Plant Circular RNA Database

Detail information of GLYMA_20G069800_circ_g.3

			
						 General Information
					
						CircRNA Name
						GLYMA_20G069800_circ_g.3
					
						ID in PlantcircBase
						gma_circ_005152
					
						Alias
						Gm20circRNA448, gma-circRNA2724
					
						Organism
						
							Glycine max						
					
						Position
						
							chr20: 24827235-24830481  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI, find_circ
					
						Parent gene
						
							GLYMA_20G069800						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							GLYMA_20G069800_circ_g.4 						
					
						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
						KRG90127:6
KRG90126:6

General Information
CircRNA Name	GLYMA_20G069800_circ_g.3
ID in PlantcircBase	gma_circ_005152
Alias	Gm20circRNA448, gma-circRNA2724
Organism	Glycine max
Position	chr20: 24827235-24830481 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI, find_circ
Parent gene	GLYMA_20G069800
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	GLYMA_20G069800_circ_g.4
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	KRG90127:6 KRG90126:6

			
						 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  
						
							CTGATCGAGACTCTGTTCAGTCAATGTCTGACTGTGATCAAGCAGTGCTTCAGTTTGCCAAGAC
AAGGAAGTTGTCAATTGAGCGTCCTGACCCACGAAAtcaccgaagatttcacttgtccattttg
tttggttaaatgcgcgtgttttaaggttaaaactactttctccttctaaataaatacttttttt
ttttagtg

									
								

					

						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: 454
Transcript exons: 24827235-24827287,24827379-24827432,24827518-24827577,24
828258-24828304,24828398-24828507,24830352-24830481
TCACCGAAGATTTCACTTGTCCATTTTGTTTGGTTAAATGCGCGTGTTTTAAGGGTCTAAGATG
TCATTTGTCATCATCACATGATCTCTTCAACTTTGAATTTTGGGTATCAGATGAATGTCACGCT
GTAAATGTGTCTGTGAAAAATGATATCTCGAGATCGGAGATTGTTTCTGATGATGTTGATCCAA
GAGTGCAAACATTTTTCTTTTGTGGAAAGCCTCTAAAGCGTAGGACAACAGCAGACCAATCTTT
GAAAAATGCAGTGGGCTTAGAGTCTTCCTTTCCTGCAGGAGGGACTGATATTTTGGAGAAGGAT
GATGGTATTTCTGCCACAATTATTCGATCACGTCCTGATCGAGACTCTGTTCAGTCAATGTCTG
ACTGTGATCAAGCAGTGCTTCAGTTTGCCAAGACAAGGAAGTTGTCAATTGAGCGTCCTGACCC
ACGAAA
						
					

