Plant Circular RNA Database

Detail information of GLYMA_20G243100_circ_g.3

			
						 General Information
					
						CircRNA Name
						GLYMA_20G243100_circ_g.3
					
						ID in PlantcircBase
						gma_circ_005345
					
						Alias
						Gm20circRNA1462
					
						Organism
						
							Glycine max						
					
						Position
						
							chr20: 47359174-47359992  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI
					
						Parent gene
						
							GLYMA_20G243100						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_20G243100_circ_g.1 GLYMA_20G243100_circ_g.2 GLYMA_20G243100_circ_g.4 GLYMA_20G243100_circ_g.5 						
					
						Support reads
						NA
					
						Tissues
						root, stem
					
						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
						KRG93006:5

General Information
CircRNA Name	GLYMA_20G243100_circ_g.3
ID in PlantcircBase	gma_circ_005345
Alias	Gm20circRNA1462
Organism	Glycine max
Position	chr20: 47359174-47359992 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI
Parent gene	GLYMA_20G243100
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_20G243100_circ_g.1 GLYMA_20G243100_circ_g.2 GLYMA_20G243100_circ_g.4 GLYMA_20G243100_circ_g.5
Support reads	NA
Tissues	root, stem
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	KRG93006:5

			
						 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  
						
							CCAATGGTTCAGCAACAAGAACGCTGTCCCCATCCATAGTGCCCACGTAAGAGAAGGCCTCAGG
AAAGCAAAGCAATTTGGCTCCAGCAGATGCTGCTTCctgtgcttcatgttggaaacgtagcaat
tggtacatctctggaaatctcaaatcatagcaaacactgaggcccaaacgtccaataggactgt
ctactgca

						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: 492
Transcript exons: 47359174-47359285,47359382-47359436,47359499-47359557,47
359658-47359786,47359856-47359992
CTGTGCTTCATGTTGGAAACGTAGCAATTGGTACATCTCTGGAAATCTCAAATCATAGCAAACA
CTGAGGCCCAAACGTCCAATAGGACTGTCTACTGCAACAATATCCAGCTCCCCCTCCCCTTTTC
CCTCAGATTTTCTAGAAAGAGAGTTACGCTGAGGGAGGACTGATTCTGTAAAACTACTTTCTTT
GTATACCCTTCCACCAGGAACATCTACGTCAAACAGGTGTATCTTTCTATAAGAGCTTATAATT
TTGCCGGTGTCATCTACGATAACATGAGTATTACACAAGTGTTGAGGATCGGATCCAATCTCTT
GGAAGCCTCCAAGTGACAACCAAATGTCGGATTCTCTGGCCAAAGAGCAGTAGTGGTTCATAAT
AGGTCCATCCAATGGTTCAGCAACAAGAACGCTGTCCCCATCCATAGTGCCCACGTAAGAGAAG
GCCTCAGGAAAGCAAAGCAATTTGGCTCCAGCAGATGCTGCTTC
						
						Genomic sequence
						
							CTGTGCTTCATGTTGGAAACGTAGCAATTGGTACATCTCTGGAAATCTCAAATCATAGCAAACA
CTGAGGCCCAAACGTCCAATAGGACTGTCTACTGCAACAATATCCAGCCTGAAAACATCCCCAA
AACAGAAGAAATTCACATGAAAGCCCCATCCTTCATGGTGCATATCATATCCAAGTGTGCTTAT
CTTCTCTTTCAAACACTCCCCCTCCCCTTTTCCCTCAGATTTTCTAGAAAGAGAGTTACGCTGA
GGGAGGACTAAAGCAAGGCAAAAGGTTCATCATCTAGTCTTAATACTGCATAGAGAGTAAATAT
CCTACCTGATTCTGTAAAACTACTTTCTTTGTATACCCTTCCACCAGGAACATCTACGTCAAAC
CTTCAAATAACAGAAAATGAATAAAATATCAACAGCATAAAGAAAAAGCAGTAAAATTTCTCAA
TTCAGGAGGAGCATACCAAATAGTTAGTGATCTTGCAGGTGTATCTTTCTATAAGAGCTTATAA
TTTTGCCGGTGTCATCTACGATAACATGAGTATTACACAAGTGTTGAGGATCGGATCCAATCTC
TTGGAAGCCTCCAAGTGACAACCAAATGTCGGATTCTCTGAAGTGAATAGTATTGTGTAAGAGA
AGGGGAGAGTAAAAAAAAGGCAAAAAAAAGAAAGAATAGAACCTGGCCAAAGAGCAGTAGTGGT
TCATAATAGGTCCATCCAATGGTTCAGCAACAAGAACGCTGTCCCCATCCATAGTGCCCACGTA
AGAGAAGGCCTCAGGAAAGCAAAGCAATTTGGCTCCAGCAGATGCTGCTTC

