Plant Circular RNA Database

Detail information of Os12g0405100_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os12g0405100_circ_g.1
					
						ID in PlantcircBase
						osa_circ_011273
					
						Alias
						Os12circ05177/Os_ciR7301
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 12196956-12199362  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, find_circ
					
						Parent gene
						
							Os12g0405100						
					
						Parent gene annotation
						
							Similar to Floral homeotic protein HUA1. (Os12t0405100-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0405100_circ_g.2 Os12g0405100_circ_g.3 						
					
						Support reads
						3/2/8
					
						Tissues
						leaf and panicle/root/shoot, seed
					
						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
						Os12t0405100-01:4

General Information
CircRNA Name	Os12g0405100_circ_g.1
ID in PlantcircBase	osa_circ_011273
Alias	Os12circ05177/Os_ciR7301
Organism	Oryza sativa
Position	chr12: 12196956-12199362 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, find_circ
Parent gene	Os12g0405100
Parent gene annotation	Similar to Floral homeotic protein HUA1. (Os12t0405100-01)
Parent gene strand	+
Alternative splicing	Os12g0405100_circ_g.2 Os12g0405100_circ_g.3
Support reads	3/2/8
Tissues	leaf and panicle/root/shoot, seed
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	Os12t0405100-01:4

			
						 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  
						
							ATCATTTATTGCAAGCCCCAGGTGGCCTGGCCATTCAGGCTATGCACAAGTAATCGTTCCCCAG
GGCCTTGTTCAAGTTCCAGGGTGGAATCCTTATGCTaagcaatgtggcaaatgactttaggagg
aggagagtctatggagtccactccataccctgagcggataggagagccagactgcagttattat
atgaggac

									
								

					

						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: 638
Transcript exons: 12196956-12197113,12198078-12198140,12198827-12198946,12
199066-12199362
AAGCAATGTGGCAAATGACTTTAGGAGGAGGAGAGTCTATGGAGTCCACTCCATACCCTGAGCG
GATAGGAGAGCCAGACTGCAGTTATTATATGAGGACTGGACTATGTAGGTTTGGGATGACCTGC
AAATTCAATCACCCCCCAAATAGAAAACTGGCTGTTGCTGCTGCAAGGATGAATGGAGAGTATC
CTTATAGAGTTGGTCAACCTGAGTGTCAATACTACTTGAAAACTGGAACGTGCAAGTTTGGTGC
AACATGCAAGTTTCATCACCCCAGGGAGAAGGCTGCACTTGCAAACCGTGTACAGTTAAATGTT
CTAGGCTACCCGATGCGTCCGAATGAGAAGGAATGTGCTTACTACTTAAGAACAGGGCAGTGTA
AATTTGCAAGCACATGTAAGTTTCATCATCCACAGCCCTCTAATACAATGGTTGCTGTACGGAA
CTCTATGTATTCACCTGGACAGTCTGCAACCTCTCCTGGTCAACATACTTATCCTGGGGCCGTA
ACAAACTGGACCTTGTCAAGATCTGCATCATTTATTGCAAGCCCCAGGTGGCCTGGCCATTCAG
GCTATGCACAAGTAATCGTTCCCCAGGGCCTTGTTCAAGTTCCAGGGTGGAATCCTTATGCT
						
					

