Plant Circular RNA Database

Detail information of GLYMA_11G154700_circ_g.2

			
						 General Information
					
						CircRNA Name
						GLYMA_11G154700_circ_g.2
					
						ID in PlantcircBase
						gma_circ_003093
					
						Alias
						Gm11circRNA1177
					
						Organism
						
							Glycine max						
					
						Position
						
							chr11: 12539404-12540944  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat
					
						Parent gene
						
							GLYMA_11G154700						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_11G154700_circ_g.3 						
					
						Support reads
						NA
					
						Tissues
						root
					
						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
						KRH30051:3
KRH30050:3
KRH30044:3
KRH30049:3
KRH30052:3
KRH30045:3
KRH30046:3
KRH30047:3
KRH30048:3
KRH30043:3

General Information
CircRNA Name	GLYMA_11G154700_circ_g.2
ID in PlantcircBase	gma_circ_003093
Alias	Gm11circRNA1177
Organism	Glycine max
Position	chr11: 12539404-12540944 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat
Parent gene	GLYMA_11G154700
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_11G154700_circ_g.3
Support reads	NA
Tissues	root
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	KRH30051:3 KRH30050:3 KRH30044:3 KRH30049:3 KRH30052:3 KRH30045:3 KRH30046:3 KRH30047:3 KRH30048:3 KRH30043:3

			
						 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  
						
							GATTCCACTCTTTTATGTTGCTAACATCTTCATTTACCTCTGGATATGGCACAATATGATCAAC
ACTCTCACCTCCTTCACCCCATATTATGTTAGCTAGctgctgttcctttcctggaggcttactt
ctaactccatcatttcccactttagctgtgattgtgcatgcattttctataacctgggatgcag
gaccccca

									
								

					

						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: 780
Transcript exons: 12539404-12539710,12540284-12540413,12540602-12540944
CTGCTGTTCCTTTCCTGGAGGCTTACTTCTAACTCCATCATTTCCCACTTTAGCTGTGATTGTG
CATGCATTTTCTATAACCTGGGATGCAGGACCCCCAATCTTCTCATTGTTGAGGTCCAATGATT
CATCACTACATTGAGCATATTCTTCTTTGATTTCCAAAGGCTCAGTTCTGTTCCTTAAAGCACC
TGATGAACTTGGTGTGTCCAATGGTAAAGGTGCTGCATTTTTACTCACATCTTTAGAGGACCAA
AGCTCATTAGAATTATCAAGACTTGCATGGCCAAATATAGGGTCATCATTGCTAAAAATTTGAT
CAAGGTCATCAAAACTTCCTATGTTGACCCATCCATAATCAACAAAATCACCTTGCTCTTTACC
TTCATGAGCAGTTTGGAAAATTTCAGCATCCTTTTCATGTTGTGTAGTTTCTTCTCTTGATGAA
CTGAATTTGCTAAGTTCACTTAAATTTTTAGATACTTCAGTACCCAGGGAACCCTGATCAATGT
TAGCTGAAGTGGATAAAGACAAGTCAGGCCATGCATTTGTTCCATATCCTGAGGTTAGTAGTTC
TCCACTATTATCAAGGTTGGAACTGCTTCCTAGCTTTCTTTCATGAAAATCAGTTTTAGCCTCT
GGCCTCTTCAGCTTGGTGAGCTTAGTCGCAGCAGCTTCTTGATTCCACTCTTTTATGTTGCTAA
CATCTTCATTTACCTCTGGATATGGCACAATATGATCAACACTCTCACCTCCTTCACCCCATAT
TATGTTAGCTAG
						
					

