Plant Circular RNA Database

Detail information of GLYMA_20G004000_circ_g.2

			
						 General Information
					
						CircRNA Name
						GLYMA_20G004000_circ_g.2
					
						ID in PlantcircBase
						gma_circ_007712
					
						Alias
						gma-circRNA2763
					
						Organism
						
							Glycine max						
					
						Position
						
							chr20: 382159-391464  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							GLYMA_20G004000						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							GLYMA_20G004000_circ_g.1 GLYMA_20G004000_circ_g.3 GLYMA_20G004000_circ_g.4 GLYMA_20G004000_circ_g.5 GLYMA_20G004000_circ_g.6 GLYMA_20G004000_circ_g.7 GLYMA_20G004000_circ_g.8 						
					
						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
						KRG89144:6
KRG89142:8
KRG89143:6

General Information
CircRNA Name	GLYMA_20G004000_circ_g.2
ID in PlantcircBase	gma_circ_007712
Alias	gma-circRNA2763
Organism	Glycine max
Position	chr20: 382159-391464 JBrowse»
Reference genome	v2.0.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	GLYMA_20G004000
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	GLYMA_20G004000_circ_g.1 GLYMA_20G004000_circ_g.3 GLYMA_20G004000_circ_g.4 GLYMA_20G004000_circ_g.5 GLYMA_20G004000_circ_g.6 GLYMA_20G004000_circ_g.7 GLYMA_20G004000_circ_g.8
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	KRG89144:6 KRG89142:8 KRG89143:6

			
						 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  
						
							ATGTGGAAAAATTGTTGATGTTCGTCTACATCGGAATCACAATGGTAGGTTAAATGGCTTTGGA
CAAGTTGAGTTTGCAACAGCAGAAGCTGCGAAAAAAgctcttcagttaaattatacagaattgt
taagatgccgcatcagagttgttttagctccacaaaagcataagcatactgccaatagaaggta
atttacga

						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: 822
Transcript exons: 382159-382247,384307-384412,385523-385614,385688-385805,
387389-387477,390527-390644,391181-391272,391347-391464
GCTCTTCAGTTAAATTATACAGAATTGTTAAGATGCCGCATCAGAGTTGTTTTAGCTCCACAAA
AGCATAAGCATACTGCCAATAGAAGCTTCCATGTTAATTCTAGCAACTTGAGTCACTCATTTCA
AAGGAGTGAAAGAACTCAGCCTGTGAAAGCTTCAGAGATTTCAGGGGACTGGGAACAAGAAACT
GAGTCAAAAATAATTGCTAACTGCAAAGACCTAAGTGCTACTTCAAAGACAATATATGCTTCAA
ACTTGGCATACAGTATGGAGAAGGATGATATGGAGTTTCTTTTCAAAAATTGTGGAGAAATTGT
TGATATCCGCCTACATACAGATCATAACGGGCGGTTTAAAGGCCATGGACATGTTGAGTTTGCA
ACCACAGAAGCTGCACAAAAAGCTCTTGAATTGAATAATAAAGTATATCTGGGACGTCCTGTTG
GAGTTTTTATTGCTAAAGGAAAGGGTGAATATACCTCCAATAGAAGCAACTGGAGCAAGTCATT
CCACCAGAGTGAACAAACTAAGCCCATCAAAAGTACAGAGAGTTCAGAGTACTGTGAGGAAGAG
GTTGAGGGAAAAGCCTCCAATAGTTATTGGGAAAGTTCTAAAAGGGTAGCTACTCTGAAAGAAC
AAAATGCTCCACCAAAGACAATATATGTCAGAAACTTGTCATACAGAGTGGAACAGGCTGATAT
GGAAAATCTTTTCAAAGAATGTGGAAAAATTGTTGATGTTCGTCTACATCGGAATCACAATGGT
AGGTTAAATGGCTTTGGACAAGTTGAGTTTGCAACAGCAGAAGCTGCGAAAAAA
						
						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	ATGTGGAAAAATTGTTGATGTTCGTCTACATCGGAATCACAATGGTAGGTTAAATGGCTTTGGA CAAGTTGAGTTTGCAACAGCAGAAGCTGCGAAAAAAgctcttcagttaaattatacagaattgt taagatgccgcatcagagttgttttagctccacaaaagcataagcatactgccaatagaaggta atttacga
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: 822 Transcript exons: 382159-382247,384307-384412,385523-385614,385688-385805, 387389-387477,390527-390644,391181-391272,391347-391464 GCTCTTCAGTTAAATTATACAGAATTGTTAAGATGCCGCATCAGAGTTGTTTTAGCTCCACAAA AGCATAAGCATACTGCCAATAGAAGCTTCCATGTTAATTCTAGCAACTTGAGTCACTCATTTCA AAGGAGTGAAAGAACTCAGCCTGTGAAAGCTTCAGAGATTTCAGGGGACTGGGAACAAGAAACT GAGTCAAAAATAATTGCTAACTGCAAAGACCTAAGTGCTACTTCAAAGACAATATATGCTTCAA ACTTGGCATACAGTATGGAGAAGGATGATATGGAGTTTCTTTTCAAAAATTGTGGAGAAATTGT TGATATCCGCCTACATACAGATCATAACGGGCGGTTTAAAGGCCATGGACATGTTGAGTTTGCA ACCACAGAAGCTGCACAAAAAGCTCTTGAATTGAATAATAAAGTATATCTGGGACGTCCTGTTG GAGTTTTTATTGCTAAAGGAAAGGGTGAATATACCTCCAATAGAAGCAACTGGAGCAAGTCATT CCACCAGAGTGAACAAACTAAGCCCATCAAAAGTACAGAGAGTTCAGAGTACTGTGAGGAAGAG GTTGAGGGAAAAGCCTCCAATAGTTATTGGGAAAGTTCTAAAAGGGTAGCTACTCTGAAAGAAC AAAATGCTCCACCAAAGACAATATATGTCAGAAACTTGTCATACAGAGTGGAACAGGCTGATAT GGAAAATCTTTTCAAAGAATGTGGAAAAATTGTTGATGTTCGTCTACATCGGAATCACAATGGT AGGTTAAATGGCTTTGGACAAGTTGAGTTTGCAACAGCAGAAGCTGCGAAAAAA
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
						0.139852227

