Plant Circular RNA Database

Detail information of orai.004G261500_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.004G261500_circ_g.1
					
						ID in PlantcircBase
						gra_circ_000404
					
						Alias
						Chr04:59684563|59691222
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr04: 59684563-59691222  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.004G261500						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						3/2
					
						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
						Gorai.004G261500.1:13

General Information
CircRNA Name	orai.004G261500_circ_g.1
ID in PlantcircBase	gra_circ_000404
Alias	Chr04:59684563\|59691222
Organism	Gossypium raimondii
Position	chrChr04: 59684563-59691222 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.004G261500
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	NA
Support reads	3/2
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	Gorai.004G261500.1:13

			
						 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  
						
							CCGAGTCAATTGTGGTACCTTTGGTATTTTGTCTTGGCTAACTATTTGGTCTGTTTCTGTATTG
CAGAAACCTCGTCGTCCACAAGATCCTAGAGTGGAAatacctctgattgctgaacggaaaggtt
ggggttcatgtctttgtagcattgttccagccactgctttgctctctatagtttaccttctagg
gttttcaa

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CCGAGTCAATTGTGGTACCTTTGGTATTTTGTCTTGGCTAACTATTTGGTCTGTTTCTGTATTG CAGAAACCTCGTCGTCCACAAGATCCTAGAGTGGAAatacctctgattgctgaacggaaaggtt ggggttcatgtctttgtagcattgttccagccactgctttgctctctatagtttaccttctagg gttttcaa
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	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.09562549

Conservation Information
Conserved circRNAs	NA
PMCS	0.09562549

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							59685268-59691219(+)
59689988-59684569(+)
59684613-59690012(-)
						
					

						Potential amino acid sequence
						
							MRPLWGFPEKENTSTSLFAVAVGIKQKDLVDKMVKMFLSSDFVVMLFHYDGIVDEWKHFEWCDK
VIHVSARNQTKWWFAKRFLHPDIVSEYSYIFLWDEDLGVEHFHPKVYMSIIEHEGLEISQPALD
RSKSEVHHQITARESKSIVHRTAFKPGANGKHCDAHSKGPPCTGWIEMMAPVFSRAAWRCVWYM
IQNDLIHAWGIDMQVGYCAQGDRTKNIGIVDAEYVVHHNRPTLGGMGAKNRSTAGGRRLDKGDR
IKGIVVNDAYILRHYVKAKKKKKPRRPQDPRVEIPLIAERKGWGSCLCSIVPATALLSIVYLLG
FSNVETENRETWGLADILQSSNVGNCKNQCKPPGTAPLPEGIIENTSNLEMRPLWGFPEKENTS
TSLFAVAVGIKQKDLVDKMVKMFLSSDFVVMLFHYDGIVDEWKHFEWCDKVIHVSARNQTKWWF
AKRFLHPDIVSEYSYIFLWDEDLGVEHFHPKVYMSIIEHEGLEISQPALDRSKSEVHHQITARE
SKSIVHRTAFKPGANGKHCDAHSKGPPCTGWIEMMAPVFSRAAWRCVWYMIQNDLIHAWGIDMQ
VGYCAQGDRTKNIGIVDAEYVVHHNRPTLGGMGAKNRSTAGGRRLDKGDRIKGIVVNDAYILRH
YVKAKKKKKPRRPQDPRVEIPLIAERKGWGSCLCSIVPATALLSIVYLLGFSNVETENRETWGL
ADILQSSNVGNCKNQCKPPGTAPLPEGIIENTSNLEMRPLWGFPEKENTSTSLFAVAVGIKQKD
LVDKMVKMFLSSDFVVMLFHYDGIVDEWKHFEWCDKVIHVSARNQTKWWFAKRFLHPDIVSEYS
YIFLWDEDLGVEHFHPKVYMSIIEHEGLEISQPALDRSKSEVHHQITARESKSIVHRTAFKPGA
NGKHCDAHSKGPPCTGWIEMMAPVFSRAAWRCVWYMIQNDLIHAWGIDMQVGYCAQGDRTKNIG
IVDAEYVVHHNRPTLGGMGAKNRSTAGGRRLDKGDRIKGIVVNDAYILRHYVKAKKKKKPRRPQ
DPRVEIPLIAERKGWGSCLCSIVPATALLSIVYLLGFSNVETENRETWGLADILQSSNVGNCKN
QCKPPGTAPLPEGIIENTSNLEMRPLWGFPEKENTSTSLFAVAVGIKQKDLVDKMVKMFLSSDF
VVMLFHYDGIVDEWKHFEWCDKVIHVSARNQTKWWFAKRFLHPDIVSEYSYIFLWDEDLGVEHF
HPKVYMSIIEHEGLEISQPALDRSKSEVHHQITARESKSIVHRTAFKPGANGKHCDAHSKGPPC
TGWIEMMAPVFSRAAWRCVWYMIQNDLIHAWGIDMQVGYCAQGDRTKNIGIVDAEYVVHHNRPT
LGGMGAKNRSTAGGRRLDKGDRIKGIVVNDAYILRHYVKAKKKKKPRRPQDPRVE(+)
MMHTYCATMLKQRKKRNLVVHKILEWKYL*(+)
MLQRHEPQPFRSAIRGISTLGSCGRRGFFFFFALT*(-)
						
