Plant Circular RNA Database

Detail information of Os06g0171900_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os06g0171900_circ_g.3
					
						ID in PlantcircBase
						osa_circ_029844
					
						Alias
						Os06circ03883/Os_ciR1619
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 3634540-3636569  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os06g0171900						
					
						Parent gene annotation
						
							WD40 subfamily protein, Salt stress (Os06t0171900-01);Similar to
 GAMYB-binding protein (Fragment). (Os06t0171900-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os06g0171900_circ_g.1 Os06g0171900_circ_g.2 Os06g0171900_circ_g.4 						
					
						Support reads
						2/8/2
					
						Tissues
						leaf and panicle/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  
						
							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
						Os06t0171900-02:5
Os06t0171900-01:7

General Information
CircRNA Name	Os06g0171900_circ_g.3
ID in PlantcircBase	osa_circ_029844
Alias	Os06circ03883/Os_ciR1619
Organism	Oryza sativa
Position	chr6: 3634540-3636569 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl, find_circ
Parent gene	Os06g0171900
Parent gene annotation	WD40 subfamily protein, Salt stress (Os06t0171900-01);Similar to GAMYB-binding protein (Fragment). (Os06t0171900-02)
Parent gene strand	+
Alternative splicing	Os06g0171900_circ_g.1 Os06g0171900_circ_g.2 Os06g0171900_circ_g.4
Support reads	2/8/2
Tissues	leaf and panicle/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	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	Os06t0171900-02:5 Os06t0171900-01:7

			
						 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  
						
							TACTCCTATGCAGCACACATCTGTGAGCCCTGATAGGAAACTTCTGGCAGTAGTTGGAGATGAT
CGGGATGCTCTTCTTGTTGATTCAAGAAATGGAAAGctcactaggataactgatacatcagcag
ctgaagcaagagcaggaaaggatatacaaggtataccatgggagaggttacaaataaccaggag
cgattaca

									
								

					

						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: 786
Transcript exons: 3634540-3634707,3634805-3634891,3635505-3635639,3635774-
3635884,3636122-3636213,3636296-3636401,3636483-3636569
CTCACTAGGATAACTGATACATCAGCAGCTGAAGCAAGAGCAGGAAAGGATATACAAGGTATAC
CATGGGAGAGGTTACAAATAACCAGGAGCGATTACAGAAAAGCTAGGTTGGTACAGTACAAAAA
CTACGAAAACTTCCCTCAATCAGGAGAGCTCATGGATAAGATATGCAAGCAAGTGGATAAGATC
AGCAAGTATTATGAATTTCACTACAACACTAGATTAGTGAAGCCATCAATCCTCCACTTTCAGC
TTAGGAATTTGTTATGGGCAACGTCGAAGCATGATGTCTACTTCATGTCAAATTCCACAGTAGG
CCACTGGTCATCATTGTCTCACAATCTATCAGAGGTTCTTGATTTCTCCGGGCATGTTGCTCCT
GCGCAGAAACACCCTGGCAGTTTACTGGAAGGGTTTAGCGGGGTTCAAGTTAGCACACTTTCAG
TGAATGAGGGTTTATTGGTTGCTGGTGGTTTTCAGGGAGAACTAATTTGCAAGGTTGTGGGAGA
CCGTGATGTTAAGTTCTGCACAAGGACAACTTTAAGCGACAATGCTATCACAAATGCGATAGAT
ATACACAGATCTGCAAGTGGAAGCTTGCGTGTTACCGTGTCCAACAATGATTGTGGTGTTCGTG
AATTTGACATGGAAACATTTCAGCTCTTGAACCACTTCAGTTATAACTGGCCAGTAAATCACAC
ATCTGTGAGCCCTGATAGGAAACTTCTGGCAGTAGTTGGAGATGATCGGGATGCTCTTCTTGTT
GATTCAAGAAATGGAAAG
						
					

