Plant Circular RNA Database

Detail information of Os01g0924300_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os01g0924300_circ_g.2
					
						ID in PlantcircBase
						osa_circ_005577
					
						Alias
						Os_ciR2107
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 40464492-40465446  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os01g0924300						
					
						Parent gene annotation
						
							WD40 repeat-like domain containing protein. (Os01t0924300-01);Si
milar to periodic tryptophan protein 1. (Os01t0924300-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0924300_circ_g.1 						
					
						Support reads
						7/3
					
						Tissues
						root/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
						Os01t0924300-02:2
Os01t0924300-01:4

General Information
CircRNA Name	Os01g0924300_circ_g.2
ID in PlantcircBase	osa_circ_005577
Alias	Os_ciR2107
Organism	Oryza sativa
Position	chr1: 40464492-40465446 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os01g0924300
Parent gene annotation	WD40 repeat-like domain containing protein. (Os01t0924300-01);Si milar to periodic tryptophan protein 1. (Os01t0924300-02)
Parent gene strand	-
Alternative splicing	Os01g0924300_circ_g.1
Support reads	7/3
Tissues	root/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	Os01t0924300-02:2 Os01t0924300-01:4

			
						 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  
						
							GTATTATCACTTGAGTAGAGAACTAAACGCACCTCACCTCCTTGTTCCATGCAAGACCAAGCAC
AGAACTTCTATGACTTCCCTTCTTGTACTTTTTTGCcatgaaggagtgctcattatgcggatcc
caagctaagctttctacatctgcttcaacagaccatttattacaactctgtccaccatctttca
tgtcattc

						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: 339
Transcript exons: 40464492-40464590,40465044-40465118,40465197-40465293,40
465379-40465446
CATGAAGGAGTGCTCATTATGCGGATCCCAAGCTAAGCTTTCTACATCTGCTTCAACAGACCAT
TTATTACAACTCTGTCCACCATCTTTCATGTCATTCATGGCAACTGATTTATCGAACGATCCGC
TTAGAAGAACTTCAGGCGATTGTCGGCTCCAAGCAACAGATTGAACCTTGTCATCATGATGTTC
CAATGTGACTGCACATTTGCCAACAGATACATCCCAAATCTTAACAGTTTTGTCTGCACTTGCA
CTAGCTAGAACATTCCTCACCTCCTTGTTCCATGCAAGACCAAGCACAGAACTTCTATGACTTC
CCTTCTTGTACTTTTTTGC
						
						Genomic sequence
						
							CATGAAGGAGTGCTCATTATGCGGATCCCAAGCTAAGCTTTCTACATCTGCTTCAACAGACCAT
TTATTACAACTCTGTCCACCATCTTTCATGTCATTCTGTAATACAGCAGTAGCCATTGTGAGTT
TTCAGTTAATGTAAGTATACATAAGTTATCACAATAATGTGACAGCCTTCAACAGGATAATCGA
AATGAAACTATAACTTGGTCCTTTATATACCATGAGAGAAAGAAAATAAGGGCTTACAAGAAAA
TTCCTCTGAACCAAAAAAATATATATTGTACAATTAGCATGGCACAAGCATATTCAGTTCTCGA
TTTATCAGTTATCATCTAAATGCCTCTATCCAAGTACAGAACAAAACAAGATTATTAATTACAC
ATCCTTTTAATTATCACACTGCTTATAGTCTGGTCAGAAACAATATGATACATATAATGTAAGA
TAATTTTCTAAATAGCATCTAAAATTAAGAAGTACAACAGCAGCAGAACAAATTTCAGGAAACA
AATCAACAATAGAACTCATTATGATTAGTAGATCCATTACCATGGCAACTGATTTATCGAACGA
TCCGCTTAGAAGAACTTCAGGCGATTGTCGGCTCCAAGCAACAGATTGAACCTACATGCCAATG
TAAGGAAAAATCAAATGTCTCAGAAACAAAAATGCAGTAAGTAAACAAAAGTAGTAAACCATTA
CCTTGTCATCATGATGTTCCAATGTGACTGCACATTTGCCAACAGATACATCCCAAATCTTAAC
AGTTTTGTCTGCACTTGCACTAGCTAGAACATTCCTGTGGCTCATAAGAACAGCAAGTCGTTCA
TGATGGGGCCATTAAGAGAAGATGTATTATCACTTGAGTAGAGAACTAAACGCACCTCACCTCC
TTGTTCCATGCAAGACCAAGCACAGAACTTCTATGACTTCCCTTCTTGTACTTTTTTGC

