Plant Circular RNA Database

Detail information of orai.004G129800_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.004G129800_circ_g.1
					
						ID in PlantcircBase
						gra_circ_000368
					
						Alias
						Chr04:34961818|34964089
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr04: 34961818-34964089  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.004G129800						
					
						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.004G129800.2:7
Gorai.004G129800.3:7
Gorai.004G129800.4:7
Gorai.004G129800.6:6
Gorai.004G129800.1:7
Gorai.004G129800.5:7

General Information
CircRNA Name	orai.004G129800_circ_g.1
ID in PlantcircBase	gra_circ_000368
Alias	Chr04:34961818\|34964089
Organism	Gossypium raimondii
Position	chrChr04: 34961818-34964089 JBrowse»
Reference genome	Graimondii_221
Type	ue-circRNA
Identification method	CIRI
Parent gene	Gorai.004G129800
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.004G129800.2:7 Gorai.004G129800.3:7 Gorai.004G129800.4:7 Gorai.004G129800.6:6 Gorai.004G129800.1:7 Gorai.004G129800.5:7

			
						 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  
						
							GGATGGGTATCTTACTGCACCACCAGTAGGAAATTCAATGGCTCCTCATGGTGCTTGGAAGAGA
ACAGAGTTCTTTTTGAATCATGAAGCACTTCAACAGgcaacaaaaaactatgaaaaagctgtcc
agctcaactggaatagcccccaggtatattagaagtaattgtttcttttagtcttgtaattctc
ccaactat

									
								

					

						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: 34961818-34961868,34961984-34962013,34962148-34962210,34
962349-34962414,34962585-34962710,34962939-34962974,3496
3970-34964089
GCAACAAAAAACTATGAAAAAGCTGTCCAGCTCAACTGGAATAGCCCCCAGGCTCTAAACAATT
GGGGACTTGCTCTTCAGGAACTCAGTGCTATTGTTCCAGCTCGGGAGAAGCAAAAAATTGTCAG
GACTGCAATTAGTAAGTTTCGTGCTGCAATACAGTTGCAATTTGATTTCCATCGAGCAATATAC
AACCTTGGAACTGTTCTGTATGGACTAGCTGAGGATACCTTAAGACAAGGTTCGCCGAATCTGA
AAGAAGTTTCCCCAGATGAGCTGTATAGCCAGTCTGCTATCTATATTGCGGCTGCTCATGCACT
GAAACCAAATTACTCGGTTTACAGCAGTGCCTTGAGGCTTGTTCGTTCAATGCTACCTTTACCC
CATCTTAAGGATGGGTATCTTACTGCACCACCAGTAGGAAATTCAATGGCTCCTCATGGTGCTT
GGAAGAGAACAGAGTTCTTTTTGAATCATGAAGCACTTCAACAG
						
					

