Plant Circular RNA Database

Detail information of Os03g0239400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os03g0239400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_018789
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 7360252-7363992  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os03g0239400						
					
						Parent gene annotation
						
							Similar to Transcription factor HBP-1a(C14). (Os03t0239400-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0239400_circ_g.1 Os03g0239400_circ_g.2 Os03g0239400_circ_g.4 Os03g0239400_circ_g.5 Os03g0239400_circ_g.6 Os03g0239400_circ_g.7 Os03g0239400_circ_g.8 						
					
						Support reads
						2
					
						Tissues
						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
						Os03t0239400-01:11

General Information
CircRNA Name	Os03g0239400_circ_g.3
ID in PlantcircBase	osa_circ_018789
Alias	NA
Organism	Oryza sativa
Position	chr3: 7360252-7363992 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os03g0239400
Parent gene annotation	Similar to Transcription factor HBP-1a(C14). (Os03t0239400-01)
Parent gene strand	-
Alternative splicing	Os03g0239400_circ_g.1 Os03g0239400_circ_g.2 Os03g0239400_circ_g.4 Os03g0239400_circ_g.5 Os03g0239400_circ_g.6 Os03g0239400_circ_g.7 Os03g0239400_circ_g.8
Support reads	2
Tissues	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	Os03t0239400-01:11

			
						 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  
						
							CCTACAAGACACCTTTGATCTTCTATATTTTCTTGGTCAATGAAGCAGTGGAGTCTCTAAGTAT
CATGGATGCGGCAGAAAATTTTCTTATTGGCTAGCActgcttgcgtaatcttgaacgtcgagct
gattccctatttgattgcttccgcttttgtctcttcagttctcgctcatcctgcattaaaaata
aaatacag