Sequences
Splice junction sequence	CCAATGGTTCAGCAACAAGAACGCTGTCCCCATCCATAGTGCCCACGTAAGAGAAGGCCTCAGG AAAGCAAAGCAATTTGGCTCCAGCAGATGCTGCTTCctgtgcttcatgttggaaacgtagcaat tggtacatctctggaaatctcaaatcatagcaaacactgaggcccaaacgtccaataggactgt ctactgca
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: 492 Transcript exons: 47359174-47359285,47359382-47359436,47359499-47359557,47 359658-47359786,47359856-47359992 CTGTGCTTCATGTTGGAAACGTAGCAATTGGTACATCTCTGGAAATCTCAAATCATAGCAAACA CTGAGGCCCAAACGTCCAATAGGACTGTCTACTGCAACAATATCCAGCTCCCCCTCCCCTTTTC CCTCAGATTTTCTAGAAAGAGAGTTACGCTGAGGGAGGACTGATTCTGTAAAACTACTTTCTTT GTATACCCTTCCACCAGGAACATCTACGTCAAACAGGTGTATCTTTCTATAAGAGCTTATAATT TTGCCGGTGTCATCTACGATAACATGAGTATTACACAAGTGTTGAGGATCGGATCCAATCTCTT GGAAGCCTCCAAGTGACAACCAAATGTCGGATTCTCTGGCCAAAGAGCAGTAGTGGTTCATAAT AGGTCCATCCAATGGTTCAGCAACAAGAACGCTGTCCCCATCCATAGTGCCCACGTAAGAGAAG GCCTCAGGAAAGCAAAGCAATTTGGCTCCAGCAGATGCTGCTTC
Genomic sequence	CTGTGCTTCATGTTGGAAACGTAGCAATTGGTACATCTCTGGAAATCTCAAATCATAGCAAACA CTGAGGCCCAAACGTCCAATAGGACTGTCTACTGCAACAATATCCAGCCTGAAAACATCCCCAA AACAGAAGAAATTCACATGAAAGCCCCATCCTTCATGGTGCATATCATATCCAAGTGTGCTTAT CTTCTCTTTCAAACACTCCCCCTCCCCTTTTCCCTCAGATTTTCTAGAAAGAGAGTTACGCTGA GGGAGGACTAAAGCAAGGCAAAAGGTTCATCATCTAGTCTTAATACTGCATAGAGAGTAAATAT CCTACCTGATTCTGTAAAACTACTTTCTTTGTATACCCTTCCACCAGGAACATCTACGTCAAAC CTTCAAATAACAGAAAATGAATAAAATATCAACAGCATAAAGAAAAAGCAGTAAAATTTCTCAA TTCAGGAGGAGCATACCAAATAGTTAGTGATCTTGCAGGTGTATCTTTCTATAAGAGCTTATAA TTTTGCCGGTGTCATCTACGATAACATGAGTATTACACAAGTGTTGAGGATCGGATCCAATCTC TTGGAAGCCTCCAAGTGACAACCAAATGTCGGATTCTCTGAAGTGAATAGTATTGTGTAAGAGA AGGGGAGAGTAAAAAAAAGGCAAAAAAAAGAAAGAATAGAACCTGGCCAAAGAGCAGTAGTGGT TCATAATAGGTCCATCCAATGGTTCAGCAACAAGAACGCTGTCCCCATCCATAGTGCCCACGTA AGAGAAGGCCTCAGGAAAGCAAAGCAATTTGGCTCCAGCAGATGCTGCTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.161261193

