Plant Circular RNA Database

Detail information of GLYMA_19G116700_circ_g.3

			
						 General Information
					
						CircRNA Name
						GLYMA_19G116700_circ_g.3
					
						ID in PlantcircBase
						gma_circ_004937
					
						Alias
						Gm19circRNA2415, gma-circRNA2582
					
						Organism
						
							Glycine max						
					
						Position
						
							chr19: 37222664-37225402  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI, find_circ
					
						Parent gene
						
							GLYMA_19G116700						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_19G116700_circ_g.2 GLYMA_19G116700_circ_g.4 GLYMA_19G116700_circ_g.5 						
					
						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
						KRG94904:3
KRG94903:3

General Information
CircRNA Name	GLYMA_19G116700_circ_g.3
ID in PlantcircBase	gma_circ_004937
Alias	Gm19circRNA2415, gma-circRNA2582
Organism	Glycine max
Position	chr19: 37222664-37225402 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI, find_circ
Parent gene	GLYMA_19G116700
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_19G116700_circ_g.2 GLYMA_19G116700_circ_g.4 GLYMA_19G116700_circ_g.5
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	KRG94904:3 KRG94903:3

			
						 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  
						
							GTTCAAGGGATCTCTCAGCAAGCATCCCATGACCAATTTCTCTTCTACTTGGGGCACCAATCCG
GCCAACTTCCCCAACACATGAAGGAGGAAATGAATActtaatgtccatttgaaatgcagttatg
ccatcttcatttccagcaacctgcattttatcatcgtcaaaacatctttttagcattatgatat
caaacaat

									
								

					

						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: 411
Transcript exons: 37222664-37222711,37222893-37223076,37225224-37225402
CTTAATGTCCATTTGAAATGCAGTTATGCCATCTTCATTTCCAGCAACCTTGAAATCCATATCT
CCAGATGCATCTTCAGATCCAGTTATGTCAGACAGAATAAGCGGAGTTCCATCTCCACCAAATT
CCTTGGTGTCCAGTACCATACCCATTGCAATTCCAGCAATAGAACCCTTAATAGGAACCCCAGC
ATCTTGCAATGCTAAGCAACCTCCACAAACAGAAGCCATGCTTGAAGAGCCATTGCTTTCTGTG
ATAGTACTCTCAACACGTATAGTGTAAGGGAAATCATCTTCAGAAGGCAAAATTGGTTCAAGGG
ATCTCTCAGCAAGCATCCCATGACCAATTTCTCTTCTACTTGGGGCACCAATCCGGCCAACTTC
CCCAACACATGAAGGAGGAAATGAATA
						
					

