Plant Circular RNA Database

Detail information of orai.004G201800_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.004G201800_circ_g.1
					
						ID in PlantcircBase
						gra_circ_000384
					
						Alias
						Chr04:52978532|52979810
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr04: 52978532-52979810  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.004G201800						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2
					
						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
						Gorai.004G201800.2:5
Gorai.004G201800.1:5
Gorai.004G201800.5:5
Gorai.004G201800.3:4
Gorai.004G201800.4:5
Gorai.004G201800.6:5

General Information
CircRNA Name	orai.004G201800_circ_g.1
ID in PlantcircBase	gra_circ_000384
Alias	Chr04:52978532\|52979810
Organism	Gossypium raimondii
Position	chrChr04: 52978532-52979810 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.004G201800
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	NA
Support reads	2
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	Gorai.004G201800.2:5 Gorai.004G201800.1:5 Gorai.004G201800.5:5 Gorai.004G201800.3:4 Gorai.004G201800.4:5 Gorai.004G201800.6:5

			
						 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  
						
							CCGTATTGAGGAACACCGTAGGAAATATGATAGATTGCACAAAGAGAGAGAAGATAGAAAGATT
GAGCGTGAGAGACGTCGTCGTCGTGCTCAAGCTCAGatgggagacccttctgtggaggttaccg
atgataaccttgatgcttcccattcagctaaggccaaagccatggatgccatttctgaaggtaa
ataatcac

									
								

					

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 492
Transcript exons: 52978532-52978619,52978699-52978779,52978923-52978987,52
979255-52979395,52979694-52979810
ATGGGAGACCCTTCTGTGGAGGTTACCGATGATAACCTTGATGCTTCCCATTCAGCTAAGGCCA
AAGCCATGGATGCCATTTCTGAAGGGAAGTTTGAGGAAGCTATTGAGAACCTGACACAGGCGAT
TTTGCTGAATCCGACTTCGGCAATCATGTATGGCACACGAGCCAGTGTTTACATTAAGATGAAA
AAGCCCAATGCTGCTATTCGAGATGCCAATGCTGCTTTGGAGATAAACCCAGATTCTGCTAAGG
GCTACAAGTCTCGTGGCATTGCACGTGCAATGCTCGGTCAATGGGAAGATGCTGCCAAGGACCT
ACACATGGCATCAAAGCTGGATTATGATGAGGAAATAAAAAATTGGCTTAAGAAGGTTGAACCC
AACGCACACCGTATTGAGGAACACCGTAGGAAATATGATAGATTGCACAAAGAGAGAGAAGATA
GAAAGATTGAGCGTGAGAGACGTCGTCGTCGTGCTCAAGCTCAG
						
					

						Genomic sequence
						
							ATGGGAGACCCTTCTGTGGAGGTTACCGATGATAACCTTGATGCTTCCCATTCAGCTAAGGCCA
AAGCCATGGATGCCATTTCTGAAGGTAAATAATCACAACTTACCATTTATTTACTTATTTTTAT
TTGTTTGAGTTTGTATTATGCTAAATCATTGTAATGCAGGGAAGTTTGAGGAAGCTATTGAGAA
CCTGACACAGGCGATTTTGCTGAATCCGACTTCGGCAATCATGTATGGCACACGAGGTTAGCAT
TTCTTAGTTTAGCCTTATATTCTCCCTTTCCACTAGTATTTTTTTTTGTTGACATGCATTCCTT
ATCTTTTTTAGAATGATTCTTATATTTGATAGAATGATTCAGTTGCTTCGTGGTCTTTTTTCTC
CTTTCAGCCAGTGTTTACATTAAGATGAAAAAGCCCAATGCTGCTATTCGAGATGCCAATGCTG
CTTTGGAGGTTTGTGTGTATATGTATATATATGTTTAGCTTAGTATTGATCTGGTTTTTTTACT
TGCTTGTATGATAAAATAATTAATGGTAATCATGAACTTCGTTAACTGTGTGTCTTGGATTATT
GGTTCATTCAAGGCAATATATGTAAGGGATTTCTGCTGAACATATTGTGTTCAATATGGTTTCA
TCTTGTTTTAGGGTTTTCCTGGAAATAGCAAGGCCGTATTTGAGTAGGAAATAATTTTAATTAT
CCTCATTCATGTCTTGCAGATAAACCCAGATTCTGCTAAGGGCTACAAGTCTCGTGGCATTGCA
CGTGCAATGCTCGGTCAATGGGAAGATGCTGCCAAGGACCTACACATGGCATCAAAGCTGGATT
ATGATGAGGAAATAAAAAATTGGCTTAAGAAGGTTTGCTCTTATCTGTCCTTTTTCACCCTTCC
CTTTGAAAGTTTCAGTCCATGCAGTATAATTGAAGAGATGAGATTTCAAAGACCAGAGCATGTC
ATGTGATTTTAAGCATAATTTGACACAATTTGGTCATTTTGTACATCTGAATTATTGCATCACT
ATATGTGAGTGTAATTCTCTGCCACCAATGTTAGTATTTTTTGGCTGTACCTGCATCACTATAT
ATGAGTGACAAGACCACTGTTGTTGGGTGTAATTCCTACTTTGACGGATCACATCGATTTCATT
GATTAAACAGGTTGAACCCAACGCACACCGTATTGAGGAACACCGTAGGAAATATGATAGATTG
CACAAAGAGAGAGAAGATAGAAAGATTGAGCGTGAGAGACGTCGTCGTCGTGCTCAAGCTCAG
						
