Plant Circular RNA Database

Detail information of orai.003G171400_circ_g.2

			
						 General Information
					
						CircRNA Name
						orai.003G171400_circ_g.2
					
						ID in PlantcircBase
						gra_circ_000286
					
						Alias
						Chr03:44273623|44276122
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr03: 44273623-44276122  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.003G171400						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							orai.003G171400_circ_g.1 						
					
						Support reads
						2
					
						Tissues
						leaf
					
						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.003G171400.1:3
Gorai.003G171400.2:3

General Information
CircRNA Name	orai.003G171400_circ_g.2
ID in PlantcircBase	gra_circ_000286
Alias	Chr03:44273623\|44276122
Organism	Gossypium raimondii
Position	chrChr03: 44273623-44276122 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.003G171400
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	orai.003G171400_circ_g.1
Support reads	2
Tissues	leaf
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.003G171400.1:3 Gorai.003G171400.2:3

			
						 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  
						
							TGGGTCAATACTCCAGGATTGTCTATTCTTACACCTACTTTGACAATCTCGTTGCTCAAGGCGG
TTGGGACGACTGGGACCATGTTAACAACCAGAATAAagagaaggtggtggtgccggcgacgaag
ccatacataacgtttcaaggtgccggtagagagacgacgtttattgagtggcacgacagagctt
gtgaccga

									
								

					

						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: 636
Transcript exons: 44273623-44273812,44274631-44274837,44275884-44276122
AGAGAAGGTGGTGGTGCCGGCGACGAAGCCATACATAACGTTTCAAGGTGCCGGTAGAGAGACG
ACGTTTATTGAGTGGCACGACAGAGCTTGTGACCGAGGGTCTAATGGTCAACAGTTGCGTACTT
ATCAAACGGCTTCCGTTACTGTGTATGCTAATTATTTCTCTGCTAGAAATATTAGCTTCAAGAA
TACAGCACCGGCTCCGAAGCCGGGAATGCAAGGGTGGCAAGCTGTGGCGTTCCGTATTTCTGGT
GACAAGGCATATTTCTCGGGGTGTGGATTCTACGGTGCACAAGACACTCTTTGCGACGATGCCG
GACGTCATTATTTCAAGCAATGTTATATTGAGGGTTCCATCGACTTCATCTTCGGGAATGGCCG
TTCCATGTACAAAGAATGTGAATTACACTCCATAGCTACGAGATTTGGATCCATAGCAGCCCAT
GACAGGAAATCACCAGATGAGAAAAGCGGGTTTGCTTTTGTAAACTGCACAGTGACGGGTACTG
GCCCACTTTATGTCGGTCGAGCCATGGGTCAATACTCCAGGATTGTCTATTCTTACACCTACTT
TGACAATCTCGTTGCTCAAGGCGGTTGGGACGACTGGGACCATGTTAACAACCAGAATAA
						
					

