Plant Circular RNA Database

Detail information of GLYMA_04G096600_circ_g.4

			
						 General Information
					
						CircRNA Name
						GLYMA_04G096600_circ_g.4
					
						ID in PlantcircBase
						gma_circ_008136
					
						Alias
						circRNA4040
					
						Organism
						
							Glycine max						
					
						Position
						
							chr4: 8718117-8720640  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI, CIRCexplorer
					
						Parent gene
						
							GLYMA_04G096600						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_04G096600_circ_g.3 						
					
						Support reads
						NA
					
						Tissues
						pod
					
						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
						KRH62260:3

General Information
CircRNA Name	GLYMA_04G096600_circ_g.4
ID in PlantcircBase	gma_circ_008136
Alias	circRNA4040
Organism	Glycine max
Position	chr4: 8718117-8720640 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	CIRI, CIRCexplorer
Parent gene	GLYMA_04G096600
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_04G096600_circ_g.3
Support reads	NA
Tissues	pod
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	KRH62260:3

			
						 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  
						
							CTTTGATGGACTCTTGCTCTTCAAAAGCAACTCTTCGTTCAAATTCACAGTGACCTCTCCACTG
GAAATGTCCATATTCTTAATAACTATGCCCACTTCTctgtatcgggatatatacaaaagagatc
aaatccaacttcaatatctccaagatagaagaaccagcttctctaagaagctgtaataacaatc
aggcaaaa

									
								

					

						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
						
							CTGTATCGGGATATATACAAAAGAGATCAAATCCAACTTCAATATCTCCAAGATAGAAGAACCA
GCTTCTCTAAGAAGCTGTAATAACAATCAGGCAAAAGAAAACTTGTCAGCAAGAAACAAAACAG
TGAAAAGTAGGAATCATATCACAAGCTCTGCCAAAATAAACAGTCACACTCCATACATGAATTT
CACTAAACTCCAGTTGGAAATCAAGGCGTGTACTCTCCCCAAGATCCTCAGTGGATCGTGATTT
GGTGCTTTTCAATTGGATGCCCATGATGTTGTTTTCAATATAAAGACCATGCTCACGATGCACA
AAACTCACATCCAGCTTTGGTAGATTGAAGCTGACCTATCAACAAAAATATACTAATACAGTTG
ACATTAAAACAATTTAAAAAACCCTTAAAAGCATTTTTAAACTAACTTTAGATTAGATAAAACC
AACAAACATAACCAAAATTGACAATCAATTTAAGCATTATAAAGTGTATAAACAATTTGAATTT
CAATGGGACACCAGACTTAATTAAATGCTCAACGGAAGCCAAAATTCACCAAGAACACAAACAC
CGGAACACATACTCAGAGAGACTTACAAGTGAAGGAACCACATTTTGCCCAAAAGCCAAATTCT
AGTGTCCAGCAAGCCATAAACAGTAACAGAATCAAGACTTTGAAGCAACAAGATCATAATTTAT
GCAGTTTCTCTACCCTTCATATTTCTGAAAAAAAATAAAGTTGCTTGAAAAACTAGAGCTATCC
ACAACAAGGAAACCCATAACCAAAGCACCACATAAAGAACATAAAGTTTGGGAAAAGGTGCACA
AAGGTGCATCATTACACCACACAATCAACCAAAAAGATAAAGTGATGATATAATGCATCTTTCT
AATTAGGTAGACCAATATTCTGGACAATACACAAAAAATTTTGCAACATTTTGAAATTAGTTAC
ACTTACACATAATGGAAATAAAATGGGTAAATAGGAAACCACTTGGCAACAATGATATTTGGGG
GGGAGGGGGGGATTCAACTAATTTGAACTAACAGCAAAATCAATGCACTAAATGTTCGTCATAA
AAAATAAAGTTGCCACCAACACATTTTTTAGTTCATAAAAGAAGAAACCATTAGAGAAGAGAAA
GGCAGAAGTGTTACATTTCAGCTTAAAACAAATTGGCACTAAGTGAAGTAGCCCAACAAATGTA
TAAGTTGCACCACGAGAACTGAGGTAGATAATGTGGGCCTTCCTAACACTCCCGCCCCCCCCCC
CCTCCCCCTCCCCAAATGCCTGCCAGAACAGGCGAGCCTACTAGAATAGGCAAAGAACCAAGAT
GGGCTATAGGCTCTGATATCATGTTAGATTTCAACTTAAAACCAATTAGCATCAAGTGAAGTTG
CCCAACAGATATATGAGTACCCTGAGAATTGAGGCAAGCAATGTGGGACTTCCTAACATGAAGT
ACAACATTTCATTTGTTCTATTGCCCCTAGACACAACAAAAAGCAGGTTTATCTGAAACGGAGC
AGATACTAGACCTATAAGTGCTACACTAGTATCCAGGCCTGTATGTTAGTGTGACATATGAGAG
AAAACAGAGAAAATAAAACCATGCCAGAATGTCCAGGCAAAAAGTCATAGATGAATTTACTCAG
AAAACATCAAGAAGAAGAAGGCTACTAGAAGGGAAATTGAAAAGCATATAGGCTAAACCTACAG
AATTCAGCAAGGGTAATTGTTTCAATATTTTCAGAACTACGTTATTTTTCTTAGTTTCTAAGAT
ACATGTTCCACCTTGTTCTCAAGGAGAAGGGAAATTCTGTCTTCAAATATTTTTCAGTGAATAA
CAACAATATATCAAAAAACTGTCAAGAGAGCATCACCTGAGAGATTCCTTTTCTAGGAAACATC
AAGACCAACCAAAAGACTAATATGAACCAAAGGAATAAATTCCAATCTAACCAACCAGAAAGAA
TGAAGAAATACAAGTAATAGATTTATAAGAGAGTATAAGATTCGAGCAAAATACATGAAGTGAT
ACATGTCCTAGAGACAGTAATATGTAATCTTTCGATATCCAGTTAAAATGAATTACGTCTCTTA
GAACGTAAAAATGAATGGTAATGAAAAAAATTGTTTAATTATTGTATTGATGTACTTCCAATGT
TTCTTATATGTTTTTCAGTTTTTAGTTGTTTGGGAGGATTACTTATCTTTTGCATTTGATTTCT
ATTTCTCCCTCATTATTATAAAAGTGATGATTAGAAACAGGAAGTAGGTTAAATTCACAACCTT
TTCAGGAAACATAGAGCTGTACTTGGAGAAAGCTGCAAGTGTTTGCTGCTTCTTTGATGGCCTT
TTTGTGCTTGTAGAATCAGCATGTGACCCCACTTTACTGTCAGAACCAGAAGAAGACTTTGATG
GACTCTTGCTCTTCAAAAGCAACTCTTCGTTCAAATTCACAGTGACCTCTCCACTGGAAATGTC
CATATTCTTAATAACTATGCCCACTTCT
						
