Plant Circular RNA Database

Detail information of Os03g0254700_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os03g0254700_circ_g.3
					
						ID in PlantcircBase
						osa_circ_018900
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 8168177-8170175  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os03g0254700						
					
						Parent gene annotation
						
							WD40 repeat-like domain containing protein. (Os03t0254700-01);Si
milar to predicted protein. (Os03t0254700-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0254700_circ_g.4 Os03g0254700_circ_g.5 Os03g0254700_circ_g.6 Os03g0254700_circ_g.7 Os03g0254700_circ_g.8 Os03g0254700_circ_g.9 Os03g0254700_circ_g.10 Os03g0254700_circ_g.11 Os03g0254700_circ_g.12 						
					
						Support reads
						14
					
						Tissues
						root, 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  
						
							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
						Os03t0254700-02:2
Os03t0254700-01:4

General Information
CircRNA Name	Os03g0254700_circ_g.3
ID in PlantcircBase	osa_circ_018900
Alias	NA
Organism	Oryza sativa
Position	chr3: 8168177-8170175 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os03g0254700
Parent gene annotation	WD40 repeat-like domain containing protein. (Os03t0254700-01);Si milar to predicted protein. (Os03t0254700-02)
Parent gene strand	-
Alternative splicing	Os03g0254700_circ_g.4 Os03g0254700_circ_g.5 Os03g0254700_circ_g.6 Os03g0254700_circ_g.7 Os03g0254700_circ_g.8 Os03g0254700_circ_g.9 Os03g0254700_circ_g.10 Os03g0254700_circ_g.11 Os03g0254700_circ_g.12
Support reads	14
Tissues	root, 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	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	Os03t0254700-02:2 Os03t0254700-01:4

			
						 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  
						
							GTGCAGTTATTGCCGGTGGAGCAGCATTTCCTGAACTAGTCCCGGCAGCAGCAGCTGACGCCGC
CGCAGCAGCAGCAGCAGTCAATGGATTCATTAGGGGcttaaaagtcatcatgttgaacagagat
attttccctccagatgcagacatgacatatgaatcattctttgacaaagcaaagcaatggacag
cttcttca

									
								

					

						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: 537
Transcript exons: 8168177-8168353,8168486-8168596,8169822-8169968,8170074-
8170175
CTTAAAAGTCATCATGTTGAACAGAGATATTTTCCCTCCAGATGCAGACATGACATATGAATCA
TTCTTTGACAAAGCAAAGCAATGGACAGCTTCTTCAGGGTTGTCAGTTATGTCATTAGTCATGA
GGATGCCGCTTGGAGGTTGCCATAATTGAGGAGAAACACTTGCAGTAGCCTTTCCACTTGAGTT
TCGGTCATTGCGAGGCCATTTCCAGAGCAGATGAACAGCATTTGAAGCTAAAGCCAAGATAGCG
ACACCAGAATTTGTGTAAATAAGTCTTGAAATCTTGCTTGTCCTCATATTATCTGTTAATTTCA
ATGATCTGCACTGACTTGACTCGGTTATCTCCATAAGTTTCCAGACTTTTGATTTATCCAATGG
CTCATCAGCTATTCTAGGCTTTACATCAACCAAGCTTCGGCTATCCCCATTCAGTGCAGTTATT
GCCGGTGGAGCAGCATTTCCTGAACTAGTCCCGGCAGCAGCAGCTGACGCCGCCGCAGCAGCAG
CAGCAGTCAATGGATTCATTAGGGG
						
					