						Genomic sequence
						
							AGAGAAGGTGGTGGTGCCGGCGACGAAGCCATACATAACGTTTCAAGGTGCCGGTAGAGAGACG
ACGTTTATTGAGTGGCACGACAGAGCTTGTGACCGAGGGTCTAATGGTCAACAGTTGCGTACTT
ATCAAACGGCTTCCGTTACTGTGTATGCTAATTATTTCTCTGCTAGAAATATTAGCTTCAAGGT
AAATATAAAGAAAGGTTAAATTATGATTTTGGTATTGAGAATTTAATATTTTAATTTGCTATAA
GTTTGTGTTTAAATAGCTAAATATTATTGTACTGAGGCTTGAACTTTTTTTTGTTTAAGTTAAT
TCCTAAATTCGATAATTATTCTCATATTGGGGCCTGAATTTGACAATTGTTCCCACATTAGGGG
TCTAAACTTTAGGATTTTTAAGGAAATATCAGGGATTAACTTTGACCAAAAAAGTGTTTAGGCC
CCAAAGTGAGAACAATTATCAAGTCTAGGGATTAATTTTGACAAAAGAAAATCCAAGTCTCAAT
GTGGAAATAATTACCAAATTTAGTCCCCAAAAGTGATTTAACCCCTTTTTTTTAAAACTAGAAT
AGGAAGCAAGGTTAACTATTTAGATTAACTAATGATATTAGAAAAGCAAATATCAAATTATGTT
AGATTAAAGTATAAGGATTAGATCTTAAATTTGAACATATTAGAAGGACCAAAACTATAATTTG
ACTAATAAGAGAAACATTTCTCTTCTTAATGTTGCAAATAAGCTTCGTGTGTATAATTCTATGC
TTTATTAATGGTTATGATGATAACCCATCAAACTTAGAAGATTGTTGATTATGCGACCTCATCT
AGTTTATTAGCTCGGCATAAAATTATAAAATTATACACCCTCAATGCATTAATACCGTATTATA
ATATATATATATATATAATATAGCCGATGTAGCTAGAATTCAAACCCTAGTAACTCATCGTCTA
AATTTGTAATGATAGAGAGAAAAGGTTACAATGCATTAAATCATGCAGAATACAGCACCGGCTC
CGAAGCCGGGAATGCAAGGGTGGCAAGCTGTGGCGTTCCGTATTTCTGGTGACAAGGCATATTT
CTCGGGGTGTGGATTCTACGGTGCACAAGACACTCTTTGCGACGATGCCGGACGTCATTATTTC
AAGCAATGTTATATTGAGGGTTCCATCGACTTCATCTTCGGGAATGGCCGTTCCATGTACAAAG
TAAGAACAAATACTATTTTTATTATTTAGGGTAAAATATGTCATAAGTCTCTATACATTTTGTA
AATTTAAAATTTAATCGTTGTACTTTTTATTTCAATAACTCAGTTACTCTACTTTTCAGATTTA
AAAATTTAAGTCGAGTTGTTAATGTTGTTAAAATTATTTTAGCTACCGAGTTTTTTTTAATTTT
AAAATGTCATACCAATAAATTTAATTAGATAATTTTTAACAATGTTAGCAATTAAACTTGAATT
TTTAAAAATGAAAAGTGGAGGGGCTAAGTTTTTAAAAATAAAATCACAAAGACAATTCTAAATT
TTTGAAAAGTATAGGGACTTATGGAGTATTTTAACCTATTATTTATTATTTATTATTTATTATT
ATAGTGTAGGGCCAATCTGACTCTCTTATCCATAAAAGCTTCAAAAAAACCAAAAGGAAAAGGA
AAAGATCTTTTCTATGTCAGAAAGTTGTTCATTTTAAATTTTAAAAAATTTTAATTTATTTTGA
GTTGTTTTGTTTTTCTGCTATTTGGGGTAAGAAATATTTTACGTTTGAGTAATTAGAGTTTATC
AATTAAGTTTTTTAGATTTGGATAATTTTGAGTTTTGTTATTCGATTTTGGAACATTTAGATCT
TAATTGAGATATTTTAGGGTTTTATCATTTGAGTTCGAGATTATTTTAAAATACGAATGGAATG
AGTTCAATTTGTTGACTATTTATAGTCAAATTATGATAAGTCGAGTTAAGATTCAGATTAATCC
AATCAAGCTTTTGAGTTCAGATATGAATTGAGAGGTCTACTCATACTAGGTTGAATCCAAAGGG
GTCATGAATTGGCTTTGGTCCTTCCTTCGTTTAAATGGTTAAATTACTTTTTTACCCCTTCACA
AAAAATTATAATTCAATTTAAGCCTTCTTAATAAAAAAATTTATGCCTTTAGCTCAAGATTTTT
TTTTTAATTTTTAGTTTAGGGTTTAAATATTATTACTTGCAATATGAGACTAAAATAAAATTGT
GAGAAATGGAATGTTTTACAGGAATGTGAATTACACTCCATAGCTACGAGATTTGGATCCATAG
CAGCCCATGACAGGAAATCACCAGATGAGAAAAGCGGGTTTGCTTTTGTAAACTGCACAGTGAC
GGGTACTGGCCCACTTTATGTCGGTCGAGCCATGGGTCAATACTCCAGGATTGTCTATTCTTAC
ACCTACTTTGACAATCTCGTTGCTCAAGGCGGTTGGGACGACTGGGACCATGTTAACAACCAGA
ATAA
						
					

			
		

