Plant Circular RNA Database

Detail information of GLYMA_17G239500_circ_g.2

			
						 General Information
					
						CircRNA Name
						GLYMA_17G239500_circ_g.2
					
						ID in PlantcircBase
						gma_circ_004583
					
						Alias
						Gm17circRNA2241
					
						Organism
						
							Glycine max						
					
						Position
						
							chr17: 39508152-39509813  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI
					
						Parent gene
						
							GLYMA_17G239500						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_17G239500_circ_g.3 GLYMA_17G239500_circ_g.4 						
					
						Support reads
						NA
					
						Tissues
						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  
						
							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
						KRH05643:5
KRH05641:5
KRH05644:5
KRH05642:5
KRH05645:5

General Information
CircRNA Name	GLYMA_17G239500_circ_g.2
ID in PlantcircBase	gma_circ_004583
Alias	Gm17circRNA2241
Organism	Glycine max
Position	chr17: 39508152-39509813 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI
Parent gene	GLYMA_17G239500
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_17G239500_circ_g.3 GLYMA_17G239500_circ_g.4
Support reads	NA
Tissues	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	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	KRH05643:5 KRH05641:5 KRH05644:5 KRH05642:5 KRH05645:5

			
						 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  
						
							CAACAAGGGACACAACACATTCATCGAACATTGCAGATGAGGGAGAACCAGTGCTCCCATAAAC
ATGATCAAATGTAAATGAATGTGCACCAATTTGTACctgcaaaagcctagtaagtttactatcc
ctataaggaacatgaacaccttcttttctcttcttttcatcaccaagcgcactaataacattac
caagcgct

									
								

					

						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: 858
Transcript exons: 39508152-39508276,39508361-39508542,39509072-39509325,39
509426-39509575,39509667-39509813
CTGCAAAAGCCTAGTAAGTTTACTATCCCTATAAGGAACATGAACACCTTCTTTTCTCTTCTTT
TCATCACCAAGCGCACTAATAACATTACCAAGCGCTAGAAGGCCTTTGTTAATGTGGACTCCTT
CCTTAAATCGCAGACCATCAGACCCGGTTCTTTTAGCTCGTTCTGATCCAGCAAGATCTACCAA
GTGCAACTTGGCACAAAGATATTCTTCATTCATTGTATCATTTAAACTGATCTCACCAGGACTA
TTGAGCTTTCGCATTTGTTCTAATGTGATGGTGAAGATAGCATGTGAACGACTGGATTGGTTGT
TCATATTTGTACTCCCAGTTGCTCTACTTAATGATCCTTGTTCTAGGCAAGCAGCCATTTCTTT
TAGGGTTGTAACACTGACTTCAGTACATCCTGCTAGAGTAATGACACCATTTGATGACTCACGG
ATTTGTATTGGTGGTTTCCCAGGAATAGTCACTTTCCCTGCATGTCCATTTGCAGTTTCTGGTT
TGTTCATAGAGGATGGGTCCAACAAGTCTCTTACTTCTTCTTTTAGAATCTCAATAAAGGAAAC
ATGCAGCTGAAATTCAATCTGATGCTTTAAGGTGTCAATTTTGTTAAACAGGGAACTCATAACT
AGAGGTATTATTCCCTCTTGGCAACCATCTTTAAAGCCAGTGCCCATGGTGTATGTTTTCCCAG
AACCTGTCTGACCATATGCAAGAACAGTAGCATTATATCCTTGGAACAAACCATCAACAAGGGA
CACAACACATTCATCGAACATTGCAGATGAGGGAGAACCAGTGCTCCCATAAACATGATCAAAT
GTAAATGAATGTGCACCAATTTGTAC
						
					

