Plant Circular RNA Database

Detail information of GLYMA_16G122200_circ_g.3

			
						 General Information
					
						CircRNA Name
						GLYMA_16G122200_circ_g.3
					
						ID in PlantcircBase
						gma_circ_004314
					
						Alias
						Gm16circRNA1347
					
						Organism
						
							Glycine max						
					
						Position
						
							chr16: 27105552-27109402  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI
					
						Parent gene
						
							GLYMA_16G122200						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_16G122200_circ_g.1 GLYMA_16G122200_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						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  
						
							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
						KRH07984:2

General Information
CircRNA Name	GLYMA_16G122200_circ_g.3
ID in PlantcircBase	gma_circ_004314
Alias	Gm16circRNA1347
Organism	Glycine max
Position	chr16: 27105552-27109402 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI
Parent gene	GLYMA_16G122200
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_16G122200_circ_g.1 GLYMA_16G122200_circ_g.2
Support reads	NA
Tissues	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	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	KRH07984:2

			
						 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  
						
							GGCCACTGTTTGGTAACCACTGACAAAAAACCTTCTTCTGTGGCTTGGTATGCCTTCCGAATAA
CCTCCTCAGACATGGACTTCTGCTCAGATGCAAATCattgtgtgggttgttttgaactatatca
acagcatcctgattgctaaggtgttcccaaagaccatcagaagcaaatatgagaaattgatcat
gctgttga

									
								

					

