Plant Circular RNA Database

Detail information of orai.004G033500_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.004G033500_circ_g.1
					
						ID in PlantcircBase
						gra_circ_000318
					
						Alias
						Chr04:2741075|2742425
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr04: 2741075-2742425  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.004G033500						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							orai.004G033500_circ_g.2 						
					
						Support reads
						3
					
						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.004G033500.3:4
Gorai.004G033500.2:4
Gorai.004G033500.1:4

General Information
CircRNA Name	orai.004G033500_circ_g.1
ID in PlantcircBase	gra_circ_000318
Alias	Chr04:2741075\|2742425
Organism	Gossypium raimondii
Position	chrChr04: 2741075-2742425 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.004G033500
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	orai.004G033500_circ_g.2
Support reads	3
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.004G033500.3:4 Gorai.004G033500.2:4 Gorai.004G033500.1:4

			
						 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  
						
							CTGCTGAACTTACTGCTGGTTACTACAACACGGCTCTGAGAGATGGTTATGATCCAGTTGTCTC
AGTGTTGTCTCGACATGGAGCTGCTTTGCATATTCCattggtgatgtaaataaagatatatact
atagagatcaacaggggttctccaacaatgattatctcacactaggggtggatcatgttcctct
gttatctg

									
								

					

						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: 725
Transcript exons: 2741075-2741295,2741401-2741478,2741539-2741710,2742172-
2742425
ATTGGTGATGTAAATAAAGATATATACTATAGAGATCAACAGGGGTTCTCCAACAATGATTATC
TCACACTAGGGGTGGATCATGTTCCTCTGTTATCTGGGCGGACTGCCCTCCAGTGTTATGAAGA
TTTCATGCTTAGTTTTGTTAACAAATTTGAATCCTTTATTGGAACTGTAATTGAAGAAATAAGC
ATCGGTCTTGGTCCTTCTGGAGAACTTAGGTATCCTGCTCATCCTTTTGGTGATGGTAGATGGA
AATTCCCTGGCATCGGTGAATTCCAGTGTTATGATAAGTACATTTTTGCTTGCAGGATGGAGGA
CTTAAAGATGGCTGCATGCCGAGAAGGAAAACCTCAATGGGGGGACAAAGGGCCACAGAATGCT
GGCTGTTACAACAGTCTTCCATCTGGGGTGCCCTTCTTTGAAGAGGGAAAGGAGAGCTTTCTAT
CTGATTATGGCCGTTTCTTCCTGGAATGGTACAGTGGTAGGCTGATTTGTCATGCAGATGCCAT
TCTTGCAAAGGCAGCAAAGATACTGAAAAAATACCAAGAAAATGAGCAAACTTCTGTTATGTTG
GTGGCTAAAATTAGTGGAATTTATTGGTGGTACCAGACTGTATCACACCCTGCTGAACTTACTG
CTGGTTACTACAACACGGCTCTGAGAGATGGTTATGATCCAGTTGTCTCAGTGTTGTCTCGACA
TGGAGCTGCTTTGCATATTCC
						
					