						Genomic sequence
						
							CTGCAAAAGCCTAGTAAGTTTACTATCCCTATAAGGAACATGAACACCTTCTTTTCTCTTCTTT
TCATCACCAAGCGCACTAATAACATTACCAAGCGCTAGAAGGCCTTTGTTAATGTGGACTCCTG
ATTGAAAGAAAAAATTATTAGAGAATTCATAATGATCAAAAGCAAGTTTAGAAGAAACAAGTGA
AAATTGTCGTGCCTAACCTTCCTTAAATCGCAGACCATCAGACCCGGTTCTTTTAGCTCGTTCT
GATCCAGCAAGATCTACCAAGTGCAACTTGGCACAAAGATATTCTTCATTCATTGTATCATTTA
AACTGATCTCACCAGGACTATTGAGCTTTCGCATTTGTTCTAATGTGATGGTGAAGATAGCATG
TGAACGACTGGTTGGACACATAACAGAAGAAGAATAAGTAATAGAAGAGAACTCCAGAAAGATA
AATGTAACAACATTTCGATGAACAACTTTTAACCCTGAAGGCTGAACTGATGCCAACAAGTAAA
TTCTGGATTGATTCATTAACAAAATCATTAGAAGTGCAGGAGACTGCGAGCATTCATACAAATT
GCAATACCAATCGCTCCATCTATTAGTTATTCCCTTAACTAACAAGAAACAGAAAATATTTGAT
ATGGAATTGGCTTCAAAGGAAAAAATTGAAAGCTCAGATTGATTGTGGAAAGCTTAAGCCATCA
GAAAGTTTAAAACCAAAAAGTAATTTATGTTTTATACATCACATCTTCTCTTAGTTTTTGCTTT
ATTATCAAAATGTCACATTATACAGCTCATGCTCTAACAAATTTCCCTAGCCTATTTATCCAAA
ATTAGCTTAAGAATCCAAAAGTGAGATAAAAAATATTTCATTAGAGATGAGTTTATGCAGTTAA
AAGGAGGGAAAATGCATAAGCAACCTGGATTGGTTGTTCATATTTGTACTCCCAGTTGCTCTAC
TTAATGATCCTTGTTCTAGGCAAGCAGCCATTTCTTTTAGGGTTGTAACACTGACTTCAGTACA
TCCTGCTAGAGTAATGACACCATTTGATGACTCACGGATTTGTATTGGTGGTTTCCCAGGAATA
GTCACTTTCCCTGCATGTCCATTTGCAGTTTCTGGTTTGTTCATAGAGGATGGGTCCAACAAGT
CTCTTACTTCTTCTTTTAGAATCTTTAATCAATCAAAATTTTTTGTTAGATGCTTCATCTAAAC
AATTTCACAAACATGAAATCTTTTAATTTCAGATATTAAAGCAAAGCTATTAACTGACCTCAAT
AAAGGAAACATGCAGCTGAAATTCAATCTGATGCTTTAAGGTGTCAATTTTGTTAAACAGGGAA
CTCATAACTAGAGGTATTATTCCCTCTTGGCAACCATCTTTAAAGCCAGTGCCCATGGTGTATG
TTTTCCCAGAACCTGTCTGCAATGGAGTGAAAATGTCATATACCAAGGAGGAAGAAGTCATAAG
TGTAATGGCATTTAACTTGTTTTTCCTTTAGCTGTAATTATACCTGACCATATGCAAGAACAGT
AGCATTATATCCTTGGAACAAACCATCAACAAGGGACACAACACATTCATCGAACATTGCAGAT
GAGGGAGAACCAGTGCTCCCATAAACATGATCAAATGTAAATGAATGTGCACCAATTTGTAC
						
					

			
		