Sequences
Splice junction sequence	TGGGTCAATACTCCAGGATTGTCTATTCTTACACCTACTTTGACAATCTCGTTGCTCAAGGCGG TTGGGACGACTGGGACCATGTTAACAACCAGAATAAagagaaggtggtggtgccggcgacgaag ccatacataacgtttcaaggtgccggtagagagacgacgtttattgagtggcacgacagagctt gtgaccga
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: 636 Transcript exons: 44273623-44273812,44274631-44274837,44275884-44276122 AGAGAAGGTGGTGGTGCCGGCGACGAAGCCATACATAACGTTTCAAGGTGCCGGTAGAGAGACG ACGTTTATTGAGTGGCACGACAGAGCTTGTGACCGAGGGTCTAATGGTCAACAGTTGCGTACTT ATCAAACGGCTTCCGTTACTGTGTATGCTAATTATTTCTCTGCTAGAAATATTAGCTTCAAGAA TACAGCACCGGCTCCGAAGCCGGGAATGCAAGGGTGGCAAGCTGTGGCGTTCCGTATTTCTGGT GACAAGGCATATTTCTCGGGGTGTGGATTCTACGGTGCACAAGACACTCTTTGCGACGATGCCG GACGTCATTATTTCAAGCAATGTTATATTGAGGGTTCCATCGACTTCATCTTCGGGAATGGCCG TTCCATGTACAAAGAATGTGAATTACACTCCATAGCTACGAGATTTGGATCCATAGCAGCCCAT GACAGGAAATCACCAGATGAGAAAAGCGGGTTTGCTTTTGTAAACTGCACAGTGACGGGTACTG GCCCACTTTATGTCGGTCGAGCCATGGGTCAATACTCCAGGATTGTCTATTCTTACACCTACTT TGACAATCTCGTTGCTCAAGGCGGTTGGGACGACTGGGACCATGTTAACAACCAGAATAA
Genomic sequence	AGAGAAGGTGGTGGTGCCGGCGACGAAGCCATACATAACGTTTCAAGGTGCCGGTAGAGAGACG ACGTTTATTGAGTGGCACGACAGAGCTTGTGACCGAGGGTCTAATGGTCAACAGTTGCGTACTT ATCAAACGGCTTCCGTTACTGTGTATGCTAATTATTTCTCTGCTAGAAATATTAGCTTCAAGGT AAATATAAAGAAAGGTTAAATTATGATTTTGGTATTGAGAATTTAATATTTTAATTTGCTATAA GTTTGTGTTTAAATAGCTAAATATTATTGTACTGAGGCTTGAACTTTTTTTTGTTTAAGTTAAT TCCTAAATTCGATAATTATTCTCATATTGGGGCCTGAATTTGACAATTGTTCCCACATTAGGGG TCTAAACTTTAGGATTTTTAAGGAAATATCAGGGATTAACTTTGACCAAAAAAGTGTTTAGGCC CCAAAGTGAGAACAATTATCAAGTCTAGGGATTAATTTTGACAAAAGAAAATCCAAGTCTCAAT GTGGAAATAATTACCAAATTTAGTCCCCAAAAGTGATTTAACCCCTTTTTTTTAAAACTAGAAT AGGAAGCAAGGTTAACTATTTAGATTAACTAATGATATTAGAAAAGCAAATATCAAATTATGTT AGATTAAAGTATAAGGATTAGATCTTAAATTTGAACATATTAGAAGGACCAAAACTATAATTTG ACTAATAAGAGAAACATTTCTCTTCTTAATGTTGCAAATAAGCTTCGTGTGTATAATTCTATGC