Plant Circular RNA Database

Detail information of AT4G13250_circ_g.7

			
						 General Information
					
						CircRNA Name
						AT4G13250_circ_g.7
					
						ID in PlantcircBase
						ath_circ_030660
					
						Alias
						At_ciR1564, Ath_circ_FC2619
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 7685165-7685745  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT4G13250						
					
						Parent gene annotation
						
							Probable chlorophyll(ide) b reductase NYC1, chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G13250_circ_g.1 AT4G13250_circ_g.2 AT4G13250_circ_g.3 AT4G13250_circ_g.4 AT4G13250_circ_g.5 AT4G13250_circ_g.6 AT4G13250_circ_g.8 AT4G13250_circ_g.9 AT4G13250_circ_g.10 AT4G13250_circ_g.11 AT4G13250_circ_g.12 AT4G13250_circ_g.13 AT4G13250_circ_g.14 AT4G13250_circ_g.15 						
					
						Support reads
						7
					
						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  
						
							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
						AT4G13250.2:3
AT4G13250.1:3

General Information
CircRNA Name	AT4G13250_circ_g.7
ID in PlantcircBase	ath_circ_030660
Alias	At_ciR1564, Ath_circ_FC2619
Organism	Arabidpsis thaliana
Position	chr4: 7685165-7685745 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ
Parent gene	AT4G13250
Parent gene annotation	Probable chlorophyll(ide) b reductase NYC1, chloroplastic
Parent gene strand	-
Alternative splicing	AT4G13250_circ_g.1 AT4G13250_circ_g.2 AT4G13250_circ_g.3 AT4G13250_circ_g.4 AT4G13250_circ_g.5 AT4G13250_circ_g.6 AT4G13250_circ_g.8 AT4G13250_circ_g.9 AT4G13250_circ_g.10 AT4G13250_circ_g.11 AT4G13250_circ_g.12 AT4G13250_circ_g.13 AT4G13250_circ_g.14 AT4G13250_circ_g.15
Support reads	7
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	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	AT4G13250.2:3 AT4G13250.1:3

			
						 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  
						
							AGCATCACTCAGTTTCTTTCTAGCTGACTCGCTAGCGTTACTCATAATCTCTTTGAGATTTTGC
TCTAGCTCTTTGACAGTCATATCAACAGATTCAGAAacggcagtgagaggagtacttgaacctc
cagagccagcaccatccatgttaaagatgtgtccaccactgtgctgtctgctcatcacatccat
agcccctc

						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: 405
Transcript exons: 7685165-7685304,7685391-7685459,7685550-7685745
ACGGCAGTGAGAGGAGTACTTGAACCTCCAGAGCCAGCACCATCCATGTTAAAGATGTGTCCAC
CACTGTGCTGTCTGCTCATCACATCCATAGCCCCTCGTGTACATAGAATTGATCCAATCAAATT
TGTGGAGACAATCTGTGTGATATCTTCTTCCGTGAACTCGAGTAGCGGTCTAAAACCTTTGTTA
GTACCAGCATTGTTTATCCATATGTTGATGGAACCAAGCTCTTTTACAGCGAAATTCGACAGCT
TCTCAACGTCTTCGGGTTTGCAAACATCACAGGCAATACCAACTACCTTAGCATCACTCAGTTT
CTTTCTAGCTGACTCGCTAGCGTTACTCATAATCTCTTTGAGATTTTGCTCTAGCTCTTTGACA
GTCATATCAACAGATTCAGAA
						
						Genomic sequence
						
							ACGGCAGTGAGAGGAGTACTTGAACCTCCAGAGCCAGCACCATCCATGTTAAAGATGTGTCCAC
CACTGTGCTGTCTGCTCATCACATCCATAGCCCCTCGTGTACATAGAATTGATCCAATCAAATT
TGTGGAGACAATCTACAAAATAATAGTTACAATTAGACTAATGAACTTCACCATAAGCTCAAGC
TGAAATTAAGCTTTAGGTTCAAAAAGGATTTTACCTGTGTGATATCTTCTTCCGTGAACTCGAG
TAGCGGTCTAAAACCTTTGTTAGTACCAGCATTGTTTATCTATCCAAATGAATATAGACAGTGA
GCAAACATATGACTAAAGATACAAAAAAAGTTACAAACTGTACAAAAAGAAATATGTTTCTTTA
CCCATATGTTGATGGAACCAAGCTCTTTTACAGCGAAATTCGACAGCTTCTCAACGTCTTCGGG
TTTGCAAACATCACAGGCAATACCAACTACCTTAGCATCACTCAGTTTCTTTCTAGCTGACTCG
CTAGCGTTACTCATAATCTCTTTGAGATTTTGCTCTAGCTCTTTGACAGTCATATCAACAGATT
CAGAA