Sequences
Splice junction sequence	CAACAAGGGACACAACACATTCATCGAACATTGCAGATGAGGGAGAACCAGTGCTCCCATAAAC ATGATCAAATGTAAATGAATGTGCACCAATTTGTACctgcaaaagcctagtaagtttactatcc ctataaggaacatgaacaccttcttttctcttcttttcatcaccaagcgcactaataacattac caagcgct
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: 858 Transcript exons: 39508152-39508276,39508361-39508542,39509072-39509325,39 509426-39509575,39509667-39509813 CTGCAAAAGCCTAGTAAGTTTACTATCCCTATAAGGAACATGAACACCTTCTTTTCTCTTCTTT TCATCACCAAGCGCACTAATAACATTACCAAGCGCTAGAAGGCCTTTGTTAATGTGGACTCCTT CCTTAAATCGCAGACCATCAGACCCGGTTCTTTTAGCTCGTTCTGATCCAGCAAGATCTACCAA GTGCAACTTGGCACAAAGATATTCTTCATTCATTGTATCATTTAAACTGATCTCACCAGGACTA TTGAGCTTTCGCATTTGTTCTAATGTGATGGTGAAGATAGCATGTGAACGACTGGATTGGTTGT TCATATTTGTACTCCCAGTTGCTCTACTTAATGATCCTTGTTCTAGGCAAGCAGCCATTTCTTT TAGGGTTGTAACACTGACTTCAGTACATCCTGCTAGAGTAATGACACCATTTGATGACTCACGG ATTTGTATTGGTGGTTTCCCAGGAATAGTCACTTTCCCTGCATGTCCATTTGCAGTTTCTGGTT TGTTCATAGAGGATGGGTCCAACAAGTCTCTTACTTCTTCTTTTAGAATCTCAATAAAGGAAAC ATGCAGCTGAAATTCAATCTGATGCTTTAAGGTGTCAATTTTGTTAAACAGGGAACTCATAACT AGAGGTATTATTCCCTCTTGGCAACCATCTTTAAAGCCAGTGCCCATGGTGTATGTTTTCCCAG AACCTGTCTGACCATATGCAAGAACAGTAGCATTATATCCTTGGAACAAACCATCAACAAGGGA CACAACACATTCATCGAACATTGCAGATGAGGGAGAACCAGTGCTCCCATAAACATGATCAAAT GTAAATGAATGTGCACCAATTTGTAC
Genomic sequence	CTGCAAAAGCCTAGTAAGTTTACTATCCCTATAAGGAACATGAACACCTTCTTTTCTCTTCTTT TCATCACCAAGCGCACTAATAACATTACCAAGCGCTAGAAGGCCTTTGTTAATGTGGACTCCTG ATTGAAAGAAAAAATTATTAGAGAATTCATAATGATCAAAAGCAAGTTTAGAAGAAACAAGTGA AAATTGTCGTGCCTAACCTTCCTTAAATCGCAGACCATCAGACCCGGTTCTTTTAGCTCGTTCT GATCCAGCAAGATCTACCAAGTGCAACTTGGCACAAAGATATTCTTCATTCATTGTATCATTTA AACTGATCTCACCAGGACTATTGAGCTTTCGCATTTGTTCTAATGTGATGGTGAAGATAGCATG TGAACGACTGGTTGGACACATAACAGAAGAAGAATAAGTAATAGAAGAGAACTCCAGAAAGATA AATGTAACAACATTTCGATGAACAACTTTTAACCCTGAAGGCTGAACTGATGCCAACAAGTAAA TTCTGGATTGATTCATTAACAAAATCATTAGAAGTGCAGGAGACTGCGAGCATTCATACAAATT GCAATACCAATCGCTCCATCTATTAGTTATTCCCTTAACTAACAAGAAACAGAAAATATTTGAT ATGGAATTGGCTTCAAAGGAAAAAATTGAAAGCTCAGATTGATTGTGGAAAGCTTAAGCCATCA GAAAGTTTAAAACCAAAAAGTAATTTATGTTTTATACATCACATCTTCTCTTAGTTTTTGCTTT ATTATCAAAATGTCACATTATACAGCTCATGCTCTAACAAATTTCCCTAGCCTATTTATCCAAA ATTAGCTTAAGAATCCAAAAGTGAGATAAAAAATATTTCATTAGAGATGAGTTTATGCAGTTAA AAGGAGGGAAAATGCATAAGCAACCTGGATTGGTTGTTCATATTTGTACTCCCAGTTGCTCTAC TTAATGATCCTTGTTCTAGGCAAGCAGCCATTTCTTTTAGGGTTGTAACACTGACTTCAGTACA TCCTGCTAGAGTAATGACACCATTTGATGACTCACGGATTTGTATTGGTGGTTTCCCAGGAATA GTCACTTTCCCTGCATGTCCATTTGCAGTTTCTGGTTTGTTCATAGAGGATGGGTCCAACAAGT CTCTTACTTCTTCTTTTAGAATCTTTAATCAATCAAAATTTTTTGTTAGATGCTTCATCTAAAC AATTTCACAAACATGAAATCTTTTAATTTCAGATATTAAAGCAAAGCTATTAACTGACCTCAAT AAAGGAAACATGCAGCTGAAATTCAATCTGATGCTTTAAGGTGTCAATTTTGTTAAACAGGGAA CTCATAACTAGAGGTATTATTCCCTCTTGGCAACCATCTTTAAAGCCAGTGCCCATGGTGTATG TTTTCCCAGAACCTGTCTGCAATGGAGTGAAAATGTCATATACCAAGGAGGAAGAAGTCATAAG TGTAATGGCATTTAACTTGTTTTTCCTTTAGCTGTAATTATACCTGACCATATGCAAGAACAGT AGCATTATATCCTTGGAACAAACCATCAACAAGGGACACAACACATTCATCGAACATTGCAGAT GAGGGAGAACCAGTGCTCCCATAAACATGATCAAATGTAAATGAATGTGCACCAATTTGTAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.383106864

