Plant Circular RNA Database

Detail information of Cotton_A_26942_circ_g.1

			
						 General Information
					
						CircRNA Name
						Cotton_A_26942_circ_g.1
					
						ID in PlantcircBase
						gar_circ_000125
					
						Alias
						CA_chr10_BGI-A2_v1.0:45454814|45457315
					
						Organism
						
							Gossypium arboreum						
					
						Position
						
							chrCA_chr10_BGI-A2_v1.0: 45454814-45457315  JBrowse»						
					
						Reference genome
						
							BGI-A2_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Cotton_A_26942						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						6/7
					
						Tissues
						leaf/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
						Cotton_A_26942:7

General Information
CircRNA Name	Cotton_A_26942_circ_g.1
ID in PlantcircBase	gar_circ_000125
Alias	CA_chr10_BGI-A2_v1.0:45454814\|45457315
Organism	Gossypium arboreum
Position	chrCA_chr10_BGI-A2_v1.0: 45454814-45457315 JBrowse»
Reference genome	BGI-A2_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	Cotton_A_26942
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	NA
Support reads	6/7
Tissues	leaf/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	Cotton_A_26942:7

			
						 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  
						
							TAGTGCTTAAAGAGTTAGCTTCGCCATCTGCAACAAATAGAAGGAATGCTGCATTTTGTGCTGG
AGAGCTGGCCAAAAATGGAGGAGAGACAACTTTGAActatttggaggaatcactgaagattttg
gagagacattctggttactttcatgaagatgttcggcttcaggcaatcattgctttgaaacgtt
agtaccat

									
								

					

						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
						
							CTATTTGGAGGAATCACTGAAGATTTTGGAGAGACATTCTGGTTACTTTCATGAAGATGTTCGG
CTTCAGGCAATCATTGCTTTGAAACGTTAGTACCATGCTTGTATCTGGATTATGTACCTCCCAA
CTTATATTATCAACATTTTTGGTTATCATAGATGGAAAGAAATTGATTATTGCTGTCCTTGATA
GTGACTCTTATATTAAAAAAGCCACCGTCTACAGCAATTAACTTGTCTTCTGTTCTGGAAAGTA
ATCATTTTAGCCTTTGGTCTGCTATCATGGCTCCATCGACAAACTCTCACCTCCTCTCTTCCCC
TTAAAAGATGAACATTCTAGAACCTAATGATGCCCTCACCATGATGATCTGTGAGGGAGGGAGA
GAGAACTATCATCCAAAAAGAAAATGAAGTGCCACTGTGGTAGGCGTAATTCTTTTGCATGTCT
