Plant Circular RNA Database

Detail information of GLYMA_20G004000_circ_g.4

			
						 General Information
					
						CircRNA Name
						GLYMA_20G004000_circ_g.4
					
						ID in PlantcircBase
						gma_circ_005105
					
						Alias
						Gm20circRNA1422, gma-circRNA2766
					
						Organism
						
							Glycine max						
					
						Position
						
							chr20: 384307-391464  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						Tophat, CIRI, 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.2 GLYMA_20G004000_circ_g.3 GLYMA_20G004000_circ_g.5 GLYMA_20G004000_circ_g.6 GLYMA_20G004000_circ_g.7 GLYMA_20G004000_circ_g.8 						
					
						Support reads
						NA
					
						Tissues
						leaf, root, stem, 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
						KRG89143:6
KRG89144:6
KRG89142:7

General Information
CircRNA Name	GLYMA_20G004000_circ_g.4
ID in PlantcircBase	gma_circ_005105
Alias	Gm20circRNA1422, gma-circRNA2766
Organism	Glycine max
Position	chr20: 384307-391464 JBrowse»
Reference genome	v2.0.38
Type	ue-circRNA
Identification method	Tophat, CIRI, 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.2 GLYMA_20G004000_circ_g.3 GLYMA_20G004000_circ_g.5 GLYMA_20G004000_circ_g.6 GLYMA_20G004000_circ_g.7 GLYMA_20G004000_circ_g.8
Support reads	NA
Tissues	leaf, root, stem, 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	KRG89143:6 KRG89144:6 KRG89142:7

			
						 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
CAAGTTGAGTTTGCAACAGCAGAAGCTGCGAAAAAActtccatgttaattctagcaacttgagt
cactcatttcaaaggagtgaaagaactcagcctgtgaaagcttcagagatttcaggggactggg
aacaagaa

						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: 733
Transcript exons: 384307-384412,385523-385614,385688-385805,387389-387477,
390527-390644,391181-391272,391347-391464
CTTCCATGTTAATTCTAGCAACTTGAGTCACTCATTTCAAAGGAGTGAAAGAACTCAGCCTGTG
AAAGCTTCAGAGATTTCAGGGGACTGGGAACAAGAAACTGAGTCAAAAATAATTGCTAACTGCA
AAGACCTAAGTGCTACTTCAAAGACAATATATGCTTCAAACTTGGCATACAGTATGGAGAAGGA
TGATATGGAGTTTCTTTTCAAAAATTGTGGAGAAATTGTTGATATCCGCCTACATACAGATCAT
AACGGGCGGTTTAAAGGCCATGGACATGTTGAGTTTGCAACCACAGAAGCTGCACAAAAAGCTC
TTGAATTGAATAATAAAGTATATCTGGGACGTCCTGTTGGAGTTTTTATTGCTAAAGGAAAGGG
TGAATATACCTCCAATAGAAGCAACTGGAGCAAGTCATTCCACCAGAGTGAACAAACTAAGCCC
ATCAAAAGTACAGAGAGTTCAGAGTACTGTGAGGAAGAGGTTGAGGGAAAAGCCTCCAATAGTT
ATTGGGAAAGTTCTAAAAGGGTAGCTACTCTGAAAGAACAAAATGCTCCACCAAAGACAATATA
TGTCAGAAACTTGTCATACAGAGTGGAACAGGCTGATATGGAAAATCTTTTCAAAGAATGTGGA
AAAATTGTTGATGTTCGTCTACATCGGAATCACAATGGTAGGTTAAATGGCTTTGGACAAGTTG
AGTTTGCAACAGCAGAAGCTGCGAAAAAA
						