Sequences
Splice junction sequence	AGCATCACTCAGTTTCTTTCTAGCTGACTCGCTAGCGTTACTCATAATCTCTTTGAGATTTTGC TCTAGCTCTTTGACAGTCATATCAACAGATTCAGAAacggcagtgagaggagtacttgaacctc cagagccagcaccatccatgttaaagatgtgtccaccactgtgctgtctgctcatcacatccat agcccctc
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: 405 Transcript exons: 7685165-7685304,7685391-7685459,7685550-7685745 ACGGCAGTGAGAGGAGTACTTGAACCTCCAGAGCCAGCACCATCCATGTTAAAGATGTGTCCAC CACTGTGCTGTCTGCTCATCACATCCATAGCCCCTCGTGTACATAGAATTGATCCAATCAAATT TGTGGAGACAATCTGTGTGATATCTTCTTCCGTGAACTCGAGTAGCGGTCTAAAACCTTTGTTA GTACCAGCATTGTTTATCCATATGTTGATGGAACCAAGCTCTTTTACAGCGAAATTCGACAGCT TCTCAACGTCTTCGGGTTTGCAAACATCACAGGCAATACCAACTACCTTAGCATCACTCAGTTT CTTTCTAGCTGACTCGCTAGCGTTACTCATAATCTCTTTGAGATTTTGCTCTAGCTCTTTGACA GTCATATCAACAGATTCAGAA
Genomic sequence	ACGGCAGTGAGAGGAGTACTTGAACCTCCAGAGCCAGCACCATCCATGTTAAAGATGTGTCCAC CACTGTGCTGTCTGCTCATCACATCCATAGCCCCTCGTGTACATAGAATTGATCCAATCAAATT TGTGGAGACAATCTACAAAATAATAGTTACAATTAGACTAATGAACTTCACCATAAGCTCAAGC TGAAATTAAGCTTTAGGTTCAAAAAGGATTTTACCTGTGTGATATCTTCTTCCGTGAACTCGAG TAGCGGTCTAAAACCTTTGTTAGTACCAGCATTGTTTATCTATCCAAATGAATATAGACAGTGA GCAAACATATGACTAAAGATACAAAAAAAGTTACAAACTGTACAAAAAGAAATATGTTTCTTTA CCCATATGTTGATGGAACCAAGCTCTTTTACAGCGAAATTCGACAGCTTCTCAACGTCTTCGGG TTTGCAAACATCACAGGCAATACCAACTACCTTAGCATCACTCAGTTTCTTTCTAGCTGACTCG CTAGCGTTACTCATAATCTCTTTGAGATTTTGCTCTAGCTCTTTGACAGTCATATCAACAGATT CAGAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.306624562

Conservation Information
Conserved circRNAs	NA
PMCS	0.306624562

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7685730-7685167(-)
7685210-7685742(+)
						
