Plant Circular RNA Database

Detail information of GLYMA_18G118100_circ_g.1

			
						 General Information
					
						CircRNA Name
						GLYMA_18G118100_circ_g.1
					
						ID in PlantcircBase
						gma_circ_007531
					
						Alias
						gma-circRNA2454
					
						Organism
						
							Glycine max						
					
						Position
						
							chr18: 14576883-14578195  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							GLYMA_18G118100						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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
						KRG99063:4
KRG99065:4
KRG99064:4

General Information
CircRNA Name	GLYMA_18G118100_circ_g.1
ID in PlantcircBase	gma_circ_007531
Alias	gma-circRNA2454
Organism	Glycine max
Position	chr18: 14576883-14578195 JBrowse»
Reference genome	v2.0.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	GLYMA_18G118100
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	NA
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	KRG99063:4 KRG99065:4 KRG99064:4

			
						 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  
						
							TGATATTGTTGTGCTGCGGAATCTTCTAAAGCCAATTTGTGACCTGAATGATGCAACCTCATTA
TGCAGACATCTTGAATCCTTTTACATCTTACGCAAGactgtctggagcaaattgatgcacaaag
ggtgttaggatatgttcttttcaaggacgggaaaaaaactaagctgccttatcctttggagaac
tttcatgc

									
								

					

						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: 842
Transcript exons: 14576883-14577057,14577214-14577385,14577546-14577764,14
577920-14578195
ACTGTCTGGAGCAAATTGATGCACAAAGGGTGTTAGGATATGTTCTTTTCAAGGACGGGAAAAA
AACTAAGCTGCCTTATCCTTTGGAGAACTTTCATGCTGATGTGGCTGGTAGGAGCTTCCATAAC
GGACGGTTTATACAGAGGATGAGAGAAAAAGCTGCTACTCTGCACCATGTACGAATGGAGCAGG
GCACTGTAACATCTCTTCTTGAACAGGATAATGGAACTATTATAGGGGTTCAGTACAAAACTAA
AGATGGCCAAAAACTTAAAGCATATGCTCCCTTCACAATTGTTTGTGATGGCTGTTTCTCAAAT
CTACGTCGGTCTCTCTGCTACCCCAAGGTAGAAGTACCCTCCTGTTTCGTGGGTTTAGTTCTGG
AGAATTGTCAACTCCCACTTGAAAATTACGGGCATGTTATTTTGGCTGATCCTTCCCCTATCTT
ATTTTATCGCATCAGCAGCACTGAAGTTCGGTGCTTAGTTGATATACCTGGTCAAAAAGTTTCT
CCTGTTGGTAAAGGTGGAATGGCCAACTACCTTAGGGCTATGGTGGCTTCCCAGATTCCACCCG
AGCTTCGTGATGCTTTCATATCTGCAATTGATCGAGGAAATATCAGAACCATGCCTAACAGTAG
CATGGCAGCAGATCCATATCCTACTCCTGGAGCTCTGTTAATGGGTGATGCTTTCAACATGCGT
CATCCTTTGACTGGTGGAGGAATGACAGTGGCACTGTCTGATATTGTTGTGCTGCGGAATCTTC
TAAAGCCAATTTGTGACCTGAATGATGCAACCTCATTATGCAGACATCTTGAATCCTTTTACAT
CTTACGCAAG
						
					

