Plant Circular RNA Database

Detail information of GLYMA_06G290300_circ_g.1

			
						 General Information
					
						CircRNA Name
						GLYMA_06G290300_circ_g.1
					
						ID in PlantcircBase
						gma_circ_001566
					
						Alias
						Gm06circRNA1670
					
						Organism
						
							Glycine max						
					
						Position
						
							chr6: 47920738-47922115  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat
					
						Parent gene
						
							GLYMA_06G290300						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							GLYMA_06G290300_circ_g.2 GLYMA_06G290300_circ_g.3 						
					
						Support reads
						NA
					
						Tissues
						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  
						
							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
						KRH55927:6
KRH55926:6
KRH55925:6

General Information
CircRNA Name	GLYMA_06G290300_circ_g.1
ID in PlantcircBase	gma_circ_001566
Alias	Gm06circRNA1670
Organism	Glycine max
Position	chr6: 47920738-47922115 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat
Parent gene	GLYMA_06G290300
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	GLYMA_06G290300_circ_g.2 GLYMA_06G290300_circ_g.3
Support reads	NA
Tissues	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	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	KRH55927:6 KRH55926:6 KRH55925:6

			
						 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  
						
							TCAGAGGATTCGCCCACCTAGGGTGAAGAGTAGTGCTGAGCTTGAGGAAGAAATGATGGCTAAA
ATTCCAAAATTCAAGGCTCGACCAGTGAATAAGAAGcattcatgcctaaaatcaagactggtag
atctattactgtggataccttgtgtgattttaatgaagctgacaaaatgcagaaggtacttgct
tcaatttt

						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
						
							CATTCATGCCTAAAATCAAGACTGGTAGATCTATTACTGTGGATACCTTGTGTGATTTTAATGA
AGCTGACAAAATGCAGAAGGTACTTGCTTCAATTTTGATGATATAGATATGTACTTTAATTTTG
ACTCCTTTAACTGATAATCTATTGTTTTAATAGATGTTAGCTAGTGTTGATGATAATGTTCTGG
AAACCAATATACAACAACAGAGCATGACTACCAAAGCAAAGGAAGATGAAGCTGACAAAGTGCA
GAAGGTACGTTGCTTCAATTTTGATGATATACATGCACATAGATTTGGTTCCTTTGACTGATTA
TATTTTATTTTTACTAGACGTCAGCAAATGTTGAGGATATAGTTCTGGAAACCAATATAAAACC
ACAGTGTGTGACTACTGTAAAGGAAGATGATGCACCTTGCCCTGACAAGGAAAGAAGTGAGAAT
GATTATAAAGAAGATAGTGCATGCTTAAAGGTTTCATCTGGAGAAGCATTCGTTGAAGTAGCAA
AAGATGCTTGCACGCCAAAACCAGCACTACTGAAAAAAGTTGCCACATCCACTAATTCCAAGAA
GACACAAAATAAGAAGATGGCCACGAATACAAAAACTCAGTTAAAGTCAGCAACAGTGAAGAGC
ATTGCAGGGACTCCTCACTTGGTCCAAGAGAATCAAGCCATTAAGAGGCAAAAATTGGATGGAG
GAAAATCTAGACAGGTAACTTTTATCTTCACAGTTTAAAGTTATTTTTGGGATCTTACTTGAAA
TATATTCTTATTTACTTTTTTAACTTTCCAGATACTGAATGCCAAGCATCAGACATTGCCTCAT
AATAAGTCAAAATTGGGTTTAACCGTGTCTGCTAGCACCAGTAAATATAACAAAGAGGACAGAA
AGGTTTGTTTTGTGCCCTTAATTTTCATATATTAAATCTAATCCTTTCTGTACCAAATTTTTAG
CTGTCTGTTTTATTTTTTACTTAGTTTATTGAATTGTGTATTGAAAGGTTTATGTTCGTGAAAC
ACCAACAACACCAGCCTCTGTACCATTTGTATCAATGGCAGAAATGATGAAAAAATTTCAATCT
AGTACCAGAGACCTGTCATTGCCCAGCTTTGTTTCTCACGTAATATACGGATCCAACTTTTTTA
CCCCCATTTCTTCTTTTTATTACACCATGTTTGAATAAATTTTTACTAAATATTCATTATGTGT
TTGATCCAGACAAAACCAAAACTCACATTGACTAGGCCTAAGGAGCCTGAATTTGAGACATCTC
AGAGGATTCGCCCACCTAGGGTGAAGAGTAGTGCTGAGCTTGAGGAAGAAATGATGGCTAAAAT
TCCAAAATTCAAGGCTCGACCAGTGAATAAGAAG

