Plant Circular RNA Database

Detail information of Os09g0436400_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os09g0436400_circ_g.2
					
						ID in PlantcircBase
						osa_circ_039293
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 16051358-16054468  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os09g0436400						
					
						Parent gene annotation
						
							PDZ/DHR/GLGF domain containing protein. (Os09t0436400-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os09g0436400_circ_g.1 Os09g0436400_circ_g.3 						
					
						Support reads
						1
					
						Tissues
						shoot, root
					
						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
						Os09t0436400-01:4

General Information
CircRNA Name	Os09g0436400_circ_g.2
ID in PlantcircBase	osa_circ_039293
Alias	NA
Organism	Oryza sativa
Position	chr9: 16051358-16054468 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os09g0436400
Parent gene annotation	PDZ/DHR/GLGF domain containing protein. (Os09t0436400-01)
Parent gene strand	+
Alternative splicing	Os09g0436400_circ_g.1 Os09g0436400_circ_g.3
Support reads	1
Tissues	shoot, root
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	Os09t0436400-01:4

			
						 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  
						
							GCTTGGCCTGAGGATTGGATCACTGAAACATGAAAAACTGGATATCCGTGAACAAATACATGGA
AGCTTCTCCAACACAGGTGGCATTTATGTAAAAGAGggcgaacgagactgtttgcatgcacggg
tacaattatggagtatggaccatctaaaatgagcattctgacttccgctagtttggttagatgc
actaaaga

									
								

					

						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: 170
Transcript exons: 16051358-16051477,16054419-16054468
GGCGAACGAGACTGTTTGCATGCACGGGTACAATTATGGAGTATGGACCATCTAAAATGAGCAT
TCTGACTTCCGCTAGTTTGGTTAGATGCACTAAAGATGAAAACAAGACAGATGAAAAACAAATA
CATGGAAGCTTCTCCAACACAGGTGGCATTTATGTAAAAGAG
Transcript length: 662
Transcript exons: 16051358-16051485,16051570-16051854,16052042-16052172,16
054351-16054468
GGCGAACGAGACTGTTTGCATGCACGGGTACAATTATGGAGTATGGACCATCTAAAATGAGCAT
TCTGACTTCCGCTAGTTTGGTTAGATGCACTAAAGATGAAAACAAGACAGATGAAAAATTAAAG
ATTAAGGTGCGCCTACCCAATGGCAAGCTTACCGAAGGAAAACTGTGGAACTATGATTTATATT
ATAATATTGCTGTTGTCAAAATCAAGTATTTCCCAGAACTTAGTACAGCACAGATACATAATCA
AGGGCAATCTAATGTTAAATTATCTCAAAGTAAACTGGTCGCTGTTGGACGTGGCTATGAATCT
GGAGAACTAATGGCTACAGGTGGGACACTGCTGTACAAACCTAGCAAACTTGACTGCAAGGAAC
TCATGACCTCCACTTGTAAGATCACAAAGGCTGGGATTGGTGGTCCCCTTGTTGGGTTTGATGG
AAACTTTGTTGGCATGAACTTTTGTGATAAGAAGGAAACTCCTTTCTTACCAATCAATATAATT
CGGAAATGTTTAAAGCACTTTGATATGTTTGGGAGAGTTGTTCAGCCATGGCTTGGCCTGAGGA
TTGGATCACTGAAACATGAAAAACTGGATATCCGTGAACAAATACATGGAAGCTTCTCCAACAC
AGGTGGCATTTATGTAAAAGAG
						
					

