Plant Circular RNA Database

Detail information of Os03g0738400_circ_g.28

			
						 General Information
					
						CircRNA Name
						Os03g0738400_circ_g.28
					
						ID in PlantcircBase
						osa_circ_041555
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 30302271-30303320  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI-long
					
						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.13 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.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
						NA
					
						Tissues
						leaf
					
						Exon boundary  
						
							No-No							"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
						Os03t0738400-01:5
Os03t0738400-03:5

General Information
CircRNA Name	Os03g0738400_circ_g.28
ID in PlantcircBase	osa_circ_041555
Alias	NA
Organism	Oryza sativa
Position	chr3: 30302271-30303320 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRI-long
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.13 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.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	NA
Tissues	leaf
Exon boundary	No-No "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	Os03t0738400-01:5 Os03t0738400-03:5

			
						 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  
						
							TCATGCAGGAACCCCAGCACTGACCTCAAGAGGATTTGTTGAGGAGGACTTTGCTAAGGTTGCT
GATTTCTTCGATGCAGCAGTGAACTTGGCTTTGAAGgtctgcaaggtggaccacataatcatac
cattactggcttagctgttgcgcttaagcaggtctgtagcacttctgatccctgatgttttata
ttttatag

									
								

					

						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: 407
Transcript exons: 30302271-30302329,30302423-30302488,30302696-30302773,30
303032-30303143,30303229-30303320
GTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGGCAAC
TACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGAGC
TTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCATTTAGTGTTGGTAAATC
TCAAGAGCAAGGGCATAGATGGTTCAAGAGTGGAGAAGGTTTTAGAAAACGTGCACATTGCAGC
AAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTACCAGGAGGCATCAGGATGGGAACC
CCAGCACTGACCTCAAGAGGATTTGTTGAGGAGGACTTTGCTAAGGTTGCTGATTTCTTCGATG
CAGCAGTGAACTTGGCTTTGAAG
						
					

						Genomic sequence
						
							GTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGGTCTG
TAGCACTTCTGATCCCTGATGTTTTATATTTTATAGATCACATTGTTTGCCTTTGTCTTGGACT
CTAAAAGGACTTTCTAACTTCCAGGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTA
TGAGTAACTGTGCAAAATTTGCACAGGTATGTGTTCAAATTTTGCTAGGTTTTTTTTTTTATCT
ACAATATGGCTTGATCTTTCTTTATTTCACAACACTTAATAATGATTTTGTTCTTCACTTAGTT
CACCTCAGCATGTTACGAATTGCAAATTATTGGTTTTTCAACATGATGAATTGTGCTTTAACAT
TTGAACCACTTCCTTATCTGGTGGCAATTTATCACTTCCAGAGCTTGACAGCAAAAGGCTACGA
ACTTGTCTCTGGTGGGACTGACAACCATTTAGTGTTGGTAAATCTCAAGAGCAAGGTAAGACAA
ACATGTGGGACGCTTTGGGTGTTTTGAGATATTTTAGTTCTATCTTTCAGTTTCTCTTATGAGT
GCTCACCAATAAACTTTCAGCTGCTTCCTTTTAAAAAATATCGATTGATGTCTATTTAACCTCA
AGCTTGCTGTTTCTGTATATAAATGATAGCTAAATGTGCTTTGCAGATAAACTTGTTTTTTTTT
TTCAAATTTTTATGCCATATGGGGACAATTATCATCCTCTTCAAATTTCATGTTTAGGGCATAG
ATGGTTCAAGAGTGGAGAAGGTTTTAGAAAACGTGCACATTGCAGCAAACAAGAACACAGTTCC
TGGTGATGTTTCAGCTATGGTACCAGGAGGCATCAGGATGGGTAAAATCTGCCCCTATGTGGTT
TTTTTTTTAATTTACTTAAAATAGATTTGCAAAATCTCAATATCAGCTCCATGATCATGCAGGA
ACCCCAGCACTGACCTCAAGAGGATTTGTTGAGGAGGACTTTGCTAAGGTTGCTGATTTCTTCG
ATGCAGCAGTGAACTTGGCTTTGAAG
						
					

			
		

Sequences
Splice junction sequence	TCATGCAGGAACCCCAGCACTGACCTCAAGAGGATTTGTTGAGGAGGACTTTGCTAAGGTTGCT GATTTCTTCGATGCAGCAGTGAACTTGGCTTTGAAGgtctgcaaggtggaccacataatcatac cattactggcttagctgttgcgcttaagcaggtctgtagcacttctgatccctgatgttttata ttttatag
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: 407 Transcript exons: 30302271-30302329,30302423-30302488,30302696-30302773,30 303032-30303143,30303229-30303320 GTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGGCAAC TACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGAGC TTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCATTTAGTGTTGGTAAATC TCAAGAGCAAGGGCATAGATGGTTCAAGAGTGGAGAAGGTTTTAGAAAACGTGCACATTGCAGC AAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTACCAGGAGGCATCAGGATGGGAACC CCAGCACTGACCTCAAGAGGATTTGTTGAGGAGGACTTTGCTAAGGTTGCTGATTTCTTCGATG CAGCAGTGAACTTGGCTTTGAAG
Genomic sequence	GTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGGTCTG TAGCACTTCTGATCCCTGATGTTTTATATTTTATAGATCACATTGTTTGCCTTTGTCTTGGACT CTAAAAGGACTTTCTAACTTCCAGGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTA TGAGTAACTGTGCAAAATTTGCACAGGTATGTGTTCAAATTTTGCTAGGTTTTTTTTTTTATCT ACAATATGGCTTGATCTTTCTTTATTTCACAACACTTAATAATGATTTTGTTCTTCACTTAGTT CACCTCAGCATGTTACGAATTGCAAATTATTGGTTTTTCAACATGATGAATTGTGCTTTAACAT TTGAACCACTTCCTTATCTGGTGGCAATTTATCACTTCCAGAGCTTGACAGCAAAAGGCTACGA ACTTGTCTCTGGTGGGACTGACAACCATTTAGTGTTGGTAAATCTCAAGAGCAAGGTAAGACAA ACATGTGGGACGCTTTGGGTGTTTTGAGATATTTTAGTTCTATCTTTCAGTTTCTCTTATGAGT GCTCACCAATAAACTTTCAGCTGCTTCCTTTTAAAAAATATCGATTGATGTCTATTTAACCTCA AGCTTGCTGTTTCTGTATATAAATGATAGCTAAATGTGCTTTGCAGATAAACTTGTTTTTTTTT TTCAAATTTTTATGCCATATGGGGACAATTATCATCCTCTTCAAATTTCATGTTTAGGGCATAG ATGGTTCAAGAGTGGAGAAGGTTTTAGAAAACGTGCACATTGCAGCAAACAAGAACACAGTTCC TGGTGATGTTTCAGCTATGGTACCAGGAGGCATCAGGATGGGTAAAATCTGCCCCTATGTGGTT TTTTTTTTAATTTACTTAAAATAGATTTGCAAAATCTCAATATCAGCTCCATGATCATGCAGGA ACCCCAGCACTGACCTCAAGAGGATTTGTTGAGGAGGACTTTGCTAAGGTTGCTGATTTCTTCG ATGCAGCAGTGAACTTGGCTTTGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.160228317

Conservation Information
Conserved circRNAs	NA
PMCS	0.160228317

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						this study

circRNA

Detail information of Os03g0738400_circ_g.28

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