Plant Circular RNA Database

Detail information of Cotton_A_16260_circ_g.1

			
						 General Information
					
						CircRNA Name
						Cotton_A_16260_circ_g.1
					
						ID in PlantcircBase
						gar_circ_000298
					
						Alias
						CA_chr12_BGI-A2_v1.0:17108675|17110775
					
						Organism
						
							Gossypium arboreum						
					
						Position
						
							chrCA_chr12_BGI-A2_v1.0: 17108675-17110775  JBrowse»						
					
						Reference genome
						
							BGI-A2_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Cotton_A_16260						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						3
					
						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  
						
							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
						Cotton_A_16260:7

General Information
CircRNA Name	Cotton_A_16260_circ_g.1
ID in PlantcircBase	gar_circ_000298
Alias	CA_chr12_BGI-A2_v1.0:17108675\|17110775
Organism	Gossypium arboreum
Position	chrCA_chr12_BGI-A2_v1.0: 17108675-17110775 JBrowse»
Reference genome	BGI-A2_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	Cotton_A_16260
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	NA
Support reads	3
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	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	Cotton_A_16260:7

			
						 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  
						
							TTAGATGATTCAAATGTGGATGCATGGGGTATGCACGGCCTCGAAAATCAAGATTGTGAGGATA
ATAAAAGCCTTCCTCATTTTCCATTTTCCGAGCCACtttagcagtataacaagctgcagaaaat
agcagcctatcatcagttatatgacccttctcctctaatcttcgttttatttgctcacgtgccc
caacaaaa

									
								

					

						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
						
							TTTAGCAGTATAACAAGCTGCAGAAAATAGCAGCCTATCATCAGTTATATGACCCTTCTCCTCT
AATCTTCGTTTTATTTGCTCACGTGCCCCAACAAAAGTTACACCATATACCGAAGTCATTACCG
TCTGCTTTACTAATTTTCGATCCACCTGAAAGTTTCCAACATTTTCATCTGTTAGTTTAAGGGG
GGAAGTCCTAACTCAAAATCAAGTGTAAATAGTTTAGATGTTAACTGTTCAAGGAAATCTAGTA
AATTTAGTAAATAAAACCAAGTCCAACCTGATCAATTAAGAGCTTTGCCAATAAAGCATTGGGA
TTCGTTGCAGGATCCTTGTTACTGTCCCTCTTCATTATATTGTGAACCCTGTTCAGCCCCAGAA
GATATAAACAGTGAGGGCATCCTTTGTTTCTCATTTTCTAGTACTAAATTTCAGAATACATAGA
AATAGATTTTTTTTCCCCAGAAACTAAAGCAGCAGCAAAGAGAAATGAGGCTGACATAAAATAT
ATATAGGACTAAACATTAAAGGTTAGAATTTTCCTTTGTTACTTCAATAAAGAAGCAGTACGTT
TATGCCTTTGGTTGCTTTTTCTCCTTTCCTCATTTTTAAGCAACAACTAAATGCAGCCAACAAT
ATCAACAAGAAAATTTCTGAATGGAGCAAGACAAGTTTATATGCAGCATGCTTATATATGCCCT
ATAACGAGTTTTCTAGATAATAACTAAAAGGATTTAATATACCTCACAGCGATTTCAGAATAAA
CATCAGCTGGTTTCTCTCCAGCAACCAAGTTAACTGCTGCAGCTTCCAACTACGGGAACAGATA
AAAGATGTGAGACCATAGATGCACTTTTAATAACTAATCCAGAAAAACTGGCTAACCATAAACT
GATAATTAGTGGGTAATAATTTTGTAAAAAAGATAAGTTGAACTGGAACACAACTTCAGATTCT
AAAATATATTGAGAAAACATGTATCTGTGTGTAACCCAAACATGACAATATCAATTGTGGATTA
TTTAGAACAAGGAAAAAAAATTATCAACAAACCACAAACATACATCGTCTCTTCCCAAGGCTGC
ATAGTGCTGTAAGCCATTGCAGGAACCATCCTGTAATAATTTTTTAAGGGAGAGAAGGAAAGGA
AAAGAAGCGTGAGGCACATGAAGCAGTTACGGTGAAAAAATGAAATGAGAAACTGCTACGATCT
TAGCATCCACAACAGAAACAAGAAACAATAAAGCTAATTAAACAACTAAGAGAAGATAATTTTA
AAATGTTCACGTAAGGTATTGAAGAGGAAAAAGATTCAAATGCATGTAAGGGGAACTGATAAAC
AATACCCTTTAACCAGGGAGAATAGAATCAGAATAATGCAGGTAATTTCTAACCAATCATTTAT
ATAAGTTACAATCCTAAGATGTGGCAGCAGTAAAAGGTCACTACAAGCAACGAACATATCATGT
CATTCACAGAACACAAAACTATTGAAATTGGATGATCATGGCAAAAGAGATAAGTAAATTATTT
AAATCAATTGCATTTTGACTTTGAAATGTTGATTGTGCAGAACTGTAACTCAACAAGCAACCTA
GAGAAATTTACTTATCATATGTTTCAGCTTAGGCATATGAAAATTGTCCTTTTCTTTGCTTCAA
GGACCCTAATGAAAATTTACCTGATGAATTGGCAGGTAAGAGATCGTACTATGTGGAGATGTGC
TCTTTAAGGCTTCTGACAGGTTCATACAAGCAGCTAAGCACTGAAAAGGATCCTCAGCGGTTAA
CCACCATCGGTTTCCATTAATAGGGTTTTCTGCTGAATCAAATATTTCATCTAAATGGTTATCA
ACAAATGCCAGACGCCCGTCATGGGAAAGCTTTTCAACACCTCCTGAGTACAGGTTTGCTAAAT
GTATTTTCAGCCAATGTAATCCTGATCTCCCCAATGGTCGTCCTTCAGCAAATTCAAGAACTCC
TCGACAGAGATCAGAACTTAGATGATTCAAATGTGGATGCATGGGGTATGCACGGCCTCGAAAA
TCAAGATTGTGAGGATAATAAAAGCCTTCCTCATTTTCCATTTTCCGAGCCAC
						