						Genomic sequence
						
							GGCGAACGAGACTGTTTGCATGCACGGGTACAATTATGGAGTATGGACCATCTAAAATGAGCAT
TCTGACTTCCGCTAGTTTGGTTAGATGCACTAAAGATGAAAACAAGACAGATGAAAAATTAAAG
GTCAGCATTCAGCCATATTTTCTCTTCTGTTACTTCTTTATGGTCTTAGCTTCATGAGATGATA
TTGTTGTCACTTGGTTGTAGATTAAGGTGCGCCTACCCAATGGCAAGCTTACCGAAGGAAAACT
GTGGAACTATGATTTATATTATAATATTGCTGTTGTCAAAATCAAGTATTTCCCAGAACTTAGT
ACAGCACAGATACATAATCAAGGGCAATCTAATGTTAAATTATCTCAAAGTAAACTGGTCGCTG
TTGGACGTGGCTATGAATCTGGAGAACTAATGGCTACAGGTGGGACACTGCTGTACAAACCTAG
CAAACTTGACTGCAAGGAACTCATGACCTCCACTTGTAAGATCACAAAGGTATTACCTCTCATT
TATTTAGTACTATGGATAGATTATGATTGCGGTTGGTTTATATTGTTAATATGCATATTATTCA
CGTTGAACCGCCTTTTAAAAAAAGATCATATGGAAAGACATTAATAGTGCAGTTTAAAATGGAA
TCTGTTATGCAGCAGTTGTTCACCATCATTTTATTTTGTTACAGGCTGGGATTGGTGGTCCCCT
TGTTGGGTTTGATGGAAACTTTGTTGGCATGAACTTTTGTGATAAGAAGGAAACTCCTTTCTTA
CCAATCAATATAATTCGGAAATGTTTAAAGCACTTTGATATGTTTGGGTATGTTTTCTAGTTCT
TATTAATGTACTTCCAATAATCTTCACTTGCAATCATGTGTGCTAATGGACAAATTTGTTCTCC
TTGACCGTCCACTCTTTGAACACTAGCTTGATTGTGGAGAGATTATGTCAGGACTCGTGATGGA
AATACTTGTTGGCTTGTTTAGTTGATACTTAGACTGGTAGTTTATTGCTTAAATAATTTGGATA
GGTCAAAACTCAAAACCAACATTCTAAGATGAGTCATCATATCCTGATCAATCAAATTTGCATT
GCCATTTTCTTTTAAGCGAGTTGTAGTGAATGCAAAAAAATTGTATTGGATAAATGCTGTGAGC
TCCTCAGTTTCCTTTCAACTGTCAGAACCATTTTTACTAAGCAAGAATTATGAATTACTATGCA
GTATGACTCAAAAGCTGACCAACCTTAGTTTCATGGCTTCATCTTTCCCCTGAGATCCATCCAC
CCTTGAGTCATTGCCATCTGGCACTACTCAGTGCAATGTTTATGCCTATTATGAATTAGACCAT
TTTGGTTGGTACTTGGTCTGAAAGATGAAATATTTACAAATACCATCGCATGTGTCATTGACAT
GTGGGCCCTGGTCCAAAGTGTCATTCTCACATGCAATGGTATTTACATCTTTGTGATGGTACAA
ACCTATTTTTCTCAATGAATGATTTTCATAACATTTGGTATCTGAGCAGTTGATTCATGGCATT
TGGTATCTGAGCAGTTGATCCTGCACGCCTTGTACTGCTAATTATCCCTTTGATAAAGCATTGG
CTGTATGCAGAATACCCAAATGGCCGTGCCATTGCTGCCAATATGTTGGGATTTGAGGATTCCT
GAGTTTGACTTATTGCATGTCTCGATTTCCTTTAACGTGCCAATAAGTTATATACAACATTAAG
ATGAATTTACACAATAGCATGAATAAACAAAGACAAGCTTCTATAAGTTTTGGCCACATATGGT
CGAATTCGGCAACCAAAGTTTACATGTTTTCCTATATGTCATGGAATATGGTTCAGTATATTTT
TCCTGTGAAATTCCTACTAAATGAAACCAATCAGGGCTTCAGGACTAATAGAAACCCCAAGTGT
GTTACAGAAGAGCATGAATAAATAAATACAAATTTCTGTAAAATTTGGCCAGATATGGTCGAAT
TTGGCAACAAAGTTCATATGTTATCCTAGATGTCATGGTACACAGTTCACTATTTTTCTTTTTG
TAAAGTTTCTACTAGTTGAAACCAATCAGGGTTTCAGGACTCAGAGAGTACTCCAGTGTGTTAA
ATCCTTCAGTAAGCTTTAAGCAAGTGAGATGTCTCATATTATTTCCTTTTTAACTTTGGCTAGA
AATTCGATTTATCATGACAGGAGCTGATTTTTTTATCTTGTTTCATTGATTATCAAATGTATAA
AATGTGATATTGCTTGTGCATTACATGCTTTCTCTGGTGGATGTACCAAGATTTTTTTTATGGT
ACAACTTTTGCATTGTTGCGGTGCAATTGTACAGCCCTGTGAGATGCCACCCCATGGTTTGACT
TGGACAATGCTGTTCAGTGGTTCATTTGTTGGGTGTAAAATAGAATGGCTCAGTTAGTGATAGG
TGATCCATCGCATCACAATTCACAACAAGCAGGACATATAGATATAATTTTCCTGCTACCTCAG
TTTTCCCTTTGTGATGGCTGCTACCTCAGTTTTCCCTTTGTGATGGGATCTACATCCATAAACA
TCAGCAGCACACTGCTCTGCCACCTTCTCGGATGTTCAGCAGTGCCACAATCGCTGCATAGCAG
GCTCGTTGGACTGCCAACTACTGAGAAGAGGACCGACAATACTCATAATCTCCATAATTACATT
CTATTAATCTGAGCCGCCAGACTCAGCTGTTTCTCCAAGCCATTAGCAGTCATCAAGTGTAGTT
GCAGTCCCCATACTGAGCAAATCACTGTTCCTCCAGCAGTCCGCTAGTCCCAAAACTGCTTAGC
CTGGTTCTTTACTTATGCGGGTCATTTGCACAAAATCTATTTGATGTGTTGAACCTATATGCAA
TTTTGTATAGTTATGTTTTCTGTATTGCTAGTTTATTTTAAAATTATTCAATGTAGTCCGAGTG
CCTCAGTCTAAATATTTCAATCATCTGCTAAATTTTGAGATATATGCAGGAGAGTTGTTCAGCC
ATGGCTTGGCCTGAGGATTGGATCACTGAAACATGAAAAACTGGATATCCGTGAACAAATACAT
GGAAGCTTCTCCAACACAGGTGGCATTTATGTAAAAGAG
						
