Plant Circular RNA Database

Detail information of GLYMA_19G249900_circ_g.3

			
						 General Information
					
						CircRNA Name
						GLYMA_19G249900_circ_g.3
					
						ID in PlantcircBase
						gma_circ_005077
					
						Alias
						Gm19circRNA1518
					
						Organism
						
							Glycine max						
					
						Position
						
							chr19: 49576200-49577860  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI
					
						Parent gene
						
							GLYMA_19G249900						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_19G249900_circ_g.4 GLYMA_19G249900_circ_g.5 GLYMA_19G249900_circ_g.6 						
					
						Support reads
						NA
					
						Tissues
						leaf, 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
						KRG97071:4

General Information
CircRNA Name	GLYMA_19G249900_circ_g.3
ID in PlantcircBase	gma_circ_005077
Alias	Gm19circRNA1518
Organism	Glycine max
Position	chr19: 49576200-49577860 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI
Parent gene	GLYMA_19G249900
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_19G249900_circ_g.4 GLYMA_19G249900_circ_g.5 GLYMA_19G249900_circ_g.6
Support reads	NA
Tissues	leaf, 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	KRG97071:4

			
						 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  
						
							CTAAAGCTATTCCTTGCCTACCCAGCCAACCAGCATCAACATTGACATCTCCAACACCCATGTC
CCGAATATACAACGAAAATAAAGTGGAAAGGGACTCttgttttgattgcattaatggagataag
cacgcagagactgccctttgaactgcttcagaaggagtatttaaaacatccaacaatttgtcca
caacagca

									
								

					

						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: 498
Transcript exons: 49576200-49576316,49576408-49576488,49576629-49576751,49
577684-49577860
TTGTTTTGATTGCATTAATGGAGATAAGCACGCAGAGACTGCCCTTTGAACTGCTTCAGAAGGA
GTATTTAAAACATCCAACAATTTGTCCACAACAGCATGAACCTTAGGATCATCCTTTGCCAAGT
GTTTTGCCAGAGCTCCAGTGAAGATAACCACACCCTCACGAACCAAGTCATATTTTTCTTCATC
TGGAGCAGTTTTGTTTAAGTAGTTCTCAAAGATAGGGAATAACAATGAGACATTATCTTTTCCA
TTTTTATCAATGATCAATATACCAGCATTAATCATTCTGCCTCTAACATCAGCATTCGGATCAG
CCAGTGCTCTTGATATTAGAAATGTCATGACAACAGGTAAGTCTTTCGTCCCCAAAATATCAGC
AGCAGAATGTAATGCTAAAGCTATTCCTTGCCTACCCAGCCAACCAGCATCAACATTGACATCT
CCAACACCCATGTCCCGAATATACAACGAAAATAAAGTGGAAAGGGACTC
						
					

						Genomic sequence
						
							TTGTTTTGATTGCATTAATGGAGATAAGCACGCAGAGACTGCCCTTTGAACTGCTTCAGAAGGA
GTATTTAAAACATCCAACAATTTGTCCACAACAGCATGAACCTTAGGATCATCCTGCTCCAAAA
GGAATATAAATAATAGCAAAAGTTTTAAAATTCAACTAGCTACCAAAATTAGGAAACGAGGAAC
AAACTTTAATACTAACCTTTGCCAAGTGTTTTGCCAGAGCTCCAGTGAAGATAACCACACCCTC
ACGAACCAAGTCATATTTTTCTTCATCTGGAGCCTAAGACATTGAGGGAAAATCTATTAATAAA
GCATCACATACAACTCTTAAAAAAGTTTGAAGGGCCAAACTACAAAGAAAGAAAAGAACAATAG
GACGAGTATCCAGCAGATCAATCTCCCAAATGATAAGGAACTCACAGTTTTGTTTAAGTAGTTC
TCAAAGATAGGGAATAACAATGAGACATTATCTTTTCCATTTTTATCAATGATCAATATACCAG
CATTAATCATTCTGCCTCTAACATCAGCATTCGGATCAGCCTGCAAATGAAATCAATCCCCAAA
GTCAAACGTTTGGTAGAAAAGTTACCCTATAGATGAAGGTAACAGTTCACAGACAGCATCGATA
CAAAGCACACTACAACCAAAAGAGTTGATCAGATTACCTAAACATTCTCGTTTACTTTCAACTT
TAAGCGGATTCTTTTATTTCGTAACATTAACATCTATTATTGAGAGTATCAAGCATTAAAAAGT
TTTTAATTTATCTCATTTCATTTGAAGACAAGGGACATTTTATTGCACCTTCCTGAACCTGTGT
TGAATATGGGCTAAGGATTATCATATTTAGGTGTTTATAGTGGTTTGTTTCAACATCCAAGTTT
CCCTTTTGTTTAGTAGTCTGTCAACCTTTATAACAGTAGAATTCAATCCCTAATTACTCAAGGA
TATGTATTTTTTTGTGGTGGAGAGAGCACATTGCTCACTCCTAGAATGGGTTGCATGATTTACA
ATACAATTTGGTATGAACCATGAGGTATGGGTTACTTATGTGGCACAACATTTTGCTAGGAACA
TGGATGAATCCCTAATACCCTGATATGCAATCAATGAACCTTAAATAACACTGTTGTCCATCAT
ATATTCACCCCAAGAAAATTCTTATTCTACGTTGATGAATGAACCTTGTAAGGCAAAAATTGAA
AATTCACCGCAAAATTATTGCTATATTCGTCTGAAATAAGCTCAATTGTGCACAATTCGCACTG
AACAGAAAAAAAATGGATGGAGACAACAATAAGTAATATCAAATATTAACTGGATAACAAATTA
TGATTATCTCAACAGTGAAAAATATTTTCATTTTTGAGTCATATATTAGTTCTTACAAAAGATG
TTGATTCCAAATGATAATAGGTTTCAGTTCCAGGATTATAATGAAAATCAAAAAATAAATGTCA
GTAAAAATTTACCAGTGCTCTTGATATTAGAAATGTCATGACAACAGGTAAGTCTTTCGTCCCC
AAAATATCAGCAGCAGAATGTAATGCTAAAGCTATTCCTTGCCTACCCAGCCAACCAGCATCAA
CATTGACATCTCCAACACCCATGTCCCGAATATACAACGAAAATAAAGTGGAAAGGGACTC
						