					

			
		

Sequences
Splice junction sequence	TTAGATGATTCAAATGTGGATGCATGGGGTATGCACGGCCTCGAAAATCAAGATTGTGAGGATA ATAAAAGCCTTCCTCATTTTCCATTTTCCGAGCCACtttagcagtataacaagctgcagaaaat agcagcctatcatcagttatatgacccttctcctctaatcttcgttttatttgctcacgtgccc caacaaaa
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	TTTAGCAGTATAACAAGCTGCAGAAAATAGCAGCCTATCATCAGTTATATGACCCTTCTCCTCT AATCTTCGTTTTATTTGCTCACGTGCCCCAACAAAAGTTACACCATATACCGAAGTCATTACCG TCTGCTTTACTAATTTTCGATCCACCTGAAAGTTTCCAACATTTTCATCTGTTAGTTTAAGGGG GGAAGTCCTAACTCAAAATCAAGTGTAAATAGTTTAGATGTTAACTGTTCAAGGAAATCTAGTA AATTTAGTAAATAAAACCAAGTCCAACCTGATCAATTAAGAGCTTTGCCAATAAAGCATTGGGA TTCGTTGCAGGATCCTTGTTACTGTCCCTCTTCATTATATTGTGAACCCTGTTCAGCCCCAGAA GATATAAACAGTGAGGGCATCCTTTGTTTCTCATTTTCTAGTACTAAATTTCAGAATACATAGA AATAGATTTTTTTTCCCCAGAAACTAAAGCAGCAGCAAAGAGAAATGAGGCTGACATAAAATAT ATATAGGACTAAACATTAAAGGTTAGAATTTTCCTTTGTTACTTCAATAAAGAAGCAGTACGTT TATGCCTTTGGTTGCTTTTTCTCCTTTCCTCATTTTTAAGCAACAACTAAATGCAGCCAACAAT ATCAACAAGAAAATTTCTGAATGGAGCAAGACAAGTTTATATGCAGCATGCTTATATATGCCCT ATAACGAGTTTTCTAGATAATAACTAAAAGGATTTAATATACCTCACAGCGATTTCAGAATAAA CATCAGCTGGTTTCTCTCCAGCAACCAAGTTAACTGCTGCAGCTTCCAACTACGGGAACAGATA AAAGATGTGAGACCATAGATGCACTTTTAATAACTAATCCAGAAAAACTGGCTAACCATAAACT GATAATTAGTGGGTAATAATTTTGTAAAAAAGATAAGTTGAACTGGAACACAACTTCAGATTCT AAAATATATTGAGAAAACATGTATCTGTGTGTAACCCAAACATGACAATATCAATTGTGGATTA TTTAGAACAAGGAAAAAAAATTATCAACAAACCACAAACATACATCGTCTCTTCCCAAGGCTGC ATAGTGCTGTAAGCCATTGCAGGAACCATCCTGTAATAATTTTTTAAGGGAGAGAAGGAAAGGA AAAGAAGCGTGAGGCACATGAAGCAGTTACGGTGAAAAAATGAAATGAGAAACTGCTACGATCT TAGCATCCACAACAGAAACAAGAAACAATAAAGCTAATTAAACAACTAAGAGAAGATAATTTTA AAATGTTCACGTAAGGTATTGAAGAGGAAAAAGATTCAAATGCATGTAAGGGGAACTGATAAAC AATACCCTTTAACCAGGGAGAATAGAATCAGAATAATGCAGGTAATTTCTAACCAATCATTTAT ATAAGTTACAATCCTAAGATGTGGCAGCAGTAAAAGGTCACTACAAGCAACGAACATATCATGT CATTCACAGAACACAAAACTATTGAAATTGGATGATCATGGCAAAAGAGATAAGTAAATTATTT AAATCAATTGCATTTTGACTTTGAAATGTTGATTGTGCAGAACTGTAACTCAACAAGCAACCTA GAGAAATTTACTTATCATATGTTTCAGCTTAGGCATATGAAAATTGTCCTTTTCTTTGCTTCAA GGACCCTAATGAAAATTTACCTGATGAATTGGCAGGTAAGAGATCGTACTATGTGGAGATGTGC TCTTTAAGGCTTCTGACAGGTTCATACAAGCAGCTAAGCACTGAAAAGGATCCTCAGCGGTTAA CCACCATCGGTTTCCATTAATAGGGTTTTCTGCTGAATCAAATATTTCATCTAAATGGTTATCA ACAAATGCCAGACGCCCGTCATGGGAAAGCTTTTCAACACCTCCTGAGTACAGGTTTGCTAAAT GTATTTTCAGCCAATGTAATCCTGATCTCCCCAATGGTCGTCCTTCAGCAAATTCAAGAACTCC TCGACAGAGATCAGAACTTAGATGATTCAAATGTGGATGCATGGGGTATGCACGGCCTCGAAAA TCAAGATTGTGAGGATAATAAAAGCCTTCCTCATTTTCCATTTTCCGAGCCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							gra_circ_000910* 						
					
