Plant Circular RNA Database

Detail information of GLYMA_04G096600_circ_g.3

			
						 General Information
					
						CircRNA Name
						GLYMA_04G096600_circ_g.3
					
						ID in PlantcircBase
						gma_circ_000865
					
						Alias
						Gm04circRNA85
					
						Organism
						
							Glycine max						
					
						Position
						
							chr4: 8715129-8718471  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat
					
						Parent gene
						
							GLYMA_04G096600						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_04G096600_circ_g.4 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						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
						KRH62260:3

General Information
CircRNA Name	GLYMA_04G096600_circ_g.3
ID in PlantcircBase	gma_circ_000865
Alias	Gm04circRNA85
Organism	Glycine max
Position	chr4: 8715129-8718471 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat
Parent gene	GLYMA_04G096600
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_04G096600_circ_g.4
Support reads	NA
Tissues	leaf
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	KRH62260:3

			
						 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  
						
							TGGTGCTTTTCAATTGGATGCCCATGATGTTGTTTTCAATATAAAGACCATGCTCACGATGCAC
AAAACTCACATCCAGCTTTGGTAGATTGAAGCTGACatgatacaccggagaaccagccatattg
aaaagcactattgtcatctcaggagctgagacattgcatgtccacatgatggtcttgccatcgg
ttgattga

									
								

					