						Genomic sequence
						
							AAGCAATGTGGCAAATGACTTTAGGAGGAGGAGAGTCTATGGAGTCCACTCCATACCCTGAGCG
GATAGGAGAGCCAGACTGCAGTTATTATATGAGGACTGGACTATGTAGGTTTGGGATGACCTGC
AAATTCAATCACCCCCCAAATAGAAAACTGGTAATGTTACTTGTGCATCATGTATTATTTGTTT
GGGTAAAGTCTTTTTGATCCTTGAACTTTGCTCAAAGTTTTTTTTTTCACCCCTGAAATACAAT
ACCGGTTTTTTTTCACCCCTAGCTTCGAAAACCGGCCATATTAGGTCCCGGAAATTTGGCTGAT
ATTTGTAATGTGTATATATCTTGAATAGACCTAATTTGTCTTTTCCTTTTTATCTTTCTTTCTA
AATTCTCAGCTGCTGAATTTTTTGGGTTAAGAATCAACCACTCCATATGTTACAGAAATTGTAA
AGAGACCACTCAATGTTTATGGTCATTGATTGCATCATTGTTCATAATGATGTTAATCTGAAAA
TTGCAAGATAATGTTGCTTGGAAAGATTGTGAAATTTGAAGTGGCCCCAAAACTAAATTGGGCA
AACATACAAAGAATTTGGATTCTTTAGTCACTCATTTAACTATATCAAATTCCTGGTGGAGAGT
TGTTTGTACTTTGTACACTCATTTAGGTAGCTTCTAAATATCTAATTTGATGCATTTAAGCTGC
CATACGTTCTGCTGTATACTATTGTATATTATATAGCGCACTCTAGCTAGAGCTGTTCCCACTT
TTCCTTATGTAAATAATAGGTGGTGTATTGTCAATTTTTTTCATAACTATTATTTGCATAGAAA
TATAAAATTAGAATGCAATTTAAGTGCCCAGGGGTTCCCATCCCAGGTCTCAATATGCAGAAAG
TGTATAACACCATTATCCTACATCCATGATTTTTTTGGTTATTATTGACACAGTATGTTGCGCA
CTTTTCACAAACATGGATGCGACAGCACCTGGGCAAACGATATGCCAAATATGGTCCACTTTTT
TGTTTGAATGTTAGAAATCATATGATTTTGTTTCCTTATCCCTTTTTTGCTTGATTCTAATTTT
TATCTTTACCCAATTTTTTTTATTGAATTATCAGGCTGTTGCTGCTGCAAGGATGAATGGAGAG
TATCCTTATAGAGTTGGTCAACCTGAGTGTCAAGTGGGTACTAAATCTTTTATTAACTTAATAA
ATCAATTTGTCTTATTTTTTTTCTTCTTTGCCATGTGGTGTGTGATTAACTTTTAACAGTTTGC
TGGGTTTCAATACTCTGGCTGATAATTAATATGTTTGATCTAAGTTTAATTTAAACTTAAGCTC
ATCTGTTTACAATGTTGGTAATCTATCAGTAAAAAAATTTTGAACATGAGCCATTTGAGTACAG
TTCCTAGCAACATATTTTGTGGCAGCCTGGCAGGTTGGCAAAAATATTTGCTTGCATTCTTTGT
AAGTTAACAAGAATTAGCTTTAAAGAGAAATAACTTTGTGAACAATATCAGTCAGTACCATGTT
ACATTGCAAGAGCACTCTCTGTTTCTCTGACTATACATGTATTCAGAAGAATCAACCTTAACAT
TTTGCTATTATGATGTAATATTTTCTGTTGTTTTAGTAAATAATATAGCTGTTAACACATTTTT
CTATGAGTATTTTTTTCTACTAGCCTTTCATTCTTATCAGCTATAAATGAACTTCGTTTTTAAA
ATTTGCCATATCCTTCATCTTTTTATAGAACCTCGACTGCTATTTATGCCTCATCTTTTGATAT
TCTACTATTTTGTACTGAAACTGGCTTTTACATGTCATGAACGTTATGCTTAGAGTTCTCATAT
TTTCTGCTCTTTCAGTACTACTTGAAAACTGGAACGTGCAAGTTTGGTGCAACATGCAAGTTTC
ATCACCCCAGGGAGAAGGCTGCACTTGCAAACCGTGTACAGTTAAATGTTCTAGGCTACCCGAT
GCGTCCGGTTTGTTCCATAATTCTATAATTTAGTTGTCACCTGATTGCTTAATCGTAATATCTG
TTCTCTACCTCTTAGCTTGCATGCAAGATTAGCTTTCATTAACTTGCAGTTTATTACTGCAGAA
TGAGAAGGAATGTGCTTACTACTTAAGAACAGGGCAGTGTAAATTTGCAAGCACATGTAAGTTT
CATCATCCACAGCCCTCTAATACAATGGTTGCTGTACGGAACTCTATGTATTCACCTGGACAGT
CTGCAACCTCTCCTGGTCAACATACTTATCCTGGGGCCGTAACAAACTGGACCTTGTCAAGATC
TGCATCATTTATTGCAAGCCCCAGGTGGCCTGGCCATTCAGGCTATGCACAAGTAATCGTTCCC
CAGGGCCTTGTTCAAGTTCCAGGGTGGAATCCTTATGCT
						
					

			
		

