Plant Circular RNA Database

Detail information of GLYMA_01G207400_circ_g.1

			
						 General Information
					
						CircRNA Name
						GLYMA_01G207400_circ_g.1
					
						ID in PlantcircBase
						gma_circ_000224
					
						Alias
						Gm01circRNA861
					
						Organism
						
							Glycine max						
					
						Position
						
							chr1: 53934829-53936075  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI
					
						Parent gene
						
							GLYMA_01G207400						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							GLYMA_01G207400_circ_g.2 GLYMA_01G207400_circ_g.3 						
					
						Support reads
						NA
					
						Tissues
						leaf, root, stem
					
						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
						KRH77334:2
KRH77333:3
KRH77332:3

General Information
CircRNA Name	GLYMA_01G207400_circ_g.1
ID in PlantcircBase	gma_circ_000224
Alias	Gm01circRNA861
Organism	Glycine max
Position	chr1: 53934829-53936075 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI
Parent gene	GLYMA_01G207400
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	GLYMA_01G207400_circ_g.2 GLYMA_01G207400_circ_g.3
Support reads	NA
Tissues	leaf, root, stem
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	KRH77334:2 KRH77333:3 KRH77332:3

			
						 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  
						
							TCAGATTCTGGGTTACTATCCCTTCAAAAATCTTCGTTCTGCTGTTGACTTGCTCTTTTTACGT
GGAGGCTCTGATATGGTGATTGCAAAACAGGCCATTacatcacagatgtatgtatggatgaaac
tgctgtttccagtgatcctgtcattgcatttttgttggatgaagtggtagtgaaggattggtgc
aagaggac

									
								

					

						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: 713
Transcript exons: 53934829-53934963,53935062-53935237,53935674-53936075
ACATCACAGATGTATGTATGGATGAAACTGCTGTTTCCAGTGATCCTGTCATTGCATTTTTGTT
GGATGAAGTGGTAGTGAAGGATTGGTGCAAGAGGACATTCAAAAACATCATTGCTGAACTGCAG
GGAATTTATAATATGGACATTTTAGGCTTGAAAGAGAGATTGAGTTTACTTCTGAAATTTTCAT
TATACTTGAAGGGCATATCAAATGTGCTAGACATTTTGGAGTCATCTTTTAAGGGTACTCTTTC
AGCACAACTTCACGATTTGCAGAATCTCCAAGAGAGCATCATGAAGACAAAGCAGCATATGGAT
GTTATTATTTGGTGTACGAGACATCAATTTTTGGAAGATGTGAGATCACGTTTTACTGATAGTT
CGTCATGGTCATCAGTTGTTCGGACAAGGAAATCAGAAGCAATTAGACGTGCTTGGCCTGATCC
AATAAATCAATCTGTGGAGTCATCAGGACATGATGGGTCTCTATTTATTGAAGATGCAATGAAT
AATCTTGATCTGGAGGAGGGGTTTAGGAATGAAATTGTAGAGGGATTGGAAATTGCATCCTTGC
AGAAGGACAGTGAATCATTTTTGGGGTCAAATACTGATCAGATTCTGGGTTACTATCCCTTCAA
AAATCTTCGTTCTGCTGTTGACTTGCTCTTTTTACGTGGAGGCTCTGATATGGTGATTGCAAAA
CAGGCCATT
						
					