CGAGAAACTCTAGACTATGTTAAAATTTGGAGTAGGATGCTGATTTGCTGAGACTGAACATTTA
GTTTCTTGCTTCTGTTGAAGCAACTGTTGTTTCCATTGTATGCAATATTAAATCTTATTGCATT
TGGATTGTGTGCAGGTTGACCAGCTTCATGAGTTTAATAGTTATTAACTCTTACATTGATATAT
TCATCATATGCAAATCTCACAGTTAACTTTTTTCCTTGATTGAAATTGCAGATATTTTAACAGC
AGCACATGCTATCTTTCAGTGCCAGAATGTGAGTTATATTGGCTTTATTCGTTTTCTTTCCTTT
CTCTGGTTTTTTTCATTGACATCTCTGGTGGAATATTCTCTTAGTTTCTGCCCGCTAGAATGCA
GGAAAATAAGGGTCAGAACAGAGGGGTGGGTAAATGTTCTGGTTGTCAAGTTTTCCGCATAATG
ATTAATCCTTATGGAATATGAACGAATAAATTTACTTTCATGTGATCTGACCATTATTGTGGGT
TTGATTTGTGCTGGATATTTATCCATTCCAATGAAGTTTGGAATTTTGTGTATTAAACTTGGCT
GCCTTTGAGCACAAATATTTTTTTCACTGAATACACCCAACTGCCCTTCACTTAGGCTTTTAGT
TATTGAAGCCCCTCTGTTAGATTGGTAAATTTGTTTTATGAGTTAATTGGTTTGAGAAACTGCA
CATGTACATGCAGGTACATGTGCTTTTTTCCCAGAATAGCGTGTACCTAAACTGGCATAGACTA
TTGACAGTCAGACAGTAGCACATGCATGCAAATATGTACATATAAATGTATTATGCATGGATAC
ACGGTGAATAGTGACCTCAGACTGCTGATATGAGTTTAACGTTTTCTGCTGTGCAGGATGGGTC
GGTGAAGGCGAAAGAAGTTCTTGGTATTAACATAAAATCTTTTATTTCTATGCTTCCCCTGGTT
TGCAATTGGTAATAGAGTTCTGATTAAGCTCATTGATTTTGTAGATATGGTGATGAATATCTAT
ATCAAGACCATGACTGAAGACGATGACAAGGAAGTTGTTGCCAATGCTTGTATGAGCATAGCTG
ATATTATCAAGGATTATGGTTATATGGCATTAGAACCTTGTAAGTAGTTGACTGCTCCCTGTTG
GGAATCTTCAGTGCAAAAATCTTTCAGATGTGGATATTTATTGTGAATTTCATTCCCATTTATT
TGGTTTTCAGATATGTCTCGGCTTGTGGATGCAACTTTGACTTTGCTTCGAGAGGAATCAGCTT
GTCAGCAATTAGAGAATGGAAGTGATATTGATGATGAGGATGATACTGAACATGATGAAATTCT
TATGGATGCAGTTTCGGACCTTTTACCTGCCTTTGCTAAGTCAATGGGTTATCACTTTGCTCCT
ATATTTGCAAAACTATTTGAACCTTTGATGAAATTTGCGGTGGGTATAATTGTCAAGTATGAAG
TTATGATTTCTATAATTAGCATCTTATATTTGTTTGTTGGCAAGTGTAGAAAGCTTCACGTCCT
CCACAAGATCGAACTATGGTGGTTGCTTGTCTTGCTGAAGTTGCACAGGACATGGGTGCTCCAA
TTGCAAGCTATATTGATGTAATTTAATCATAACGTTCAATTGTTTAGGCTTTATTTGGTTCTCA
CTTTTATCATGTGCTTTTTGTTGCCTAAAAGGCTGCTATAGGACAAACATGAAGCATAGGGAGA
AAAATGTTGACTAAAGTCTTTTAAAATAATAACAAAATGCAATAGCAATTTTAAAATAAATGGT
CTGTAGAAAAACCATGCATTTTGTTATAAAATTTACTTTTGAAGTTTTAGTTGTTGAATAGTAT
TTAGTTTTTTACATGAAAAGTATTTAATATCTTTGTTGGTTTTCAGATATGCTGCAGTTTACTA
AAACTTTTTTGTGTGTTTCAGAGACTGATGCCCCTAGTGCTTAAAGAGTTAGCTTCGCCATCTG
CAACAAATAGAAGGAATGCTGCATTTTGTGCTGGAGAGCTGGCCAAAAATGGAGGAGAGACAAC
TTTGAA
						
