Plant Circular RNA Database

Detail information of GLYMA_03G121500_circ_g.1

			
						 General Information
					
						CircRNA Name
						GLYMA_03G121500_circ_g.1
					
						ID in PlantcircBase
						gma_circ_000615
					
						Alias
						Gm03circRNA1783, gma-circRNA0321
					
						Organism
						
							Glycine max						
					
						Position
						
							chr3: 33388790-33391348  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, find_circ
					
						Parent gene
						
							GLYMA_03G121500						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_03G121300_circ_ag.1 GLYMA_03G121500_circ_g.2 GLYMA_03G121500_circ_g.3 						
					
						Support reads
						NA
					
						Tissues
						stem, 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
						KRH66676:4
KRH66675:3

General Information
CircRNA Name	GLYMA_03G121500_circ_g.1
ID in PlantcircBase	gma_circ_000615
Alias	Gm03circRNA1783, gma-circRNA0321
Organism	Glycine max
Position	chr3: 33388790-33391348 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, find_circ
Parent gene	GLYMA_03G121500
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_03G121300_circ_ag.1 GLYMA_03G121500_circ_g.2 GLYMA_03G121500_circ_g.3
Support reads	NA
Tissues	stem, 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	KRH66676:4 KRH66675:3

			
						 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  
						
							CATGTGCTTTTGCAAGTGTAGGACCAATTTCCTCCATTAGGTTAGTGGCAAGCAAAGCTTGAAT
AACCAAACTAGCATCCCATCCTTGGCTACCAAAACTttccaaccattcttgagttcctgatggt
tcccatgctgctaaaccaccttttctactctgcaataattaagagaaaaaagaaccacagttgc
atcaaaag

									
								

					

						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: 300
Transcript exons: 33388790-33388846,33390754-33390876,33391229-33391348
TTCCAACCATTCTTGAGTTCCTGATGGTTCCCATGCTGCTAAACCACCTTTTCTACTATTCAAA
GTTTCTGCCGTGCAATCAGAAACTTGCCATCCCTGATCTTGATCAGAGAATGTCCAAGACCCTT
TAGAAATATGACGATACATACTCTTAAAATCTCCTAAAGGGTCATCCTTCACCTGAGTCTTCTT
GATGAAATCATGTGCTTTTGCAAGTGTAGGACCAATTTCCTCCATTAGGTTAGTGGCAAGCAAA
GCTTGAATAACCAAACTAGCATCCCATCCTTGGCTACCAAAACT
						
					