						Genomic sequence
						
							GCAACAAAAAACTATGAAAAAGCTGTCCAGCTCAACTGGAATAGCCCCCAGGTATATTAGAAGT
AATTGTTTCTTTTAGTCTTGTAATTCTCCCAACTATAATGACTACATCTTTCATTTTTATTCTA
CATCTTAGTGGTTTTAAGGATTCATAAATCTCTTTCAGGCTCTAAACAATTGGGGACTTGCTCT
TCAGGTAAACTATGTTTTAGTGATGTTGATATTGTAATCAGCTTCATTTTATTTCCATATCTTT
CAAATTTCTGAGTCTACTTCTATGAAATCCTGGAACGCTATGCTTACTTTCATGTTCTATCATG
CATGCTTTAGGAACTCAGTGCTATTGTTCCAGCTCGGGAGAAGCAAAAAATTGTCAGGACTGCA
ATTAGTAAGGTACAAAAGTCATTTGGAGCAATCAGGGTGCTCAGATGACTATAGTAACAAGCTG
CAAAGTAATTTGACATCTGATAAGTCCTAAAAGAAGTTCACTTTGCATTTCAATTCTTACAGTA
CCCTTTGCTTTAAATGCAGTTTCGTGCTGCAATACAGTTGCAATTTGATTTCCATCGAGCAATA
TACAACCTTGGAACTGTTCTGGTAAGTTTGTTGGTTATTACTAGTCGTGATACTGGATGGCATG
ATCCTATCCTCACCTATGATACATTCATTTGTGAAATTAATGAGATTAGATAATGACCTTATCA
AGTGAAATTTCAAACAAGTGAAGCATTGATTTGGAAATTGAAATATTTCTATTTCTAATGCAGT
ATGGACTAGCTGAGGATACCTTAAGACAAGGTTCGCCGAATCTGAAAGAAGTTTCCCCAGATGA
GCTGTATAGCCAGTCTGCTATCTATATTGCGGCTGCTCATGCACTGAAACCAAATTACTCGGTA
AGAGATCAATGTATTTTTCTGGACTACCGAGGTTTACCCTACATTCAGGCTATATATGTGGCAC
AATTATTGGCTAATGAAATTTTGTCACATGAGTTTAATAAAGAAAGCTAATGTTATACTTCTTA
ATTTTCTCCTTAATTTAAAAGTTCCAGTGTTCTGCATTTTGATTTCCTATCTTAGTTTTGTGGA
TATGTTCTTATTTGATGTTTTAAATACATCCAGGTTTACAGCAGTGCCTTGAGGCTTGTTCGTT
CAATGGTCAGTATTTAATCTTTAAACAATGTTTTTTTAGGTTTATTTTGTTTTCTAAATTGATT
GAATCTTCCATAAGAAATGTTGAGTCTGTTAGAATGAAAACGACTTCTGTTCCTTTACCTGGTT
AATTATCATTTATTACTACTGTAGGAGTATTTTTGGCGTAATCCTTCTAGTTCTGAAGTTCTTT
CTTGTCAGTCATTAGTGCTGTTTTTAACTGTCAATTATCAGTGCACCACAACTATATCTTTGAG
CTGCACCAGAAACTTCGGTTTGATGCAAAATATCCTTTCACATGCTTTCCAATGCTTTTTCAAA
TAGTATTCCTTTGGCTTGAAATGTGAACCTATTCAATGATTGGCCAATCCATGCTTACCCCCAA
CAATGTTCATTTATTTTTCCTCGCAACATAAGCGAGGATGCATTGTTTGAAAATCTGAAGTTAA
AAAGGTTGTGTGATAAAACACATATAAATGTAAAATTTGTGATTATTTTGCAGGTTCTTGGATT
TGTCAGATGCCTATTTTGGTGGTGAATTTAAAATTCCCATACATATTTGTGATTTTGAAAATCA
TGCTTTTATACCTTTCAAATATGTAATCATATTGAATCTTAATTTTTATATATAATGTATGCGC
TTCATTCTCACTATATATAGCAAATGAAATACAATTGATGTTCCCAAACATGGCATTAACTAAT
TTGGCCTAGCAATACCTCCTTGGCTTAGTGATCTTGTATTCAAATCAAAAGAAACATAATTTTA
TTTAAAAATGTAATTGCAAGCTGCTGTAATTGTATTCTTTCACCCTCTTCATTTTCCAGTGCCT
GTCTTCTTGAAGATTATTTTTTTCTCATTTGCTCGTTCATGTTTAAACCAGATGGCTCACCTGG
TTAAGAGAACTATTATTGCGGAAGCCATCACTCTGTTTATTCTCAATTGAATTAGCTGGGCAAC
TCATTTAATATTATGTCTAACTGAAATAAAATTTTGACAGCTACCTTTACCCCATCTTAAGGAT
GGGTATCTTACTGCACCACCAGTAGGAAATTCAATGGCTCCTCATGGTGCTTGGAAGAGAACAG
AGTTCTTTTTGAATCATGAAGCACTTCAACAG
						
