Plant Circular RNA Database

Detail information of GLYMA_04G146900_circ_g.2

			
						 General Information
					
						CircRNA Name
						GLYMA_04G146900_circ_g.2
					
						ID in PlantcircBase
						gma_circ_005792
					
						Alias
						gma-circRNA0446
					
						Organism
						
							Glycine max						
					
						Position
						
							chr4: 28671067-28672737  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							GLYMA_04G146900						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							GLYMA_04G146900_circ_g.1 						
					
						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
						KRH62987:2
KRH62986:2

General Information
CircRNA Name	GLYMA_04G146900_circ_g.2
ID in PlantcircBase	gma_circ_005792
Alias	gma-circRNA0446
Organism	Glycine max
Position	chr4: 28671067-28672737 JBrowse»
Reference genome	v2.0.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	GLYMA_04G146900
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	GLYMA_04G146900_circ_g.1
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	KRH62987:2 KRH62986:2

			
						 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  
						
							TGCATTGCCACATGAGCTTCCGAAAGTTTCAAATGAACAAAGGCTTGAAGAGTCGACTGGGGCC
ATATGGGGAACCTCAACACCTCTTGGTCTGTCAAAGcttttggcatccaagtcatctgaaatgg
ctagtactgatgacatcagtggtaaactgaaaagcagttcagacttggttatgtccagacaaga
taaacaag

									
								

					

						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: 381
Transcript exons: 28671067-28671233,28672524-28672737
CTTTTGGCATCCAAGTCATCTGAAATGGCTAGTACTGATGACATCAGTGGTAAACTGAAAAGCA
GTTCAGACTTGGTTATGTCCAGACAAGATAAACAAGTAGATAAATCTGATAAAAATGGGCTTTC
TGATATTGAGCAGCTGGTGCAAGGGAAGAAATTCTCTAGAGATGAATTTGATCGTTTAGTGGCG
GTATTAAATTTGAGGGTGATGGACCTTTCTAATGTTGAACAAGGAAAGAAAATTACAAATTTGA
GTTCTAGGAAAGATGATGAGGGGATTGCATTGCCACATGAGCTTCCGAAAGTTTCAAATGAACA
AAGGCTTGAAGAGTCGACTGGGGCCATATGGGGAACCTCAACACCTCTTGGTCTGTCAAAG
						
					

						Genomic sequence
						
							CTTTTGGCATCCAAGTCATCTGAAATGGCTAGTACTGATGACATCAGTGGTAAACTGAAAAGCA
GTTCAGACTTGGTTATGTCCAGACAAGATAAACAAGTAGATAAATCTGATAAAAATGGGCTTTC
TGATATTGAGCAGCTGGTGCAAGGGAAGAAATTCTCTAGGTACATTAGTTTAATTTGTTATAAT
TTTTTCATCCTTTTTTTTTTCTTTGAAAAAGGCATGCAAAGCATTAGGATAAAGTATAAAATCC
CAACTATGTTGGCACCTATACCCTATCCTTCATCTACCGCATACCTGAATTTATTAATTTTTTC
CCTCCCTTGATTGAATGACTCATTTCTTAATTTTACGGTGAAAGTTATTCTTGTTGTAGATCAA
ATCATTTACCCCCATATCTTTGAGCTTTATTGTCATCATTCTTGCACAGTAATAACTTTTTTGT
TTTGCTGTTGAAGTGAAAAGCTTTTTTGTTATAAATTTTTTTGATTAATAAATTTATTTTTATC
CATACAATAGATGTGGGAATGCCTTAGAGCACCAAAACATGTCTCATTTAGATATTGCATCCAT
ACATTGGTATGATATTAGCAAACATGTCTCCTATTTGGTGAAGCTAGGGATCATTAAGATTTTT
GGCCCAACGAGTTAGGTTCAAATTTGTTACTAAATAATGTCTTAGAGCATCTAAACATGTCTCA
TTTAGATATTGCATCCATACATTGTTATGATATTAGCAAACATGTCTCCTATTTGGTGAAGCTG
GGGATCATTAAGATTTTTGGCCCAACGAGTTAGGTTCAAATTTGTTACTAAATAAAATCTTTTT
TATATATATTTATTTCCAAGGTAATATAGACTAAAAAAATTATATCAAATGCGAATATATATTA
AATTAAAACATTATTGTTATGTACACATGCAAACATTAACATACCCTTTGAACTGACTCATGAG
TTAATGAGTCAATGATGTGATTGTGAAAGCTTTGGTTTGGCTCATTTAACAATCAAACGATTAT
TCTCATCTGATTGAGTTAATGAATTGGGCCGTGTAGTAGGATCAAGGGATGACTTGGCTTACCT
TCATCCTAGCTTTGTATGCTCGTGCTGTTAGAAAATCTGTTCATGTACTCTCTTATTTAGGGTG
TGTTAGGATGGAGGGGTTGGAAAGAGGATGAGGAGGGTTAATTTTTCATTTCTAAATTGAGTAG
AGACTGTAGAGTATGAGGAGGGTTAATTTTATAAATAGGAATAAGGGTCATTTGGGAGGTTACA
TGACAGTCTCATTTTATTCCATTTTTGTTTTTTTTCCTAATAAAAGAATATTTACTTAAGAAAT
GAAATTTTTTACCTCTCATCCTTTCCTTTCCAAGCATACCCTTAGTGAAGAAAACTATTTTTTT
GTTATTTATGGATGTACCATGTCTAAAAATCTTCAATCTCCTCGTGTAGAGATGAATTTGATCG
TTTAGTGGCGGTATTAAATTTGAGGGTGATGGACCTTTCTAATGTTGAACAAGGAAAGAAAATT
ACAAATTTGAGTTCTAGGAAAGATGATGAGGGGATTGCATTGCCACATGAGCTTCCGAAAGTTT
CAAATGAACAAAGGCTTGAAGAGTCGACTGGGGCCATATGGGGAACCTCAACACCTCTTGGTCT
GTCAAAG
						