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CTGCTTGCGTAATCTTGAACGTCGAGCTGATTCCCTATTTGATTGCTTCCGCTTTTGTCTCTTC
AGTTCTCGCTCATCCTGCATTAAAAATAAAATACAGCCCTAAGGAAATTGCAAGGTTGGTTCCT
GTAACACAGCAAAAACAAGAAACAAATCCTGCACAGCAATAAACCTGTATGGCTGGATCACTGA
GAACAACATCACGAGAGTTTGATGAAGGAGCTGATGCTGGTGCTGCAATAACTTTATTATGCAT
GGGTACTGAAGTAGGAGTACCCCAGTAATCCATTCCCATGTTTACACCAGTTGCTGGGCCAGCC
ATGGGAGGAGGGACAGGCCAGTATGGCATCATAGGGTTAAGCACAACTGGCCCAGTAGATGCTT
GTACGGGCTCAACCGCAGAACTCTGAGCAGTAGCTCCTTTGTTGCTAGCATCTGGACAAAAAGG
TAATTAGATTGCAGTCAATCCTTACTACATGAGAAAAATTTCTTATTGTCTTAACTAATATATT
TATTAATTGCTTATAACAAAAACAAGCATAGTTTCACAATTTTATTCTTCAATAAAGCTACCAA
TGGCAGGTTGTAGAATATGTTCAGTACTATACTAGGAGTAAACCCCTAATATACCACTGGAAAT
TTCGTCGGTTCCTAATATGTCATCAAAATTTTGCTTGTACCAAATATGCCACTTTGAATCCAAA
TCTAAACCCACACCCAATATGCCAACGGATGATGATTGCATATGGTACTTCCTCGCCCTTGCTT
TCTTAAAAACCTTGTGTCTAAACAGTGATTTTTGCCATATGTGTTTTCAACACGGAAAATGTTT
TTCAGGCATGCCTCCTGCACCACTATAATATTCATGAGTTTTTGCAGAATCTTTTATGAGCTAC
AGATTTTCCTTGAAAATTCTACTGTTTTATATAAAAAAAAGAGAGGTTCTTAATCCTACCATTA
CCCTGGCCATGCTCAGAACCATCCTTTGTCCTTGAACCCTGCAAGCAAATTGTTTGTACATATT
TGTCTTAGGTTAGCAAGAAAATGATCGTATGAAGCAAAAGGAGCAAAAAGGAAAAAAAAAAAAA
CATAGAGGATTGAGTGCATCCATATACTTTGTTCACAGGCTAGAAGGCTATAGTGCATTTTGAA
AGTAGTGGCAACCATGGATACACCCAGCACAAAAAGGTACCAAACATGCATGCAACAAAAAAAA
AAGATCCATTCTTTCAAAAAAAAAAAAGATCCACATACTATAAGTATTTGGTGGGGAAAACAAG
TTCCTAAGGGTTTCAGAACAATCGATCAACACTAATTATTAAAGGGTACAACACATGTGGCGAG
AGCAAAGAATAATCAACTCGAGTCTAATAACTAACGACTATGCGAATGGTCAAGAACTTTAATA
GAAGGGCTCACCATTCGATTTTTTTTTAGTATCACCAAAAATCAGACTGTTTCATTATCAGTTG
GGATCCTCTTATTACAAGATTTGCACTTTGCAGATCTTTATTTTGCAAACATCCAGAACCTTGA
AGAGAAGTACAACCCAACTAGTCTAGGTGGGTTTCTGATGGCCAATATGCAGAGCCAGTGTGCA
ACCCTAGTACCCAACTAACTTGCACCTCTAAATAGTGTACCAGTTCAGTACAGGTGCCGTAAGC
AATAATACAAAGGCTTAGACTCTAGATATTGCGCATGACAAACAAGACCTTCAGTAGGGGGGGG
GGATGCCAGAGTGGTAAAACAAAAGGCATGCTGCCTTTGGAATTTGTACTGGTGAGAAAAATGA
AGTAACTGAAGTAACATAACAAAGCGGTATGATAGAGTGACATACACTTTTTGAATTTGTACTG
CTTCCTTCAGAAGAACTTCCACTTCCGCTCTCACTGCATATCATATGTTAAAAAAAAGTCAGCG
TTTATCCATTATAATCACAGAGACAGAAGAAAAGGAGCTACCTGTGTGAAGAACCTTCATTGGA
TGAGGATGCTGAAGGTTTTGCGGGCGCCTTTTTATTTTTTGTTGCAACTACATCAAGATTACCT
AAGCTTCCTTTCGATCTCTTCAGGGGAGTCTTCCGCTTACTTTTGCCTGACTTATCTGTCTCTG
TTCCGCCAGCAGATGTCTAACAACATGATTTTCAACCACAATCATATCTAATCTAAGTAGACAG
GTAATGAAATAAAGGTGCAAATCAAACCAATTAATTTTTACATGAAAATGTAGCTAAATTATGA
TAGCATAAGCAACAATTTTGACAGCAAGATCACTGAAACTGGAATAAACGGACACAACTAAAAG
ACCCAGGGAAGCAAAAAAAAAAGATTAGATGAAATTCTTCTTGCCTTCTACAACTACAGAGCAG
ATAAAAGATGCCCAAGAACTTACAGGAGTTTGAACTGTCCCATTTGGTGATTGCCCGGGATAAG
GATTGTATGGGTGTGAACCCTGGTATAGAGACAATTAGAATGAAATTCTTTGGTAAGAGCTATT
CACATAACATGACAAAAACTATTTCATTAAGTAAAATGTAAGAGTGAGTACCGGTAGCATAGGT
GCCTGCTGATATGGTGTCCCTTGCGCATACATCGCCGCATATGGCGGCGGTGTTCCATAGGGAG
GCATCATCTGACACGAGCAATTCACATCACATGTTAAAACTGATTTTCCATAGCTTCAGAGTAG
CTAACAGCATCCTTCATACAAAAGAAAAACTACCAAAACCCTAAGGCCAAAGGTTAAAAGGACT
GGGTAACTCAAATGAATGCAGCGGAAAGGTCCATGCTACCATTTGCTTATTATCACTCATGCTT
AGACTTATCTAGACATAATTCTGATAAAACAGCAGAAATGGTAGTGGTATGACCAGAACACTGC
ATCTATAGCAAGAAATTAATGTGAATGTACCTGTGGACCCCACATATATGGGTGCCCCTGAGGA
CTTGGAGCCACATTTGGATGGAAAAAGCCCGGTGGGGTCATTGGAGCTGTCCCAGCAGGATTAT
AGTATGCCTACAGATTGATACTAACCAGTACAGTAAACAATATAGTGGAAAAAGTTAAATGGAT
GCAAGATGAACTCATTTTATGAACCTGAAATTGAGACCAGTCCGGATATGCAGTAGGAGGATTA
GTGGGTGTACTCTGTTCATTCTAAAACAAGCAAAACAAGGTAAGAGAATTTCACTAATTAGTAA
TTAGTCTTGTAGTTTCAGATTGTTGTACATACCTGTGTCGCCGATGATTTTTGAGATTTGGACC
TAGTGGCTACCTCTCCTTTTCCCATGCTTTATTCCTCCCTAGATTACTCTATTCCTTTTAACAC
CTAAGTTCTGAAAATAAGACAAATTTATGAAGTGATCATTAATCATGTGTCTCAATGGTTTTTA
AAATAATGTTTTCCGAAACGCTTAAATTAGATCTTCCTTGCCTTTAAGGAAGTGAAAAATAAAA
GGATTTCAGCAAGCAAACAAATTGTGTCATGGATAAAATAATTTTGAAAGGAGAGATGACTATT
AATCATTATCAGAGCATAGAATAATACACAAGTGCAGAAAAACACTCGGAACCCAACAAACATG
GAAAAAAAATTATCAGGTGAAACGATGAATATATAAACAACCGGCAGAAGCTTCCTACCTACAA
GACACCTTTGATCTTCTATATTTTCTTGGTCAATGAAGCAGTGGAGTCTCTAAGTATCATGGAT
GCGGCAGAAAATTTTCTTATTGGCTAGCA
						