						Genomic sequence
						
							CTGCTGTTCCTTTCCTGGAGGCTTACTTCTAACTCCATCATTTCCCACTTTAGCTGTGATTGTG
CATGCATTTTCTATAACCTGGGATGCAGGACCCCCAATCTTCTCATTGTTGAGGTCCAATGATT
CATCACTACATTGAGCATATTCTTCTTTGATTTCCAAAGGCTCAGTTCTGTTCCTTAAAGCACC
TGATGAACTTGGTGTGTCCAATGGTAAAGGTGCTGCATTTTTACTCACATCTTTAGAGGACCAA
AGCTCATTAGAATTATCAAGACTTGCATGGCCAAATATAGGGTCATCATTGCTGCAAAATCATC
ACTTGTAGAATATTCAGTCAGACAGATGCCATTGTAAAATACATGACTAATAACTAAAAGTATA
GATGTATGTCTACAAACATTCACTGTTAATCAGGACTTCACATCTCTCCAATGTTATCCATCAC
ATGCACTGTATAATGAAGACCAAGGCACGTAAAACTACCAACTGGCAATCTTTCTAAGTTCAAA
CTTTGGTGAAATGAAGTCTTCCTAGTTTAGTGTAAAATTGTTCAAAGACTTAATATTGTAATTA
TTCCCATATTTTCCCTTTTAATGATGGTACTTTATCATTGAACGACGAATGTGCACAGCTGCAC
ATATTTTTCCATTCAAGTTTGATAGAAGGAACTTAAATGAAGATTGAGTAAAGTATAAGCAGTT
TTGAAAAGTGAAGAATACAACAGTTCTCATAAATAGGAAAACAGGAGAGAAGTTTAGTCCAATT
TTAGATTTCAGTAATTCAGTAAAAAGAATGACATGATATTAAATACACTGGTGATCATAATGCT
ATCTGATACACATGCATTCTATAATGCGATAGAGATAATCTACATTACCTAAAAATTTGATCAA
GGTCATCAAAACTTCCTATGTTGACCCATCCATAATCAACAAAATCACCTTGCTCTTTACCTTC
ATGAGCAGTTTGGAAAATTTCAGCATCCTTTTCATGTTGTGTAGTTTCTTCTGTCAGACATTAA
TACAATTAGAAATGGCAAAATATAACTACATATCATGCATGTTTATTATTTTTCATAAAATGAT
GGTGAGACAAGCAGAAAAGACATCAACAGACAGAGGCCTGTACAAACACAAAAATGAATAGACA
CACATGTTATCTAGTCATTATTCCAGCAAATTGGCAATTTTACCACCTCTTGATGAACTGAATT
TGCTAAGTTCACTTAAATTTTTAGATACTTCAGTACCCAGGGAACCCTGATCAATGTTAGCTGA
AGTGGATAAAGACAAGTCAGGCCATGCATTTGTTCCATATCCTGAGGTTAGTAGTTCTCCACTA
TTATCAAGGTTGGAACTGCTTCCTAGCTTTCTTTCATGAAAATCAGTTTTAGCCTCTGGCCTCT
TCAGCTTGGTGAGCTTAGTCGCAGCAGCTTCTTGATTCCACTCTTTTATGTTGCTAACATCTTC
ATTTACCTCTGGATATGGCACAATATGATCAACACTCTCACCTCCTTCACCCCATATTATGTTA
GCTAG
						
					

			
		