					

			
		

Sequences
Splice junction sequence	TGCATTGCCACATGAGCTTCCGAAAGTTTCAAATGAACAAAGGCTTGAAGAGTCGACTGGGGCC ATATGGGGAACCTCAACACCTCTTGGTCTGTCAAAGcttttggcatccaagtcatctgaaatgg ctagtactgatgacatcagtggtaaactgaaaagcagttcagacttggttatgtccagacaaga taaacaag
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: 381 Transcript exons: 28671067-28671233,28672524-28672737 CTTTTGGCATCCAAGTCATCTGAAATGGCTAGTACTGATGACATCAGTGGTAAACTGAAAAGCA GTTCAGACTTGGTTATGTCCAGACAAGATAAACAAGTAGATAAATCTGATAAAAATGGGCTTTC TGATATTGAGCAGCTGGTGCAAGGGAAGAAATTCTCTAGAGATGAATTTGATCGTTTAGTGGCG GTATTAAATTTGAGGGTGATGGACCTTTCTAATGTTGAACAAGGAAAGAAAATTACAAATTTGA GTTCTAGGAAAGATGATGAGGGGATTGCATTGCCACATGAGCTTCCGAAAGTTTCAAATGAACA AAGGCTTGAAGAGTCGACTGGGGCCATATGGGGAACCTCAACACCTCTTGGTCTGTCAAAG
Genomic sequence	CTTTTGGCATCCAAGTCATCTGAAATGGCTAGTACTGATGACATCAGTGGTAAACTGAAAAGCA GTTCAGACTTGGTTATGTCCAGACAAGATAAACAAGTAGATAAATCTGATAAAAATGGGCTTTC TGATATTGAGCAGCTGGTGCAAGGGAAGAAATTCTCTAGGTACATTAGTTTAATTTGTTATAAT TTTTTCATCCTTTTTTTTTTCTTTGAAAAAGGCATGCAAAGCATTAGGATAAAGTATAAAATCC CAACTATGTTGGCACCTATACCCTATCCTTCATCTACCGCATACCTGAATTTATTAATTTTTTC CCTCCCTTGATTGAATGACTCATTTCTTAATTTTACGGTGAAAGTTATTCTTGTTGTAGATCAA ATCATTTACCCCCATATCTTTGAGCTTTATTGTCATCATTCTTGCACAGTAATAACTTTTTTGT TTTGCTGTTGAAGTGAAAAGCTTTTTTGTTATAAATTTTTTTGATTAATAAATTTATTTTTATC CATACAATAGATGTGGGAATGCCTTAGAGCACCAAAACATGTCTCATTTAGATATTGCATCCAT ACATTGGTATGATATTAGCAAACATGTCTCCTATTTGGTGAAGCTAGGGATCATTAAGATTTTT GGCCCAACGAGTTAGGTTCAAATTTGTTACTAAATAATGTCTTAGAGCATCTAAACATGTCTCA TTTAGATATTGCATCCATACATTGTTATGATATTAGCAAACATGTCTCCTATTTGGTGAAGCTG GGGATCATTAAGATTTTTGGCCCAACGAGTTAGGTTCAAATTTGTTACTAAATAAAATCTTTTT TATATATATTTATTTCCAAGGTAATATAGACTAAAAAAATTATATCAAATGCGAATATATATTA AATTAAAACATTATTGTTATGTACACATGCAAACATTAACATACCCTTTGAACTGACTCATGAG TTAATGAGTCAATGATGTGATTGTGAAAGCTTTGGTTTGGCTCATTTAACAATCAAACGATTAT TCTCATCTGATTGAGTTAATGAATTGGGCCGTGTAGTAGGATCAAGGGATGACTTGGCTTACCT TCATCCTAGCTTTGTATGCTCGTGCTGTTAGAAAATCTGTTCATGTACTCTCTTATTTAGGGTG