TTTATTAATGGTTATGATGATAACCCATCAAACTTAGAAGATTGTTGATTATGCGACCTCATCT AGTTTATTAGCTCGGCATAAAATTATAAAATTATACACCCTCAATGCATTAATACCGTATTATA ATATATATATATATATAATATAGCCGATGTAGCTAGAATTCAAACCCTAGTAACTCATCGTCTA AATTTGTAATGATAGAGAGAAAAGGTTACAATGCATTAAATCATGCAGAATACAGCACCGGCTC CGAAGCCGGGAATGCAAGGGTGGCAAGCTGTGGCGTTCCGTATTTCTGGTGACAAGGCATATTT CTCGGGGTGTGGATTCTACGGTGCACAAGACACTCTTTGCGACGATGCCGGACGTCATTATTTC AAGCAATGTTATATTGAGGGTTCCATCGACTTCATCTTCGGGAATGGCCGTTCCATGTACAAAG TAAGAACAAATACTATTTTTATTATTTAGGGTAAAATATGTCATAAGTCTCTATACATTTTGTA AATTTAAAATTTAATCGTTGTACTTTTTATTTCAATAACTCAGTTACTCTACTTTTCAGATTTA AAAATTTAAGTCGAGTTGTTAATGTTGTTAAAATTATTTTAGCTACCGAGTTTTTTTTAATTTT AAAATGTCATACCAATAAATTTAATTAGATAATTTTTAACAATGTTAGCAATTAAACTTGAATT TTTAAAAATGAAAAGTGGAGGGGCTAAGTTTTTAAAAATAAAATCACAAAGACAATTCTAAATT TTTGAAAAGTATAGGGACTTATGGAGTATTTTAACCTATTATTTATTATTTATTATTTATTATT ATAGTGTAGGGCCAATCTGACTCTCTTATCCATAAAAGCTTCAAAAAAACCAAAAGGAAAAGGA AAAGATCTTTTCTATGTCAGAAAGTTGTTCATTTTAAATTTTAAAAAATTTTAATTTATTTTGA GTTGTTTTGTTTTTCTGCTATTTGGGGTAAGAAATATTTTACGTTTGAGTAATTAGAGTTTATC AATTAAGTTTTTTAGATTTGGATAATTTTGAGTTTTGTTATTCGATTTTGGAACATTTAGATCT TAATTGAGATATTTTAGGGTTTTATCATTTGAGTTCGAGATTATTTTAAAATACGAATGGAATG AGTTCAATTTGTTGACTATTTATAGTCAAATTATGATAAGTCGAGTTAAGATTCAGATTAATCC AATCAAGCTTTTGAGTTCAGATATGAATTGAGAGGTCTACTCATACTAGGTTGAATCCAAAGGG GTCATGAATTGGCTTTGGTCCTTCCTTCGTTTAAATGGTTAAATTACTTTTTTACCCCTTCACA AAAAATTATAATTCAATTTAAGCCTTCTTAATAAAAAAATTTATGCCTTTAGCTCAAGATTTTT TTTTTAATTTTTAGTTTAGGGTTTAAATATTATTACTTGCAATATGAGACTAAAATAAAATTGT GAGAAATGGAATGTTTTACAGGAATGTGAATTACACTCCATAGCTACGAGATTTGGATCCATAG CAGCCCATGACAGGAAATCACCAGATGAGAAAAGCGGGTTTGCTTTTGTAAACTGCACAGTGAC GGGTACTGGCCCACTTTATGTCGGTCGAGCCATGGGTCAATACTCCAGGATTGTCTATTCTTAC ACCTACTTTGACAATCTCGTTGCTCAAGGCGGTTGGGACGACTGGGACCATGTTAACAACCAGA ATAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							ghi_circ_000034 						
					