						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
						
							ATGATACACCGGAGAACCAGCCATATTGAAAAGCACTATTGTCATCTCAGGAGCTGAGACATTG
CATGTCCACATGATGGTCTTGCCATCGGTTGATTGAGGCCTTGCAACCACAGAAGCTTCTTGTC
GAAGTACCATTTTTTTCTTCTTAGACGAGTGGAGGACCAACCAAGGCTTTAACCTGCTCATTAT
GATGTTGCACTGAGTACCTCCTAGCTTGATTTCAGATTCAGCTCTAACAGGTGATATTGGCTGA
TTCAGAGGAAGCATCCCCGACAACAAATAACAGTAAGTTCCCAAAGCAAATAAAAAGGAACATT
CAAACTCCATATGTAAAAACAAAAGAGGGGAGTTGAGCAGTATGCGAAAATGGCAAAACATGAG
CACATATGAAGTTACAGTTTTTAGAGTACCAAATAAAAAGTCGTTTTCTTGAGAATTTTGTTTC
CTTTTTGACAACTAGATTCTTTTATTCACTTCAAAACAGGATATATTTATTTTTTCAATCCTTC
TGGAAGAATATTAGGGTCAATTGTCTTATTGTTTGTGGATTTAGGCTCCTACTAGCAACACTAG
TACTTGACCTAATTATTAGTATAACAGAAGCATTAGGTTAGGCCATTTTATCATGTCATCCCTC
AATCATAATTCATATATCCCAATTCTAGTCAAAATGGAAGCAAAGACACATTTCATTTGGGGGG
AGAGTGACATTAATATAGTCAGTACTAACATCAATTCCTATCTATTTCTTTTCTTTTTTCAGGG
TGCCTCAGTCCGTGGTGGATAAGCTAGTGAAAATACAACGTCGATTTCTATGGGGAGGTGGTCC
TGACCAAAACAAGATTGCATGGATTAGGTGGGACAAAGTGTGCTTACCCAAAGAAAGGGGAGGG
CTTGGCATCAAGGACATCAACACTTTTAATCTCGCTCTGCTAGGCAAATGGAAGTTGCATCTTT
TACAGTGCCAAGGAGATCTTTGGGCTAGAGTATTGGAGTCTAAATATGGTGGATGGAGGGGTGG
GGAGGAAGTTGGAAGGACAGCCAATGAATCTATTTGGTGGAGGGATATAAAAAGGGCTATGGGT
CATTCATACCAGGGTAGAGCTCTCCAAGATGGATTCCGATGGAAGGTAGGAGCTGGAGACAGGA
TTAAATTTTGGGAGGATAGGTGGTTATGTCAGGAGGAATCATTAGCAGAAAAATATCCTAGAAT
TTATCTCATCTCATCACAGCAGCACCAACCTATCCGACAAGTGGGATCTCACAAGGATAATGGT
TGGGAGTGGCCTTTCCTATGGAGAAGACCATTGTTTGACTCTGAAATTGATTCAGCTATCAGTT
TCCTTGAAGAGGTCAAAGGCAGGCACATACAGCAACAGGGAGATGATGTATGGGAGTGGATAGG
ACACCCTTCAGGCACAGACTCTACAAGCAGTGCCTATCAATTGTTATGGGAGGGGGGAGCAGCT
GGAAGTAAGGAGGACTGTTTTGAGGAGATTTGGAAGTTAAAGATTCCTAGAAAATTCGCTGTAT
TTGCATGGAGATTGTTTAGGGATAGATTGCCAACTAAGAAGAATCTGCAGAGGAGACACGTGCA
GATAGTGGATTTAACATGTCCTTTCTGTGGTAGGGTAGAGGAGGAGGCATCTCATTTATTCATT
CACTGCATAAAAATCCTGCCCATTTGGTGGGAAACCATGTCTTGGATGAATATTAAAAGTGCCC
TTCCATTAAACCCAAAATGTCATTTCCTCCAACACTCATGTTCAGGTGGATGGCATAAGGGTAA
AGAGATGGCAATGTTGGTGGTTGGTTGTGGTATGGTCCATATGGCAGATGCGCAACAGAATTAT
ATTCTCTAATGCTATTTTCAATGGCAACAAGCTGATTGAGGATGCAATGTTTTTAATCTGGACT
TGGCTCAGATACTTAGAGAAGGATTTCTCCCTGCATTTTAATCACTGGTCAAGCCATATTAGAC
AGGATTTTTTGTATCAGTAGAGGGTAGCTTTTATTGGCTTTTAGCCGCTGTAAATTAAACATGT
AGCCATAATATGGTTCCTATTCATTGAGGAACCATATTTATGGAATTCTATTTTTGTACAAAGT
ACCTCTGGTACTCCATTGCTATTATATATATATATACTTATCTTTGCCGATCAAAAAAAAATAT
ATCCCAATTCTAGTGATAGTTCCCTCCCTTAATGAAAAGAGAAATATCAGTTTACTGTAAAGCA
TATAGGCAAACTTCCTTAAGTCCAAGTAAACATATCAATCATAATTAGAGAAAATACTATTGCA
CAAAACTATCAGGGTCGCAATAATTTCTGCATTGACATTGACATCTTGCCACTTAAATAAAAAT
CTCAGCAAAAATTCTGCATCTTTTTGTGTGTGTGTGTGTGTCTGTGTGTGTGTGTGTGTGTGTG
TGTGTGTGTCTGTGTGTGTGTCTGTGTGTCTGTGTGTCTGTCTGTGTCTGTGTGTGTCTGTGTG
TGTGTCTGTGTGTGTGTCTGTGTGTCTGTGTGTGTGTCTGTGTGTCTGTCTGTGTCTGTGTGTG
TGTCTGTGTGTGTGTCTGTGTGTGTGTGTGTGTGTGTGTGTCTGTGTCTGTGTGTGTGTCTGTG
TGTGTCTGTGTGTGTGTCTGTGTGTGTGTGTGTCTGTGTGTGTGTCTGTGTGTCTGTCTGTGTC
TGTGTGTGTCTGTGTGTGTGTCTGTGTGTGTGTCTGTGTGTGTGTGTGTGTCTGTGTGTGTGTG
TGTCTGGGTGTGTGTGTGTGTCTGTGTGTGTGTCTGTGTGTGTGTGTGTCTGTGTGTGTGTGTG
TGTCTGTGTGTGTCTGTGTGTGTGTGTCAGTGTGTGTGTCTGTGTGTGTGTGTGTGTGTGTGTG
TGTTTTCATTTTTAACTTTGAGTATATTTGTCAGGTGGAGCAAACACAAAGGAATATCAATTTT
AAAGTGATGCAAAAGCTACTTTACATGGATACCAAATCACTTACCTGTATCGGGATATATACAA
AAGAGATCAAATCCAACTTCAATATCTCCAAGATAGAAGAACCAGCTTCTCTAAGAAGCTGTAA
TAACAATCAGGCAAAAGAAAACTTGTCAGCAAGAAACAAAACAGTGAAAAGTAGGAATCATATC
ACAAGCTCTGCCAAAATAAACAGTCACACTCCATACATGAATTTCACTAAACTCCAGTTGGAAA
TCAAGGCGTGTACTCTCCCCAAGATCCTCAGTGGATCGTGATTTGGTGCTTTTCAATTGGATGC
CCATGATGTTGTTTTCAATATAAAGACCATGCTCACGATGCACAAAACTCACATCCAGCTTTGG
TAGATTGAAGCTGAC
						