					

			
		

Sequences
Splice junction sequence	CTAAAGCTATTCCTTGCCTACCCAGCCAACCAGCATCAACATTGACATCTCCAACACCCATGTC CCGAATATACAACGAAAATAAAGTGGAAAGGGACTCttgttttgattgcattaatggagataag cacgcagagactgccctttgaactgcttcagaaggagtatttaaaacatccaacaatttgtcca caacagca
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: 498 Transcript exons: 49576200-49576316,49576408-49576488,49576629-49576751,49 577684-49577860 TTGTTTTGATTGCATTAATGGAGATAAGCACGCAGAGACTGCCCTTTGAACTGCTTCAGAAGGA GTATTTAAAACATCCAACAATTTGTCCACAACAGCATGAACCTTAGGATCATCCTTTGCCAAGT GTTTTGCCAGAGCTCCAGTGAAGATAACCACACCCTCACGAACCAAGTCATATTTTTCTTCATC TGGAGCAGTTTTGTTTAAGTAGTTCTCAAAGATAGGGAATAACAATGAGACATTATCTTTTCCA TTTTTATCAATGATCAATATACCAGCATTAATCATTCTGCCTCTAACATCAGCATTCGGATCAG CCAGTGCTCTTGATATTAGAAATGTCATGACAACAGGTAAGTCTTTCGTCCCCAAAATATCAGC AGCAGAATGTAATGCTAAAGCTATTCCTTGCCTACCCAGCCAACCAGCATCAACATTGACATCT CCAACACCCATGTCCCGAATATACAACGAAAATAAAGTGGAAAGGGACTC
Genomic sequence	TTGTTTTGATTGCATTAATGGAGATAAGCACGCAGAGACTGCCCTTTGAACTGCTTCAGAAGGA GTATTTAAAACATCCAACAATTTGTCCACAACAGCATGAACCTTAGGATCATCCTGCTCCAAAA GGAATATAAATAATAGCAAAAGTTTTAAAATTCAACTAGCTACCAAAATTAGGAAACGAGGAAC AAACTTTAATACTAACCTTTGCCAAGTGTTTTGCCAGAGCTCCAGTGAAGATAACCACACCCTC ACGAACCAAGTCATATTTTTCTTCATCTGGAGCCTAAGACATTGAGGGAAAATCTATTAATAAA GCATCACATACAACTCTTAAAAAAGTTTGAAGGGCCAAACTACAAAGAAAGAAAAGAACAATAG GACGAGTATCCAGCAGATCAATCTCCCAAATGATAAGGAACTCACAGTTTTGTTTAAGTAGTTC TCAAAGATAGGGAATAACAATGAGACATTATCTTTTCCATTTTTATCAATGATCAATATACCAG CATTAATCATTCTGCCTCTAACATCAGCATTCGGATCAGCCTGCAAATGAAATCAATCCCCAAA GTCAAACGTTTGGTAGAAAAGTTACCCTATAGATGAAGGTAACAGTTCACAGACAGCATCGATA CAAAGCACACTACAACCAAAAGAGTTGATCAGATTACCTAAACATTCTCGTTTACTTTCAACTT TAAGCGGATTCTTTTATTTCGTAACATTAACATCTATTATTGAGAGTATCAAGCATTAAAAAGT TTTTAATTTATCTCATTTCATTTGAAGACAAGGGACATTTTATTGCACCTTCCTGAACCTGTGT TGAATATGGGCTAAGGATTATCATATTTAGGTGTTTATAGTGGTTTGTTTCAACATCCAAGTTT CCCTTTTGTTTAGTAGTCTGTCAACCTTTATAACAGTAGAATTCAATCCCTAATTACTCAAGGA TATGTATTTTTTTGTGGTGGAGAGAGCACATTGCTCACTCCTAGAATGGGTTGCATGATTTACA ATACAATTTGGTATGAACCATGAGGTATGGGTTACTTATGTGGCACAACATTTTGCTAGGAACA TGGATGAATCCCTAATACCCTGATATGCAATCAATGAACCTTAAATAACACTGTTGTCCATCAT ATATTCACCCCAAGAAAATTCTTATTCTACGTTGATGAATGAACCTTGTAAGGCAAAAATTGAA AATTCACCGCAAAATTATTGCTATATTCGTCTGAAATAAGCTCAATTGTGCACAATTCGCACTG AACAGAAAAAAAATGGATGGAGACAACAATAAGTAATATCAAATATTAACTGGATAACAAATTA TGATTATCTCAACAGTGAAAAATATTTTCATTTTTGAGTCATATATTAGTTCTTACAAAAGATG TTGATTCCAAATGATAATAGGTTTCAGTTCCAGGATTATAATGAAAATCAAAAAATAAATGTCA GTAAAAATTTACCAGTGCTCTTGATATTAGAAATGTCATGACAACAGGTAAGTCTTTCGTCCCC AAAATATCAGCAGCAGAATGTAATGCTAAAGCTATTCCTTGCCTACCCAGCCAACCAGCATCAA CATTGACATCTCCAACACCCATGTCCCGAATATACAACGAAAATAAAGTGGAAAGGGACTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.205292515