Sequences
Splice junction sequence	TCAGAGGATTCGCCCACCTAGGGTGAAGAGTAGTGCTGAGCTTGAGGAAGAAATGATGGCTAAA ATTCCAAAATTCAAGGCTCGACCAGTGAATAAGAAGcattcatgcctaaaatcaagactggtag atctattactgtggataccttgtgtgattttaatgaagctgacaaaatgcagaaggtacttgct tcaatttt
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	CATTCATGCCTAAAATCAAGACTGGTAGATCTATTACTGTGGATACCTTGTGTGATTTTAATGA AGCTGACAAAATGCAGAAGGTACTTGCTTCAATTTTGATGATATAGATATGTACTTTAATTTTG ACTCCTTTAACTGATAATCTATTGTTTTAATAGATGTTAGCTAGTGTTGATGATAATGTTCTGG AAACCAATATACAACAACAGAGCATGACTACCAAAGCAAAGGAAGATGAAGCTGACAAAGTGCA GAAGGTACGTTGCTTCAATTTTGATGATATACATGCACATAGATTTGGTTCCTTTGACTGATTA TATTTTATTTTTACTAGACGTCAGCAAATGTTGAGGATATAGTTCTGGAAACCAATATAAAACC ACAGTGTGTGACTACTGTAAAGGAAGATGATGCACCTTGCCCTGACAAGGAAAGAAGTGAGAAT GATTATAAAGAAGATAGTGCATGCTTAAAGGTTTCATCTGGAGAAGCATTCGTTGAAGTAGCAA AAGATGCTTGCACGCCAAAACCAGCACTACTGAAAAAAGTTGCCACATCCACTAATTCCAAGAA GACACAAAATAAGAAGATGGCCACGAATACAAAAACTCAGTTAAAGTCAGCAACAGTGAAGAGC ATTGCAGGGACTCCTCACTTGGTCCAAGAGAATCAAGCCATTAAGAGGCAAAAATTGGATGGAG GAAAATCTAGACAGGTAACTTTTATCTTCACAGTTTAAAGTTATTTTTGGGATCTTACTTGAAA TATATTCTTATTTACTTTTTTAACTTTCCAGATACTGAATGCCAAGCATCAGACATTGCCTCAT AATAAGTCAAAATTGGGTTTAACCGTGTCTGCTAGCACCAGTAAATATAACAAAGAGGACAGAA AGGTTTGTTTTGTGCCCTTAATTTTCATATATTAAATCTAATCCTTTCTGTACCAAATTTTTAG CTGTCTGTTTTATTTTTTACTTAGTTTATTGAATTGTGTATTGAAAGGTTTATGTTCGTGAAAC ACCAACAACACCAGCCTCTGTACCATTTGTATCAATGGCAGAAATGATGAAAAAATTTCAATCT AGTACCAGAGACCTGTCATTGCCCAGCTTTGTTTCTCACGTAATATACGGATCCAACTTTTTTA CCCCCATTTCTTCTTTTTATTACACCATGTTTGAATAAATTTTTACTAAATATTCATTATGTGT TTGATCCAGACAAAACCAAAACTCACATTGACTAGGCCTAAGGAGCCTGAATTTGAGACATCTC AGAGGATTCGCCCACCTAGGGTGAAGAGTAGTGCTGAGCTTGAGGAAGAAATGATGGCTAAAAT TCCAAAATTCAAGGCTCGACCAGTGAATAAGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.188374057

Conservation Information
Conserved circRNAs	NA
PMCS	0.188374057

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							47920744-47920902(+)
47920956-47922092(-)
47920742-47921843(-)
						
						Potential amino acid sequence
						
							MPKIKTGRSITVDTLCDFNEADKMQKMLASVDDNVLETNIQQQSMTTKAKEDEADKVQKTSANV
EDIVLETNIKPQCVTTVKEDDAPCPDKERSENDYKEDSACLKVSSGEAFVEVAKDACTPKPALL
KKVATSTNSKKTQNKKMATNTKTQLKSATVKSIAGTPHLVQENQAIKRQKLDGGKSRQILNAKH
QTLPHNKSKLGLTVSASTSKYNKEDRKVYVRETPTTPASVPFVSMAEMMKKFQSSTRDLSLPSF
VSHTKPKLTLTRPKEPEFETSQRIRPPRVKSSAELEEEMMAKIPKFKARPVNKKHSCLKSRLVD
LLLWIPCVILMKLTKCRRC*(+)
MLCCCILVSRTLSSTLANIFCILSASLKSHKVSTVIDLPVLILGMNASYSLVEP*(-)
MLLIHWSSLEFWNFSHHFFLKLSTTLHPRWANPLRCLKFRLLRPSQCEFWFCVRNKAGQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	47920744-47920902(+) 47920956-47922092(-) 47920742-47921843(-)
Potential amino acid sequence	MPKIKTGRSITVDTLCDFNEADKMQKMLASVDDNVLETNIQQQSMTTKAKEDEADKVQKTSANV EDIVLETNIKPQCVTTVKEDDAPCPDKERSENDYKEDSACLKVSSGEAFVEVAKDACTPKPALL KKVATSTNSKKTQNKKMATNTKTQLKSATVKSIAGTPHLVQENQAIKRQKLDGGKSRQILNAKH QTLPHNKSKLGLTVSASTSKYNKEDRKVYVRETPTTPASVPFVSMAEMMKKFQSSTRDLSLPSF VSHTKPKLTLTRPKEPEFETSQRIRPPRVKSSAELEEEMMAKIPKFKARPVNKKHSCLKSRLVD LLLWIPCVILMKLTKCRRC(+) MLCCCILVSRTLSSTLANIFCILSASLKSHKVSTVIDLPVLILGMNASYSLVEP(-) MLLIHWSSLEFWNFSHHFFLKLSTTLHPRWANPLRCLKFRLLRPSQCEFWFCVRNKAGQ*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_06G290300_circ_g.1

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