					

			
		

Sequences
Splice junction sequence	CCTACAAGACACCTTTGATCTTCTATATTTTCTTGGTCAATGAAGCAGTGGAGTCTCTAAGTAT CATGGATGCGGCAGAAAATTTTCTTATTGGCTAGCActgcttgcgtaatcttgaacgtcgagct gattccctatttgattgcttccgcttttgtctcttcagttctcgctcatcctgcattaaaaata aaatacag
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CTGCTTGCGTAATCTTGAACGTCGAGCTGATTCCCTATTTGATTGCTTCCGCTTTTGTCTCTTC AGTTCTCGCTCATCCTGCATTAAAAATAAAATACAGCCCTAAGGAAATTGCAAGGTTGGTTCCT GTAACACAGCAAAAACAAGAAACAAATCCTGCACAGCAATAAACCTGTATGGCTGGATCACTGA GAACAACATCACGAGAGTTTGATGAAGGAGCTGATGCTGGTGCTGCAATAACTTTATTATGCAT GGGTACTGAAGTAGGAGTACCCCAGTAATCCATTCCCATGTTTACACCAGTTGCTGGGCCAGCC ATGGGAGGAGGGACAGGCCAGTATGGCATCATAGGGTTAAGCACAACTGGCCCAGTAGATGCTT GTACGGGCTCAACCGCAGAACTCTGAGCAGTAGCTCCTTTGTTGCTAGCATCTGGACAAAAAGG TAATTAGATTGCAGTCAATCCTTACTACATGAGAAAAATTTCTTATTGTCTTAACTAATATATT TATTAATTGCTTATAACAAAAACAAGCATAGTTTCACAATTTTATTCTTCAATAAAGCTACCAA TGGCAGGTTGTAGAATATGTTCAGTACTATACTAGGAGTAAACCCCTAATATACCACTGGAAAT TTCGTCGGTTCCTAATATGTCATCAAAATTTTGCTTGTACCAAATATGCCACTTTGAATCCAAA TCTAAACCCACACCCAATATGCCAACGGATGATGATTGCATATGGTACTTCCTCGCCCTTGCTT TCTTAAAAACCTTGTGTCTAAACAGTGATTTTTGCCATATGTGTTTTCAACACGGAAAATGTTT TTCAGGCATGCCTCCTGCACCACTATAATATTCATGAGTTTTTGCAGAATCTTTTATGAGCTAC AGATTTTCCTTGAAAATTCTACTGTTTTATATAAAAAAAAGAGAGGTTCTTAATCCTACCATTA CCCTGGCCATGCTCAGAACCATCCTTTGTCCTTGAACCCTGCAAGCAAATTGTTTGTACATATT TGTCTTAGGTTAGCAAGAAAATGATCGTATGAAGCAAAAGGAGCAAAAAGGAAAAAAAAAAAAA CATAGAGGATTGAGTGCATCCATATACTTTGTTCACAGGCTAGAAGGCTATAGTGCATTTTGAA AGTAGTGGCAACCATGGATACACCCAGCACAAAAAGGTACCAAACATGCATGCAACAAAAAAAA AAGATCCATTCTTTCAAAAAAAAAAAAGATCCACATACTATAAGTATTTGGTGGGGAAAACAAG TTCCTAAGGGTTTCAGAACAATCGATCAACACTAATTATTAAAGGGTACAACACATGTGGCGAG AGCAAAGAATAATCAACTCGAGTCTAATAACTAACGACTATGCGAATGGTCAAGAACTTTAATA GAAGGGCTCACCATTCGATTTTTTTTTAGTATCACCAAAAATCAGACTGTTTCATTATCAGTTG GGATCCTCTTATTACAAGATTTGCACTTTGCAGATCTTTATTTTGCAAACATCCAGAACCTTGA AGAGAAGTACAACCCAACTAGTCTAGGTGGGTTTCTGATGGCCAATATGCAGAGCCAGTGTGCA ACCCTAGTACCCAACTAACTTGCACCTCTAAATAGTGTACCAGTTCAGTACAGGTGCCGTAAGC AATAATACAAAGGCTTAGACTCTAGATATTGCGCATGACAAACAAGACCTTCAGTAGGGGGGGG