					

						Sponge-miRNAs
						
							gra-miR157b 						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	59685268-59691219(+) 59689988-59684569(+) 59684613-59690012(-)
Potential amino acid sequence	MRPLWGFPEKENTSTSLFAVAVGIKQKDLVDKMVKMFLSSDFVVMLFHYDGIVDEWKHFEWCDK VIHVSARNQTKWWFAKRFLHPDIVSEYSYIFLWDEDLGVEHFHPKVYMSIIEHEGLEISQPALD RSKSEVHHQITARESKSIVHRTAFKPGANGKHCDAHSKGPPCTGWIEMMAPVFSRAAWRCVWYM IQNDLIHAWGIDMQVGYCAQGDRTKNIGIVDAEYVVHHNRPTLGGMGAKNRSTAGGRRLDKGDR IKGIVVNDAYILRHYVKAKKKKKPRRPQDPRVEIPLIAERKGWGSCLCSIVPATALLSIVYLLG FSNVETENRETWGLADILQSSNVGNCKNQCKPPGTAPLPEGIIENTSNLEMRPLWGFPEKENTS TSLFAVAVGIKQKDLVDKMVKMFLSSDFVVMLFHYDGIVDEWKHFEWCDKVIHVSARNQTKWWF AKRFLHPDIVSEYSYIFLWDEDLGVEHFHPKVYMSIIEHEGLEISQPALDRSKSEVHHQITARE SKSIVHRTAFKPGANGKHCDAHSKGPPCTGWIEMMAPVFSRAAWRCVWYMIQNDLIHAWGIDMQ VGYCAQGDRTKNIGIVDAEYVVHHNRPTLGGMGAKNRSTAGGRRLDKGDRIKGIVVNDAYILRH YVKAKKKKKPRRPQDPRVEIPLIAERKGWGSCLCSIVPATALLSIVYLLGFSNVETENRETWGL ADILQSSNVGNCKNQCKPPGTAPLPEGIIENTSNLEMRPLWGFPEKENTSTSLFAVAVGIKQKD LVDKMVKMFLSSDFVVMLFHYDGIVDEWKHFEWCDKVIHVSARNQTKWWFAKRFLHPDIVSEYS YIFLWDEDLGVEHFHPKVYMSIIEHEGLEISQPALDRSKSEVHHQITARESKSIVHRTAFKPGA NGKHCDAHSKGPPCTGWIEMMAPVFSRAAWRCVWYMIQNDLIHAWGIDMQVGYCAQGDRTKNIG IVDAEYVVHHNRPTLGGMGAKNRSTAGGRRLDKGDRIKGIVVNDAYILRHYVKAKKKKKPRRPQ DPRVEIPLIAERKGWGSCLCSIVPATALLSIVYLLGFSNVETENRETWGLADILQSSNVGNCKN QCKPPGTAPLPEGIIENTSNLEMRPLWGFPEKENTSTSLFAVAVGIKQKDLVDKMVKMFLSSDF VVMLFHYDGIVDEWKHFEWCDKVIHVSARNQTKWWFAKRFLHPDIVSEYSYIFLWDEDLGVEHF HPKVYMSIIEHEGLEISQPALDRSKSEVHHQITARESKSIVHRTAFKPGANGKHCDAHSKGPPC TGWIEMMAPVFSRAAWRCVWYMIQNDLIHAWGIDMQVGYCAQGDRTKNIGIVDAEYVVHHNRPT LGGMGAKNRSTAGGRRLDKGDRIKGIVVNDAYILRHYVKAKKKKKPRRPQDPRVE(+) MMHTYCATMLKQRKKRNLVVHKILEWKYL(+) MLQRHEPQPFRSAIRGISTLGSCGRRGFFFFFALT(-)
Sponge-miRNAs	gra-miR157b
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.004G261500_circ_g.1

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