Plant Circular RNA Database

Detail information of Os03g0355600_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os03g0355600_circ_g.4
					
						ID in PlantcircBase
						osa_circ_019868
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 13588998-13590276  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os03g0355600						
					
						Parent gene annotation
						
							Similar to Adapter-related protein complex 2 beta 1 subunit (Bet
a-adaptin) (Plasma membrane adaptor HA2/AP2 adaptin beta subunit
) (Clathrin assembly protein complex 2 beta large chain) (AP105B
) (Fragment). (Os03t0355600-01);Similar to predicted protein. (O
s03t0355600-02);Similar to predicted protein. (Os03t0355600-03);
Similar to predicted protein. (Os03t0355600-04)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0355600_circ_g.1 Os03g0355600_circ_g.2 Os03g0355600_circ_g.3 Os03g0355600_circ_g.5 Os03g0355600_circ_g.6 						
					
						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
						Os03t0355600-01:5
Os03t0355600-03:3
Os03t0355600-02:4

General Information
CircRNA Name	Os03g0355600_circ_g.4
ID in PlantcircBase	osa_circ_019868
Alias	NA
Organism	Oryza sativa
Position	chr3: 13588998-13590276 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os03g0355600
Parent gene annotation	Similar to Adapter-related protein complex 2 beta 1 subunit (Bet a-adaptin) (Plasma membrane adaptor HA2/AP2 adaptin beta subunit ) (Clathrin assembly protein complex 2 beta large chain) (AP105B ) (Fragment). (Os03t0355600-01);Similar to predicted protein. (O s03t0355600-02);Similar to predicted protein. (Os03t0355600-03); Similar to predicted protein. (Os03t0355600-04)
Parent gene strand	-
Alternative splicing	Os03g0355600_circ_g.1 Os03g0355600_circ_g.2 Os03g0355600_circ_g.3 Os03g0355600_circ_g.5 Os03g0355600_circ_g.6
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	Os03t0355600-01:5 Os03t0355600-03:3 Os03t0355600-02:4

			
						 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  
						
							GTTCTGCTGACAAAAGCGTAACAAGAGGGGGTGCCATTTTCTTACAGAGATTACGGACAACATC
TGTGCTAGTAATGAGCTCCATTTGTAAAAGGATTATctgtatcatctgttgaggcccctcagtt
ggctttttaaggaacaacttaacagttgccgttagtaactgcaattgaactaatgctggttctt
ctgggaat

									
								

					

						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: 729
Transcript exons: 13588998-13589177,13589249-13589312,13589437-13589648,13
589920-13590012,13590097-13590276
CTGTATCATCTGTTGAGGCCCCTCAGTTGGCTTTTTAAGGAACAACTTAACAGTTGCCGTTAGT
AACTGCAATTGAACTAATGCTGGTTCTTCTGGGAATGTTTCCAAGAAGCTCTCAAGAAGTTCGT
CAGCATTGTCAATCCTTTCAGCATATTCTCCAATAATCCAAATCATTGATGCCTTAGCCTCTGG
TTCATCTAAGGTGTCTAGGCTTTCACAGAGTGTTGCGATGATCGACTCATACGTATTAGGGTAG
CGCCTGAAGATGTCCTTAATAACAATTATAGCCTCCTGCACAACATAATTAACCTTTATCTTAA
TCAGCTCAAGCAAAACACTGATACACCTTTCAGCAGCTCTCTCCAACTTAATTGCACATCTTCC
AATAGCACGAACAGCTTTGCGGACAAAGTCAACATCCACCTCTGTGGCATACTCTTTGAATTCC
AATAGAACCTGATCTATGTTTCTGTCAGAGGCAAGCTTTATCATAATCTCCAGCTTTTCCATCT
TAACATATATTGGGTCATTATACTTGCAAAAGAAGACCTTAATTTCATGTGCAAGTATAGTAGG
CCTTTTCTGAACAATCAGATTAATGTTCCTTAACGCTACATACTGAATCTCAGGTTCTGCTGAC
AAAAGCGTAACAAGAGGGGGTGCCATTTTCTTACAGAGATTACGGACAACATCTGTGCTAGTAA
TGAGCTCCATTTGTAAAAGGATTAT
						