					

			
		

Sequences
Splice junction sequence	TGGTGCTTTTCAATTGGATGCCCATGATGTTGTTTTCAATATAAAGACCATGCTCACGATGCAC AAAACTCACATCCAGCTTTGGTAGATTGAAGCTGACatgatacaccggagaaccagccatattg aaaagcactattgtcatctcaggagctgagacattgcatgtccacatgatggtcttgccatcgg ttgattga
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	ATGATACACCGGAGAACCAGCCATATTGAAAAGCACTATTGTCATCTCAGGAGCTGAGACATTG CATGTCCACATGATGGTCTTGCCATCGGTTGATTGAGGCCTTGCAACCACAGAAGCTTCTTGTC GAAGTACCATTTTTTTCTTCTTAGACGAGTGGAGGACCAACCAAGGCTTTAACCTGCTCATTAT GATGTTGCACTGAGTACCTCCTAGCTTGATTTCAGATTCAGCTCTAACAGGTGATATTGGCTGA TTCAGAGGAAGCATCCCCGACAACAAATAACAGTAAGTTCCCAAAGCAAATAAAAAGGAACATT CAAACTCCATATGTAAAAACAAAAGAGGGGAGTTGAGCAGTATGCGAAAATGGCAAAACATGAG CACATATGAAGTTACAGTTTTTAGAGTACCAAATAAAAAGTCGTTTTCTTGAGAATTTTGTTTC CTTTTTGACAACTAGATTCTTTTATTCACTTCAAAACAGGATATATTTATTTTTTCAATCCTTC TGGAAGAATATTAGGGTCAATTGTCTTATTGTTTGTGGATTTAGGCTCCTACTAGCAACACTAG TACTTGACCTAATTATTAGTATAACAGAAGCATTAGGTTAGGCCATTTTATCATGTCATCCCTC AATCATAATTCATATATCCCAATTCTAGTCAAAATGGAAGCAAAGACACATTTCATTTGGGGGG AGAGTGACATTAATATAGTCAGTACTAACATCAATTCCTATCTATTTCTTTTCTTTTTTCAGGG TGCCTCAGTCCGTGGTGGATAAGCTAGTGAAAATACAACGTCGATTTCTATGGGGAGGTGGTCC TGACCAAAACAAGATTGCATGGATTAGGTGGGACAAAGTGTGCTTACCCAAAGAAAGGGGAGGG CTTGGCATCAAGGACATCAACACTTTTAATCTCGCTCTGCTAGGCAAATGGAAGTTGCATCTTT TACAGTGCCAAGGAGATCTTTGGGCTAGAGTATTGGAGTCTAAATATGGTGGATGGAGGGGTGG GGAGGAAGTTGGAAGGACAGCCAATGAATCTATTTGGTGGAGGGATATAAAAAGGGCTATGGGT CATTCATACCAGGGTAGAGCTCTCCAAGATGGATTCCGATGGAAGGTAGGAGCTGGAGACAGGA TTAAATTTTGGGAGGATAGGTGGTTATGTCAGGAGGAATCATTAGCAGAAAAATATCCTAGAAT TTATCTCATCTCATCACAGCAGCACCAACCTATCCGACAAGTGGGATCTCACAAGGATAATGGT TGGGAGTGGCCTTTCCTATGGAGAAGACCATTGTTTGACTCTGAAATTGATTCAGCTATCAGTT TCCTTGAAGAGGTCAAAGGCAGGCACATACAGCAACAGGGAGATGATGTATGGGAGTGGATAGG ACACCCTTCAGGCACAGACTCTACAAGCAGTGCCTATCAATTGTTATGGGAGGGGGGAGCAGCT GGAAGTAAGGAGGACTGTTTTGAGGAGATTTGGAAGTTAAAGATTCCTAGAAAATTCGCTGTAT