Plant Circular RNA Database

Detail information of GLYMA_19G120400_circ_g.1

			
						 General Information
					
						CircRNA Name
						GLYMA_19G120400_circ_g.1
					
						ID in PlantcircBase
						gma_circ_007628
					
						Alias
						gma-circRNA2585
					
						Organism
						
							Glycine max						
					
						Position
						
							chr19: 37808986-37816258  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							GLYMA_19G120400						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							GLYMA_19G120400_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						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
						KRG94948:5

General Information
CircRNA Name	GLYMA_19G120400_circ_g.1
ID in PlantcircBase	gma_circ_007628
Alias	gma-circRNA2585
Organism	Glycine max
Position	chr19: 37808986-37816258 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	GLYMA_19G120400
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	GLYMA_19G120400_circ_g.2
Support reads	NA
Tissues	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	KRG94948:5

			
						 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  
						
							CTGGATTGTTAAAGCATAGAGCTACATATGAAATAATGTCTCCCGAAGATATTGGTCATGAAAA
GTCCAGTGGAGTTAATATGGTACTAGGGAAGCTAAGatcggatagagagtttctttatcaaatt
ttggaagaagttatcaaagctggggcaacaactttgggcataggtgacactgtgggcataacaa
tgccattc

						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: 576
Transcript exons: 37808986-37809199,37809278-37809358,37809674-37809766,37
809867-37809953,37816158-37816258
ATCGGATAGAGAGTTTCTTTATCAAATTTTGGAAGAAGTTATCAAAGCTGGGGCAACAACTTTG
GGCATAGGTGACACTGTGGGCATAACAATGCCATTCGAGATTAGACAATTGATTGCTGATATAA
AAGCCAATGTCCCTGGAGCAGAAAATGTTATTATTTCTATGCACTGTCATAATGATCTTGGACA
TGCTACTGCAAACGCAATAGAGGCTGCTCAAGCTGGTGCAATGCAATTAGAAGTAACAATTAAT
GGGATTGGTGAAAGGGCTGGTAATGCCTCATTAGAAGAGGTTGTGATGGCCCTAAAATGCAGGG
GAGATCAAGTCTTAGGTGGTTTGTATACTGGAATTAATACAAGGCACTTATTGAAGACAAGCAA
GATGGTCGAAGAGTTTTCTGGTATGTATTTACAACCACACAAAGCTGTTGTAGGTGATAATGCC
TTTCTCCATGAAAGTGGCGTTCACCAGGCTGGATTGTTAAAGCATAGAGCTACATATGAAATAA
TGTCTCCCGAAGATATTGGTCATGAAAAGTCCAGTGGAGTTAATATGGTACTAGGGAAGCTAAG
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CTGGATTGTTAAAGCATAGAGCTACATATGAAATAATGTCTCCCGAAGATATTGGTCATGAAAA GTCCAGTGGAGTTAATATGGTACTAGGGAAGCTAAGatcggatagagagtttctttatcaaatt ttggaagaagttatcaaagctggggcaacaactttgggcataggtgacactgtgggcataacaa tgccattc
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: 576 Transcript exons: 37808986-37809199,37809278-37809358,37809674-37809766,37 809867-37809953,37816158-37816258 ATCGGATAGAGAGTTTCTTTATCAAATTTTGGAAGAAGTTATCAAAGCTGGGGCAACAACTTTG GGCATAGGTGACACTGTGGGCATAACAATGCCATTCGAGATTAGACAATTGATTGCTGATATAA AAGCCAATGTCCCTGGAGCAGAAAATGTTATTATTTCTATGCACTGTCATAATGATCTTGGACA TGCTACTGCAAACGCAATAGAGGCTGCTCAAGCTGGTGCAATGCAATTAGAAGTAACAATTAAT GGGATTGGTGAAAGGGCTGGTAATGCCTCATTAGAAGAGGTTGTGATGGCCCTAAAATGCAGGG GAGATCAAGTCTTAGGTGGTTTGTATACTGGAATTAATACAAGGCACTTATTGAAGACAAGCAA GATGGTCGAAGAGTTTTCTGGTATGTATTTACAACCACACAAAGCTGTTGTAGGTGATAATGCC TTTCTCCATGAAAGTGGCGTTCACCAGGCTGGATTGTTAAAGCATAGAGCTACATATGAAATAA TGTCTCCCGAAGATATTGGTCATGAAAAGTCCAGTGGAGTTAATATGGTACTAGGGAAGCTAAG
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.330276897