						Genomic sequence
						
							CTCACTAGGATAACTGATACATCAGCAGCTGAAGCAAGAGCAGGAAAGGATATACAAGGTATAC
CATGGGAGAGGTTACAAATAACCAGGAGCGATTACAGAAAAGCTAGGTTGGTACAGTACAAAAA
CTACGAAAACTTCCCTCAATCAGGAGAGCTCATGGATAAGGTCTCTATTATCATGAAATTTTAT
CTATCAATGTTTGTTTTTTTTGCTCTATGGATGTTCCAAATTCCTGAAAAAAAATGCATCTTAC
ATTTTTCAGATATGCAAGCAAGTGGATAAGATCAGCAAGTATTATGAATTTCACTACAACACTA
GATTAGTGAAGCCATCAATCCTCCACTTTCAGGTGAGTTGCATTCTTTCTTAGCTGACAAATAC
TCCTTTTTATCAATCCTCCACTAGATTAATGCGGGATAAGCTATTTTTCTTAGCTGTTAGCATT
AGTTGTGTATCATCGGAGTTGTTACACCTCATTTACTTGTCTTACGTATGTGGCCATGTCAATA
AGAACTACAAAGATAAAAAATGTTGTATGATCATTAGGGAAAGGGAACCTTTAACAAATTGTGA
AATTGGCCTCTAAACAAGAAAACTACTGTTCCAGAGCATAGAATTAGTTCAATTGTTTTGCAGG
ATTCTGGTTCAGTTATGTTGGTAAAAAGGTTTTGGGATATTTCAAAGGGAATGCTGTAGTGGCT
AAATACTTGGATGTTTTCATGGAACTGTTAAACACATGAAATCATGGCTTACACAATCTTGCCA
GTGAAAAATTAAGTTTAAAGTTCTTCATACAAGCGAATTTTGAACTATGACTGGATATAATCAA
TGATGCAAACTTAAACACTTTTGCCTTGATGTCTTCATTATTATGAGGTCCATTCTTCTTTATA
GCAGCTATCTGAATTTGTCTTGTCATATGAGTCCCAAGGCTGCTCAGTACTGACGAACTGCTTC
TGTAGCTTAGGAATTTGTTATGGGCAACGTCGAAGCATGATGTCTACTTCATGTCAAATTCCAC
AGTAGGCCACTGGTCATCATTGTCTCACAATCTATCAGAGGTTCTTGATTTCTCCGGGCATGTT
GCTCCTGCGCAGGTTTTCTTCTTTTTCATTTCCTGCTTGTGTTTATTTGAACTAAAGATCTTTT
TTTTATTAGTGATGTTTCTCCCAAGTTCAATTACTCTTGTTTTTTTATGTAAAATTATTCTGAA
ATTAATGTTGTCACACAGAAACACCCTGGCAGTTTACTGGAAGGGTTTAGCGGGGTTCAAGTTA
GCACACTTTCAGTGAATGAGGGTTTATTGGTTGCTGGTGGTTTTCAGGGAGAACTAATTTGCAA
GGTAAGGTGCTGTTTCCCCTACTTTTGCTTTATAATAAGTACCTGCTTTAATGAAAAAAAAGCA
AGCCATGAGTATCATCAGGCTTACATGCTCAGTATTTGCCAGTCTTGCTACAGGTTTGGGGATC
CTTTACCTTTTCTTAATAAAAGAGGCAACCATGAATATTGTTTTTTTAAATAGAAAAGGCAAAC
CTTAAATATCAGGTTTACGTGCTCAATATTTTTTATCTTTGTACAGGTTGTGGGAGACCGTGAT
GTTAAGTTCTGCACAAGGACAACTTTAAGCGACAATGCTATCACAAATGCGATAGATATACACA
GATCTGCAAGGTAAAAATATACCAGCTTAAATCTTTGGCTGAAGATGTACCTATCATTACAGAA
ATCTAAAGCCCTAAAATTGTCCATGTAGTGGAAGCTTGCGTGTTACCGTGTCCAACAATGATTG
TGGTGTTCGTGAATTTGACATGGAAACATTTCAGCTCTTGAACCACTTCAGTTATAACTGGCCA
GTAAATGTAAGTCATCTCTCTTCAATATCCACACAACGCTTTTATGTCCAGCCATCCTTGTTTG
ACTTCCTTACTACTCCTATGCAGCACACATCTGTGAGCCCTGATAGGAAACTTCTGGCAGTAGT
TGGAGATGATCGGGATGCTCTTCTTGTTGATTCAAGAAATGGAAAG
						