						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
						
							ATTGTGTGGGTTGTTTTGAACTATATCAACAGCATCCTGATTGCTAAGGTGTTCCCAAAGACCA
TCAGAAGCAAATATGAGAAATTGATCATGCTGTTGAATTTCATGAACGGAAATTGATGGGTCAG
AGCTCAAAATGGGCCTCTTAAAACCTTCCCGCACACGGAACTTAGCATACAATGGTTCCTTGTT
GAATTCAGCCTTTTTTAGGTAAACATCGCCAATGGATCTAGAAATCTGCCACATAAAAATTTCA
TAATTGAGTTGTATTATACATGATAAGTTTAATCAAGTGATTAGACACAAGTAAATTAATGTGC
TGAAGTTAAGGTTGAATCGTTCGGGTAGTATCCGAGTTTGATCCTTTGCGGAAACAATTCTTGA
CCAGGCTTTACTTACCTCCTGGTCGAACTCCGGATTAGTCAGGGGTCCCTTTCCCCTAATGAAC
CAGAGGGTTAAGACCAAAAAAAAATACATGATAAGTTTATGGTAATGTTTATCTAGCTTTTTTT
TTCTCCTTAAAAAGAAGAAATTTGGCCAACACTTTTTGTGAAAAGCTCTTAAAAGTTAAGTAGA
TTAATTTCTATAAAGGAAAAGGAAAACAAATAGCATTTTAAAAAAGGCTAGCTGAAGGAGCTTT
TAGAATAAAGTTGGCTTCTCCCTCTTTCACTCCACTCCCCACTCTCTCTCCCTTTCTCTCTCAC
TCTCCTCTCTCTCCCCATTTTTCTTTTCATGTCTCTCTCTACCTCCTCTCTTTCTCTCACTCTC
TCCTCTCTCTCGCCCCACTCGCTCTCTTATCTCTTCTTTCTCTTTCTTTCTGCTCTCACTCTCA
CTCACTCTCTTTATCCCTGCTTTCTCTACTCTATCAAGTCATTTCTTAAGCTAAAAGAAATGAA
AATTATCAAATAATTTCTACTTTATTCTTAAATCTCTTGTTTTGAGCTTTAATTTTGAAGTAAC
TTTTAAGGCAAAAAAAAGGTTGGGCCAAACATAACCTATATAATTTAATATCATTATACAGACA
AAATTCACTGAAATTAGCATCTTTTATGTATCTTTCATTTGCTTTGTTGGAAAATCTTGAATCA
TGAACTTAGTAAAGCTACATTCTAGGTTTGGGCACTTGGCAGTTTCACCCCAACCCACTATGAG
GCTGCATAGGTGCAGGTTTAGGCATCAACTCACCCTTCCCTGCAGTCCTGCACTCCTCATTTAA
AACATTGTGCTTATCCCCCTTTGTTACTGATAAAGTCTACTATATTAATTTATCTTTCACTAGT
TCGTGACTGCAGACAATAGTGCTTTAGAAGCTCTGAAATAAACAGCTACCTCTTTTGCATTGTC
AGGTAAGCAGCTTTGATGTAAGCTGTGTGTACACTGCAGGGTATTTACCTAAATTGGAAGTCTT
TTTCTCTACTTATTATAAAGGTTTTGGAGGTTGAGAGGATAATTTTTTTAAAGAAAAAAAGTGC
TTTTGTACTGAGCACTTAGATATAGTTTTGTGTATTTTGCTGCAGCATAATTCTAGAATTTTAG
CCATAACTATCATCCTCCACAACCATATGTAATGAGATCATTTTCTTCTCCTTAGCCTCCTAGA
GAGTTTCAGTTCACAGGTTTTTCTAAGGATGCTCCTAGGTCAGACTTATAAAGGGGACTATTGC
TCTTTGAGCTGATGACAGTTTCCTTGTGATCTTGAAGCCTTTGGAGGATTCTTGATCCTCTTGT
TTTGTTCTCTTTCCTTTCTTAATGCATTCTTTCCATTTGAAGTGTAAGGCTTTGATGGAAAATA
GACAAAACATATCTGAATGATAATTGTATGATGTGATATCAAAAACTAAAACTAAAACCAAAAC
CTATTAGTATTCATTGTTCATACTACCAGACAAGATCAAGTACTAGTACAAACCCAGTTCAACA
AGACTAGTAACATAACATGATCTTGAACACATGAATAATCCTCATATTCTAGCACTCCTCTTTA
TGCTAAAGCTTACAAGGCTTTTTTATTTTGTTACAAATAAACATTTAAAGAAAACAATCTAAAA
ATATAAGGTGGGTTCAAAATGAAACTTGGAATGACAACTCGGTAAAACCTCCATATAAACACTG
GTATAAGAGATCACGGAGAGGTGATACACAAAAATGAGCATGGTTAGAAAGATAGCTCAACAAA
ATAGCTGGAATGACGCACAACCATAAAAGCTATTGCAATGTTGCATGGCCATAGACAAGGAGTA
AGAGAACCACTGGAATGACAGGCAGTGAAAATTGCCTGGCAAGCAATCATACAAGGCCAAAACT
TCTCCAGGTTCACTAAATGAAAGGTATTTGGAATTTTCAACCAGCAAGAATAACCTCAAATTTG
AATTCAGAAGACAGAAAAACCATCTAAAACATGTCTGAAAAGTGGATAACTGATTCGGGTTTGA
ATTCACTCAAAAACTACTATAATTGACTCAATCAATAGCTAGCTGCTAGAAGAACTTATAATAA
CAACGCAACTGCAGAACTAAACAGTAGAAAAAATTCAGTGAGACTAAATAAGCTCTAAATAGCC
CTAACAGAGACAATGGAGCAGATGTAAACTAAAAGGCTAAAGTGATGCATAAGCATAGGCAAAC
AGAGGACAAACAGCAAAAAAGAAACAAAGTCAAGTAACTGAACAAAGACGCCGTGAAAGGATTT
TAAAATTTTGGATACCCCACAGGCAGCAGCAGCAGAATAGTTATGGTATTAGGTCAAGGAGAAT
GGATGAATGGTAGAACTGTAACATCAAGTTGAAATACAGCGGTTTGATGGAAAAGAAGAGAGGA
GAAAGAACATGTCTTATTGATATTCATATGATATGATATATTTGATATAATAAAAAGCTAGATA
GGCTAGAATTTTTTATAGGATAAGTTGGATTGGTTAGTGGTCCCTATTGCTTTAACTTATCCAA
CAACCATTCTTGAATTGAATCCGGCAGAATTCCATCAAAATTTTGATGAGTTTTTAAAGCTTTG
TATCATTAATTTAGTGGGGGGAAAAAAAGAACCAATAATTCCTAGTTATATTACTAATCCAAGT
ATTAGTGTAGCACAAGCCCAACCAATAAAACGACCAATATAACAAAACTCAATAACACATGATC
AACCCAAATTTTGTAAAATAATATATATTAGATCACAGGCAATACATCTACGATCTACCAAAAA
AAGATCATAGGTGATGCTTTCATCTATTAACTAATACAATAATATGGAAATCCTTTATACCAAT
AAAAAGGCTGCACAAGGCTACAACATCAAAAATAGTAAAAAGAAATATTGACAATATGTAGTCT
AATAACACATCACATCAAGTTTATGATAAACTGAAAACAATAAATCAAATTTTCCAATTTCAAA
AGCAAAAGGACAGAAGAATTTGGGAAAGATGTGGATTGCGTTTTATTTAAAAACAAAAAACAAA
TCACCAAGTTTCGCATGAAAAACTTACCTGTATCAGACCCTTCACCCGCCATACATTGTGCTTT
AGAACCACAATTTTTGAGTCATCCGGATGCAAAGAATGCATCTCTTGTCTCACAGATTCTCTGG
CCACATTATGCTCTGACGAAAGCTGGATCGCCAAAACCTCCCCGGTTGCTCTGACAACCCGGCC
AAGCACAGCACGGGAATCGCCAAGGTTAGCAATGTAGAGGATACCACCACAAATCACACCAACC
AAACAACAAGATCCCACAGCAGCAATTTGGGGATTCATGGGCCACTGTTTGGTAACCACTGACA
AAAAACCTTCTTCTGTGGCTTGGTATGCCTTCCGAATAACCTCCTCAGACATGGACTTCTGCTC
AGATGCAAATC
						
