Plant Circular RNA Database

Detail information of Os07g0558500_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os07g0558500_circ_g.3
					
						ID in PlantcircBase
						osa_circ_034254
					
						Alias
						Os07circ12932/Os_ciR11007
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 22319740-22321911  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os07g0558500						
					
						Parent gene annotation
						
							Inositol phosphatase-like protein. (Os07t0558500-01);Similar to 
Protein THYLAKOID FORMATION1, chloroplastic. (Os07t0558500-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os07g0558500_circ_g.4 Os07g0558500_circ_g.5 						
					
						Support reads
						2/2/3
					
						Tissues
						leaf/root/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  
						
							CT-AC							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
						Os07t0558500-02:1
Os07t0558500-01:3

General Information
CircRNA Name	Os07g0558500_circ_g.3
ID in PlantcircBase	osa_circ_034254
Alias	Os07circ12932/Os_ciR11007
Organism	Oryza sativa
Position	chr7: 22319740-22321911 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl, find_circ
Parent gene	Os07g0558500
Parent gene annotation	Inositol phosphatase-like protein. (Os07t0558500-01);Similar to Protein THYLAKOID FORMATION1, chloroplastic. (Os07t0558500-02)
Parent gene strand	-
Alternative splicing	Os07g0558500_circ_g.4 Os07g0558500_circ_g.5
Support reads	2/2/3
Tissues	leaf/root/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	CT-AC 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	Os07t0558500-02:1 Os07t0558500-01:3

			
						 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  
						
							ACCAAAAGTTCTTGTAGAACTGTACTGTAAATGCTTAGGATAGGACGCTTGTATGACTTGAGAA
AATTCATCTTTGTTTCTGCGACAGTGGGTGGAACATctttccacgtattccttgagaagttcct
tagcctggaccaatttggagagtatgttccggtaaacatcgagatccctgtcgacacttctttt
gttgatgt

									
								

					

						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: 604
Transcript exons: 22319740-22319855,22320981-22321197,22321641-22321911
CTTTCCACGTATTCCTTGAGAAGTTCCTTAGCCTGGACCAATTTGGAGAGTATGTTCCGGTAAA
CATCGAGATCCCTGTCGACACTTCTTTTGTTGATGTTTAGAGCAGCGCAAAGCTTGTCTAGTAT
GGTTGGCTCTGTTGCATTTGCAAGCTCAAGCAAACGGAACAAGCCAACTGCAAAGAACCGGCTG
TAGCTGAAGCTTCCCTTACCCTGGGCCCTTTCTGAAATATCTTTCAGAATGGCCTCTATTTCTC
CATCTTTGGATGAAAACTCAACTAAAGAATTACCATTCTGGGAACGAGCCCACTCTTCCATCTT
TTGTGCGTCAGCTCTGTATTGCTCAGGGTCTTCGTTTAACGCTGTTATATATGCTTTGAAGATT
GCATCCCTATCCTCATTGCTAGGGTACCCTTCCATGAGTTGGTCATAGACGGTCACAAAACCAA
GAGCAAACACCGCATCATATTGATATGTTGTTTTGTATCTCATCAGATGTTGCTGTACCAAAAG
TTCTTGTAGAACTGTACTGTAAATGCTTAGGATAGGACGCTTGTATGACTTGAGAAAATTCATC
TTTGTTTCTGCGACAGTGGGTGGAACAT
						
					