					

			
		

Sequences
Splice junction sequence	CTTTGATGGACTCTTGCTCTTCAAAAGCAACTCTTCGTTCAAATTCACAGTGACCTCTCCACTG GAAATGTCCATATTCTTAATAACTATGCCCACTTCTctgtatcgggatatatacaaaagagatc aaatccaacttcaatatctccaagatagaagaaccagcttctctaagaagctgtaataacaatc aggcaaaa
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	CTGTATCGGGATATATACAAAAGAGATCAAATCCAACTTCAATATCTCCAAGATAGAAGAACCA GCTTCTCTAAGAAGCTGTAATAACAATCAGGCAAAAGAAAACTTGTCAGCAAGAAACAAAACAG TGAAAAGTAGGAATCATATCACAAGCTCTGCCAAAATAAACAGTCACACTCCATACATGAATTT CACTAAACTCCAGTTGGAAATCAAGGCGTGTACTCTCCCCAAGATCCTCAGTGGATCGTGATTT GGTGCTTTTCAATTGGATGCCCATGATGTTGTTTTCAATATAAAGACCATGCTCACGATGCACA AAACTCACATCCAGCTTTGGTAGATTGAAGCTGACCTATCAACAAAAATATACTAATACAGTTG ACATTAAAACAATTTAAAAAACCCTTAAAAGCATTTTTAAACTAACTTTAGATTAGATAAAACC AACAAACATAACCAAAATTGACAATCAATTTAAGCATTATAAAGTGTATAAACAATTTGAATTT CAATGGGACACCAGACTTAATTAAATGCTCAACGGAAGCCAAAATTCACCAAGAACACAAACAC CGGAACACATACTCAGAGAGACTTACAAGTGAAGGAACCACATTTTGCCCAAAAGCCAAATTCT AGTGTCCAGCAAGCCATAAACAGTAACAGAATCAAGACTTTGAAGCAACAAGATCATAATTTAT GCAGTTTCTCTACCCTTCATATTTCTGAAAAAAAATAAAGTTGCTTGAAAAACTAGAGCTATCC ACAACAAGGAAACCCATAACCAAAGCACCACATAAAGAACATAAAGTTTGGGAAAAGGTGCACA AAGGTGCATCATTACACCACACAATCAACCAAAAAGATAAAGTGATGATATAATGCATCTTTCT AATTAGGTAGACCAATATTCTGGACAATACACAAAAAATTTTGCAACATTTTGAAATTAGTTAC ACTTACACATAATGGAAATAAAATGGGTAAATAGGAAACCACTTGGCAACAATGATATTTGGGG GGGAGGGGGGGATTCAACTAATTTGAACTAACAGCAAAATCAATGCACTAAATGTTCGTCATAA AAAATAAAGTTGCCACCAACACATTTTTTAGTTCATAAAAGAAGAAACCATTAGAGAAGAGAAA GGCAGAAGTGTTACATTTCAGCTTAAAACAAATTGGCACTAAGTGAAGTAGCCCAACAAATGTA TAAGTTGCACCACGAGAACTGAGGTAGATAATGTGGGCCTTCCTAACACTCCCGCCCCCCCCCC CCTCCCCCTCCCCAAATGCCTGCCAGAACAGGCGAGCCTACTAGAATAGGCAAAGAACCAAGAT GGGCTATAGGCTCTGATATCATGTTAGATTTCAACTTAAAACCAATTAGCATCAAGTGAAGTTG CCCAACAGATATATGAGTACCCTGAGAATTGAGGCAAGCAATGTGGGACTTCCTAACATGAAGT ACAACATTTCATTTGTTCTATTGCCCCTAGACACAACAAAAAGCAGGTTTATCTGAAACGGAGC AGATACTAGACCTATAAGTGCTACACTAGTATCCAGGCCTGTATGTTAGTGTGACATATGAGAG