						Genomic sequence
						
							ACTGTCTGGAGCAAATTGATGCACAAAGGGTGTTAGGATATGTTCTTTTCAAGGACGGGAAAAA
AACTAAGCTGCCTTATCCTTTGGAGAACTTTCATGCTGATGTGGCTGGTAGGAGCTTCCATAAC
GGACGGTTTATACAGAGGATGAGAGAAAAAGCTGCTACTCTGCACCAGTAGTCCTTCTTAATCT
ATTGTGATTGTTAATTTACTTGTTAAAGTTACTTTGGCTACAAAAAAAGCCAAAAGCTAGCTAA
TTTGTCATTGAAATTATTGTTTGTGCAGTGTATTCTTTTTGTCTGATAGTATCATCTGCTTTGT
TTACTGTTCAGTGTACGAATGGAGCAGGGCACTGTAACATCTCTTCTTGAACAGGATAATGGAA
CTATTATAGGGGTTCAGTACAAAACTAAAGATGGCCAAAAACTTAAAGCATATGCTCCCTTCAC
AATTGTTTGTGATGGCTGTTTCTCAAATCTACGTCGGTCTCTCTGCTACCCCAAGGTTGAACTG
TTCTAAATAAGTTGAGTTGCAAAAATATCATTTTTCTTTTTTAATGATATCAATTCAAAGACAG
TTTGCCGAAACTGCAAAATCTATAGAATTTTGTCAGTTGTGTACCAGTTTGCTTGACTTGCCTG
ATATATTATTGAACACTTGCCAGGTAGAAGTACCCTCCTGTTTCGTGGGTTTAGTTCTGGAGAA
TTGTCAACTCCCACTTGAAAATTACGGGCATGTTATTTTGGCTGATCCTTCCCCTATCTTATTT
TATCGCATCAGCAGCACTGAAGTTCGGTGCTTAGTTGATATACCTGGTCAAAAAGTTTCTCCTG
TTGGTAAAGGTGGAATGGCCAACTACCTTAGGGCTATGGTGGCTTCCCAGGTATCTGTTATGAT
CCTGCATTCCTGCTTGAGTTGTGGATGGTCCATCTGTGATTTGTCATTACTTTTCTGTCCACAT
GTATTCAATTAAGAGGGAAAATAATTGATTTCTGCCTTCATCTTCCTATGTATCTGGTGTAACT
TTTCATTGTCCAGATTCCACCCGAGCTTCGTGATGCTTTCATATCTGCAATTGATCGAGGAAAT
ATCAGAACCATGCCTAACAGTAGCATGGCAGCAGATCCATATCCTACTCCTGGAGCTCTGTTAA
TGGGTGATGCTTTCAACATGCGTCATCCTTTGACTGGTGGAGGAATGACAGTGGCACTGTCTGA
TATTGTTGTGCTGCGGAATCTTCTAAAGCCAATTTGTGACCTGAATGATGCAACCTCATTATGC
AGACATCTTGAATCCTTTTACATCTTACGCAAG
						
					

			
		