GGATGCCAGAGTGGTAAAACAAAAGGCATGCTGCCTTTGGAATTTGTACTGGTGAGAAAAATGA AGTAACTGAAGTAACATAACAAAGCGGTATGATAGAGTGACATACACTTTTTGAATTTGTACTG CTTCCTTCAGAAGAACTTCCACTTCCGCTCTCACTGCATATCATATGTTAAAAAAAAGTCAGCG TTTATCCATTATAATCACAGAGACAGAAGAAAAGGAGCTACCTGTGTGAAGAACCTTCATTGGA TGAGGATGCTGAAGGTTTTGCGGGCGCCTTTTTATTTTTTGTTGCAACTACATCAAGATTACCT AAGCTTCCTTTCGATCTCTTCAGGGGAGTCTTCCGCTTACTTTTGCCTGACTTATCTGTCTCTG TTCCGCCAGCAGATGTCTAACAACATGATTTTCAACCACAATCATATCTAATCTAAGTAGACAG GTAATGAAATAAAGGTGCAAATCAAACCAATTAATTTTTACATGAAAATGTAGCTAAATTATGA TAGCATAAGCAACAATTTTGACAGCAAGATCACTGAAACTGGAATAAACGGACACAACTAAAAG ACCCAGGGAAGCAAAAAAAAAAGATTAGATGAAATTCTTCTTGCCTTCTACAACTACAGAGCAG ATAAAAGATGCCCAAGAACTTACAGGAGTTTGAACTGTCCCATTTGGTGATTGCCCGGGATAAG GATTGTATGGGTGTGAACCCTGGTATAGAGACAATTAGAATGAAATTCTTTGGTAAGAGCTATT CACATAACATGACAAAAACTATTTCATTAAGTAAAATGTAAGAGTGAGTACCGGTAGCATAGGT GCCTGCTGATATGGTGTCCCTTGCGCATACATCGCCGCATATGGCGGCGGTGTTCCATAGGGAG GCATCATCTGACACGAGCAATTCACATCACATGTTAAAACTGATTTTCCATAGCTTCAGAGTAG CTAACAGCATCCTTCATACAAAAGAAAAACTACCAAAACCCTAAGGCCAAAGGTTAAAAGGACT GGGTAACTCAAATGAATGCAGCGGAAAGGTCCATGCTACCATTTGCTTATTATCACTCATGCTT AGACTTATCTAGACATAATTCTGATAAAACAGCAGAAATGGTAGTGGTATGACCAGAACACTGC ATCTATAGCAAGAAATTAATGTGAATGTACCTGTGGACCCCACATATATGGGTGCCCCTGAGGA CTTGGAGCCACATTTGGATGGAAAAAGCCCGGTGGGGTCATTGGAGCTGTCCCAGCAGGATTAT AGTATGCCTACAGATTGATACTAACCAGTACAGTAAACAATATAGTGGAAAAAGTTAAATGGAT GCAAGATGAACTCATTTTATGAACCTGAAATTGAGACCAGTCCGGATATGCAGTAGGAGGATTA GTGGGTGTACTCTGTTCATTCTAAAACAAGCAAAACAAGGTAAGAGAATTTCACTAATTAGTAA TTAGTCTTGTAGTTTCAGATTGTTGTACATACCTGTGTCGCCGATGATTTTTGAGATTTGGACC TAGTGGCTACCTCTCCTTTTCCCATGCTTTATTCCTCCCTAGATTACTCTATTCCTTTTAACAC CTAAGTTCTGAAAATAAGACAAATTTATGAAGTGATCATTAATCATGTGTCTCAATGGTTTTTA AAATAATGTTTTCCGAAACGCTTAAATTAGATCTTCCTTGCCTTTAAGGAAGTGAAAAATAAAA GGATTTCAGCAAGCAAACAAATTGTGTCATGGATAAAATAATTTTGAAAGGAGAGATGACTATT AATCATTATCAGAGCATAGAATAATACACAAGTGCAGAAAAACACTCGGAACCCAACAAACATG GAAAAAAAATTATCAGGTGAAACGATGAATATATAAACAACCGGCAGAAGCTTCCTACCTACAA GACACCTTTGATCTTCTATATTTTCTTGGTCAATGAAGCAGTGGAGTCTCTAAGTATCATGGAT GCGGCAGAAAATTTTCTTATTGGCTAGCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.106990802

