Plant Circular RNA Database

Detail information of Os11g0533100_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os11g0533100_circ_g.3
					
						ID in PlantcircBase
						osa_circ_009491
					
						Alias
						Os11circ06428
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 19425868-19426875  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os11g0533100						
					
						Parent gene annotation
						
							Similar to CarD-like transcriptional regulator family protein, e
xpressed. (Os11t0533100-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os11g0533100_circ_g.1 Os11g0533100_circ_g.2 Os11g0533100_circ_g.4 Os11g0533100_circ_g.5 Os11g0533100_circ_g.6 Os11g0533100_circ_g.7 						
					
						Support reads
						2/1
					
						Tissues
						leaf/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  
						
							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
						Os11t0533100-01:3

General Information
CircRNA Name	Os11g0533100_circ_g.3
ID in PlantcircBase	osa_circ_009491
Alias	Os11circ06428
Organism	Oryza sativa
Position	chr11: 19425868-19426875 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os11g0533100
Parent gene annotation	Similar to CarD-like transcriptional regulator family protein, e xpressed. (Os11t0533100-01)
Parent gene strand	-
Alternative splicing	Os11g0533100_circ_g.1 Os11g0533100_circ_g.2 Os11g0533100_circ_g.4 Os11g0533100_circ_g.5 Os11g0533100_circ_g.6 Os11g0533100_circ_g.7
Support reads	2/1
Tissues	leaf/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	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	Os11t0533100-01:3

			
						 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  
						
							CGAGATACAAAGTACGTGGAATGGGTGTTGCAGACAGTGTGAGAACATCAATAGAAGCCTTGTA
TGATGCAATCTTCTCCTTTTGTTGGACACCAAACTTctttccatgagcaacagccattggaaca
tctggaagagaatccttgagaaattgcagcacatcatctattgctgtcgcatgatgaaataaat
tattaaac

						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: 336
Transcript exons: 19425868-19425938,19426219-19426358,19426751-19426875
CTTTCCATGAGCAACAGCCATTGGAACATCTGGAAGAGAATCCTTGAGAAATTGCAGCACATCA
TCTATTGCTTTTATTCGAGGAACAACATAGAAAACTTGACCACCACGTGCCAACTCAAACTTAA
TAGCTGATAGAGCCCTTTCTTTGCTAAATCCTGACACGTAGGTCCTTACAGCAACTCTTTCTGG
AGGCGGCGTAGACATTAAACTGGCATCACGGAAACCTGTCAACGCGAGATACAAAGTACGTGGA
ATGGGTGTTGCAGACAGTGTGAGAACATCAATAGAAGCCTTGTATGATGCAATCTTCTCCTTTT
GTTGGACACCAAACTT
						
						Genomic sequence
						
							CTTTCCATGAGCAACAGCCATTGGAACATCTGGAAGAGAATCCTTGAGAAATTGCAGCACATCA
TCTATTGCTGTCGCATGATGAAATAAATTATTAAACATAAATGCAGATTTGCAATCTAAATTAT
TGAATGACTTTGCATGATATTGCAGCTTCTATATGGACAGTATAGATTGTTAGTGAACGCATCC
AGCAATAGGCTAATTGTTAGAACAATCTGCAATCGCAAGTCCAACTTGCTGAGTACTAAACTGA
GATTGGGAATATTGAGAAAAAAATTGTTTTCAGGTTCATGCATCACAAGTATATGCTGTGAACA
ATAAGTCATCTGAAGATAACAAAGTTTCCACCTTTTATTCGAGGAACAACATAGAAAACTTGAC
CACCACGTGCCAACTCAAACTTAATAGCTGATAGAGCCCTTTCTTTGCTAAATCCTGACACGTA
GGTCCTTACAGCAACTCTTTCTGGAGGCGGCGTAGACATTAAACTGAAATCATAATACATATGC
TTGTGTCATGGAAAAAAATGAAAACAATTCCGAGATTAAATGCATCCAAGGTATTGGAGTTATG
AAGAATGAATTAAATATAGAGTCAGCAGAATAGCGCTATGATCACATTAAATGCACGAATTATC
TCAAGAAAACAGTAGTAACTATTGCAAATGTAATAAAATGGCTCAAGTGAATCCCCTAAAAAAA
CTCTAGTGATTACTCGTAACCATTGTCCACAAATTATCTCAAGAAAACAGTGGTAATAAATTAG
CAATATCTCGTAATAAATTGTGGACAATGGTTACGAGTAATAAATTAGCAATATCTCGTCCAAT
ATCTCGTCCAACAGAAAACAGAAGAAAAAAATAGTATTGTTGCCATCTTACCTGGCATCACGGA
AACCTGTCAACGCGAGATACAAAGTACGTGGAATGGGTGTTGCAGACAGTGTGAGAACATCAAT
AGAAGCCTTGTATGATGCAATCTTCTCCTTTTGTTGGACACCAAACTT