AAAACAGAGAAAATAAAACCATGCCAGAATGTCCAGGCAAAAAGTCATAGATGAATTTACTCAG AAAACATCAAGAAGAAGAAGGCTACTAGAAGGGAAATTGAAAAGCATATAGGCTAAACCTACAG AATTCAGCAAGGGTAATTGTTTCAATATTTTCAGAACTACGTTATTTTTCTTAGTTTCTAAGAT ACATGTTCCACCTTGTTCTCAAGGAGAAGGGAAATTCTGTCTTCAAATATTTTTCAGTGAATAA CAACAATATATCAAAAAACTGTCAAGAGAGCATCACCTGAGAGATTCCTTTTCTAGGAAACATC AAGACCAACCAAAAGACTAATATGAACCAAAGGAATAAATTCCAATCTAACCAACCAGAAAGAA TGAAGAAATACAAGTAATAGATTTATAAGAGAGTATAAGATTCGAGCAAAATACATGAAGTGAT ACATGTCCTAGAGACAGTAATATGTAATCTTTCGATATCCAGTTAAAATGAATTACGTCTCTTA GAACGTAAAAATGAATGGTAATGAAAAAAATTGTTTAATTATTGTATTGATGTACTTCCAATGT TTCTTATATGTTTTTCAGTTTTTAGTTGTTTGGGAGGATTACTTATCTTTTGCATTTGATTTCT ATTTCTCCCTCATTATTATAAAAGTGATGATTAGAAACAGGAAGTAGGTTAAATTCACAACCTT TTCAGGAAACATAGAGCTGTACTTGGAGAAAGCTGCAAGTGTTTGCTGCTTCTTTGATGGCCTT TTTGTGCTTGTAGAATCAGCATGTGACCCCACTTTACTGTCAGAACCAGAAGAAGACTTTGATG GACTCTTGCTCTTCAAAAGCAACTCTTCGTTCAAATTCACAGTGACCTCTCCACTGGAAATGTC CATATTCTTAATAACTATGCCCACTTCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.089461328

Conservation Information
Conserved circRNAs	NA
PMCS	0.089461328

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8720609-8718366(+)
8720617-8720622(-)
						
						Potential amino acid sequence
						
							MSIFLITMPTSLYRDIYKRDQIQLQYLQDRRTSFSKKMNFTKLQLEIKACTLPKILSGS*(+)
MDISSGEVTVNLNEELLLKSKSPSKSSSGSDSKVGSHADSTSTKRPSKKQQTLAAFSKYSSMFP
EKVSFNLPKLDVSFVHREHGLYIENNIMGIQLKSTKSRSTEDLGESTRLDFQLEFSEIHLLREA
GSSILEILKLDLISFVYIPIQRSGHSY*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8720609-8718366(+) 8720617-8720622(-)
Potential amino acid sequence	MSIFLITMPTSLYRDIYKRDQIQLQYLQDRRTSFSKKMNFTKLQLEIKACTLPKILSGS(+) MDISSGEVTVNLNEELLLKSKSPSKSSSGSDSKVGSHADSTSTKRPSKKQQTLAAFSKYSSMFP EKVSFNLPKLDVSFVHREHGLYIENNIMGIQLKSTKSRSTEDLGESTRLDFQLEFSEIHLLREA GSSILEILKLDLISFVYIPIQRSGHSY(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021a

circRNA

Detail information of GLYMA_04G096600_circ_g.4

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