					

						Genomic sequence
						
							CTGTATCATCTGTTGAGGCCCCTCAGTTGGCTTTTTAAGGAACAACTTAACAGTTGCCGTTAGT
AACTGCAATTGAACTAATGCTGGTTCTTCTGGGAATGTTTCCAAGAAGCTCTCAAGAAGTTCGT
CAGCATTGTCAATCCTTTCAGCATATTCTCCAATAATCCAAATCATTGATGCCTGGAGAAAAAT
AAACATGTAATTGCACAAAAATGCAATAGATTACCTAGACAGTTTTCATAGAATAATACCTTAG
CCTCTGGTTCATCTAAGGTGTCTAGGCTTTCACAGAGTGTTGCGATGATCGACTCATACCTGCA
TTTTGGCAAGAAAACAGTTAGTTTTATAGATGCAATTCTTGAGCAAAAACAATAAAAAAATTGA
AGAGTTCCTTTGTTACATAATATAGAACATTGATCTGTCATGCCACAGTACTCACGTATTAGGG
TAGCGCCTGAAGATGTCCTTAATAACAATTATAGCCTCCTGCACAACATAATTAACCTTTATCT
TAATCAGCTCAAGCAAAACACTGATACACCTTTCAGCAGCTCTCTCCAACTTAATTGCACATCT
TCCAATAGCACGAACAGCTTTGCGGACAAAGTCAACATCCACCTCTGTGGCATACTCTTTGAAT
TCCAATAGAACCTATAGAAGGAGCTCTGTTAGCTTCTTGAACAAAATTTACAGAAAAGAAACCA
TCTGCTCCACAAGGAGTAAGACATTCAACATGGTTGGCAAGTTAATCCAATTTTTGAAACTGAT
ATAATAATTGTTTAGCCTTTCTTCCAACAATACAAAAGCACTTCTGGTAGACATGAGACCATAC
AAAAGCAGAAAAACATTTAGTTAAGGAAATCTTTCACTGCAACTAACATGCGCTGGACACAATA
ATAATATAAAACAGCAGATTTTTTACCTGATCTATGTTTCTGTCAGAGGCAAGCTTTATCATAA
TCTCCAGCTTTTCCATCTTAACATATATTGGGTCATTATACTTGCAAAAGAAGACCTGTTGCAA
GAACAGCCTGTTGGGTCAGTAACACATTTGCGTTACTGGAAATGAGTGGCTCAGATGAGGAAGA
AAATATATCACCTTAATTTCATGTGCAAGTATAGTAGGCCTTTTCTGAACAATCAGATTAATGT
TCCTTAACGCTACATACTGAATCTCAGGTTCTGCTGACAAAAGCGTAACAAGAGGGGGTGCCAT
TTTCTTACAGAGATTACGGACAACATCTGTGCTAGTAATGAGCTCCATTTGTAAAAGGATTAT
						
					

			
		