						PMCS

Conservation Information
Conserved circRNAs	gra_circ_000910*
PMCS

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							17110764-17108677(-)
17108716-17110687(-)
17110680-17108701(+)
17110535-17108676(+)
						
					

						Potential amino acid sequence
						
							MENEEGFYYPHNLDFRGRAYPMHPHLNHLSSDLCRGVLEFAEGRPLGRSGLHWLKIHLANLYSG
GVEKLSHDGRLAFVDNHLDEIFDSAENPINGNRWWLTAEDPFQCLAACMNLSEALKSTSPHSTI
SYLPIHQFPLHAFESFSSSIPYVNILKLSSLSCLISFIVSCFCYRSSFSFHFFTVTASCASRFF
SFPSLLKKLLQDGSCNGLQHYAALGRDDVCLWFLEAAAVNLVAGEKPADVYSEIAVRVHNIMKR
DSNKDPATNPNALLAKLLIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRLLF
SAACYTAKVARKMENEEGFYYPHNLDFRGRAYPMHPHLNHLSSDLCRGVLEFAEGRPLGRSGLH
WLKIHLANLYSGGVEKLSHDGRLAFVDNHLDEIFDSAENPINGNRWWLTAEDPFQCLAACMNLS
EALKSTSPHSTISYLPIHQFPLHAFESFSSSIPYVNILKLSSLSCLISFIVSCFCYRSSFSFHF
FTVTASCASRFFSFPSLLKKLLQDGSCNGLQHYAALGRDDVCLWFLEAAAVNLVAGEKPADVYS
EIAVRVHNIMKRDSNKDPATNPNALLAKLLIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLE
EKGHITDDRLLFSAACYTAKVARKMENEEGFYYPHNLDFRGRAYPMHPHLNHLSSDLCRGVLEF
AEGRPLGRSGLHWLKIHLANLYSGGVEKLSHDGRLAFVDNHLDEIFDSAENPINGNRWWLTAED
PFQCLAACMNLSEALKSTSPHSTISYLPIHQFPLHAFESFSSSIPYVNILKLSSLSCLISFIVS
CFCYRSSFSFHFFTVTASCASRFFSFPSLLKKLLQDGSCNGLQHYAALGRDDVCLWFLEAAAVN
LVAGEKPADVYSEIAVRVHNIMKRDSNKDPATNPNALLAKLLIDQVDRKLVKQTVMTSVYGVTF
VGAREQIKRRLEEKGHITDDRLLFSAACYTAKVARKMENEEGFYYPHNLDFRGRAYPMHPHLNH
LSSDLCRGVLEFAEGRPLGRSGLHWLKIHLANLYSGGVEKLSHDGRLAFVDNHLDEIFDSAENP
INGNRWWLTAEDPFQCLAACMNLSEALKSTSPHSTISYLPIHQFPLHAFESFSSSIPYVNILKL
SSLSCLISFIVSCFCYRSSFSFHFFTVTASCASRFFSFPSLLKKLLQDGSCNGLQHYAALGRDD
VCLWFLEAAAVNLVAGEKPADVYSEIAVRVHNIMKRDSNKDPATNPNALLAKLLIDQVDRKLVK
QTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRLLFSAACYTAK(-)
MIGCYFLQLVILLKWLGKWKMRKAFIILTILIFEAVHTPCIHI*(-)
MIQMWMHGVCTASKIKIVRIIKAFLIFHFPSHFSSITSCRK*(+)
MPDARHGKAFQHLLSTGLLNVFSANVILISPMVVLQQIQELLDRDQNLDDSNVDAWGMHGLENQ