						Genomic sequence
						
							CTTTCCACGTATTCCTTGAGAAGTTCCTTAGCCTGGACCAATTTGGAGAGTATGTTCCGGTAAA
CATCGAGATCCCTGTCGACACTTCTTTTGTTGATGTTTAGAGCAGCGCAAAGCTGTCAAGGAAG
CCATTGAAAATATTAGTGAGGTAAGTAGGTAACATCAAAGTGCACATTACATTTTGAGTTCACC
AAATGACAAACATAACTGGCTTAAATGTTTCCTGAAATTATCATTGGACACTGAAAAAATTACT
TGACTTGTACTATACTAGAATGCCTCAAGAATGCTTTTGGAGTTTTATCCTGTATGGAATCTCC
CTATCTCCAATGAGTCCTCCCACAGAAAAGTCCAGATATGCCCCCAACATTGGTACTAAGTTAG
AAGCCAAAACTGAACTCGAACCTCCTTAGTGCTATTTCCTATTCTGGCTTAAGAAACATCATAA
ATAATAGAAACCATCACAAACTTGAATTGTCAGTTGATCACATGCCATAACGATTAGAACATTT
GCTAACCTCAACGTTTGAGGAGAAATATTTAGGAAAGCAGTTCGTGCGCACTCAGCTAGGGTAG
TTAGATTTTAGAGGTGGGAGCTGTGGTTCTGAAGTGATAGGAATGAATGATGGAGTCGAGTAAG
AGGCTTAGTCAATAGGAAAGTATGATGGAGTCGAGTCAGAGGCTTAGTCAATAGGTATGGAGGG
CATGTTTGGTAGAGCTCCAACTCCTAAAATTTAACTCTAGGAGTTGGGTTCGGAGTGGAGTTGT
GGAGCTGCCTAAACCCAAGCTCCACCTCTCTAGTTCATTTTGTGAGAGCGCTCCACCCAGCTCC
ACTCCCATTTTAGGTGGAGTTGAACTATTTGGCTGGGCTCCAACTCCAGGAGAGGCGGAACTGG
AGTTAGAACTGTGCCAAACAGGCCCGTACGCTGTAGGATGGAATAGAGTCAGACTTAGTCCTTT
ACTAGTAATCTAGCATATCAGCGAAGTAGTAGGTTAAAAAGAACACCGCATAGACACTTAACCA
GCTGTGGTTGCAAGATATTAGACAGCAGACACAAGCCAACCCCTTAATTGATTTGAGATAAATC
CTTTCTTTCTGCGAAAACTAAAATGTATTGGAAACATGCTCTCTAAAATATAACTTGAGAAACA
CACATAAGCGTTATTAGAAGATATAATTTGGAAGTGAAGCAAAAATAAGTATGATAGTCAGAAA
CAAAATTATTAATGGCAATAACAACCTTGTCTAGTATGGTTGGCTCTGTTGCATTTGCAAGCTC
AAGCAAACGGAACAAGCCAACTGCAAAGAACCGGCTGTAGCTGAAGCTTCCCTTACCCTGGGCC
CTTTCTGAAATATCTTTCAGAATGGCCTCTATTTCTCCATCTTTGGATGAAAACTCAACTAAAG
AATTACCATTCTGGGAACGAGCCCACTCTTCCATCTTTTGTGCGTCAGCTCTGAAGAAAGAACA
GAAAACACTTACTATGATTGCTTGGAAAGACACCTCTGTTGATGCCAAAACAAACTAGTAACCC
AATAATACATTAGCTTTCATTGACGCAAATAAAGCAGATAATTGGTGATCCACAAATAAGCAAA
GCATGCAACAAATAGATAGTGCAAAATGTGACATTTTTTACAGCGGCAAGATAGATAATTGCTA
CTATCTCTATAGGAAAAGGCTATGGTTGACATATGAATTCAACGAATTGGGGGTAATATTTATG
CTGAAAATTCATGGCTGTGAATTATATAAATCTATAAAAAAATTACTTGGATCAATTAAGTGTA
GGATATTGTTTGAAGGTTCAATTTGGTTATGAGAAATCTAATTGAATATAAAACAAGAAGATGC
TAACATCACTGTGAATAAAAAACAGTTGTAAGTTACAGTAGGCACCTGTATTGCTCAGGGTCTT
CGTTTAACGCTGTTATATATGCTTTGAAGATTGCATCCCTATCCTCATTGCTAGGGTACCCTTC
CATGAGTTGGTCATAGACGGTCACAAAACCAAGAGCAAACACCGCATCATATTGATATGTTGTT
TTGTATCTCATCAGATGTTGCTGTACCAAAAGTTCTTGTAGAACTGTACTGTAAATGCTTAGGA
TAGGACGCTTGTATGACTTGAGAAAATTCATCTTTGTTTCTGCGACAGTGGGTGGAACAT
						
					

			
		