Sequences
Splice junction sequence	GTATTATCACTTGAGTAGAGAACTAAACGCACCTCACCTCCTTGTTCCATGCAAGACCAAGCAC AGAACTTCTATGACTTCCCTTCTTGTACTTTTTTGCcatgaaggagtgctcattatgcggatcc caagctaagctttctacatctgcttcaacagaccatttattacaactctgtccaccatctttca tgtcattc
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: 339 Transcript exons: 40464492-40464590,40465044-40465118,40465197-40465293,40 465379-40465446 CATGAAGGAGTGCTCATTATGCGGATCCCAAGCTAAGCTTTCTACATCTGCTTCAACAGACCAT TTATTACAACTCTGTCCACCATCTTTCATGTCATTCATGGCAACTGATTTATCGAACGATCCGC TTAGAAGAACTTCAGGCGATTGTCGGCTCCAAGCAACAGATTGAACCTTGTCATCATGATGTTC CAATGTGACTGCACATTTGCCAACAGATACATCCCAAATCTTAACAGTTTTGTCTGCACTTGCA CTAGCTAGAACATTCCTCACCTCCTTGTTCCATGCAAGACCAAGCACAGAACTTCTATGACTTC CCTTCTTGTACTTTTTTGC
Genomic sequence	CATGAAGGAGTGCTCATTATGCGGATCCCAAGCTAAGCTTTCTACATCTGCTTCAACAGACCAT TTATTACAACTCTGTCCACCATCTTTCATGTCATTCTGTAATACAGCAGTAGCCATTGTGAGTT TTCAGTTAATGTAAGTATACATAAGTTATCACAATAATGTGACAGCCTTCAACAGGATAATCGA AATGAAACTATAACTTGGTCCTTTATATACCATGAGAGAAAGAAAATAAGGGCTTACAAGAAAA TTCCTCTGAACCAAAAAAATATATATTGTACAATTAGCATGGCACAAGCATATTCAGTTCTCGA TTTATCAGTTATCATCTAAATGCCTCTATCCAAGTACAGAACAAAACAAGATTATTAATTACAC ATCCTTTTAATTATCACACTGCTTATAGTCTGGTCAGAAACAATATGATACATATAATGTAAGA TAATTTTCTAAATAGCATCTAAAATTAAGAAGTACAACAGCAGCAGAACAAATTTCAGGAAACA AATCAACAATAGAACTCATTATGATTAGTAGATCCATTACCATGGCAACTGATTTATCGAACGA TCCGCTTAGAAGAACTTCAGGCGATTGTCGGCTCCAAGCAACAGATTGAACCTACATGCCAATG TAAGGAAAAATCAAATGTCTCAGAAACAAAAATGCAGTAAGTAAACAAAAGTAGTAAACCATTA CCTTGTCATCATGATGTTCCAATGTGACTGCACATTTGCCAACAGATACATCCCAAATCTTAAC AGTTTTGTCTGCACTTGCACTAGCTAGAACATTCCTGTGGCTCATAAGAACAGCAAGTCGTTCA TGATGGGGCCATTAAGAGAAGATGTATTATCACTTGAGTAGAGAACTAAACGCACCTCACCTCC TTGTTCCATGCAAGACCAAGCACAGAACTTCTATGACTTCCCTTCTTGTACTTTTTTGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002643* osi_circ_011128 						
					
						PMCS
						0.356750122

Conservation Information
Conserved circRNAs	osi_circ_002643* osi_circ_011128
PMCS	0.356750122

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							40465421-40464524(+)
40465048-40464494(-)
40464510-40465382(-)
						
						Potential amino acid sequence
						
							MTSLLVLFCHEGVLIMRIPS*(+)
MNDMKDGGQSCNKWSVEADVESLAWDPHNEHSFMAKKYKKGSHRSSVLGLAWNKEVRNVLASAS
ADKTVKIWDVSVGKCAVTLEHHDDKVQSVAWSRQSPEVLLSGSFDKSVAMNDMKDGGQSCNKWS
VEADVESLAWDPHNEHSFMAKKYKKGSHRSSVLGLAWNKEVRNVLASASADKTVKIWDVSVGKC
AVTLEHHDDKVQSVAWSRQSPEVLLSGSFDKSVAMNDMKDGGQSCNKWSVEADVESLAWDPHNE
HSFMAKKYKKGSHRSSVLGLAWNKEVRNVLASASADKTVKIWDVSVGKCAVTLEHHDDKVQSVA
WSRQSPEVLLSGSFDKSVAMNDMKDGGQSCNKWSVEADVESLAWDPHNEHSFM(-)
MSTPSWQKSTRREVIEVLCLVLHGTRR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	40465421-40464524(+) 40465048-40464494(-) 40464510-40465382(-)
Potential amino acid sequence	MTSLLVLFCHEGVLIMRIPS(+) MNDMKDGGQSCNKWSVEADVESLAWDPHNEHSFMAKKYKKGSHRSSVLGLAWNKEVRNVLASAS ADKTVKIWDVSVGKCAVTLEHHDDKVQSVAWSRQSPEVLLSGSFDKSVAMNDMKDGGQSCNKWS VEADVESLAWDPHNEHSFMAKKYKKGSHRSSVLGLAWNKEVRNVLASASADKTVKIWDVSVGKC AVTLEHHDDKVQSVAWSRQSPEVLLSGSFDKSVAMNDMKDGGQSCNKWSVEADVESLAWDPHNE HSFMAKKYKKGSHRSSVLGLAWNKEVRNVLASASADKTVKIWDVSVGKCAVTLEHHDDKVQSVA WSRQSPEVLLSGSFDKSVAMNDMKDGGQSCNKWSVEADVESLAWDPHNEHSFM(-) MSTPSWQKSTRREVIEVLCLVLHGTRR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os01g0924300_circ_g.2

Address

Any questions?

Supported by