Sequences
Splice junction sequence	TGATATTGTTGTGCTGCGGAATCTTCTAAAGCCAATTTGTGACCTGAATGATGCAACCTCATTA TGCAGACATCTTGAATCCTTTTACATCTTACGCAAGactgtctggagcaaattgatgcacaaag ggtgttaggatatgttcttttcaaggacgggaaaaaaactaagctgccttatcctttggagaac tttcatgc
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: 842 Transcript exons: 14576883-14577057,14577214-14577385,14577546-14577764,14 577920-14578195 ACTGTCTGGAGCAAATTGATGCACAAAGGGTGTTAGGATATGTTCTTTTCAAGGACGGGAAAAA AACTAAGCTGCCTTATCCTTTGGAGAACTTTCATGCTGATGTGGCTGGTAGGAGCTTCCATAAC GGACGGTTTATACAGAGGATGAGAGAAAAAGCTGCTACTCTGCACCATGTACGAATGGAGCAGG GCACTGTAACATCTCTTCTTGAACAGGATAATGGAACTATTATAGGGGTTCAGTACAAAACTAA AGATGGCCAAAAACTTAAAGCATATGCTCCCTTCACAATTGTTTGTGATGGCTGTTTCTCAAAT CTACGTCGGTCTCTCTGCTACCCCAAGGTAGAAGTACCCTCCTGTTTCGTGGGTTTAGTTCTGG AGAATTGTCAACTCCCACTTGAAAATTACGGGCATGTTATTTTGGCTGATCCTTCCCCTATCTT ATTTTATCGCATCAGCAGCACTGAAGTTCGGTGCTTAGTTGATATACCTGGTCAAAAAGTTTCT CCTGTTGGTAAAGGTGGAATGGCCAACTACCTTAGGGCTATGGTGGCTTCCCAGATTCCACCCG AGCTTCGTGATGCTTTCATATCTGCAATTGATCGAGGAAATATCAGAACCATGCCTAACAGTAG CATGGCAGCAGATCCATATCCTACTCCTGGAGCTCTGTTAATGGGTGATGCTTTCAACATGCGT CATCCTTTGACTGGTGGAGGAATGACAGTGGCACTGTCTGATATTGTTGTGCTGCGGAATCTTC TAAAGCCAATTTGTGACCTGAATGATGCAACCTCATTATGCAGACATCTTGAATCCTTTTACAT CTTACGCAAG
Genomic sequence	ACTGTCTGGAGCAAATTGATGCACAAAGGGTGTTAGGATATGTTCTTTTCAAGGACGGGAAAAA AACTAAGCTGCCTTATCCTTTGGAGAACTTTCATGCTGATGTGGCTGGTAGGAGCTTCCATAAC GGACGGTTTATACAGAGGATGAGAGAAAAAGCTGCTACTCTGCACCAGTAGTCCTTCTTAATCT ATTGTGATTGTTAATTTACTTGTTAAAGTTACTTTGGCTACAAAAAAAGCCAAAAGCTAGCTAA TTTGTCATTGAAATTATTGTTTGTGCAGTGTATTCTTTTTGTCTGATAGTATCATCTGCTTTGT TTACTGTTCAGTGTACGAATGGAGCAGGGCACTGTAACATCTCTTCTTGAACAGGATAATGGAA CTATTATAGGGGTTCAGTACAAAACTAAAGATGGCCAAAAACTTAAAGCATATGCTCCCTTCAC AATTGTTTGTGATGGCTGTTTCTCAAATCTACGTCGGTCTCTCTGCTACCCCAAGGTTGAACTG TTCTAAATAAGTTGAGTTGCAAAAATATCATTTTTCTTTTTTAATGATATCAATTCAAAGACAG TTTGCCGAAACTGCAAAATCTATAGAATTTTGTCAGTTGTGTACCAGTTTGCTTGACTTGCCTG ATATATTATTGAACACTTGCCAGGTAGAAGTACCCTCCTGTTTCGTGGGTTTAGTTCTGGAGAA TTGTCAACTCCCACTTGAAAATTACGGGCATGTTATTTTGGCTGATCCTTCCCCTATCTTATTT TATCGCATCAGCAGCACTGAAGTTCGGTGCTTAGTTGATATACCTGGTCAAAAAGTTTCTCCTG TTGGTAAAGGTGGAATGGCCAACTACCTTAGGGCTATGGTGGCTTCCCAGGTATCTGTTATGAT CCTGCATTCCTGCTTGAGTTGTGGATGGTCCATCTGTGATTTGTCATTACTTTTCTGTCCACAT GTATTCAATTAAGAGGGAAAATAATTGATTTCTGCCTTCATCTTCCTATGTATCTGGTGTAACT TTTCATTGTCCAGATTCCACCCGAGCTTCGTGATGCTTTCATATCTGCAATTGATCGAGGAAAT ATCAGAACCATGCCTAACAGTAGCATGGCAGCAGATCCATATCCTACTCCTGGAGCTCTGTTAA TGGGTGATGCTTTCAACATGCGTCATCCTTTGACTGGTGGAGGAATGACAGTGGCACTGTCTGA TATTGTTGTGCTGCGGAATCTTCTAAAGCCAATTTGTGACCTGAATGATGCAACCTCATTATGC AGACATCTTGAATCCTTTTACATCTTACGCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.392120479

Conservation Information
Conserved circRNAs	NA
PMCS	0.392120479

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							14578144-14576898(+)
14577030-14576915(+)
						
						Potential amino acid sequence
						
							MMQPHYADILNPFTSYARLSGAN*(+)
MREKAATLHHVRMEQGTVTSLLEQDNGTIIGVQYKTKDGQKLKAYAPFTIVCDGCFSNLRRSLC
YPKVEVPSCFVGLVLENCQLPLENYGHVILADPSPILFYRISSTEVRCLVDIPGQKVSPVGKGG
MANYLRAMVASQIPPELRDAFISAIDRGNIRTMPNSSMAADPYPTPGALLMGDAFNMRHPLTGG
GMTVALSDIVVLRNLLKPICDLNDATSLCRHLESFYILRKTVWSKLMHKGC*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						cytoplasmic male sterility

Functional Information
Coding potential	Y
Potential coding position	14578144-14576898(+) 14577030-14576915(+)
Potential amino acid sequence	MMQPHYADILNPFTSYARLSGAN(+) MREKAATLHHVRMEQGTVTSLLEQDNGTIIGVQYKTKDGQKLKAYAPFTIVCDGCFSNLRRSLC YPKVEVPSCFVGLVLENCQLPLENYGHVILADPSPILFYRISSTEVRCLVDIPGQKVSPVGKGG MANYLRAMVASQIPPELRDAFISAIDRGNIRTMPNSSMAADPYPTPGALLMGDAFNMRHPLTGG GMTVALSDIVVLRNLLKPICDLNDATSLCRHLESFYILRKTVWSKLMHKGC(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	cytoplasmic male sterility

			
						 Other Information
					
						References
						Chen et al., 2018

circRNA

Detail information of GLYMA_18G118100_circ_g.1

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