Sequences
Splice junction sequence	ACCAAAAGTTCTTGTAGAACTGTACTGTAAATGCTTAGGATAGGACGCTTGTATGACTTGAGAA AATTCATCTTTGTTTCTGCGACAGTGGGTGGAACATctttccacgtattccttgagaagttcct tagcctggaccaatttggagagtatgttccggtaaacatcgagatccctgtcgacacttctttt gttgatgt
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: 604 Transcript exons: 22319740-22319855,22320981-22321197,22321641-22321911 CTTTCCACGTATTCCTTGAGAAGTTCCTTAGCCTGGACCAATTTGGAGAGTATGTTCCGGTAAA CATCGAGATCCCTGTCGACACTTCTTTTGTTGATGTTTAGAGCAGCGCAAAGCTTGTCTAGTAT GGTTGGCTCTGTTGCATTTGCAAGCTCAAGCAAACGGAACAAGCCAACTGCAAAGAACCGGCTG TAGCTGAAGCTTCCCTTACCCTGGGCCCTTTCTGAAATATCTTTCAGAATGGCCTCTATTTCTC CATCTTTGGATGAAAACTCAACTAAAGAATTACCATTCTGGGAACGAGCCCACTCTTCCATCTT TTGTGCGTCAGCTCTGTATTGCTCAGGGTCTTCGTTTAACGCTGTTATATATGCTTTGAAGATT GCATCCCTATCCTCATTGCTAGGGTACCCTTCCATGAGTTGGTCATAGACGGTCACAAAACCAA GAGCAAACACCGCATCATATTGATATGTTGTTTTGTATCTCATCAGATGTTGCTGTACCAAAAG TTCTTGTAGAACTGTACTGTAAATGCTTAGGATAGGACGCTTGTATGACTTGAGAAAATTCATC TTTGTTTCTGCGACAGTGGGTGGAACAT
Genomic sequence	CTTTCCACGTATTCCTTGAGAAGTTCCTTAGCCTGGACCAATTTGGAGAGTATGTTCCGGTAAA CATCGAGATCCCTGTCGACACTTCTTTTGTTGATGTTTAGAGCAGCGCAAAGCTGTCAAGGAAG CCATTGAAAATATTAGTGAGGTAAGTAGGTAACATCAAAGTGCACATTACATTTTGAGTTCACC AAATGACAAACATAACTGGCTTAAATGTTTCCTGAAATTATCATTGGACACTGAAAAAATTACT TGACTTGTACTATACTAGAATGCCTCAAGAATGCTTTTGGAGTTTTATCCTGTATGGAATCTCC CTATCTCCAATGAGTCCTCCCACAGAAAAGTCCAGATATGCCCCCAACATTGGTACTAAGTTAG AAGCCAAAACTGAACTCGAACCTCCTTAGTGCTATTTCCTATTCTGGCTTAAGAAACATCATAA ATAATAGAAACCATCACAAACTTGAATTGTCAGTTGATCACATGCCATAACGATTAGAACATTT GCTAACCTCAACGTTTGAGGAGAAATATTTAGGAAAGCAGTTCGTGCGCACTCAGCTAGGGTAG TTAGATTTTAGAGGTGGGAGCTGTGGTTCTGAAGTGATAGGAATGAATGATGGAGTCGAGTAAG AGGCTTAGTCAATAGGAAAGTATGATGGAGTCGAGTCAGAGGCTTAGTCAATAGGTATGGAGGG CATGTTTGGTAGAGCTCCAACTCCTAAAATTTAACTCTAGGAGTTGGGTTCGGAGTGGAGTTGT GGAGCTGCCTAAACCCAAGCTCCACCTCTCTAGTTCATTTTGTGAGAGCGCTCCACCCAGCTCC ACTCCCATTTTAGGTGGAGTTGAACTATTTGGCTGGGCTCCAACTCCAGGAGAGGCGGAACTGG AGTTAGAACTGTGCCAAACAGGCCCGTACGCTGTAGGATGGAATAGAGTCAGACTTAGTCCTTT ACTAGTAATCTAGCATATCAGCGAAGTAGTAGGTTAAAAAGAACACCGCATAGACACTTAACCA GCTGTGGTTGCAAGATATTAGACAGCAGACACAAGCCAACCCCTTAATTGATTTGAGATAAATC CTTTCTTTCTGCGAAAACTAAAATGTATTGGAAACATGCTCTCTAAAATATAACTTGAGAAACA CACATAAGCGTTATTAGAAGATATAATTTGGAAGTGAAGCAAAAATAAGTATGATAGTCAGAAA CAAAATTATTAATGGCAATAACAACCTTGTCTAGTATGGTTGGCTCTGTTGCATTTGCAAGCTC AAGCAAACGGAACAAGCCAACTGCAAAGAACCGGCTGTAGCTGAAGCTTCCCTTACCCTGGGCC CTTTCTGAAATATCTTTCAGAATGGCCTCTATTTCTCCATCTTTGGATGAAAACTCAACTAAAG AATTACCATTCTGGGAACGAGCCCACTCTTCCATCTTTTGTGCGTCAGCTCTGAAGAAAGAACA GAAAACACTTACTATGATTGCTTGGAAAGACACCTCTGTTGATGCCAAAACAAACTAGTAACCC AATAATACATTAGCTTTCATTGACGCAAATAAAGCAGATAATTGGTGATCCACAAATAAGCAAA GCATGCAACAAATAGATAGTGCAAAATGTGACATTTTTTACAGCGGCAAGATAGATAATTGCTA CTATCTCTATAGGAAAAGGCTATGGTTGACATATGAATTCAACGAATTGGGGGTAATATTTATG CTGAAAATTCATGGCTGTGAATTATATAAATCTATAAAAAAATTACTTGGATCAATTAAGTGTA GGATATTGTTTGAAGGTTCAATTTGGTTATGAGAAATCTAATTGAATATAAAACAAGAAGATGC TAACATCACTGTGAATAAAAAACAGTTGTAAGTTACAGTAGGCACCTGTATTGCTCAGGGTCTT CGTTTAACGCTGTTATATATGCTTTGAAGATTGCATCCCTATCCTCATTGCTAGGGTACCCTTC CATGAGTTGGTCATAGACGGTCACAAAACCAAGAGCAAACACCGCATCATATTGATATGTTGTT TTGTATCTCATCAGATGTTGCTGTACCAAAAGTTCTTGTAGAACTGTACTGTAAATGCTTAGGA TAGGACGCTTGTATGACTTGAGAAAATTCATCTTTGTTTCTGCGACAGTGGGTGGAACAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_017202 						
					