					

			
		

Sequences
Splice junction sequence	GCTTGGCCTGAGGATTGGATCACTGAAACATGAAAAACTGGATATCCGTGAACAAATACATGGA AGCTTCTCCAACACAGGTGGCATTTATGTAAAAGAGggcgaacgagactgtttgcatgcacggg tacaattatggagtatggaccatctaaaatgagcattctgacttccgctagtttggttagatgc actaaaga
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: 170 Transcript exons: 16051358-16051477,16054419-16054468 GGCGAACGAGACTGTTTGCATGCACGGGTACAATTATGGAGTATGGACCATCTAAAATGAGCAT TCTGACTTCCGCTAGTTTGGTTAGATGCACTAAAGATGAAAACAAGACAGATGAAAAACAAATA CATGGAAGCTTCTCCAACACAGGTGGCATTTATGTAAAAGAG Transcript length: 662 Transcript exons: 16051358-16051485,16051570-16051854,16052042-16052172,16 054351-16054468 GGCGAACGAGACTGTTTGCATGCACGGGTACAATTATGGAGTATGGACCATCTAAAATGAGCAT TCTGACTTCCGCTAGTTTGGTTAGATGCACTAAAGATGAAAACAAGACAGATGAAAAATTAAAG ATTAAGGTGCGCCTACCCAATGGCAAGCTTACCGAAGGAAAACTGTGGAACTATGATTTATATT ATAATATTGCTGTTGTCAAAATCAAGTATTTCCCAGAACTTAGTACAGCACAGATACATAATCA AGGGCAATCTAATGTTAAATTATCTCAAAGTAAACTGGTCGCTGTTGGACGTGGCTATGAATCT GGAGAACTAATGGCTACAGGTGGGACACTGCTGTACAAACCTAGCAAACTTGACTGCAAGGAAC TCATGACCTCCACTTGTAAGATCACAAAGGCTGGGATTGGTGGTCCCCTTGTTGGGTTTGATGG AAACTTTGTTGGCATGAACTTTTGTGATAAGAAGGAAACTCCTTTCTTACCAATCAATATAATT CGGAAATGTTTAAAGCACTTTGATATGTTTGGGAGAGTTGTTCAGCCATGGCTTGGCCTGAGGA TTGGATCACTGAAACATGAAAAACTGGATATCCGTGAACAAATACATGGAAGCTTCTCCAACAC AGGTGGCATTTATGTAAAAGAG
Genomic sequence	GGCGAACGAGACTGTTTGCATGCACGGGTACAATTATGGAGTATGGACCATCTAAAATGAGCAT TCTGACTTCCGCTAGTTTGGTTAGATGCACTAAAGATGAAAACAAGACAGATGAAAAATTAAAG GTCAGCATTCAGCCATATTTTCTCTTCTGTTACTTCTTTATGGTCTTAGCTTCATGAGATGATA TTGTTGTCACTTGGTTGTAGATTAAGGTGCGCCTACCCAATGGCAAGCTTACCGAAGGAAAACT GTGGAACTATGATTTATATTATAATATTGCTGTTGTCAAAATCAAGTATTTCCCAGAACTTAGT ACAGCACAGATACATAATCAAGGGCAATCTAATGTTAAATTATCTCAAAGTAAACTGGTCGCTG TTGGACGTGGCTATGAATCTGGAGAACTAATGGCTACAGGTGGGACACTGCTGTACAAACCTAG CAAACTTGACTGCAAGGAACTCATGACCTCCACTTGTAAGATCACAAAGGTATTACCTCTCATT TATTTAGTACTATGGATAGATTATGATTGCGGTTGGTTTATATTGTTAATATGCATATTATTCA CGTTGAACCGCCTTTTAAAAAAAGATCATATGGAAAGACATTAATAGTGCAGTTTAAAATGGAA TCTGTTATGCAGCAGTTGTTCACCATCATTTTATTTTGTTACAGGCTGGGATTGGTGGTCCCCT TGTTGGGTTTGATGGAAACTTTGTTGGCATGAACTTTTGTGATAAGAAGGAAACTCCTTTCTTA CCAATCAATATAATTCGGAAATGTTTAAAGCACTTTGATATGTTTGGGTATGTTTTCTAGTTCT TATTAATGTACTTCCAATAATCTTCACTTGCAATCATGTGTGCTAATGGACAAATTTGTTCTCC