Conservation Information
Conserved circRNAs	NA
PMCS	0.330276897

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							37809078-37816255(+)
37809180-37816256(-)
						
						Potential amino acid sequence
						
							MPFEIRQLIADIKANVPGAENVIISMHCHNDLGHATANAIEAAQAGAMQLEVTINGIGERAGNA
SLEEVVMALKCRGDQVLGGLYTGINTRHLLKTSKMVEEFSGMYLQPHKAVVGDNAFLHESGVHQ
AGLLKHRATYEIMSPEDIGHEKSSGVNMVLGKLRSDREFLYQILEEVIKAGATTLGIGDTVGIT
MPFEIRQLIADIKANVPGAENVIISMHCHNDLGHATANAIEAAQAGAMQLEVTINGIGERAGNA
SLEEVVMALKCRGDQVLGGLYTGINTRHLLKTSKMVEEFSGMYLQPHKAVVGDNAFLHESGVHQ
AGLLKHRATYEIMSPEDIGHEKSSGVNMVLGKLRSDREFLYQILEEVIKAGATTLGIGDTVGIT
MPFEIRQLIADIKANVPGAENVIISMHCHNDLGHATANAIEAAQAGAMQLEVTINGIGERAGNA
SLEEVVMALKCRGDQVLGGLYTGINTRHLLKTSKMVEEFSGMYLQPHKAVVGDNAFLHESGVHQ
AGLLKHRATYEIMSPEDIGHEKSSGVNMVLGKLRSDREFLYQILEEVIKAGATTLGIGDTVGIT
MPFEIRQLIADIKANVPGAENVIISMHCHNDLGHATANAIEAAQAGAMQLEVTINGIGERAGNA
SLEEVVMALKCRGDQVLGGLYTGINTRHLLKTSKMVEEFSGMYLQPHKAVVGDNAFLHESGVHQ
AGLLKHRATYEIMSPEDIGHEKSSGVNMVLGKL(+)
MSKIIMTVHRNNNIFCSRDIGFYISNQLSNLEWHCYAHSVTYAQSCCPSFDNFFQNLIKKLSIR
S*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						cytoplasmic male sterility

Functional Information
Coding potential	Y
Potential coding position	37809078-37816255(+) 37809180-37816256(-)
Potential amino acid sequence	MPFEIRQLIADIKANVPGAENVIISMHCHNDLGHATANAIEAAQAGAMQLEVTINGIGERAGNA SLEEVVMALKCRGDQVLGGLYTGINTRHLLKTSKMVEEFSGMYLQPHKAVVGDNAFLHESGVHQ AGLLKHRATYEIMSPEDIGHEKSSGVNMVLGKLRSDREFLYQILEEVIKAGATTLGIGDTVGIT MPFEIRQLIADIKANVPGAENVIISMHCHNDLGHATANAIEAAQAGAMQLEVTINGIGERAGNA SLEEVVMALKCRGDQVLGGLYTGINTRHLLKTSKMVEEFSGMYLQPHKAVVGDNAFLHESGVHQ AGLLKHRATYEIMSPEDIGHEKSSGVNMVLGKLRSDREFLYQILEEVIKAGATTLGIGDTVGIT MPFEIRQLIADIKANVPGAENVIISMHCHNDLGHATANAIEAAQAGAMQLEVTINGIGERAGNA SLEEVVMALKCRGDQVLGGLYTGINTRHLLKTSKMVEEFSGMYLQPHKAVVGDNAFLHESGVHQ AGLLKHRATYEIMSPEDIGHEKSSGVNMVLGKLRSDREFLYQILEEVIKAGATTLGIGDTVGIT MPFEIRQLIADIKANVPGAENVIISMHCHNDLGHATANAIEAAQAGAMQLEVTINGIGERAGNA SLEEVVMALKCRGDQVLGGLYTGINTRHLLKTSKMVEEFSGMYLQPHKAVVGDNAFLHESGVHQ AGLLKHRATYEIMSPEDIGHEKSSGVNMVLGKL(+) MSKIIMTVHRNNNIFCSRDIGFYISNQLSNLEWHCYAHSVTYAQSCCPSFDNFFQNLIKKLSIR S*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	cytoplasmic male sterility

			
						 Other Information
					
						References
						Chen et al., 2018

circRNA

Detail information of GLYMA_19G120400_circ_g.1

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