						Genomic sequence
						
							TTCCAACCATTCTTGAGTTCCTGATGGTTCCCATGCTGCTAAACCACCTTTTCTACTCTGCAAT
AATTAAGAGAAAAAAGAACCACAGTTGCATCAAAAGTAAATATTCTAGTAGTAAAAGTAAATCA
AACATCAATTATTAATGTCGTCTGCGCTAACCCCAACTTCCCAATGATAAAAGATTAAACAAAG
AGAAGGACCATCAATTGATTGATTTATTAATTAATTAAAAGCATATGACCATGAATTTAGGAGA
AATACAATATGGTACCAAACAAATTTCACGAATCTTGAATAAATGATGTGGCATTGGATTTGAG
ACAGGGAGTCTATCATATCAACATATGTCAGCTATTAGCCATTAATTTATAGACAACTTACTAT
AACATATTTCATAATATTAAGTATTTATCTAAATTGTCAGAAATTGAGATCTTTCCTCAAATTA
TATTAAAAGTTGCTTGTGTAAGAAATAACTAGTTGTAGGCTAATGGTGTTAACATTTGCAAATT
TCTAAATGAGTAAATATTTTTTACCTCGGAGGGGTAATTTTTGGAAATATTATCAAAATGAGTA
AATATTTTTTTAAAAATTATTTAAATTGGGGTAAATCATGTTTATGAAACATGACTTCTAAATG
GAAGTTGTATACTATTATGTGACTTTTGGATTTACTAAGTAAACAAGATTTTCATTTTTTTTTA
CGAAGTTGTGTTTTACTTTTACAACTTTTATTTGTTTTTATTTTTTATTCTAAATATCTTTAAC
AGTTTTTTTACAGAGTTCATGCCGTAAAACCCAAGGTTGCTTTATTTTTTATTATTTTATTTCA
TTTACTGAAGTTGTCATATGAAACACCAATTTCTTTTATATTTTTTTAAAAAATAATAAAAACT
AAATTAAAGAAAATTACAAAAGCTACATTTATAATTTTTTATTTATTAATTGAAGTCGTGTATG
CATATATTAAGTCATGCTCACACCCATGACTTCTATTAATTTTTGTTTTTCATTTATTAAGTGA
ATTGGTGAATCTTTATGTTTGCAATGAATTCATTTTATTTTTTTATAGACCTAATGTATCTTTC
ACGGAAAATAATTTTGTTATCACTAAGGAAAAAACTCTCCCTCCTAGTATTTAATGTAGATGTA
TGCCAAAAACTCAAACTTAAAACCTTTGATTAAGTTAGGACAATCCCGTGCCAGTTCGTCTACG
CATTCGATGGTAAATGAATTTGTTAATAAAGAAAAAGAAAGAAAAGTGGTATAAATTTTATAAA
ACTAACTTCAAAAATTAAAAAAAAAATAAAATGAAAGAATACTTATTGTGTACAATAATGGCCA
CTCATGATCCTTTTAAAAAAAAGGTGTGCATTGATGACCACTCAAATTAATTTAACTTGTATAA
TAATAAAAGAATTATCTAAAACTTGAACTCAAAATCCGGATTAGGAGGATCAAATCTAGTAACA
CTCGAACCAATAATTTATTTAAATTTGAATAATTTTTTAAAATTATCCATTTTGATATATTTTT
CTAAATTACCCTTATAGGGTTAAAAGAAACCTAAAATGAGTAATGATTGTTCTATTTCTGTGTC
CAATCAAGGGCTTTAATTTTAATAGCTAGCTTTTGTATTTAAGCAACTTGCAATTACACTTTTA
GTGTATGCTATTCATATCGTAACAATTTTATGTTTCTATATTTTTTGTTTGATGTTGTTTTCTT
CCAAATCGTTTTGTGTTCAATTTTCTACCAAAATTTAATGTTACTTACTTGAAGTGACAATAGG
ATATTGACTGAATCATATAACCTTTGAGGTTCCATCTTTTCTCCTACAATCTCTGATGGCAATA
TGGATAGAAGTAGACAACACTAAAAAAAAAAAAGCTAAATTAACATATATTTGTAGTGATTGAT
AAAGCTTATAACAAATTAAGTTGTTTATGAGCTAAGTTAGTTACATTCAAAGTTTCTGCCGTGC
AATCAGAAACTTGCCATCCCTGATCTTGATCAGAGAATGTCCAAGACCCTTTAGAAATATGACG
ATACATACTCTTAAAATCTCCTAAAGGGTCATCCTTCACCTGTGAAATAAGAGTGTTAGTTCAT
TACTGCTATGTAAAGCTAGCAAATTACATATTAATCAATAATCTAATGAACACTAAATTCGTCG
TCCAATTTAAATATGCATTTTAATTCGAATAATATAGTTATGCTAGTTTTAATTAATATTATTA
GTTAGCTGGTAAATTAGTTAGTAAATTGATTACTTAATAGGTTAAATCACTCTATAAATAAGAC
CCAAGTATATTTTGAATATTTCCAATTAGTGAATTGTATAACTTAAATAAACTAGGTTCATTGG
GGAATTTACACTCCTTAACTAGAAGGAGAATTATGATTTTTTTATATGCTTGTAATAAAAATTA
AGCAAACCTGAGTCTTCTTGATGAAATCATGTGCTTTTGCAAGTGTAGGACCAATTTCCTCCAT
TAGGTTAGTGGCAAGCAAAGCTTGAATAACCAAACTAGCATCCCATCCTTGGCTACCAAAACT
						
					

			
		

