Plant Circular RNA Database

Detail information of Os04g0496800_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os04g0496800_circ_g.4
					
						ID in PlantcircBase
						osa_circ_024397
					
						Alias
						Os_ciR4817
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 24851199-24852872  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0496800						
					
						Parent gene annotation
						
							LETM1-like domain containing protein. (Os04t0496800-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0496800_circ_g.3 						
					
						Support reads
						4/1
					
						Tissues
						root/shoot
					
						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
						Os04t0496800-01:5

General Information
CircRNA Name	Os04g0496800_circ_g.4
ID in PlantcircBase	osa_circ_024397
Alias	Os_ciR4817
Organism	Oryza sativa
Position	chr4: 24851199-24852872 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0496800
Parent gene annotation	LETM1-like domain containing protein. (Os04t0496800-01)
Parent gene strand	-
Alternative splicing	Os04g0496800_circ_g.3
Support reads	4/1
Tissues	root/shoot
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	Os04t0496800-01:5

			
						 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  
						
							AGCATACTTCCTTCTCCTAATGATCGCCCTCGAGGCCATTTTTGGTTGCTTCTTCCTTTTCTCA
AGAGAATGTCAGGGTTATGCCTTTCCGGGTAGAACCtcttgcaatttcttccgaagcatgaatg
tcaggtagtggtctgtaccaaaaggttggatccccatatatttacacatatttaccaaccgtgc
tctgcagg

									
								

					

						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: 1278
Transcript exons: 24851199-24851291,24851371-24851459,24851567-24851713,24
851810-24852122,24852237-24852872
TCTTGCAATTTCTTCCGAAGCATGAATGTCAGGTAGTGGTCTGTACCAAAAGGTTGGATCCCCA
TATATTTACACATATTTACCAACCGTGCTCTGTTCATGTTATCCAAAGTCAGTTCATCATTAAA
CAGCTTTGCAAAGCTCAAAATTTCTTCATTTGAGACATGTCCACCTTTCCTAACCTTGTTCAAA
AATTCATCCAGATCTTCAGCTGTCTGTTTCATTTCTCCACTACGTGACGTCTGCACTTCCTTTG
CCATTTCTTTTGCAGTATCTTGTAAAAATCTTGCATATTCCATCCTTGCTTTCAATTTCCTTTT
CAATGCCTCCTCTTCCTTCATCTTGTCCTGGAAAGTCGATGGCAACATGTTAGGGAACATCTTG
AGGAAGACTGGTAGTAAAAATTCCATGAAGGGAACAATGATGAACACAGCAAAAGGTACAAGCC
TAAACAAATCAGCTGTTGTGCGTGTAAGCTGTTGCCTCTCTCTTCTTGTTAGGCTCTTTCCACC
AGCAAGTTTCACTAACAATCTAGATGAAATCCTAACATCTGCCCACAGCAGCTTAGTTCCCAAC
CAATAATGCTGCAGTGTAGAAACAAACTCATCCTTCCAATGCTTCAATTTTGCAGCCCAGTCAG
CCCTGCTCATTGAAGCAACAGCACGCAGAGCAGGTCCAATACCTAGAAGTATTGCCCAAAATTT
ATGTATGATTGACTGGTCAGACTTTTGTACTTCCTGCACCAGCTTAGCTTTAGCTTTAGCTTTT
GCAGTGCTTAAGCCTTCCACCGCCTGATCACACTCTTCTGGGGATGCCTCCTTTTTCCCCTGAT
TCTGGTTCTGGTTCTCGCTCCGCTCGTCCAGAATACCAACTTTAGGCTGCCCAGCAGTGCTTGA
TGTTGGGCGTACTGACTGTAGGAAATACCTGGCTCCCAAGGGGAAACCAAAAGTCTGTGGTTTA
GATTCATAAGAAGCAAGTGAAGCACCACGAGTTGGGTGACACAGGATACTAAGGCCCAAAAGTC
CTTGTTTCCTTAAGATGTATTGTGCCTTCTCATGGTTTGATTCTCTTGAGTTTTGAGATGCAGT
GCTTTGCTCAATTTCACATCCAAACTTTTCTTGCCCAAAAGTAGAAATAGATGAATGTCGTAAT
AAAACAGGGATATTAGTATGCTCCAGAGCATACTTCCTTCTCCTAATGATCGCCCTCGAGGCCA
TTTTTGGTTGCTTCTTCCTTTTCTCAAGAGAATGTCAGGGTTATGCCTTTCCGGGTAGAACC
Transcript length: 136
Transcript exons: 24851199-24851262,24852801-24852872
TCTTGCAATTTCTTCCGAAGCATGAATGTCAGGTAGTGGTCTGTACCAAAAGGTTGGATCCCCA
CTCGAGGCCATTTTTGGTTGCTTCTTCCTTTTCTCAAGAGAATGTCAGGGTTATGCCTTTCCGG
GTAGAACC
						