						Genomic sequence
						
							ATTGGTGATGTAAATAAAGATATATACTATAGAGATCAACAGGGGTTCTCCAACAATGATTATC
TCACACTAGGGGTGGATCATGTTCCTCTGTTATCTGGGCGGACTGCCCTCCAGTGTTATGAAGA
TTTCATGCTTAGTTTTGTTAACAAATTTGAATCCTTTATTGGAACTGTAATTGAAGAAATAAGC
ATCGGTCTTGGTCCTTCTGGAGAACTTAGGTACTTTATGGTTCTTATGTTATTCTTTTCCTTTT
TTTTTGTTCAGTCTATGAAGTTATTGTTGAAACATGATTATGAAGTCATTGCATGATTGTCTTA
GTGCAGGTATCCTGCTCATCCTTTTGGTGATGGTAGATGGAAATTCCCTGGCATCGGTGAATTC
CAGTGTTATGATAAGTACATGTAGGCATAAACTGTTTCCATCCTAATACAAGGTCAGGTGTTTC
ATTATTCTCAAGATAGTTTTGCTTGCAGGATGGAGGACTTAAAGATGGCTGCATGCCGAGAAGG
AAAACCTCAATGGGGGGACAAAGGGCCACAGAATGCTGGCTGTTACAACAGTCTTCCATCTGGG
GTGCCCTTCTTTGAAGAGGGAAAGGAGAGCTTTCTATCTGATTATGGCCGTTTCTTCCTGGTAC
TATGCTTTATCTGTAATATTTTCGTACCAGATTTATGTCTGTACATTGTGCAGGTTAATATTCT
ACAACATTCATGCACCAATATAATATGTACTGCTACCATGCATTAACTTATGGTATTCAAACCG
TCCATTTGAATTTAATCCATTGACCAGATATCTGCAATATAGAAGAGTGGTGCTGAATTTACTG
ACTGTCATATTGAGAGGTTATTTATGATCATTGCTACATTTTTATTTTCTAAGTTACTCGTCTA
CTAAAATGGTAATATATGGGGTAGAGCTCCTTTTGGCTGGAGCTCATAGTGATATACAAATAGG
TATGTATTTATTGGGGAAAGTGCGTGATAACATCATGTTTTCAGAAATCCAATATGCAATCCCC
AGCCTCAGATTAAACATGATTATGGAAACAAACTTAGCATTTAAAAACCATACTTGGGAATGAT
CTTTTGCAGGAATGGTACAGTGGTAGGCTGATTTGTCATGCAGATGCCATTCTTGCAAAGGCAG
CAAAGATACTGAAAAAATACCAAGAAAATGAGCAAACTTCTGTTATGTTGGTGGCTAAAATTAG
TGGAATTTATTGGTGGTACCAGACTGTATCACACCCTGCTGAACTTACTGCTGGTTACTACAAC
ACGGCTCTGAGAGATGGTTATGATCCAGTTGTCTCAGTGTTGTCTCGACATGGAGCTGCTTTGC
ATATTCC
						
					

			
		

