Plant Circular RNA Database

Detail information of GLYMA_20G004000_circ_g.3

			
						 General Information
					
						CircRNA Name
						GLYMA_20G004000_circ_g.3
					
						ID in PlantcircBase
						gma_circ_005104
					
						Alias
						Gm20circRNA1421, gma-circRNA2765
					
						Organism
						
							Glycine max						
					
						Position
						
							chr20: 384307-387477  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						Tophat, CIRI, find_circ
					
						Parent gene
						
							GLYMA_20G004000						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							GLYMA_20G004000_circ_g.1 GLYMA_20G004000_circ_g.2 GLYMA_20G004000_circ_g.4 GLYMA_20G004000_circ_g.5 GLYMA_20G004000_circ_g.6 GLYMA_20G004000_circ_g.7 GLYMA_20G004000_circ_g.8 						
					
						Support reads
						NA
					
						Tissues
						leaf, root, 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  
						
							GT-AG							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
						KRG89142:4
KRG89144:3
KRG89143:3

General Information
CircRNA Name	GLYMA_20G004000_circ_g.3
ID in PlantcircBase	gma_circ_005104
Alias	Gm20circRNA1421, gma-circRNA2765
Organism	Glycine max
Position	chr20: 384307-387477 JBrowse»
Reference genome	v2.0.38
Type	ue-circRNA
Identification method	Tophat, CIRI, find_circ
Parent gene	GLYMA_20G004000
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	GLYMA_20G004000_circ_g.1 GLYMA_20G004000_circ_g.2 GLYMA_20G004000_circ_g.4 GLYMA_20G004000_circ_g.5 GLYMA_20G004000_circ_g.6 GLYMA_20G004000_circ_g.7 GLYMA_20G004000_circ_g.8
Support reads	NA
Tissues	leaf, root, 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	GT-AG 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	KRG89142:4 KRG89144:3 KRG89143:3

			
						 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  
						
							GGTAATCACAGGCTCTTGAATTGAATAATAAAGTATATCTGGGACGTCCTGTTGGAGTTTTTAT
TGCTAAAGGAAAGGGTGAATATACCTCCAATAGAAGcttccatgttaattctagcaacttgagt
cactcatttcaaaggagtgaaagaactcagcctgtgaaagcttcagagatttcaggggactggg
aacaagaa

									
								

					

						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: 405
Transcript exons: 384307-384412,385523-385614,385688-385805,387389-387477
CTTCCATGTTAATTCTAGCAACTTGAGTCACTCATTTCAAAGGAGTGAAAGAACTCAGCCTGTG
AAAGCTTCAGAGATTTCAGGGGACTGGGAACAAGAAACTGAGTCAAAAATAATTGCTAACTGCA
AAGACCTAAGTGCTACTTCAAAGACAATATATGCTTCAAACTTGGCATACAGTATGGAGAAGGA
TGATATGGAGTTTCTTTTCAAAAATTGTGGAGAAATTGTTGATATCCGCCTACATACAGATCAT
AACGGGCGGTTTAAAGGCCATGGACATGTTGAGTTTGCAACCACAGAAGCTGCACAAAAAGCTC
TTGAATTGAATAATAAAGTATATCTGGGACGTCCTGTTGGAGTTTTTATTGCTAAAGGAAAGGG
TGAATATACCTCCAATAGAAG
						
					

