Plant Circular RNA Database

Detail information of GLYMA_17G259400_circ_g.1

			
						 General Information
					
						CircRNA Name
						GLYMA_17G259400_circ_g.1
					
						ID in PlantcircBase
						gma_circ_004603
					
						Alias
						Gm17circRNA379, gma-circRNA2412
					
						Organism
						
							Glycine max						
					
						Position
						
							chr17: 41354458-41356841  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, find_circ
					
						Parent gene
						
							GLYMA_17G259400						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							GLYMA_17G259400_circ_g.2 GLYMA_17G259400_circ_g.3 						
					
						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
						KRH05975:3

General Information
CircRNA Name	GLYMA_17G259400_circ_g.1
ID in PlantcircBase	gma_circ_004603
Alias	Gm17circRNA379, gma-circRNA2412
Organism	Glycine max
Position	chr17: 41354458-41356841 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, find_circ
Parent gene	GLYMA_17G259400
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	GLYMA_17G259400_circ_g.2 GLYMA_17G259400_circ_g.3
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	KRH05975:3

			
						 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  
						
							GAACTGTGGGGATATTTTTTGTGACAAATGCACACGTGGTAGAATTGCTCTTACTTCTGATGAG
GATGCTCTGCAAGTACGAGTTTGTGATCGATGCATGttcaaggaaatgggtggaagcaggaggc
cttccgaatcattgagaacaaacgaacagcctacagaaaaaaagagaggatttggtgattggat
gaatttga

									
								

					

						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: 309
Transcript exons: 41354458-41354589,41356585-41356650,41356731-41356841
TTCAAGGAAATGGGTGGAAGCAGGAGGCCTTCCGAATCATTGAGAACAAACGAACAGCCTACAG
AAAAAAAGAGAGGATTTGGTGATTGGATGAATTTGATTAAACCTGCCGATGAAGAGAAGGATCA
TTGGGTCCCAGATGAAGCAGTCTTAAAATGTACAGCATGCGGAGTAGATTTTGGGGCTTTTCTT
CGCAGACATCACTGTAGGAACTGTGGGGATATTTTTTGTGACAAATGCACACGTGGTAGAATTG
CTCTTACTTCTGATGAGGATGCTCTGCAAGTACGAGTTTGTGATCGATGCATG
						
					

