Plant Circular RNA Database

Detail information of BGIOSGA012350_circ_g.2

			
						 General Information
					
						CircRNA Name
						BGIOSGA012350_circ_g.2
					
						ID in PlantcircBase
						osi_circ_004727
					
						Alias
						3:10401147|10401939
					
						Organism
						
							Oryza sativa ssp. indica						
					
						Position
						
							chr3: 10401147-10401939  JBrowse»						
					
						Reference genome
						
							Oryza_indica.ASM465v1.42						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							BGIOSGA012350						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							BGIOSGA012350_circ_g.1 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						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
						BGIOSGA012350-TA:4

General Information
CircRNA Name	BGIOSGA012350_circ_g.2
ID in PlantcircBase	osi_circ_004727
Alias	3:10401147\|10401939
Organism	Oryza sativa ssp. indica
Position	chr3: 10401147-10401939 JBrowse»
Reference genome	Oryza_indica.ASM465v1.42
Type	e-circRNA
Identification method	find_circ
Parent gene	BGIOSGA012350
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	BGIOSGA012350_circ_g.1
Support reads	NA
Tissues	leaf
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	BGIOSGA012350-TA: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  
						
							CAGCGCACCGTGGATGGCAAGAACTACTGGACATTTGAGTACGATCTTGAGGCCCCGGGCTACG
GCGTGTCCGCATTTGCGACGGTTGCCATTGGAAACGaagtgccaaagaattacaagtcttatgt
ggattcaaaagatggatattcatacctgtatccagctgattggagggtaggttgcaatattttc
gtcttgaa

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							AAGTGCCAAAGAATTACAAGTCTTATGTGGATTCAAAAGATGGATATTCATACCTGTATCCAGC
TGATTGGAGGGTAGGTTGCAATATTTTCGTCTTGAAGAACAGAGATGTCAGTTCCAATGACTGT
GTTTTCGGTGGTACATGGTATTGATGTATGCCCTTTGTTTTGATGTGTCACTTCAGGATTTCGA
CTTCCTGGGGCATGATTCAGCGTTCAAAGATCGTAATGTAGCGCTGCAGTGCGTGCGTGTGGGC
TTCATTCCTACTACAAAAACAGATATCCGTGACCTTGGTCCAATGGATGAGGTAGGATTTCATG
CGATATCTGATAATATCTTTCTTGGTAATGTAAAGGAATCAGGCAATTTTTTTAGCCTTTTCTT
TTGTTATACATCATAGATTTTTTTTATTCTGACAATTTACATACTCCTCTATCAGGCGATCTTC
AATTTGGTGAACAATGTTTATGCTGCTCCAAATCAAATACCAACTGTCTATGACATGCAAGAGG
TTTGCCATTTATCCATCTCCTTCAATCAATACTATTTAGCCATATGATCTATCTGAGTATACCA
AACTGTCGCTGCATTGCTCTTTCGCTGATTAATTTACGTCTGATCTCATTGGAATGGCTATAAC
AAAGACTGCAACAACTCTGCAAGCAAAATAAGCAACTGAGTTGTTGTGATTCGCAGCGCACCGT
GGATGGCAAGAACTACTGGACATTTGAGTACGATCTTGAGGCCCCGGGCTACGGCGTGTCCGCA
TTTGCGACGGTTGCCATTGGAAACG