						Genomic sequence
						
							CTTAATGTCCATTTGAAATGCAGTTATGCCATCTTCATTTCCAGCAACCTGCATTTTATCATCG
TCAAAACATCTTTTTAGCATTATGATATCAAACAATGTTGATCAAATATAAATTAACTAAAAAC
GAAAATATACAACAAACCAAACTGAATTCCCCAAATTACTTATCATCCAAATAATCATGTGAGG
AAATAAGTATCACAAGTTCAATCATGTAAATTATAACCTTGAAATCCATATCTCCAGATGCATC
TTCAGATCCAGTTATGTCAGACAGAATAAGCGGAGTTCCATCTCCACCAAATTCCTTGGTGTCC
AGTACCATACCCATTGCAATTCCAGCAATAGAACCCTTAATAGGAACCCCAGCATCTTGCAATG
CTAAGCAACCTCCACAAACAGAAGCCATGCTAAAATAAAAATATATATATAAATAAAATGTGGA
AACTTCAAAGCTATGTAAGAAAAAAGAACAGTATAGTGTGCAAAAATATAAAACAGTGAATCAG
AGGTGGGAGAATATGGCATCTTCCTGAAATAGTAAAACTATTACATTGACTGGAAAATAGCCAT
GAGCCCATGAGCTTTAGATCTGCGTTTTATCAATAAATGCTAAACAATAGCAAAAATTGCATAG
CTTCGGAATGTCTTCTGCTTCTTACCCATCACAAAACCATGATTAATTATATGTTGCGAATCAA
TCTAAATATTCTGAAATTTATTGTATAATGGAAACAAAATCTGATTTATAGGAACAAAATCTCC
TATAAGCAATTGTATTTATGATTATAGACCTATATAATAAAATCAATGATGTGTAGCTGATACA
CGGTTTCAGTAAACCTGTCATCTGCTTCCTTATGGTATCTAAGCTTAAAACAGAGGCAGCCCCA
GAACCGTGCCTACCCGCAAAACTCTCCTTTTGTTTCAGTTCATTTAGATATTTAGGGTCCTAGT
AGTGTCACTTTTCACTTAGGCATTTCAATATTAAAACAGCAGCCCCAGAACCGTGCCCACCCGC
AAAACTCTCCTTTTGTTTCAGTTCATTTAGATATTTAGGGTCCTAGTAGTGTCACTGTCACTTT
GGCACTTCAATATTTTGTTACTTCTATTGACAATGATTTTCATTCTATTTGGTTCTTCCTATCA
AGAAATTATTCAAAACACTGTCCCAGCTTCCAATGTTTTTACTCTGAGATTAAAATCTATGCAA
ATATGTGACCTATATTAAGGTGATACCTTTTCTATTGGCTTGGTTACTCATATCAGTTAAATGT
TTATTGGCCAGGATCCCCATCATATAAGAGTTCAATCTCAGAGGGTAATTTGTGTTTGCTGGAG
CTTAATTTCATGGAATGTTAAGAAACATAATGAAGCAGCTAGATGCATGCAGAGGCTGGACATC
AAGGGTAAGTAAGGATGGCAACGGGACAGGTAGTAGCTACCTGCTACCTGCCAGATAATTATCC
ACCCCGTACGGGCACAGCCGCACAGGTACCCATTAAGCGGATACTGGTGGATTTTTTCAATATT
TGTGGATATCCATGAATATTTACTGTAAAAAAAACAGTTTAAAATACAATTTAACCCATTTTTT
AATTATTTTAACAATTTCTTCAAAAACATAGTTCAAAGGTCAAAATTAAAATTATTCAAATATT
TTACACAATTATCCCAATCTAAATTATTCAGTTTTGAAACTAAATTTAAATTTAAAATACTTCA
ATCTCATAAGTAAATAAACTAAAATAATTCAATCTCACAAGTCCAAACAAAATTACTTAAACAA
TAACATTTAAGTAATTTTAATATAATGGGTGTTTAACAAGTCCAAGCTGTCCTACATTTTGCTT
ACAACCCTCCTTTTCATTATTACCATTTAATGATTTGCTTACTATAGGCTTTGTTATCTCGAGC
CAGATTTCCCAAAATATTAACTAAGTTCCTTACAGTTAGCTGTCCTCAGGTTGACCTTGCTTGT
AATAAATTTGATGTGTGTGAGAAGAGAGAAACAGATTTTATTTTCTCAATTTGCTTGAGTTTAC
CACTCTGCAGAGTGATCTATTTATTATAATAATAATGATTACAAAGATAATAAATAACTACTAC
TATTTCAATAGAACTACTTCCGAAAGAGAACTACTTCCTATTTCCTAAGATACAATGAACTTAG
CTAAACACAATAACTAAGCTACTGGGAAAAGTAATAATCATTAAATGCTCCTATTTCCAAATAA
TATGTATGCTCAATCTTGCAGAGAAGTATTAGACTTAAGCTTTAGAAAATCTGTAAATATACAA
TCAACTGTATTTATGCTGATTAGATTAGATCAATAAATAATTATTACTTTATTAGGCCAGAGAT
TAGTTTGTGATTAGCACAATTAATTCTTTAATTACTCTGATTGTAAATTAAACTATAATACCAG
AACCAGAGCATGTGCGTATCTGAACACAAATTTTCATTCAATCTTCATCTTTTTCTGAGAATAA
TGATGACAATTGACAAACAAATAAAAAAAATTGGAAATTGAAAATGGAATTAAAAAAAACTCAC
CTTGAAGAGCCATTGCTTTCTGTGATAGTACTCTCAACACGTATAGTGTAAGGGAAATCATCTT
CAGAAGGCAAAATTGGTTCAAGGGATCTCTCAGCAAGCATCCCATGACCAATTTCTCTTCTACT
TGGGGCACCAATCCGGCCAACTTCCCCAACACATGAAGGAGGAAATGAATA
						
					

			
		