TTGCATGGAGATTGTTTAGGGATAGATTGCCAACTAAGAAGAATCTGCAGAGGAGACACGTGCA GATAGTGGATTTAACATGTCCTTTCTGTGGTAGGGTAGAGGAGGAGGCATCTCATTTATTCATT CACTGCATAAAAATCCTGCCCATTTGGTGGGAAACCATGTCTTGGATGAATATTAAAAGTGCCC TTCCATTAAACCCAAAATGTCATTTCCTCCAACACTCATGTTCAGGTGGATGGCATAAGGGTAA AGAGATGGCAATGTTGGTGGTTGGTTGTGGTATGGTCCATATGGCAGATGCGCAACAGAATTAT ATTCTCTAATGCTATTTTCAATGGCAACAAGCTGATTGAGGATGCAATGTTTTTAATCTGGACT TGGCTCAGATACTTAGAGAAGGATTTCTCCCTGCATTTTAATCACTGGTCAAGCCATATTAGAC AGGATTTTTTGTATCAGTAGAGGGTAGCTTTTATTGGCTTTTAGCCGCTGTAAATTAAACATGT AGCCATAATATGGTTCCTATTCATTGAGGAACCATATTTATGGAATTCTATTTTTGTACAAAGT ACCTCTGGTACTCCATTGCTATTATATATATATATACTTATCTTTGCCGATCAAAAAAAAATAT ATCCCAATTCTAGTGATAGTTCCCTCCCTTAATGAAAAGAGAAATATCAGTTTACTGTAAAGCA TATAGGCAAACTTCCTTAAGTCCAAGTAAACATATCAATCATAATTAGAGAAAATACTATTGCA CAAAACTATCAGGGTCGCAATAATTTCTGCATTGACATTGACATCTTGCCACTTAAATAAAAAT CTCAGCAAAAATTCTGCATCTTTTTGTGTGTGTGTGTGTGTCTGTGTGTGTGTGTGTGTGTGTG TGTGTGTGTCTGTGTGTGTGTCTGTGTGTCTGTGTGTCTGTCTGTGTCTGTGTGTGTCTGTGTG TGTGTCTGTGTGTGTGTCTGTGTGTCTGTGTGTGTGTCTGTGTGTCTGTCTGTGTCTGTGTGTG TGTCTGTGTGTGTGTCTGTGTGTGTGTGTGTGTGTGTGTGTCTGTGTCTGTGTGTGTGTCTGTG TGTGTCTGTGTGTGTGTCTGTGTGTGTGTGTGTCTGTGTGTGTGTCTGTGTGTCTGTCTGTGTC TGTGTGTGTCTGTGTGTGTGTCTGTGTGTGTGTCTGTGTGTGTGTGTGTGTCTGTGTGTGTGTG TGTCTGGGTGTGTGTGTGTGTCTGTGTGTGTGTCTGTGTGTGTGTGTGTCTGTGTGTGTGTGTG TGTCTGTGTGTGTCTGTGTGTGTGTGTCAGTGTGTGTGTCTGTGTGTGTGTGTGTGTGTGTGTG TGTTTTCATTTTTAACTTTGAGTATATTTGTCAGGTGGAGCAAACACAAAGGAATATCAATTTT AAAGTGATGCAAAAGCTACTTTACATGGATACCAAATCACTTACCTGTATCGGGATATATACAA AAGAGATCAAATCCAACTTCAATATCTCCAAGATAGAAGAACCAGCTTCTCTAAGAAGCTGTAA TAACAATCAGGCAAAAGAAAACTTGTCAGCAAGAAACAAAACAGTGAAAAGTAGGAATCATATC ACAAGCTCTGCCAAAATAAACAGTCACACTCCATACATGAATTTCACTAAACTCCAGTTGGAAA TCAAGGCGTGTACTCTCCCCAAGATCCTCAGTGGATCGTGATTTGGTGCTTTTCAATTGGATGC CCATGATGTTGTTTTCAATATAAAGACCATGCTCACGATGCACAAAACTCACATCCAGCTTTGG TAGATTGAAGCTGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.008702607