					

			
		

Sequences
Splice junction sequence	TACTCCTATGCAGCACACATCTGTGAGCCCTGATAGGAAACTTCTGGCAGTAGTTGGAGATGAT CGGGATGCTCTTCTTGTTGATTCAAGAAATGGAAAGctcactaggataactgatacatcagcag ctgaagcaagagcaggaaaggatatacaaggtataccatgggagaggttacaaataaccaggag cgattaca
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: 786 Transcript exons: 3634540-3634707,3634805-3634891,3635505-3635639,3635774- 3635884,3636122-3636213,3636296-3636401,3636483-3636569 CTCACTAGGATAACTGATACATCAGCAGCTGAAGCAAGAGCAGGAAAGGATATACAAGGTATAC CATGGGAGAGGTTACAAATAACCAGGAGCGATTACAGAAAAGCTAGGTTGGTACAGTACAAAAA CTACGAAAACTTCCCTCAATCAGGAGAGCTCATGGATAAGATATGCAAGCAAGTGGATAAGATC AGCAAGTATTATGAATTTCACTACAACACTAGATTAGTGAAGCCATCAATCCTCCACTTTCAGC TTAGGAATTTGTTATGGGCAACGTCGAAGCATGATGTCTACTTCATGTCAAATTCCACAGTAGG CCACTGGTCATCATTGTCTCACAATCTATCAGAGGTTCTTGATTTCTCCGGGCATGTTGCTCCT GCGCAGAAACACCCTGGCAGTTTACTGGAAGGGTTTAGCGGGGTTCAAGTTAGCACACTTTCAG TGAATGAGGGTTTATTGGTTGCTGGTGGTTTTCAGGGAGAACTAATTTGCAAGGTTGTGGGAGA CCGTGATGTTAAGTTCTGCACAAGGACAACTTTAAGCGACAATGCTATCACAAATGCGATAGAT ATACACAGATCTGCAAGTGGAAGCTTGCGTGTTACCGTGTCCAACAATGATTGTGGTGTTCGTG AATTTGACATGGAAACATTTCAGCTCTTGAACCACTTCAGTTATAACTGGCCAGTAAATCACAC ATCTGTGAGCCCTGATAGGAAACTTCTGGCAGTAGTTGGAGATGATCGGGATGCTCTTCTTGTT GATTCAAGAAATGGAAAG
Genomic sequence	CTCACTAGGATAACTGATACATCAGCAGCTGAAGCAAGAGCAGGAAAGGATATACAAGGTATAC CATGGGAGAGGTTACAAATAACCAGGAGCGATTACAGAAAAGCTAGGTTGGTACAGTACAAAAA CTACGAAAACTTCCCTCAATCAGGAGAGCTCATGGATAAGGTCTCTATTATCATGAAATTTTAT CTATCAATGTTTGTTTTTTTTGCTCTATGGATGTTCCAAATTCCTGAAAAAAAATGCATCTTAC ATTTTTCAGATATGCAAGCAAGTGGATAAGATCAGCAAGTATTATGAATTTCACTACAACACTA GATTAGTGAAGCCATCAATCCTCCACTTTCAGGTGAGTTGCATTCTTTCTTAGCTGACAAATAC TCCTTTTTATCAATCCTCCACTAGATTAATGCGGGATAAGCTATTTTTCTTAGCTGTTAGCATT