Plant Circular RNA Database

Detail information of Os03g0182400_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os03g0182400_circ_g.6
					
						ID in PlantcircBase
						osa_circ_018226
					
						Alias
						Os_ciR2988
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 4330248-4331670  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os03g0182400						
					
						Parent gene annotation
						
							Similar to SAC domain protein 1 (FIG4-like protein AtFIG4). (Os0
3t0182400-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0182400_circ_g.1 Os03g0182400_circ_g.2 Os03g0182400_circ_g.3 Os03g0182400_circ_g.4 Os03g0182400_circ_g.5 Os03g0182400_circ_g.7 Os03g0182400_circ_g.8 Os03g0182400_circ_g.9 Os03g0182400_circ_g.10 Os03g0182400_circ_g.11 Os03g0182400_circ_g.12 Os03g0182400_circ_g.13 Os03g0182400_circ_g.14 Os03g0182400_circ_g.15 Os03g0182400_circ_g.16 Os03g0182400_circ_g.17 Os03g0182400_circ_g.18 Os03g0182400_circ_g.19 Os03g0182400_circ_g.20 Os03g0182400_circ_g.21 						
					
						Support reads
						4/1
					
						Tissues
						root/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
						Os03t0182400-01:4

General Information
CircRNA Name	Os03g0182400_circ_g.6
ID in PlantcircBase	osa_circ_018226
Alias	Os_ciR2988
Organism	Oryza sativa
Position	chr3: 4330248-4331670 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os03g0182400
Parent gene annotation	Similar to SAC domain protein 1 (FIG4-like protein AtFIG4). (Os0 3t0182400-01)
Parent gene strand	+
Alternative splicing	Os03g0182400_circ_g.1 Os03g0182400_circ_g.2 Os03g0182400_circ_g.3 Os03g0182400_circ_g.4 Os03g0182400_circ_g.5 Os03g0182400_circ_g.7 Os03g0182400_circ_g.8 Os03g0182400_circ_g.9 Os03g0182400_circ_g.10 Os03g0182400_circ_g.11 Os03g0182400_circ_g.12 Os03g0182400_circ_g.13 Os03g0182400_circ_g.14 Os03g0182400_circ_g.15 Os03g0182400_circ_g.16 Os03g0182400_circ_g.17 Os03g0182400_circ_g.18 Os03g0182400_circ_g.19 Os03g0182400_circ_g.20 Os03g0182400_circ_g.21
Support reads	4/1
Tissues	root/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	Os03t0182400-01:4

			
						 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  
						
							TGCAGTGAAACCGGATGTAGACTACAAGACAACTCGCCTTCATTTTGAGAACCTTGCACTTAGA
TATGGGAACCCAATAATTATCTTAAACTTGATCAAGatataaacggctcctttgctcggtcgat
ctctcgaaagacttcttcttcagctactcttacaatatcatgcgcagccttcagaagaacataa
ctgacaag

									
								

					

						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: 583
Transcript exons: 4330248-4330470,4331104-4331180,4331304-4331491,4331576-
4331670
ATATAAACGGCTCCTTTGCTCGGTCGATCTCTCGAAAGACTTCTTCTTCAGCTACTCTTACAAT
ATCATGCGCAGCCTTCAGAAGAACATAACTGACAAGAATACTGGGCAAGTTGTTTATGAGACAA
TGTTTGTTTGGAACGAGTTTCTGTCTCGAGCTATCCGGAACCATCTCAAGAATACAACGTGGAC
TGTTGCCTTAATCCATGGATTTTTTAAACAGTCAAAGCTCTCAGTAGCTGGGAAGGAATTCTGG
TTGACACTTATAGCAAGGCGCTCACGTCATTTTGCTGGAACCAGATTCTTGAAAAGAGGTGTTA
ATGAAAAGGGTAGGGTTGCCAATGATGTTGAGACTGAACAAATTGTTTTTGAGGACACACCAGA
TGAAATACCACATCAGATATCATCTGTTGTACAACATAGAGGATCCATACCTCTTATATGGTTT
CAGGAAACTTCAAGACTCAACATTAGGCCAGATATCATACTGAAACCGGATGTAGACTACAAGA
CAACTCGCCTTCATTTTGAGAACCTTGCACTTAGATATGGGAACCCAATAATTATCTTAAACTT
GATCAAG
						
					