DCEDNKSLPHFPFSEPL*(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	17110764-17108677(-) 17108716-17110687(-) 17110680-17108701(+) 17110535-17108676(+)
Potential amino acid sequence	MENEEGFYYPHNLDFRGRAYPMHPHLNHLSSDLCRGVLEFAEGRPLGRSGLHWLKIHLANLYSG GVEKLSHDGRLAFVDNHLDEIFDSAENPINGNRWWLTAEDPFQCLAACMNLSEALKSTSPHSTI SYLPIHQFPLHAFESFSSSIPYVNILKLSSLSCLISFIVSCFCYRSSFSFHFFTVTASCASRFF SFPSLLKKLLQDGSCNGLQHYAALGRDDVCLWFLEAAAVNLVAGEKPADVYSEIAVRVHNIMKR DSNKDPATNPNALLAKLLIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRLLF SAACYTAKVARKMENEEGFYYPHNLDFRGRAYPMHPHLNHLSSDLCRGVLEFAEGRPLGRSGLH WLKIHLANLYSGGVEKLSHDGRLAFVDNHLDEIFDSAENPINGNRWWLTAEDPFQCLAACMNLS EALKSTSPHSTISYLPIHQFPLHAFESFSSSIPYVNILKLSSLSCLISFIVSCFCYRSSFSFHF FTVTASCASRFFSFPSLLKKLLQDGSCNGLQHYAALGRDDVCLWFLEAAAVNLVAGEKPADVYS EIAVRVHNIMKRDSNKDPATNPNALLAKLLIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLE EKGHITDDRLLFSAACYTAKVARKMENEEGFYYPHNLDFRGRAYPMHPHLNHLSSDLCRGVLEF AEGRPLGRSGLHWLKIHLANLYSGGVEKLSHDGRLAFVDNHLDEIFDSAENPINGNRWWLTAED PFQCLAACMNLSEALKSTSPHSTISYLPIHQFPLHAFESFSSSIPYVNILKLSSLSCLISFIVS CFCYRSSFSFHFFTVTASCASRFFSFPSLLKKLLQDGSCNGLQHYAALGRDDVCLWFLEAAAVN LVAGEKPADVYSEIAVRVHNIMKRDSNKDPATNPNALLAKLLIDQVDRKLVKQTVMTSVYGVTF VGAREQIKRRLEEKGHITDDRLLFSAACYTAKVARKMENEEGFYYPHNLDFRGRAYPMHPHLNH LSSDLCRGVLEFAEGRPLGRSGLHWLKIHLANLYSGGVEKLSHDGRLAFVDNHLDEIFDSAENP INGNRWWLTAEDPFQCLAACMNLSEALKSTSPHSTISYLPIHQFPLHAFESFSSSIPYVNILKL SSLSCLISFIVSCFCYRSSFSFHFFTVTASCASRFFSFPSLLKKLLQDGSCNGLQHYAALGRDD VCLWFLEAAAVNLVAGEKPADVYSEIAVRVHNIMKRDSNKDPATNPNALLAKLLIDQVDRKLVK QTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRLLFSAACYTAK(-) MIGCYFLQLVILLKWLGKWKMRKAFIILTILIFEAVHTPCIHI(-) MIQMWMHGVCTASKIKIVRIIKAFLIFHFPSHFSSITSCRK(+) MPDARHGKAFQHLLSTGLLNVFSANVILISPMVVLQQIQELLDRDQNLDDSNVDAWGMHGLENQ DCEDNKSLPHFPFSEPL*(+)
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_16260_circ_g.1

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