Conservation Information
Conserved circRNAs	NA
PMCS	0.106990802

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7363963-7360440(+)
7363542-7363989(-)
						
						Potential amino acid sequence
						
							MRQKIFLLASTACVILNVELIPYLIASAFVSSVLAHPVWLDH*(+)
MGKGEVATRSKSQKSSATQNEQSTPTNPPTAYPDWSQFQAYYNPAGTAPMTPPGFFHPNVAPSP
QGHPYMWGPQMMPPYGTPPPYAAMYAQGTPYQQAPMLPGSHPYNPYPGQSPNGTVQTPTSAGGT
ETDKSGKSKRKTPLKRSKGSLGNLDVVATKNKKAPAKPSASSSNEGSSHSESGSGSSSEGSSTN
SKSGSRTKDGSEHGQGNDASNKGATAQSSAVEPVQASTGPVVLNPMMPYWPVPPPMAGPATGVN
MGMDYWGTPTSVPMHNKVIAAPASAPSSNSRDVVLSDPAIQDERELKRQKRKQSNRESARRSRL
RKQC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7363963-7360440(+) 7363542-7363989(-)
Potential amino acid sequence	MRQKIFLLASTACVILNVELIPYLIASAFVSSVLAHPVWLDH(+) MGKGEVATRSKSQKSSATQNEQSTPTNPPTAYPDWSQFQAYYNPAGTAPMTPPGFFHPNVAPSP QGHPYMWGPQMMPPYGTPPPYAAMYAQGTPYQQAPMLPGSHPYNPYPGQSPNGTVQTPTSAGGT ETDKSGKSKRKTPLKRSKGSLGNLDVVATKNKKAPAKPSASSSNEGSSHSESGSGSSSEGSSTN SKSGSRTKDGSEHGQGNDASNKGATAQSSAVEPVQASTGPVVLNPMMPYWPVPPPMAGPATGVN MGMDYWGTPTSVPMHNKVIAAPASAPSSNSRDVVLSDPAIQDERELKRQKRKQSNRESARRSRL RKQC(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0239400_circ_g.3

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