Sequences
Splice junction sequence	GTTCAAGGGATCTCTCAGCAAGCATCCCATGACCAATTTCTCTTCTACTTGGGGCACCAATCCG GCCAACTTCCCCAACACATGAAGGAGGAAATGAATActtaatgtccatttgaaatgcagttatg ccatcttcatttccagcaacctgcattttatcatcgtcaaaacatctttttagcattatgatat caaacaat
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: 411 Transcript exons: 37222664-37222711,37222893-37223076,37225224-37225402 CTTAATGTCCATTTGAAATGCAGTTATGCCATCTTCATTTCCAGCAACCTTGAAATCCATATCT CCAGATGCATCTTCAGATCCAGTTATGTCAGACAGAATAAGCGGAGTTCCATCTCCACCAAATT CCTTGGTGTCCAGTACCATACCCATTGCAATTCCAGCAATAGAACCCTTAATAGGAACCCCAGC ATCTTGCAATGCTAAGCAACCTCCACAAACAGAAGCCATGCTTGAAGAGCCATTGCTTTCTGTG ATAGTACTCTCAACACGTATAGTGTAAGGGAAATCATCTTCAGAAGGCAAAATTGGTTCAAGGG ATCTCTCAGCAAGCATCCCATGACCAATTTCTCTTCTACTTGGGGCACCAATCCGGCCAACTTC CCCAACACATGAAGGAGGAAATGAATA
Genomic sequence	CTTAATGTCCATTTGAAATGCAGTTATGCCATCTTCATTTCCAGCAACCTGCATTTTATCATCG TCAAAACATCTTTTTAGCATTATGATATCAAACAATGTTGATCAAATATAAATTAACTAAAAAC GAAAATATACAACAAACCAAACTGAATTCCCCAAATTACTTATCATCCAAATAATCATGTGAGG AAATAAGTATCACAAGTTCAATCATGTAAATTATAACCTTGAAATCCATATCTCCAGATGCATC TTCAGATCCAGTTATGTCAGACAGAATAAGCGGAGTTCCATCTCCACCAAATTCCTTGGTGTCC AGTACCATACCCATTGCAATTCCAGCAATAGAACCCTTAATAGGAACCCCAGCATCTTGCAATG CTAAGCAACCTCCACAAACAGAAGCCATGCTAAAATAAAAATATATATATAAATAAAATGTGGA AACTTCAAAGCTATGTAAGAAAAAAGAACAGTATAGTGTGCAAAAATATAAAACAGTGAATCAG AGGTGGGAGAATATGGCATCTTCCTGAAATAGTAAAACTATTACATTGACTGGAAAATAGCCAT GAGCCCATGAGCTTTAGATCTGCGTTTTATCAATAAATGCTAAACAATAGCAAAAATTGCATAG CTTCGGAATGTCTTCTGCTTCTTACCCATCACAAAACCATGATTAATTATATGTTGCGAATCAA TCTAAATATTCTGAAATTTATTGTATAATGGAAACAAAATCTGATTTATAGGAACAAAATCTCC TATAAGCAATTGTATTTATGATTATAGACCTATATAATAAAATCAATGATGTGTAGCTGATACA CGGTTTCAGTAAACCTGTCATCTGCTTCCTTATGGTATCTAAGCTTAAAACAGAGGCAGCCCCA GAACCGTGCCTACCCGCAAAACTCTCCTTTTGTTTCAGTTCATTTAGATATTTAGGGTCCTAGT AGTGTCACTTTTCACTTAGGCATTTCAATATTAAAACAGCAGCCCCAGAACCGTGCCCACCCGC AAAACTCTCCTTTTGTTTCAGTTCATTTAGATATTTAGGGTCCTAGTAGTGTCACTGTCACTTT GGCACTTCAATATTTTGTTACTTCTATTGACAATGATTTTCATTCTATTTGGTTCTTCCTATCA AGAAATTATTCAAAACACTGTCCCAGCTTCCAATGTTTTTACTCTGAGATTAAAATCTATGCAA ATATGTGACCTATATTAAGGTGATACCTTTTCTATTGGCTTGGTTACTCATATCAGTTAAATGT TTATTGGCCAGGATCCCCATCATATAAGAGTTCAATCTCAGAGGGTAATTTGTGTTTGCTGGAG CTTAATTTCATGGAATGTTAAGAAACATAATGAAGCAGCTAGATGCATGCAGAGGCTGGACATC AAGGGTAAGTAAGGATGGCAACGGGACAGGTAGTAGCTACCTGCTACCTGCCAGATAATTATCC ACCCCGTACGGGCACAGCCGCACAGGTACCCATTAAGCGGATACTGGTGGATTTTTTCAATATT TGTGGATATCCATGAATATTTACTGTAAAAAAAACAGTTTAAAATACAATTTAACCCATTTTTT AATTATTTTAACAATTTCTTCAAAAACATAGTTCAAAGGTCAAAATTAAAATTATTCAAATATT TTACACAATTATCCCAATCTAAATTATTCAGTTTTGAAACTAAATTTAAATTTAAAATACTTCA ATCTCATAAGTAAATAAACTAAAATAATTCAATCTCACAAGTCCAAACAAAATTACTTAAACAA TAACATTTAAGTAATTTTAATATAATGGGTGTTTAACAAGTCCAAGCTGTCCTACATTTTGCTT ACAACCCTCCTTTTCATTATTACCATTTAATGATTTGCTTACTATAGGCTTTGTTATCTCGAGC CAGATTTCCCAAAATATTAACTAAGTTCCTTACAGTTAGCTGTCCTCAGGTTGACCTTGCTTGT AATAAATTTGATGTGTGTGAGAAGAGAGAAACAGATTTTATTTTCTCAATTTGCTTGAGTTTAC CACTCTGCAGAGTGATCTATTTATTATAATAATAATGATTACAAAGATAATAAATAACTACTAC TATTTCAATAGAACTACTTCCGAAAGAGAACTACTTCCTATTTCCTAAGATACAATGAACTTAG CTAAACACAATAACTAAGCTACTGGGAAAAGTAATAATCATTAAATGCTCCTATTTCCAAATAA TATGTATGCTCAATCTTGCAGAGAAGTATTAGACTTAAGCTTTAGAAAATCTGTAAATATACAA TCAACTGTATTTATGCTGATTAGATTAGATCAATAAATAATTATTACTTTATTAGGCCAGAGAT TAGTTTGTGATTAGCACAATTAATTCTTTAATTACTCTGATTGTAAATTAAACTATAATACCAG AACCAGAGCATGTGCGTATCTGAACACAAATTTTCATTCAATCTTCATCTTTTTCTGAGAATAA TGATGACAATTGACAAACAAATAAAAAAAATTGGAAATTGAAAATGGAATTAAAAAAAACTCAC CTTGAAGAGCCATTGCTTTCTGTGATAGTACTCTCAACACGTATAGTGTAAGGGAAATCATCTT CAGAAGGCAAAATTGGTTCAAGGGATCTCTCAGCAAGCATCCCATGACCAATTTCTCTTCTACT TGGGGCACCAATCCGGCCAACTTCCCCAACACATGAAGGAGGAAATGAATA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.290665574