Sequences
Splice junction sequence	GTTCTGCTGACAAAAGCGTAACAAGAGGGGGTGCCATTTTCTTACAGAGATTACGGACAACATC TGTGCTAGTAATGAGCTCCATTTGTAAAAGGATTATctgtatcatctgttgaggcccctcagtt ggctttttaaggaacaacttaacagttgccgttagtaactgcaattgaactaatgctggttctt ctgggaat
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: 729 Transcript exons: 13588998-13589177,13589249-13589312,13589437-13589648,13 589920-13590012,13590097-13590276 CTGTATCATCTGTTGAGGCCCCTCAGTTGGCTTTTTAAGGAACAACTTAACAGTTGCCGTTAGT AACTGCAATTGAACTAATGCTGGTTCTTCTGGGAATGTTTCCAAGAAGCTCTCAAGAAGTTCGT CAGCATTGTCAATCCTTTCAGCATATTCTCCAATAATCCAAATCATTGATGCCTTAGCCTCTGG TTCATCTAAGGTGTCTAGGCTTTCACAGAGTGTTGCGATGATCGACTCATACGTATTAGGGTAG CGCCTGAAGATGTCCTTAATAACAATTATAGCCTCCTGCACAACATAATTAACCTTTATCTTAA TCAGCTCAAGCAAAACACTGATACACCTTTCAGCAGCTCTCTCCAACTTAATTGCACATCTTCC AATAGCACGAACAGCTTTGCGGACAAAGTCAACATCCACCTCTGTGGCATACTCTTTGAATTCC AATAGAACCTGATCTATGTTTCTGTCAGAGGCAAGCTTTATCATAATCTCCAGCTTTTCCATCT TAACATATATTGGGTCATTATACTTGCAAAAGAAGACCTTAATTTCATGTGCAAGTATAGTAGG CCTTTTCTGAACAATCAGATTAATGTTCCTTAACGCTACATACTGAATCTCAGGTTCTGCTGAC AAAAGCGTAACAAGAGGGGGTGCCATTTTCTTACAGAGATTACGGACAACATCTGTGCTAGTAA TGAGCTCCATTTGTAAAAGGATTAT
Genomic sequence	CTGTATCATCTGTTGAGGCCCCTCAGTTGGCTTTTTAAGGAACAACTTAACAGTTGCCGTTAGT AACTGCAATTGAACTAATGCTGGTTCTTCTGGGAATGTTTCCAAGAAGCTCTCAAGAAGTTCGT CAGCATTGTCAATCCTTTCAGCATATTCTCCAATAATCCAAATCATTGATGCCTGGAGAAAAAT AAACATGTAATTGCACAAAAATGCAATAGATTACCTAGACAGTTTTCATAGAATAATACCTTAG CCTCTGGTTCATCTAAGGTGTCTAGGCTTTCACAGAGTGTTGCGATGATCGACTCATACCTGCA TTTTGGCAAGAAAACAGTTAGTTTTATAGATGCAATTCTTGAGCAAAAACAATAAAAAAATTGA AGAGTTCCTTTGTTACATAATATAGAACATTGATCTGTCATGCCACAGTACTCACGTATTAGGG TAGCGCCTGAAGATGTCCTTAATAACAATTATAGCCTCCTGCACAACATAATTAACCTTTATCT TAATCAGCTCAAGCAAAACACTGATACACCTTTCAGCAGCTCTCTCCAACTTAATTGCACATCT TCCAATAGCACGAACAGCTTTGCGGACAAAGTCAACATCCACCTCTGTGGCATACTCTTTGAAT TCCAATAGAACCTATAGAAGGAGCTCTGTTAGCTTCTTGAACAAAATTTACAGAAAAGAAACCA TCTGCTCCACAAGGAGTAAGACATTCAACATGGTTGGCAAGTTAATCCAATTTTTGAAACTGAT ATAATAATTGTTTAGCCTTTCTTCCAACAATACAAAAGCACTTCTGGTAGACATGAGACCATAC AAAAGCAGAAAAACATTTAGTTAAGGAAATCTTTCACTGCAACTAACATGCGCTGGACACAATA ATAATATAAAACAGCAGATTTTTTACCTGATCTATGTTTCTGTCAGAGGCAAGCTTTATCATAA TCTCCAGCTTTTCCATCTTAACATATATTGGGTCATTATACTTGCAAAAGAAGACCTGTTGCAA GAACAGCCTGTTGGGTCAGTAACACATTTGCGTTACTGGAAATGAGTGGCTCAGATGAGGAAGA AAATATATCACCTTAATTTCATGTGCAAGTATAGTAGGCCTTTTCTGAACAATCAGATTAATGT TCCTTAACGCTACATACTGAATCTCAGGTTCTGCTGACAAAAGCGTAACAAGAGGGGGTGCCAT TTTCTTACAGAGATTACGGACAACATCTGTGCTAGTAATGAGCTCCATTTGTAAAAGGATTAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.350542637

Conservation Information
Conserved circRNAs	NA
PMCS	0.350542637

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13590263-13589000(-)
						