						Genomic sequence
						
							CTTCCATGTTAATTCTAGCAACTTGAGTCACTCATTTCAAAGGAGTGAAAGAACTCAGCCTGTG
AAAGCTTCAGAGATTTCAGGGGACTGGGAACAAGAAACTGAGGTAAAAGCCTCCAGAACTTGTC
CAAAAAGTGTAAACATTTCATAATGCATATACCTAGGGCTGCTGAAACTTCATTTGTTCCATGA
CTTGTTTGAATGCCTCGTAACATCAATATTTTTTTTTTTTGAACGGCCAAAAGTATTCATATAT
TAGATATGGATAGTACCAGAGGTACTACAAAGATACATATAGGATGCCATTTGCTGAGGAATAT
TATATCTTAAAATGTTGTAGAGTATCTTAGAAATTATATCTTGGGATTAGTTAATGTAATTCCA
TAGCTTCATGATTTCTAATATTTTATGATTAGTTTTCTTATTTAGTTTGGATTATTAGTATGAA
TAGGGGTGAGTGTTTTAGGTTTTATCATCACATTATCTTATTATAAATTATAATACAACACAAT
ACGCAAGTAAATATTATTCATTAATCTCTTTTCTTTGTATTCTCTCCATACATTCCTAAAATAT
CATAATTTCTACTTGACTTTGAAGTATATACTCCCTTCAGTCGTTACCCAATTAACTAATTCAC
AAGGATTGAGAAAATTAGGTATTTTAGGTAGTAACATTAAATTTTTCCTAAATTTACATGTTCT
TTAAAAGTTACCCTTAACATTAATGAGACATACTTGTTTTCTTTTTTTTCAAATATTTTTATTG
ACTTCAATTCTATCAATCTCTCTAATAAGTAATATATTTATTGCTTTAATTTTTACTGGCAATG
TATGTGAAGAGGTGAAGTAAAATTTCAAAAATTCTCTCTATAGTCTATACAAGGTTAGACACCA
AAGAGCCTAAGACATTATTGCACCCCACCTACTATTTATTGAACTCAGAGAAATGACTAATAAT
TAAGGGTATTTTTGTAAAAAAATAATTAATGTAGCAGACATTGTAGATTAATTCTTATAAAAAA
GGGCCAAACCAAACCTCTAATTTGGTTCTTATAAAATGAGAGTAATTGACTTGAGTGAAAGAGG
TTAAGGATATGGAGATGATTGGTGCAGCCTCCATCAGAAAGAAAGCTATAACTGAACAGTATCC
CCTCTCCCTGCAATGTAAACTATCAAATCTGTCATATAATATATTGTTTCCTGGAATTTTGCAG
TCAAAAATAATTGCTAACTGCAAAGACCTAAGTGCTACTTCAAAGACAATATATGCTTCAAACT
TGGCATACAGTATGGAGAAGGATGATATGTATGTATTATTTTTCATGCTGGTGGTTTTTGATTA
TTTTGTGTACTGTTTTTTTAATTTCGATATTGTCCAGGGAGTTTCTTTTCAAAAATTGTGGAGA
AATTGTTGATATCCGCCTACATACAGATCATAACGGGCGGTTTAAAGGCCATGGACATGTTGAG
TTTGCAACCACAGAAGCTGCACAAAAAGTAAGCTATATCATCTTGTGTAGCCTGTGCAAATCAT
TTTGGAACTGCCAAAATCATTTCAAAGATAGTTGTATCTTTGGAAGCAACAATTGCATATATTT
ATTTCATTGGTAAAGTTTTAACAAATTGGTTTATTGAAATATTTGGCATTCATCATATTTTCAA
TGAAATTTATTAAATTTAATAGCTGAAGCAAATTGCTACCCTGTAATTATTTGTGGTTGAGACT
TTATTTCTGTTGATATTGCGAAATGCCTAAACCTGCATTTTTTACAGGCATGGCATAGTTCACG
TTTGTTTATAGCCTTGTCTTTGGAATCCAATGTTGGATTGGCATCGTGAATGTGCATATATAAA
TATCTGGTTGATGTGTGAATATGATGCTGTTGTGGATGGGATGTGCATGGCCGTGAGGAAAAGA
AGAAATTCCTCCTAATCTTTTTTTTTTAAAATTTGTTCAACCTTTGATTGTAAAGATCCTATTT
GTATCATTGGTATGATCTTTTACAATATCTTTGGTGGAGATGACTTGCAAACATTTTGTTTGTT
TGTATTATTATATAATGCATTTTGATGATATGGAATTAATAAGTATTGGCCAATAGTTCATGTA
ATTTTTTTTTTCAATTCATGTAATGGTATATTGTTTTAATTGGTTGATAGGTTACAACTAGTTT
TTGTCATGTAGGGTCTCAAGAAATAAACACACTGAATTCTGAATAAATAATTGAAATAATCTGA
TTTGATTACAAAGATGAAAAACACAGGGTTTCCCCCTAGCAAGGATTTTCCTCCTACAAAACAC
TAGAAACAACAATTTTACACCTTAATTTCCTTCAACAATTTGACACCTTGATAAAAAATAATTT
ATACCAATCAGCTTATTAAATATGTTTTTATTTTTCTTGAAAGTATTTAGATTAATTTTTTTTT
TTTTTGAAAAACACGGGTTTAAATTGGTTCTTTACACCGGTTTTGAACCAGTGTTCATCGGTTC
TGAGAACACCCTATGTTTTAGAGTTAACGGAATGATCACCAGGCCGTTCCCGGTTGAACTGGCT
GGTCCAGTTTTCAAAACTATGTGAATTAATTTAAAAGAACTGCATAATAACTGCCTAATTCAGA
ACATGGCCTATCAATGCCTCTTGACACAAAAGTATCCTCATCCTCAATTTCGTTTTTATATTTC
CATTTCCTATTTTCATTTTCTTGTTCACATAATCATCTTGCCTTTTCGAGCCTTCTACTCTCGA
GTACATCCTCGTGAAGAAATAAACACTGAATTTTTAACAAATAGAAATAGTCAGGTTTTTTGGC
CATATTTGGGTACAAACATGAAGAAGAAACACAGGGTTTCCCTAACAAGGGGTTTCATCCTTCA
AAACACTAGAAATAACAATCTGATACCTTAATTTTGTCACAATCTATGTAACACTATAATTGTG
TGTGTGTGTGTATATATATATGTATATATAATGTATTGCCTTTTCTATGCCTCATCATGATCTG
TGGGCTATGCTTGTTGAGCCCTTTTTCTATGTGAAGACATTTACCTGAAAATCAATTTTCTTTG
GTAATCACAGGCTCTTGAATTGAATAATAAAGTATATCTGGGACGTCCTGTTGGAGTTTTTATT
GCTAAAGGAAAGGGTGAATATACCTCCAATAGAAG
						
