Plant Circular RNA Database

Detail information of GLYMA_08G2649001_circ_g.1

			
						 General Information
					
						CircRNA Name
						GLYMA_08G2649001_circ_g.1
					
						ID in PlantcircBase
						gma_circ_002150
					
						Alias
						Gm08circRNA1979, gma-circRNA1100
					
						Organism
						
							Glycine max						
					
						Position
						
							chr8: 30760157-30761961  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, find_circ
					
						Parent gene
						
							GLYMA_08G2649001						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_08G2649001_circ_igg.1 GLYMA_08G2649001_circ_g.2 GLYMA_08G2649001_circ_g.3 						
					
						Support reads
						NA
					
						Tissues
						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  
						
							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
						KRH45323:5
KRH45324:5
KRH45325:5
KRH45328:5
KRH45327:5
KRH45326:5

General Information
CircRNA Name	GLYMA_08G2649001_circ_g.1
ID in PlantcircBase	gma_circ_002150
Alias	Gm08circRNA1979, gma-circRNA1100
Organism	Glycine max
Position	chr8: 30760157-30761961 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, find_circ
Parent gene	GLYMA_08G2649001
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_08G2649001_circ_igg.1 GLYMA_08G2649001_circ_g.2 GLYMA_08G2649001_circ_g.3
Support reads	NA
Tissues	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	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	KRH45323:5 KRH45324:5 KRH45325:5 KRH45328:5 KRH45327:5 KRH45326:5

			
						 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  
						
							AGTATAGTTTATCAACTGTACAGTGATTTCCCTTTGTTCTCTGATAGCATCCCTTATCCTGGAA
ACAGTTGCCTGATCTGTTTCTGGTCCTTGAAGAAACcttttgtattgctatccaagaaggattg
tcctttttgtgaggtcgtggaaagacaggttgggaatgaattgcccacaaatcttctggtctct
gcaacaaa

									
								

					

						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: 412
Transcript exons: 30760157-30760246,30760416-30760475,30761339-30761443,30
761570-30761619,30761855-30761961
CTTTTGTATTGCTATCCAAGAAGGATTGTCCTTTTTGTGAGGTCGTGGAAAGACAGGTTGGGAA
TGAATTGCCCACAAATCTTCTGGTCTCAAGTTGGCATCTGGAAGTTCTCGGACAGCTTCATCAA
CATTTTCTGCAGTGGCTTTCACCAACTTAGCACTTTGTTGCTCAGTTGTCTCAGACAGGCGGTT
TTTTAAGGGTTCTACATGATCACTTCCATCTAGTTGAACACCAATGAAGTATTGAAGTTCACCC
TTTTGGTCACGCATAGGTTGCAAGTGAAACAAATTCCAGAACTTTTTCCCACTCTTAGTATAGT
TTATCAACTGTACAGTGATTTCCCTTTGTTCTCTGATAGCATCCCTTATCCTGGAAACAGTTGC
CTGATCTGTTTCTGGTCCTTGAAGAAAC
						
					