TGTTAGGATGGAGGGGTTGGAAAGAGGATGAGGAGGGTTAATTTTTCATTTCTAAATTGAGTAG AGACTGTAGAGTATGAGGAGGGTTAATTTTATAAATAGGAATAAGGGTCATTTGGGAGGTTACA TGACAGTCTCATTTTATTCCATTTTTGTTTTTTTTCCTAATAAAAGAATATTTACTTAAGAAAT GAAATTTTTTACCTCTCATCCTTTCCTTTCCAAGCATACCCTTAGTGAAGAAAACTATTTTTTT GTTATTTATGGATGTACCATGTCTAAAAATCTTCAATCTCCTCGTGTAGAGATGAATTTGATCG TTTAGTGGCGGTATTAAATTTGAGGGTGATGGACCTTTCTAATGTTGAACAAGGAAAGAAAATT ACAAATTTGAGTTCTAGGAAAGATGATGAGGGGATTGCATTGCCACATGAGCTTCCGAAAGTTT CAAATGAACAAAGGCTTGAAGAGTCGACTGGGGCCATATGGGGAACCTCAACACCTCTTGGTCT GTCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.190005984

Conservation Information
Conserved circRNAs	NA
PMCS	0.190005984

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28671092-28672734(+)
28672626-28671121(+)
28672705-28671069(-)
28671087-28672618(-)
						
						Potential amino acid sequence
						
							MASTDDISGKLKSSSDLVMSRQDKQVDKSDKNGLSDIEQLVQGKKFSRDEFDRLVAVLNLRVMD
LSNVEQGKKITNLSSRKDDEGIALPHELPKVSNEQRLEESTGAIWGTSTPLGLSKLLASKSSEM
ASTDDISGKLKSSSDLVMSRQDKQVDKSDKNGLSDIEQLVQGKKFSRDEFDRLVAVLNLRVMDL
SNVEQGKKITNLSSRKDDEGIALPHELPKVSNEQRLEESTGAIWGTSTPLGLSKLLASKSSEMA
STDDISGKLKSSSDLVMSRQDKQVDKSDKNGLSDIEQLVQGKKFSRDEFDRLVAVLNLRVMDLS
NVEQGKKITNLSSRKDDEGIALPHELPKVSNEQRLEESTGAIWGTSTPLGLSKLLASKSSEMAS
TDDISGKLKSSSDLVMSRQDKQVDKSDKNGLSDIEQLVQGKKFSRDEFDRLVAVLNLRVMDLSN
VEQGKKITNLSSRKDDEGIALPHELPKVSNEQRLEESTGAIWGTSTPLGLSK(+)
MMRGLHCHMSFRKFQMNKGLKSRLGPYGEPQHLLVCQSFWHPSHLKWLVLMTSVVN*(+)
MAPVDSSSLCSFETFGSSCGNAIPSSSFLELKFVIFFPCSTLERSITLKFNTATKRSNSSLENF
FPCTSCSISESPFLSDLSTCLSCLDITKSELLFSLPLMSSVLAISDDLDAKSFDRPRGVEVPHM
APVDSSSLCSFETFGSSCGNAIPSSSFLELKFVIFFPCSTLERSITLKFNTATKRSNSSLENFF
PCTSCSISESPFLSDLSTCLSCLDITKSELLFSLPLMSSVLAISDDLDAKSFDRPRGVEVPHMA
PVDSSSLCSFETFGSSCGNAIPSSSFLELKFVIFFPCSTLERSITLKFNTATKRSNSSLENFFP
CTSCSISESPFLSDLSTCLSCLDITKSELLFSLPLMSSVLAISDDLDAKSFDRPRGVEVPHMAP
VDSSSLCSFETFGSSCGNAIPSSSFLELKFVIFFPCSTLERSITLKFNTATKRSNSSLENFFPC
TSCSISESPFLSDLSTCLSCLDITKSELLFSLPLMSSVLAISDDLDAK(-)
MTWMPKALTDQEVLRFPIWPQSTLQAFVHLKLSEAHVAMQSPHHLS*(-)
						
