Plant Circular RNA Database

Detail information of Os04g0620000_circ_g.17

			
						 General Information
					
						CircRNA Name
						Os04g0620000_circ_g.17
					
						ID in PlantcircBase
						osa_circ_025328
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 31509926-31510659  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0620000						
					
						Parent gene annotation
						
							C-type ATP-binding cassette (ABC) transporter, Arsenic (As) deto
xification, Reduction of As in grains (Os04t0620000-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0620000_circ_g.7 Os04g0620000_circ_g.8 Os04g0620000_circ_g.9 Os04g0620000_circ_g.10 Os04g0620000_circ_g.11 Os04g0620000_circ_g.12 Os04g0620000_circ_g.13 Os04g0620000_circ_g.14 Os04g0620000_circ_g.15 Os04g0620000_circ_g.16 Os04g0620000_circ_g.18 Os04g0620000_circ_g.19 Os04g0620000_circ_g.20 Os04g0620000_circ_g.21 Os04g0620000_circ_g.22 Os04g0620000_circ_g.23 Os04g0620000_circ_g.24 Os04g0620000_circ_g.25 Os04g0620000_circ_g.26 Os04g0620000_circ_g.27 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os04t0620000-01:3

General Information
CircRNA Name	Os04g0620000_circ_g.17
ID in PlantcircBase	osa_circ_025328
Alias	NA
Organism	Oryza sativa
Position	chr4: 31509926-31510659 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0620000
Parent gene annotation	C-type ATP-binding cassette (ABC) transporter, Arsenic (As) deto xification, Reduction of As in grains (Os04t0620000-01)
Parent gene strand	-
Alternative splicing	Os04g0620000_circ_g.7 Os04g0620000_circ_g.8 Os04g0620000_circ_g.9 Os04g0620000_circ_g.10 Os04g0620000_circ_g.11 Os04g0620000_circ_g.12 Os04g0620000_circ_g.13 Os04g0620000_circ_g.14 Os04g0620000_circ_g.15 Os04g0620000_circ_g.16 Os04g0620000_circ_g.18 Os04g0620000_circ_g.19 Os04g0620000_circ_g.20 Os04g0620000_circ_g.21 Os04g0620000_circ_g.22 Os04g0620000_circ_g.23 Os04g0620000_circ_g.24 Os04g0620000_circ_g.25 Os04g0620000_circ_g.26 Os04g0620000_circ_g.27
Support reads	1
Tissues	shoot
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	Os04t0620000-01:3

			
						 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  
						
							TATCCATTGCAGCTAATATTTCATTCATTAGACTGATTCTCCTGTCAGTCCTTTGCAACCCTTC
CTTGGTAAGTTTTTGCATTTTGCTTATGATAACAGTctgagttatcagatttggcagcataaaa
agtggaaatcttaagacagcaaacagtgaaagtgatgtgaacgcctttgctggtgtcaagtcac
ctcccagc

						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: 369
Transcript exons: 31509926-31510093,31510376-31510469,31510553-31510659
CTGAGTTATCAGATTTGGCAGCATAAAAAGTGGAAATCTTAAGACAGCAAACAGTGAAAGTGAT
GTGAACGCCTTTGCTGGTGTCAAGTCACCTCCCAGCAGAGAGTATACACCAAATGAAACCACAG
TGACAATAACGGGGATACTGTTTAGGATGAAGCTATTCAGCGCAGCAAGCAATTGAGCGCTGCG
GAACCATGAAATTTCATCATCACGGATGTCCTGCACTTTTGACTGGAAACTTTGCTCCCAAGCA
TAACATTTGACCGTATCCATTGCAGCTAATATTTCATTCATTAGACTGATTCTCCTGTCAGTCC
TTTGCAACCCTTCCTTGGTAAGTTTTTGCATTTTGCTTATGATAACAGT
						
						Genomic sequence
						
							CTGAGTTATCAGATTTGGCAGCATAAAAAGTGGAAATCTTAAGACAGCAAACAGTGAAAGTGAT
GTGAACGCCTTTGCTGGTGTCAAGTCACCTCCCAGCAGAGAGTATACACCAAATGAAACCACAG
TGACAATAACGGGGATACTGTTTAGGATGAAGCTATTCAGCTGCAGCAGACAAGGAAAAATACA
AAAGATAATAGTGAGCCGACAATAAGGGATGCAACAACTCATTCTCATATCTATTTTAAGTTTG
AGTAACTAAGTAAATTATTGTAAACAAACTTTATAGGACCAGGAAGCACCAGTACAATCGATAC
TATAGCATGCAACTCCAAAACTTATTGTGTAATAAGGAGAGTTCATGGATGCACGATTAAAAAA
GAGATCATATATAGCAGAATGAAATTGACACAAGTGAAAGATAACTTAAATACAAAATGGACAT
ACCGCAGCAAGCAATTGAGCGCTGCGGAACCATGAAATTTCATCATCACGGATGTCCTGCACTT
TTGACTGGAAACTTTGCTCCCAAGCATAACATCTAACCAAGAAAATGTTTGGAACAGTTTATAC
CAAAATTTTAGTACTACTTCTAGTAAAAACACAAGTAAATGTAAAGCATACTTGACCGTATCCA
TTGCAGCTAATATTTCATTCATTAGACTGATTCTCCTGTCAGTCCTTTGCAACCCTTCCTTGGT
AAGTTTTTGCATTTTGCTTATGATAACAGT