AGTTGTGTATCATCGGAGTTGTTACACCTCATTTACTTGTCTTACGTATGTGGCCATGTCAATA AGAACTACAAAGATAAAAAATGTTGTATGATCATTAGGGAAAGGGAACCTTTAACAAATTGTGA AATTGGCCTCTAAACAAGAAAACTACTGTTCCAGAGCATAGAATTAGTTCAATTGTTTTGCAGG ATTCTGGTTCAGTTATGTTGGTAAAAAGGTTTTGGGATATTTCAAAGGGAATGCTGTAGTGGCT AAATACTTGGATGTTTTCATGGAACTGTTAAACACATGAAATCATGGCTTACACAATCTTGCCA GTGAAAAATTAAGTTTAAAGTTCTTCATACAAGCGAATTTTGAACTATGACTGGATATAATCAA TGATGCAAACTTAAACACTTTTGCCTTGATGTCTTCATTATTATGAGGTCCATTCTTCTTTATA GCAGCTATCTGAATTTGTCTTGTCATATGAGTCCCAAGGCTGCTCAGTACTGACGAACTGCTTC TGTAGCTTAGGAATTTGTTATGGGCAACGTCGAAGCATGATGTCTACTTCATGTCAAATTCCAC AGTAGGCCACTGGTCATCATTGTCTCACAATCTATCAGAGGTTCTTGATTTCTCCGGGCATGTT GCTCCTGCGCAGGTTTTCTTCTTTTTCATTTCCTGCTTGTGTTTATTTGAACTAAAGATCTTTT TTTTATTAGTGATGTTTCTCCCAAGTTCAATTACTCTTGTTTTTTTATGTAAAATTATTCTGAA ATTAATGTTGTCACACAGAAACACCCTGGCAGTTTACTGGAAGGGTTTAGCGGGGTTCAAGTTA GCACACTTTCAGTGAATGAGGGTTTATTGGTTGCTGGTGGTTTTCAGGGAGAACTAATTTGCAA GGTAAGGTGCTGTTTCCCCTACTTTTGCTTTATAATAAGTACCTGCTTTAATGAAAAAAAAGCA AGCCATGAGTATCATCAGGCTTACATGCTCAGTATTTGCCAGTCTTGCTACAGGTTTGGGGATC CTTTACCTTTTCTTAATAAAAGAGGCAACCATGAATATTGTTTTTTTAAATAGAAAAGGCAAAC CTTAAATATCAGGTTTACGTGCTCAATATTTTTTATCTTTGTACAGGTTGTGGGAGACCGTGAT GTTAAGTTCTGCACAAGGACAACTTTAAGCGACAATGCTATCACAAATGCGATAGATATACACA GATCTGCAAGGTAAAAATATACCAGCTTAAATCTTTGGCTGAAGATGTACCTATCATTACAGAA ATCTAAAGCCCTAAAATTGTCCATGTAGTGGAAGCTTGCGTGTTACCGTGTCCAACAATGATTG TGGTGTTCGTGAATTTGACATGGAAACATTTCAGCTCTTGAACCACTTCAGTTATAACTGGCCA GTAAATGTAAGTCATCTCTCTTCAATATCCACACAACGCTTTTATGTCCAGCCATCCTTGTTTG ACTTCCTTACTACTCCTATGCAGCACACATCTGTGAGCCCTGATAGGAAACTTCTGGCAGTAGT TGGAGATGATCGGGATGCTCTTCTTGTTGATTCAAGAAATGGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_016714 						
					