						Sponge-miRNAs
						
							gma-miR4372b 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28671092-28672734(+) 28672626-28671121(+) 28672705-28671069(-) 28671087-28672618(-)
Potential amino acid sequence	MASTDDISGKLKSSSDLVMSRQDKQVDKSDKNGLSDIEQLVQGKKFSRDEFDRLVAVLNLRVMD LSNVEQGKKITNLSSRKDDEGIALPHELPKVSNEQRLEESTGAIWGTSTPLGLSKLLASKSSEM ASTDDISGKLKSSSDLVMSRQDKQVDKSDKNGLSDIEQLVQGKKFSRDEFDRLVAVLNLRVMDL SNVEQGKKITNLSSRKDDEGIALPHELPKVSNEQRLEESTGAIWGTSTPLGLSKLLASKSSEMA STDDISGKLKSSSDLVMSRQDKQVDKSDKNGLSDIEQLVQGKKFSRDEFDRLVAVLNLRVMDLS NVEQGKKITNLSSRKDDEGIALPHELPKVSNEQRLEESTGAIWGTSTPLGLSKLLASKSSEMAS TDDISGKLKSSSDLVMSRQDKQVDKSDKNGLSDIEQLVQGKKFSRDEFDRLVAVLNLRVMDLSN VEQGKKITNLSSRKDDEGIALPHELPKVSNEQRLEESTGAIWGTSTPLGLSK(+) MMRGLHCHMSFRKFQMNKGLKSRLGPYGEPQHLLVCQSFWHPSHLKWLVLMTSVVN(+) MAPVDSSSLCSFETFGSSCGNAIPSSSFLELKFVIFFPCSTLERSITLKFNTATKRSNSSLENF FPCTSCSISESPFLSDLSTCLSCLDITKSELLFSLPLMSSVLAISDDLDAKSFDRPRGVEVPHM APVDSSSLCSFETFGSSCGNAIPSSSFLELKFVIFFPCSTLERSITLKFNTATKRSNSSLENFF PCTSCSISESPFLSDLSTCLSCLDITKSELLFSLPLMSSVLAISDDLDAKSFDRPRGVEVPHMA PVDSSSLCSFETFGSSCGNAIPSSSFLELKFVIFFPCSTLERSITLKFNTATKRSNSSLENFFP CTSCSISESPFLSDLSTCLSCLDITKSELLFSLPLMSSVLAISDDLDAKSFDRPRGVEVPHMAP VDSSSLCSFETFGSSCGNAIPSSSFLELKFVIFFPCSTLERSITLKFNTATKRSNSSLENFFPC TSCSISESPFLSDLSTCLSCLDITKSELLFSLPLMSSVLAISDDLDAK(-) MTWMPKALTDQEVLRFPIWPQSTLQAFVHLKLSEAHVAMQSPHHLS(-)
Sponge-miRNAs	gma-miR4372b
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2018

circRNA

Detail information of GLYMA_04G146900_circ_g.2

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