Sequences
Splice junction sequence	ATCATTTATTGCAAGCCCCAGGTGGCCTGGCCATTCAGGCTATGCACAAGTAATCGTTCCCCAG GGCCTTGTTCAAGTTCCAGGGTGGAATCCTTATGCTaagcaatgtggcaaatgactttaggagg aggagagtctatggagtccactccataccctgagcggataggagagccagactgcagttattat atgaggac
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: 638 Transcript exons: 12196956-12197113,12198078-12198140,12198827-12198946,12 199066-12199362 AAGCAATGTGGCAAATGACTTTAGGAGGAGGAGAGTCTATGGAGTCCACTCCATACCCTGAGCG GATAGGAGAGCCAGACTGCAGTTATTATATGAGGACTGGACTATGTAGGTTTGGGATGACCTGC AAATTCAATCACCCCCCAAATAGAAAACTGGCTGTTGCTGCTGCAAGGATGAATGGAGAGTATC CTTATAGAGTTGGTCAACCTGAGTGTCAATACTACTTGAAAACTGGAACGTGCAAGTTTGGTGC AACATGCAAGTTTCATCACCCCAGGGAGAAGGCTGCACTTGCAAACCGTGTACAGTTAAATGTT CTAGGCTACCCGATGCGTCCGAATGAGAAGGAATGTGCTTACTACTTAAGAACAGGGCAGTGTA AATTTGCAAGCACATGTAAGTTTCATCATCCACAGCCCTCTAATACAATGGTTGCTGTACGGAA CTCTATGTATTCACCTGGACAGTCTGCAACCTCTCCTGGTCAACATACTTATCCTGGGGCCGTA ACAAACTGGACCTTGTCAAGATCTGCATCATTTATTGCAAGCCCCAGGTGGCCTGGCCATTCAG GCTATGCACAAGTAATCGTTCCCCAGGGCCTTGTTCAAGTTCCAGGGTGGAATCCTTATGCT
Genomic sequence	AAGCAATGTGGCAAATGACTTTAGGAGGAGGAGAGTCTATGGAGTCCACTCCATACCCTGAGCG GATAGGAGAGCCAGACTGCAGTTATTATATGAGGACTGGACTATGTAGGTTTGGGATGACCTGC AAATTCAATCACCCCCCAAATAGAAAACTGGTAATGTTACTTGTGCATCATGTATTATTTGTTT GGGTAAAGTCTTTTTGATCCTTGAACTTTGCTCAAAGTTTTTTTTTTCACCCCTGAAATACAAT ACCGGTTTTTTTTCACCCCTAGCTTCGAAAACCGGCCATATTAGGTCCCGGAAATTTGGCTGAT ATTTGTAATGTGTATATATCTTGAATAGACCTAATTTGTCTTTTCCTTTTTATCTTTCTTTCTA AATTCTCAGCTGCTGAATTTTTTGGGTTAAGAATCAACCACTCCATATGTTACAGAAATTGTAA AGAGACCACTCAATGTTTATGGTCATTGATTGCATCATTGTTCATAATGATGTTAATCTGAAAA TTGCAAGATAATGTTGCTTGGAAAGATTGTGAAATTTGAAGTGGCCCCAAAACTAAATTGGGCA AACATACAAAGAATTTGGATTCTTTAGTCACTCATTTAACTATATCAAATTCCTGGTGGAGAGT TGTTTGTACTTTGTACACTCATTTAGGTAGCTTCTAAATATCTAATTTGATGCATTTAAGCTGC CATACGTTCTGCTGTATACTATTGTATATTATATAGCGCACTCTAGCTAGAGCTGTTCCCACTT TTCCTTATGTAAATAATAGGTGGTGTATTGTCAATTTTTTTCATAACTATTATTTGCATAGAAA TATAAAATTAGAATGCAATTTAAGTGCCCAGGGGTTCCCATCCCAGGTCTCAATATGCAGAAAG TGTATAACACCATTATCCTACATCCATGATTTTTTTGGTTATTATTGACACAGTATGTTGCGCA CTTTTCACAAACATGGATGCGACAGCACCTGGGCAAACGATATGCCAAATATGGTCCACTTTTT TGTTTGAATGTTAGAAATCATATGATTTTGTTTCCTTATCCCTTTTTTGCTTGATTCTAATTTT TATCTTTACCCAATTTTTTTTATTGAATTATCAGGCTGTTGCTGCTGCAAGGATGAATGGAGAG TATCCTTATAGAGTTGGTCAACCTGAGTGTCAAGTGGGTACTAAATCTTTTATTAACTTAATAA ATCAATTTGTCTTATTTTTTTTCTTCTTTGCCATGTGGTGTGTGATTAACTTTTAACAGTTTGC TGGGTTTCAATACTCTGGCTGATAATTAATATGTTTGATCTAAGTTTAATTTAAACTTAAGCTC ATCTGTTTACAATGTTGGTAATCTATCAGTAAAAAAATTTTGAACATGAGCCATTTGAGTACAG TTCCTAGCAACATATTTTGTGGCAGCCTGGCAGGTTGGCAAAAATATTTGCTTGCATTCTTTGT AAGTTAACAAGAATTAGCTTTAAAGAGAAATAACTTTGTGAACAATATCAGTCAGTACCATGTT ACATTGCAAGAGCACTCTCTGTTTCTCTGACTATACATGTATTCAGAAGAATCAACCTTAACAT TTTGCTATTATGATGTAATATTTTCTGTTGTTTTAGTAAATAATATAGCTGTTAACACATTTTT CTATGAGTATTTTTTTCTACTAGCCTTTCATTCTTATCAGCTATAAATGAACTTCGTTTTTAAA ATTTGCCATATCCTTCATCTTTTTATAGAACCTCGACTGCTATTTATGCCTCATCTTTTGATAT TCTACTATTTTGTACTGAAACTGGCTTTTACATGTCATGAACGTTATGCTTAGAGTTCTCATAT TTTCTGCTCTTTCAGTACTACTTGAAAACTGGAACGTGCAAGTTTGGTGCAACATGCAAGTTTC ATCACCCCAGGGAGAAGGCTGCACTTGCAAACCGTGTACAGTTAAATGTTCTAGGCTACCCGAT GCGTCCGGTTTGTTCCATAATTCTATAATTTAGTTGTCACCTGATTGCTTAATCGTAATATCTG TTCTCTACCTCTTAGCTTGCATGCAAGATTAGCTTTCATTAACTTGCAGTTTATTACTGCAGAA TGAGAAGGAATGTGCTTACTACTTAAGAACAGGGCAGTGTAAATTTGCAAGCACATGTAAGTTT CATCATCCACAGCCCTCTAATACAATGGTTGCTGTACGGAACTCTATGTATTCACCTGGACAGT CTGCAACCTCTCCTGGTCAACATACTTATCCTGGGGCCGTAACAAACTGGACCTTGTCAAGATC TGCATCATTTATTGCAAGCCCCAGGTGGCCTGGCCATTCAGGCTATGCACAAGTAATCGTTCCC CAGGGCCTTGTTCAAGTTCCAGGGTGGAATCCTTATGCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_003413* osi_circ_010453 						
					