					

						Genomic sequence
						
							TCTTGCAATTTCTTCCGAAGCATGAATGTCAGGTAGTGGTCTGTACCAAAAGGTTGGATCCCCA
TATATTTACACATATTTACCAACCGTGCTCTGCAGGCAAAAAAGGACTGATCAGAAAGATGTGA
AAACCAAGGGCTAGGGCTAAGCTAGATGTTCAAGAAACATCAACCTGTTCATGTTATCCAAAGT
CAGTTCATCATTAAACAGCTTTGCAAAGCTCAAAATTTCTTCATTTGAGACATGTCCACCTTTC
CTAACCTAGTTACAAAGTTAAGAATAGATTACTAGGAAATCAATAAAACAAACACTTAATGATC
TATGTATTCAACTTGAGGTAACAAACAAAACATGTATGAACCCAAAACCTTGTTCAAAAATTCA
TCCAGATCTTCAGCTGTCTGTTTCATTTCTCCACTACGTGACGTCTGCACTTCCTTTGCCATTT
CTTTTGCAGTATCTTGTAAAAATCTTGCATATTCCATCCTTGCTTTCAATTTCCTTTTCAATGC
CTCCTGCACGTATCAAAAAAAAAAAATGTTGACCTGAGTCAATCTGTTTGTATTTAGCAAATAC
AGTGGCAAGATATCATAACATGTCTTGGTCAGTACCTCTTCCTTCATCTTGTCCTGGAAAGTCG
ATGGCAACATGTTAGGGAACATCTTGAGGAAGACTGGTAGTAAAAATTCCATGAAGGGAACAAT
GATGAACACAGCAAAAGGTACAAGCCTAAACAAATCAGCTGTTGTGCGTGTAAGCTGTTGCCTC
TCTCTTCTTGTTAGGCTCTTTCCACCAGCAAGTTTCACTAACAATCTAGATGAAATCCTAACAT
CTGCCCACAGCAGCTTAGTTCCCAACCAATAATGCTGCAGTGTAGAAACAAACTCATCCTTCCA
ATGCTTCAATTTTGCAGCCCAGTCAGCCCTTCGATTCACAAGATAAATATAAATCAAAACATTG
GATATGAATGTATAATCCATGGAAAGGGGCAAGACAGCAATTGCAAATATACTTCAATATACTG
AAGGGAACTGAGACCTGCTCATTGAAGCAACAGCACGCAGAGCAGGTCCAATACCTAGAAGTAT
TGCCCAAAATTTATGTATGATTGACTGGTCAGACTTTTGTACTTCCTGCACCAGCTTAGCTTTA
GCTTTAGCTTTTGCAGTGCTTAAGCCTTCCACCGCCTGATCACACTCTTCTGGGGATGCCTCCT
TTTTCCCCTGATTCTGGTTCTGGTTCTCGCTCCGCTCGTCCAGAATACCAACTTTAGGCTGCCC
AGCAGTGCTTGATGTTGGGCGTACTGACTGTAGGAAATACCTGGCTCCCAAGGGGAAACCAAAA
GTCTGTGGTTTAGATTCATAAGAAGCAAGTGAAGCACCACGAGTTGGGTGACACAGGATACTAA
GGCCCAAAAGTCCTTGTTTCCTTAAGATGTATTGTGCCTTCTCATGGTTTGATTCTCTTGAGTT
TTGAGATGCAGTGCTTTGCTCAATTTCACATCCAAACTTTTCTTGCCCAAAAGTAGAAATAGAT
GAATGTCGTAATAAAACAGGGATATTAGTATGCTCCAGAGCATACTTCCTTCTCCTAATGATCG
CCCTCGAGGCCATTTTTGGTTGCTTCTTCCTTTTCTCAAGAGAATGTCAGGGTTATGCCTTTCC
GGGTAGAACC
						
					

			
		