						Genomic sequence
						
							ATATAAACGGCTCCTTTGCTCGGTCGATCTCTCGAAAGACTTCTTCTTCAGCTACTCTTACAAT
ATCATGCGCAGCCTTCAGAAGAACATAACTGACAAGAATACTGGGCAAGTTGTTTATGAGACAA
TGTTTGTTTGGAACGAGTTTCTGTCTCGAGCTATCCGGAACCATCTCAAGAATACAACGTGGAC
TGTTGCCTTAATCCATGGATTTTTTAAACAGGTATTCTGCTGCAACATTCTAAGTCTCCGATAC
TGCATTTGATGCGATCCATTCTTTTCATCTCTAATTGATGAGCTTATGCATATCCAGCACTGTC
TATTCATCAACGAAGACCACAAGTAGGGATACTGCTAACTCAATGCCATCCCACTAACTTTTGT
GTTTTACTCCACAATGTGTGACCTGACATGTAGTGAAAGCTCGAAATAAAGGGTTTGCAAAGGC
ATGGCTTTGTATAACCTGCTGACATTTATCAGTTTGAGCTTCTTGAGGCTTTCCCGAGTCGAAA
ATTTTGCTCGTAAGTCTCAGCAGACTGTTAATGCTTTTCCTAAGTTGTTAAATTCCCCTTTGTG
CAGTCTTAGCAAACCAATGCTTAGATGTGAAATTACAGCGCTATTTATACTTATCTGTAATGTT
TATTAAACGGTAAGCGTTGTGCCGTTGAGGTTCTTTGGTCCTGGTTCAAGACCTTTGAATTAGG
ACATGTATGATTGGCAGTTCTAAATGTTTCTGATAAATAGGAACTTCTTATTGCTACTCTATTT
GCATTTTCATTATGTAAGTACTGTGTTTCATACTTTCATCTGTCAAGTATTATACACAGAGCCA
TGCTAAACATATTTTGTTGCACAGTCAAAGCTCTCAGTAGCTGGGAAGGAATTCTGGTTGACAC
TTATAGCAAGGCGCTCACGTCATTTTGCTGGAACCAGGTTTGCATTACAATCCTTTGGGTTTAG
CACCCTAATTTATGTTGAAAAGAATGGAGCCTAAACAATGTAATCTATGTCGCCTGATCTTACA
ATGTTAATTTTGCATGTCATTTTCAAATACAGATTCTTGAAAAGAGGTGTTAATGAAAAGGGTA
GGGTTGCCAATGATGTTGAGACTGAACAAATTGTTTTTGAGGACACACCAGATGAAATACCACA
TCAGATATCATCTGTTGTACAACATAGAGGATCCATACCTCTTATATGGTTTCAGGAAACTTCA
AGACTCAACATTAGGCCAGATATCATACGTAAGTTCTAGACTGTCAGTCTGTCATGCATTTGCC
ATCTGTAGACTGTCTTCTCTAATACTCCAATCACCTTGCTACCTGCAGTGAAACCGGATGTAGA
CTACAAGACAACTCGCCTTCATTTTGAGAACCTTGCACTTAGATATGGGAACCCAATAATTATC
TTAAACTTGATCAAG
						
					

			
		