Sequences
Splice junction sequence	CATGTGCTTTTGCAAGTGTAGGACCAATTTCCTCCATTAGGTTAGTGGCAAGCAAAGCTTGAAT AACCAAACTAGCATCCCATCCTTGGCTACCAAAACTttccaaccattcttgagttcctgatggt tcccatgctgctaaaccaccttttctactctgcaataattaagagaaaaaagaaccacagttgc atcaaaag
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: 300 Transcript exons: 33388790-33388846,33390754-33390876,33391229-33391348 TTCCAACCATTCTTGAGTTCCTGATGGTTCCCATGCTGCTAAACCACCTTTTCTACTATTCAAA GTTTCTGCCGTGCAATCAGAAACTTGCCATCCCTGATCTTGATCAGAGAATGTCCAAGACCCTT TAGAAATATGACGATACATACTCTTAAAATCTCCTAAAGGGTCATCCTTCACCTGAGTCTTCTT GATGAAATCATGTGCTTTTGCAAGTGTAGGACCAATTTCCTCCATTAGGTTAGTGGCAAGCAAA GCTTGAATAACCAAACTAGCATCCCATCCTTGGCTACCAAAACT
Genomic sequence	TTCCAACCATTCTTGAGTTCCTGATGGTTCCCATGCTGCTAAACCACCTTTTCTACTCTGCAAT AATTAAGAGAAAAAAGAACCACAGTTGCATCAAAAGTAAATATTCTAGTAGTAAAAGTAAATCA AACATCAATTATTAATGTCGTCTGCGCTAACCCCAACTTCCCAATGATAAAAGATTAAACAAAG AGAAGGACCATCAATTGATTGATTTATTAATTAATTAAAAGCATATGACCATGAATTTAGGAGA AATACAATATGGTACCAAACAAATTTCACGAATCTTGAATAAATGATGTGGCATTGGATTTGAG ACAGGGAGTCTATCATATCAACATATGTCAGCTATTAGCCATTAATTTATAGACAACTTACTAT AACATATTTCATAATATTAAGTATTTATCTAAATTGTCAGAAATTGAGATCTTTCCTCAAATTA TATTAAAAGTTGCTTGTGTAAGAAATAACTAGTTGTAGGCTAATGGTGTTAACATTTGCAAATT TCTAAATGAGTAAATATTTTTTACCTCGGAGGGGTAATTTTTGGAAATATTATCAAAATGAGTA AATATTTTTTTAAAAATTATTTAAATTGGGGTAAATCATGTTTATGAAACATGACTTCTAAATG GAAGTTGTATACTATTATGTGACTTTTGGATTTACTAAGTAAACAAGATTTTCATTTTTTTTTA CGAAGTTGTGTTTTACTTTTACAACTTTTATTTGTTTTTATTTTTTATTCTAAATATCTTTAAC AGTTTTTTTACAGAGTTCATGCCGTAAAACCCAAGGTTGCTTTATTTTTTATTATTTTATTTCA TTTACTGAAGTTGTCATATGAAACACCAATTTCTTTTATATTTTTTTAAAAAATAATAAAAACT AAATTAAAGAAAATTACAAAAGCTACATTTATAATTTTTTATTTATTAATTGAAGTCGTGTATG CATATATTAAGTCATGCTCACACCCATGACTTCTATTAATTTTTGTTTTTCATTTATTAAGTGA ATTGGTGAATCTTTATGTTTGCAATGAATTCATTTTATTTTTTTATAGACCTAATGTATCTTTC ACGGAAAATAATTTTGTTATCACTAAGGAAAAAACTCTCCCTCCTAGTATTTAATGTAGATGTA TGCCAAAAACTCAAACTTAAAACCTTTGATTAAGTTAGGACAATCCCGTGCCAGTTCGTCTACG CATTCGATGGTAAATGAATTTGTTAATAAAGAAAAAGAAAGAAAAGTGGTATAAATTTTATAAA ACTAACTTCAAAAATTAAAAAAAAAATAAAATGAAAGAATACTTATTGTGTACAATAATGGCCA CTCATGATCCTTTTAAAAAAAAGGTGTGCATTGATGACCACTCAAATTAATTTAACTTGTATAA TAATAAAAGAATTATCTAAAACTTGAACTCAAAATCCGGATTAGGAGGATCAAATCTAGTAACA CTCGAACCAATAATTTATTTAAATTTGAATAATTTTTTAAAATTATCCATTTTGATATATTTTT CTAAATTACCCTTATAGGGTTAAAAGAAACCTAAAATGAGTAATGATTGTTCTATTTCTGTGTC CAATCAAGGGCTTTAATTTTAATAGCTAGCTTTTGTATTTAAGCAACTTGCAATTACACTTTTA GTGTATGCTATTCATATCGTAACAATTTTATGTTTCTATATTTTTTGTTTGATGTTGTTTTCTT CCAAATCGTTTTGTGTTCAATTTTCTACCAAAATTTAATGTTACTTACTTGAAGTGACAATAGG ATATTGACTGAATCATATAACCTTTGAGGTTCCATCTTTTCTCCTACAATCTCTGATGGCAATA TGGATAGAAGTAGACAACACTAAAAAAAAAAAAGCTAAATTAACATATATTTGTAGTGATTGAT AAAGCTTATAACAAATTAAGTTGTTTATGAGCTAAGTTAGTTACATTCAAAGTTTCTGCCGTGC AATCAGAAACTTGCCATCCCTGATCTTGATCAGAGAATGTCCAAGACCCTTTAGAAATATGACG ATACATACTCTTAAAATCTCCTAAAGGGTCATCCTTCACCTGTGAAATAAGAGTGTTAGTTCAT TACTGCTATGTAAAGCTAGCAAATTACATATTAATCAATAATCTAATGAACACTAAATTCGTCG TCCAATTTAAATATGCATTTTAATTCGAATAATATAGTTATGCTAGTTTTAATTAATATTATTA GTTAGCTGGTAAATTAGTTAGTAAATTGATTACTTAATAGGTTAAATCACTCTATAAATAAGAC CCAAGTATATTTTGAATATTTCCAATTAGTGAATTGTATAACTTAAATAAACTAGGTTCATTGG GGAATTTACACTCCTTAACTAGAAGGAGAATTATGATTTTTTTATATGCTTGTAATAAAAATTA AGCAAACCTGAGTCTTCTTGATGAAATCATGTGCTTTTGCAAGTGTAGGACCAATTTCCTCCAT TAGGTTAGTGGCAAGCAAAGCTTGAATAACCAAACTAGCATCCCATCCTTGGCTACCAAAACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.161952911

