Plant Circular RNA Database

Detail information of Cotton_A_15992_circ_g.1

			
						 General Information
					
						CircRNA Name
						Cotton_A_15992_circ_g.1
					
						ID in PlantcircBase
						gar_circ_000372
					
						Alias
						CA_chr12_BGI-A2_v1.0:138211108|138213453
					
						Organism
						
							Gossypium arboreum						
					
						Position
						
							chrCA_chr12_BGI-A2_v1.0: 138211108-138213453  JBrowse»						
					
						Reference genome
						
							BGI-A2_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Cotton_A_15992						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						8
					
						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_15992:4

General Information
CircRNA Name	Cotton_A_15992_circ_g.1
ID in PlantcircBase	gar_circ_000372
Alias	CA_chr12_BGI-A2_v1.0:138211108\|138213453
Organism	Gossypium arboreum
Position	chrCA_chr12_BGI-A2_v1.0: 138211108-138213453 JBrowse»
Reference genome	BGI-A2_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	Cotton_A_15992
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	NA
Support reads	8
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_15992:4

			
						 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  
						
							CAGTTGTGAAATTATAGAAGAATTTGCTTGTCCAAATCCTAGTATCCCATCTAGTGCTTCACTT
GATGATCCTAATTCCCCAGATTGTCTAGCACCGCACacgaatttggaatgtatactcatgggga
aaaactgttaaaacaagggaatcttcaaaatggaactttacgactggaaatccactatcaacac
tgcaagag

									
								

					

						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
						
							ACGAATTTGGAATGTATACTCATGGGGAAAAACTGTTAAAACAAGGGAATCTTCAAAATGGAAC
TTTACGACTGGAAATCCACTATCAACACTGCAAGAGCACATAACAAAAGGAAGCAGCAAGTCTC
AAACAAAGTAATTCACAGGAATTAATGAAAGAAAAAGCCAATGATCAGTCCAACAAAAGTATTG
ACCTTGAGGCAAAGAAATGAAAGAATCAAGGCAAACAAAATATAAATTAAGAATTTTCCTTTTT
TTTTTTTTTTTTTGGCTAGACCATCAATAAAAAATTATGTTTAAGCGCAAGAAGGCAGCAATTT
ATTATAAATCTGTCCTAAGATTTCTGAAAAGCACGAGAGAGCAACAGTTAAAAAGAAAACAAGA
AACAAAAGTGAAGTAAAAACATGTTCTTGAAAAGTCACAATCACATTGTACATCTTTTTGACAA
GAGTGGGATGAAAAATCTATTTATCACTGACTACAATTTTGCCATATTTCTCCAAGTCCTAAGA
GATTCCAAGTTACAGTAAAACTTTCTAGTCATTCTGGTTCAAAATAAAGAAAAATATGCAATAA
ACATATGTGTTCTTATCTCACAATTTCTTTTACGTAAATCAGTATTGCATGACTGCATTTGACT
GTTTAATTTTTTTTCCTTATAACTGCATCCTCGATCAAATGCACATTTTTTATTGTTAGTGTTA
GGGAATATAAGGAATAACACCTCAATTTGGAATTGTATATAAAATGAGATATAATATTAAAGCA
TGAAATGTTCAAATTAAAGTAAACCTTGGGAAATGTAACATTCGGAACATCAGAAATTGCAAAC
ATTGCAGATAAAGCTATTATCCATATCATGAACAAATAAATGATGTGTATTACCGACATATTTA
CCAGAGACTACAATTGCAGTATCTTACCTTCCCGCAAACTGAAAACATGTAAATTGGTCTTCTA
CAGTATGCAAGTTCAACGCAGGTTGCTGGGAGAGAATCTATTGACAGAAGAGACGATGTAATTA
GTAATGGATAATGTCAAAATCAAAGTAAGATAAGTGGTAATGTTTACCTTTGTCATTAGTGGTT
CATAAATTGATGATGGGAGATATGCTAAGGTTGTACCACTATCCACTATTGTTCCCTTTTGATC
TCCACTATCAAAAATATCACTTGGAAGTCGCAGTAGATCACCACCGACCTCAATATCCTTCATT
ACAATATTGTAATGTGCCCTAAGAGTGTCGATAAAAATATATTTATGAATTTATAAACCAAAAG
ACCTGATTGATGAAAAAGAGTAAGACCTTAAACAAAAAGTTGAAAACCACAAGGCAATCCATGA
ACAAACACAAGTAAATAGCAAAATGGTTTAATTTGTCAATCATGATCATCTAGAAAAATTTTAT
TCCTGCGTTATGAAAGAAACACAGCATTTATATTGTTTCCCAATGATGAGATGCACCAGAAACT
TGAAAACATTTTAGCTATGAATTAAATCTATACTGCTCTCTTCCTAAATTCCATAAGCCTCATT
TGGGACACAAGAAATTGATAGGATTGATTTGCATTCACTTTGATATGCATAAATAAGAATGAAT
GCAGACAATAAAAGAAGACACTTTGTAAACTGTTTATCAGAGGGAGTACGACAGATTGAGTTTA
ACATAGGTGTTTCAGATTAACAATGTAATAGAGATCTATCAAATCCTAGATTTGAATGTAATCA
TGGTCATCATCCAATATAATAGTCAATGTAAAGAATTACTATAGCCAACAACTTGAAGCGCAAT
TTGCCATTTACAAATGCTAGTTTGGGGAAGTAAAATACAATTTAGACATTAAACTATGAGATAA
AGAAACCACAATATATGCTTATTCCATTCTAAAAAATTGAGCTTGACCTAAAGCAGGCAACATT
TATGCTTTACAACCAAGCATGCAACAGTGAAACAATCTTGCACCTAAATCCCCCCCCCAAAAAA
AAAAAAAGCAAAATTAGGAAGCCCCAACTAGAATTTCTTGGTCATTATCACCCTCAATGAGAAA
AAAGTTTAAGCTACAAACCATCAATCATAAAACATAGATATAAAAAAAGAAGCTTTTAAGATAG
ACCACTTACTGGTTTTGAACCATAGGTGTCCTTTTGACTTTCGGAGATACCACTTCACCAATCG
CAAAGATTCCACCTCCCTCTATATTATCCAAACAGTGTGCAAACGATTTTTTTACTTTCCCAGA
TGCAGCCAGTTGTGAAATTATAGAAGAATTTGCTTGTCCAAATCCTAGTATCCCATCTAGTGCT
TCACTTGATGATCCTAATTCCCCAGATTGTCTAGCACCGCAC
						