						Genomic sequence
						
							TTCAAGGAAATGGGTGGAAGCAGGAGGCCTTCCGAATCATTGAGAACAAACGAACAGCCTACAG
AAAAAAAGAGAGGATTTGGTGATTGGATGAATTTGATTAAACCTGCCGATGAAGAGAAGGATCA
TTGGGTAACATTAGATGCAAATTATGTTTTCTTTTGCTTTTTTCTGAACCCCATACCAGATTTG
GCTCCTTTAAAGTGAATGGGCACTATAAAGGATAAAATGCAGAGATATAACTGTTGATTGAAAA
AACAATGCTTGAAATTATGATAAAATACATGCACATATAAAATAAACTATGAAATTTTTAAAAT
ATACTCCATTGATTTTCCAATCAACAGTGATAATTTCACACCTTACCTTCAGAAGTGCATCCCT
TGTTTTAAAGGAGCCAAATTCCCTCTTACCCTTCCCCTAAAATGGCTTGTAGGGCTTTAGCAGA
ATATTTTTGGTTGAACTATTTATTTAATTACTAGGATTCAATGTTATTATATATTGCTGCTTGG
TTATGATTGTTGGGACAAGGGTGTATTGCTGTTGCCATTATTTTTACAACAAGAAAAACAACCA
AGCCTTTCTCACTACATGAGGTCAGCTAGATGAATCAAATGATGTCATAATATTTTATCGTAAA
TTATGGCTATGATCAAACTATTGACCCAAAAAATCTTCTTAATGGTTTCACCCATACTTTTTTT
CATGATCTTCCTTTGTCTCTAGTGTTTGGGCTACCCTCCATAGAGCTGTTCCAAAATTCTTTTA
TATCTAATATGTTTACTCATCCAACACAGCATTCTCCTTTTTGCTACCTTGAGCTTATTCCGTT
GTTGGCTTTTTAATGCCCAATGTTTAGTCTCATACAATATTGCAGGTTTTTTAACTGTGATAAA
GTTTTTAAGCTTGAGTGATACTTTTTAGTCATAGATAACACCTGAAGCACTCCTCCAATTCATC
TACCTGCTTGAATCCTGTGGTTTACATCTTCCTCAATTTCTCTGCCGTTCTGTATGAAGGGCCC
TAAATACTTAAACTCTGTTACTTGTATTAAAGTATGTTCTCGGGACTTTTACTTTTAAGCTAGG
CTTGTTGTTCTTCATGCTAAACTTACATTCCATGTACTTGGTGTTACTTTTACTTAAGCAAAAT
CCACGAGTTTTCAAAGCTTGTCCCCATTTCTCCAATTCCCATTTATTTCCTCACTTGATTCTTC
AACTTGAACTATATCGTCTTATAAAAAGCATGCATCATAGCACTGCCTCTTGGATGTGCTCAGT
TAGCAAGCCTAAGACCAAAATAAAGAGGTAAGGACTCAAAGCTGACCCTTGACCCAGCCCTATG
GTTGTTGGAAAATTTTAAATTTGTTGTGACCCAATCTTGTGTTCTCACCATATTCATGCCTCCC
TTATACATATCCTTGATTGCTCAAGTATTGCACATAGGAACTCTGGCCTTCCACAAAATCTGAC
ACCGTTTTCCCTCATCAATTTAATTTTTAGGCTAAAATGCATTTTTTGTCCCCCTATTTTTTCA
AATATGTGATTTTAGTCCCCCTACATTTTAATTGAGACATTTCATCCCTCACTTTTAAAAAATT
CGCGATTTTAGTCCTCCGTTTTATAATTGAGCATTTTGTCCCCCACTTTTAAAAAAGCCACAAT
TTTAATCCTTGTAGCCAATTTCAAACATTGATCTATGCATTCTGTAAAGGTTGAATGACACGTG
TCTATTTATTATCCACATGACAAATGTTTTTTTTAATTATTTAATTGCTAACAAACTTAATTTA
TTAAAAAAAATAATTAAAAAGTACATAGTTAAGTCTGGAATTGAAAAGGGGACTAAAATCACAG
ATTTTTAAAAAGTGTGGGATGAAATGTCTCAATTAAAAAATAGGGGGACTAAAATTGCGGATTT
AGAAAAATGGGAGGACGAAAATTGCATTTTAGCCTAACTTTTACAATGCTAATGTGTTTGTTAC
ACTTATAACCCTTGGAAAGTGCAAATTGTCTAAATGTAACTTGATCTTAATGAAAATGAAAGCT
ACATCAACTTAAACTACACTCAGTTTTCATTTTTGCTTGTACTCAATTGGAGTTCTTATGAGGT
TCAATTTATGCATAGGTCCCAGATGAAGCAGTCTTAAAATGTACAGCATGCGGAGTAGATTTTG
GGGCTTTTCTTCGCAGAGTTGATCTCCTGTTTCTTTTAATTATGTTTTATATTGTGTGGTTTGG
GTGCTAATGTTTGATCATCTATGCTTTGGACAGCATCACTGTAGGAACTGTGGGGATATTTTTT
GTGACAAATGCACACGTGGTAGAATTGCTCTTACTTCTGATGAGGATGCTCTGCAAGTACGAGT
TTGTGATCGATGCATG
						
					

			
		

