Plant Circular RNA Database

Detail information of Os03g0738400_circ_g.13

			
						 General Information
					
						CircRNA Name
						Os03g0738400_circ_g.13
					
						ID in PlantcircBase
						osa_circ_021781
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 30301385-30302101  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os03g0738400						
					
						Parent gene annotation
						
							Similar to Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.
1) (Serine methylase) (Glycine hydroxymethyltransferase) (SHMT).
 (Os03t0738400-01);Similar to Serine hydroxymethyltransferase. (
Os03t0738400-02);Similar to Serine hydroxymethyltransferase. (Os
03t0738400-03)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0738400_circ_g.14 Os03g0738400_circ_g.15 Os03g0738400_circ_g.16 Os03g0738400_circ_g.17 Os03g0738400_circ_g.18 Os03g0738400_circ_g.19 Os03g0738400_circ_g.20 Os03g0738400_circ_g.21 Os03g0738400_circ_g.22 Os03g0738400_circ_g.23 Os03g0738400_circ_g.24 Os03g0738400_circ_g.25 Os03g0738400_circ_g.26 Os03g0738400_circ_g.27 Os03g0738400_circ_g.28 Os03g0738400_circ_g.29 Os03g0738400_circ_g.30 Os03g0738400_circ_g.31 Os03g0738400_circ_g.32 Os03g0738400_circ_g.33 Os03g0738400_circ_g.34 Os03g0738400_circ_g.35 						
					
						Support reads
						2
					
						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  
						
							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
						Os03t0738400-01:3
Os03t0738400-03:3

General Information
CircRNA Name	Os03g0738400_circ_g.13
ID in PlantcircBase	osa_circ_021781
Alias	NA
Organism	Oryza sativa
Position	chr3: 30301385-30302101 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os03g0738400
Parent gene annotation	Similar to Serine hydroxymethyltransferase, cytosolic (EC 2.1.2. 1) (Serine methylase) (Glycine hydroxymethyltransferase) (SHMT). (Os03t0738400-01);Similar to Serine hydroxymethyltransferase. ( Os03t0738400-02);Similar to Serine hydroxymethyltransferase. (Os 03t0738400-03)
Parent gene strand	+
Alternative splicing	Os03g0738400_circ_g.14 Os03g0738400_circ_g.15 Os03g0738400_circ_g.16 Os03g0738400_circ_g.17 Os03g0738400_circ_g.18 Os03g0738400_circ_g.19 Os03g0738400_circ_g.20 Os03g0738400_circ_g.21 Os03g0738400_circ_g.22 Os03g0738400_circ_g.23 Os03g0738400_circ_g.24 Os03g0738400_circ_g.25 Os03g0738400_circ_g.26 Os03g0738400_circ_g.27 Os03g0738400_circ_g.28 Os03g0738400_circ_g.29 Os03g0738400_circ_g.30 Os03g0738400_circ_g.31 Os03g0738400_circ_g.32 Os03g0738400_circ_g.33 Os03g0738400_circ_g.34 Os03g0738400_circ_g.35
Support reads	2
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	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	Os03t0738400-01:3 Os03t0738400-03:3

			
						 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  
						
							TGTAGTGACTACCACTACTCACAAGTCACTCCGTGGACCACGTGGAGCCATGATCTTTTACAGG
AAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGactgatactaagaagatttcagcagttt
cgatattctttgagacaatgccctacagattggatgaaagcactggcttgattgattatgatca
ggtgcaat

						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: 384
Transcript exons: 30301385-30301477,30301728-30301820,30301904-30302101
ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATG
AAAGCACTGGCTTGATTGATTATGATCAGATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTT
GATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGGTTTGT
GACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGTGGGCTTGTCGCAGCTGGTG
TTGTTCCATCTCCTTTTGATTATGCAGATGTAGTGACTACCACTACTCACAAGTCACTCCGTGG
ACCACGTGGAGCCATGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG
						
						Genomic sequence
						
							ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATG
AAAGCACTGGCTTGATTGATTATGATCAGGTGCAATGTCCTCCTTATCTGTTTTGTTTTAATGC
CATTTAACTTATTGAATTCTCTATCATTCTTTTATAGGTATGAGTTTTCATTGGACAAAACGTG
TTCTTTTTGCATCTAGCAGATTCCACAGCTGAAAATATGGTTTCAAGTAGCATTATCTAGGATA
TTTTTCATTGCCTCATATCTCTTTCAATTGTGAAATTATTTCAAGATGAATTTCTGCTGACATG
CTTGATTTGCTACTTCTGCACAGATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGT
TGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGGTGAATTTTACT
GCTCAATAGTGCATGCTGAATCTTCACCTTCTGTAATCAGTCAAATAATTCACTTGTTATGCAA
TCTGCAGGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGTGGGCTT
GTCGCAGCTGGTGTTGTTCCATCTCCTTTTGATTATGCAGATGTAGTGACTACCACTACTCACA
AGTCACTCCGTGGACCACGTGGAGCCATGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAA
GCAAGGCAAAGAG