					

			
		

Sequences
Splice junction sequence	GGCCACTGTTTGGTAACCACTGACAAAAAACCTTCTTCTGTGGCTTGGTATGCCTTCCGAATAA CCTCCTCAGACATGGACTTCTGCTCAGATGCAAATCattgtgtgggttgttttgaactatatca acagcatcctgattgctaaggtgttcccaaagaccatcagaagcaaatatgagaaattgatcat gctgttga
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	ATTGTGTGGGTTGTTTTGAACTATATCAACAGCATCCTGATTGCTAAGGTGTTCCCAAAGACCA TCAGAAGCAAATATGAGAAATTGATCATGCTGTTGAATTTCATGAACGGAAATTGATGGGTCAG AGCTCAAAATGGGCCTCTTAAAACCTTCCCGCACACGGAACTTAGCATACAATGGTTCCTTGTT GAATTCAGCCTTTTTTAGGTAAACATCGCCAATGGATCTAGAAATCTGCCACATAAAAATTTCA TAATTGAGTTGTATTATACATGATAAGTTTAATCAAGTGATTAGACACAAGTAAATTAATGTGC TGAAGTTAAGGTTGAATCGTTCGGGTAGTATCCGAGTTTGATCCTTTGCGGAAACAATTCTTGA CCAGGCTTTACTTACCTCCTGGTCGAACTCCGGATTAGTCAGGGGTCCCTTTCCCCTAATGAAC CAGAGGGTTAAGACCAAAAAAAAATACATGATAAGTTTATGGTAATGTTTATCTAGCTTTTTTT TTCTCCTTAAAAAGAAGAAATTTGGCCAACACTTTTTGTGAAAAGCTCTTAAAAGTTAAGTAGA TTAATTTCTATAAAGGAAAAGGAAAACAAATAGCATTTTAAAAAAGGCTAGCTGAAGGAGCTTT TAGAATAAAGTTGGCTTCTCCCTCTTTCACTCCACTCCCCACTCTCTCTCCCTTTCTCTCTCAC TCTCCTCTCTCTCCCCATTTTTCTTTTCATGTCTCTCTCTACCTCCTCTCTTTCTCTCACTCTC TCCTCTCTCTCGCCCCACTCGCTCTCTTATCTCTTCTTTCTCTTTCTTTCTGCTCTCACTCTCA CTCACTCTCTTTATCCCTGCTTTCTCTACTCTATCAAGTCATTTCTTAAGCTAAAAGAAATGAA AATTATCAAATAATTTCTACTTTATTCTTAAATCTCTTGTTTTGAGCTTTAATTTTGAAGTAAC TTTTAAGGCAAAAAAAAGGTTGGGCCAAACATAACCTATATAATTTAATATCATTATACAGACA AAATTCACTGAAATTAGCATCTTTTATGTATCTTTCATTTGCTTTGTTGGAAAATCTTGAATCA TGAACTTAGTAAAGCTACATTCTAGGTTTGGGCACTTGGCAGTTTCACCCCAACCCACTATGAG GCTGCATAGGTGCAGGTTTAGGCATCAACTCACCCTTCCCTGCAGTCCTGCACTCCTCATTTAA AACATTGTGCTTATCCCCCTTTGTTACTGATAAAGTCTACTATATTAATTTATCTTTCACTAGT TCGTGACTGCAGACAATAGTGCTTTAGAAGCTCTGAAATAAACAGCTACCTCTTTTGCATTGTC AGGTAAGCAGCTTTGATGTAAGCTGTGTGTACACTGCAGGGTATTTACCTAAATTGGAAGTCTT TTTCTCTACTTATTATAAAGGTTTTGGAGGTTGAGAGGATAATTTTTTTAAAGAAAAAAAGTGC TTTTGTACTGAGCACTTAGATATAGTTTTGTGTATTTTGCTGCAGCATAATTCTAGAATTTTAG CCATAACTATCATCCTCCACAACCATATGTAATGAGATCATTTTCTTCTCCTTAGCCTCCTAGA GAGTTTCAGTTCACAGGTTTTTCTAAGGATGCTCCTAGGTCAGACTTATAAAGGGGACTATTGC TCTTTGAGCTGATGACAGTTTCCTTGTGATCTTGAAGCCTTTGGAGGATTCTTGATCCTCTTGT TTTGTTCTCTTTCCTTTCTTAATGCATTCTTTCCATTTGAAGTGTAAGGCTTTGATGGAAAATA