Plant Circular RNA Database

Detail information of orai.003G035200_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.003G035200_circ_g.1
					
						ID in PlantcircBase
						gra_circ_000232
					
						Alias
						Chr03:3575491|3578134
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr03: 3575491-3578134  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.003G035200						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							orai.003G035200_circ_g.2 orai.003G035200_circ_g.3 						
					
						Support reads
						2
					
						Tissues
						ovule
					
						Exon boundary  
						
							Yes-No							"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
						Gorai.003G035200.6:8
Gorai.003G035200.2:8
Gorai.003G035200.4:8
Gorai.003G035200.1:8
Gorai.003G035200.5:8
Gorai.003G035200.7:8
Gorai.003G035200.3:8

General Information
CircRNA Name	orai.003G035200_circ_g.1
ID in PlantcircBase	gra_circ_000232
Alias	Chr03:3575491\|3578134
Organism	Gossypium raimondii
Position	chrChr03: 3575491-3578134 JBrowse»
Reference genome	Graimondii_221
Type	ue-circRNA
Identification method	CIRI
Parent gene	Gorai.003G035200
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	orai.003G035200_circ_g.2 orai.003G035200_circ_g.3
Support reads	2
Tissues	ovule
Exon boundary	Yes-No "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	Gorai.003G035200.6:8 Gorai.003G035200.2:8 Gorai.003G035200.4:8 Gorai.003G035200.1:8 Gorai.003G035200.5:8 Gorai.003G035200.7:8 Gorai.003G035200.3:8

			
						 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  
						
							CGTCATGACAGATTCCACCGTTCTTCTGCGTCTGAATCCTCGCCAACGGACTCTTCGGCGTCGT
CGAAACTCCGTTCCCATTGGCCGCCATATCTTCCCTctgtaactgatttgtcaccataatccac
ctctctcgtatgttcatcgaaaacaacattttccaacactgcagaaacaaagaattcaaaaaga
tcaaaaac

									
								

					

