Plant Circular RNA Database

Detail information of GLYMA_19G116700_circ_g.2

			
						 General Information
					
						CircRNA Name
						GLYMA_19G116700_circ_g.2
					
						ID in PlantcircBase
						gma_circ_004936
					
						Alias
						Gm19circRNA2414
					
						Organism
						
							Glycine max						
					
						Position
						
							chr19: 37215477-37243090  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI
					
						Parent gene
						
							GLYMA_19G116700						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_19G116700_circ_g.3 GLYMA_19G116700_circ_g.4 GLYMA_19G116700_circ_g.5 						
					
						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  
						
							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
						KRG94904:10
KRG94903:10

General Information
CircRNA Name	GLYMA_19G116700_circ_g.2
ID in PlantcircBase	gma_circ_004936
Alias	Gm19circRNA2414
Organism	Glycine max
Position	chr19: 37215477-37243090 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI
Parent gene	GLYMA_19G116700
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_19G116700_circ_g.3 GLYMA_19G116700_circ_g.4 GLYMA_19G116700_circ_g.5
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	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	KRG94904:10 KRG94903:10

			
						 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  
						
							AAAGTTCGGGAGGAGGCAACTTGATGGCATCCAACATCTTTGGCTTCCCACATTTCTTAACCAA
AGCTTCTACCTCATTACAGATTGCTCGCACTGCATTcttcataacatgaatcagaggagcatac
ttcgaaagtctttttgctggaggaggtgaggaattcatcattgctccttgattaggtaatagaa
gggagaac

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AAAGTTCGGGAGGAGGCAACTTGATGGCATCCAACATCTTTGGCTTCCCACATTTCTTAACCAA AGCTTCTACCTCATTACAGATTGCTCGCACTGCATTcttcataacatgaatcagaggagcatac ttcgaaagtctttttgctggaggaggtgaggaattcatcattgctccttgattaggtaatagaa gggagaac
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	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.001799125

Conservation Information
Conserved circRNAs	NA
PMCS	0.001799125

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							37242984-37215530(+)
37243015-37215486(+)
37243029-37215479(-)
						
					

						Potential amino acid sequence
						
							MFIKFGRRQLDGIQHLWLPTFLNQSFYLITDCSHCILHNMNQRSILRKSFCWRR*(+)
MASNIFGFPHFLTKASTSLQIARTAFFIT*(+)
MLDAIKLPPPELYEHVEAIASDELVKVLQIRNKIPRRKALSSLEEKVLKILTENGFVSNDSTLR
SNSETIAEILEVEDEDEEVIVDGEVDEGDVHIKPTPRKPALLFSEVDVKLVFKEVTSKYWRKRM
VEGGKRSDGRTPDGIRPIYSRCGLLPRAHGSTLFTRGETQALAVVTLGDKQMAQRIDSLDGVDE
FKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERSLEPILPSEDDFPYTIRVESTITESNG
SSSMASVCGGCLALQDAGVPIKGSIAGIAMGMVLDTKEFGGDGTPLILSDITGSEDASGDMDFK
VAGNEDGITAFQMDIKVGGITLPIMRKALLQARDGRKHILGAMMNSSPPPAKRLSKYAPLIHVM
KNAVRAICNEVEALVKKCGKPKMLDAIKLPPPELYEHVEAIASDELVKVLQIRNKIPRRKALSS
LEEKVLKILTENGFVSNDSTLRSNSETIAEILEVEDEDEEVIVDGEVDEGDVHIKPTPRKPALL
FSEVDVKLVFKEVTSKYWRKRMVEGGKRSDGRTPDGIRPIYSRCGLLPRAHGSTLFTRGETQAL
AVVTLGDKQMAQRIDSLDGVDEFKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERSLEPI
LPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKGSIAGIAMGMVLDTKEFGGD
GTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPIMRKALLQARDGRKHILGA
MMNSSPPPAKRLSKYAPLIHVMKNAVRAICNEVEALVKKCGKPKMLDAIKLPPPELYEHVEAIA
SDELVKVLQIRNKIPRRKALSSLEEKVLKILTENGFVSNDSTLRSNSETIAEILEVEDEDEEVI
VDGEVDEGDVHIKPTPRKPALLFSEVDVKLVFKEVTSKYWRKRMVEGGKRSDGRTPDGIRPIYS
RCGLLPRAHGSTLFTRGETQALAVVTLGDKQMAQRIDSLDGVDEFKRFYLQYSFPPSCVGEVGR
IGAPSRREIGHGMLAERSLEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVP
IKGSIAGIAMGMVLDTKEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGI
TLPIMRKALLQARDGRKHILGAMMNSSPPPAKRLSKYAPLIHVMKNAVRAICNEVEALVKKCGK
PKMLDAIKLPPPELYEHVEAIASDELVKVLQIRNKIPRRKALSSLEEKVLKILTENGFVSNDST
LRSNSETIAEILEVEDEDEEVIVDGEVDEGDVHIKPTPRKPALLFSEVDVKLVFKEVTSKYWRK
RMVEGGKRSDGRTPDGIRPIYSRCGLLPRAHGSTLFTRGETQALAVVTLGDKQMAQRIDSLDGV
DEFKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERSLEPILPSEDDFPYTIRVESTITES
NGSSSMASVCGGCLALQDAGVPIKGSIAGIAMGMVLDTKEFGGDGTPLILSDITGSEDASGDMD
FKVAGNEDGITAFQMDIKVGGITLPIMRKALLQARDGRKHILGAMMNSSPPPAKRLSKYAPLIH
VMK(-)
						
