Plant Circular RNA Database

Detail information of GLYMA_18G179800_circ_g.2

			
						 General Information
					
						CircRNA Name
						GLYMA_18G179800_circ_g.2
					
						ID in PlantcircBase
						gma_circ_007546
					
						Alias
						gma-circRNA2485
					
						Organism
						
							Glycine max						
					
						Position
						
							chr18: 43345766-43346768  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							GLYMA_18G179800						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						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
						KRG99917:5
KRG99916:5

General Information
CircRNA Name	GLYMA_18G179800_circ_g.2
ID in PlantcircBase	gma_circ_007546
Alias	gma-circRNA2485
Organism	Glycine max
Position	chr18: 43345766-43346768 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	GLYMA_18G179800
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
Tissues	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	KRG99917:5 KRG99916:5

			
						 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  
						
							AAAGGAGATTGGAATGTTTATAGATTCATGCTTCGTCCATTGCCAGACTGAGATGGAAGTGACG
TGGCATTCACCCAACTCTCCTAAAATAAATGATAAGgaaggatattagtggaaacagtacaatg
agatctttctatcatgatgttgcccagcttcaggtattgtggtgcttgcttatatatttataac
aatatttc

						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: 445
Transcript exons: 43345766-43345826,43345975-43346028,43346154-43346231,43
346327-43346432,43346623-43346768
GAAGGATATTAGTGGAAACAGTACAATGAGATCTTTCTATCATGATGTTGCCCAGCTTCAGGGT
CTTGCAAAAAGTTTGCACAAAGATTGCATTGCTAAAATGGAACCATCTAAGTGTCTCTTTCCAT
CAGAAATTGCTAAAAACATAAAGACTCCACTGTTCCTTGTTCATCCAGCTTATGATTTCTGGCA
GATACGCAATATTTTGGTGCCTCAAGGATCAGATCCTGATGGTCACTGGCAAAGGTGCAGACTG
GACATTCGCAGTTGTAATGCTAATATGATTGATAAACTTGACAGTTACCGTGGCTCTTTGCTGA
AGGCTGTGAATGAATTCCAACAACGAAAGGAGATTGGAATGTTTATAGATTCATGCTTCGTCCA
TTGCCAGACTGAGATGGAAGTGACGTGGCATTCACCCAACTCTCCTAAAATAAATGATAAG
						
						Genomic sequence
						
							GAAGGATATTAGTGGAAACAGTACAATGAGATCTTTCTATCATGATGTTGCCCAGCTTCAGGTA
TTGTGGTGCTTGCTTATATATTTATAACAATATTTCTTTAAGGAACTACAATTATACTTATCTG
TTAAGTTTATTAGTATAAATAAAAAAAGTAGAATGTGATTTTTTCAGTTAATTATATAATATTC
GCATATCTTGTTGTTAGGGTCTTGCAAAAAGTTTGCACAAAGATTGCATTGCTAAAATGGAACC
ATCTAAGGCAGGTTTTTTAGTTTCTCAAATCTTGTTGCCTCACCCTTCGATATAATTTGTAAGA
GTAAAATTTGGTTAGTTGGTTCATATATTTCATCTAAAAGAACAACCAACTGTGTATTTGTAAT
GCAGTGTCTCTTTCCATCAGAAATTGCTAAAAACATAAAGACTCCACTGTTCCTTGTTCATCCA
GCTTATGATTTCTGGCAGGTAAGTCCCTTAGTATTCATGTTTCATTGTCATAAAACATTTTTTT
TTCTAATTTTTCTGTGATGGACATTTGATGCTAATTAAAACGTATTTAGATACGCAATATTTTG
GTGCCTCAAGGATCAGATCCTGATGGTCACTGGCAAAGGTGCAGACTGGACATTCGCAGTTGTA
ATGCTAATATGATTGATAAACTTGACAGTAAGTATTCGCTATAGCTACCATATAGTTTCTGGAT
ATGTTGTTGTAGTCTTGGTTTATTAACTTCTGTAAGCCTTCAATTGGATTAGATTTGGAATGCT
GCAGATATTGATTAATGATGATCTAACCTGGAACCTAAATGTAGTAGCCACGCTGAGGCATGGA
TAACTTGAGAAATTATCATTGTCAGGTTACCGTGGCTCTTTGCTGAAGGCTGTGAATGAATTCC
AACAACGAAAGGAGATTGGAATGTTTATAGATTCATGCTTCGTCCATTGCCAGACTGAGATGGA
AGTGACGTGGCATTCACCCAACTCTCCTAAAATAAATGATAAG