						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 CAAGTTGAGTTTGCAACAGCAGAAGCTGCGAAAAAActtccatgttaattctagcaacttgagt cactcatttcaaaggagtgaaagaactcagcctgtgaaagcttcagagatttcaggggactggg aacaagaa
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: 733 Transcript exons: 384307-384412,385523-385614,385688-385805,387389-387477, 390527-390644,391181-391272,391347-391464 CTTCCATGTTAATTCTAGCAACTTGAGTCACTCATTTCAAAGGAGTGAAAGAACTCAGCCTGTG AAAGCTTCAGAGATTTCAGGGGACTGGGAACAAGAAACTGAGTCAAAAATAATTGCTAACTGCA AAGACCTAAGTGCTACTTCAAAGACAATATATGCTTCAAACTTGGCATACAGTATGGAGAAGGA TGATATGGAGTTTCTTTTCAAAAATTGTGGAGAAATTGTTGATATCCGCCTACATACAGATCAT AACGGGCGGTTTAAAGGCCATGGACATGTTGAGTTTGCAACCACAGAAGCTGCACAAAAAGCTC TTGAATTGAATAATAAAGTATATCTGGGACGTCCTGTTGGAGTTTTTATTGCTAAAGGAAAGGG TGAATATACCTCCAATAGAAGCAACTGGAGCAAGTCATTCCACCAGAGTGAACAAACTAAGCCC ATCAAAAGTACAGAGAGTTCAGAGTACTGTGAGGAAGAGGTTGAGGGAAAAGCCTCCAATAGTT ATTGGGAAAGTTCTAAAAGGGTAGCTACTCTGAAAGAACAAAATGCTCCACCAAAGACAATATA TGTCAGAAACTTGTCATACAGAGTGGAACAGGCTGATATGGAAAATCTTTTCAAAGAATGTGGA AAAATTGTTGATGTTCGTCTACATCGGAATCACAATGGTAGGTTAAATGGCTTTGGACAAGTTG AGTTTGCAACAGCAGAAGCTGCGAAAAAA
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
						0.150653115

Conservation Information
Conserved circRNAs	NA
PMCS	0.150653115

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							385599-384315(+)
391419-384315(+)
384315-391360(-)
						
						Potential amino acid sequence
						
							MEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELNNKVYLGRPVGVFIA
KGKGEYTSNRSNWSKSFHQSEQTKPIKSTESSEYCEEEVEGKASNSYWESSKRVATLKEQNAPP
KTIYVRNLSYRVEQADMENLFKECGKIVDVRLHRNHNGRLNGFGQVEFATAEAAKKLPC*(+)
MALDKLSLQQQKLRKNFHVNSSNLSHSFQRSERTQPVKASEISGDWEQETESKIIANCKDLSAT
SKTIYASNLAYSMEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELNNK
VYLGRPVGVFIAKGKGEYTSNRSNWSKSFHQSEQTKPIKSTESSEYCEEEVEGKASNSYWESSK
RVATLKEQNAPPKTIYVRNLSYRVEQADMENLFKECGKIVDVRLHRNHNGRLNGFGQVEFATAE
AAKKLPC*(+)
MEVFSQLLLLQTQLVQSHLTYHCDSDVDEHQQFFHIL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						cytoplasmic male sterility

Functional Information
Coding potential	Y
Potential coding position	385599-384315(+) 391419-384315(+) 384315-391360(-)
Potential amino acid sequence	MEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELNNKVYLGRPVGVFIA KGKGEYTSNRSNWSKSFHQSEQTKPIKSTESSEYCEEEVEGKASNSYWESSKRVATLKEQNAPP KTIYVRNLSYRVEQADMENLFKECGKIVDVRLHRNHNGRLNGFGQVEFATAEAAKKLPC(+) MALDKLSLQQQKLRKNFHVNSSNLSHSFQRSERTQPVKASEISGDWEQETESKIIANCKDLSAT SKTIYASNLAYSMEKDDMEFLFKNCGEIVDIRLHTDHNGRFKGHGHVEFATTEAAQKALELNNK VYLGRPVGVFIAKGKGEYTSNRSNWSKSFHQSEQTKPIKSTESSEYCEEEVEGKASNSYWESSK RVATLKEQNAPPKTIYVRNLSYRVEQADMENLFKECGKIVDVRLHRNHNGRLNGFGQVEFATAE AAKKLPC(+) MEVFSQLLLLQTQLVQSHLTYHCDSDVDEHQQFFHIL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	cytoplasmic male sterility

			
						 Other Information
					
						References
						Zhao et al., 2017a; Chen et al., 2018

circRNA

Detail information of GLYMA_20G004000_circ_g.4

Address

Any questions?

Supported by