						Potential amino acid sequence
						
							MTVKELEQNLKEIMSNASESARKKLSDAKVVGIACDVCKPEDVEKLSNFAVKELGSINIWINNA
GTNKGFRPLLEFTEEDITQIVSTNLIGSILCTRGAMDVMSRQHSGGHIFNMDGAGSGGSSTPLT
AVSESVDMTVKELEQNLKEIMSNASESARKKLSDAKVVGIACDVCKPEDVEKLSNFAVKELGSI
NIWINNAGTNKGFRPLLEFTEEDITQIVSTNLIGSILCTRGAMDVMSRQHSGGHIFNMDGAGSG
GSSTPLTAVSESVDMTVKELEQNLKEIMSNASESARKKLSDAKVVGIACDVCKPEDVEKLSNFA
VKELGSINIWINNAGTNKGFRPLLEFTEEDITQIVSTNLIGSILCTRGAMDVMSRQHSGGHIFN
MDGAGSGGSSTPLTAVSESVDMTVKELEQNLKEIMSNASESARKKLSDAKVVGIACDVCKPEDV
EKLSNFAVKELGSINIWINNAGTNKGFRPLLEFTEEDITQIVSTNLIGSILCTRGAMDVMSRQH
SGGHIFNMDGAGSGGSSTPLTA(-)
MLKMCPPLCCLLITSIAPRVHRIDPIKFVETICVISSSVNSSSGLKPLLVPALFIHMLMEPSSF
TAKFDSFSTSSGLQTSQAIPTTLASLSFFLADSLALLIISLRFCSSSLTVISTDSETAVRGVLE
PPEPAPSMLKMCPPLCCLLITSIAPRVHRIDPIKFVETICVISSSVNSSSGLKPLLVPALFIHM
LMEPSSFTAKFDSFSTSSGLQTSQAIPTTLASLSFFLADSLALLIISLRFCSSSLTVISTDSET
AVRGVLEPPEPAPSMLKMCPPLCCLLITSIAPRVHRIDPIKFVETICVISSSVNSSSGLKPLLV
PALFIHMLMEPSSFTAKFDSFSTSSGLQTSQAIPTTLASLSFFLADSLALLIISLRFCSSSLTV
ISTDSETAVRGVLEPPEPAPSMLKMCPPLCCLLITSIAPRVHRIDPIKFVETICVISSSVNSSS
GLKPLLVPALFIHMLMEPSSFTAKFDSFSTSSGLQTSQAIPTTLASLSFFLADSLALLIISLRF
CSSSLTVISTDSE(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7685730-7685167(-) 7685210-7685742(+)
Potential amino acid sequence	MTVKELEQNLKEIMSNASESARKKLSDAKVVGIACDVCKPEDVEKLSNFAVKELGSINIWINNA GTNKGFRPLLEFTEEDITQIVSTNLIGSILCTRGAMDVMSRQHSGGHIFNMDGAGSGGSSTPLT AVSESVDMTVKELEQNLKEIMSNASESARKKLSDAKVVGIACDVCKPEDVEKLSNFAVKELGSI NIWINNAGTNKGFRPLLEFTEEDITQIVSTNLIGSILCTRGAMDVMSRQHSGGHIFNMDGAGSG GSSTPLTAVSESVDMTVKELEQNLKEIMSNASESARKKLSDAKVVGIACDVCKPEDVEKLSNFA VKELGSINIWINNAGTNKGFRPLLEFTEEDITQIVSTNLIGSILCTRGAMDVMSRQHSGGHIFN MDGAGSGGSSTPLTAVSESVDMTVKELEQNLKEIMSNASESARKKLSDAKVVGIACDVCKPEDV EKLSNFAVKELGSINIWINNAGTNKGFRPLLEFTEEDITQIVSTNLIGSILCTRGAMDVMSRQH SGGHIFNMDGAGSGGSSTPLTA(-) MLKMCPPLCCLLITSIAPRVHRIDPIKFVETICVISSSVNSSSGLKPLLVPALFIHMLMEPSSF TAKFDSFSTSSGLQTSQAIPTTLASLSFFLADSLALLIISLRFCSSSLTVISTDSETAVRGVLE PPEPAPSMLKMCPPLCCLLITSIAPRVHRIDPIKFVETICVISSSVNSSSGLKPLLVPALFIHM LMEPSSFTAKFDSFSTSSGLQTSQAIPTTLASLSFFLADSLALLIISLRFCSSSLTVISTDSET AVRGVLEPPEPAPSMLKMCPPLCCLLITSIAPRVHRIDPIKFVETICVISSSVNSSSGLKPLLV PALFIHMLMEPSSFTAKFDSFSTSSGLQTSQAIPTTLASLSFFLADSLALLIISLRFCSSSLTV ISTDSETAVRGVLEPPEPAPSMLKMCPPLCCLLITSIAPRVHRIDPIKFVETICVISSSVNSSS GLKPLLVPALFIHMLMEPSSFTAKFDSFSTSSGLQTSQAIPTTLASLSFFLADSLALLIISLRF CSSSLTVISTDSE(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chen et al., 2017a

circRNA

Detail information of AT4G13250_circ_g.7

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