Plant Circular RNA Database

Detail information of Os03g0109400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os03g0109400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_017505
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 550721-551584  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os03g0109400						
					
						Parent gene annotation
						
							Similar to cDNA clone:J033091P14, full insert sequence. (Os03t01
09400-01);Homeodomain-related domain containing protein. (Os03t0
109400-02);Similar to cDNA clone:J033091P14, full insert sequenc
e. (Os03t0109400-03)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0108800_circ_ag.1 Os03g0109300_circ_g.1 Os03g0109300_circ_g.2 Os03g0109300_circ_g.3 Os03g0109300_circ_g.4 Os03g0109400_circ_g.1 Os03g0109400_circ_g.2 Os03g0109400_circ_g.4 Os03g0109400_circ_g.5 Os03g0109400_circ_g.6 Os03g0109600_circ_g.1 Os03g0109600_circ_g.2 Os03g0109900_circ_g.1 Os03g0109900_circ_g.2 Os03g0109900_circ_g.3 Os03g0109900_circ_g.4 Os03g0109900_circ_g.5 Os03g0109900_circ_g.6 Os03g0110400_circ_g.1 Os03g0110400_circ_g.2 Os03g0110400_circ_g.3 Os03g0110400_circ_g.4 Os03g0110400_circ_g.5 Os03g0110500_circ_g.1 Os03g0110900_circ_g.1 Os03g0111100_circ_g.1 Os03g0111100_circ_g.2 Os03g0111100_circ_g.3 Os03g0111100_circ_g.4 Os03g0111100_circ_g.5 Os03g0111100_circ_g.6 Os03g0111100_circ_g.7 Os03g0111100_circ_g.8 Os03g0111100_circ_g.9 Os03g0111100_circ_g.10 Os03g0111100_circ_g.11 Os03g0111200_circ_g.1 Os03g0111200_circ_g.2 Os03g0111200_circ_g.3 Os03g0111400_circ_g.1 Os03g0111400_circ_g.2 Os03g0111500_circ_g.1 Os03g0111500_circ_g.2 Os03g0111500_circ_g.3 Os03g0111600_circ_g.1 Os03g0111600_circ_g.2 Os03g0111700_circ_g.1 Os03g0111700_circ_g.2 Os03g0111800_circ_g.1 Os03g0112101_circ_g.1 Os03g0112101_circ_g.2 Os03g0112101_circ_igg.1 Os03g0112101_circ_ig.1 Os03g0112101_circ_ig.2 Os03g0112101_circ_ig.3 Os03g0112101_circ_ig.4 Os03g0112101_circ_ig.5 Os03g0112101_circ_ig.6 Os03g0112101_circ_ig.7 Os03g0112101_circ_ig.8 Os03g0112400_circ_g.1 Os03g0112400_circ_igg.1 EPlOSAG00000048437_circ_ig.1 EPlOSAG00000048437_circ_ig.2 Os03g0112600_circ_ig.1 Os03g0112700_circ_g.1 Os03g0112700_circ_g.2 Os03g0112700_circ_g.3 Os03g0112700_circ_g.4 Os03g0112700_circ_g.5 Os03g0112700_circ_g.6 Os03g0112700_circ_g.7 Os03g0112800_circ_g.1 Os03g0112800_circ_g.2 Os03g0113500_circ_g.1 Os03g0113500_circ_g.2 Os03g0113500_circ_g.3 Os03g0113500_circ_g.4 Os03g0113500_circ_g.5 Os03g0113700_circ_g.1 Os03g0113800_circ_g.1 Os03g0113800_circ_g.2 Os03g0113800_circ_g.3 Os03g0113800_circ_g.4 Os03g0113800_circ_g.5 Os03g0113800_circ_g.6 Os03g0113800_circ_g.7 EPlOSAG00000003330_circ_ig.1 Os03g0114000_circ_g.1 Os03g0114300_circ_g.1 Os03g0114300_circ_g.2 Os03g0114300_circ_g.3 Os03g0114300_circ_g.4 Os03g0114300_circ_g.5 Os03g0114300_circ_g.6 Os03g0114300_circ_g.7 Os03g0114300_circ_g.8 Os03g0114300_circ_g.9 Os03g0114300_circ_g.10 Os03g0114300_circ_g.11 Os03g0115100_circ_g.1 Os03g0115400_circ_g.1 Os03g0115400_circ_g.2 Os03g0115400_circ_ig.1 Os03g0115700_circ_g.1 Os03g0116000_circ_g.1 Os03g0116000_circ_g.2 Os03g0116300_circ_g.1 Os03g0116300_circ_g.2 Os03g0116300_circ_g.3 Os03g0116300_circ_g.4 Os03g0116300_circ_g.5 Os03g0116300_circ_g.6 Os03g0116400_circ_g.1 Os03g0116400_circ_g.2 Os03g0116700_circ_g.1 Os03g0116700_circ_g.2 Os03g0116900_circ_igg.1 Os03g0117100_circ_g.1 Os03g0117100_circ_g.2 Os03g0117100_circ_g.3 Os03g0117100_circ_g.4 Os03g0117800_circ_g.1 Os03g0117800_circ_g.2 Os03g0118400_circ_g.1 						
					