Conservation Information
Conserved circRNAs	NA
PMCS	0.161952911

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							33391287-33388792(-)
						
						Potential amino acid sequence
						
							MEEIGPTLAKAHDFIKKTQVKDDPLGDFKSMYRHISKGSWTFSDQDQGWQVSDCTAETLNSRKG
GLAAWEPSGTQEWLESFGSQGWDASLVIQALLATNLMEEIGPTLAKAHDFIKKTQVKDDPLGDF
KSMYRHISKGSWTFSDQDQGWQVSDCTAETLNSRKGGLAAWEPSGTQEWLESFGSQGWDASLVI
QALLATNLMEEIGPTLAKAHDFIKKTQVKDDPLGDFKSMYRHISKGSWTFSDQDQGWQVSDCTA
ETLNSRKGGLAAWEPSGTQEWLESFGSQGWDASLVIQALLATNLMEEIGPTLAKAHDFIKKTQV
KDDPLGDFKSMYRHISKGSWTFSDQDQGWQVSDCTAETLNSRKGGLAAWEPSGTQEWLE(-)
						
						Sponge-miRNAs
						
							gma-miR1533 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	33391287-33388792(-)
Potential amino acid sequence	MEEIGPTLAKAHDFIKKTQVKDDPLGDFKSMYRHISKGSWTFSDQDQGWQVSDCTAETLNSRKG GLAAWEPSGTQEWLESFGSQGWDASLVIQALLATNLMEEIGPTLAKAHDFIKKTQVKDDPLGDF KSMYRHISKGSWTFSDQDQGWQVSDCTAETLNSRKGGLAAWEPSGTQEWLESFGSQGWDASLVI QALLATNLMEEIGPTLAKAHDFIKKTQVKDDPLGDFKSMYRHISKGSWTFSDQDQGWQVSDCTA ETLNSRKGGLAAWEPSGTQEWLESFGSQGWDASLVIQALLATNLMEEIGPTLAKAHDFIKKTQV KDDPLGDFKSMYRHISKGSWTFSDQDQGWQVSDCTAETLNSRKGGLAAWEPSGTQEWLE(-)
Sponge-miRNAs	gma-miR1533
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a; Chen et al., 2018

circRNA

Detail information of GLYMA_03G121500_circ_g.1

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