Sequences
Splice junction sequence	AGCATACTTCCTTCTCCTAATGATCGCCCTCGAGGCCATTTTTGGTTGCTTCTTCCTTTTCTCA AGAGAATGTCAGGGTTATGCCTTTCCGGGTAGAACCtcttgcaatttcttccgaagcatgaatg tcaggtagtggtctgtaccaaaaggttggatccccatatatttacacatatttaccaaccgtgc tctgcagg
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: 1278 Transcript exons: 24851199-24851291,24851371-24851459,24851567-24851713,24 851810-24852122,24852237-24852872 TCTTGCAATTTCTTCCGAAGCATGAATGTCAGGTAGTGGTCTGTACCAAAAGGTTGGATCCCCA TATATTTACACATATTTACCAACCGTGCTCTGTTCATGTTATCCAAAGTCAGTTCATCATTAAA CAGCTTTGCAAAGCTCAAAATTTCTTCATTTGAGACATGTCCACCTTTCCTAACCTTGTTCAAA AATTCATCCAGATCTTCAGCTGTCTGTTTCATTTCTCCACTACGTGACGTCTGCACTTCCTTTG CCATTTCTTTTGCAGTATCTTGTAAAAATCTTGCATATTCCATCCTTGCTTTCAATTTCCTTTT CAATGCCTCCTCTTCCTTCATCTTGTCCTGGAAAGTCGATGGCAACATGTTAGGGAACATCTTG AGGAAGACTGGTAGTAAAAATTCCATGAAGGGAACAATGATGAACACAGCAAAAGGTACAAGCC TAAACAAATCAGCTGTTGTGCGTGTAAGCTGTTGCCTCTCTCTTCTTGTTAGGCTCTTTCCACC AGCAAGTTTCACTAACAATCTAGATGAAATCCTAACATCTGCCCACAGCAGCTTAGTTCCCAAC CAATAATGCTGCAGTGTAGAAACAAACTCATCCTTCCAATGCTTCAATTTTGCAGCCCAGTCAG CCCTGCTCATTGAAGCAACAGCACGCAGAGCAGGTCCAATACCTAGAAGTATTGCCCAAAATTT ATGTATGATTGACTGGTCAGACTTTTGTACTTCCTGCACCAGCTTAGCTTTAGCTTTAGCTTTT GCAGTGCTTAAGCCTTCCACCGCCTGATCACACTCTTCTGGGGATGCCTCCTTTTTCCCCTGAT TCTGGTTCTGGTTCTCGCTCCGCTCGTCCAGAATACCAACTTTAGGCTGCCCAGCAGTGCTTGA TGTTGGGCGTACTGACTGTAGGAAATACCTGGCTCCCAAGGGGAAACCAAAAGTCTGTGGTTTA GATTCATAAGAAGCAAGTGAAGCACCACGAGTTGGGTGACACAGGATACTAAGGCCCAAAAGTC CTTGTTTCCTTAAGATGTATTGTGCCTTCTCATGGTTTGATTCTCTTGAGTTTTGAGATGCAGT GCTTTGCTCAATTTCACATCCAAACTTTTCTTGCCCAAAAGTAGAAATAGATGAATGTCGTAAT AAAACAGGGATATTAGTATGCTCCAGAGCATACTTCCTTCTCCTAATGATCGCCCTCGAGGCCA TTTTTGGTTGCTTCTTCCTTTTCTCAAGAGAATGTCAGGGTTATGCCTTTCCGGGTAGAACC Transcript length: 136 Transcript exons: 24851199-24851262,24852801-24852872 TCTTGCAATTTCTTCCGAAGCATGAATGTCAGGTAGTGGTCTGTACCAAAAGGTTGGATCCCCA CTCGAGGCCATTTTTGGTTGCTTCTTCCTTTTCTCAAGAGAATGTCAGGGTTATGCCTTTCCGG GTAGAACC
Genomic sequence	TCTTGCAATTTCTTCCGAAGCATGAATGTCAGGTAGTGGTCTGTACCAAAAGGTTGGATCCCCA TATATTTACACATATTTACCAACCGTGCTCTGCAGGCAAAAAAGGACTGATCAGAAAGATGTGA AAACCAAGGGCTAGGGCTAAGCTAGATGTTCAAGAAACATCAACCTGTTCATGTTATCCAAAGT CAGTTCATCATTAAACAGCTTTGCAAAGCTCAAAATTTCTTCATTTGAGACATGTCCACCTTTC CTAACCTAGTTACAAAGTTAAGAATAGATTACTAGGAAATCAATAAAACAAACACTTAATGATC TATGTATTCAACTTGAGGTAACAAACAAAACATGTATGAACCCAAAACCTTGTTCAAAAATTCA TCCAGATCTTCAGCTGTCTGTTTCATTTCTCCACTACGTGACGTCTGCACTTCCTTTGCCATTT CTTTTGCAGTATCTTGTAAAAATCTTGCATATTCCATCCTTGCTTTCAATTTCCTTTTCAATGC CTCCTGCACGTATCAAAAAAAAAAAATGTTGACCTGAGTCAATCTGTTTGTATTTAGCAAATAC AGTGGCAAGATATCATAACATGTCTTGGTCAGTACCTCTTCCTTCATCTTGTCCTGGAAAGTCG ATGGCAACATGTTAGGGAACATCTTGAGGAAGACTGGTAGTAAAAATTCCATGAAGGGAACAAT GATGAACACAGCAAAAGGTACAAGCCTAAACAAATCAGCTGTTGTGCGTGTAAGCTGTTGCCTC TCTCTTCTTGTTAGGCTCTTTCCACCAGCAAGTTTCACTAACAATCTAGATGAAATCCTAACAT CTGCCCACAGCAGCTTAGTTCCCAACCAATAATGCTGCAGTGTAGAAACAAACTCATCCTTCCA ATGCTTCAATTTTGCAGCCCAGTCAGCCCTTCGATTCACAAGATAAATATAAATCAAAACATTG GATATGAATGTATAATCCATGGAAAGGGGCAAGACAGCAATTGCAAATATACTTCAATATACTG AAGGGAACTGAGACCTGCTCATTGAAGCAACAGCACGCAGAGCAGGTCCAATACCTAGAAGTAT TGCCCAAAATTTATGTATGATTGACTGGTCAGACTTTTGTACTTCCTGCACCAGCTTAGCTTTA GCTTTAGCTTTTGCAGTGCTTAAGCCTTCCACCGCCTGATCACACTCTTCTGGGGATGCCTCCT TTTTCCCCTGATTCTGGTTCTGGTTCTCGCTCCGCTCGTCCAGAATACCAACTTTAGGCTGCCC AGCAGTGCTTGATGTTGGGCGTACTGACTGTAGGAAATACCTGGCTCCCAAGGGGAAACCAAAA GTCTGTGGTTTAGATTCATAAGAAGCAAGTGAAGCACCACGAGTTGGGTGACACAGGATACTAA GGCCCAAAAGTCCTTGTTTCCTTAAGATGTATTGTGCCTTCTCATGGTTTGATTCTCTTGAGTT TTGAGATGCAGTGCTTTGCTCAATTTCACATCCAAACTTTTCTTGCCCAAAAGTAGAAATAGAT GAATGTCGTAATAAAACAGGGATATTAGTATGCTCCAGAGCATACTTCCTTCTCCTAATGATCG CCCTCGAGGCCATTTTTGGTTGCTTCTTCCTTTTCTCAAGAGAATGTCAGGGTTATGCCTTTCC GGGTAGAACC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.478291796