Sequences
Splice junction sequence	CTGCTGAACTTACTGCTGGTTACTACAACACGGCTCTGAGAGATGGTTATGATCCAGTTGTCTC AGTGTTGTCTCGACATGGAGCTGCTTTGCATATTCCattggtgatgtaaataaagatatatact atagagatcaacaggggttctccaacaatgattatctcacactaggggtggatcatgttcctct gttatctg
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: 725 Transcript exons: 2741075-2741295,2741401-2741478,2741539-2741710,2742172- 2742425 ATTGGTGATGTAAATAAAGATATATACTATAGAGATCAACAGGGGTTCTCCAACAATGATTATC TCACACTAGGGGTGGATCATGTTCCTCTGTTATCTGGGCGGACTGCCCTCCAGTGTTATGAAGA TTTCATGCTTAGTTTTGTTAACAAATTTGAATCCTTTATTGGAACTGTAATTGAAGAAATAAGC ATCGGTCTTGGTCCTTCTGGAGAACTTAGGTATCCTGCTCATCCTTTTGGTGATGGTAGATGGA AATTCCCTGGCATCGGTGAATTCCAGTGTTATGATAAGTACATTTTTGCTTGCAGGATGGAGGA CTTAAAGATGGCTGCATGCCGAGAAGGAAAACCTCAATGGGGGGACAAAGGGCCACAGAATGCT GGCTGTTACAACAGTCTTCCATCTGGGGTGCCCTTCTTTGAAGAGGGAAAGGAGAGCTTTCTAT CTGATTATGGCCGTTTCTTCCTGGAATGGTACAGTGGTAGGCTGATTTGTCATGCAGATGCCAT TCTTGCAAAGGCAGCAAAGATACTGAAAAAATACCAAGAAAATGAGCAAACTTCTGTTATGTTG GTGGCTAAAATTAGTGGAATTTATTGGTGGTACCAGACTGTATCACACCCTGCTGAACTTACTG CTGGTTACTACAACACGGCTCTGAGAGATGGTTATGATCCAGTTGTCTCAGTGTTGTCTCGACA TGGAGCTGCTTTGCATATTCC
Genomic sequence	ATTGGTGATGTAAATAAAGATATATACTATAGAGATCAACAGGGGTTCTCCAACAATGATTATC TCACACTAGGGGTGGATCATGTTCCTCTGTTATCTGGGCGGACTGCCCTCCAGTGTTATGAAGA TTTCATGCTTAGTTTTGTTAACAAATTTGAATCCTTTATTGGAACTGTAATTGAAGAAATAAGC ATCGGTCTTGGTCCTTCTGGAGAACTTAGGTACTTTATGGTTCTTATGTTATTCTTTTCCTTTT TTTTTGTTCAGTCTATGAAGTTATTGTTGAAACATGATTATGAAGTCATTGCATGATTGTCTTA GTGCAGGTATCCTGCTCATCCTTTTGGTGATGGTAGATGGAAATTCCCTGGCATCGGTGAATTC CAGTGTTATGATAAGTACATGTAGGCATAAACTGTTTCCATCCTAATACAAGGTCAGGTGTTTC ATTATTCTCAAGATAGTTTTGCTTGCAGGATGGAGGACTTAAAGATGGCTGCATGCCGAGAAGG AAAACCTCAATGGGGGGACAAAGGGCCACAGAATGCTGGCTGTTACAACAGTCTTCCATCTGGG GTGCCCTTCTTTGAAGAGGGAAAGGAGAGCTTTCTATCTGATTATGGCCGTTTCTTCCTGGTAC TATGCTTTATCTGTAATATTTTCGTACCAGATTTATGTCTGTACATTGTGCAGGTTAATATTCT ACAACATTCATGCACCAATATAATATGTACTGCTACCATGCATTAACTTATGGTATTCAAACCG TCCATTTGAATTTAATCCATTGACCAGATATCTGCAATATAGAAGAGTGGTGCTGAATTTACTG ACTGTCATATTGAGAGGTTATTTATGATCATTGCTACATTTTTATTTTCTAAGTTACTCGTCTA CTAAAATGGTAATATATGGGGTAGAGCTCCTTTTGGCTGGAGCTCATAGTGATATACAAATAGG TATGTATTTATTGGGGAAAGTGCGTGATAACATCATGTTTTCAGAAATCCAATATGCAATCCCC AGCCTCAGATTAAACATGATTATGGAAACAAACTTAGCATTTAAAAACCATACTTGGGAATGAT CTTTTGCAGGAATGGTACAGTGGTAGGCTGATTTGTCATGCAGATGCCATTCTTGCAAAGGCAG CAAAGATACTGAAAAAATACCAAGAAAATGAGCAAACTTCTGTTATGTTGGTGGCTAAAATTAG TGGAATTTATTGGTGGTACCAGACTGTATCACACCCTGCTGAACTTACTGCTGGTTACTACAAC ACGGCTCTGAGAGATGGTTATGATCCAGTTGTCTCAGTGTTGTCTCGACATGGAGCTGCTTTGC ATATTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.53378548

Conservation Information
Conserved circRNAs	NA
PMCS	0.53378548

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2741207-2741084(+)
2742368-2741079(+)
2741077-2742337(-)
						
						Potential amino acid sequence
						
							MLSFVNKFESFIGTVIEEISIGLGPSGELRYPAHPFGDGRWKFPGIGEFQCYDKYMMEDLKMAA
CREGKPQWGDKGPQNAGCYNSLPSGVPFFEEGKESFLSDYGRFFLEWYSGRLICHADAILAKAA
KILKKYQENEQTSVMLVAKISGIYWWYQTVSHPAELTAGYYNTALRDGYDPVVSVLSRHGAALH
IPLVM*(+)
MVMIQLSQCCLDMELLCIFHW*(+)
MEYAKQLHVETTLRQLDHNHLSEPCCSNQQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2741207-2741084(+) 2742368-2741079(+) 2741077-2742337(-)
Potential amino acid sequence	MLSFVNKFESFIGTVIEEISIGLGPSGELRYPAHPFGDGRWKFPGIGEFQCYDKYMMEDLKMAA CREGKPQWGDKGPQNAGCYNSLPSGVPFFEEGKESFLSDYGRFFLEWYSGRLICHADAILAKAA KILKKYQENEQTSVMLVAKISGIYWWYQTVSHPAELTAGYYNTALRDGYDPVVSVLSRHGAALH IPLVM(+) MVMIQLSQCCLDMELLCIFHW(+) MEYAKQLHVETTLRQLDHNHLSEPCCSNQQ*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.004G033500_circ_g.1

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