GACAAAACATATCTGAATGATAATTGTATGATGTGATATCAAAAACTAAAACTAAAACCAAAAC CTATTAGTATTCATTGTTCATACTACCAGACAAGATCAAGTACTAGTACAAACCCAGTTCAACA AGACTAGTAACATAACATGATCTTGAACACATGAATAATCCTCATATTCTAGCACTCCTCTTTA TGCTAAAGCTTACAAGGCTTTTTTATTTTGTTACAAATAAACATTTAAAGAAAACAATCTAAAA ATATAAGGTGGGTTCAAAATGAAACTTGGAATGACAACTCGGTAAAACCTCCATATAAACACTG GTATAAGAGATCACGGAGAGGTGATACACAAAAATGAGCATGGTTAGAAAGATAGCTCAACAAA ATAGCTGGAATGACGCACAACCATAAAAGCTATTGCAATGTTGCATGGCCATAGACAAGGAGTA AGAGAACCACTGGAATGACAGGCAGTGAAAATTGCCTGGCAAGCAATCATACAAGGCCAAAACT TCTCCAGGTTCACTAAATGAAAGGTATTTGGAATTTTCAACCAGCAAGAATAACCTCAAATTTG AATTCAGAAGACAGAAAAACCATCTAAAACATGTCTGAAAAGTGGATAACTGATTCGGGTTTGA ATTCACTCAAAAACTACTATAATTGACTCAATCAATAGCTAGCTGCTAGAAGAACTTATAATAA CAACGCAACTGCAGAACTAAACAGTAGAAAAAATTCAGTGAGACTAAATAAGCTCTAAATAGCC CTAACAGAGACAATGGAGCAGATGTAAACTAAAAGGCTAAAGTGATGCATAAGCATAGGCAAAC AGAGGACAAACAGCAAAAAAGAAACAAAGTCAAGTAACTGAACAAAGACGCCGTGAAAGGATTT TAAAATTTTGGATACCCCACAGGCAGCAGCAGCAGAATAGTTATGGTATTAGGTCAAGGAGAAT GGATGAATGGTAGAACTGTAACATCAAGTTGAAATACAGCGGTTTGATGGAAAAGAAGAGAGGA GAAAGAACATGTCTTATTGATATTCATATGATATGATATATTTGATATAATAAAAAGCTAGATA GGCTAGAATTTTTTATAGGATAAGTTGGATTGGTTAGTGGTCCCTATTGCTTTAACTTATCCAA CAACCATTCTTGAATTGAATCCGGCAGAATTCCATCAAAATTTTGATGAGTTTTTAAAGCTTTG TATCATTAATTTAGTGGGGGGAAAAAAAGAACCAATAATTCCTAGTTATATTACTAATCCAAGT ATTAGTGTAGCACAAGCCCAACCAATAAAACGACCAATATAACAAAACTCAATAACACATGATC AACCCAAATTTTGTAAAATAATATATATTAGATCACAGGCAATACATCTACGATCTACCAAAAA AAGATCATAGGTGATGCTTTCATCTATTAACTAATACAATAATATGGAAATCCTTTATACCAAT AAAAAGGCTGCACAAGGCTACAACATCAAAAATAGTAAAAAGAAATATTGACAATATGTAGTCT AATAACACATCACATCAAGTTTATGATAAACTGAAAACAATAAATCAAATTTTCCAATTTCAAA AGCAAAAGGACAGAAGAATTTGGGAAAGATGTGGATTGCGTTTTATTTAAAAACAAAAAACAAA TCACCAAGTTTCGCATGAAAAACTTACCTGTATCAGACCCTTCACCCGCCATACATTGTGCTTT AGAACCACAATTTTTGAGTCATCCGGATGCAAAGAATGCATCTCTTGTCTCACAGATTCTCTGG CCACATTATGCTCTGACGAAAGCTGGATCGCCAAAACCTCCCCGGTTGCTCTGACAACCCGGCC AAGCACAGCACGGGAATCGCCAAGGTTAGCAATGTAGAGGATACCACCACAAATCACACCAACC AAACAACAAGATCCCACAGCAGCAATTTGGGGATTCATGGGCCACTGTTTGGTAACCACTGACA AAAAACCTTCTTCTGTGGCTTGGTATGCCTTCCGAATAACCTCCTCAGACATGGACTTCTGCTC AGATGCAAATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.041978681