Sequences
Splice junction sequence	TATCCATTGCAGCTAATATTTCATTCATTAGACTGATTCTCCTGTCAGTCCTTTGCAACCCTTC CTTGGTAAGTTTTTGCATTTTGCTTATGATAACAGTctgagttatcagatttggcagcataaaa agtggaaatcttaagacagcaaacagtgaaagtgatgtgaacgcctttgctggtgtcaagtcac ctcccagc
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: 369 Transcript exons: 31509926-31510093,31510376-31510469,31510553-31510659 CTGAGTTATCAGATTTGGCAGCATAAAAAGTGGAAATCTTAAGACAGCAAACAGTGAAAGTGAT GTGAACGCCTTTGCTGGTGTCAAGTCACCTCCCAGCAGAGAGTATACACCAAATGAAACCACAG TGACAATAACGGGGATACTGTTTAGGATGAAGCTATTCAGCGCAGCAAGCAATTGAGCGCTGCG GAACCATGAAATTTCATCATCACGGATGTCCTGCACTTTTGACTGGAAACTTTGCTCCCAAGCA TAACATTTGACCGTATCCATTGCAGCTAATATTTCATTCATTAGACTGATTCTCCTGTCAGTCC TTTGCAACCCTTCCTTGGTAAGTTTTTGCATTTTGCTTATGATAACAGT
Genomic sequence	CTGAGTTATCAGATTTGGCAGCATAAAAAGTGGAAATCTTAAGACAGCAAACAGTGAAAGTGAT GTGAACGCCTTTGCTGGTGTCAAGTCACCTCCCAGCAGAGAGTATACACCAAATGAAACCACAG TGACAATAACGGGGATACTGTTTAGGATGAAGCTATTCAGCTGCAGCAGACAAGGAAAAATACA AAAGATAATAGTGAGCCGACAATAAGGGATGCAACAACTCATTCTCATATCTATTTTAAGTTTG AGTAACTAAGTAAATTATTGTAAACAAACTTTATAGGACCAGGAAGCACCAGTACAATCGATAC TATAGCATGCAACTCCAAAACTTATTGTGTAATAAGGAGAGTTCATGGATGCACGATTAAAAAA GAGATCATATATAGCAGAATGAAATTGACACAAGTGAAAGATAACTTAAATACAAAATGGACAT ACCGCAGCAAGCAATTGAGCGCTGCGGAACCATGAAATTTCATCATCACGGATGTCCTGCACTT TTGACTGGAAACTTTGCTCCCAAGCATAACATCTAACCAAGAAAATGTTTGGAACAGTTTATAC CAAAATTTTAGTACTACTTCTAGTAAAAACACAAGTAAATGTAAAGCATACTTGACCGTATCCA TTGCAGCTAATATTTCATTCATTAGACTGATTCTCCTGTCAGTCCTTTGCAACCCTTCCTTGGT AAGTTTTTGCATTTTGCTTATGATAACAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.28908305

Conservation Information
Conserved circRNAs	NA
PMCS	0.28908305

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							31510643-31509928(-)
						
						Potential amino acid sequence
						
							MQKLTKEGLQRTDRRISLMNEILAAMDTVKCYAWEQSFQSKVQDIRDDEISWFRSAQLLAALNS
FILNSIPVIVTVVSFGVYSLLGGDLTPAKAFTSLSLFAVLRFPLFMLPNLITQTVIISKMQKLT
KEGLQRTDRRISLMNEILAAMDTVKCYAWEQSFQSKVQDIRDDEISWFRSAQLLAALNSFILNS
IPVIVTVVSFGVYSLLGGDLTPAKAFTSLSLFAVLRFPLFMLPNLITQTVIISKMQKLTKEGLQ
RTDRRISLMNEILAAMDTVKCYAWEQSFQSKVQDIRDDEISWFRSAQLLAALNSFILNSIPVIV
TVVSFGVYSLLGGDLTPAKAFTSLSLFAVLRFPLFMLPNLITQTVIISKMQKLTKEGLQRTDRR
ISLMNEILAAMDTVKCYAWEQSFQSKVQDIRDDEISWFRSAQLLAALNSFILNSIPVIVTVVSF
GVYSLLGGDLTPAKAFTSLSLFAVLRFPLFMLPNLITQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	31510643-31509928(-)
Potential amino acid sequence	MQKLTKEGLQRTDRRISLMNEILAAMDTVKCYAWEQSFQSKVQDIRDDEISWFRSAQLLAALNS FILNSIPVIVTVVSFGVYSLLGGDLTPAKAFTSLSLFAVLRFPLFMLPNLITQTVIISKMQKLT KEGLQRTDRRISLMNEILAAMDTVKCYAWEQSFQSKVQDIRDDEISWFRSAQLLAALNSFILNS IPVIVTVVSFGVYSLLGGDLTPAKAFTSLSLFAVLRFPLFMLPNLITQTVIISKMQKLTKEGLQ RTDRRISLMNEILAAMDTVKCYAWEQSFQSKVQDIRDDEISWFRSAQLLAALNSFILNSIPVIV TVVSFGVYSLLGGDLTPAKAFTSLSLFAVLRFPLFMLPNLITQTVIISKMQKLTKEGLQRTDRR ISLMNEILAAMDTVKCYAWEQSFQSKVQDIRDDEISWFRSAQLLAALNSFILNSIPVIVTVVSF GVYSLLGGDLTPAKAFTSLSLFAVLRFPLFMLPNLITQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0620000_circ_g.17

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