TTGACCGTCCACTCTTTGAACACTAGCTTGATTGTGGAGAGATTATGTCAGGACTCGTGATGGA AATACTTGTTGGCTTGTTTAGTTGATACTTAGACTGGTAGTTTATTGCTTAAATAATTTGGATA GGTCAAAACTCAAAACCAACATTCTAAGATGAGTCATCATATCCTGATCAATCAAATTTGCATT GCCATTTTCTTTTAAGCGAGTTGTAGTGAATGCAAAAAAATTGTATTGGATAAATGCTGTGAGC TCCTCAGTTTCCTTTCAACTGTCAGAACCATTTTTACTAAGCAAGAATTATGAATTACTATGCA GTATGACTCAAAAGCTGACCAACCTTAGTTTCATGGCTTCATCTTTCCCCTGAGATCCATCCAC CCTTGAGTCATTGCCATCTGGCACTACTCAGTGCAATGTTTATGCCTATTATGAATTAGACCAT TTTGGTTGGTACTTGGTCTGAAAGATGAAATATTTACAAATACCATCGCATGTGTCATTGACAT GTGGGCCCTGGTCCAAAGTGTCATTCTCACATGCAATGGTATTTACATCTTTGTGATGGTACAA ACCTATTTTTCTCAATGAATGATTTTCATAACATTTGGTATCTGAGCAGTTGATTCATGGCATT TGGTATCTGAGCAGTTGATCCTGCACGCCTTGTACTGCTAATTATCCCTTTGATAAAGCATTGG CTGTATGCAGAATACCCAAATGGCCGTGCCATTGCTGCCAATATGTTGGGATTTGAGGATTCCT GAGTTTGACTTATTGCATGTCTCGATTTCCTTTAACGTGCCAATAAGTTATATACAACATTAAG ATGAATTTACACAATAGCATGAATAAACAAAGACAAGCTTCTATAAGTTTTGGCCACATATGGT CGAATTCGGCAACCAAAGTTTACATGTTTTCCTATATGTCATGGAATATGGTTCAGTATATTTT TCCTGTGAAATTCCTACTAAATGAAACCAATCAGGGCTTCAGGACTAATAGAAACCCCAAGTGT GTTACAGAAGAGCATGAATAAATAAATACAAATTTCTGTAAAATTTGGCCAGATATGGTCGAAT TTGGCAACAAAGTTCATATGTTATCCTAGATGTCATGGTACACAGTTCACTATTTTTCTTTTTG TAAAGTTTCTACTAGTTGAAACCAATCAGGGTTTCAGGACTCAGAGAGTACTCCAGTGTGTTAA ATCCTTCAGTAAGCTTTAAGCAAGTGAGATGTCTCATATTATTTCCTTTTTAACTTTGGCTAGA AATTCGATTTATCATGACAGGAGCTGATTTTTTTATCTTGTTTCATTGATTATCAAATGTATAA AATGTGATATTGCTTGTGCATTACATGCTTTCTCTGGTGGATGTACCAAGATTTTTTTTATGGT ACAACTTTTGCATTGTTGCGGTGCAATTGTACAGCCCTGTGAGATGCCACCCCATGGTTTGACT TGGACAATGCTGTTCAGTGGTTCATTTGTTGGGTGTAAAATAGAATGGCTCAGTTAGTGATAGG TGATCCATCGCATCACAATTCACAACAAGCAGGACATATAGATATAATTTTCCTGCTACCTCAG TTTTCCCTTTGTGATGGCTGCTACCTCAGTTTTCCCTTTGTGATGGGATCTACATCCATAAACA TCAGCAGCACACTGCTCTGCCACCTTCTCGGATGTTCAGCAGTGCCACAATCGCTGCATAGCAG GCTCGTTGGACTGCCAACTACTGAGAAGAGGACCGACAATACTCATAATCTCCATAATTACATT CTATTAATCTGAGCCGCCAGACTCAGCTGTTTCTCCAAGCCATTAGCAGTCATCAAGTGTAGTT GCAGTCCCCATACTGAGCAAATCACTGTTCCTCCAGCAGTCCGCTAGTCCCAAAACTGCTTAGC CTGGTTCTTTACTTATGCGGGTCATTTGCACAAAATCTATTTGATGTGTTGAACCTATATGCAA TTTTGTATAGTTATGTTTTCTGTATTGCTAGTTTATTTTAAAATTATTCAATGTAGTCCGAGTG CCTCAGTCTAAATATTTCAATCATCTGCTAAATTTTGAGATATATGCAGGAGAGTTGTTCAGCC ATGGCTTGGCCTGAGGATTGGATCACTGAAACATGAAAAACTGGATATCCGTGAACAAATACAT GGAAGCTTCTCCAACACAGGTGGCATTTATGTAAAAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.316673318