						Genomic sequence
						
							ACATCACAGATGTATGTATGGATGAAACTGCTGTTTCCAGTGATCCTGTCATTGCATTTTTGTT
GGATGAAGTGGTAGTGAAGGATTGGTGCAAGAGGACATTCAAAAACATCATTGCTGAACTGCAG
GGAATTTGTATCCTTAAACCTTGTTTTTTTGTTGATATCTAAAGCTAATTATTAGTATGACCTT
TTTCCATAATTATATTTGTTCTCCCTAACAATTTTCACTAGATAATATGGACATTTTAGGCTTG
AAAGAGAGATTGAGTTTACTTCTGAAATTTTCATTATACTTGAAGGGCATATCAAATGTGCTAG
ACATTTTGGAGTCATCTTTTAAGGGTACTCTTTCAGCACAACTTCACGATTTGCAGAATCTCCA
AGAGAGCATCATGAAGACAAAGCAGGTTTGGTTTTGCAAGAATTCATGTTCAATGGAGTCATTG
CTTAACCGTTATGATTTTTGCATTAATATTTGATTTTTGACACATTTCTTGCTTGGCTGATGTG
CTGCCAAGTGTCAAGTCATCACAATAAATTCGTACATATTATCTATTTTTTAAATGATTCTGTG
TGATTTTTGTTGGAAGGGGCTTTATACCTAATCTTCAAAAGTGTTGATGACAATGGGTAACCTT
TGTTGTTGTAGTTCACTATGATGAAGTATATAAGAGGGACGTTTGTAGAAATGACTGTTATTTG
GCCTTGCACTTTAATTAATATTGCTTATAAAGAGTGGTTTGCTGGATTTAGTCTTCCTCTATCT
GTCTGTATGTAGCTCCAAAATTAGAGTAGCTCATTGCAATCTTCATCCTGGTGTTTAATTTTTG
TTGTTTTACCCAGCATATGGATGTTATTATTTGGTGTACGAGACATCAATTTTTGGAAGATGTG
AGATCACGTTTTACTGATAGTTCGTCATGGTCATCAGTTGTTCGGACAAGGAAATCAGAAGCAA
TTAGACGTGCTTGGCCTGATCCAATAAATCAATCTGTGGAGTCATCAGGACATGATGGGTCTCT
ATTTATTGAAGATGCAATGAATAATCTTGATCTGGAGGAGGGGTTTAGGAATGAAATTGTAGAG
GGATTGGAAATTGCATCCTTGCAGAAGGACAGTGAATCATTTTTGGGGTCAAATACTGATCAGA
TTCTGGGTTACTATCCCTTCAAAAATCTTCGTTCTGCTGTTGACTTGCTCTTTTTACGTGGAGG
CTCTGATATGGTGATTGCAAAACAGGCCATT
						
					

			
		