Conservation Information
Conserved circRNAs	NA
PMCS	0.008702607

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8718398-8715131(-)
						
						Potential amino acid sequence
						
							MGIQLKSTKSRSTEDLGESTRLDFQLEFSEIHLLREAGSSILEILKLDLISFVYIPIQPISPVR
AESEIKLGGTQCNIIMSRLKPWLVLHSSKKKKMVLRQEASVVARPQSTDGKTIMWTCNVSAPEM
TIVLFNMAGSPVYHVSFNLPKLDVSFVHREHGLYIENNIMGIQLKSTKSRSTEDLGESTRLDFQ
LEFSEIHLLREAGSSILEILKLDLISFVYIPIQPISPVRAESEIKLGGTQCNIIMSRLKPWLVL
HSSKKKKMVLRQEASVVARPQSTDGKTIMWTCNVSAPEMTIVLFNMAGSPVYHVSFNLPKLDVS
FVHREHGLYIENNIMGIQLKSTKSRSTEDLGESTRLDFQLEFSEIHLLREAGSSILEILKLDLI
SFVYIPIQPISPVRAESEIKLGGTQCNIIMSRLKPWLVLHSSKKKKMVLRQEASVVARPQSTDG
KTIMWTCNVSAPEMTIVLFNMAGSPVYHVSFNLPKLDVSFVHREHGLYIENNIMGIQLKSTKSR
STEDLGESTRLDFQLEFSEIHLLREAGSSILEILKLDLISFVYIPIQPISPVRAESEIKLGGTQ
CNIIMSRLKPWLVLHSSKKKKMVLRQEASVVARPQSTDGKTIMWTCNVSAPEMTIVLFNMAGSP
VYH(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8718398-8715131(-)
Potential amino acid sequence	MGIQLKSTKSRSTEDLGESTRLDFQLEFSEIHLLREAGSSILEILKLDLISFVYIPIQPISPVR AESEIKLGGTQCNIIMSRLKPWLVLHSSKKKKMVLRQEASVVARPQSTDGKTIMWTCNVSAPEM TIVLFNMAGSPVYHVSFNLPKLDVSFVHREHGLYIENNIMGIQLKSTKSRSTEDLGESTRLDFQ LEFSEIHLLREAGSSILEILKLDLISFVYIPIQPISPVRAESEIKLGGTQCNIIMSRLKPWLVL HSSKKKKMVLRQEASVVARPQSTDGKTIMWTCNVSAPEMTIVLFNMAGSPVYHVSFNLPKLDVS FVHREHGLYIENNIMGIQLKSTKSRSTEDLGESTRLDFQLEFSEIHLLREAGSSILEILKLDLI SFVYIPIQPISPVRAESEIKLGGTQCNIIMSRLKPWLVLHSSKKKKMVLRQEASVVARPQSTDG KTIMWTCNVSAPEMTIVLFNMAGSPVYHVSFNLPKLDVSFVHREHGLYIENNIMGIQLKSTKSR STEDLGESTRLDFQLEFSEIHLLREAGSSILEILKLDLISFVYIPIQPISPVRAESEIKLGGTQ CNIIMSRLKPWLVLHSSKKKKMVLRQEASVVARPQSTDGKTIMWTCNVSAPEMTIVLFNMAGSP VYH(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_04G096600_circ_g.3

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