						Genomic sequence
						
							CTTTTGTATTGCTATCCAAGAAGGATTGTCCTTTTTGTGAGGTCGTGGAAAGACAGGTTGGGAA
TGAATTGCCCACAAATCTTCTGGTCTCTGCAACAAAACAGATTCATATGATATCATCAAATATA
ACTGACAAAAAGCACCTTACCACTCTTCTTCAAATGACAGCTATGAAAAACATAAAATAATGCA
TTAAAGGAAATCTGAAAAATATATGCATAGGTAGGGTGTTGCTAACCCAAAAAAAGGAATACCT
TACCAAGTTGGCATCTGGAAGTTCTCGGACAGCTTCATCAACATTTTCTGCAGTGGCTTTCACC
TGATATGAAGATAATCAAGTATGTAAGAAATTTACAAATAAGAGGAACTCAATTGTATACTGAG
ATTCTATGACAATCTCATGGGGAACAACGTTTGATATCGAGATCAGAAACACATGTTAAACCAA
TAATAGTAGTAGTGAGAGTTGCTAACAGTTTGCAGCTATCTGCAGCTATTACCATCATAGAAAT
AAAGCAATTTTATATTTTCTGATGTCTCCTCAGCCTCCAATCTAACAAAGTATTTCTAGCATTT
TATAAAAATTCTTAGATGATAAATGGATGAAGATGCATATACAAAGTAGTAAGTACTAAGTAGA
TGTGACAGATATGAAAATTTACAGAATATGAACAACAGTGCTAAATCTAGCATTCACTTCTAAC
TCTATTATTTTCTAGGTGATTTCTACTCTGGTACTGCCAAATGCAACTCAACTAATAAGCAGGC
ATCTTCTACCAACTTCTACAGTGAAACAAGGAATAATAGTACTTACATGGTGGGAAAAGAAAGA
CAATGCACAATTGACAAATATAGACCTATGAACAAGTTATGCTAATCATGGAGACTAAAAAGCA
AGAACACAGCAGAATAAATTTTCATAGGTTGCACATATTATGCACATTGTCTTCCATAATATTT
AAACTGAAATTTTTGCTATTGAATAATGGTTATGCTAAATACTTATTGAAAGTATTCAAGAAAA
CATCTTAATAAGGGAACTTTCTAGTAACTCAAGTTATGTTAAAATGTAGAATTTGCATATTCTT
AGTTTTGCATATCACAAAGTGAAATATAAAAACAAAGCATCAAAGTAACTTGAACCAGTAAGTA
CAAAGCTAAGACTGAGAAGACAATACTCACCAACTTAGCACTTTGTTGCTCAGTTGTCTCAGAC
AGGCGGTTTTTTAAGGGTTCTACATGATCACTTCCATCTAGTTGAACACCAATGAAGTATTGAA
GTTCACCCTAAATACAAATCATTGAGAAAAACATTAGAAACTAAAAAGGGGGGAACACAATGTA
TTGTTTAATAGATATTGAATGTTCATGATTCAGATTAATTGTTTTCTACCATAACAGTATCACA
TTCACCTTTTGGTCACGCATAGGTTGCAAGTGAAACAAATTCCAGAACTTTTTCCCTACATATT
ATAAATTAGAAGAGTTTAACATGTAAACAATAAAATAAAACAAAAGATTAAAAAAAAAAAAGCA
TTTATATCTACATCAGTCAATTTCCACACTACTTTCATAATGTAACTTTTAATAAAAAAATGAA
TAAAGAGAAATACAACTTCTAGGAGGAAGGACAAGTCATCCTCCAACGAAAAGAGAGAGACAGT
TAGAAGTATAGTTATAATTTGACCAGTTATTTACCACTCTTAGTATAGTTTATCAACTGTACAG
TGATTTCCCTTTGTTCTCTGATAGCATCCCTTATCCTGGAAACAGTTGCCTGATCTGTTTCTGG
TCCTTGAAGAAAC
						
					

			
		