					

			
		

Sequences
Splice junction sequence	CCGTATTGAGGAACACCGTAGGAAATATGATAGATTGCACAAAGAGAGAGAAGATAGAAAGATT GAGCGTGAGAGACGTCGTCGTCGTGCTCAAGCTCAGatgggagacccttctgtggaggttaccg atgataaccttgatgcttcccattcagctaaggccaaagccatggatgccatttctgaaggtaa ataatcac
Assembled circRNA sequence	Yes 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	Transcript length: 492 Transcript exons: 52978532-52978619,52978699-52978779,52978923-52978987,52 979255-52979395,52979694-52979810 ATGGGAGACCCTTCTGTGGAGGTTACCGATGATAACCTTGATGCTTCCCATTCAGCTAAGGCCA AAGCCATGGATGCCATTTCTGAAGGGAAGTTTGAGGAAGCTATTGAGAACCTGACACAGGCGAT TTTGCTGAATCCGACTTCGGCAATCATGTATGGCACACGAGCCAGTGTTTACATTAAGATGAAA AAGCCCAATGCTGCTATTCGAGATGCCAATGCTGCTTTGGAGATAAACCCAGATTCTGCTAAGG GCTACAAGTCTCGTGGCATTGCACGTGCAATGCTCGGTCAATGGGAAGATGCTGCCAAGGACCT ACACATGGCATCAAAGCTGGATTATGATGAGGAAATAAAAAATTGGCTTAAGAAGGTTGAACCC AACGCACACCGTATTGAGGAACACCGTAGGAAATATGATAGATTGCACAAAGAGAGAGAAGATA GAAAGATTGAGCGTGAGAGACGTCGTCGTCGTGCTCAAGCTCAG
Genomic sequence	ATGGGAGACCCTTCTGTGGAGGTTACCGATGATAACCTTGATGCTTCCCATTCAGCTAAGGCCA AAGCCATGGATGCCATTTCTGAAGGTAAATAATCACAACTTACCATTTATTTACTTATTTTTAT TTGTTTGAGTTTGTATTATGCTAAATCATTGTAATGCAGGGAAGTTTGAGGAAGCTATTGAGAA CCTGACACAGGCGATTTTGCTGAATCCGACTTCGGCAATCATGTATGGCACACGAGGTTAGCAT TTCTTAGTTTAGCCTTATATTCTCCCTTTCCACTAGTATTTTTTTTTGTTGACATGCATTCCTT ATCTTTTTTAGAATGATTCTTATATTTGATAGAATGATTCAGTTGCTTCGTGGTCTTTTTTCTC CTTTCAGCCAGTGTTTACATTAAGATGAAAAAGCCCAATGCTGCTATTCGAGATGCCAATGCTG CTTTGGAGGTTTGTGTGTATATGTATATATATGTTTAGCTTAGTATTGATCTGGTTTTTTTACT TGCTTGTATGATAAAATAATTAATGGTAATCATGAACTTCGTTAACTGTGTGTCTTGGATTATT GGTTCATTCAAGGCAATATATGTAAGGGATTTCTGCTGAACATATTGTGTTCAATATGGTTTCA TCTTGTTTTAGGGTTTTCCTGGAAATAGCAAGGCCGTATTTGAGTAGGAAATAATTTTAATTAT CCTCATTCATGTCTTGCAGATAAACCCAGATTCTGCTAAGGGCTACAAGTCTCGTGGCATTGCA CGTGCAATGCTCGGTCAATGGGAAGATGCTGCCAAGGACCTACACATGGCATCAAAGCTGGATT ATGATGAGGAAATAAAAAATTGGCTTAAGAAGGTTTGCTCTTATCTGTCCTTTTTCACCCTTCC CTTTGAAAGTTTCAGTCCATGCAGTATAATTGAAGAGATGAGATTTCAAAGACCAGAGCATGTC ATGTGATTTTAAGCATAATTTGACACAATTTGGTCATTTTGTACATCTGAATTATTGCATCACT ATATGTGAGTGTAATTCTCTGCCACCAATGTTAGTATTTTTTGGCTGTACCTGCATCACTATAT ATGAGTGACAAGACCACTGTTGTTGGGTGTAATTCCTACTTTGACGGATCACATCGATTTCATT GATTAAACAGGTTGAACCCAACGCACACCGTATTGAGGAACACCGTAGGAAATATGATAGATTG CACAAAGAGAGAGAAGATAGAAAGATTGAGCGTGAGAGACGTCGTCGTCGTGCTCAAGCTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.451811324