Sequences
Splice junction sequence	CGAGATACAAAGTACGTGGAATGGGTGTTGCAGACAGTGTGAGAACATCAATAGAAGCCTTGTA TGATGCAATCTTCTCCTTTTGTTGGACACCAAACTTctttccatgagcaacagccattggaaca tctggaagagaatccttgagaaattgcagcacatcatctattgctgtcgcatgatgaaataaat tattaaac
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: 336 Transcript exons: 19425868-19425938,19426219-19426358,19426751-19426875 CTTTCCATGAGCAACAGCCATTGGAACATCTGGAAGAGAATCCTTGAGAAATTGCAGCACATCA TCTATTGCTTTTATTCGAGGAACAACATAGAAAACTTGACCACCACGTGCCAACTCAAACTTAA TAGCTGATAGAGCCCTTTCTTTGCTAAATCCTGACACGTAGGTCCTTACAGCAACTCTTTCTGG AGGCGGCGTAGACATTAAACTGGCATCACGGAAACCTGTCAACGCGAGATACAAAGTACGTGGA ATGGGTGTTGCAGACAGTGTGAGAACATCAATAGAAGCCTTGTATGATGCAATCTTCTCCTTTT GTTGGACACCAAACTT
Genomic sequence	CTTTCCATGAGCAACAGCCATTGGAACATCTGGAAGAGAATCCTTGAGAAATTGCAGCACATCA TCTATTGCTGTCGCATGATGAAATAAATTATTAAACATAAATGCAGATTTGCAATCTAAATTAT TGAATGACTTTGCATGATATTGCAGCTTCTATATGGACAGTATAGATTGTTAGTGAACGCATCC AGCAATAGGCTAATTGTTAGAACAATCTGCAATCGCAAGTCCAACTTGCTGAGTACTAAACTGA GATTGGGAATATTGAGAAAAAAATTGTTTTCAGGTTCATGCATCACAAGTATATGCTGTGAACA ATAAGTCATCTGAAGATAACAAAGTTTCCACCTTTTATTCGAGGAACAACATAGAAAACTTGAC CACCACGTGCCAACTCAAACTTAATAGCTGATAGAGCCCTTTCTTTGCTAAATCCTGACACGTA GGTCCTTACAGCAACTCTTTCTGGAGGCGGCGTAGACATTAAACTGAAATCATAATACATATGC TTGTGTCATGGAAAAAAATGAAAACAATTCCGAGATTAAATGCATCCAAGGTATTGGAGTTATG AAGAATGAATTAAATATAGAGTCAGCAGAATAGCGCTATGATCACATTAAATGCACGAATTATC TCAAGAAAACAGTAGTAACTATTGCAAATGTAATAAAATGGCTCAAGTGAATCCCCTAAAAAAA CTCTAGTGATTACTCGTAACCATTGTCCACAAATTATCTCAAGAAAACAGTGGTAATAAATTAG CAATATCTCGTAATAAATTGTGGACAATGGTTACGAGTAATAAATTAGCAATATCTCGTCCAAT ATCTCGTCCAACAGAAAACAGAAGAAAAAAATAGTATTGTTGCCATCTTACCTGGCATCACGGA AACCTGTCAACGCGAGATACAAAGTACGTGGAATGGGTGTTGCAGACAGTGTGAGAACATCAAT AGAAGCCTTGTATGATGCAATCTTCTCCTTTTGTTGGACACCAAACTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_003172* osi_circ_009077 						
					
						PMCS
						0.246153423

Conservation Information
Conserved circRNAs	osi_circ_003172* osi_circ_009077
PMCS	0.246153423

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							19426797-19425874(+)
19426840-19425911(+)
19426356-19425870(-)
19425934-19426772(-)
						
						Potential amino acid sequence
						
							MGVADSVRTSIEALYDAIFSFCWTPNFFP*(+)
MMQSSPFVGHQTSFHEQQPLEHLEENP*(+)
MSTPPPERVAVRTYVSGFSKERALSAIKFELARGGQVFYVVPRIKAIDDVLQFLKDSLPDVPMA
VAHGKKFGVQQKEKIASYKASIDVLTLSATPIPRTLYLALTGFRDASLMSTPPPERVAVRTYVS
GFSKERALSAIKFELARGGQVFYVVPRIKAIDDVLQFLKDSLPDVPMAVAHGKKFGVQQKEKIA
SYKASIDVLTLSATPIPRTLYLALTGFRDASLMSTPPPERVAVRTYVSGFSKERALSAIKFELA
RGGQVFYVVPRIKAIDDVLQFLKDSLPDVPMAVAHGKKFGVQQKEKIASYKASIDVLTLSATPI
PRTLYLALTGFRDASLMSTPPPERVAVRTYVSGFSKERALSAIKFELARGGQVFYVVPRIKAID
DVLQFLKDSLPDVPMAVAHGK(-)
MMCCNFSRILFQMFQWLLLMERSLVSNKRRRLHHTRLLLMFSHCLQHPFHVLCISR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	19426797-19425874(+) 19426840-19425911(+) 19426356-19425870(-) 19425934-19426772(-)
Potential amino acid sequence	MGVADSVRTSIEALYDAIFSFCWTPNFFP(+) MMQSSPFVGHQTSFHEQQPLEHLEENP(+) MSTPPPERVAVRTYVSGFSKERALSAIKFELARGGQVFYVVPRIKAIDDVLQFLKDSLPDVPMA VAHGKKFGVQQKEKIASYKASIDVLTLSATPIPRTLYLALTGFRDASLMSTPPPERVAVRTYVS GFSKERALSAIKFELARGGQVFYVVPRIKAIDDVLQFLKDSLPDVPMAVAHGKKFGVQQKEKIA SYKASIDVLTLSATPIPRTLYLALTGFRDASLMSTPPPERVAVRTYVSGFSKERALSAIKFELA RGGQVFYVVPRIKAIDDVLQFLKDSLPDVPMAVAHGKKFGVQQKEKIASYKASIDVLTLSATPI PRTLYLALTGFRDASLMSTPPPERVAVRTYVSGFSKERALSAIKFELARGGQVFYVVPRIKAID DVLQFLKDSLPDVPMAVAHGK(-) MMCCNFSRILFQMFQWLLLMERSLVSNKRRRLHHTRLLLMFSHCLQHPFHVLCISR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os11g0533100_circ_g.3

Address

Any questions?

Supported by