					

			
		

Sequences
Splice junction sequence	TAGTGCTTAAAGAGTTAGCTTCGCCATCTGCAACAAATAGAAGGAATGCTGCATTTTGTGCTGG AGAGCTGGCCAAAAATGGAGGAGAGACAACTTTGAActatttggaggaatcactgaagattttg gagagacattctggttactttcatgaagatgttcggcttcaggcaatcattgctttgaaacgtt agtaccat
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	CTATTTGGAGGAATCACTGAAGATTTTGGAGAGACATTCTGGTTACTTTCATGAAGATGTTCGG CTTCAGGCAATCATTGCTTTGAAACGTTAGTACCATGCTTGTATCTGGATTATGTACCTCCCAA CTTATATTATCAACATTTTTGGTTATCATAGATGGAAAGAAATTGATTATTGCTGTCCTTGATA GTGACTCTTATATTAAAAAAGCCACCGTCTACAGCAATTAACTTGTCTTCTGTTCTGGAAAGTA ATCATTTTAGCCTTTGGTCTGCTATCATGGCTCCATCGACAAACTCTCACCTCCTCTCTTCCCC TTAAAAGATGAACATTCTAGAACCTAATGATGCCCTCACCATGATGATCTGTGAGGGAGGGAGA GAGAACTATCATCCAAAAAGAAAATGAAGTGCCACTGTGGTAGGCGTAATTCTTTTGCATGTCT CGAGAAACTCTAGACTATGTTAAAATTTGGAGTAGGATGCTGATTTGCTGAGACTGAACATTTA GTTTCTTGCTTCTGTTGAAGCAACTGTTGTTTCCATTGTATGCAATATTAAATCTTATTGCATT TGGATTGTGTGCAGGTTGACCAGCTTCATGAGTTTAATAGTTATTAACTCTTACATTGATATAT TCATCATATGCAAATCTCACAGTTAACTTTTTTCCTTGATTGAAATTGCAGATATTTTAACAGC AGCACATGCTATCTTTCAGTGCCAGAATGTGAGTTATATTGGCTTTATTCGTTTTCTTTCCTTT CTCTGGTTTTTTTCATTGACATCTCTGGTGGAATATTCTCTTAGTTTCTGCCCGCTAGAATGCA GGAAAATAAGGGTCAGAACAGAGGGGTGGGTAAATGTTCTGGTTGTCAAGTTTTCCGCATAATG ATTAATCCTTATGGAATATGAACGAATAAATTTACTTTCATGTGATCTGACCATTATTGTGGGT TTGATTTGTGCTGGATATTTATCCATTCCAATGAAGTTTGGAATTTTGTGTATTAAACTTGGCT GCCTTTGAGCACAAATATTTTTTTCACTGAATACACCCAACTGCCCTTCACTTAGGCTTTTAGT TATTGAAGCCCCTCTGTTAGATTGGTAAATTTGTTTTATGAGTTAATTGGTTTGAGAAACTGCA CATGTACATGCAGGTACATGTGCTTTTTTCCCAGAATAGCGTGTACCTAAACTGGCATAGACTA TTGACAGTCAGACAGTAGCACATGCATGCAAATATGTACATATAAATGTATTATGCATGGATAC ACGGTGAATAGTGACCTCAGACTGCTGATATGAGTTTAACGTTTTCTGCTGTGCAGGATGGGTC GGTGAAGGCGAAAGAAGTTCTTGGTATTAACATAAAATCTTTTATTTCTATGCTTCCCCTGGTT TGCAATTGGTAATAGAGTTCTGATTAAGCTCATTGATTTTGTAGATATGGTGATGAATATCTAT ATCAAGACCATGACTGAAGACGATGACAAGGAAGTTGTTGCCAATGCTTGTATGAGCATAGCTG ATATTATCAAGGATTATGGTTATATGGCATTAGAACCTTGTAAGTAGTTGACTGCTCCCTGTTG GGAATCTTCAGTGCAAAAATCTTTCAGATGTGGATATTTATTGTGAATTTCATTCCCATTTATT TGGTTTTCAGATATGTCTCGGCTTGTGGATGCAACTTTGACTTTGCTTCGAGAGGAATCAGCTT GTCAGCAATTAGAGAATGGAAGTGATATTGATGATGAGGATGATACTGAACATGATGAAATTCT TATGGATGCAGTTTCGGACCTTTTACCTGCCTTTGCTAAGTCAATGGGTTATCACTTTGCTCCT ATATTTGCAAAACTATTTGAACCTTTGATGAAATTTGCGGTGGGTATAATTGTCAAGTATGAAG TTATGATTTCTATAATTAGCATCTTATATTTGTTTGTTGGCAAGTGTAGAAAGCTTCACGTCCT CCACAAGATCGAACTATGGTGGTTGCTTGTCTTGCTGAAGTTGCACAGGACATGGGTGCTCCAA TTGCAAGCTATATTGATGTAATTTAATCATAACGTTCAATTGTTTAGGCTTTATTTGGTTCTCA CTTTTATCATGTGCTTTTTGTTGCCTAAAAGGCTGCTATAGGACAAACATGAAGCATAGGGAGA AAAATGTTGACTAAAGTCTTTTAAAATAATAACAAAATGCAATAGCAATTTTAAAATAAATGGT CTGTAGAAAAACCATGCATTTTGTTATAAAATTTACTTTTGAAGTTTTAGTTGTTGAATAGTAT TTAGTTTTTTACATGAAAAGTATTTAATATCTTTGTTGGTTTTCAGATATGCTGCAGTTTACTA AAACTTTTTTGTGTGTTTCAGAGACTGATGCCCCTAGTGCTTAAAGAGTTAGCTTCGCCATCTG CAACAAATAGAAGGAATGCTGCATTTTGTGCTGGAGAGCTGGCCAAAAATGGAGGAGAGACAAC TTTGAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							gra_circ_001009 ghi_circ_000290 						
					