Conservation Information
Conserved circRNAs	NA
PMCS	0.161261193

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							47359984-47359238(+)
47359931-47359176(-)
47359186-47359880(-)
						
						Potential amino acid sequence
						
							MLLPVLHVGNVAIGTSLEISNHSKH*(+)
MDGDSVLVAEPLDGPIMNHYCSLARESDIWLSLGGFQEIGSDPQHLCNTHVIVDDTGKIISSYR
KIHLFDVDVPGGRVYKESSFTESVLPQRNSLSRKSEGKGEGELDIVAVDSPIGRLGLSVCYDLR
FPEMYQLLRFQHEAQEAASAGAKLLCFPEAFSYVGTMDGDSVLVAEPLDGPIMNHYCSLARESD
IWLSLGGFQEIGSDPQHLCNTHVIVDDTGKIISSYRKIHLFDVDVPGGRVYKESSFTESVLPQR
NSLSRKSEGKGEGELDIVAVDSPIGRLGLSVCYDLRFPEMYQLLRFQHEAQEAASAGAKLLCFP
EAFSYVGTMDGDSVLVAEPLDGPIMNHYCSLARESDIWLSLGGFQEIGSDPQHLCNTHVIVDDT
GKIISSYRKIHLFDVDVPGGRVYKESSFTESVLPQRNSLSRKSEGKGEGELDIVAVDSPIGRLG
LSVCYDLRFPEMYQLLRFQHEAQEAASAGAKLLCFPEAFSYVGTMDGDSVLVAEPLDGPIMNHY
CSLARESDIWLSLGGFQEIGSDPQHLCNTHVIVDDTGKIISSYRKIHLFDVDVPGGRVYKESSF
TESVLPQRNSLSRKSEGKGEGELDIVAVDSPIGRLGLSVCYDLRFPEMYQLLRFQHEAQ(-)
MKHRKQHLLEPNCFAFLRPSLTWALWMGTAFLLLNHWMDLL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	47359984-47359238(+) 47359931-47359176(-) 47359186-47359880(-)
Potential amino acid sequence	MLLPVLHVGNVAIGTSLEISNHSKH(+) MDGDSVLVAEPLDGPIMNHYCSLARESDIWLSLGGFQEIGSDPQHLCNTHVIVDDTGKIISSYR KIHLFDVDVPGGRVYKESSFTESVLPQRNSLSRKSEGKGEGELDIVAVDSPIGRLGLSVCYDLR FPEMYQLLRFQHEAQEAASAGAKLLCFPEAFSYVGTMDGDSVLVAEPLDGPIMNHYCSLARESD IWLSLGGFQEIGSDPQHLCNTHVIVDDTGKIISSYRKIHLFDVDVPGGRVYKESSFTESVLPQR NSLSRKSEGKGEGELDIVAVDSPIGRLGLSVCYDLRFPEMYQLLRFQHEAQEAASAGAKLLCFP EAFSYVGTMDGDSVLVAEPLDGPIMNHYCSLARESDIWLSLGGFQEIGSDPQHLCNTHVIVDDT GKIISSYRKIHLFDVDVPGGRVYKESSFTESVLPQRNSLSRKSEGKGEGELDIVAVDSPIGRLG LSVCYDLRFPEMYQLLRFQHEAQEAASAGAKLLCFPEAFSYVGTMDGDSVLVAEPLDGPIMNHY CSLARESDIWLSLGGFQEIGSDPQHLCNTHVIVDDTGKIISSYRKIHLFDVDVPGGRVYKESSF TESVLPQRNSLSRKSEGKGEGELDIVAVDSPIGRLGLSVCYDLRFPEMYQLLRFQHEAQ(-) MKHRKQHLLEPNCFAFLRPSLTWALWMGTAFLLLNHWMDLL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_20G243100_circ_g.3

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