Conservation Information
Conserved circRNAs	NA
PMCS	0.451811324

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							52978560-52978705(+)
52979737-52978705(+)
52978583-52979353(-)
52978612-52979809(-)
						
						Potential amino acid sequence
						
							MITLMLPIQLRPKPWMPFLKFEEAIENLTQAILLNPTSAIMYGTRASVYIKMKKPNAAIRDANA
ALEINPDSAKGYKSRGIARAMLGQWEDAAKDLHMASKLDYDEEIKNWLKKVEPNAHRIEEHRRK
YDRLHKEREDRKIERERRRRRAQAQMGDPSVEVTDDNLDASHSAKAKAMDAISEV*(+)
MIDCTKREKIERLSVRDVVVVLKLRWETLLWRLPMITLMLPIQLRPKPWMPFLKFEEAIENLTQ
AILLNPTSAIMYGTRASVYIKMKKPNAAIRDANAALEINPDSAKGYKSRGIARAMLGQWEDAAK
DLHMASKLDYDEEIKNWLKKVEPNAHRIEEHRRKYDRLHKEREDRKIERERRRRRAQAQMGDPS
VEVTDDNLDASHSAKAKAMDAISEV*(+)
MGSIKVIIGNLHRRVSHLSLSTTTTSLTLNLSIFSLFVQSIIFPTVFLNTVCVGFNLLKPIFYF
LIIIQL*(-)
MASMALALAEWEASRLSSVTSTEGSPI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	52978560-52978705(+) 52979737-52978705(+) 52978583-52979353(-) 52978612-52979809(-)
Potential amino acid sequence	MITLMLPIQLRPKPWMPFLKFEEAIENLTQAILLNPTSAIMYGTRASVYIKMKKPNAAIRDANA ALEINPDSAKGYKSRGIARAMLGQWEDAAKDLHMASKLDYDEEIKNWLKKVEPNAHRIEEHRRK YDRLHKEREDRKIERERRRRRAQAQMGDPSVEVTDDNLDASHSAKAKAMDAISEV(+) MIDCTKREKIERLSVRDVVVVLKLRWETLLWRLPMITLMLPIQLRPKPWMPFLKFEEAIENLTQ AILLNPTSAIMYGTRASVYIKMKKPNAAIRDANAALEINPDSAKGYKSRGIARAMLGQWEDAAK DLHMASKLDYDEEIKNWLKKVEPNAHRIEEHRRKYDRLHKEREDRKIERERRRRRAQAQMGDPS VEVTDDNLDASHSAKAKAMDAISEV(+) MGSIKVIIGNLHRRVSHLSLSTTTTSLTLNLSIFSLFVQSIIFPTVFLNTVCVGFNLLKPIFYF LIIIQL(-) MASMALALAEWEASRLSSVTSTEGSPI(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.004G201800_circ_g.1

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