Conservation Information
Conserved circRNAs	NA
PMCS	0.383106864

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							39509797-39508250(+)
39509746-39508154(-)
39508242-39509514(-)
						
					

						Potential amino acid sequence
						
							MCTNLYLQKPSKFTIPIRNMNTFFSLLFITKRTNNITKR*(+)
MFDECVVSLVDGLFQGYNATVLAYGQTGSGKTYTMGTGFKDGCQEGIIPLVMSSLFNKIDTLKH
QIEFQLHVSFIEILKEEVRDLLDPSSMNKPETANGHAGKVTIPGKPPIQIRESSNGVITLAGCT
EVSVTTLKEMAACLEQGSLSRATGSTNMNNQSSRSHAIFTITLEQMRKLNSPGEISLNDTMNEE
YLCAKLHLVDLAGSERAKRTGSDGLRFKEGVHINKGLLALGNVISALGDEKKRKEGVHVPYRDS
KLTRLLQVQIGAHSFTFDHVYGSTGSPSSAMFDECVVSLVDGLFQGYNATVLAYGQTGSGKTYT
MGTGFKDGCQEGIIPLVMSSLFNKIDTLKHQIEFQLHVSFIEILKEEVRDLLDPSSMNKPETAN
GHAGKVTIPGKPPIQIRESSNGVITLAGCTEVSVTTLKEMAACLEQGSLSRATGSTNMNNQSSR
SHAIFTITLEQMRKLNSPGEISLNDTMNEEYLCAKLHLVDLAGSERAKRTGSDGLRFKEGVHIN
KGLLALGNVISALGDEKKRKEGVHVPYRDSKLTRLLQVQIGAHSFTFDHVYGSTGSPSSAMFDE
CVVSLVDGLFQGYNATVLAYGQTGSGKTYTMGTGFKDGCQEGIIPLVMSSLFNKIDTLKHQIEF
QLHVSFIEILKEEVRDLLDPSSMNKPETANGHAGKVTIPGKPPIQIRESSNGVITLAGCTEVSV
TTLKEMAACLEQGSLSRATGSTNMNNQSSRSHAIFTITLEQMRKLNSPGEISLNDTMNEEYLCA
KLHLVDLAGSERAKRTGSDGLRFKEGVHINKGLLALGNVISALGDEKKRKEGVHVPYRDSKLTR
LLQVQIGAHSFTFDHVYGSTGSPSSAMFDECVVSLVDGLFQGYNATVLAYGQTGSGKTYTMGTG
FKDGCQEGIIPLVMSSLFNKIDTLKHQIEFQLHVSFIEILKEEVRDLLDPSSMNKPETANGHAG
KVTIPGKPPIQIRESSNGVITLAGCTEVSVTTLKEMAACLEQGSLSRATGSTNMNNQSSRSHAI
FTITLEQMRKLNSPGEISLNDTMNEEYLCAKLHLVDLAGSERAKRTGSDGLRFKEGVHINKGLL
ALGNVISALGDEKKRKEGVHVPYRDSKLTRLLQ(-)
MLLVRLVMKRREKKVFMFLIGIVNLLGFCRYKLVHIHLHLIMFMGALVLPHLQCSMNVLCPLLM