Sequences
Splice junction sequence	GAACTGTGGGGATATTTTTTGTGACAAATGCACACGTGGTAGAATTGCTCTTACTTCTGATGAG GATGCTCTGCAAGTACGAGTTTGTGATCGATGCATGttcaaggaaatgggtggaagcaggaggc cttccgaatcattgagaacaaacgaacagcctacagaaaaaaagagaggatttggtgattggat gaatttga
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: 309 Transcript exons: 41354458-41354589,41356585-41356650,41356731-41356841 TTCAAGGAAATGGGTGGAAGCAGGAGGCCTTCCGAATCATTGAGAACAAACGAACAGCCTACAG AAAAAAAGAGAGGATTTGGTGATTGGATGAATTTGATTAAACCTGCCGATGAAGAGAAGGATCA TTGGGTCCCAGATGAAGCAGTCTTAAAATGTACAGCATGCGGAGTAGATTTTGGGGCTTTTCTT CGCAGACATCACTGTAGGAACTGTGGGGATATTTTTTGTGACAAATGCACACGTGGTAGAATTG CTCTTACTTCTGATGAGGATGCTCTGCAAGTACGAGTTTGTGATCGATGCATG
Genomic sequence	TTCAAGGAAATGGGTGGAAGCAGGAGGCCTTCCGAATCATTGAGAACAAACGAACAGCCTACAG AAAAAAAGAGAGGATTTGGTGATTGGATGAATTTGATTAAACCTGCCGATGAAGAGAAGGATCA TTGGGTAACATTAGATGCAAATTATGTTTTCTTTTGCTTTTTTCTGAACCCCATACCAGATTTG GCTCCTTTAAAGTGAATGGGCACTATAAAGGATAAAATGCAGAGATATAACTGTTGATTGAAAA AACAATGCTTGAAATTATGATAAAATACATGCACATATAAAATAAACTATGAAATTTTTAAAAT ATACTCCATTGATTTTCCAATCAACAGTGATAATTTCACACCTTACCTTCAGAAGTGCATCCCT TGTTTTAAAGGAGCCAAATTCCCTCTTACCCTTCCCCTAAAATGGCTTGTAGGGCTTTAGCAGA ATATTTTTGGTTGAACTATTTATTTAATTACTAGGATTCAATGTTATTATATATTGCTGCTTGG TTATGATTGTTGGGACAAGGGTGTATTGCTGTTGCCATTATTTTTACAACAAGAAAAACAACCA AGCCTTTCTCACTACATGAGGTCAGCTAGATGAATCAAATGATGTCATAATATTTTATCGTAAA TTATGGCTATGATCAAACTATTGACCCAAAAAATCTTCTTAATGGTTTCACCCATACTTTTTTT CATGATCTTCCTTTGTCTCTAGTGTTTGGGCTACCCTCCATAGAGCTGTTCCAAAATTCTTTTA TATCTAATATGTTTACTCATCCAACACAGCATTCTCCTTTTTGCTACCTTGAGCTTATTCCGTT GTTGGCTTTTTAATGCCCAATGTTTAGTCTCATACAATATTGCAGGTTTTTTAACTGTGATAAA GTTTTTAAGCTTGAGTGATACTTTTTAGTCATAGATAACACCTGAAGCACTCCTCCAATTCATC TACCTGCTTGAATCCTGTGGTTTACATCTTCCTCAATTTCTCTGCCGTTCTGTATGAAGGGCCC TAAATACTTAAACTCTGTTACTTGTATTAAAGTATGTTCTCGGGACTTTTACTTTTAAGCTAGG CTTGTTGTTCTTCATGCTAAACTTACATTCCATGTACTTGGTGTTACTTTTACTTAAGCAAAAT CCACGAGTTTTCAAAGCTTGTCCCCATTTCTCCAATTCCCATTTATTTCCTCACTTGATTCTTC AACTTGAACTATATCGTCTTATAAAAAGCATGCATCATAGCACTGCCTCTTGGATGTGCTCAGT TAGCAAGCCTAAGACCAAAATAAAGAGGTAAGGACTCAAAGCTGACCCTTGACCCAGCCCTATG GTTGTTGGAAAATTTTAAATTTGTTGTGACCCAATCTTGTGTTCTCACCATATTCATGCCTCCC TTATACATATCCTTGATTGCTCAAGTATTGCACATAGGAACTCTGGCCTTCCACAAAATCTGAC ACCGTTTTCCCTCATCAATTTAATTTTTAGGCTAAAATGCATTTTTTGTCCCCCTATTTTTTCA AATATGTGATTTTAGTCCCCCTACATTTTAATTGAGACATTTCATCCCTCACTTTTAAAAAATT CGCGATTTTAGTCCTCCGTTTTATAATTGAGCATTTTGTCCCCCACTTTTAAAAAAGCCACAAT TTTAATCCTTGTAGCCAATTTCAAACATTGATCTATGCATTCTGTAAAGGTTGAATGACACGTG TCTATTTATTATCCACATGACAAATGTTTTTTTTAATTATTTAATTGCTAACAAACTTAATTTA TTAAAAAAAATAATTAAAAAGTACATAGTTAAGTCTGGAATTGAAAAGGGGACTAAAATCACAG ATTTTTAAAAAGTGTGGGATGAAATGTCTCAATTAAAAAATAGGGGGACTAAAATTGCGGATTT AGAAAAATGGGAGGACGAAAATTGCATTTTAGCCTAACTTTTACAATGCTAATGTGTTTGTTAC ACTTATAACCCTTGGAAAGTGCAAATTGTCTAAATGTAACTTGATCTTAATGAAAATGAAAGCT ACATCAACTTAAACTACACTCAGTTTTCATTTTTGCTTGTACTCAATTGGAGTTCTTATGAGGT TCAATTTATGCATAGGTCCCAGATGAAGCAGTCTTAAAATGTACAGCATGCGGAGTAGATTTTG GGGCTTTTCTTCGCAGAGTTGATCTCCTGTTTCTTTTAATTATGTTTTATATTGTGTGGTTTGG GTGCTAATGTTTGATCATCTATGCTTTGGACAGCATCACTGTAGGAACTGTGGGGATATTTTTT GTGACAAATGCACACGTGGTAGAATTGCTCTTACTTCTGATGAGGATGCTCTGCAAGTACGAGT TTGTGATCGATGCATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.574622109

