Plant Circular RNA Database

Detail information of Os04g0244400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0244400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_023173
					
						Alias
						Os_ciR1314
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 9341030-9342346  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, circseq_cup, find_circ
					
						Parent gene
						
							Os04g0244400						
					
						Parent gene annotation
						
							Thioredoxin fold domain containing protein. (Os04t0244400-01);Th
ioredoxin fold domain containing protein. (Os04t0244400-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0244400_circ_g.2 						
					
						Support reads
						14/3/3
					
						Tissues
						root/root/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  
						
							GT-AG							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
						Os04t0244400-02:3
Os04t0244400-01:3

General Information
CircRNA Name	Os04g0244400_circ_g.3
ID in PlantcircBase	osa_circ_023173
Alias	Os_ciR1314
Organism	Oryza sativa
Position	chr4: 9341030-9342346 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, circseq_cup, find_circ
Parent gene	Os04g0244400
Parent gene annotation	Thioredoxin fold domain containing protein. (Os04t0244400-01);Th ioredoxin fold domain containing protein. (Os04t0244400-02)
Parent gene strand	+
Alternative splicing	Os04g0244400_circ_g.2
Support reads	14/3/3
Tissues	root/root/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	GT-AG 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	Os04t0244400-02:3 Os04t0244400-01:3

			
						 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  
						
							TTTAGGTGGGTTGATGAGCACCTTGTGCATGTCTTGTCGCCAAATATATATCGGACAACTTCAG
AGGCCTTGGAATCTTTTGATTATATTTCAAAACATGctttcctagactatcatgatatacccta
caaggttgtggaagttaatccattgagcaagaaggaaatcaagtggtctgagtacaagaaggtc
ccaatact

									
								

					

						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: 155
Transcript exons: 9341030-9341099,9342262-9342346
CTTTCCTAGACTATCATGATATACCCTACAAGGTTGTGGAAGTTAATCCATTGAGCAAGAAGGA
AATCAAGAGCACCTTGTGCATGTCTTGTCGCCAAATATATATCGGACAACTTCAGAGGCCTTGG
AATCTTTTGATTATATTTCAAAACATG
Transcript length: 306
Transcript exons: 9341030-9341164,9341296-9341371,9342252-9342346
CTTTCCTAGACTATCATGATATACCCTACAAGGTTGTGGAAGTTAATCCATTGAGCAAGAAGGA
AATCAAGTGGTCTGAGTACAAGAAGGTCCCAATACTGATGGTAGATGGTGAACAGCTGGTTGAT
TCATCAGATATAATCAATATATTACAGCAAAGGGTCCGCCCTGATGATAAAGCCACTAATGAAG
AGGAAGAAAAATGGCGCAGGTGGGTTGATGAGCACCTTGTGCATGTCTTGTCGCCAAATATATA
TCGGACAACTTCAGAGGCCTTGGAATCTTTTGATTATATTTCAAAACATG
						
					