					

						Sponge-miRNAs
						
							gma-miR169l-3p 						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	37242984-37215530(+) 37243015-37215486(+) 37243029-37215479(-)
Potential amino acid sequence	MFIKFGRRQLDGIQHLWLPTFLNQSFYLITDCSHCILHNMNQRSILRKSFCWRR(+) MASNIFGFPHFLTKASTSLQIARTAFFIT(+) MLDAIKLPPPELYEHVEAIASDELVKVLQIRNKIPRRKALSSLEEKVLKILTENGFVSNDSTLR SNSETIAEILEVEDEDEEVIVDGEVDEGDVHIKPTPRKPALLFSEVDVKLVFKEVTSKYWRKRM VEGGKRSDGRTPDGIRPIYSRCGLLPRAHGSTLFTRGETQALAVVTLGDKQMAQRIDSLDGVDE FKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERSLEPILPSEDDFPYTIRVESTITESNG SSSMASVCGGCLALQDAGVPIKGSIAGIAMGMVLDTKEFGGDGTPLILSDITGSEDASGDMDFK VAGNEDGITAFQMDIKVGGITLPIMRKALLQARDGRKHILGAMMNSSPPPAKRLSKYAPLIHVM KNAVRAICNEVEALVKKCGKPKMLDAIKLPPPELYEHVEAIASDELVKVLQIRNKIPRRKALSS LEEKVLKILTENGFVSNDSTLRSNSETIAEILEVEDEDEEVIVDGEVDEGDVHIKPTPRKPALL FSEVDVKLVFKEVTSKYWRKRMVEGGKRSDGRTPDGIRPIYSRCGLLPRAHGSTLFTRGETQAL AVVTLGDKQMAQRIDSLDGVDEFKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERSLEPI LPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKGSIAGIAMGMVLDTKEFGGD GTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPIMRKALLQARDGRKHILGA MMNSSPPPAKRLSKYAPLIHVMKNAVRAICNEVEALVKKCGKPKMLDAIKLPPPELYEHVEAIA SDELVKVLQIRNKIPRRKALSSLEEKVLKILTENGFVSNDSTLRSNSETIAEILEVEDEDEEVI VDGEVDEGDVHIKPTPRKPALLFSEVDVKLVFKEVTSKYWRKRMVEGGKRSDGRTPDGIRPIYS RCGLLPRAHGSTLFTRGETQALAVVTLGDKQMAQRIDSLDGVDEFKRFYLQYSFPPSCVGEVGR IGAPSRREIGHGMLAERSLEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVP IKGSIAGIAMGMVLDTKEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGI TLPIMRKALLQARDGRKHILGAMMNSSPPPAKRLSKYAPLIHVMKNAVRAICNEVEALVKKCGK PKMLDAIKLPPPELYEHVEAIASDELVKVLQIRNKIPRRKALSSLEEKVLKILTENGFVSNDST LRSNSETIAEILEVEDEDEEVIVDGEVDEGDVHIKPTPRKPALLFSEVDVKLVFKEVTSKYWRK RMVEGGKRSDGRTPDGIRPIYSRCGLLPRAHGSTLFTRGETQALAVVTLGDKQMAQRIDSLDGV DEFKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERSLEPILPSEDDFPYTIRVESTITES NGSSSMASVCGGCLALQDAGVPIKGSIAGIAMGMVLDTKEFGGDGTPLILSDITGSEDASGDMD FKVAGNEDGITAFQMDIKVGGITLPIMRKALLQARDGRKHILGAMMNSSPPPAKRLSKYAPLIH VMK(-)
Sponge-miRNAs	gma-miR169l-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_19G116700_circ_g.2

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