Conservation Information
Conserved circRNAs	NA
PMCS	0.139852227

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							385599-391461(+)
						
						Potential amino acid sequence
						
							MEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELNNKVYLGRPVGVFIA
KGKGEYTSNRSNWSKSFHQSEQTKPIKSTESSEYCEEEVEGKASNSYWESSKRVATLKEQNAPP
KTIYVRNLSYRVEQADMENLFKECGKIVDVRLHRNHNGRLNGFGQVEFATAEAAKKALQLNYTE
LLRCRIRVVLAPQKHKHTANRSFHVNSSNLSHSFQRSERTQPVKASEISGDWEQETESKIIANC
KDLSATSKTIYASNLAYSMEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKA
LELNNKVYLGRPVGVFIAKGKGEYTSNRSNWSKSFHQSEQTKPIKSTESSEYCEEEVEGKASNS
YWESSKRVATLKEQNAPPKTIYVRNLSYRVEQADMENLFKECGKIVDVRLHRNHNGRLNGFGQV
EFATAEAAKKALQLNYTELLRCRIRVVLAPQKHKHTANRSFHVNSSNLSHSFQRSERTQPVKAS
EISGDWEQETESKIIANCKDLSATSKTIYASNLAYSMEKDDMEFLFKNCGEIVDIRLHTDHNGR
FKGHGHVEFATTEAAQKALELNNKVYLGRPVGVFIAKGKGEYTSNRSNWSKSFHQSEQTKPIKS
TESSEYCEEEVEGKASNSYWESSKRVATLKEQNAPPKTIYVRNLSYRVEQADMENLFKECGKIV
DVRLHRNHNGRLNGFGQVEFATAEAAKKALQLNYTELLRCRIRVVLAPQKHKHTANRSFHVNSS
NLSHSFQRSERTQPVKASEISGDWEQETESKIIANCKDLSATSKTIYASNLAYSMEKDDMEFLF
KNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELNNKVYLGRPVGVFIAKGKGEYTSNR
SNWSKSFHQSEQTKPIKSTESSEYCEEEVEGKASNSYWESSKRVATLKEQNAPPKTIYVRNLSY
RVEQADMENLFKECGKIVDVRLHRNHNGRLNGFGQVEFATAEAAKK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	385599-391461(+)
Potential amino acid sequence	MEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELNNKVYLGRPVGVFIA KGKGEYTSNRSNWSKSFHQSEQTKPIKSTESSEYCEEEVEGKASNSYWESSKRVATLKEQNAPP KTIYVRNLSYRVEQADMENLFKECGKIVDVRLHRNHNGRLNGFGQVEFATAEAAKKALQLNYTE LLRCRIRVVLAPQKHKHTANRSFHVNSSNLSHSFQRSERTQPVKASEISGDWEQETESKIIANC KDLSATSKTIYASNLAYSMEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKA LELNNKVYLGRPVGVFIAKGKGEYTSNRSNWSKSFHQSEQTKPIKSTESSEYCEEEVEGKASNS YWESSKRVATLKEQNAPPKTIYVRNLSYRVEQADMENLFKECGKIVDVRLHRNHNGRLNGFGQV EFATAEAAKKALQLNYTELLRCRIRVVLAPQKHKHTANRSFHVNSSNLSHSFQRSERTQPVKAS EISGDWEQETESKIIANCKDLSATSKTIYASNLAYSMEKDDMEFLFKNCGEIVDIRLHTDHNGR FKGHGHVEFATTEAAQKALELNNKVYLGRPVGVFIAKGKGEYTSNRSNWSKSFHQSEQTKPIKS TESSEYCEEEVEGKASNSYWESSKRVATLKEQNAPPKTIYVRNLSYRVEQADMENLFKECGKIV DVRLHRNHNGRLNGFGQVEFATAEAAKKALQLNYTELLRCRIRVVLAPQKHKHTANRSFHVNSS NLSHSFQRSERTQPVKASEISGDWEQETESKIIANCKDLSATSKTIYASNLAYSMEKDDMEFLF KNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELNNKVYLGRPVGVFIAKGKGEYTSNR SNWSKSFHQSEQTKPIKSTESSEYCEEEVEGKASNSYWESSKRVATLKEQNAPPKTIYVRNLSY RVEQADMENLFKECGKIVDVRLHRNHNGRLNGFGQVEFATAEAAKK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2018

circRNA

Detail information of GLYMA_20G004000_circ_g.2

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