Conservation Information
Conserved circRNAs	NA
PMCS	0.316673318

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16051394-16051414(+)
16051423-16052132(-)
16051380-16054390(-)
						
						Potential amino acid sequence
						
							MEYGPSKMSILTSASLVRCTKDENKTDEKLKIKVRLPNGKLTEGKLWNYDLYYNIAVVKIKYFP
ELSTAQIHNQGQSNVKLSQSKLVAVGRGYESGELMATGGTLLYKPSKLDCKELMTSTCKITKAG
IGGPLVGFDGNFVGMNFCDKKETPFLPINIIRKCLKHFDMFGRVVQPWLGLRIGSLKHEKLDIR
EQIHGSFSNTGGIYVKEGERDCLHARVQLWSMDHLK*(+)
MLILDGPYSIIVPVHANSLVRPLLHKCHLCWRSFHVFVHGYPVFHVSVIQSSGQAMAEQLSQTY
QSALNISELY*(-)
MQTVSFALFYINATCVGEASMYLFTDIQFFMFQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	16051394-16051414(+) 16051423-16052132(-) 16051380-16054390(-)
Potential amino acid sequence	MEYGPSKMSILTSASLVRCTKDENKTDEKLKIKVRLPNGKLTEGKLWNYDLYYNIAVVKIKYFP ELSTAQIHNQGQSNVKLSQSKLVAVGRGYESGELMATGGTLLYKPSKLDCKELMTSTCKITKAG IGGPLVGFDGNFVGMNFCDKKETPFLPINIIRKCLKHFDMFGRVVQPWLGLRIGSLKHEKLDIR EQIHGSFSNTGGIYVKEGERDCLHARVQLWSMDHLK(+) MLILDGPYSIIVPVHANSLVRPLLHKCHLCWRSFHVFVHGYPVFHVSVIQSSGQAMAEQLSQTY QSALNISELY(-) MQTVSFALFYINATCVGEASMYLFTDIQFFMFQ*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os09g0436400_circ_g.2

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