						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
						
							CTGTAACTGATTTGTCACCATAATCCACCTCTCTCGTATGTTCATCGAAAACAACATTTTCCAA
CACTGCAGAAACAAAGAATTCAAAAAGATCAAAAACCAAGCACAACAGTTTTATACTGGGTATA
GTATGATCTAAGAAAACCGAGGGACAGAGAATTTCACCAGTTCCAAACTTAATGGCATTCCAGA
TATCAGGCTCCTTCTCCCTTGAAAGATCAATACACTTGGCATAGCAACCACCTTCGATGTTCGA
CACACCATTGTCACTCCAACAATGCTCGTCATCACCGATCAGATACCTGTTGTGATCGGTAGAC
AAAGTGGTCTTACCCGTACCTGTTTTGCATGTAAACTCATTAGTAACAATGCAAAGCCGACTAT
CCACATATCGGGAGCAGAGTTAAGAGAACACATATCGGTTTTCAGGAACTAAGCACCACATCAT
GTGACCTTTGATCCGGCGATACTATACCTGACAATCCAAAGAAGAGGGCAACATCTCCATCTTT
TCCCATATTGCATCCAGAATGTAACGAGAGGATTTGACGCATAGGCATGAGATAATGCATAACA
CTGAAAAGACCCTTCTTCATTTCCCCGGCGTATTGAGTGCCGAGGATGACCATTTCCCTCCTAG
CAAGATTAAGGTCTATGCTAGTAGAGGATGTCATGTAGTGTGTATAACGATTACACGGGAACTG
CCCAGCATTGTATATAGTGAAGTCCGGAGTACCGAAATTCTCCAGCTCTTCAGGAGTGGGTCGG
ATACACCTGTCACCCACCCAATTATCCAATTGTACACTAAGCTTTACCTTTTTACCATTTTTAA
TTTTATCTTATTGCCTTAGGGAAATTCTATATGGATTATAAAACTCAAACACATTATACATACT
ACATCGATAAAGAGACTTATCTGGGGTAGGCTTAGACCTGTGAAACAAAACACACACACAAAGA
AAGGCTTATAAAACTTCAAAATCACGTAGTTTTTACTTACATGTTATGCATGAACAATGAATGA
TAAGCTCTAGCAGACACAATCCGAACTTTGATTCTGTTCTGTGGATCCCAGTTCAAGAATTGAT
CATTCACGAAAACCTGTAAAAAGTGATTACATGAACAAACTGAACTAAACCTCAGATTCATGTA
TATATATATATGTAAACATAATTTCATATTTTCCCAATGAAAAACATCGATGATAACATCTAGA
CGGTATCCGAATAAACATGACAAAAATTGCTTCTCCCAATGTATTAGGATGCCCCTAGTACAAC
TTGTTGAAAACTAAAAGACAAAAATGATACCATATGACCATACCCCTCCATCAACATCATCTTC
CAAAAACCTTTTTTACTAAATTCGAAATCAAGCCAAATAAAACTAATTTACTATGATACCCCTA
TACCTTGTCCAGAGAATTCAAGTAATCAACAGCTCTTTCTCTGTTCACCATGAAGGTATGCTCG
TCCATTTCAATATTGGGTGAGCCCCTGTTATACAGATCCCAAAATATTTAGATTTCAATGCATT
ATTACATCAACAATCACTAAACATTTTTCACTGTATCCACACTTACTTTCCCCACCAAAGCTCA
TCTTGGGTGGAGTCATCGATAACAACTCTCTTATCTCTCGGTGACCGACCGGTTTTGGCTCCGG
ATAGGGTGGCGAGTGCACCGGTTGAAGTAATGAAAGAACCCTTCTCATACTTTATTGCCTGCTC
ATACAACTCTGCACCAAAGGAAGAAAAAAATATTACATATATATATGAAAATCCAAAAATTTTT
CAGCTGGTTTTGTTCTGTTCTGTTTTGGTGGATTTTATTACGTTACCTGCAGGAGAGAGGTTGT
ATAGGACGTGAGTGAATTTCAAGGAACTGTCACTGACGCTAATGGTTGGCGCCTCGATATGGTG
GTGGTGCGCCACATGCGACACCGATTGAACCTTCCCTGCCGGGTCCCCTCTCACCACTTTCGGC
CCTGTTCCTCGAGTGAGTGACGCCAACGATGCACTGTTCACAAACAGTAAATTAAAGCTTGCAA
AATCAGTTATGGAAATTTTGTAAGAAACCCAAAATTAAAAATAAAAGATTTACATAAAGTTTTA
ATCTTTTCTTTGCTAGTCCATTTTCGTTTTCATGTGATTCTCGGGAACCAAACAAGAGCTCATA
AATTTGTTGGCATATCTGAGAAATTTCACGTGGACCCCACATAAAATCCACCCGAATCATCCAT
CATGTTCATTGATTTTCAATTTTCCACCGTCTGATTATATTACGGAAGGGGTCCACTTCATAGG
AATTTTATTTTTCATCTTTAAATTTTAACTTCAAATTTCTTTCTTCCTTTTTTTTTTTTTGCTG
CTGCTATGGAGGCGTGTAGTACCTGATGGACTGGAGCTGCTGCCTCTGGCGCTCATCTTCAGAA
ATGGTGGCAAAGGTACCCTGAACGCCGTCAAGAGGAGTCGTCGGCGCCGATCTCTTCTTCTGCA
AAGAGTGAAGCTCATCGATCGTCTGAGCCTTAACAGGCTTCCCGCTATCGTCATGACAGATTCC
ACCGTTCTTCTGCGTCTGAATCCTCGCCAACGGACTCTTCGGCGTCGTCGAAACTCCGTTCCCA
TTGGCCGCCATATCTTCCCT
						
					

			
		