Sequences
Splice junction sequence	CAGCGCACCGTGGATGGCAAGAACTACTGGACATTTGAGTACGATCTTGAGGCCCCGGGCTACG GCGTGTCCGCATTTGCGACGGTTGCCATTGGAAACGaagtgccaaagaattacaagtcttatgt ggattcaaaagatggatattcatacctgtatccagctgattggagggtaggttgcaatattttc gtcttgaa
Assembled circRNA sequence	NA 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	NA
Genomic sequence	AAGTGCCAAAGAATTACAAGTCTTATGTGGATTCAAAAGATGGATATTCATACCTGTATCCAGC TGATTGGAGGGTAGGTTGCAATATTTTCGTCTTGAAGAACAGAGATGTCAGTTCCAATGACTGT GTTTTCGGTGGTACATGGTATTGATGTATGCCCTTTGTTTTGATGTGTCACTTCAGGATTTCGA CTTCCTGGGGCATGATTCAGCGTTCAAAGATCGTAATGTAGCGCTGCAGTGCGTGCGTGTGGGC TTCATTCCTACTACAAAAACAGATATCCGTGACCTTGGTCCAATGGATGAGGTAGGATTTCATG CGATATCTGATAATATCTTTCTTGGTAATGTAAAGGAATCAGGCAATTTTTTTAGCCTTTTCTT TTGTTATACATCATAGATTTTTTTTATTCTGACAATTTACATACTCCTCTATCAGGCGATCTTC AATTTGGTGAACAATGTTTATGCTGCTCCAAATCAAATACCAACTGTCTATGACATGCAAGAGG TTTGCCATTTATCCATCTCCTTCAATCAATACTATTTAGCCATATGATCTATCTGAGTATACCA AACTGTCGCTGCATTGCTCTTTCGCTGATTAATTTACGTCTGATCTCATTGGAATGGCTATAAC AAAGACTGCAACAACTCTGCAAGCAAAATAAGCAACTGAGTTGTTGTGATTCGCAGCGCACCGT GGATGGCAAGAACTACTGGACATTTGAGTACGATCTTGAGGCCCCGGGCTACGGCGTGTCCGCA TTTGCGACGGTTGCCATTGGAAACG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_019186* 						
					
						PMCS

Conservation Information
Conserved circRNAs	osa_circ_019186*
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10401199-10401595(-)
10401609-10401376(+)
10401446-10401936(+)
						
						Potential amino acid sequence
						
							MNIHLLNPHKTCNSLALRFQWQPSQMRTRRSPGPQDRTQMSSSSCHPRCALACHRQLVFDLEQH
KHCSPN*(-)
MFMLLQIKYQLSMTCKSAPWMARTTGHLSTILRPRATACPHLRRLPLETKCQRITSLMWIQKMD
IHTCIQLIGGISTSWGMIQRSKIVM*(+)
MDEAIFNLVNNVYAAPNQIPTVYDMQERTVDGKNYWTFEYDLEAPGYGVSAFATVAIGNEVPKN
YKSYVDSKDGYSYLYPADWRDFDFLGHDSAFKDRNVALQCVRVGFIPTTKTDIRDLGPMDEAIF
NLVNNVYAAPNQIPTVYDMQERTVDGKNYWTFEYDLEAPGYGVSAFATVAIGNEVPKNYKSYVD
SKDGYSYLYPADWRDFDFLGHDSAFKDRNVALQCVRVGFIPTTKTDIRDLGPMDEAIFNLVNNV
YAAPNQIPTVYDMQERTVDGKNYWTFEYDLEAPGYGVSAFATVAIGNEVPKNYKSYVDSKDGYS
YLYPADWRDFDFLGHDSAFKDRNVALQCVRVGFIPTTKTDIRDLGPMDEAIFNLVNNVYAAPNQ
IPTVYDMQERTVDGKNYWTFEYDLEAPGYGVSAFATVAIGN(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	10401199-10401595(-) 10401609-10401376(+) 10401446-10401936(+)
Potential amino acid sequence	MNIHLLNPHKTCNSLALRFQWQPSQMRTRRSPGPQDRTQMSSSSCHPRCALACHRQLVFDLEQH KHCSPN(-) MFMLLQIKYQLSMTCKSAPWMARTTGHLSTILRPRATACPHLRRLPLETKCQRITSLMWIQKMD IHTCIQLIGGISTSWGMIQRSKIVM(+) MDEAIFNLVNNVYAAPNQIPTVYDMQERTVDGKNYWTFEYDLEAPGYGVSAFATVAIGNEVPKN YKSYVDSKDGYSYLYPADWRDFDFLGHDSAFKDRNVALQCVRVGFIPTTKTDIRDLGPMDEAIF NLVNNVYAAPNQIPTVYDMQERTVDGKNYWTFEYDLEAPGYGVSAFATVAIGNEVPKNYKSYVD SKDGYSYLYPADWRDFDFLGHDSAFKDRNVALQCVRVGFIPTTKTDIRDLGPMDEAIFNLVNNV YAAPNQIPTVYDMQERTVDGKNYWTFEYDLEAPGYGVSAFATVAIGNEVPKNYKSYVDSKDGYS YLYPADWRDFDFLGHDSAFKDRNVALQCVRVGFIPTTKTDIRDLGPMDEAIFNLVNNVYAAPNQ IPTVYDMQERTVDGKNYWTFEYDLEAPGYGVSAFATVAIGN(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Huang et al., 2021

circRNA

Detail information of BGIOSGA012350_circ_g.2

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