					

			
		

Sequences
Splice junction sequence	GGTAATCACAGGCTCTTGAATTGAATAATAAAGTATATCTGGGACGTCCTGTTGGAGTTTTTAT TGCTAAAGGAAAGGGTGAATATACCTCCAATAGAAGcttccatgttaattctagcaacttgagt cactcatttcaaaggagtgaaagaactcagcctgtgaaagcttcagagatttcaggggactggg aacaagaa
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: 405 Transcript exons: 384307-384412,385523-385614,385688-385805,387389-387477 CTTCCATGTTAATTCTAGCAACTTGAGTCACTCATTTCAAAGGAGTGAAAGAACTCAGCCTGTG AAAGCTTCAGAGATTTCAGGGGACTGGGAACAAGAAACTGAGTCAAAAATAATTGCTAACTGCA AAGACCTAAGTGCTACTTCAAAGACAATATATGCTTCAAACTTGGCATACAGTATGGAGAAGGA TGATATGGAGTTTCTTTTCAAAAATTGTGGAGAAATTGTTGATATCCGCCTACATACAGATCAT AACGGGCGGTTTAAAGGCCATGGACATGTTGAGTTTGCAACCACAGAAGCTGCACAAAAAGCTC TTGAATTGAATAATAAAGTATATCTGGGACGTCCTGTTGGAGTTTTTATTGCTAAAGGAAAGGG TGAATATACCTCCAATAGAAG
Genomic sequence	CTTCCATGTTAATTCTAGCAACTTGAGTCACTCATTTCAAAGGAGTGAAAGAACTCAGCCTGTG AAAGCTTCAGAGATTTCAGGGGACTGGGAACAAGAAACTGAGGTAAAAGCCTCCAGAACTTGTC CAAAAAGTGTAAACATTTCATAATGCATATACCTAGGGCTGCTGAAACTTCATTTGTTCCATGA CTTGTTTGAATGCCTCGTAACATCAATATTTTTTTTTTTTGAACGGCCAAAAGTATTCATATAT TAGATATGGATAGTACCAGAGGTACTACAAAGATACATATAGGATGCCATTTGCTGAGGAATAT TATATCTTAAAATGTTGTAGAGTATCTTAGAAATTATATCTTGGGATTAGTTAATGTAATTCCA TAGCTTCATGATTTCTAATATTTTATGATTAGTTTTCTTATTTAGTTTGGATTATTAGTATGAA TAGGGGTGAGTGTTTTAGGTTTTATCATCACATTATCTTATTATAAATTATAATACAACACAAT ACGCAAGTAAATATTATTCATTAATCTCTTTTCTTTGTATTCTCTCCATACATTCCTAAAATAT CATAATTTCTACTTGACTTTGAAGTATATACTCCCTTCAGTCGTTACCCAATTAACTAATTCAC AAGGATTGAGAAAATTAGGTATTTTAGGTAGTAACATTAAATTTTTCCTAAATTTACATGTTCT TTAAAAGTTACCCTTAACATTAATGAGACATACTTGTTTTCTTTTTTTTCAAATATTTTTATTG ACTTCAATTCTATCAATCTCTCTAATAAGTAATATATTTATTGCTTTAATTTTTACTGGCAATG TATGTGAAGAGGTGAAGTAAAATTTCAAAAATTCTCTCTATAGTCTATACAAGGTTAGACACCA AAGAGCCTAAGACATTATTGCACCCCACCTACTATTTATTGAACTCAGAGAAATGACTAATAAT TAAGGGTATTTTTGTAAAAAAATAATTAATGTAGCAGACATTGTAGATTAATTCTTATAAAAAA GGGCCAAACCAAACCTCTAATTTGGTTCTTATAAAATGAGAGTAATTGACTTGAGTGAAAGAGG TTAAGGATATGGAGATGATTGGTGCAGCCTCCATCAGAAAGAAAGCTATAACTGAACAGTATCC CCTCTCCCTGCAATGTAAACTATCAAATCTGTCATATAATATATTGTTTCCTGGAATTTTGCAG