Conservation Information
Conserved circRNAs	NA
PMCS	0.041978681

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							27109301-27105595(+)
27109395-27105668(+)
27109381-27109300(-)
						
						Potential amino acid sequence
						
							MGHCLVTTDKKPSSVAWYAFRITSSDMDFCSDANHCVGCFELYQQHPDC*(+)
MQIIVWVVLNYINSILIAKVFPKTIRSKYEKLIMLLNFMNGN*(+)
MSEEVIRKAYQATEEGFLSVVTKQWPMNPQIAAVGSCCLVGVICGGILYIANLGDSRAVLGRVV
RATGEVLAIQLSSEHNVARESVRQEMHSLHPDDSKIVVLKHNVWRVKGLIQISRSIGDVYLKKA
EFNKEPLYAKFRVREGFKRPILSSDPSISVHEIQQHDQFLIFASDGLWEHLSNQDAVDIVQNNP
HNDLHLSRSPCLRRLFGRHTKPQKKVFCQWLPNSGP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	27109301-27105595(+) 27109395-27105668(+) 27109381-27109300(-)
Potential amino acid sequence	MGHCLVTTDKKPSSVAWYAFRITSSDMDFCSDANHCVGCFELYQQHPDC(+) MQIIVWVVLNYINSILIAKVFPKTIRSKYEKLIMLLNFMNGN(+) MSEEVIRKAYQATEEGFLSVVTKQWPMNPQIAAVGSCCLVGVICGGILYIANLGDSRAVLGRVV RATGEVLAIQLSSEHNVARESVRQEMHSLHPDDSKIVVLKHNVWRVKGLIQISRSIGDVYLKKA EFNKEPLYAKFRVREGFKRPILSSDPSISVHEIQQHDQFLIFASDGLWEHLSNQDAVDIVQNNP HNDLHLSRSPCLRRLFGRHTKPQKKVFCQWLPNSGP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_16G122200_circ_g.3

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