					

			
		

Sequences
Splice junction sequence	CAGTTGTGAAATTATAGAAGAATTTGCTTGTCCAAATCCTAGTATCCCATCTAGTGCTTCACTT GATGATCCTAATTCCCCAGATTGTCTAGCACCGCACacgaatttggaatgtatactcatgggga aaaactgttaaaacaagggaatcttcaaaatggaactttacgactggaaatccactatcaacac tgcaagag
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	ACGAATTTGGAATGTATACTCATGGGGAAAAACTGTTAAAACAAGGGAATCTTCAAAATGGAAC TTTACGACTGGAAATCCACTATCAACACTGCAAGAGCACATAACAAAAGGAAGCAGCAAGTCTC AAACAAAGTAATTCACAGGAATTAATGAAAGAAAAAGCCAATGATCAGTCCAACAAAAGTATTG ACCTTGAGGCAAAGAAATGAAAGAATCAAGGCAAACAAAATATAAATTAAGAATTTTCCTTTTT TTTTTTTTTTTTTGGCTAGACCATCAATAAAAAATTATGTTTAAGCGCAAGAAGGCAGCAATTT ATTATAAATCTGTCCTAAGATTTCTGAAAAGCACGAGAGAGCAACAGTTAAAAAGAAAACAAGA AACAAAAGTGAAGTAAAAACATGTTCTTGAAAAGTCACAATCACATTGTACATCTTTTTGACAA GAGTGGGATGAAAAATCTATTTATCACTGACTACAATTTTGCCATATTTCTCCAAGTCCTAAGA GATTCCAAGTTACAGTAAAACTTTCTAGTCATTCTGGTTCAAAATAAAGAAAAATATGCAATAA ACATATGTGTTCTTATCTCACAATTTCTTTTACGTAAATCAGTATTGCATGACTGCATTTGACT GTTTAATTTTTTTTCCTTATAACTGCATCCTCGATCAAATGCACATTTTTTATTGTTAGTGTTA GGGAATATAAGGAATAACACCTCAATTTGGAATTGTATATAAAATGAGATATAATATTAAAGCA TGAAATGTTCAAATTAAAGTAAACCTTGGGAAATGTAACATTCGGAACATCAGAAATTGCAAAC ATTGCAGATAAAGCTATTATCCATATCATGAACAAATAAATGATGTGTATTACCGACATATTTA CCAGAGACTACAATTGCAGTATCTTACCTTCCCGCAAACTGAAAACATGTAAATTGGTCTTCTA CAGTATGCAAGTTCAACGCAGGTTGCTGGGAGAGAATCTATTGACAGAAGAGACGATGTAATTA GTAATGGATAATGTCAAAATCAAAGTAAGATAAGTGGTAATGTTTACCTTTGTCATTAGTGGTT CATAAATTGATGATGGGAGATATGCTAAGGTTGTACCACTATCCACTATTGTTCCCTTTTGATC TCCACTATCAAAAATATCACTTGGAAGTCGCAGTAGATCACCACCGACCTCAATATCCTTCATT ACAATATTGTAATGTGCCCTAAGAGTGTCGATAAAAATATATTTATGAATTTATAAACCAAAAG ACCTGATTGATGAAAAAGAGTAAGACCTTAAACAAAAAGTTGAAAACCACAAGGCAATCCATGA ACAAACACAAGTAAATAGCAAAATGGTTTAATTTGTCAATCATGATCATCTAGAAAAATTTTAT TCCTGCGTTATGAAAGAAACACAGCATTTATATTGTTTCCCAATGATGAGATGCACCAGAAACT TGAAAACATTTTAGCTATGAATTAAATCTATACTGCTCTCTTCCTAAATTCCATAAGCCTCATT TGGGACACAAGAAATTGATAGGATTGATTTGCATTCACTTTGATATGCATAAATAAGAATGAAT GCAGACAATAAAAGAAGACACTTTGTAAACTGTTTATCAGAGGGAGTACGACAGATTGAGTTTA