Sequences
Splice junction sequence	AAAGGAGATTGGAATGTTTATAGATTCATGCTTCGTCCATTGCCAGACTGAGATGGAAGTGACG TGGCATTCACCCAACTCTCCTAAAATAAATGATAAGgaaggatattagtggaaacagtacaatg agatctttctatcatgatgttgcccagcttcaggtattgtggtgcttgcttatatatttataac aatatttc
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: 445 Transcript exons: 43345766-43345826,43345975-43346028,43346154-43346231,43 346327-43346432,43346623-43346768 GAAGGATATTAGTGGAAACAGTACAATGAGATCTTTCTATCATGATGTTGCCCAGCTTCAGGGT CTTGCAAAAAGTTTGCACAAAGATTGCATTGCTAAAATGGAACCATCTAAGTGTCTCTTTCCAT CAGAAATTGCTAAAAACATAAAGACTCCACTGTTCCTTGTTCATCCAGCTTATGATTTCTGGCA GATACGCAATATTTTGGTGCCTCAAGGATCAGATCCTGATGGTCACTGGCAAAGGTGCAGACTG GACATTCGCAGTTGTAATGCTAATATGATTGATAAACTTGACAGTTACCGTGGCTCTTTGCTGA AGGCTGTGAATGAATTCCAACAACGAAAGGAGATTGGAATGTTTATAGATTCATGCTTCGTCCA TTGCCAGACTGAGATGGAAGTGACGTGGCATTCACCCAACTCTCCTAAAATAAATGATAAG
Genomic sequence	GAAGGATATTAGTGGAAACAGTACAATGAGATCTTTCTATCATGATGTTGCCCAGCTTCAGGTA TTGTGGTGCTTGCTTATATATTTATAACAATATTTCTTTAAGGAACTACAATTATACTTATCTG TTAAGTTTATTAGTATAAATAAAAAAAGTAGAATGTGATTTTTTCAGTTAATTATATAATATTC GCATATCTTGTTGTTAGGGTCTTGCAAAAAGTTTGCACAAAGATTGCATTGCTAAAATGGAACC ATCTAAGGCAGGTTTTTTAGTTTCTCAAATCTTGTTGCCTCACCCTTCGATATAATTTGTAAGA GTAAAATTTGGTTAGTTGGTTCATATATTTCATCTAAAAGAACAACCAACTGTGTATTTGTAAT GCAGTGTCTCTTTCCATCAGAAATTGCTAAAAACATAAAGACTCCACTGTTCCTTGTTCATCCA GCTTATGATTTCTGGCAGGTAAGTCCCTTAGTATTCATGTTTCATTGTCATAAAACATTTTTTT TTCTAATTTTTCTGTGATGGACATTTGATGCTAATTAAAACGTATTTAGATACGCAATATTTTG GTGCCTCAAGGATCAGATCCTGATGGTCACTGGCAAAGGTGCAGACTGGACATTCGCAGTTGTA ATGCTAATATGATTGATAAACTTGACAGTAAGTATTCGCTATAGCTACCATATAGTTTCTGGAT ATGTTGTTGTAGTCTTGGTTTATTAACTTCTGTAAGCCTTCAATTGGATTAGATTTGGAATGCT GCAGATATTGATTAATGATGATCTAACCTGGAACCTAAATGTAGTAGCCACGCTGAGGCATGGA TAACTTGAGAAATTATCATTGTCAGGTTACCGTGGCTCTTTGCTGAAGGCTGTGAATGAATTCC AACAACGAAAGGAGATTGGAATGTTTATAGATTCATGCTTCGTCCATTGCCAGACTGAGATGGA AGTGACGTGGCATTCACCCAACTCTCCTAAAATAAATGATAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.171755567

Conservation Information
Conserved circRNAs	NA
PMCS	0.171755567

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							43345792-43345774(+)
43346762-43345774(+)
						
						Potential amino acid sequence
						
							MRSFYHDVAQLQGLAKSLHKDCIAKMEPSKCLFPSEIAKNIKTPLFLVHPAYDFWQIRNILVPQ
GSDPDGHWQRCRLDIRSCNANMIDKLDSYRGSLLKAVNEFQQRKEIGMFIDSCFVHCQTEMEVT
WHSPNSPKINDKEGY*(+)
MIRKDISGNSTMRSFYHDVAQLQGLAKSLHKDCIAKMEPSKCLFPSEIAKNIKTPLFLVHPAYD
FWQIRNILVPQGSDPDGHWQRCRLDIRSCNANMIDKLDSYRGSLLKAVNEFQQRKEIGMFIDSC
FVHCQTEMEVTWHSPNSPKINDKEGY*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						playing a post-transcriptional regulatory role in soybean oil synthesis; cytoplasmic male sterility

Functional Information
Coding potential	Y
Potential coding position	43345792-43345774(+) 43346762-43345774(+)
Potential amino acid sequence	MRSFYHDVAQLQGLAKSLHKDCIAKMEPSKCLFPSEIAKNIKTPLFLVHPAYDFWQIRNILVPQ GSDPDGHWQRCRLDIRSCNANMIDKLDSYRGSLLKAVNEFQQRKEIGMFIDSCFVHCQTEMEVT WHSPNSPKINDKEGY(+) MIRKDISGNSTMRSFYHDVAQLQGLAKSLHKDCIAKMEPSKCLFPSEIAKNIKTPLFLVHPAYD FWQIRNILVPQGSDPDGHWQRCRLDIRSCNANMIDKLDSYRGSLLKAVNEFQQRKEIGMFIDSC FVHCQTEMEVTWHSPNSPKINDKEGY(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	playing a post-transcriptional regulatory role in soybean oil synthesis; cytoplasmic male sterility

			
						 Other Information
					
						References
						Chen et al., 2018

circRNA

Detail information of GLYMA_18G179800_circ_g.2

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