Plant Circular RNA Database

Detail information of Gh_D12G2141_circ_g.2

			
						 General Information
					
						CircRNA Name
						Gh_D12G2141_circ_g.2
					
						ID in PlantcircBase
						ghi_circ_003444
					
						Alias
						D12:54449907|54451069
					
						Organism
						
							Gossypium hirsutum						
					
						Position
						
							chrD12: 54449907-54451069  JBrowse»						
					
						Reference genome
						
							v1.1						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gh_D12G2141						
					
						Parent gene annotation
						
							SIMILAR TO: AT2G39810, ubiquitin-protein ligases
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Gh_D12G2141_circ_g.1 						
					
						Support reads
						19
					
						Tissues
						ovule
					
						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
						Gh_D12G2141:3

General Information
CircRNA Name	Gh_D12G2141_circ_g.2
ID in PlantcircBase	ghi_circ_003444
Alias	D12:54449907\|54451069
Organism	Gossypium hirsutum
Position	chrD12: 54449907-54451069 JBrowse»
Reference genome	v1.1
Type	e-circRNA
Identification method	CIRI
Parent gene	Gh_D12G2141
Parent gene annotation	SIMILAR TO: AT2G39810, ubiquitin-protein ligases
Parent gene strand	+
Alternative splicing	Gh_D12G2141_circ_g.1
Support reads	19
Tissues	ovule
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	Gh_D12G2141:3

			
						 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  
						
							TGGAATTACAGGATATTATCCTTTTGAAAGTCTTCGAGCTGCTGTGGATATCCTCTTTCTACGT
GGTGGTTCTGATTTGGTGGTTGCCAAGCAAGCGATTatgttacagatgtatgtatggatgaaac
tgctgtttccagtgatgttgtcactgctttgttgctggatgagaaggttgttaaggattgggtc
aagcggac

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							ATGTTACAGATGTATGTATGGATGAAACTGCTGTTTCCAGTGATGTTGTCACTGCTTTGTTGCT
GGATGAGAAGGTTGTTAAGGATTGGGTCAAGCGGACATTTAAAAACATGGCAACAGAACTTCAG
CGTATATGTATCCTTGAAAATTTATGAAATGCTTTGAGAACTATGCTATTTTAGTAATTTGTAT
ATACAATGCTTGTTGGGTGTTCCGTAACTGTTTTTATCAGATTATCTTGAGATAGAAGAGATGA
AAAATCGGTTGGGTTTGCTTCTAAAATTTTCTGTACGTCTGACCAGTTTATCCAGTGTACTTGA
AGTTTTGGAGTCTTCTTTCAAGGGCCGTCTTTCAGCAGAGCTTCATGACTTGCACCACCTTCAA
GAGAGTATATTGAAGACAAAGCAGGTTTGATTCAGTTAAGCGAATGGTTCATCATATTTTAGCA
TAATTTAAGAGCAATGTGATTTTAGCAAAGTCTCAGAACCTGCAATCATGAAAAGCAGCTGAGT
AAAGAGTAATAGCAGTTTGAGTTCAGAATTTGTGAGAAATTAATGGCTGCCATTTGATCATTGC
TCTTATTTGAACTTCTTATGACAATGTTGCTATGTCCACCTTTTGTCTTTTAGTACTGTACATT
ATTGTATCATTAATATTTCATTGAAGACTCATTTTGACCTTTCACCGGGCAAAATAAACAAAAT
ATAGAATTTTAACGTCATGCAATAATCACCATTTTCCACAATATTTGTTTTAATTTTCAGCATC
TTGAGATCACAATGTGGTGTATAAGGCACCACTTCTTGGAACAAGTGAGGTCTCGTCATGCTGA
TTTCACATCCTGGCGTAATCATGTCCGTGAAAGGAAATCAGCTGCAATCGTGCGGGCGTGGCCT
CCTCCTGATGTGTTAGATCTCTCAACCAACTCCACTGGACAGGAAGCTTCTCTTTTCATTGAGG
ATGCACTAGAAAATCTTGACATATACGAGAAGATAGGAGACGAGTCAGATTTTGCATTTTTGCA
GAAGAATGGCGCCTTGTCCTTTCTTCAGTCTAAAATAGGTGGAATTACAGGATATTATCCTTTT
GAAAGTCTTCGAGCTGCTGTGGATATCCTCTTTCTACGTGGTGGTTCTGATTTGGTGGTTGCCA
AGCAAGCGATT