VCSKDIMLLFLHMVRQVLGKHTPWALALKMVAKRE*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	39509797-39508250(+) 39509746-39508154(-) 39508242-39509514(-)
Potential amino acid sequence	MCTNLYLQKPSKFTIPIRNMNTFFSLLFITKRTNNITKR(+) MFDECVVSLVDGLFQGYNATVLAYGQTGSGKTYTMGTGFKDGCQEGIIPLVMSSLFNKIDTLKH QIEFQLHVSFIEILKEEVRDLLDPSSMNKPETANGHAGKVTIPGKPPIQIRESSNGVITLAGCT EVSVTTLKEMAACLEQGSLSRATGSTNMNNQSSRSHAIFTITLEQMRKLNSPGEISLNDTMNEE YLCAKLHLVDLAGSERAKRTGSDGLRFKEGVHINKGLLALGNVISALGDEKKRKEGVHVPYRDS KLTRLLQVQIGAHSFTFDHVYGSTGSPSSAMFDECVVSLVDGLFQGYNATVLAYGQTGSGKTYT MGTGFKDGCQEGIIPLVMSSLFNKIDTLKHQIEFQLHVSFIEILKEEVRDLLDPSSMNKPETAN GHAGKVTIPGKPPIQIRESSNGVITLAGCTEVSVTTLKEMAACLEQGSLSRATGSTNMNNQSSR SHAIFTITLEQMRKLNSPGEISLNDTMNEEYLCAKLHLVDLAGSERAKRTGSDGLRFKEGVHIN KGLLALGNVISALGDEKKRKEGVHVPYRDSKLTRLLQVQIGAHSFTFDHVYGSTGSPSSAMFDE CVVSLVDGLFQGYNATVLAYGQTGSGKTYTMGTGFKDGCQEGIIPLVMSSLFNKIDTLKHQIEF QLHVSFIEILKEEVRDLLDPSSMNKPETANGHAGKVTIPGKPPIQIRESSNGVITLAGCTEVSV TTLKEMAACLEQGSLSRATGSTNMNNQSSRSHAIFTITLEQMRKLNSPGEISLNDTMNEEYLCA KLHLVDLAGSERAKRTGSDGLRFKEGVHINKGLLALGNVISALGDEKKRKEGVHVPYRDSKLTR LLQVQIGAHSFTFDHVYGSTGSPSSAMFDECVVSLVDGLFQGYNATVLAYGQTGSGKTYTMGTG FKDGCQEGIIPLVMSSLFNKIDTLKHQIEFQLHVSFIEILKEEVRDLLDPSSMNKPETANGHAG KVTIPGKPPIQIRESSNGVITLAGCTEVSVTTLKEMAACLEQGSLSRATGSTNMNNQSSRSHAI FTITLEQMRKLNSPGEISLNDTMNEEYLCAKLHLVDLAGSERAKRTGSDGLRFKEGVHINKGLL ALGNVISALGDEKKRKEGVHVPYRDSKLTRLLQ(-) MLLVRLVMKRREKKVFMFLIGIVNLLGFCRYKLVHIHLHLIMFMGALVLPHLQCSMNVLCPLLM VCSKDIMLLFLHMVRQVLGKHTPWALALKMVAKRE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_17G239500_circ_g.2

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