						Potential amino acid sequence
						
							MELITSTDVVRNLCKKMAPPLVTLLSAEPEIQYVALRNINLIVQKRPTILAHEIKVFFCKYNDP
IYVKMEKLEIMIKLASDRNIDQVLLEFKEYATEVDVDFVRKAVRAIGRCAIKLERAAERCISVL
LELIKIKVNYVVQEAIIVIKDIFRRYPNTYESIIATLCESLDTLDEPEAKASMIWIIGEYAERI
DNADELLESFLETFPEEPALVQLQLLTATVKLFLKKPTEGPQQMIQIILLQMELITSTDVVRNL
CKKMAPPLVTLLSAEPEIQYVALRNINLIVQKRPTILAHEIKVFFCKYNDPIYVKMEKLEIMIK
LASDRNIDQVLLEFKEYATEVDVDFVRKAVRAIGRCAIKLERAAERCISVLLELIKIKVNYVVQ
EAIIVIKDIFRRYPNTYESIIATLCESLDTLDEPEAKASMIWIIGEYAERIDNADELLESFLET
FPEEPALVQLQLLTATVKLFLKKPTEGPQQMIQIILLQMELITSTDVVRNLCKKMAPPLVTLLS
AEPEIQYVALRNINLIVQKRPTILAHEIKVFFCKYNDPIYVKMEKLEIMIKLASDRNIDQVLLE
FKEYATEVDVDFVRKAVRAIGRCAIKLERAAERCISVLLELIKIKVNYVVQEAIIVIKDIFRRY
PNTYESIIATLCESLDTLDEPEAKASMIWIIGEYAERIDNADELLESFLETFPEEPALVQLQLL
TATVKLFLKKPTEGPQQMIQIILLQMELITSTDVVRNLCKKMAPPLVTLLSAEPEIQYVALRNI
NLIVQKRPTILAHEIKVFFCKYNDPIYVKMEKLEIMIKLASDRNIDQVLLEFKEYATEVDVDFV
RKAVRAIGRCAIKLERAAERCISVLLELIKIKVNYVVQEAIIVIKDIFRRYPNTYESIIATLCE
SLDTLDEPEAKASMIWIIGEYAERIDNADELLESFLETFPEEPALVQLQLLTATVKLFLKKPTE
GPQQMIQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13590263-13589000(-)
Potential amino acid sequence	MELITSTDVVRNLCKKMAPPLVTLLSAEPEIQYVALRNINLIVQKRPTILAHEIKVFFCKYNDP IYVKMEKLEIMIKLASDRNIDQVLLEFKEYATEVDVDFVRKAVRAIGRCAIKLERAAERCISVL LELIKIKVNYVVQEAIIVIKDIFRRYPNTYESIIATLCESLDTLDEPEAKASMIWIIGEYAERI DNADELLESFLETFPEEPALVQLQLLTATVKLFLKKPTEGPQQMIQIILLQMELITSTDVVRNL CKKMAPPLVTLLSAEPEIQYVALRNINLIVQKRPTILAHEIKVFFCKYNDPIYVKMEKLEIMIK LASDRNIDQVLLEFKEYATEVDVDFVRKAVRAIGRCAIKLERAAERCISVLLELIKIKVNYVVQ EAIIVIKDIFRRYPNTYESIIATLCESLDTLDEPEAKASMIWIIGEYAERIDNADELLESFLET FPEEPALVQLQLLTATVKLFLKKPTEGPQQMIQIILLQMELITSTDVVRNLCKKMAPPLVTLLS AEPEIQYVALRNINLIVQKRPTILAHEIKVFFCKYNDPIYVKMEKLEIMIKLASDRNIDQVLLE FKEYATEVDVDFVRKAVRAIGRCAIKLERAAERCISVLLELIKIKVNYVVQEAIIVIKDIFRRY PNTYESIIATLCESLDTLDEPEAKASMIWIIGEYAERIDNADELLESFLETFPEEPALVQLQLL TATVKLFLKKPTEGPQQMIQIILLQMELITSTDVVRNLCKKMAPPLVTLLSAEPEIQYVALRNI NLIVQKRPTILAHEIKVFFCKYNDPIYVKMEKLEIMIKLASDRNIDQVLLEFKEYATEVDVDFV RKAVRAIGRCAIKLERAAERCISVLLELIKIKVNYVVQEAIIVIKDIFRRYPNTYESIIATLCE SLDTLDEPEAKASMIWIIGEYAERIDNADELLESFLETFPEEPALVQLQLLTATVKLFLKKPTE GPQQMIQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0355600_circ_g.4

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