Conservation Information
Conserved circRNAs	NA
PMCS	0.478291796

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24852793-24851231(+)
24852813-24852853(-)
						
						Potential amino acid sequence
						
							MIALEAIFGCFFLFSRECQGYAFPGRTSCNFFRSMNVR*(+)
MASRAIIRRRKYALEHTNIPVLLRHSSISTFGQEKFGCEIEQSTASQNSRESNHEKAQYILRKQ
GLLGLSILCHPTRGASLASYESKPQTFGFPLGARYFLQSVRPTSSTAGQPKVGILDERSENQNQ
NQGKKEASPEECDQAVEGLSTAKAKAKAKLVQEVQKSDQSIIHKFWAILLGIGPALRAVASMSR
ADWAAKLKHWKDEFVSTLQHYWLGTKLLWADVRISSRLLVKLAGGKSLTRRERQQLTRTTADLF
RLVPFAVFIIVPFMEFLLPVFLKMFPNMLPSTFQDKMKEEEALKRKLKARMEYARFLQDTAKEM
AKEVQTSRSGEMKQTAEDLDEFLNKVRKGGHVSNEEILSFAKLFNDELTLDNMNRARLVNMCKY
MGIQPFGTDHYLTFMLRKKLQEVLPGKA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24852793-24851231(+) 24852813-24852853(-)
Potential amino acid sequence	MIALEAIFGCFFLFSRECQGYAFPGRTSCNFFRSMNVR(+) MASRAIIRRRKYALEHTNIPVLLRHSSISTFGQEKFGCEIEQSTASQNSRESNHEKAQYILRKQ GLLGLSILCHPTRGASLASYESKPQTFGFPLGARYFLQSVRPTSSTAGQPKVGILDERSENQNQ NQGKKEASPEECDQAVEGLSTAKAKAKAKLVQEVQKSDQSIIHKFWAILLGIGPALRAVASMSR ADWAAKLKHWKDEFVSTLQHYWLGTKLLWADVRISSRLLVKLAGGKSLTRRERQQLTRTTADLF RLVPFAVFIIVPFMEFLLPVFLKMFPNMLPSTFQDKMKEEEALKRKLKARMEYARFLQDTAKEM AKEVQTSRSGEMKQTAEDLDEFLNKVRKGGHVSNEEILSFAKLFNDELTLDNMNRARLVNMCKY MGIQPFGTDHYLTFMLRKKLQEVLPGKA(-)
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 Os04g0496800_circ_g.4

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