Sequences
Splice junction sequence	TGGAATTACAGGATATTATCCTTTTGAAAGTCTTCGAGCTGCTGTGGATATCCTCTTTCTACGT GGTGGTTCTGATTTGGTGGTTGCCAAGCAAGCGATTatgttacagatgtatgtatggatgaaac tgctgtttccagtgatgttgtcactgctttgttgctggatgagaaggttgttaaggattgggtc aagcggac
Assembled circRNA sequence	NA 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	NA
Genomic sequence	ATGTTACAGATGTATGTATGGATGAAACTGCTGTTTCCAGTGATGTTGTCACTGCTTTGTTGCT GGATGAGAAGGTTGTTAAGGATTGGGTCAAGCGGACATTTAAAAACATGGCAACAGAACTTCAG CGTATATGTATCCTTGAAAATTTATGAAATGCTTTGAGAACTATGCTATTTTAGTAATTTGTAT ATACAATGCTTGTTGGGTGTTCCGTAACTGTTTTTATCAGATTATCTTGAGATAGAAGAGATGA AAAATCGGTTGGGTTTGCTTCTAAAATTTTCTGTACGTCTGACCAGTTTATCCAGTGTACTTGA AGTTTTGGAGTCTTCTTTCAAGGGCCGTCTTTCAGCAGAGCTTCATGACTTGCACCACCTTCAA GAGAGTATATTGAAGACAAAGCAGGTTTGATTCAGTTAAGCGAATGGTTCATCATATTTTAGCA TAATTTAAGAGCAATGTGATTTTAGCAAAGTCTCAGAACCTGCAATCATGAAAAGCAGCTGAGT AAAGAGTAATAGCAGTTTGAGTTCAGAATTTGTGAGAAATTAATGGCTGCCATTTGATCATTGC TCTTATTTGAACTTCTTATGACAATGTTGCTATGTCCACCTTTTGTCTTTTAGTACTGTACATT ATTGTATCATTAATATTTCATTGAAGACTCATTTTGACCTTTCACCGGGCAAAATAAACAAAAT ATAGAATTTTAACGTCATGCAATAATCACCATTTTCCACAATATTTGTTTTAATTTTCAGCATC TTGAGATCACAATGTGGTGTATAAGGCACCACTTCTTGGAACAAGTGAGGTCTCGTCATGCTGA TTTCACATCCTGGCGTAATCATGTCCGTGAAAGGAAATCAGCTGCAATCGTGCGGGCGTGGCCT CCTCCTGATGTGTTAGATCTCTCAACCAACTCCACTGGACAGGAAGCTTCTCTTTTCATTGAGG ATGCACTAGAAAATCTTGACATATACGAGAAGATAGGAGACGAGTCAGATTTTGCATTTTTGCA GAAGAATGGCGCCTTGTCCTTTCTTCAGTCTAAAATAGGTGGAATTACAGGATATTATCCTTTT GAAAGTCTTCGAGCTGCTGTGGATATCCTCTTTCTACGTGGTGGTTCTGATTTGGTGGTTGCCA AGCAAGCGATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							gra_circ_000873* gar_circ_000746* gra_circ_000288 gma_circ_000224* 
gma_circ_002912 						
					
						PMCS

Conservation Information
Conserved circRNAs	gra_circ_000873* gar_circ_000746* gra_circ_000288 gma_circ_000224* gma_circ_002912
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							54449925-54450150(+)
						
						Potential amino acid sequence
						
							MDETAVSSDVVTALLLDEKVVKDWVKRTFKNMATELQRIYYLEIEEMKNRLGLLLKFSVRLTSL
SSVLEVLESSFKGRLSAELHDLHHLQESILKTKQHLEITMWCIRHHFLEQVRSRHADFTSWRNH
VRERKSAAIVRAWPPPDVLDLSTNSTGQEASLFIEDALENLDIYEKIGDESDFAFLQKNGALSF
LQSKIGGITGYYPFESLRAAVDILFLRGGSDLVVAKQAIMLQMYVWMKLLFPVMLSLLCCWMRR
LLRIGSSGHLKTWQQNFSVYIILR*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	54449925-54450150(+)
Potential amino acid sequence	MDETAVSSDVVTALLLDEKVVKDWVKRTFKNMATELQRIYYLEIEEMKNRLGLLLKFSVRLTSL SSVLEVLESSFKGRLSAELHDLHHLQESILKTKQHLEITMWCIRHHFLEQVRSRHADFTSWRNH VRERKSAAIVRAWPPPDVLDLSTNSTGQEASLFIEDALENLDIYEKIGDESDFAFLQKNGALSF LQSKIGGITGYYPFESLRAAVDILFLRGGSDLVVAKQAIMLQMYVWMKLLFPVMLSLLCCWMRR LLRIGSSGHLKTWQQNFSVYIILR*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of Gh_D12G2141_circ_g.2

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