						Genomic sequence
						
							TCACCGAAGATTTCACTTGTCCATTTTGTTTGGTTAAATGCGCGTGTTTTAAGGTTAAAACTAC
TTTCTCCTTCTAAATAAATACTTTTTTTTTTTAGTGTTGAAACCTGTTTCTAATGCTCTTCTGA
CATGACCTTTTTTTAGGGTCTAAGATGTCATTTGTCATCATCACATGATCTCTTCAACTTTGAA
TTTTGGGTCAGTAATCTTTAAATCTCTTGCTGGCATTCTATTCACTGAGCTGTATTGAACCATC
AGTAATCAAGTACAAATAATTTTTCAGGTATCAGATGAATGTCACGCTGTAAATGTGTCTGTGA
AAAATGATATCTCGAGATCGGAGGTGAGAGGATAGTTTATGCTCAATTATTTTCTTTTGCATAT
ATATATATATATATACACATTATATTTAATTACTATCTAATTAGTTATTAGTTATACTGTCTAT
TTACAACTCTAAATGTTGTGGAAGATTTGTCTTTCATTTGGGATCTCTAATTTGTTCTTGGACT
TTATTGATTATATGATTTTTGGCCCTATTTAAATTTCTCCTTCACCTTTTTTTATTCGTTTTCA
TATTTTTGACTCACCAACAATGTTGCCTTGTCCCACTTTCATTTGGGTTTAGCAATGTAGATCA
ATGACAGCTTTAAGCTTTATAAAAAATACTAAATTTCTATTAATCCATTTGGTGTAAGGTCTTC
TTCAAATATTTTTCCTAGTATTCTTTGGTCTTCTGCTACCACTTTCGATTGGCCTATATTTATT
TCATTCACTTTTTGCACCAGGATTACCTTTAGTCTTCCCCTGACGTGACAAAACAACTTTAGAT
TTCTGTCATCTTCTCTTAAAAAATTGCTACACCAAATTTCTTCTAGATACCTTCATATCTTGAT
TTAACAAACATGCATGCATCTCAACATTTGGTAACATAGTGTGCTGCCAGTCTTATTGCTGTGA
GCTAGAATTCCTCTTTAAGTTCAAGAGGGACTCTATGATCACAAACATTATCTTTTTGTCCAGA
TTGTTTCTGATGATGTTGATCCAAGAGTGCAAACATTTTTCTTTTGGTAAGCTATTTTATTTCT
TCTAAAATTTTGATGGCTCCGGATTCTTTCATAACATGGTATGAGATTCAGTTGTGATACCATG
CCTATATGCAGTGGAAAGCCTCTAAAGCGTAGGACAACAGCAGACCAATCTTTGAAAAATGCAG
TGGGCTTAGAGTCTTCCTTTCCTGCAGGAGGGACTGATATTTTGGAGAAGGATGATGGTATGTA
GCTAGCTTTTGCAACAATATCAACTATATAAGTCAATCCATTAATTCTCTTAAAAATTTGTAGA
AGGGGCAAATGTATATAGTTTTCAGATGTTGAAAATCATAATACGATATTCTGATTTATTAATA
ATAGTGGTTTATAGGCACATAATTTTTTATTTAGAGGAAACATAATATCCTCTATTATGTATAA
TTAATGTAATTAACCTGCATAAACATGCATCCGCTGTGTATTCATACAGTTTTCTGTCAATTAC
CCCTCTGACTCCTATTTTAACATGGTATCCAGAGCTTAACAGAGGTATCATGAAAATTGTGCTT
CACCAGGGACCAACTGTTCCCAGTGGACCCTTCTGCTCTTTGCCCTTCTGCCTATTTGTTTTCG
TTTTTCAGCAGATTTTCCACCACCGCCCACTGCCATGGGCCACTGGTGCGTCGTCGGCGAGTTT
TCTAGTGAGACCACCACCATCAGGATCGAAATATTCTGATCTACCTGTCCTCGAAGTTACAGTC
CTGGCCTCCCATCCACGTGCGTGGTTTTACATGCGCCAAGCAACATCTTTTGTTGGGGCTTCTT
GGCGGCGAATCCGATCATCTTTTCGGCTGCTGTTTTTAGTGACAGACTCGCCGGACCGAGGCAC
ACAAAGCCCAGTCGGTTTCGGGCCATTCTGAGATTGTGTCGTTTGCCGGGCCTTATTTTAGTTT
GCGTTTTTTGGTCATTGTTTTGTCCTTGTTTTCTAGTTCGACAGTTGCTTCCATTGTCCCGGTC
TTTGTCCCGGATGCACCGACCCCGGCTATGTCCTAGTTGCACTAGTCCCGGCTATGTCCTAGAT
GCCTTGGTCTTGTCTTGGTCCCAGAAGCAGTAGACTAGTTTCAAGTTTAAATGATTTGGGTCTC
CTACATTGCTGGTTTGAAGATTCCAATCCTTGTCCAACATGCTATTCTTTGTCTAGCTCCTTTT
TGTTGGCTGCCAAGGGCCTAACACAACAACCCTCCTTTACTTGAGCTTGGGATTGGCTATGATA
CCGTACATAGTGTTTAAATATTAATCATTAGTTAAGATGATGAGTTTATATATTTAATGTTAAA
TATCAAATATTAATTATTAAAATTACTTAATAACAATGCTAATTATTAATTAGTACTTAAAATA
ATACTTTAAAATAATTAAATGTCACTATATATTATGAAAAGTTAATAGAAATTATTGAATCTTA
AATAATATTGAATTATATTCTTAATAAAATCATAAAATAAAAGTACATAGAATAAAAATCATAT
GAATCTTTTATAGCATAAAAAGCACTGTCGTAATAGGTTAAAAATAAATTTAAATGACGTTTTC
TTCTTTTGTTTTTACTCTATTTACGCAATTTACATGCAACTATTAAATTATATTGAAAAGTTAA
AAATACTAACCAATTTGATAATTTATATAATTGTAAAATTTTGATAAAATTACGTATATTTGTA
TTGTTTTTTTTTAAATAAATAAAGAATTTATAATATTTTCATTTTATTTTTTTAAACATAAAAA
ATCAATTCAAACTTATTCCTGTAAAATATTTATAACAAGTTAAAAAATTAATTAGTATGTTAAA
TTAAAAATAAGCTTTGCAACACATAGAATAAAGTATCTCACTTTAGCTAATCTTAACTCAAACT
TTCACAATTAGGTTCTGTTTTTCATACTTTTGTTAATTGATTTTCCTTATATGGTCCTGGTCAT
ATTTGTTAATATTTCTTTTGAGTTGGGGTTCTTGCTCCAAAATGTTGCAATAGTGCTGCTTGAG
TTTTACTGTGTTAGGAATATGTTACATGCTGCTATGGCATTGCAGGTATTTCTGCCACAATTAT
TCGATCACGTCCTGATCGAGACTCTGTTCAGTCAATGTCTGACTGTGATCAAGCAGTGCTTCAG
TTTGCCAAGACAAGGAAGTTGTCAATTGAGCGTCCTGACCCACGAAA
						