						PMCS
						0.231408168

Conservation Information
Conserved circRNAs	osi_circ_017202
PMCS	0.231408168

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22321843-22319840(+)
22319808-22321772(-)
22321884-22321772(-)
						
						Potential amino acid sequence
						
							MLRIGRLYDLRKFIFVSATVGGTSFHVFLEKFLSLDQFGEYVPVNIEIPVDTSFVDV*(+)
MFTGTYSPNWSRLRNFSRNTWKDVPPTVAETKMNFLKSYKRPILSIYSTVLQELLVQQHLMRYK
TTYQYDAVFALGFVTVYDQLMEGYPSNEDRDAIFKAYITALNEDPEQYRADAQKMEEWARSQNG
NSLVEFSSKDGEIEAILKDISERAQGKGSFSYSRFFAVGLFRLLELANATEPTILDKLCAALNI
NKRSVDRDLDVYRNILSKLVQAKELLKEYVERCSTHCRRNKDEFSQVIQASYPKHLQYSSTRTF
GTATSDEIQNNISI*(-)
MNFLKSYKRPILSIYSTVLQELLVQQHLMRYKTTYQYDAVFALGFVTVYDQLMEGYPSNEDRDA
IFKAYITALNEDPEQYRADAQKMEEWARSQNGNSLVEFSSKDGEIEAILKDISERAQGKGSFSY
SRFFAVGLFRLLELANATEPTILDKLCAALNINKRSVDRDLDVYRNILSKLVQAKELLKEYVER
CSTHCRRNKDEFSQVIQASYPKHLQYSSTRTFGTATSDEIQNNISI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22321843-22319840(+) 22319808-22321772(-) 22321884-22321772(-)
Potential amino acid sequence	MLRIGRLYDLRKFIFVSATVGGTSFHVFLEKFLSLDQFGEYVPVNIEIPVDTSFVDV(+) MFTGTYSPNWSRLRNFSRNTWKDVPPTVAETKMNFLKSYKRPILSIYSTVLQELLVQQHLMRYK TTYQYDAVFALGFVTVYDQLMEGYPSNEDRDAIFKAYITALNEDPEQYRADAQKMEEWARSQNG NSLVEFSSKDGEIEAILKDISERAQGKGSFSYSRFFAVGLFRLLELANATEPTILDKLCAALNI NKRSVDRDLDVYRNILSKLVQAKELLKEYVERCSTHCRRNKDEFSQVIQASYPKHLQYSSTRTF GTATSDEIQNNISI(-) MNFLKSYKRPILSIYSTVLQELLVQQHLMRYKTTYQYDAVFALGFVTVYDQLMEGYPSNEDRDA IFKAYITALNEDPEQYRADAQKMEEWARSQNGNSLVEFSSKDGEIEAILKDISERAQGKGSFSY SRFFAVGLFRLLELANATEPTILDKLCAALNINKRSVDRDLDVYRNILSKLVQAKELLKEYVER CSTHCRRNKDEFSQVIQASYPKHLQYSSTRTFGTATSDEIQNNISI*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os07g0558500_circ_g.3

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