					

			
		

Sequences
Splice junction sequence	GGATGGGTATCTTACTGCACCACCAGTAGGAAATTCAATGGCTCCTCATGGTGCTTGGAAGAGA ACAGAGTTCTTTTTGAATCATGAAGCACTTCAACAGgcaacaaaaaactatgaaaaagctgtcc agctcaactggaatagcccccaggtatattagaagtaattgtttcttttagtcttgtaattctc ccaactat
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: 34961818-34961868,34961984-34962013,34962148-34962210,34 962349-34962414,34962585-34962710,34962939-34962974,3496 3970-34964089 GCAACAAAAAACTATGAAAAAGCTGTCCAGCTCAACTGGAATAGCCCCCAGGCTCTAAACAATT GGGGACTTGCTCTTCAGGAACTCAGTGCTATTGTTCCAGCTCGGGAGAAGCAAAAAATTGTCAG GACTGCAATTAGTAAGTTTCGTGCTGCAATACAGTTGCAATTTGATTTCCATCGAGCAATATAC AACCTTGGAACTGTTCTGTATGGACTAGCTGAGGATACCTTAAGACAAGGTTCGCCGAATCTGA AAGAAGTTTCCCCAGATGAGCTGTATAGCCAGTCTGCTATCTATATTGCGGCTGCTCATGCACT GAAACCAAATTACTCGGTTTACAGCAGTGCCTTGAGGCTTGTTCGTTCAATGCTACCTTTACCC CATCTTAAGGATGGGTATCTTACTGCACCACCAGTAGGAAATTCAATGGCTCCTCATGGTGCTT GGAAGAGAACAGAGTTCTTTTTGAATCATGAAGCACTTCAACAG
Genomic sequence	GCAACAAAAAACTATGAAAAAGCTGTCCAGCTCAACTGGAATAGCCCCCAGGTATATTAGAAGT AATTGTTTCTTTTAGTCTTGTAATTCTCCCAACTATAATGACTACATCTTTCATTTTTATTCTA CATCTTAGTGGTTTTAAGGATTCATAAATCTCTTTCAGGCTCTAAACAATTGGGGACTTGCTCT TCAGGTAAACTATGTTTTAGTGATGTTGATATTGTAATCAGCTTCATTTTATTTCCATATCTTT CAAATTTCTGAGTCTACTTCTATGAAATCCTGGAACGCTATGCTTACTTTCATGTTCTATCATG CATGCTTTAGGAACTCAGTGCTATTGTTCCAGCTCGGGAGAAGCAAAAAATTGTCAGGACTGCA ATTAGTAAGGTACAAAAGTCATTTGGAGCAATCAGGGTGCTCAGATGACTATAGTAACAAGCTG CAAAGTAATTTGACATCTGATAAGTCCTAAAAGAAGTTCACTTTGCATTTCAATTCTTACAGTA CCCTTTGCTTTAAATGCAGTTTCGTGCTGCAATACAGTTGCAATTTGATTTCCATCGAGCAATA TACAACCTTGGAACTGTTCTGGTAAGTTTGTTGGTTATTACTAGTCGTGATACTGGATGGCATG ATCCTATCCTCACCTATGATACATTCATTTGTGAAATTAATGAGATTAGATAATGACCTTATCA AGTGAAATTTCAAACAAGTGAAGCATTGATTTGGAAATTGAAATATTTCTATTTCTAATGCAGT ATGGACTAGCTGAGGATACCTTAAGACAAGGTTCGCCGAATCTGAAAGAAGTTTCCCCAGATGA GCTGTATAGCCAGTCTGCTATCTATATTGCGGCTGCTCATGCACTGAAACCAAATTACTCGGTA AGAGATCAATGTATTTTTCTGGACTACCGAGGTTTACCCTACATTCAGGCTATATATGTGGCAC AATTATTGGCTAATGAAATTTTGTCACATGAGTTTAATAAAGAAAGCTAATGTTATACTTCTTA ATTTTCTCCTTAATTTAAAAGTTCCAGTGTTCTGCATTTTGATTTCCTATCTTAGTTTTGTGGA