					

			
		

Sequences
Splice junction sequence	CTGATCGAGACTCTGTTCAGTCAATGTCTGACTGTGATCAAGCAGTGCTTCAGTTTGCCAAGAC AAGGAAGTTGTCAATTGAGCGTCCTGACCCACGAAAtcaccgaagatttcacttgtccattttg tttggttaaatgcgcgtgttttaaggttaaaactactttctccttctaaataaatacttttttt ttttagtg
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: 454 Transcript exons: 24827235-24827287,24827379-24827432,24827518-24827577,24 828258-24828304,24828398-24828507,24830352-24830481 TCACCGAAGATTTCACTTGTCCATTTTGTTTGGTTAAATGCGCGTGTTTTAAGGGTCTAAGATG TCATTTGTCATCATCACATGATCTCTTCAACTTTGAATTTTGGGTATCAGATGAATGTCACGCT GTAAATGTGTCTGTGAAAAATGATATCTCGAGATCGGAGATTGTTTCTGATGATGTTGATCCAA GAGTGCAAACATTTTTCTTTTGTGGAAAGCCTCTAAAGCGTAGGACAACAGCAGACCAATCTTT GAAAAATGCAGTGGGCTTAGAGTCTTCCTTTCCTGCAGGAGGGACTGATATTTTGGAGAAGGAT GATGGTATTTCTGCCACAATTATTCGATCACGTCCTGATCGAGACTCTGTTCAGTCAATGTCTG ACTGTGATCAAGCAGTGCTTCAGTTTGCCAAGACAAGGAAGTTGTCAATTGAGCGTCCTGACCC ACGAAA
Genomic sequence	TCACCGAAGATTTCACTTGTCCATTTTGTTTGGTTAAATGCGCGTGTTTTAAGGTTAAAACTAC TTTCTCCTTCTAAATAAATACTTTTTTTTTTTAGTGTTGAAACCTGTTTCTAATGCTCTTCTGA CATGACCTTTTTTTAGGGTCTAAGATGTCATTTGTCATCATCACATGATCTCTTCAACTTTGAA TTTTGGGTCAGTAATCTTTAAATCTCTTGCTGGCATTCTATTCACTGAGCTGTATTGAACCATC AGTAATCAAGTACAAATAATTTTTCAGGTATCAGATGAATGTCACGCTGTAAATGTGTCTGTGA AAAATGATATCTCGAGATCGGAGGTGAGAGGATAGTTTATGCTCAATTATTTTCTTTTGCATAT ATATATATATATATACACATTATATTTAATTACTATCTAATTAGTTATTAGTTATACTGTCTAT TTACAACTCTAAATGTTGTGGAAGATTTGTCTTTCATTTGGGATCTCTAATTTGTTCTTGGACT TTATTGATTATATGATTTTTGGCCCTATTTAAATTTCTCCTTCACCTTTTTTTATTCGTTTTCA TATTTTTGACTCACCAACAATGTTGCCTTGTCCCACTTTCATTTGGGTTTAGCAATGTAGATCA ATGACAGCTTTAAGCTTTATAAAAAATACTAAATTTCTATTAATCCATTTGGTGTAAGGTCTTC TTCAAATATTTTTCCTAGTATTCTTTGGTCTTCTGCTACCACTTTCGATTGGCCTATATTTATT TCATTCACTTTTTGCACCAGGATTACCTTTAGTCTTCCCCTGACGTGACAAAACAACTTTAGAT TTCTGTCATCTTCTCTTAAAAAATTGCTACACCAAATTTCTTCTAGATACCTTCATATCTTGAT TTAACAAACATGCATGCATCTCAACATTTGGTAACATAGTGTGCTGCCAGTCTTATTGCTGTGA GCTAGAATTCCTCTTTAAGTTCAAGAGGGACTCTATGATCACAAACATTATCTTTTTGTCCAGA TTGTTTCTGATGATGTTGATCCAAGAGTGCAAACATTTTTCTTTTGGTAAGCTATTTTATTTCT TCTAAAATTTTGATGGCTCCGGATTCTTTCATAACATGGTATGAGATTCAGTTGTGATACCATG CCTATATGCAGTGGAAAGCCTCTAAAGCGTAGGACAACAGCAGACCAATCTTTGAAAAATGCAG