-37000637 TGGTTCGAGGTGCTGGATGGGCTACTGGGCCCGTACTGGAAGGCGGCCGGACTCGCCTTCAACT GCACGTTCCTCCTCTTCGGCTCCGTCATCCAGCTGATCGCCTGCGCGAGTAACATCTACTACAT CAACGACCGGCTGGACAAGCGGACGTGGACGTACATCTTCGGCGCGTGCTGCGCCACCACGGTG TTCATCCCGTCGTTCCACAACTACCGGATCTGGTCCTTCCTGGGCCTCGGCATGACCACCTATA CCGCTTGGTACCTCGCCATCGCCGCCCTCCTCAACGGCCAGGCCGAAGGCATCACCCACACCGG TCCAACCAAGCTGGTGCTGTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCAC GCCGTCACAGT
Genomic sequence	TGGTTCGAGGTGCTGGATGGGCTACTGGGCCCGTACTGGAAGGCGGCCGGACTCGCCTTCAACT GCACGTTCCTCCTCTTCGGCTCCGTCATCCAGCTGATCGCCTGCGCGAGGTCAAATTCCTTTCC TCCCCAACTCAACCAACCAACCATCACTCTCCCACTGTCACTTCGCAGCGCCAGTGTAAATATG TAGCCGTGCTGCTGCGCAACAGTGTGTCGTGGTGACAGATTGGGTTTGTGCGGATGGGCTGAAA ACCTGACCGATAATTTGGTGGTGTTTTCTTCAGTAACATCTACTACATCAACGACCGGCTGGAC AAGCGGACGTGGACGTACATCTTCGGCGCGTGCTGCGCCACCACGGTGTTCATCCCGTCGTTCC ACAACTACCGGATCTGGTCCTTCCTGGGCCTCGGCATGACCACCTATACCGCTTGGTACCTCGC CATCGCCGCCCTCCTCAACGGCCAGGTGAGATAAGAAGAGGGAAACTGTCCTTGTCACTTTCTC GATCATCCATCGCGTCTACTACATGTCCATTTAGCTTGGGTTTGCAGTGACTGATGATCGTTTG CGTCGCAGGCCGAAGGCATCACCCACACCGGTCCAACCAAGCTGGTGCTGTACTTCACCGGCGC CACCAACATCCTCTACACCTTCGGCGGCCACGCCGTCACAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							zma_circ_007738 zma_circ_001456 						
					
						PMCS
						0.291196347

Conservation Information
Conserved circRNAs	zma_circ_007738 zma_circ_001456
PMCS	0.291196347

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							37000376-37000052(+)
37000252-37000633(-)
						
						Potential amino acid sequence
						
							MTTYTAWYLAIAALLNGQAEGITHTGPTKLVLYFTGATNILYTFGGHAVTVGSRCWMGYWARTG
RRPDSPSTARSSSSAPSSS*(+)
MLLAQAISWMTEPKRRNVQLKASPAAFQYGPSSPSSTSNQL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	37000376-37000052(+) 37000252-37000633(-)
Potential amino acid sequence	MTTYTAWYLAIAALLNGQAEGITHTGPTKLVLYFTGATNILYTFGGHAVTVGSRCWMGYWARTG RRPDSPSTARSSSSAPSSS(+) MLLAQAISWMTEPKRRNVQLKASPAAFQYGPSSPSSTSNQL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0856500_circ_g.4

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