						Support reads
						1
					
						Tissues
						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
						Os03t0109400-01:2
Os03t0109400-02:2

General Information
CircRNA Name	Os03g0109400_circ_g.3
ID in PlantcircBase	osa_circ_017505
Alias	NA
Organism	Oryza sativa
Position	chr3: 550721-551584 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os03g0109400
Parent gene annotation	Similar to cDNA clone:J033091P14, full insert sequence. (Os03t01 09400-01);Homeodomain-related domain containing protein. (Os03t0 109400-02);Similar to cDNA clone:J033091P14, full insert sequenc e. (Os03t0109400-03)
Parent gene strand	+
Alternative splicing	Os03g0108800_circ_ag.1 Os03g0109300_circ_g.1 Os03g0109300_circ_g.2 Os03g0109300_circ_g.3 Os03g0109300_circ_g.4 Os03g0109400_circ_g.1 Os03g0109400_circ_g.2 Os03g0109400_circ_g.4 Os03g0109400_circ_g.5 Os03g0109400_circ_g.6 Os03g0109600_circ_g.1 Os03g0109600_circ_g.2 Os03g0109900_circ_g.1 Os03g0109900_circ_g.2 Os03g0109900_circ_g.3 Os03g0109900_circ_g.4 Os03g0109900_circ_g.5 Os03g0109900_circ_g.6 Os03g0110400_circ_g.1 Os03g0110400_circ_g.2 Os03g0110400_circ_g.3 Os03g0110400_circ_g.4 Os03g0110400_circ_g.5 Os03g0110500_circ_g.1 Os03g0110900_circ_g.1 Os03g0111100_circ_g.1 Os03g0111100_circ_g.2 Os03g0111100_circ_g.3 Os03g0111100_circ_g.4 Os03g0111100_circ_g.5 Os03g0111100_circ_g.6 Os03g0111100_circ_g.7 Os03g0111100_circ_g.8 Os03g0111100_circ_g.9 Os03g0111100_circ_g.10 Os03g0111100_circ_g.11 Os03g0111200_circ_g.1 Os03g0111200_circ_g.2 Os03g0111200_circ_g.3 Os03g0111400_circ_g.1 Os03g0111400_circ_g.2 Os03g0111500_circ_g.1 Os03g0111500_circ_g.2 Os03g0111500_circ_g.3 Os03g0111600_circ_g.1 Os03g0111600_circ_g.2 Os03g0111700_circ_g.1 Os03g0111700_circ_g.2 Os03g0111800_circ_g.1 Os03g0112101_circ_g.1 Os03g0112101_circ_g.2 Os03g0112101_circ_igg.1 Os03g0112101_circ_ig.1 Os03g0112101_circ_ig.2 Os03g0112101_circ_ig.3 Os03g0112101_circ_ig.4 Os03g0112101_circ_ig.5 Os03g0112101_circ_ig.6 Os03g0112101_circ_ig.7 Os03g0112101_circ_ig.8 Os03g0112400_circ_g.1 Os03g0112400_circ_igg.1 EPlOSAG00000048437_circ_ig.1 EPlOSAG00000048437_circ_ig.2 Os03g0112600_circ_ig.1 Os03g0112700_circ_g.1 Os03g0112700_circ_g.2 Os03g0112700_circ_g.3 Os03g0112700_circ_g.4 Os03g0112700_circ_g.5 Os03g0112700_circ_g.6 Os03g0112700_circ_g.7 Os03g0112800_circ_g.1 Os03g0112800_circ_g.2 Os03g0113500_circ_g.1 Os03g0113500_circ_g.2 Os03g0113500_circ_g.3 Os03g0113500_circ_g.4 Os03g0113500_circ_g.5 Os03g0113700_circ_g.1 Os03g0113800_circ_g.1 Os03g0113800_circ_g.2 Os03g0113800_circ_g.3 Os03g0113800_circ_g.4 Os03g0113800_circ_g.5 Os03g0113800_circ_g.6 Os03g0113800_circ_g.7 EPlOSAG00000003330_circ_ig.1 Os03g0114000_circ_g.1 Os03g0114300_circ_g.1 Os03g0114300_circ_g.2 Os03g0114300_circ_g.3 Os03g0114300_circ_g.4 Os03g0114300_circ_g.5 Os03g0114300_circ_g.6 Os03g0114300_circ_g.7 Os03g0114300_circ_g.8 Os03g0114300_circ_g.9 Os03g0114300_circ_g.10 Os03g0114300_circ_g.11 Os03g0115100_circ_g.1 Os03g0115400_circ_g.1 Os03g0115400_circ_g.2 Os03g0115400_circ_ig.1 Os03g0115700_circ_g.1 Os03g0116000_circ_g.1 Os03g0116000_circ_g.2 Os03g0116300_circ_g.1 Os03g0116300_circ_g.2 Os03g0116300_circ_g.3 Os03g0116300_circ_g.4 Os03g0116300_circ_g.5 Os03g0116300_circ_g.6 Os03g0116400_circ_g.1 Os03g0116400_circ_g.2 Os03g0116700_circ_g.1 Os03g0116700_circ_g.2 Os03g0116900_circ_igg.1 Os03g0117100_circ_g.1 Os03g0117100_circ_g.2 Os03g0117100_circ_g.3 Os03g0117100_circ_g.4 Os03g0117800_circ_g.1 Os03g0117800_circ_g.2 Os03g0118400_circ_g.1
Support reads	1
Tissues	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	Os03t0109400-01:2 Os03t0109400-02:2

