Plant Circular RNA Database

Detail information of Os12g0299700_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os12g0299700_circ_g.3
					
						ID in PlantcircBase
						osa_circ_011270
					
						Alias
						Os12circ05157/Os_ciR1084
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 11917245-11917664  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ
					
						Parent gene
						
							Os12g0299700						
					
						Parent gene annotation
						
							NOP5, N-terminal domain containing protein. (Os12t0299700-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0299700_circ_g.2 						
					
						Support reads
						6/18/5/5
					
						Tissues
						leaf and panicle/root/root/shoot, root, seed, pistil
					
						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
						Os12t0299700-01:2

General Information
CircRNA Name	Os12g0299700_circ_g.3
ID in PlantcircBase	osa_circ_011270
Alias	Os12circ05157/Os_ciR1084
Organism	Oryza sativa
Position	chr12: 11917245-11917664 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ
Parent gene	Os12g0299700
Parent gene annotation	NOP5, N-terminal domain containing protein. (Os12t0299700-01)
Parent gene strand	+
Alternative splicing	Os12g0299700_circ_g.2
Support reads	6/18/5/5
Tissues	leaf and panicle/root/root/shoot, root, seed, pistil
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	Os12t0299700-01:2

			
						 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  
						
							CCAAGAAAAAATGAAGTTGAGCAAGGACGACTACCTCCCAATGAGCCAAGGATTGTACATGCTC
CTTAACCGCTATGGTTTGGATGTCAAACCAGAGATGttcatttggctgaaggaatttcgagaaa
tcaaggacaagtccagtgccattaatcatgatactggtgtcagttgcgaccttgctgagatgat
catgaagt

						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: 177
Transcript exons: 11917245-11917274,11917518-11917664
TTCATTTGGCTGAAGGAATTTCGAGAAATCATGGAAGTGATGTGGGGCCTGAAGAATCTGATGC
ATGTTTTAGTACCCCAAGAAAAAATGAAGTTGAGCAAGGACGACTACCTCCCAATGAGCCAAGG
ATTGTACATGCTCCTTAACCGCTATGGTTTGGATGTCAAACCAGAGATG
Transcript length: 205
Transcript exons: 11917245-11917369,11917585-11917664
TTCATTTGGCTGAAGGAATTTCGAGAAATCAAGGACAAGTCCAGTGCCATTAATCATGATACTG
GTGTCAGTTGCGACCTTGCTGAGATGATCATGAAGTGGCATCACCCTGGGCAGAAAATGGCGCA
AGGACGACTACCTCCCAATGAGCCAAGGATTGTACATGCTCCTTAACCGCTATGGTTTGGATGT
CAAACCAGAGATG
Transcript length: 345
Transcript exons: 11917245-11917412,11917488-11917664
TTCATTTGGCTGAAGGAATTTCGAGAAATCAAGGACAAGTCCAGTGCCATTAATCATGATACTG
GTGTCAGTTGCGACCTTGCTGAGATGATCATGAAGTGGCATCACCCTGGGCAGAAAATGGCCGT
TGGAAAACCCGAATATAAAGAAATCATTGAAAGAAGCTTGAGTGTGCCCTGCATGTTTGATGAA
ATTGTGATGGAAGTGATGTGGGGCCTGAAGAATCTGATGCATGTTTTAGTACCCCAAGAAAAAA
TGAAGTTGAGCAAGGACGACTACCTCCCAATGAGCCAAGGATTGTACATGCTCCTTAACCGCTA
TGGTTTGGATGTCAAACCAGAGATG
						
						Genomic sequence
						
							TTCATTTGGCTGAAGGAATTTCGAGAAATCAAGGACAAGTCCAGTGCCATTAATCATGATACTG
GTGTCAGTTGCGACCTTGCTGAGATGATCATGAAGTGGCATCACCCTGGGCAGAAAATGGCCGT
TGGAAAACCCGAATATAAAGAAATCATTGAAAGAAGCTTGGTTAGTGTTCAGCTCCCTTGTTTG
CTTTTCTTAGTGGACAACCTTGAGCACCAATTTTGCTGTCATTTCTTTCAGAGTGTGCCCTGCA
TGTTTGATGAAATTGTGATGGAAGTGATGTGGGGCCTGAAGAATCTGATGCATGTTTTAGTACC
CCAAGAAAAAATGAAGTTGAGCAAGGACGACTACCTCCCAATGAGCCAAGGATTGTACATGCTC
CTTAACCGCTATGGTTTGGATGTCAAACCAGAGATG