TCAAAAATAATTGCTAACTGCAAAGACCTAAGTGCTACTTCAAAGACAATATATGCTTCAAACT TGGCATACAGTATGGAGAAGGATGATATGTATGTATTATTTTTCATGCTGGTGGTTTTTGATTA TTTTGTGTACTGTTTTTTTAATTTCGATATTGTCCAGGGAGTTTCTTTTCAAAAATTGTGGAGA AATTGTTGATATCCGCCTACATACAGATCATAACGGGCGGTTTAAAGGCCATGGACATGTTGAG TTTGCAACCACAGAAGCTGCACAAAAAGTAAGCTATATCATCTTGTGTAGCCTGTGCAAATCAT TTTGGAACTGCCAAAATCATTTCAAAGATAGTTGTATCTTTGGAAGCAACAATTGCATATATTT ATTTCATTGGTAAAGTTTTAACAAATTGGTTTATTGAAATATTTGGCATTCATCATATTTTCAA TGAAATTTATTAAATTTAATAGCTGAAGCAAATTGCTACCCTGTAATTATTTGTGGTTGAGACT TTATTTCTGTTGATATTGCGAAATGCCTAAACCTGCATTTTTTACAGGCATGGCATAGTTCACG TTTGTTTATAGCCTTGTCTTTGGAATCCAATGTTGGATTGGCATCGTGAATGTGCATATATAAA TATCTGGTTGATGTGTGAATATGATGCTGTTGTGGATGGGATGTGCATGGCCGTGAGGAAAAGA AGAAATTCCTCCTAATCTTTTTTTTTTAAAATTTGTTCAACCTTTGATTGTAAAGATCCTATTT GTATCATTGGTATGATCTTTTACAATATCTTTGGTGGAGATGACTTGCAAACATTTTGTTTGTT TGTATTATTATATAATGCATTTTGATGATATGGAATTAATAAGTATTGGCCAATAGTTCATGTA ATTTTTTTTTTCAATTCATGTAATGGTATATTGTTTTAATTGGTTGATAGGTTACAACTAGTTT TTGTCATGTAGGGTCTCAAGAAATAAACACACTGAATTCTGAATAAATAATTGAAATAATCTGA TTTGATTACAAAGATGAAAAACACAGGGTTTCCCCCTAGCAAGGATTTTCCTCCTACAAAACAC TAGAAACAACAATTTTACACCTTAATTTCCTTCAACAATTTGACACCTTGATAAAAAATAATTT ATACCAATCAGCTTATTAAATATGTTTTTATTTTTCTTGAAAGTATTTAGATTAATTTTTTTTT TTTTTGAAAAACACGGGTTTAAATTGGTTCTTTACACCGGTTTTGAACCAGTGTTCATCGGTTC TGAGAACACCCTATGTTTTAGAGTTAACGGAATGATCACCAGGCCGTTCCCGGTTGAACTGGCT GGTCCAGTTTTCAAAACTATGTGAATTAATTTAAAAGAACTGCATAATAACTGCCTAATTCAGA ACATGGCCTATCAATGCCTCTTGACACAAAAGTATCCTCATCCTCAATTTCGTTTTTATATTTC CATTTCCTATTTTCATTTTCTTGTTCACATAATCATCTTGCCTTTTCGAGCCTTCTACTCTCGA GTACATCCTCGTGAAGAAATAAACACTGAATTTTTAACAAATAGAAATAGTCAGGTTTTTTGGC CATATTTGGGTACAAACATGAAGAAGAAACACAGGGTTTCCCTAACAAGGGGTTTCATCCTTCA AAACACTAGAAATAACAATCTGATACCTTAATTTTGTCACAATCTATGTAACACTATAATTGTG TGTGTGTGTGTATATATATATGTATATATAATGTATTGCCTTTTCTATGCCTCATCATGATCTG TGGGCTATGCTTGTTGAGCCCTTTTTCTATGTGAAGACATTTACCTGAAAATCAATTTTCTTTG GTAATCACAGGCTCTTGAATTGAATAATAAAGTATATCTGGGACGTCCTGTTGGAGTTTTTATT GCTAAAGGAAAGGGTGAATATACCTCCAATAGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.454326924

