Plant Circular RNA Database

Detail information of GLYMA_20G250200_circ_g.1

			
						 General Information
					
						CircRNA Name
						GLYMA_20G250200_circ_g.1
					
						ID in PlantcircBase
						gma_circ_007835
					
						Alias
						gma-circRNA2838
					
						Organism
						
							Glycine max						
					
						Position
						
							chr20: 47895695-47895946  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							GLYMA_20G250200						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						flower bud
					
						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  
						
							CT-AC							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
						KRG93151:1
KRG93152:1
KRG93147:1
KRG93150:1
KRG93149:1
KRG93153:1
KRG93148:1

General Information
CircRNA Name	GLYMA_20G250200_circ_g.1
ID in PlantcircBase	gma_circ_007835
Alias	gma-circRNA2838
Organism	Glycine max
Position	chr20: 47895695-47895946 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	GLYMA_20G250200
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	NA
Support reads	NA
Tissues	flower bud
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	CT-AC 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	KRG93151:1 KRG93152:1 KRG93147:1 KRG93150:1 KRG93149:1 KRG93153:1 KRG93148:1

			
						 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  
						
							TACCAATGAATTGGTAATCAATGTGATGCTGCTCTGTTACTGATTTTACATGTGGCTCCACTGT
CTCAAGAGATTTAACTGCTTTCTTGAAGAAACACAActtcattgagttctctaatgtagaatca
tcttgctcgcattcattttgtgcatagtcaaaactcagctccccatcatcattctcatcatgac
tgtcatca

						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: 252
Transcript exons: 47895695-47895946
CTTCATTGAGTTCTCTAATGTAGAATCATCTTGCTCGCATTCATTTTGTGCATAGTCAAAACTC
AGCTCCCCATCATCATTCTCATCATGACTGTCATCATCATGATCTACATCATCTTCATCTTCAT
CCTCATCCTCATCCTCTCCTTCAATACCAATGAATTGGTAATCAATGTGATGCTGCTCTGTTAC
TGATTTTACATGTGGCTCCACTGTCTCAAGAGATTTAACTGCTTTCTTGAAGAAACACAA
						
						Genomic sequence
						
							CTTCATTGAGTTCTCTAATGTAGAATCATCTTGCTCGCATTCATTTTGTGCATAGTCAAAACTC
AGCTCCCCATCATCATTCTCATCATGACTGTCATCATCATGATCTACATCATCTTCATCTTCAT
CCTCATCCTCATCCTCTCCTTCAATACCAATGAATTGGTAATCAATGTGATGCTGCTCTGTTAC
TGATTTTACATGTGGCTCCACTGTCTCAAGAGATTTAACTGCTTTCTTGAAGAAACACAA

Sequences
Splice junction sequence	TACCAATGAATTGGTAATCAATGTGATGCTGCTCTGTTACTGATTTTACATGTGGCTCCACTGT CTCAAGAGATTTAACTGCTTTCTTGAAGAAACACAActtcattgagttctctaatgtagaatca tcttgctcgcattcattttgtgcatagtcaaaactcagctccccatcatcattctcatcatgac tgtcatca
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: 252 Transcript exons: 47895695-47895946 CTTCATTGAGTTCTCTAATGTAGAATCATCTTGCTCGCATTCATTTTGTGCATAGTCAAAACTC AGCTCCCCATCATCATTCTCATCATGACTGTCATCATCATGATCTACATCATCTTCATCTTCAT CCTCATCCTCATCCTCTCCTTCAATACCAATGAATTGGTAATCAATGTGATGCTGCTCTGTTAC TGATTTTACATGTGGCTCCACTGTCTCAAGAGATTTAACTGCTTTCTTGAAGAAACACAA
Genomic sequence	CTTCATTGAGTTCTCTAATGTAGAATCATCTTGCTCGCATTCATTTTGTGCATAGTCAAAACTC AGCTCCCCATCATCATTCTCATCATGACTGTCATCATCATGATCTACATCATCTTCATCTTCAT CCTCATCCTCATCCTCTCCTTCAATACCAATGAATTGGTAATCAATGTGATGCTGCTCTGTTAC TGATTTTACATGTGGCTCCACTGTCTCAAGAGATTTAACTGCTTTCTTGAAGAAACACAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.209828042

Conservation Information
Conserved circRNAs	NA
PMCS	0.209828042

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							47895702-47895697(-)
						
						Potential amino acid sequence
						
							MKLCFFKKAVKSLETVEPHVKSVTEQHHIDYQFIGIEGEDEDEDEDEDDVDHDDDSHDENDDGE
LSFDYAQNECEQDDSTLENSMKLCFFKKAVKSLETVEPHVKSVTEQHHIDYQFIGIEGEDEDED
EDEDDVDHDDDSHDENDDGELSFDYAQNECEQDDSTLENSMKLCFFKKAVKSLETVEPHVKSVT
EQHHIDYQFIGIEGEDEDEDEDEDDVDHDDDSHDENDDGELSFDYAQNECEQDDSTLENSMK(-
)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						cytoplasmic male sterility

Functional Information
Coding potential	Y
Potential coding position	47895702-47895697(-)
Potential amino acid sequence	MKLCFFKKAVKSLETVEPHVKSVTEQHHIDYQFIGIEGEDEDEDEDEDDVDHDDDSHDENDDGE LSFDYAQNECEQDDSTLENSMKLCFFKKAVKSLETVEPHVKSVTEQHHIDYQFIGIEGEDEDED EDEDDVDHDDDSHDENDDGELSFDYAQNECEQDDSTLENSMKLCFFKKAVKSLETVEPHVKSVT EQHHIDYQFIGIEGEDEDEDEDEDDVDHDDDSHDENDDGELSFDYAQNECEQDDSTLENSMK(- )
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	cytoplasmic male sterility

			
						 Other Information
					
						References
						Chen et al., 2018

circRNA

Detail information of GLYMA_20G250200_circ_g.1

Address

Any questions?

Supported by