Sequences
Splice junction sequence	CCAAGAAAAAATGAAGTTGAGCAAGGACGACTACCTCCCAATGAGCCAAGGATTGTACATGCTC CTTAACCGCTATGGTTTGGATGTCAAACCAGAGATGttcatttggctgaaggaatttcgagaaa tcaaggacaagtccagtgccattaatcatgatactggtgtcagttgcgaccttgctgagatgat catgaagt
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: 177 Transcript exons: 11917245-11917274,11917518-11917664 TTCATTTGGCTGAAGGAATTTCGAGAAATCATGGAAGTGATGTGGGGCCTGAAGAATCTGATGC ATGTTTTAGTACCCCAAGAAAAAATGAAGTTGAGCAAGGACGACTACCTCCCAATGAGCCAAGG ATTGTACATGCTCCTTAACCGCTATGGTTTGGATGTCAAACCAGAGATG Transcript length: 205 Transcript exons: 11917245-11917369,11917585-11917664 TTCATTTGGCTGAAGGAATTTCGAGAAATCAAGGACAAGTCCAGTGCCATTAATCATGATACTG GTGTCAGTTGCGACCTTGCTGAGATGATCATGAAGTGGCATCACCCTGGGCAGAAAATGGCGCA AGGACGACTACCTCCCAATGAGCCAAGGATTGTACATGCTCCTTAACCGCTATGGTTTGGATGT CAAACCAGAGATG Transcript length: 345 Transcript exons: 11917245-11917412,11917488-11917664 TTCATTTGGCTGAAGGAATTTCGAGAAATCAAGGACAAGTCCAGTGCCATTAATCATGATACTG GTGTCAGTTGCGACCTTGCTGAGATGATCATGAAGTGGCATCACCCTGGGCAGAAAATGGCCGT TGGAAAACCCGAATATAAAGAAATCATTGAAAGAAGCTTGAGTGTGCCCTGCATGTTTGATGAA ATTGTGATGGAAGTGATGTGGGGCCTGAAGAATCTGATGCATGTTTTAGTACCCCAAGAAAAAA TGAAGTTGAGCAAGGACGACTACCTCCCAATGAGCCAAGGATTGTACATGCTCCTTAACCGCTA TGGTTTGGATGTCAAACCAGAGATG
Genomic sequence	TTCATTTGGCTGAAGGAATTTCGAGAAATCAAGGACAAGTCCAGTGCCATTAATCATGATACTG GTGTCAGTTGCGACCTTGCTGAGATGATCATGAAGTGGCATCACCCTGGGCAGAAAATGGCCGT TGGAAAACCCGAATATAAAGAAATCATTGAAAGAAGCTTGGTTAGTGTTCAGCTCCCTTGTTTG CTTTTCTTAGTGGACAACCTTGAGCACCAATTTTGCTGTCATTTCTTTCAGAGTGTGCCCTGCA TGTTTGATGAAATTGTGATGGAAGTGATGTGGGGCCTGAAGAATCTGATGCATGTTTTAGTACC CCAAGAAAAAATGAAGTTGAGCAAGGACGACTACCTCCCAATGAGCCAAGGATTGTACATGCTC CTTAACCGCTATGGTTTGGATGTCAAACCAGAGATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.65668598

Conservation Information
Conserved circRNAs	NA
PMCS	0.65668598

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11917333-11917661(+)
11917555-11917559(-)
11917296-11917639(-)
						
						Potential amino acid sequence
						
							MIMKWHHPGQKMAVGKPEYKEIIERSLSVPCMFDEIVMEVMWGLKNLMHVLVPQEKMKLSKDDY
LPMSQGLYMLLNRYGLDVKPEMFIWLKEFREIKDKSSAINHDTGVSCDLAEMIMKWHHPGQKMA
VGKPEYKEIIERSLSVPCMFDEIVMEVMWGLKNLMHVLVPQEKMKLSKDDYLPMSQGLYMLLNR
YGLDVKPEMFIWLKEFREIKDKSSAINHDTGVSCDLAEMIMKWHHPGQKMAVGKPEYKEIIERS
LSVPCMFDEIVMEVMWGLKNLMHVLVPQEKMKLSKDDYLPMSQGLYMLLNRYGLDVKPEMFIWL
KEFREIKDKSSAINHDTGVSCDLAEMIMKWHHPGQKMAVGKPEYKEIIERSLSVPCMFDEIVME
VMWGLKNLMHVLVPQEKMKLSKDDYLPMSQGLYMLLNRYGLDVKPEM(+)
MHQILQAPHHFHHNFIKHAGHTQASFNDFFIFGFSNGHFLPRVMPLHDHLSKVATDTSIMINGT
GLVLDFSKFLQPNEHLWFDIQTIAVKEHVQSLAHWEVVVLAQLHFFLGY*(-)
MALDLSLISRNSFSQMNISGLTSKP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11917333-11917661(+) 11917555-11917559(-) 11917296-11917639(-)
Potential amino acid sequence	MIMKWHHPGQKMAVGKPEYKEIIERSLSVPCMFDEIVMEVMWGLKNLMHVLVPQEKMKLSKDDY LPMSQGLYMLLNRYGLDVKPEMFIWLKEFREIKDKSSAINHDTGVSCDLAEMIMKWHHPGQKMA VGKPEYKEIIERSLSVPCMFDEIVMEVMWGLKNLMHVLVPQEKMKLSKDDYLPMSQGLYMLLNR YGLDVKPEMFIWLKEFREIKDKSSAINHDTGVSCDLAEMIMKWHHPGQKMAVGKPEYKEIIERS LSVPCMFDEIVMEVMWGLKNLMHVLVPQEKMKLSKDDYLPMSQGLYMLLNRYGLDVKPEMFIWL KEFREIKDKSSAINHDTGVSCDLAEMIMKWHHPGQKMAVGKPEYKEIIERSLSVPCMFDEIVME VMWGLKNLMHVLVPQEKMKLSKDDYLPMSQGLYMLLNRYGLDVKPEM(+) MHQILQAPHHFHHNFIKHAGHTQASFNDFFIFGFSNGHFLPRVMPLHDHLSKVATDTSIMINGT GLVLDFSKFLQPNEHLWFDIQTIAVKEHVQSLAHWEVVVLAQLHFFLGY(-) MALDLSLISRNSFSQMNISGLTSKP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os12g0299700_circ_g.3

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