						Genomic sequence
						
							CTTTCCTAGACTATCATGATATACCCTACAAGGTTGTGGAAGTTAATCCATTGAGCAAGAAGGA
AATCAAGTGGTCTGAGTACAAGAAGGTCCCAATACTGATGGTAGATGGTGAACAGCTGGTTGAT
TCATCAGGTTACATTCATTTCATATTGGTTTATTCCGGTCTGGTTCCTTTACATTGTTGTGGTT
TCAACTTTTAAGTAAAATAACTTTTTATGTGTTAAACTCCAGAGTTAACGTATTGTTACATCTG
TTGTTGGTAGATATAATCAATATATTACAGCAAAGGGTCCGCCCTGATGATAAAGCCACTAATG
AAGAGGAAGAAAAATGGCGCAGGTATTTCTCCATTACTTGCATCTGTTTATGTGGCATTAGTAT
TTGTAATTTTTTTTTCAGGTCTTGGTTCTAGCTTCTCAAATCATTAATGTTATAGTACTCCTAT
TTCTAGAAACAAATATTGTTTAAAGTCTACTTTCCTCTTGAAATTTTTAATCATTTATATGGCA
TTAGTATGTGCAATATGTTCTACTTTTATAGTATTTCTTTACTTTTGTTTCATTGTTTTACAAT
GTAAATCAATCGGTGAACAAAAACCTTGTCCATCAGTTTTTTCTGTTTATGCATTGATAGTTAC
ATGATAGACTTCTTTCCCTGGATCTGGTCATTGTAATGTTCCAACACCAGGCAGGATCAGCATA
GCCATCACTATTACTACATTTTTTCTGCGATCTGATAGTTTATAGTTACATGTTTCCCAAGGAT
CTGGTGATAATGTTTCAAGGCCAGGCAGAATCAGTATGGCCATCAACTATCCTCTTTGCTTTAT
TTCATTGTGTTTTTACCACTAAAATTAATTGATGAAACTAAGAGCTTATCCGTTATGATCTGAT
GATTACTTTATAGACTTTTTCTCTGGATCTGGTCATAGTAGTGTTTCCAAGGCTAGAGACAACC
AGTAAGTCCATTATTATCTTGTATTAGGGGTAGTTATGCATTTTCTGGTAGGATTCACAAACTG
AAAGATGAAAAACAAAAAAGCCGACTACCACTAAATTGGCTGCATTTAGGCTTTACCCTTGATG
GAGTGAGCTGGATTCCTCTAGAAGTAGCATGGCGAACCCTGGTTGCACGAGTGACCAACATTTT
ACTCTCTTAACATTCTTACAAACTGGAGTTTATCTACGGTAACATAATTTGTCTTGAATTATTG
GTTTAGGTGGGTTGATGAGCACCTTGTGCATGTCTTGTCGCCAAATATATATCGGACAACTTCA
GAGGCCTTGGAATCTTTTGATTATATTTCAAAACATG
						
					

			
		

Sequences
Splice junction sequence	TTTAGGTGGGTTGATGAGCACCTTGTGCATGTCTTGTCGCCAAATATATATCGGACAACTTCAG AGGCCTTGGAATCTTTTGATTATATTTCAAAACATGctttcctagactatcatgatatacccta caaggttgtggaagttaatccattgagcaagaaggaaatcaagtggtctgagtacaagaaggtc ccaatact
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: 155 Transcript exons: 9341030-9341099,9342262-9342346 CTTTCCTAGACTATCATGATATACCCTACAAGGTTGTGGAAGTTAATCCATTGAGCAAGAAGGA AATCAAGAGCACCTTGTGCATGTCTTGTCGCCAAATATATATCGGACAACTTCAGAGGCCTTGG AATCTTTTGATTATATTTCAAAACATG Transcript length: 306 Transcript exons: 9341030-9341164,9341296-9341371,9342252-9342346 CTTTCCTAGACTATCATGATATACCCTACAAGGTTGTGGAAGTTAATCCATTGAGCAAGAAGGA AATCAAGTGGTCTGAGTACAAGAAGGTCCCAATACTGATGGTAGATGGTGAACAGCTGGTTGAT TCATCAGATATAATCAATATATTACAGCAAAGGGTCCGCCCTGATGATAAAGCCACTAATGAAG AGGAAGAAAAATGGCGCAGGTGGGTTGATGAGCACCTTGTGCATGTCTTGTCGCCAAATATATA TCGGACAACTTCAGAGGCCTTGGAATCTTTTGATTATATTTCAAAACATG
Genomic sequence	CTTTCCTAGACTATCATGATATACCCTACAAGGTTGTGGAAGTTAATCCATTGAGCAAGAAGGA AATCAAGTGGTCTGAGTACAAGAAGGTCCCAATACTGATGGTAGATGGTGAACAGCTGGTTGAT TCATCAGGTTACATTCATTTCATATTGGTTTATTCCGGTCTGGTTCCTTTACATTGTTGTGGTT TCAACTTTTAAGTAAAATAACTTTTTATGTGTTAAACTCCAGAGTTAACGTATTGTTACATCTG TTGTTGGTAGATATAATCAATATATTACAGCAAAGGGTCCGCCCTGATGATAAAGCCACTAATG AAGAGGAAGAAAAATGGCGCAGGTATTTCTCCATTACTTGCATCTGTTTATGTGGCATTAGTAT TTGTAATTTTTTTTTCAGGTCTTGGTTCTAGCTTCTCAAATCATTAATGTTATAGTACTCCTAT TTCTAGAAACAAATATTGTTTAAAGTCTACTTTCCTCTTGAAATTTTTAATCATTTATATGGCA TTAGTATGTGCAATATGTTCTACTTTTATAGTATTTCTTTACTTTTGTTTCATTGTTTTACAAT GTAAATCAATCGGTGAACAAAAACCTTGTCCATCAGTTTTTTCTGTTTATGCATTGATAGTTAC ATGATAGACTTCTTTCCCTGGATCTGGTCATTGTAATGTTCCAACACCAGGCAGGATCAGCATA GCCATCACTATTACTACATTTTTTCTGCGATCTGATAGTTTATAGTTACATGTTTCCCAAGGAT CTGGTGATAATGTTTCAAGGCCAGGCAGAATCAGTATGGCCATCAACTATCCTCTTTGCTTTAT TTCATTGTGTTTTTACCACTAAAATTAATTGATGAAACTAAGAGCTTATCCGTTATGATCTGAT GATTACTTTATAGACTTTTTCTCTGGATCTGGTCATAGTAGTGTTTCCAAGGCTAGAGACAACC AGTAAGTCCATTATTATCTTGTATTAGGGGTAGTTATGCATTTTCTGGTAGGATTCACAAACTG AAAGATGAAAAACAAAAAAGCCGACTACCACTAAATTGGCTGCATTTAGGCTTTACCCTTGATG GAGTGAGCTGGATTCCTCTAGAAGTAGCATGGCGAACCCTGGTTGCACGAGTGACCAACATTTT ACTCTCTTAACATTCTTACAAACTGGAGTTTATCTACGGTAACATAATTTGTCTTGAATTATTG GTTTAGGTGGGTTGATGAGCACCTTGTGCATGTCTTGTCGCCAAATATATATCGGACAACTTCA GAGGCCTTGGAATCTTTTGATTATATTTCAAAACATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005335* osi_circ_015122 zma_circ_001078 						
					