						PMCS

Conservation Information
Conserved circRNAs	gra_circ_001009 ghi_circ_000290
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							45456268-45457312(+)
						
						Potential amino acid sequence
						
							MVMNIYIKTMTEDDDKEVVANACMSIADIIKDYGYMALEPYMSRLVDATLTLLREESACQQLEN
GSDIDDEDDTEHDEILMDAVSDLLPAFAKSMGYHFAPIFAKLFEPLMKFAVASRPPQDRTMVVA
CLAEVAQDMGAPIASYIDRLMPLVLKELASPSATNRRNAAFCAGELAKNGGETTLNYLEESLKI
LERHSGYFHEDVRLQAIIALKHILTAAHAIFQCQNDGSVKAKEVLDMVMNIYIKTMTEDDDKEV
VANACMSIADIIKDYGYMALEPYMSRLVDATLTLLREESACQQLENGSDIDDEDDTEHDEILMD
AVSDLLPAFAKSMGYHFAPIFAKLFEPLMKFAVASRPPQDRTMVVACLAEVAQDMGAPIASYID
RLMPLVLKELASPSATNRRNAAFCAGELAKNGGETTLNYLEESLKILERHSGYFHEDVRLQAII
ALKHILTAAHAIFQCQNDGSVKAKEVLDMVMNIYIKTMTEDDDKEVVANACMSIADIIKDYGYM
ALEPYMSRLVDATLTLLREESACQQLENGSDIDDEDDTEHDEILMDAVSDLLPAFAKSMGYHFA
PIFAKLFEPLMKFAVASRPPQDRTMVVACLAEVAQDMGAPIASYIDRLMPLVLKELASPSATNR
RNAAFCAGELAKNGGETTLNYLEESLKILERHSGYFHEDVRLQAIIALKHILTAAHAIFQCQND
GSVKAKEVLDMVMNIYIKTMTEDDDKEVVANACMSIADIIKDYGYMALEPYMSRLVDATLTLLR
EESACQQLENGSDIDDEDDTEHDEILMDAVSDLLPAFAKSMGYHFAPIFAKLFEPLMKFAVASR
PPQDRTMVVACLAEVAQDMGAPIASYIDRLMPLVLKELASPSATNRRNAAFCAGELAKNGGETT
L(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	45456268-45457312(+)
Potential amino acid sequence	MVMNIYIKTMTEDDDKEVVANACMSIADIIKDYGYMALEPYMSRLVDATLTLLREESACQQLEN GSDIDDEDDTEHDEILMDAVSDLLPAFAKSMGYHFAPIFAKLFEPLMKFAVASRPPQDRTMVVA CLAEVAQDMGAPIASYIDRLMPLVLKELASPSATNRRNAAFCAGELAKNGGETTLNYLEESLKI LERHSGYFHEDVRLQAIIALKHILTAAHAIFQCQNDGSVKAKEVLDMVMNIYIKTMTEDDDKEV VANACMSIADIIKDYGYMALEPYMSRLVDATLTLLREESACQQLENGSDIDDEDDTEHDEILMD AVSDLLPAFAKSMGYHFAPIFAKLFEPLMKFAVASRPPQDRTMVVACLAEVAQDMGAPIASYID RLMPLVLKELASPSATNRRNAAFCAGELAKNGGETTLNYLEESLKILERHSGYFHEDVRLQAII ALKHILTAAHAIFQCQNDGSVKAKEVLDMVMNIYIKTMTEDDDKEVVANACMSIADIIKDYGYM ALEPYMSRLVDATLTLLREESACQQLENGSDIDDEDDTEHDEILMDAVSDLLPAFAKSMGYHFA PIFAKLFEPLMKFAVASRPPQDRTMVVACLAEVAQDMGAPIASYIDRLMPLVLKELASPSATNR RNAAFCAGELAKNGGETTLNYLEESLKILERHSGYFHEDVRLQAIIALKHILTAAHAIFQCQND GSVKAKEVLDMVMNIYIKTMTEDDDKEVVANACMSIADIIKDYGYMALEPYMSRLVDATLTLLR EESACQQLENGSDIDDEDDTEHDEILMDAVSDLLPAFAKSMGYHFAPIFAKLFEPLMKFAVASR PPQDRTMVVACLAEVAQDMGAPIASYIDRLMPLVLKELASPSATNRRNAAFCAGELAKNGGETT L(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of Cotton_A_26942_circ_g.1

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