Sequences
Splice junction sequence	TGCAGTGAAACCGGATGTAGACTACAAGACAACTCGCCTTCATTTTGAGAACCTTGCACTTAGA TATGGGAACCCAATAATTATCTTAAACTTGATCAAGatataaacggctcctttgctcggtcgat ctctcgaaagacttcttcttcagctactcttacaatatcatgcgcagccttcagaagaacataa ctgacaag
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: 583 Transcript exons: 4330248-4330470,4331104-4331180,4331304-4331491,4331576- 4331670 ATATAAACGGCTCCTTTGCTCGGTCGATCTCTCGAAAGACTTCTTCTTCAGCTACTCTTACAAT ATCATGCGCAGCCTTCAGAAGAACATAACTGACAAGAATACTGGGCAAGTTGTTTATGAGACAA TGTTTGTTTGGAACGAGTTTCTGTCTCGAGCTATCCGGAACCATCTCAAGAATACAACGTGGAC TGTTGCCTTAATCCATGGATTTTTTAAACAGTCAAAGCTCTCAGTAGCTGGGAAGGAATTCTGG TTGACACTTATAGCAAGGCGCTCACGTCATTTTGCTGGAACCAGATTCTTGAAAAGAGGTGTTA ATGAAAAGGGTAGGGTTGCCAATGATGTTGAGACTGAACAAATTGTTTTTGAGGACACACCAGA TGAAATACCACATCAGATATCATCTGTTGTACAACATAGAGGATCCATACCTCTTATATGGTTT CAGGAAACTTCAAGACTCAACATTAGGCCAGATATCATACTGAAACCGGATGTAGACTACAAGA CAACTCGCCTTCATTTTGAGAACCTTGCACTTAGATATGGGAACCCAATAATTATCTTAAACTT GATCAAG
Genomic sequence	ATATAAACGGCTCCTTTGCTCGGTCGATCTCTCGAAAGACTTCTTCTTCAGCTACTCTTACAAT ATCATGCGCAGCCTTCAGAAGAACATAACTGACAAGAATACTGGGCAAGTTGTTTATGAGACAA TGTTTGTTTGGAACGAGTTTCTGTCTCGAGCTATCCGGAACCATCTCAAGAATACAACGTGGAC TGTTGCCTTAATCCATGGATTTTTTAAACAGGTATTCTGCTGCAACATTCTAAGTCTCCGATAC TGCATTTGATGCGATCCATTCTTTTCATCTCTAATTGATGAGCTTATGCATATCCAGCACTGTC TATTCATCAACGAAGACCACAAGTAGGGATACTGCTAACTCAATGCCATCCCACTAACTTTTGT GTTTTACTCCACAATGTGTGACCTGACATGTAGTGAAAGCTCGAAATAAAGGGTTTGCAAAGGC ATGGCTTTGTATAACCTGCTGACATTTATCAGTTTGAGCTTCTTGAGGCTTTCCCGAGTCGAAA ATTTTGCTCGTAAGTCTCAGCAGACTGTTAATGCTTTTCCTAAGTTGTTAAATTCCCCTTTGTG CAGTCTTAGCAAACCAATGCTTAGATGTGAAATTACAGCGCTATTTATACTTATCTGTAATGTT TATTAAACGGTAAGCGTTGTGCCGTTGAGGTTCTTTGGTCCTGGTTCAAGACCTTTGAATTAGG ACATGTATGATTGGCAGTTCTAAATGTTTCTGATAAATAGGAACTTCTTATTGCTACTCTATTT GCATTTTCATTATGTAAGTACTGTGTTTCATACTTTCATCTGTCAAGTATTATACACAGAGCCA TGCTAAACATATTTTGTTGCACAGTCAAAGCTCTCAGTAGCTGGGAAGGAATTCTGGTTGACAC TTATAGCAAGGCGCTCACGTCATTTTGCTGGAACCAGGTTTGCATTACAATCCTTTGGGTTTAG CACCCTAATTTATGTTGAAAAGAATGGAGCCTAAACAATGTAATCTATGTCGCCTGATCTTACA ATGTTAATTTTGCATGTCATTTTCAAATACAGATTCTTGAAAAGAGGTGTTAATGAAAAGGGTA GGGTTGCCAATGATGTTGAGACTGAACAAATTGTTTTTGAGGACACACCAGATGAAATACCACA TCAGATATCATCTGTTGTACAACATAGAGGATCCATACCTCTTATATGGTTTCAGGAAACTTCA AGACTCAACATTAGGCCAGATATCATACGTAAGTTCTAGACTGTCAGTCTGTCATGCATTTGCC ATCTGTAGACTGTCTTCTCTAATACTCCAATCACCTTGCTACCTGCAGTGAAACCGGATGTAGA CTACAAGACAACTCGCCTTCATTTTGAGAACCTTGCACTTAGATATGGGAACCCAATAATTATC TTAAACTTGATCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_004585* osi_circ_013959 						
					
						PMCS
						0.272594337

Conservation Information
Conserved circRNAs	osi_circ_004585* osi_circ_013959
PMCS	0.272594337

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4330316-4330250(+)
4330421-4331668(-)
						
						Potential amino acid sequence
						
							MRSLQKNITDKNTGQVVYETMFVWNEFLSRAIRNHLKNTTWTVALIHGFFKQSKLSVAGKEFWL
TLIARRSRHFAGTRFLKRGVNEKGRVANDVETEQIVFEDTPDEIPHQISSVVQHRGSIPLIWFQ
ETSRLNIRPDIILKPDVDYKTTRLHFENLALRYGNPIIILNLIKI*(+)
MVPDSSRQKLVPNKHCLINNLPSILVSYVLLKAAHDIVRVAEEEVFREIDRAKEPFIS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4330316-4330250(+) 4330421-4331668(-)
Potential amino acid sequence	MRSLQKNITDKNTGQVVYETMFVWNEFLSRAIRNHLKNTTWTVALIHGFFKQSKLSVAGKEFWL TLIARRSRHFAGTRFLKRGVNEKGRVANDVETEQIVFEDTPDEIPHQISSVVQHRGSIPLIWFQ ETSRLNIRPDIILKPDVDYKTTRLHFENLALRYGNPIIILNLIKI(+) MVPDSSRQKLVPNKHCLINNLPSILVSYVLLKAAHDIVRVAEEEVFREIDRAKEPFIS(-)
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 Os03g0182400_circ_g.6

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