						PMCS
						0.441934661

Conservation Information
Conserved circRNAs	osi_circ_003413* osi_circ_010453
PMCS	0.441934661

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12199359-12197013(+)
12196962-12196970(+)
						
						Potential amino acid sequence
						
							MLSNVANDFRRRRVYGVHSIP*(+)
MWQMTLGGGESMESTPYPERIGEPDCSYYMRTGLCRFGMTCKFNHPPNRKLAVAAARMNGEYPY
RVGQPECQYYLKTGTCKFGATCKFHHPREKAALANRVQLNVLGYPMRPNEKECAYYLRTGQCKF
ASTCKFHHPQPSNTMVAVRNSMYSPGQSATSPGQHTYPGAVTNWTLSRSASFIASPRWPGHSGY
AQVIVPQGLVQVPGWNPYAKQCGK*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	12199359-12197013(+) 12196962-12196970(+)
Potential amino acid sequence	MLSNVANDFRRRRVYGVHSIP(+) MWQMTLGGGESMESTPYPERIGEPDCSYYMRTGLCRFGMTCKFNHPPNRKLAVAAARMNGEYPY RVGQPECQYYLKTGTCKFGATCKFHHPREKAALANRVQLNVLGYPMRPNEKECAYYLRTGQCKF ASTCKFHHPQPSNTMVAVRNSMYSPGQSATSPGQHTYPGAVTNWTLSRSASFIASPRWPGHSGY AQVIVPQGLVQVPGWNPYAKQCGK(+)
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 Os12g0405100_circ_g.1

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