TGGGCTTAGAGTCTTCCTTTCCTGCAGGAGGGACTGATATTTTGGAGAAGGATGATGGTATGTA GCTAGCTTTTGCAACAATATCAACTATATAAGTCAATCCATTAATTCTCTTAAAAATTTGTAGA AGGGGCAAATGTATATAGTTTTCAGATGTTGAAAATCATAATACGATATTCTGATTTATTAATA ATAGTGGTTTATAGGCACATAATTTTTTATTTAGAGGAAACATAATATCCTCTATTATGTATAA TTAATGTAATTAACCTGCATAAACATGCATCCGCTGTGTATTCATACAGTTTTCTGTCAATTAC CCCTCTGACTCCTATTTTAACATGGTATCCAGAGCTTAACAGAGGTATCATGAAAATTGTGCTT CACCAGGGACCAACTGTTCCCAGTGGACCCTTCTGCTCTTTGCCCTTCTGCCTATTTGTTTTCG TTTTTCAGCAGATTTTCCACCACCGCCCACTGCCATGGGCCACTGGTGCGTCGTCGGCGAGTTT TCTAGTGAGACCACCACCATCAGGATCGAAATATTCTGATCTACCTGTCCTCGAAGTTACAGTC CTGGCCTCCCATCCACGTGCGTGGTTTTACATGCGCCAAGCAACATCTTTTGTTGGGGCTTCTT GGCGGCGAATCCGATCATCTTTTCGGCTGCTGTTTTTAGTGACAGACTCGCCGGACCGAGGCAC ACAAAGCCCAGTCGGTTTCGGGCCATTCTGAGATTGTGTCGTTTGCCGGGCCTTATTTTAGTTT GCGTTTTTTGGTCATTGTTTTGTCCTTGTTTTCTAGTTCGACAGTTGCTTCCATTGTCCCGGTC TTTGTCCCGGATGCACCGACCCCGGCTATGTCCTAGTTGCACTAGTCCCGGCTATGTCCTAGAT GCCTTGGTCTTGTCTTGGTCCCAGAAGCAGTAGACTAGTTTCAAGTTTAAATGATTTGGGTCTC CTACATTGCTGGTTTGAAGATTCCAATCCTTGTCCAACATGCTATTCTTTGTCTAGCTCCTTTT TGTTGGCTGCCAAGGGCCTAACACAACAACCCTCCTTTACTTGAGCTTGGGATTGGCTATGATA CCGTACATAGTGTTTAAATATTAATCATTAGTTAAGATGATGAGTTTATATATTTAATGTTAAA TATCAAATATTAATTATTAAAATTACTTAATAACAATGCTAATTATTAATTAGTACTTAAAATA ATACTTTAAAATAATTAAATGTCACTATATATTATGAAAAGTTAATAGAAATTATTGAATCTTA AATAATATTGAATTATATTCTTAATAAAATCATAAAATAAAAGTACATAGAATAAAAATCATAT GAATCTTTTATAGCATAAAAAGCACTGTCGTAATAGGTTAAAAATAAATTTAAATGACGTTTTC TTCTTTTGTTTTTACTCTATTTACGCAATTTACATGCAACTATTAAATTATATTGAAAAGTTAA AAATACTAACCAATTTGATAATTTATATAATTGTAAAATTTTGATAAAATTACGTATATTTGTA TTGTTTTTTTTTAAATAAATAAAGAATTTATAATATTTTCATTTTATTTTTTTAAACATAAAAA ATCAATTCAAACTTATTCCTGTAAAATATTTATAACAAGTTAAAAAATTAATTAGTATGTTAAA TTAAAAATAAGCTTTGCAACACATAGAATAAAGTATCTCACTTTAGCTAATCTTAACTCAAACT TTCACAATTAGGTTCTGTTTTTCATACTTTTGTTAATTGATTTTCCTTATATGGTCCTGGTCAT ATTTGTTAATATTTCTTTTGAGTTGGGGTTCTTGCTCCAAAATGTTGCAATAGTGCTGCTTGAG TTTTACTGTGTTAGGAATATGTTACATGCTGCTATGGCATTGCAGGTATTTCTGCCACAATTAT TCGATCACGTCCTGATCGAGACTCTGTTCAGTCAATGTCTGACTGTGATCAAGCAGTGCTTCAG TTTGCCAAGACAAGGAAGTTGTCAATTGAGCGTCCTGACCCACGAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.46668322