ACATAGGTGTTTCAGATTAACAATGTAATAGAGATCTATCAAATCCTAGATTTGAATGTAATCA TGGTCATCATCCAATATAATAGTCAATGTAAAGAATTACTATAGCCAACAACTTGAAGCGCAAT TTGCCATTTACAAATGCTAGTTTGGGGAAGTAAAATACAATTTAGACATTAAACTATGAGATAA AGAAACCACAATATATGCTTATTCCATTCTAAAAAATTGAGCTTGACCTAAAGCAGGCAACATT TATGCTTTACAACCAAGCATGCAACAGTGAAACAATCTTGCACCTAAATCCCCCCCCCAAAAAA AAAAAAAGCAAAATTAGGAAGCCCCAACTAGAATTTCTTGGTCATTATCACCCTCAATGAGAAA AAAGTTTAAGCTACAAACCATCAATCATAAAACATAGATATAAAAAAAGAAGCTTTTAAGATAG ACCACTTACTGGTTTTGAACCATAGGTGTCCTTTTGACTTTCGGAGATACCACTTCACCAATCG CAAAGATTCCACCTCCCTCTATATTATCCAAACAGTGTGCAAACGATTTTTTTACTTTCCCAGA TGCAGCCAGTTGTGAAATTATAGAAGAATTTGCTTGTCCAAATCCTAGTATCCCATCTAGTGCT TCACTTGATGATCCTAATTCCCCAGATTGTCTAGCACCGCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							gra_circ_001301 ghi_circ_000271 						
					
						PMCS

Conservation Information
Conserved circRNAs	gra_circ_001301 ghi_circ_000271
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							138213243-138213444(-)
138211131-138213444(-)
						
						Potential amino acid sequence
						
							MVQNQAHYNIVMKDIEVGGDLLRLPSDIFDSGDQKGTIVDSGTTLAYLPSSIYEPLMTKILSQQ
PALNLHTVEDQFTCFQFAGSVDSGFPVVKFHFEDSLVLTVFPHEYTFQIRVRC*(-)
MSIHSKFVCGARQSGELGSSSEALDGILGFGQANSSIISQLAASGKVKKSFAHCLDNIEGGGIF
AIGEVVSPKVKRTPMVQNQAHYNIVMKDIEVGGDLLRLPSDIFDSGDQKGTIVDSGTTLAYLPS
SIYEPLMTKILSQQPALNLHTVEDQFTCFQFAGSVDSGFPVVKFHFEDSLVLTVFPHEYTFQIR
VRC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	138213243-138213444(-) 138211131-138213444(-)
Potential amino acid sequence	MVQNQAHYNIVMKDIEVGGDLLRLPSDIFDSGDQKGTIVDSGTTLAYLPSSIYEPLMTKILSQQ PALNLHTVEDQFTCFQFAGSVDSGFPVVKFHFEDSLVLTVFPHEYTFQIRVRC(-) MSIHSKFVCGARQSGELGSSSEALDGILGFGQANSSIISQLAASGKVKKSFAHCLDNIEGGGIF AIGEVVSPKVKRTPMVQNQAHYNIVMKDIEVGGDLLRLPSDIFDSGDQKGTIVDSGTTLAYLPS SIYEPLMTKILSQQPALNLHTVEDQFTCFQFAGSVDSGFPVVKFHFEDSLVLTVFPHEYTFQIR VRC(-)
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_15992_circ_g.1

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