			
						 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  
						
							GGCAATGAACAAGCTACTTATGGAAGAGAATGAGCGACTCCAGAAGCAGGTCTCCCAATTGGTT
CATGAGAATGCCCACATGCGACAGCAGCTGCAGAATggatctaggcgagctgaaaattgaagtg
caggcaaggagataagagcagcgtccaaattgtgagtacttcattagcaggaggtagtggttgt
gcttgctt

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							GGATCTAGGCGAGCTGAAAATTGAAGTGCAGGCAAGGAGATAAGAGCAGCGTCCAAATTGTGAG
TACTTCATTAGCAGGAGGTAGTGGTTGTGCTTGCTTGGCTCCTTTGCAATTTGGCTTTGGCGAG
GTAGCAATGGCTGCGGCAGTGGCAATGCGAGGGAGTAGCAGTGATGGAGGTGGCTATGATAAGG
TTTCCGGGATGGACTCCGGTAAATATGTGCGCTACACGCCTGAGCAGGTGGAGGCGCTTGAGCG
GGTGTACGCCGATTGCCCCAAGCCAACCTCCTCCCGCAGGCAGCAACTGCTGCGTGAGTGCCCC
ATACTTGCTAACATTGAGCCCAAGCAGATCAAGGTCTGGTTCCAGAACAGAAGGTAATGATAAT
AGAATTGAATCTTTCTACGTTTGTTCTCTGTGACAAAAACTTGTTATGGCAGTTTTCCCTGATT
GTTTCATCTGTCACCTGAAATAACATTTCGTTAGTTTCCTTCTGGGGAGGCTATGGTTCTAATA
TGCTGCGTTGTTGTTGTGATGATGAGCGGTATTTTGATATGAGGGGAGCTGCAATGCCAATTGT
TTATCATTTCATTTGTTTGCGCACCAGCAAAATGTAGTATAATTACTTTAGCTGACGGCTCTGC
ATGTATATGATTTTTTCGTTTTTCATGTTCGCTGAAGTGGATACTTGTGCTTGTGTTGCTCTAG
GTGCCGGGATAAGCAGCGGAAGGAGTCTTCACGGCTTCAGGCTGTCAACAGGAAATTGACGGCA
ATGAACAAGCTACTTATGGAAGAGAATGAGCGACTCCAGAAGCAGGTCTCCCAATTGGTTCATG
AGAATGCCCACATGCGACAGCAGCTGCAGAAT