Conservation Information
Conserved circRNAs	NA
PMCS	0.574622109

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							41354468-41356838(+)
41356802-41354497(+)
41356836-41354540(+)
						
						Potential amino acid sequence
						
							MGGSRRPSESLRTNEQPTEKKRGFGDWMNLIKPADEEKDHWVPDEAVLKCTACGVDFGAFLRRH
HCRNCGDIFCDKCTRGRIALTSDEDALQVRVCDRCMFKEMGGSRRPSESLRTNEQPTEKKRGFG
DWMNLIKPADEEKDHWVPDEAVLKCTACGVDFGAFLRRHHCRNCGDIFCDKCTRGRIALTSDED
ALQVRVCDRCMFKEMGGSRRPSESLRTNEQPTEKKRGFGDWMNLIKPADEEKDHWVPDEAVLKC
TACGVDFGAFLRRHHCRNCGDIFCDKCTRGRIALTSDEDALQVRVCDRCMFKEMGGSRRPSESL
RTNEQPTEKKRGFGDWMNLIKPADEEKDHWVPDEAVLKCTACGVDFGAFLRRHHCRNCGDIFCD
KCTRGRIALTSDEDALQVRVCDRCM(+)
MRMLCKYEFVIDACSRKWVEAGGLPNH*(+)
MHVQGNGWKQEAFRIIENKRTAYRKKERIW*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	41354468-41356838(+) 41356802-41354497(+) 41356836-41354540(+)
Potential amino acid sequence	MGGSRRPSESLRTNEQPTEKKRGFGDWMNLIKPADEEKDHWVPDEAVLKCTACGVDFGAFLRRH HCRNCGDIFCDKCTRGRIALTSDEDALQVRVCDRCMFKEMGGSRRPSESLRTNEQPTEKKRGFG DWMNLIKPADEEKDHWVPDEAVLKCTACGVDFGAFLRRHHCRNCGDIFCDKCTRGRIALTSDED ALQVRVCDRCMFKEMGGSRRPSESLRTNEQPTEKKRGFGDWMNLIKPADEEKDHWVPDEAVLKC TACGVDFGAFLRRHHCRNCGDIFCDKCTRGRIALTSDEDALQVRVCDRCMFKEMGGSRRPSESL RTNEQPTEKKRGFGDWMNLIKPADEEKDHWVPDEAVLKCTACGVDFGAFLRRHHCRNCGDIFCD KCTRGRIALTSDEDALQVRVCDRCM(+) MRMLCKYEFVIDACSRKWVEAGGLPNH(+) MHVQGNGWKQEAFRIIENKRTAYRKKERIW(+)
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_17G259400_circ_g.1

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