Plant Circular RNA Database

Detail information of Os04g0278550_circ_g.5

			
						 General Information
					
						CircRNA Name
						Os04g0278550_circ_g.5
					
						ID in PlantcircBase
						osa_circ_023264
					
						Alias
						Os_ciR1556
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 11767566-11774675  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ie-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0278550						
					
						Parent gene annotation
						
							Hypothetical protein. (Os04t0278550-00)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0278200_circ_g.1 Os04g0278550_circ_g.1 Os04g0278550_circ_g.2 Os04g0278550_circ_g.3 Os04g0278550_circ_g.4 Os04g0278550_circ_g.6 Os04g0278550_circ_g.7 Os04g0278550_circ_g.8 Os04g0278550_circ_g.9 Os04g0278550_circ_g.10 Os04g0278550_circ_g.11 Os04g0278550_circ_g.12 Os04g0278550_circ_g.13 Os04g0278550_circ_g.14 Os04g0278550_circ_g.15 Os04g0278550_circ_g.16 Os04g0278550_circ_g.17 Os04g0278550_circ_g.18 Os04g0278550_circ_g.19 						
					
						Support reads
						12/4
					
						Tissues
						root/shoot, 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
						Os04t0278200-02:7
Os04t0278200-01:7
Os04t0278550-00:4
Os04t0278200-02:7
Os04t0278200-01:7

General Information
CircRNA Name	Os04g0278550_circ_g.5
ID in PlantcircBase	osa_circ_023264
Alias	Os_ciR1556
Organism	Oryza sativa
Position	chr4: 11767566-11774675 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ie-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0278550
Parent gene annotation	Hypothetical protein. (Os04t0278550-00)
Parent gene strand	-
Alternative splicing	Os04g0278200_circ_g.1 Os04g0278550_circ_g.1 Os04g0278550_circ_g.2 Os04g0278550_circ_g.3 Os04g0278550_circ_g.4 Os04g0278550_circ_g.6 Os04g0278550_circ_g.7 Os04g0278550_circ_g.8 Os04g0278550_circ_g.9 Os04g0278550_circ_g.10 Os04g0278550_circ_g.11 Os04g0278550_circ_g.12 Os04g0278550_circ_g.13 Os04g0278550_circ_g.14 Os04g0278550_circ_g.15 Os04g0278550_circ_g.16 Os04g0278550_circ_g.17 Os04g0278550_circ_g.18 Os04g0278550_circ_g.19
Support reads	12/4
Tissues	root/shoot, 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	Os04t0278200-02:7 Os04t0278200-01:7 Os04t0278550-00:4 Os04t0278200-02:7 Os04t0278200-01:7

			
						 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  
						
							ATGTGCATGTATATGTTTGATGAGGATTTTACCATGATTTTAGGAGTCTGGGCTTGGTGAGTCA
CCAATATGCATACAAAGAATGAGGTATCTCTCCACGagaaacctagatgaagctgagaagtttt
tccaggcagccctacatgaagcgaaagaaggatttggactgagagatccacatgttgcgtcagc
ccttaaca

						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: 221
Transcript exons: 11767566-11767629,11768830-11768928,11774618-11774675
AGAAACCTAGATGAAGCTGAGAAGTTTTTCCAGGCAGCCCTACATGAAGCGAAAGAAGGATTTG
TGAGTTTTATAGGTTAAAGAAAGAATACGAGAAGGCTGAGCTATTGTATCTGGAAGCAATTGAA
ATCCTGGAAGAATCATTTGGATCGGACGATATAAGGGAGTCTGGGCTTGGTGAGTCACCAATAT
GCATACAAAGAATGAGGTATCTCTCCACG
Transcript length: 483
Transcript exons: 11767566-11767670,11768828-11768928,11771554-11771632,11
772179-11772190,11772950-11773015,11774473-11774535,1177
4619-11774675
AGAAACCTAGATGAAGCTGAGAAGTTTTTCCAGGCAGCCCTACATGAAGCGAAAGAAGGATTTG
GACTGAGAGATCCACATGTTGCGTCAGCCCTTAACAATCTGGCTGAGTTTTATAGGTTAAAGAA
AGAATACGAGAAGGCTGAGCTATTGTATCTGGAAGCAATTGAAATCCTGGAAGAATCATTTGGA
TCGGACGATATAAGGGTTGGAACTGCTTTGCATAGTCTTGGAATATGCTACCATCTTCAACGCA
AGTTTGCTCTAGCTCAGACATGTTATGAGCGTGCTTTGAAGATAGAAGGACGTGTTATGGGGAT
TGGTCATCCAGAGTATGCAAGCACAATGTACCTTCTTGGCAAGGTGTTAAGTCAACAAGGAAAA
GATGCAGAAGCCCTTATTGAAGAGTCTATCAGGATATTGGAGGAGTCTGGGCTTGGTGAGTCAC
CAATATGCATACAAAGAATGAGGTATCTCTCCACG
						