Sequences
Splice junction sequence	GGCAATGAACAAGCTACTTATGGAAGAGAATGAGCGACTCCAGAAGCAGGTCTCCCAATTGGTT CATGAGAATGCCCACATGCGACAGCAGCTGCAGAATggatctaggcgagctgaaaattgaagtg caggcaaggagataagagcagcgtccaaattgtgagtacttcattagcaggaggtagtggttgt gcttgctt
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GGATCTAGGCGAGCTGAAAATTGAAGTGCAGGCAAGGAGATAAGAGCAGCGTCCAAATTGTGAG TACTTCATTAGCAGGAGGTAGTGGTTGTGCTTGCTTGGCTCCTTTGCAATTTGGCTTTGGCGAG GTAGCAATGGCTGCGGCAGTGGCAATGCGAGGGAGTAGCAGTGATGGAGGTGGCTATGATAAGG TTTCCGGGATGGACTCCGGTAAATATGTGCGCTACACGCCTGAGCAGGTGGAGGCGCTTGAGCG GGTGTACGCCGATTGCCCCAAGCCAACCTCCTCCCGCAGGCAGCAACTGCTGCGTGAGTGCCCC ATACTTGCTAACATTGAGCCCAAGCAGATCAAGGTCTGGTTCCAGAACAGAAGGTAATGATAAT AGAATTGAATCTTTCTACGTTTGTTCTCTGTGACAAAAACTTGTTATGGCAGTTTTCCCTGATT GTTTCATCTGTCACCTGAAATAACATTTCGTTAGTTTCCTTCTGGGGAGGCTATGGTTCTAATA TGCTGCGTTGTTGTTGTGATGATGAGCGGTATTTTGATATGAGGGGAGCTGCAATGCCAATTGT TTATCATTTCATTTGTTTGCGCACCAGCAAAATGTAGTATAATTACTTTAGCTGACGGCTCTGC ATGTATATGATTTTTTCGTTTTTCATGTTCGCTGAAGTGGATACTTGTGCTTGTGTTGCTCTAG GTGCCGGGATAAGCAGCGGAAGGAGTCTTCACGGCTTCAGGCTGTCAACAGGAAATTGACGGCA ATGAACAAGCTACTTATGGAAGAGAATGAGCGACTCCAGAAGCAGGTCTCCCAATTGGTTCATG AGAATGCCCACATGCGACAGCAGCTGCAGAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.211884028

Conservation Information
Conserved circRNAs	NA
PMCS	0.211884028

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							551515-550760(+)
550856-550741(+)
550794-551500(-)
						
						Potential amino acid sequence
						
							MSDSRSRSPNWFMRMPTCDSSCRMDLGELKIEVQARR*(+)
MAAAVAMRGSSSDGGGYDKVSGMDSGKYVRYTPEQVEALERVYADCPKPTSSRRQQLLRECPIL
ANIEPKQIKVWFQNRRCRDKQRKESSRLQAVNRKLTAMNKLLMEENERLQKQVSQLVHENAHMR
QQLQNGSRRAEN*(+)
MKYSQFGRCSYLLACTSIFSSPRSILQLLSHVGILMNQLGDLLLESLILFHK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	551515-550760(+) 550856-550741(+) 550794-551500(-)
Potential amino acid sequence	MSDSRSRSPNWFMRMPTCDSSCRMDLGELKIEVQARR(+) MAAAVAMRGSSSDGGGYDKVSGMDSGKYVRYTPEQVEALERVYADCPKPTSSRRQQLLRECPIL ANIEPKQIKVWFQNRRCRDKQRKESSRLQAVNRKLTAMNKLLMEENERLQKQVSQLVHENAHMR QQLQNGSRRAEN(+) MKYSQFGRCSYLLACTSIFSSPRSILQLLSHVGILMNQLGDLLLESLILFHK*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0109400_circ_g.3

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