						Genomic sequence
						
							CTTAAAAGTCATCATGTTGAACAGAGATATTTTCCCTCCAGATGCAGACATGACATATGAATCA
TTCTTTGACAAAGCAAAGCAATGGACAGCTTCTTCAGGGTTGTCAGTTATGTCATTAGTCATGA
GGATGCCGCTTGGAGGTTGCCATAATTGAGGAGAAACACTTGCAGTAGCCTAGAAGAGTCAATA
GCAAACATAAAAAGTTAGTAACAATCATATGCACAAATTGCTTGCCCCTGGACCTGGTATACAG
AGCAGGTAGGTAAAACTGAGCATATTTATGTGCGTAAATAATCCAGATTTAACCTTTCCACTTG
AGTTTCGGTCATTGCGAGGCCATTTCCAGAGCAGATGAACAGCATTTGAAGCTAAAGCCAAGAT
AGCGACACCAGAATTTGTGTAAATAAGTCTTGAAATCTGCAGTTCAAAACAAATAAGATCTATG
GAAACCCTTACAGATAAAAACCAGCAGTTGGTACTTGGATGTGGATCAGAAGAATCTCAAGAAT
GCTAGTCAAAATATGAGGTGACAAAACATTTCATTCTATTGGGCAAGCATCATTCACGGAAACA
GTCAGTGGCTTTAGTTCAATTAACAATCATACTCTGCAATAGGGGTGGGCACTCGGTTTTTCGG
TTTAATAGGGTCGGTCTTTTAGGTTTTTTATATAACTCGGTTTATGTAAAATACTAACCGACGG
TAGCTATGGAAAAATAAAAACTGAGCTTTCCAAAACTGATTAATGTCAGTTCGGGTTTATCAGC
TTTCGGTTTTTACCGAAGAATGCCGCGCTCAACGAGGACCTACGCACACGCAGCCATGGAGCTC
GCTCGATGATGACGACATGCCTCTGATCTTCCACCGTCCAACCACTAATCACCAAAGCTGCTTA
ATCGTCCAGCACAAGCTCCAGGAGCGCTAGTCGCCAACCCCTGCTGCACTCGGCCGCGACGGCG
AGCAGCACGACCACACGAATCCCACACGACCCCACGCACAAATTAGGGATATGGGGAAAAGTTA
ATGGGCCTTGTGTAGTTGGGCCAGGAGGGAGACACACACAGATCGGTTTTCTCGGTAGTTCGGT
TTATGGCAGATGAAGACTGAAGAAAAAACCGCACACCAAATGATGTAAAAAATCAAACCGAGCA
AGCAAGCAGCCGAAGACCGAAGAAACCACCAATTCGGCTCGGTTCGGTTCGGTCTACGGTTTTC
GGTGTTTTTATGCCCACCCCTACTCTGCAATAAATCAAATAATATTAGCTATGGAAACTTGTCA
AAACATATGGTGTTTGTTCTATACACACTAAGGCTGTGTTCGGCAGACACAGTTGGGAACTAAT
CCTTGGTGCACGCAAAACAAAGCAGCTCATTAGCGTATGATTAATTAAGTATTAGCTTTTTAAA
AAAAATGGATTAATATGATTTTTTGAAGCAACTTTCCTATTGAAAACTTTTGTAAAAAAAATGC
ACCGTTTAATAGTTTGAAAAGCGTGTGCACGGAAAAAGAGGGAGATGAGTTGGGAAAGGAGAGG
AAAGAACTCAGCCTAAAAAATTACTTAATAATGTACTACAAAGTATTAATTTTATAGAACCACT
GAGACAGTTATACTGCAGATTGCAACAAGAGGGATAAAATATCACCTTGCTTGTCCTCATATTA
TCTGTTAATTTCAATGATCTGCACTGACTTGACTCGGTTATCTCCATAAGTTTCCAGACTTTTG
ATTTATCCAATGGCTCATCAGCTATTCTAGGCTTTACATCAACCAAGCTTCGGCTATCCCCATT
CTGTAGAATTTTTCCAAGAATGTACAAGTTAGTTGGGTCACTATAGAAGGTTTTCTGATAGAAA
GAGAAAGATCAATAGAAAAGGAATTGTGAATATGGTCAAACCAGTGCAGTTATTGCCGGTGGAG
CAGCATTTCCTGAACTAGTCCCGGCAGCAGCAGCTGACGCCGCCGCAGCAGCAGCAGCAGTCAA
TGGATTCATTAGGGG
						
					

			
		