Conservation Information
Conserved circRNAs	NA
PMCS	0.454326924

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							385599-387474(+)
384315-385733(-)
						
						Potential amino acid sequence
						
							MEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELNNKVYLGRPVGVFIA
KGKGEYTSNRSFHVNSSNLSHSFQRSERTQPVKASEISGDWEQETESKIIANCKDLSATSKTIY
ASNLAYSMEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELNNKVYLGR
PVGVFIAKGKGEYTSNRSFHVNSSNLSHSFQRSERTQPVKASEISGDWEQETESKIIANCKDLS
ATSKTIYASNLAYSMEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELN
NKVYLGRPVGVFIAKGKGEYTSNRSFHVNSSNLSHSFQRSERTQPVKASEISGDWEQETESKII
ANCKDLSATSKTIYASNLAYSMEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAA
QKALELNNKVYLGRPVGVFIAKGKGEYTSNR(+)
MEASIGGIFTLSFSNKNSNRTSQIYFIIQFKSFLCSFCGCKLNMSMAFKPPVMICM*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	385599-387474(+) 384315-385733(-)
Potential amino acid sequence	MEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELNNKVYLGRPVGVFIA KGKGEYTSNRSFHVNSSNLSHSFQRSERTQPVKASEISGDWEQETESKIIANCKDLSATSKTIY ASNLAYSMEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELNNKVYLGR PVGVFIAKGKGEYTSNRSFHVNSSNLSHSFQRSERTQPVKASEISGDWEQETESKIIANCKDLS ATSKTIYASNLAYSMEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELN NKVYLGRPVGVFIAKGKGEYTSNRSFHVNSSNLSHSFQRSERTQPVKASEISGDWEQETESKII ANCKDLSATSKTIYASNLAYSMEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAA QKALELNNKVYLGRPVGVFIAKGKGEYTSNR(+) MEASIGGIFTLSFSNKNSNRTSQIYFIIQFKSFLCSFCGCKLNMSMAFKPPVMICM*(-)
Sponge-miRNAs	NA
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_20G004000_circ_g.3

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