Conservation Information
Conserved circRNAs	NA
PMCS	0.205292515

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							49576697-49576245(+)
49577823-49576202(-)
						
						Potential amino acid sequence
						
							MINIPALIILPLTSAFGSASALDIRNVMTTGKSFVPKISAAECNAKAIPCLPSQPASTLTSPTP
MSRIYNENKVERDSCFDCINGDKHAETAL*(+)
MGVGDVNVDAGWLGRQGIALALHSAADILGTKDLPVVMTFLISRALADPNADVRGRMINAGILI
IDKNGKDNVSLLFPIFENYLNKTAPDEEKYDLVREGVVIFTGALAKHLAKDDPKVHAVVDKLLD
VLNTPSEAVQRAVSACLSPLMQSKQESLSTLFSLYIRDMGVGDVNVDAGWLGRQGIALALHSAA
DILGTKDLPVVMTFLISRALADPNADVRGRMINAGILIIDKNGKDNVSLLFPIFENYLNKTAPD
EEKYDLVREGVVIFTGALAKHLAKDDPKVHAVVDKLLDVLNTPSEAVQRAVSACLSPLMQSKQE
SLSTLFSLYIRDMGVGDVNVDAGWLGRQGIALALHSAADILGTKDLPVVMTFLISRALADPNAD
VRGRMINAGILIIDKNGKDNVSLLFPIFENYLNKTAPDEEKYDLVREGVVIFTGALAKHLAKDD
PKVHAVVDKLLDVLNTPSEAVQRAVSACLSPLMQSKQESLSTLFSLYIRDMGVGDVNVDAGWLG
RQGIALALHSAADILGTKDLPVVMTFLISRALADPNADVRGRMINAGILIIDKNGKDNVSLLFP
IFENYLNKTAPDEEKYDLVREGVVIFTGALAKHLAKDDPKVHAVVDKLLDVLNTPSEAVQRAVS
ACLSPLMQSKQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	49576697-49576245(+) 49577823-49576202(-)
Potential amino acid sequence	MINIPALIILPLTSAFGSASALDIRNVMTTGKSFVPKISAAECNAKAIPCLPSQPASTLTSPTP MSRIYNENKVERDSCFDCINGDKHAETAL*(+) MGVGDVNVDAGWLGRQGIALALHSAADILGTKDLPVVMTFLISRALADPNADVRGRMINAGILI IDKNGKDNVSLLFPIFENYLNKTAPDEEKYDLVREGVVIFTGALAKHLAKDDPKVHAVVDKLLD VLNTPSEAVQRAVSACLSPLMQSKQESLSTLFSLYIRDMGVGDVNVDAGWLGRQGIALALHSAA DILGTKDLPVVMTFLISRALADPNADVRGRMINAGILIIDKNGKDNVSLLFPIFENYLNKTAPD EEKYDLVREGVVIFTGALAKHLAKDDPKVHAVVDKLLDVLNTPSEAVQRAVSACLSPLMQSKQE SLSTLFSLYIRDMGVGDVNVDAGWLGRQGIALALHSAADILGTKDLPVVMTFLISRALADPNAD VRGRMINAGILIIDKNGKDNVSLLFPIFENYLNKTAPDEEKYDLVREGVVIFTGALAKHLAKDD PKVHAVVDKLLDVLNTPSEAVQRAVSACLSPLMQSKQESLSTLFSLYIRDMGVGDVNVDAGWLG RQGIALALHSAADILGTKDLPVVMTFLISRALADPNADVRGRMINAGILIIDKNGKDNVSLLFP IFENYLNKTAPDEEKYDLVREGVVIFTGALAKHLAKDDPKVHAVVDKLLDVLNTPSEAVQRAVS ACLSPLMQSKQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_19G249900_circ_g.3

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