						PMCS
						0.444741675

Conservation Information
Conserved circRNAs	osi_circ_016714
PMCS	0.444741675

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3634700-3636566(+)
						
						Potential amino acid sequence
						
							MDKICKQVDKISKYYEFHYNTRLVKPSILHFQLRNLLWATSKHDVYFMSNSTVGHWSSLSHNLS
EVLDFSGHVAPAQKHPGSLLEGFSGVQVSTLSVNEGLLVAGGFQGELICKVVGDRDVKFCTRTT
LSDNAITNAIDIHRSASGSLRVTVSNNDCGVREFDMETFQLLNHFSYNWPVNHTSVSPDRKLLA
VVGDDRDALLVDSRNGKLTRITDTSAAEARAGKDIQGIPWERLQITRSDYRKARLVQYKNYENF
PQSGELMDKICKQVDKISKYYEFHYNTRLVKPSILHFQLRNLLWATSKHDVYFMSNSTVGHWSS
LSHNLSEVLDFSGHVAPAQKHPGSLLEGFSGVQVSTLSVNEGLLVAGGFQGELICKVVGDRDVK
FCTRTTLSDNAITNAIDIHRSASGSLRVTVSNNDCGVREFDMETFQLLNHFSYNWPVNHTSVSP
DRKLLAVVGDDRDALLVDSRNGKLTRITDTSAAEARAGKDIQGIPWERLQITRSDYRKARLVQY
KNYENFPQSGELMDKICKQVDKISKYYEFHYNTRLVKPSILHFQLRNLLWATSKHDVYFMSNST
VGHWSSLSHNLSEVLDFSGHVAPAQKHPGSLLEGFSGVQVSTLSVNEGLLVAGGFQGELICKVV
GDRDVKFCTRTTLSDNAITNAIDIHRSASGSLRVTVSNNDCGVREFDMETFQLLNHFSYNWPVN
HTSVSPDRKLLAVVGDDRDALLVDSRNGKLTRITDTSAAEARAGKDIQGIPWERLQITRSDYRK
ARLVQYKNYENFPQSGELMDKICKQVDKISKYYEFHYNTRLVKPSILHFQLRNLLWATSKHDVY
FMSNSTVGHWSSLSHNLSEVLDFSGHVAPAQKHPGSLLEGFSGVQVSTLSVNEGLLVAGGFQGE
LICKVVGDRDVKFCTRTTLSDNAITNAIDIHRSASGSLRVTVSNNDCGVREFDMETFQLLNHFS
YNWPVNHTSVSPDRKLLAVVGDDRDALLVDSRNGK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3634700-3636566(+)
Potential amino acid sequence	MDKICKQVDKISKYYEFHYNTRLVKPSILHFQLRNLLWATSKHDVYFMSNSTVGHWSSLSHNLS EVLDFSGHVAPAQKHPGSLLEGFSGVQVSTLSVNEGLLVAGGFQGELICKVVGDRDVKFCTRTT LSDNAITNAIDIHRSASGSLRVTVSNNDCGVREFDMETFQLLNHFSYNWPVNHTSVSPDRKLLA VVGDDRDALLVDSRNGKLTRITDTSAAEARAGKDIQGIPWERLQITRSDYRKARLVQYKNYENF PQSGELMDKICKQVDKISKYYEFHYNTRLVKPSILHFQLRNLLWATSKHDVYFMSNSTVGHWSS LSHNLSEVLDFSGHVAPAQKHPGSLLEGFSGVQVSTLSVNEGLLVAGGFQGELICKVVGDRDVK FCTRTTLSDNAITNAIDIHRSASGSLRVTVSNNDCGVREFDMETFQLLNHFSYNWPVNHTSVSP DRKLLAVVGDDRDALLVDSRNGKLTRITDTSAAEARAGKDIQGIPWERLQITRSDYRKARLVQY KNYENFPQSGELMDKICKQVDKISKYYEFHYNTRLVKPSILHFQLRNLLWATSKHDVYFMSNST VGHWSSLSHNLSEVLDFSGHVAPAQKHPGSLLEGFSGVQVSTLSVNEGLLVAGGFQGELICKVV GDRDVKFCTRTTLSDNAITNAIDIHRSASGSLRVTVSNNDCGVREFDMETFQLLNHFSYNWPVN HTSVSPDRKLLAVVGDDRDALLVDSRNGKLTRITDTSAAEARAGKDIQGIPWERLQITRSDYRK ARLVQYKNYENFPQSGELMDKICKQVDKISKYYEFHYNTRLVKPSILHFQLRNLLWATSKHDVY FMSNSTVGHWSSLSHNLSEVLDFSGHVAPAQKHPGSLLEGFSGVQVSTLSVNEGLLVAGGFQGE LICKVVGDRDVKFCTRTTLSDNAITNAIDIHRSASGSLRVTVSNNDCGVREFDMETFQLLNHFS YNWPVNHTSVSPDRKLLAVVGDDRDALLVDSRNGK(+)
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 Os06g0171900_circ_g.3

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