Conservation Information
Conserved circRNAs	NA
PMCS	0.290665574

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							37225329-37222666(-)
						
						Potential amino acid sequence
						
							MLAERSLEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKGSIAGIAMGM
VLDTKEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKYSFPPSCVGEVGRIGA
PSRREIGHGMLAERSLEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKG
SIAGIAMGMVLDTKEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKYSFPPSC
VGEVGRIGAPSRREIGHGMLAERSLEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLAL
QDAGVPIKGSIAGIAMGMVLDTKEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMD
IKYSFPPSCVGEVGRIGAPSRREIGHGMLAERSLEPILPSEDDFPYTIRVESTITESNGSSSMA
SVCGGCLALQDAGVPIKGSIAGIAMGMVLDTKEFGGDGTPLILSDITGSEDASGDMDFKVAGNE
DGITAFQMDIK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						cytoplasmic male sterility (acting as miRNA sponges;with protein-coding potential)

Functional Information
Coding potential	Y
Potential coding position	37225329-37222666(-)
Potential amino acid sequence	MLAERSLEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKGSIAGIAMGM VLDTKEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKYSFPPSCVGEVGRIGA PSRREIGHGMLAERSLEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKG SIAGIAMGMVLDTKEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKYSFPPSC VGEVGRIGAPSRREIGHGMLAERSLEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLAL QDAGVPIKGSIAGIAMGMVLDTKEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMD IKYSFPPSCVGEVGRIGAPSRREIGHGMLAERSLEPILPSEDDFPYTIRVESTITESNGSSSMA SVCGGCLALQDAGVPIKGSIAGIAMGMVLDTKEFGGDGTPLILSDITGSEDASGDMDFKVAGNE DGITAFQMDIK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	cytoplasmic male sterility (acting as miRNA sponges;with protein-coding potential)

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

circRNA

Detail information of GLYMA_19G116700_circ_g.3

Address

Any questions?

Supported by