Sequences
Splice junction sequence	GTGCAGTTATTGCCGGTGGAGCAGCATTTCCTGAACTAGTCCCGGCAGCAGCAGCTGACGCCGC CGCAGCAGCAGCAGCAGTCAATGGATTCATTAGGGGcttaaaagtcatcatgttgaacagagat attttccctccagatgcagacatgacatatgaatcattctttgacaaagcaaagcaatggacag cttcttca
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: 537 Transcript exons: 8168177-8168353,8168486-8168596,8169822-8169968,8170074- 8170175 CTTAAAAGTCATCATGTTGAACAGAGATATTTTCCCTCCAGATGCAGACATGACATATGAATCA TTCTTTGACAAAGCAAAGCAATGGACAGCTTCTTCAGGGTTGTCAGTTATGTCATTAGTCATGA GGATGCCGCTTGGAGGTTGCCATAATTGAGGAGAAACACTTGCAGTAGCCTTTCCACTTGAGTT TCGGTCATTGCGAGGCCATTTCCAGAGCAGATGAACAGCATTTGAAGCTAAAGCCAAGATAGCG ACACCAGAATTTGTGTAAATAAGTCTTGAAATCTTGCTTGTCCTCATATTATCTGTTAATTTCA ATGATCTGCACTGACTTGACTCGGTTATCTCCATAAGTTTCCAGACTTTTGATTTATCCAATGG CTCATCAGCTATTCTAGGCTTTACATCAACCAAGCTTCGGCTATCCCCATTCAGTGCAGTTATT GCCGGTGGAGCAGCATTTCCTGAACTAGTCCCGGCAGCAGCAGCTGACGCCGCCGCAGCAGCAG CAGCAGTCAATGGATTCATTAGGGG
Genomic sequence	CTTAAAAGTCATCATGTTGAACAGAGATATTTTCCCTCCAGATGCAGACATGACATATGAATCA TTCTTTGACAAAGCAAAGCAATGGACAGCTTCTTCAGGGTTGTCAGTTATGTCATTAGTCATGA GGATGCCGCTTGGAGGTTGCCATAATTGAGGAGAAACACTTGCAGTAGCCTAGAAGAGTCAATA GCAAACATAAAAAGTTAGTAACAATCATATGCACAAATTGCTTGCCCCTGGACCTGGTATACAG AGCAGGTAGGTAAAACTGAGCATATTTATGTGCGTAAATAATCCAGATTTAACCTTTCCACTTG AGTTTCGGTCATTGCGAGGCCATTTCCAGAGCAGATGAACAGCATTTGAAGCTAAAGCCAAGAT AGCGACACCAGAATTTGTGTAAATAAGTCTTGAAATCTGCAGTTCAAAACAAATAAGATCTATG GAAACCCTTACAGATAAAAACCAGCAGTTGGTACTTGGATGTGGATCAGAAGAATCTCAAGAAT GCTAGTCAAAATATGAGGTGACAAAACATTTCATTCTATTGGGCAAGCATCATTCACGGAAACA GTCAGTGGCTTTAGTTCAATTAACAATCATACTCTGCAATAGGGGTGGGCACTCGGTTTTTCGG TTTAATAGGGTCGGTCTTTTAGGTTTTTTATATAACTCGGTTTATGTAAAATACTAACCGACGG TAGCTATGGAAAAATAAAAACTGAGCTTTCCAAAACTGATTAATGTCAGTTCGGGTTTATCAGC TTTCGGTTTTTACCGAAGAATGCCGCGCTCAACGAGGACCTACGCACACGCAGCCATGGAGCTC GCTCGATGATGACGACATGCCTCTGATCTTCCACCGTCCAACCACTAATCACCAAAGCTGCTTA ATCGTCCAGCACAAGCTCCAGGAGCGCTAGTCGCCAACCCCTGCTGCACTCGGCCGCGACGGCG AGCAGCACGACCACACGAATCCCACACGACCCCACGCACAAATTAGGGATATGGGGAAAAGTTA ATGGGCCTTGTGTAGTTGGGCCAGGAGGGAGACACACACAGATCGGTTTTCTCGGTAGTTCGGT TTATGGCAGATGAAGACTGAAGAAAAAACCGCACACCAAATGATGTAAAAAATCAAACCGAGCA AGCAAGCAGCCGAAGACCGAAGAAACCACCAATTCGGCTCGGTTCGGTTCGGTCTACGGTTTTC GGTGTTTTTATGCCCACCCCTACTCTGCAATAAATCAAATAATATTAGCTATGGAAACTTGTCA AAACATATGGTGTTTGTTCTATACACACTAAGGCTGTGTTCGGCAGACACAGTTGGGAACTAAT CCTTGGTGCACGCAAAACAAAGCAGCTCATTAGCGTATGATTAATTAAGTATTAGCTTTTTAAA AAAAATGGATTAATATGATTTTTTGAAGCAACTTTCCTATTGAAAACTTTTGTAAAAAAAATGC ACCGTTTAATAGTTTGAAAAGCGTGTGCACGGAAAAAGAGGGAGATGAGTTGGGAAAGGAGAGG AAAGAACTCAGCCTAAAAAATTACTTAATAATGTACTACAAAGTATTAATTTTATAGAACCACT GAGACAGTTATACTGCAGATTGCAACAAGAGGGATAAAATATCACCTTGCTTGTCCTCATATTA TCTGTTAATTTCAATGATCTGCACTGACTTGACTCGGTTATCTCCATAAGTTTCCAGACTTTTG ATTTATCCAATGGCTCATCAGCTATTCTAGGCTTTACATCAACCAAGCTTCGGCTATCCCCATT CTGTAGAATTTTTCCAAGAATGTACAAGTTAGTTGGGTCACTATAGAAGGTTTTCTGATAGAAA GAGAAAGATCAATAGAAAAGGAATTGTGAATATGGTCAAACCAGTGCAGTTATTGCCGGTGGAG CAGCATTTCCTGAACTAGTCCCGGCAGCAGCAGCTGACGCCGCCGCAGCAGCAGCAGCAGTCAA TGGATTCATTAGGGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.246379194