Sequences
Splice junction sequence	TCAGATTCTGGGTTACTATCCCTTCAAAAATCTTCGTTCTGCTGTTGACTTGCTCTTTTTACGT GGAGGCTCTGATATGGTGATTGCAAAACAGGCCATTacatcacagatgtatgtatggatgaaac tgctgtttccagtgatcctgtcattgcatttttgttggatgaagtggtagtgaaggattggtgc aagaggac
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: 713 Transcript exons: 53934829-53934963,53935062-53935237,53935674-53936075 ACATCACAGATGTATGTATGGATGAAACTGCTGTTTCCAGTGATCCTGTCATTGCATTTTTGTT GGATGAAGTGGTAGTGAAGGATTGGTGCAAGAGGACATTCAAAAACATCATTGCTGAACTGCAG GGAATTTATAATATGGACATTTTAGGCTTGAAAGAGAGATTGAGTTTACTTCTGAAATTTTCAT TATACTTGAAGGGCATATCAAATGTGCTAGACATTTTGGAGTCATCTTTTAAGGGTACTCTTTC AGCACAACTTCACGATTTGCAGAATCTCCAAGAGAGCATCATGAAGACAAAGCAGCATATGGAT GTTATTATTTGGTGTACGAGACATCAATTTTTGGAAGATGTGAGATCACGTTTTACTGATAGTT CGTCATGGTCATCAGTTGTTCGGACAAGGAAATCAGAAGCAATTAGACGTGCTTGGCCTGATCC AATAAATCAATCTGTGGAGTCATCAGGACATGATGGGTCTCTATTTATTGAAGATGCAATGAAT AATCTTGATCTGGAGGAGGGGTTTAGGAATGAAATTGTAGAGGGATTGGAAATTGCATCCTTGC AGAAGGACAGTGAATCATTTTTGGGGTCAAATACTGATCAGATTCTGGGTTACTATCCCTTCAA AAATCTTCGTTCTGCTGTTGACTTGCTCTTTTTACGTGGAGGCTCTGATATGGTGATTGCAAAA CAGGCCATT
Genomic sequence	ACATCACAGATGTATGTATGGATGAAACTGCTGTTTCCAGTGATCCTGTCATTGCATTTTTGTT GGATGAAGTGGTAGTGAAGGATTGGTGCAAGAGGACATTCAAAAACATCATTGCTGAACTGCAG GGAATTTGTATCCTTAAACCTTGTTTTTTTGTTGATATCTAAAGCTAATTATTAGTATGACCTT TTTCCATAATTATATTTGTTCTCCCTAACAATTTTCACTAGATAATATGGACATTTTAGGCTTG AAAGAGAGATTGAGTTTACTTCTGAAATTTTCATTATACTTGAAGGGCATATCAAATGTGCTAG ACATTTTGGAGTCATCTTTTAAGGGTACTCTTTCAGCACAACTTCACGATTTGCAGAATCTCCA AGAGAGCATCATGAAGACAAAGCAGGTTTGGTTTTGCAAGAATTCATGTTCAATGGAGTCATTG CTTAACCGTTATGATTTTTGCATTAATATTTGATTTTTGACACATTTCTTGCTTGGCTGATGTG CTGCCAAGTGTCAAGTCATCACAATAAATTCGTACATATTATCTATTTTTTAAATGATTCTGTG TGATTTTTGTTGGAAGGGGCTTTATACCTAATCTTCAAAAGTGTTGATGACAATGGGTAACCTT TGTTGTTGTAGTTCACTATGATGAAGTATATAAGAGGGACGTTTGTAGAAATGACTGTTATTTG GCCTTGCACTTTAATTAATATTGCTTATAAAGAGTGGTTTGCTGGATTTAGTCTTCCTCTATCT GTCTGTATGTAGCTCCAAAATTAGAGTAGCTCATTGCAATCTTCATCCTGGTGTTTAATTTTTG TTGTTTTACCCAGCATATGGATGTTATTATTTGGTGTACGAGACATCAATTTTTGGAAGATGTG AGATCACGTTTTACTGATAGTTCGTCATGGTCATCAGTTGTTCGGACAAGGAAATCAGAAGCAA TTAGACGTGCTTGGCCTGATCCAATAAATCAATCTGTGGAGTCATCAGGACATGATGGGTCTCT ATTTATTGAAGATGCAATGAATAATCTTGATCTGGAGGAGGGGTTTAGGAATGAAATTGTAGAG GGATTGGAAATTGCATCCTTGCAGAAGGACAGTGAATCATTTTTGGGGTCAAATACTGATCAGA TTCTGGGTTACTATCCCTTCAAAAATCTTCGTTCTGCTGTTGACTTGCTCTTTTTACGTGGAGG CTCTGATATGGTGATTGCAAAACAGGCCATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							ghi_circ_003444* gra_circ_000873* gar_circ_000746* ghi_circ_003443 
ghi_circ_001551* ghi_circ_001550 						
					
						PMCS
						0.606085151

Conservation Information
Conserved circRNAs	ghi_circ_003444* gra_circ_000873* gar_circ_000746* ghi_circ_003443 ghi_circ_001551* ghi_circ_001550
PMCS	0.606085151

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							53934847-53934903(+)
						
						Potential amino acid sequence
						
							MDETAVSSDPVIAFLLDEVVVKDWCKRTFKNIIAELQGIYNMDILGLKERLSLLLKFSLYLKGI
SNVLDILESSFKGTLSAQLHDLQNLQESIMKTKQHMDVIIWCTRHQFLEDVRSRFTDSSSWSSV
VRTRKSEAIRRAWPDPINQSVESSGHDGSLFIEDAMNNLDLEEGFRNEIVEGLEIASLQKDSES
FLGSNTDQILGYYPFKNLRSAVDLLFLRGGSDMVIAKQAITSQMYVWMKLLFPVILSLHFCWMK
W*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	53934847-53934903(+)
Potential amino acid sequence	MDETAVSSDPVIAFLLDEVVVKDWCKRTFKNIIAELQGIYNMDILGLKERLSLLLKFSLYLKGI SNVLDILESSFKGTLSAQLHDLQNLQESIMKTKQHMDVIIWCTRHQFLEDVRSRFTDSSSWSSV VRTRKSEAIRRAWPDPINQSVESSGHDGSLFIEDAMNNLDLEEGFRNEIVEGLEIASLQKDSES FLGSNTDQILGYYPFKNLRSAVDLLFLRGGSDMVIAKQAITSQMYVWMKLLFPVILSLHFCWMK W*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_01G207400_circ_g.1

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