Plant Circular RNA Database

Detail information of Bra005039_circ_g.1

			
						 General Information
					
						CircRNA Name
						Bra005039_circ_g.1
					
						ID in PlantcircBase
						bra_circ_000220
					
						Alias
						A05:3108416|3108880
					
						Organism
						
							Brassica rapa						
					
						Position
						
							chrA05: 3108416-3108880  JBrowse»						
					
						Reference genome
						
							Brassica rapa v2						
					
						Type  
						
							ie-circRNA							
									
						Identification method
						Find_circ
					
						Parent gene
						
							Bra005039						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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
						Bra0A0A50A39:2

General Information
CircRNA Name	Bra005039_circ_g.1
ID in PlantcircBase	bra_circ_000220
Alias	A05:3108416\|3108880
Organism	Brassica rapa
Position	chrA05: 3108416-3108880 JBrowse»
Reference genome	Brassica rapa v2
Type	ie-circRNA
Identification method	Find_circ
Parent gene	Bra005039
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	NA
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	Bra0A0A50A39:2

			
						 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  
						
							TGATCTTCTCTCTGGCTTCATCCTCTGGTTCACCGCCTTCTCGATGCAGACACCAAACCCGTAT
CAGTATCCCATTGGCAAGAAAAGGATGCAACCACTGgtccggaagacaatgtggcagattatta
ccagcaacaggtagagatgcttgaaggctttactgaaatggatgaactcgcagaacgtggcttt
gtccctgg

						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: 356
Transcript exons: 3108416-3108525,3108635-3108880
GTCCGGAAGACAATGTGGCAGATTATTACCAGCAACAGGTAGAGATGCTTGAAGGCTTTACTGA
AATGGATGAACTCGCAGAACGTGGCTTTGTCCCTGGAATGTCAAAGGAAGAGCAAGACAATCTG
GCTAAAAGCGAGACATTAGCCATCAGAATATCGAACATTGCAAACATGGTTCTCTTTGCTGCTA
AAGTCTATGCCTCCGTCACAAGCGGCTCTTTAGCAATCGTTGCTTCCACGTTGGACTCTCTTCT
TGATCTTCTCTCTGGCTTCATCCTCTGGTTCACCGCCTTCTCGATGCAGACACCAAACCCGTAT
CAGTATCCCATTGGCAAGAAAAGGATGCAACCACTG
						
						Genomic sequence
						
							GTCCGGAAGACAATGTGGCAGATTATTACCAGCAACAGGTAGAGATGCTTGAAGGCTTTACTGA
AATGGATGAACTCGCAGAACGTGGCTTTGTCCCTGGAATGTCAAAGGTTTAAGCTTAGATGATG
ATGATGATGATGATGACAACTTGTCTCTTATTCCACTTTTTTCTTATCTTTGTTAATTGAGATA
CTTATCTCTGTGTTGTGTTCCACATAGGAAGAGCAAGACAATCTGGCTAAAAGCGAGACATTAG
CCATCAGAATATCGAACATTGCAAACATGGTTCTCTTTGCTGCTAAAGTCTATGCCTCCGTCAC
AAGCGGCTCTTTAGCAATCGTTGCTTCCACGTTGGACTCTCTTCTTGATCTTCTCTCTGGCTTC
ATCCTCTGGTTCACCGCCTTCTCGATGCAGACACCAAACCCGTATCAGTATCCCATTGGCAAGA
AAAGGATGCAACCACTG

Sequences
Splice junction sequence	TGATCTTCTCTCTGGCTTCATCCTCTGGTTCACCGCCTTCTCGATGCAGACACCAAACCCGTAT CAGTATCCCATTGGCAAGAAAAGGATGCAACCACTGgtccggaagacaatgtggcagattatta ccagcaacaggtagagatgcttgaaggctttactgaaatggatgaactcgcagaacgtggcttt gtccctgg
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: 356 Transcript exons: 3108416-3108525,3108635-3108880 GTCCGGAAGACAATGTGGCAGATTATTACCAGCAACAGGTAGAGATGCTTGAAGGCTTTACTGA AATGGATGAACTCGCAGAACGTGGCTTTGTCCCTGGAATGTCAAAGGAAGAGCAAGACAATCTG GCTAAAAGCGAGACATTAGCCATCAGAATATCGAACATTGCAAACATGGTTCTCTTTGCTGCTA AAGTCTATGCCTCCGTCACAAGCGGCTCTTTAGCAATCGTTGCTTCCACGTTGGACTCTCTTCT TGATCTTCTCTCTGGCTTCATCCTCTGGTTCACCGCCTTCTCGATGCAGACACCAAACCCGTAT CAGTATCCCATTGGCAAGAAAAGGATGCAACCACTG
Genomic sequence	GTCCGGAAGACAATGTGGCAGATTATTACCAGCAACAGGTAGAGATGCTTGAAGGCTTTACTGA AATGGATGAACTCGCAGAACGTGGCTTTGTCCCTGGAATGTCAAAGGTTTAAGCTTAGATGATG ATGATGATGATGATGACAACTTGTCTCTTATTCCACTTTTTTCTTATCTTTGTTAATTGAGATA CTTATCTCTGTGTTGTGTTCCACATAGGAAGAGCAAGACAATCTGGCTAAAAGCGAGACATTAG CCATCAGAATATCGAACATTGCAAACATGGTTCTCTTTGCTGCTAAAGTCTATGCCTCCGTCAC AAGCGGCTCTTTAGCAATCGTTGCTTCCACGTTGGACTCTCTTCTTGATCTTCTCTCTGGCTTC ATCCTCTGGTTCACCGCCTTCTCGATGCAGACACCAAACCCGTATCAGTATCCCATTGGCAAGA AAAGGATGCAACCACTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.915398692

Conservation Information
Conserved circRNAs	NA
PMCS	0.915398692

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3108461-3108454(+)
						
						Potential amino acid sequence
						
							MLEGFTEMDELAERGFVPGMSKEEQDNLAKSETLAIRISNIANMVLFAAKVYASVTSGSLAIVA
STLDSLLDLLSGFILWFTAFSMQTPNPYQYPIGKKRMQPLVRKTMWQIITSNR*
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3108461-3108454(+)
Potential amino acid sequence	MLEGFTEMDELAERGFVPGMSKEEQDNLAKSETLAIRISNIANMVLFAAKVYASVTSGSLAIVA STLDSLLDLLSGFILWFTAFSMQTPNPYQYPIGKKRMQPLVRKTMWQIITSNR*
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Wang et al., 2019

circRNA

Detail information of Bra005039_circ_g.1

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