Sequences
Splice junction sequence	GATTCCACTCTTTTATGTTGCTAACATCTTCATTTACCTCTGGATATGGCACAATATGATCAAC ACTCTCACCTCCTTCACCCCATATTATGTTAGCTAGctgctgttcctttcctggaggcttactt ctaactccatcatttcccactttagctgtgattgtgcatgcattttctataacctgggatgcag gaccccca
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: 780 Transcript exons: 12539404-12539710,12540284-12540413,12540602-12540944 CTGCTGTTCCTTTCCTGGAGGCTTACTTCTAACTCCATCATTTCCCACTTTAGCTGTGATTGTG CATGCATTTTCTATAACCTGGGATGCAGGACCCCCAATCTTCTCATTGTTGAGGTCCAATGATT CATCACTACATTGAGCATATTCTTCTTTGATTTCCAAAGGCTCAGTTCTGTTCCTTAAAGCACC TGATGAACTTGGTGTGTCCAATGGTAAAGGTGCTGCATTTTTACTCACATCTTTAGAGGACCAA AGCTCATTAGAATTATCAAGACTTGCATGGCCAAATATAGGGTCATCATTGCTAAAAATTTGAT CAAGGTCATCAAAACTTCCTATGTTGACCCATCCATAATCAACAAAATCACCTTGCTCTTTACC TTCATGAGCAGTTTGGAAAATTTCAGCATCCTTTTCATGTTGTGTAGTTTCTTCTCTTGATGAA CTGAATTTGCTAAGTTCACTTAAATTTTTAGATACTTCAGTACCCAGGGAACCCTGATCAATGT TAGCTGAAGTGGATAAAGACAAGTCAGGCCATGCATTTGTTCCATATCCTGAGGTTAGTAGTTC TCCACTATTATCAAGGTTGGAACTGCTTCCTAGCTTTCTTTCATGAAAATCAGTTTTAGCCTCT GGCCTCTTCAGCTTGGTGAGCTTAGTCGCAGCAGCTTCTTGATTCCACTCTTTTATGTTGCTAA CATCTTCATTTACCTCTGGATATGGCACAATATGATCAACACTCTCACCTCCTTCACCCCATAT TATGTTAGCTAG
Genomic sequence	CTGCTGTTCCTTTCCTGGAGGCTTACTTCTAACTCCATCATTTCCCACTTTAGCTGTGATTGTG CATGCATTTTCTATAACCTGGGATGCAGGACCCCCAATCTTCTCATTGTTGAGGTCCAATGATT CATCACTACATTGAGCATATTCTTCTTTGATTTCCAAAGGCTCAGTTCTGTTCCTTAAAGCACC TGATGAACTTGGTGTGTCCAATGGTAAAGGTGCTGCATTTTTACTCACATCTTTAGAGGACCAA AGCTCATTAGAATTATCAAGACTTGCATGGCCAAATATAGGGTCATCATTGCTGCAAAATCATC ACTTGTAGAATATTCAGTCAGACAGATGCCATTGTAAAATACATGACTAATAACTAAAAGTATA GATGTATGTCTACAAACATTCACTGTTAATCAGGACTTCACATCTCTCCAATGTTATCCATCAC ATGCACTGTATAATGAAGACCAAGGCACGTAAAACTACCAACTGGCAATCTTTCTAAGTTCAAA CTTTGGTGAAATGAAGTCTTCCTAGTTTAGTGTAAAATTGTTCAAAGACTTAATATTGTAATTA TTCCCATATTTTCCCTTTTAATGATGGTACTTTATCATTGAACGACGAATGTGCACAGCTGCAC ATATTTTTCCATTCAAGTTTGATAGAAGGAACTTAAATGAAGATTGAGTAAAGTATAAGCAGTT TTGAAAAGTGAAGAATACAACAGTTCTCATAAATAGGAAAACAGGAGAGAAGTTTAGTCCAATT TTAGATTTCAGTAATTCAGTAAAAAGAATGACATGATATTAAATACACTGGTGATCATAATGCT ATCTGATACACATGCATTCTATAATGCGATAGAGATAATCTACATTACCTAAAAATTTGATCAA GGTCATCAAAACTTCCTATGTTGACCCATCCATAATCAACAAAATCACCTTGCTCTTTACCTTC ATGAGCAGTTTGGAAAATTTCAGCATCCTTTTCATGTTGTGTAGTTTCTTCTGTCAGACATTAA TACAATTAGAAATGGCAAAATATAACTACATATCATGCATGTTTATTATTTTTCATAAAATGAT GGTGAGACAAGCAGAAAAGACATCAACAGACAGAGGCCTGTACAAACACAAAAATGAATAGACA CACATGTTATCTAGTCATTATTCCAGCAAATTGGCAATTTTACCACCTCTTGATGAACTGAATT TGCTAAGTTCACTTAAATTTTTAGATACTTCAGTACCCAGGGAACCCTGATCAATGTTAGCTGA AGTGGATAAAGACAAGTCAGGCCATGCATTTGTTCCATATCCTGAGGTTAGTAGTTCTCCACTA TTATCAAGGTTGGAACTGCTTCCTAGCTTTCTTTCATGAAAATCAGTTTTAGCCTCTGGCCTCT TCAGCTTGGTGAGCTTAGTCGCAGCAGCTTCTTGATTCCACTCTTTTATGTTGCTAACATCTTC ATTTACCTCTGGATATGGCACAATATGATCAACACTCTCACCTCCTTCACCCCATATTATGTTA GCTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.174604175

Conservation Information
Conserved circRNAs	NA
PMCS	0.174604175

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12540935-12539542(+)
12539476-12540943(-)
						
						Potential amino acid sequence
						
							MLASCCSFPGGLLLTPSFPTLAVIVHAFSITWDAGPPIFSLLRSNDSSLH*(+)
MHAQSQLKWEMMELEVSLQERNSS*(-)
						
						Sponge-miRNAs
						
							gma-miR156r 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	12540935-12539542(+) 12539476-12540943(-)
Potential amino acid sequence	MLASCCSFPGGLLLTPSFPTLAVIVHAFSITWDAGPPIFSLLRSNDSSLH(+) MHAQSQLKWEMMELEVSLQERNSS(-)
Sponge-miRNAs	gma-miR156r
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_11G154700_circ_g.2

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