Conservation Information
Conserved circRNAs	NA
PMCS	0.46668322

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24828503-24827268(+)
24830406-24827268(+)
						
						Potential amino acid sequence
						
							MMVFLPQLFDHVLIETLFSQCLTVIKQCFSLPRQGSCQLSVLTHEITEDFTCPFCLVKCACFKG
LRCHLSSSHDLFNFEFWVSDECHAVNVSVKNDISRSEIVSDDVDPRVQTFFFCGKPLKRRTTAD
QSLKNAVGLESSFPAGGTDILEKDDGISATIIRSRPDRDSVQSMSDCDQAVLQFAKTRKLSIER
PDPRNHRRFHLSILFG*(+)
MSDCDQAVLQFAKTRKLSIERPDPRNHRRFHLSILFG*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24828503-24827268(+) 24830406-24827268(+)
Potential amino acid sequence	MMVFLPQLFDHVLIETLFSQCLTVIKQCFSLPRQGSCQLSVLTHEITEDFTCPFCLVKCACFKG LRCHLSSSHDLFNFEFWVSDECHAVNVSVKNDISRSEIVSDDVDPRVQTFFFCGKPLKRRTTAD QSLKNAVGLESSFPAGGTDILEKDDGISATIIRSRPDRDSVQSMSDCDQAVLQFAKTRKLSIER PDPRNHRRFHLSILFG(+) MSDCDQAVLQFAKTRKLSIERPDPRNHRRFHLSILFG(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of GLYMA_20G069800_circ_g.3

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