Conservation Information
Conserved circRNAs	NA
PMCS	0.246379194

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8170171-8168179(-)
						
						Potential amino acid sequence
						
							MNPLTAAAAAAASAAAAGTSSGNAAPPAITALNGDSRSLVDVKPRIADEPLDKSKVWKLMEITE
SSQCRSLKLTDNMRTSKISRLIYTNSGVAILALASNAVHLLWKWPRNDRNSSGKATASVSPQLW
QPPSGILMTNDITDNPEEAVHCFALSKNDSYVMSASGGKISLFNMMTFKPLMNPLTAAAAAAAS
AAAAGTSSGNAAPPAITALNGDSRSLVDVKPRIADEPLDKSKVWKLMEITESSQCRSLKLTDNM
RTSKISRLIYTNSGVAILALASNAVHLLWKWPRNDRNSSGKATASVSPQLWQPPSGILMTNDIT
DNPEEAVHCFALSKNDSYVMSASGGKISLFNMMTFKPLMNPLTAAAAAAASAAAAGTSSGNAAP
PAITALNGDSRSLVDVKPRIADEPLDKSKVWKLMEITESSQCRSLKLTDNMRTSKISRLIYTNS
GVAILALASNAVHLLWKWPRNDRNSSGKATASVSPQLWQPPSGILMTNDITDNPEEAVHCFALS
KNDSYVMSASGGKISLFNMMTFKPLMNPLTAAAAAAASAAAAGTSSGNAAPPAITALNGDSRSL
VDVKPRIADEPLDKSKVWKLMEITESSQCRSLKLTDNMRTSKISRLIYTNSGVAILALASNAVH
LLWKWPRNDRNSSGKATASVSPQLWQPPSGILMTNDITDNPEEAVHCFALSKNDSYVMSASGGK
ISLFNMMTFK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8170171-8168179(-)
Potential amino acid sequence	MNPLTAAAAAAASAAAAGTSSGNAAPPAITALNGDSRSLVDVKPRIADEPLDKSKVWKLMEITE SSQCRSLKLTDNMRTSKISRLIYTNSGVAILALASNAVHLLWKWPRNDRNSSGKATASVSPQLW QPPSGILMTNDITDNPEEAVHCFALSKNDSYVMSASGGKISLFNMMTFKPLMNPLTAAAAAAAS AAAAGTSSGNAAPPAITALNGDSRSLVDVKPRIADEPLDKSKVWKLMEITESSQCRSLKLTDNM RTSKISRLIYTNSGVAILALASNAVHLLWKWPRNDRNSSGKATASVSPQLWQPPSGILMTNDIT DNPEEAVHCFALSKNDSYVMSASGGKISLFNMMTFKPLMNPLTAAAAAAASAAAAGTSSGNAAP PAITALNGDSRSLVDVKPRIADEPLDKSKVWKLMEITESSQCRSLKLTDNMRTSKISRLIYTNS GVAILALASNAVHLLWKWPRNDRNSSGKATASVSPQLWQPPSGILMTNDITDNPEEAVHCFALS KNDSYVMSASGGKISLFNMMTFKPLMNPLTAAAAAAASAAAAGTSSGNAAPPAITALNGDSRSL VDVKPRIADEPLDKSKVWKLMEITESSQCRSLKLTDNMRTSKISRLIYTNSGVAILALASNAVH LLWKWPRNDRNSSGKATASVSPQLWQPPSGILMTNDITDNPEEAVHCFALSKNDSYVMSASGGK ISLFNMMTFK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0254700_circ_g.3

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