TATGTTCTTATTTGATGTTTTAAATACATCCAGGTTTACAGCAGTGCCTTGAGGCTTGTTCGTT CAATGGTCAGTATTTAATCTTTAAACAATGTTTTTTTAGGTTTATTTTGTTTTCTAAATTGATT GAATCTTCCATAAGAAATGTTGAGTCTGTTAGAATGAAAACGACTTCTGTTCCTTTACCTGGTT AATTATCATTTATTACTACTGTAGGAGTATTTTTGGCGTAATCCTTCTAGTTCTGAAGTTCTTT CTTGTCAGTCATTAGTGCTGTTTTTAACTGTCAATTATCAGTGCACCACAACTATATCTTTGAG CTGCACCAGAAACTTCGGTTTGATGCAAAATATCCTTTCACATGCTTTCCAATGCTTTTTCAAA TAGTATTCCTTTGGCTTGAAATGTGAACCTATTCAATGATTGGCCAATCCATGCTTACCCCCAA CAATGTTCATTTATTTTTCCTCGCAACATAAGCGAGGATGCATTGTTTGAAAATCTGAAGTTAA AAAGGTTGTGTGATAAAACACATATAAATGTAAAATTTGTGATTATTTTGCAGGTTCTTGGATT TGTCAGATGCCTATTTTGGTGGTGAATTTAAAATTCCCATACATATTTGTGATTTTGAAAATCA TGCTTTTATACCTTTCAAATATGTAATCATATTGAATCTTAATTTTTATATATAATGTATGCGC TTCATTCTCACTATATATAGCAAATGAAATACAATTGATGTTCCCAAACATGGCATTAACTAAT TTGGCCTAGCAATACCTCCTTGGCTTAGTGATCTTGTATTCAAATCAAAAGAAACATAATTTTA TTTAAAAATGTAATTGCAAGCTGCTGTAATTGTATTCTTTCACCCTCTTCATTTTCCAGTGCCT GTCTTCTTGAAGATTATTTTTTTCTCATTTGCTCGTTCATGTTTAAACCAGATGGCTCACCTGG TTAAGAGAACTATTATTGCGGAAGCCATCACTCTGTTTATTCTCAATTGAATTAGCTGGGCAAC TCATTTAATATTATGTCTAACTGAAATAAAATTTTGACAGCTACCTTTACCCCATCTTAAGGAT GGGTATCTTACTGCACCACCAGTAGGAAATTCAATGGCTCCTCATGGTGCTTGGAAGAGAACAG AGTTCTTTTTGAATCATGAAGCACTTCAACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.445319979

Conservation Information
Conserved circRNAs	NA
PMCS	0.445319979

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							34964027-34963503(+)
34964073-34961987(+)
						
						Potential amino acid sequence
						
							MAPHGAWKRTEFFLNHEALQQATKNYEKAVQLNWNSPQALNNWGLALQELSAIVPAREKQKIVR
TAISKFRAAIQLQFDFHRAIYNLGTVLYGLAEDTLRQGSPNLKEVSPDELYSQSAIYIAAAHAL
KPNYSVYSSALRLVRSMVLGFVRCLFWW*(+)
MKHFNRQQKTMKKLSSSTGIAPRL*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	34964027-34963503(+) 34964073-34961987(+)
Potential amino acid sequence	MAPHGAWKRTEFFLNHEALQQATKNYEKAVQLNWNSPQALNNWGLALQELSAIVPAREKQKIVR TAISKFRAAIQLQFDFHRAIYNLGTVLYGLAEDTLRQGSPNLKEVSPDELYSQSAIYIAAAHAL KPNYSVYSSALRLVRSMVLGFVRCLFWW(+) MKHFNRQQKTMKKLSSSTGIAPRL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.004G129800_circ_g.1

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