						PMCS
						0.354878278

Conservation Information
Conserved circRNAs	osi_circ_005335* osi_circ_015122 zma_circ_001078
PMCS	0.354878278

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9341333-9341035(+)
9341132-9342343(+)
						
						Potential amino acid sequence
						
							MIKPLMKRKKNGAGGLMSTLCMSCRQIYIGQLQRPWNLLIIFQNMLS*(+)
MVDGEQLVDSSDIINILQQRVRPDDKATNEEEEKWRRWVDEHLVHVLSPNIYRTTSEALESFDY
ISKHAFLDYHDIPYKVVEVNPLSKKEIKWSEYKKVPILMVDGEQLVDSSDIINILQQRVRPDDK
ATNEEEEKWRRWVDEHLVHVLSPNIYRTTSEALESFDYISKHAFLDYHDIPYKVVEVNPLSKKE
IKWSEYKKVPILMVDGEQLVDSSDIINILQQRVRPDDKATNEEEEKWRRWVDEHLVHVLSPNIY
RTTSEALESFDYISKHAFLDYHDIPYKVVEVNPLSKKEIKWSEYKKVPILMVDGEQLVDSSDII
NILQQRVRPDDKATNEEEEKWRRWVDEHLVHVLSPNIYRTTSEALESFDYISKH(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9341333-9341035(+) 9341132-9342343(+)
Potential amino acid sequence	MIKPLMKRKKNGAGGLMSTLCMSCRQIYIGQLQRPWNLLIIFQNMLS*(+) MVDGEQLVDSSDIINILQQRVRPDDKATNEEEEKWRRWVDEHLVHVLSPNIYRTTSEALESFDY ISKHAFLDYHDIPYKVVEVNPLSKKEIKWSEYKKVPILMVDGEQLVDSSDIINILQQRVRPDDK ATNEEEEKWRRWVDEHLVHVLSPNIYRTTSEALESFDYISKHAFLDYHDIPYKVVEVNPLSKKE IKWSEYKKVPILMVDGEQLVDSSDIINILQQRVRPDDKATNEEEEKWRRWVDEHLVHVLSPNIY RTTSEALESFDYISKHAFLDYHDIPYKVVEVNPLSKKEIKWSEYKKVPILMVDGEQLVDSSDII NILQQRVRPDDKATNEEEEKWRRWVDEHLVHVLSPNIYRTTSEALESFDYISKH(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os04g0244400_circ_g.3

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