Sequences
Splice junction sequence	AGTATAGTTTATCAACTGTACAGTGATTTCCCTTTGTTCTCTGATAGCATCCCTTATCCTGGAA ACAGTTGCCTGATCTGTTTCTGGTCCTTGAAGAAACcttttgtattgctatccaagaaggattg tcctttttgtgaggtcgtggaaagacaggttgggaatgaattgcccacaaatcttctggtctct gcaacaaa
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: 412 Transcript exons: 30760157-30760246,30760416-30760475,30761339-30761443,30 761570-30761619,30761855-30761961 CTTTTGTATTGCTATCCAAGAAGGATTGTCCTTTTTGTGAGGTCGTGGAAAGACAGGTTGGGAA TGAATTGCCCACAAATCTTCTGGTCTCAAGTTGGCATCTGGAAGTTCTCGGACAGCTTCATCAA CATTTTCTGCAGTGGCTTTCACCAACTTAGCACTTTGTTGCTCAGTTGTCTCAGACAGGCGGTT TTTTAAGGGTTCTACATGATCACTTCCATCTAGTTGAACACCAATGAAGTATTGAAGTTCACCC TTTTGGTCACGCATAGGTTGCAAGTGAAACAAATTCCAGAACTTTTTCCCACTCTTAGTATAGT TTATCAACTGTACAGTGATTTCCCTTTGTTCTCTGATAGCATCCCTTATCCTGGAAACAGTTGC CTGATCTGTTTCTGGTCCTTGAAGAAAC
Genomic sequence	CTTTTGTATTGCTATCCAAGAAGGATTGTCCTTTTTGTGAGGTCGTGGAAAGACAGGTTGGGAA TGAATTGCCCACAAATCTTCTGGTCTCTGCAACAAAACAGATTCATATGATATCATCAAATATA ACTGACAAAAAGCACCTTACCACTCTTCTTCAAATGACAGCTATGAAAAACATAAAATAATGCA TTAAAGGAAATCTGAAAAATATATGCATAGGTAGGGTGTTGCTAACCCAAAAAAAGGAATACCT TACCAAGTTGGCATCTGGAAGTTCTCGGACAGCTTCATCAACATTTTCTGCAGTGGCTTTCACC TGATATGAAGATAATCAAGTATGTAAGAAATTTACAAATAAGAGGAACTCAATTGTATACTGAG ATTCTATGACAATCTCATGGGGAACAACGTTTGATATCGAGATCAGAAACACATGTTAAACCAA TAATAGTAGTAGTGAGAGTTGCTAACAGTTTGCAGCTATCTGCAGCTATTACCATCATAGAAAT AAAGCAATTTTATATTTTCTGATGTCTCCTCAGCCTCCAATCTAACAAAGTATTTCTAGCATTT TATAAAAATTCTTAGATGATAAATGGATGAAGATGCATATACAAAGTAGTAAGTACTAAGTAGA TGTGACAGATATGAAAATTTACAGAATATGAACAACAGTGCTAAATCTAGCATTCACTTCTAAC TCTATTATTTTCTAGGTGATTTCTACTCTGGTACTGCCAAATGCAACTCAACTAATAAGCAGGC ATCTTCTACCAACTTCTACAGTGAAACAAGGAATAATAGTACTTACATGGTGGGAAAAGAAAGA CAATGCACAATTGACAAATATAGACCTATGAACAAGTTATGCTAATCATGGAGACTAAAAAGCA AGAACACAGCAGAATAAATTTTCATAGGTTGCACATATTATGCACATTGTCTTCCATAATATTT AAACTGAAATTTTTGCTATTGAATAATGGTTATGCTAAATACTTATTGAAAGTATTCAAGAAAA CATCTTAATAAGGGAACTTTCTAGTAACTCAAGTTATGTTAAAATGTAGAATTTGCATATTCTT AGTTTTGCATATCACAAAGTGAAATATAAAAACAAAGCATCAAAGTAACTTGAACCAGTAAGTA CAAAGCTAAGACTGAGAAGACAATACTCACCAACTTAGCACTTTGTTGCTCAGTTGTCTCAGAC AGGCGGTTTTTTAAGGGTTCTACATGATCACTTCCATCTAGTTGAACACCAATGAAGTATTGAA GTTCACCCTAAATACAAATCATTGAGAAAAACATTAGAAACTAAAAAGGGGGGAACACAATGTA TTGTTTAATAGATATTGAATGTTCATGATTCAGATTAATTGTTTTCTACCATAACAGTATCACA TTCACCTTTTGGTCACGCATAGGTTGCAAGTGAAACAAATTCCAGAACTTTTTCCCTACATATT ATAAATTAGAAGAGTTTAACATGTAAACAATAAAATAAAACAAAAGATTAAAAAAAAAAAAGCA TTTATATCTACATCAGTCAATTTCCACACTACTTTCATAATGTAACTTTTAATAAAAAAATGAA TAAAGAGAAATACAACTTCTAGGAGGAAGGACAAGTCATCCTCCAACGAAAAGAGAGAGACAGT TAGAAGTATAGTTATAATTTGACCAGTTATTTACCACTCTTAGTATAGTTTATCAACTGTACAG TGATTTCCCTTTGTTCTCTGATAGCATCCCTTATCCTGGAAACAGTTGCCTGATCTGTTTCTGG TCCTTGAAGAAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.186260928

Conservation Information
Conserved circRNAs	NA
PMCS	0.186260928

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30761586-30761862(-)
						
						Potential amino acid sequence
						
							MRDQKGELQYFIGVQLDGSDHVEPLKNRLSETTEQQSAKLVKATAENVDEAVRELPDANLRPED
LWAIHSQPVFPRPHKKDNPSWIAIQKVSSRTRNRSGNCFQDKGCYQRTKGNHCTVDKLY*(-)
						
						Sponge-miRNAs
						
							gma-miR1533 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						cytoplasmic male sterility

Functional Information
Coding potential	Y
Potential coding position	30761586-30761862(-)
Potential amino acid sequence	MRDQKGELQYFIGVQLDGSDHVEPLKNRLSETTEQQSAKLVKATAENVDEAVRELPDANLRPED LWAIHSQPVFPRPHKKDNPSWIAIQKVSSRTRNRSGNCFQDKGCYQRTKGNHCTVDKLY*(-)
Sponge-miRNAs	gma-miR1533
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_08G2649001_circ_g.1

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