						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	ATGTGCATGTATATGTTTGATGAGGATTTTACCATGATTTTAGGAGTCTGGGCTTGGTGAGTCA CCAATATGCATACAAAGAATGAGGTATCTCTCCACGagaaacctagatgaagctgagaagtttt tccaggcagccctacatgaagcgaaagaaggatttggactgagagatccacatgttgcgtcagc ccttaaca
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: 221 Transcript exons: 11767566-11767629,11768830-11768928,11774618-11774675 AGAAACCTAGATGAAGCTGAGAAGTTTTTCCAGGCAGCCCTACATGAAGCGAAAGAAGGATTTG TGAGTTTTATAGGTTAAAGAAAGAATACGAGAAGGCTGAGCTATTGTATCTGGAAGCAATTGAA ATCCTGGAAGAATCATTTGGATCGGACGATATAAGGGAGTCTGGGCTTGGTGAGTCACCAATAT GCATACAAAGAATGAGGTATCTCTCCACG Transcript length: 483 Transcript exons: 11767566-11767670,11768828-11768928,11771554-11771632,11 772179-11772190,11772950-11773015,11774473-11774535,1177 4619-11774675 AGAAACCTAGATGAAGCTGAGAAGTTTTTCCAGGCAGCCCTACATGAAGCGAAAGAAGGATTTG GACTGAGAGATCCACATGTTGCGTCAGCCCTTAACAATCTGGCTGAGTTTTATAGGTTAAAGAA AGAATACGAGAAGGCTGAGCTATTGTATCTGGAAGCAATTGAAATCCTGGAAGAATCATTTGGA TCGGACGATATAAGGGTTGGAACTGCTTTGCATAGTCTTGGAATATGCTACCATCTTCAACGCA AGTTTGCTCTAGCTCAGACATGTTATGAGCGTGCTTTGAAGATAGAAGGACGTGTTATGGGGAT TGGTCATCCAGAGTATGCAAGCACAATGTACCTTCTTGGCAAGGTGTTAAGTCAACAAGGAAAA GATGCAGAAGCCCTTATTGAAGAGTCTATCAGGATATTGGAGGAGTCTGGGCTTGGTGAGTCAC CAATATGCATACAAAGAATGAGGTATCTCTCCACG
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_005352* 						
					
						PMCS
						0.196796404

Conservation Information
Conserved circRNAs	osi_circ_005352*
PMCS	0.196796404

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11772966-11774672(+)
						
						Potential amino acid sequence
						
							MGIGHPEYASTMYLLGKVLSQQGKDAEALIEESIRILEESGLGESPICIQRMRYLSTRNLDEAE
KFFQAALHEAKEGFGLRDPHVASALNNLAEFYRLKKEYEKAELLYLEAIEILEESFGSDDIRVG
TALHSLGICYHLQRKFALAQTCYERALKIEGRVMGIGHPEYASTMYLLGKVLSQQGKDAEALIE
ESIRILEESGLGESPICIQRMRYLSTRNLDEAEKFFQAALHEAKEGFGLRDPHVASALNNLAEF
YRLKKEYEKAELLYLEAIEILEESFGSDDIRVGTALHSLGICYHLQRKFALAQTCYERALKIEG
RVMGIGHPEYASTMYLLGKVLSQQGKDAEALIEESIRILEESGLGESPICIQRMRYLSTRNLDE
AEKFFQAALHEAKEGFGLRDPHVASALNNLAEFYRLKKEYEKAELLYLEAIEILEESFGSDDIR
VGTALHSLGICYHLQRKFALAQTCYERALKIEGRVMGIGHPEYASTMYLLGKVLSQQGKDAEAL
IEESIRILEESGLGESPICIQRMRYLST(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11772966-11774672(+)
Potential amino acid sequence	MGIGHPEYASTMYLLGKVLSQQGKDAEALIEESIRILEESGLGESPICIQRMRYLSTRNLDEAE KFFQAALHEAKEGFGLRDPHVASALNNLAEFYRLKKEYEKAELLYLEAIEILEESFGSDDIRVG TALHSLGICYHLQRKFALAQTCYERALKIEGRVMGIGHPEYASTMYLLGKVLSQQGKDAEALIE ESIRILEESGLGESPICIQRMRYLSTRNLDEAEKFFQAALHEAKEGFGLRDPHVASALNNLAEF YRLKKEYEKAELLYLEAIEILEESFGSDDIRVGTALHSLGICYHLQRKFALAQTCYERALKIEG RVMGIGHPEYASTMYLLGKVLSQQGKDAEALIEESIRILEESGLGESPICIQRMRYLSTRNLDE AEKFFQAALHEAKEGFGLRDPHVASALNNLAEFYRLKKEYEKAELLYLEAIEILEESFGSDDIR VGTALHSLGICYHLQRKFALAQTCYERALKIEGRVMGIGHPEYASTMYLLGKVLSQQGKDAEAL IEESIRILEESGLGESPICIQRMRYLST(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os04g0278550_circ_g.5

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