						PMCS
						0.46109419

Conservation Information
Conserved circRNAs	ghi_circ_000034
PMCS	0.46109419

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							44274658-44276119(+)
44276008-44273657(+)
44273659-44276080(-)
44274769-44275946(-)
						
						Potential amino acid sequence
						
							MQGWQAVAFRISGDKAYFSGCGFYGAQDTLCDDAGRHYFKQCYIEGSIDFIFGNGRSMYKECEL
HSIATRFGSIAAHDRKSPDEKSGFAFVNCTVTGTGPLYVGRAMGQYSRIVYSYTYFDNLVAQGG
WDDWDHVNNQNKEKVVVPATKPYITFQGAGRETTFIEWHDRACDRGSNGQQLRTYQTASVTVYA
NYFSARNISFKNTAPAPKPGMQGWQAVAFRISGDKAYFSGCGFYGAQDTLCDDAGRHYFKQCYI
EGSIDFIFGNGRSMYKECELHSIATRFGSIAAHDRKSPDEKSGFAFVNCTVTGTGPLYVGRAMG
QYSRIVYSYTYFDNLVAQGGWDDWDHVNNQNKEKVVVPATKPYITFQGAGRETTFIEWHDRACD
RGSNGQQLRTYQTASVTVYANYFSARNISFKNTAPAPKPGMQGWQAVAFRISGDKAYFSGCGFY
GAQDTLCDDAGRHYFKQCYIEGSIDFIFGNGRSMYKECELHSIATRFGSIAAHDRKSPDEKSGF
AFVNCTVTGTGPLYVGRAMGQYSRIVYSYTYFDNLVAQGGWDDWDHVNNQNKEKVVVPATKPYI
TFQGAGRETTFIEWHDRACDRGSNGQQLRTYQTASVTVYANYFSARNISFKNTAPAPKPGMQGW
QAVAFRISGDKAYFSGCGFYGAQDTLCDDAGRHYFKQCYIEGSIDFIFGNGRSMYKECELHSIA
TRFGSIAAHDRKSPDEKSGFAFVNCTVTGTGPLYVGRAMGQYSRIVYSYTYFDNLVAQGGWDDW
DHVNNQN(+)
MSVEPWVNTPGLSILTPTLTISLLKAVGTTGTMLTTRIKRRWWCRRRSHT*(+)
MYGFVAGTTTFSLFWLLTWSQSSQPP*(-)
MTSGIVAKSVLCTVESTPREICLVTRNTERHSLPPLHSRLRSRCCILEANISSREIISIHSNGS
RLISTQLLTIRPSVTSSVVPLNKRRLSTGTLKRYVWLRRRHHHLLFILVVNMVPVVPTALSNEI
VKVGVRIDNPGVLTHGSTDIKWASTRHCAVYKSKPAFLIW*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	44274658-44276119(+) 44276008-44273657(+) 44273659-44276080(-) 44274769-44275946(-)
Potential amino acid sequence	MQGWQAVAFRISGDKAYFSGCGFYGAQDTLCDDAGRHYFKQCYIEGSIDFIFGNGRSMYKECEL HSIATRFGSIAAHDRKSPDEKSGFAFVNCTVTGTGPLYVGRAMGQYSRIVYSYTYFDNLVAQGG WDDWDHVNNQNKEKVVVPATKPYITFQGAGRETTFIEWHDRACDRGSNGQQLRTYQTASVTVYA NYFSARNISFKNTAPAPKPGMQGWQAVAFRISGDKAYFSGCGFYGAQDTLCDDAGRHYFKQCYI EGSIDFIFGNGRSMYKECELHSIATRFGSIAAHDRKSPDEKSGFAFVNCTVTGTGPLYVGRAMG QYSRIVYSYTYFDNLVAQGGWDDWDHVNNQNKEKVVVPATKPYITFQGAGRETTFIEWHDRACD RGSNGQQLRTYQTASVTVYANYFSARNISFKNTAPAPKPGMQGWQAVAFRISGDKAYFSGCGFY GAQDTLCDDAGRHYFKQCYIEGSIDFIFGNGRSMYKECELHSIATRFGSIAAHDRKSPDEKSGF AFVNCTVTGTGPLYVGRAMGQYSRIVYSYTYFDNLVAQGGWDDWDHVNNQNKEKVVVPATKPYI TFQGAGRETTFIEWHDRACDRGSNGQQLRTYQTASVTVYANYFSARNISFKNTAPAPKPGMQGW QAVAFRISGDKAYFSGCGFYGAQDTLCDDAGRHYFKQCYIEGSIDFIFGNGRSMYKECELHSIA TRFGSIAAHDRKSPDEKSGFAFVNCTVTGTGPLYVGRAMGQYSRIVYSYTYFDNLVAQGGWDDW DHVNNQN(+) MSVEPWVNTPGLSILTPTLTISLLKAVGTTGTMLTTRIKRRWWCRRRSHT(+) MYGFVAGTTTFSLFWLLTWSQSSQPP(-) MTSGIVAKSVLCTVESTPREICLVTRNTERHSLPPLHSRLRSRCCILEANISSREIISIHSNGS RLISTQLLTIRPSVTSSVVPLNKRRLSTGTLKRYVWLRRRHHHLLFILVVNMVPVVPTALSNEI VKVGVRIDNPGVLTHGSTDIKWASTRHCAVYKSKPAFLIW*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.003G171400_circ_g.2

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