Sequences
Splice junction sequence	TGTAGTGACTACCACTACTCACAAGTCACTCCGTGGACCACGTGGAGCCATGATCTTTTACAGG AAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGactgatactaagaagatttcagcagttt cgatattctttgagacaatgccctacagattggatgaaagcactggcttgattgattatgatca ggtgcaat
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: 384 Transcript exons: 30301385-30301477,30301728-30301820,30301904-30302101 ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATG AAAGCACTGGCTTGATTGATTATGATCAGATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTT GATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGGTTTGT GACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGTGGGCTTGTCGCAGCTGGTG TTGTTCCATCTCCTTTTGATTATGCAGATGTAGTGACTACCACTACTCACAAGTCACTCCGTGG ACCACGTGGAGCCATGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG
Genomic sequence	ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATG AAAGCACTGGCTTGATTGATTATGATCAGGTGCAATGTCCTCCTTATCTGTTTTGTTTTAATGC CATTTAACTTATTGAATTCTCTATCATTCTTTTATAGGTATGAGTTTTCATTGGACAAAACGTG TTCTTTTTGCATCTAGCAGATTCCACAGCTGAAAATATGGTTTCAAGTAGCATTATCTAGGATA TTTTTCATTGCCTCATATCTCTTTCAATTGTGAAATTATTTCAAGATGAATTTCTGCTGACATG CTTGATTTGCTACTTCTGCACAGATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGT TGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGGTGAATTTTACT GCTCAATAGTGCATGCTGAATCTTCACCTTCTGTAATCAGTCAAATAATTCACTTGTTATGCAA TCTGCAGGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGTGGGCTT GTCGCAGCTGGTGTTGTTCCATCTCCTTTTGATTATGCAGATGTAGTGACTACCACTACTCACA AGTCACTCCGTGGACCACGTGGAGCCATGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAA GCAAGGCAAAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005089* 						
					
						PMCS
						0.359728045

Conservation Information
Conserved circRNAs	osi_circ_005089*
PMCS	0.359728045

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30301431-30302098(+)
						
						Potential amino acid sequence
						
							MPYRLDESTGLIDYDQMEKSAVLFRPKLIVAGASAYARLYDYDRMRKVCDKQKAILLADMAHIS
GLVAAGVVPSPFDYADVVTTTTHKSLRGPRGAMIFYRKGVKGVNKQGKETDTKKISAVSIFFET
MPYRLDESTGLIDYDQMEKSAVLFRPKLIVAGASAYARLYDYDRMRKVCDKQKAILLADMAHIS
GLVAAGVVPSPFDYADVVTTTTHKSLRGPRGAMIFYRKGVKGVNKQGKETDTKKISAVSIFFET
MPYRLDESTGLIDYDQMEKSAVLFRPKLIVAGASAYARLYDYDRMRKVCDKQKAILLADMAHIS
GLVAAGVVPSPFDYADVVTTTTHKSLRGPRGAMIFYRKGVKGVNKQGKETDTKKISAVSIFFET
MPYRLDESTGLIDYDQMEKSAVLFRPKLIVAGASAYARLYDYDRMRKVCDKQKAILLADMAHIS
GLVAAGVVPSPFDYADVVTTTTHKSLRGPRGAMIFYRKGVKGVNKQGKE(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30301431-30302098(+)
Potential amino acid sequence	MPYRLDESTGLIDYDQMEKSAVLFRPKLIVAGASAYARLYDYDRMRKVCDKQKAILLADMAHIS GLVAAGVVPSPFDYADVVTTTTHKSLRGPRGAMIFYRKGVKGVNKQGKETDTKKISAVSIFFET MPYRLDESTGLIDYDQMEKSAVLFRPKLIVAGASAYARLYDYDRMRKVCDKQKAILLADMAHIS GLVAAGVVPSPFDYADVVTTTTHKSLRGPRGAMIFYRKGVKGVNKQGKETDTKKISAVSIFFET MPYRLDESTGLIDYDQMEKSAVLFRPKLIVAGASAYARLYDYDRMRKVCDKQKAILLADMAHIS GLVAAGVVPSPFDYADVVTTTTHKSLRGPRGAMIFYRKGVKGVNKQGKETDTKKISAVSIFFET MPYRLDESTGLIDYDQMEKSAVLFRPKLIVAGASAYARLYDYDRMRKVCDKQKAILLADMAHIS GLVAAGVVPSPFDYADVVTTTTHKSLRGPRGAMIFYRKGVKGVNKQGKE(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0738400_circ_g.13

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