Sequences
Splice junction sequence	CGTCATGACAGATTCCACCGTTCTTCTGCGTCTGAATCCTCGCCAACGGACTCTTCGGCGTCGT CGAAACTCCGTTCCCATTGGCCGCCATATCTTCCCTctgtaactgatttgtcaccataatccac ctctctcgtatgttcatcgaaaacaacattttccaacactgcagaaacaaagaattcaaaaaga tcaaaaac
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	CTGTAACTGATTTGTCACCATAATCCACCTCTCTCGTATGTTCATCGAAAACAACATTTTCCAA CACTGCAGAAACAAAGAATTCAAAAAGATCAAAAACCAAGCACAACAGTTTTATACTGGGTATA GTATGATCTAAGAAAACCGAGGGACAGAGAATTTCACCAGTTCCAAACTTAATGGCATTCCAGA TATCAGGCTCCTTCTCCCTTGAAAGATCAATACACTTGGCATAGCAACCACCTTCGATGTTCGA CACACCATTGTCACTCCAACAATGCTCGTCATCACCGATCAGATACCTGTTGTGATCGGTAGAC AAAGTGGTCTTACCCGTACCTGTTTTGCATGTAAACTCATTAGTAACAATGCAAAGCCGACTAT CCACATATCGGGAGCAGAGTTAAGAGAACACATATCGGTTTTCAGGAACTAAGCACCACATCAT GTGACCTTTGATCCGGCGATACTATACCTGACAATCCAAAGAAGAGGGCAACATCTCCATCTTT TCCCATATTGCATCCAGAATGTAACGAGAGGATTTGACGCATAGGCATGAGATAATGCATAACA CTGAAAAGACCCTTCTTCATTTCCCCGGCGTATTGAGTGCCGAGGATGACCATTTCCCTCCTAG CAAGATTAAGGTCTATGCTAGTAGAGGATGTCATGTAGTGTGTATAACGATTACACGGGAACTG CCCAGCATTGTATATAGTGAAGTCCGGAGTACCGAAATTCTCCAGCTCTTCAGGAGTGGGTCGG ATACACCTGTCACCCACCCAATTATCCAATTGTACACTAAGCTTTACCTTTTTACCATTTTTAA TTTTATCTTATTGCCTTAGGGAAATTCTATATGGATTATAAAACTCAAACACATTATACATACT ACATCGATAAAGAGACTTATCTGGGGTAGGCTTAGACCTGTGAAACAAAACACACACACAAAGA AAGGCTTATAAAACTTCAAAATCACGTAGTTTTTACTTACATGTTATGCATGAACAATGAATGA TAAGCTCTAGCAGACACAATCCGAACTTTGATTCTGTTCTGTGGATCCCAGTTCAAGAATTGAT CATTCACGAAAACCTGTAAAAAGTGATTACATGAACAAACTGAACTAAACCTCAGATTCATGTA TATATATATATGTAAACATAATTTCATATTTTCCCAATGAAAAACATCGATGATAACATCTAGA CGGTATCCGAATAAACATGACAAAAATTGCTTCTCCCAATGTATTAGGATGCCCCTAGTACAAC TTGTTGAAAACTAAAAGACAAAAATGATACCATATGACCATACCCCTCCATCAACATCATCTTC CAAAAACCTTTTTTACTAAATTCGAAATCAAGCCAAATAAAACTAATTTACTATGATACCCCTA TACCTTGTCCAGAGAATTCAAGTAATCAACAGCTCTTTCTCTGTTCACCATGAAGGTATGCTCG TCCATTTCAATATTGGGTGAGCCCCTGTTATACAGATCCCAAAATATTTAGATTTCAATGCATT ATTACATCAACAATCACTAAACATTTTTCACTGTATCCACACTTACTTTCCCCACCAAAGCTCA TCTTGGGTGGAGTCATCGATAACAACTCTCTTATCTCTCGGTGACCGACCGGTTTTGGCTCCGG ATAGGGTGGCGAGTGCACCGGTTGAAGTAATGAAAGAACCCTTCTCATACTTTATTGCCTGCTC ATACAACTCTGCACCAAAGGAAGAAAAAAATATTACATATATATATGAAAATCCAAAAATTTTT CAGCTGGTTTTGTTCTGTTCTGTTTTGGTGGATTTTATTACGTTACCTGCAGGAGAGAGGTTGT ATAGGACGTGAGTGAATTTCAAGGAACTGTCACTGACGCTAATGGTTGGCGCCTCGATATGGTG GTGGTGCGCCACATGCGACACCGATTGAACCTTCCCTGCCGGGTCCCCTCTCACCACTTTCGGC CCTGTTCCTCGAGTGAGTGACGCCAACGATGCACTGTTCACAAACAGTAAATTAAAGCTTGCAA AATCAGTTATGGAAATTTTGTAAGAAACCCAAAATTAAAAATAAAAGATTTACATAAAGTTTTA ATCTTTTCTTTGCTAGTCCATTTTCGTTTTCATGTGATTCTCGGGAACCAAACAAGAGCTCATA AATTTGTTGGCATATCTGAGAAATTTCACGTGGACCCCACATAAAATCCACCCGAATCATCCAT CATGTTCATTGATTTTCAATTTTCCACCGTCTGATTATATTACGGAAGGGGTCCACTTCATAGG AATTTTATTTTTCATCTTTAAATTTTAACTTCAAATTTCTTTCTTCCTTTTTTTTTTTTTGCTG CTGCTATGGAGGCGTGTAGTACCTGATGGACTGGAGCTGCTGCCTCTGGCGCTCATCTTCAGAA ATGGTGGCAAAGGTACCCTGAACGCCGTCAAGAGGAGTCGTCGGCGCCGATCTCTTCTTCTGCA AAGAGTGAAGCTCATCGATCGTCTGAGCCTTAACAGGCTTCCCGCTATCGTCATGACAGATTCC ACCGTTCTTCTGCGTCTGAATCCTCGCCAACGGACTCTTCGGCGTCGTCGAAACTCCGTTCCCA TTGGCCGCCATATCTTCCCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.158346568

Conservation Information
Conserved circRNAs	NA
PMCS	0.158346568

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3578126-3578039(-)
3575779-3578039(-)
3578039-3575493(+)
						
						Potential amino acid sequence
						
							MAANGNGVSTTPKSPLARIQTQKNGGICHDDSGKPVKAQTIDELHSLQKKRSAPTTPLDGVQGT
FATISEDERQRQQLQSISASLASLTRGTGPKVVRGDPAGKVQSVSHVAHHHHIEAPTISVSDSS
LKFTHVLYNLSPAELYEQAIKYEKGSFITSTGALATLSGAKTGRSPRDKRVVIDDSTQDELWWG
KGSPNIEMDEHTFMVNRERAVDYLNSLDKVFVNDQFLNWDPQNRIKVRIVSARAYHSLFMHNMC
IRPTPEELENFGTPDFTIYNAGQFPCNRYTHYMTSSTSIDLNLARREMVILGTQYAGEMKKGLF
SVMHYLMPMRQILSLHSGCNMGKDGDVALFFGLSGTGKTTLSTDHNRYLIGDDEHCWSDNGVSN
IEGGCYAKCIDLSREKEPDIWNAIKFGTVLENVVFDEHTREVDYGDKSVTEGRYGGQWERSFDD
AEESVGEDSDAEERWNLS*(-)
MTSIVGVTMVCRTSKVVAMPSVLIFQGRRSLISGMPLSLELCWKMLFSMNIRERWIMVTNQLQR
EDMAANGNGVSTTPKSPLARIQTQKNGGICHDDSGKPVKAQTIDELHSLQKKRSAPTTPLDGVQ
GTFATISEDERQRQQLQSISASLASLTRGTGPKVVRGDPAGKVQSVSHVAHHHHIEAPTISVSD
SSLKFTHVLYNLSPAELYEQAIKYEKGSFITSTGALATLSGAKTGRSPRDKRVVIDDSTQDELW
WGKGSPNIEMDEHTFMVNRERAVDYLNSLDKVFVNDQFLNWDPQNRIKVRIVSARAYHSLFMHN
MCIRPTPEELENFGTPDFTIYNAGQFPCNRYTHYMTSSTSIDLNLARREMVILGTQYAGEMKKG
LFSVMHYLMPMRQILSLHSGCNMGKDGDVALFFGLSGTGKTTLSTDHNRYLIGDDEHCWSDNGV
SNIEGGCYAKCIDLSREKEPDIWNAIKFGTVLENVVFDEHTREVDYGDKSVTEGRYGGQWERSF
DDAEESVGEDSDAEERWNLS*(-)
MTDSTVLLRLNPRQRTLRRRRNSVPIGRHIFPL*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3578126-3578039(-) 3575779-3578039(-) 3578039-3575493(+)
Potential amino acid sequence	MAANGNGVSTTPKSPLARIQTQKNGGICHDDSGKPVKAQTIDELHSLQKKRSAPTTPLDGVQGT FATISEDERQRQQLQSISASLASLTRGTGPKVVRGDPAGKVQSVSHVAHHHHIEAPTISVSDSS LKFTHVLYNLSPAELYEQAIKYEKGSFITSTGALATLSGAKTGRSPRDKRVVIDDSTQDELWWG KGSPNIEMDEHTFMVNRERAVDYLNSLDKVFVNDQFLNWDPQNRIKVRIVSARAYHSLFMHNMC IRPTPEELENFGTPDFTIYNAGQFPCNRYTHYMTSSTSIDLNLARREMVILGTQYAGEMKKGLF SVMHYLMPMRQILSLHSGCNMGKDGDVALFFGLSGTGKTTLSTDHNRYLIGDDEHCWSDNGVSN IEGGCYAKCIDLSREKEPDIWNAIKFGTVLENVVFDEHTREVDYGDKSVTEGRYGGQWERSFDD AEESVGEDSDAEERWNLS(-) MTSIVGVTMVCRTSKVVAMPSVLIFQGRRSLISGMPLSLELCWKMLFSMNIRERWIMVTNQLQR EDMAANGNGVSTTPKSPLARIQTQKNGGICHDDSGKPVKAQTIDELHSLQKKRSAPTTPLDGVQ GTFATISEDERQRQQLQSISASLASLTRGTGPKVVRGDPAGKVQSVSHVAHHHHIEAPTISVSD SSLKFTHVLYNLSPAELYEQAIKYEKGSFITSTGALATLSGAKTGRSPRDKRVVIDDSTQDELW WGKGSPNIEMDEHTFMVNRERAVDYLNSLDKVFVNDQFLNWDPQNRIKVRIVSARAYHSLFMHN MCIRPTPEELENFGTPDFTIYNAGQFPCNRYTHYMTSSTSIDLNLARREMVILGTQYAGEMKKG LFSVMHYLMPMRQILSLHSGCNMGKDGDVALFFGLSGTGKTTLSTDHNRYLIGDDEHCWSDNGV SNIEGGCYAKCIDLSREKEPDIWNAIKFGTVLENVVFDEHTREVDYGDKSVTEGRYGGQWERSF DDAEESVGEDSDAEERWNLS(-) MTDSTVLLRLNPRQRTLRRRRNSVPIGRHIFPL*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.003G035200_circ_g.1

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