Plant Circular RNA Database

Detail information of AT3G28860_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G28860_circ_g.3
					
						ID in PlantcircBase
						ath_circ_024256
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 10872910-10874035  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT3G28860						
					
						Parent gene annotation
						
							ABC transporter B family member 19
							
						Parent gene strand
						-
					
						Alternative splicing
						
							3_circ_ag.3 3_circ_ag.4 AT3G28830_circ_g.1 AT3G28860_circ_g.1 AT3G28860_circ_g.2 AT3G28860_circ_g.4 AT3G28860_circ_g.5 AT3G28860_circ_g.6 3_circ_ag.7 AT3G28900_circ_g.1 AT3G28900_circ_g.2 AT3G28900_circ_g.3 AT3G28910_circ_g.1 3_circ_ig.2 AT3G28930_circ_g.1 AT3G28930_circ_g.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 3_circ_ig.8 3_circ_ig.9 AT3G28940_circ_g.1 AT3G28940_circ_g.2 AT3G28940_circ_g.3 AT3G28940_circ_g.4 AT3G28950_circ_g.1 AT3G28970_circ_g.1 AT3G28970_circ_g.2 AT3G28970_circ_g.3 AT3G28970_circ_g.4 AT3G28980_circ_g.1 						
					
						Support reads
						29
					
						Tissues
						inflorescences
					
						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
						AT3G28860.1:2

General Information
CircRNA Name	AT3G28860_circ_g.3
ID in PlantcircBase	ath_circ_024256
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 10872910-10874035 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT3G28860
Parent gene annotation	ABC transporter B family member 19
Parent gene strand	-
Alternative splicing	3_circ_ag.3 3_circ_ag.4 AT3G28830_circ_g.1 AT3G28860_circ_g.1 AT3G28860_circ_g.2 AT3G28860_circ_g.4 AT3G28860_circ_g.5 AT3G28860_circ_g.6 3_circ_ag.7 AT3G28900_circ_g.1 AT3G28900_circ_g.2 AT3G28900_circ_g.3 AT3G28910_circ_g.1 3_circ_ig.2 AT3G28930_circ_g.1 AT3G28930_circ_g.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 3_circ_ig.8 3_circ_ig.9 AT3G28940_circ_g.1 AT3G28940_circ_g.2 AT3G28940_circ_g.3 AT3G28940_circ_g.4 AT3G28950_circ_g.1 AT3G28970_circ_g.1 AT3G28970_circ_g.2 AT3G28970_circ_g.3 AT3G28970_circ_g.4 AT3G28980_circ_g.1
Support reads	29
Tissues	inflorescences
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	AT3G28860.1:2

			
						 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  
						
							GTGGCAAAGAGCGCAGGTTCTTGATTCACAAGCCCGATTTGTTCACGCAAAAACTTCAACTGAA
GCGTCTTTATCTCAACACCATCCAACAGAATTTGCCctgagagcatcattcttcttactcttgt
tgtgaggttttctcccatgatgctaaagaagtaatgttggatcaaataagcacccacagcatag
agaccagc

									
								

					

						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: 1044
Transcript exons: 10872910-10873729,10873812-10874035
CTGAGAGCATCATTCTTCTTACTCTTGTTGTGAGGTTTTCTCCCATGATGCTAAAGAAGTAATG
TTGGATCAAATAAGCACCCACAGCATAGAGACCAGCACCAATGTAGATGAAGACATACTCTTTT
GTTTTCCTTTCCATTGAATCATAGTCTGTGTAGTAGAAGACTTCGATCATGTTGCTCATCACAA
TAGCAAATGTAGGACCAATGAAACCAGAAAGAATTGAGCCTACTGCTCCCATGATTGAGTAAGG
CCATTCCGGTGAATTAAGCTTGAGAAGCCTGTAGAAGTAATTTTCAGGGGCACGAGTCTTTCGG
TCAGTCTCTGCATTTGAAATCATCTCTATCCGACCATCAGCTCCAGTGCTGTAAGAATAGCTCA
GATTCCTCAAACTTCCTGATCTTAAACTGAGTGATTTCGTTGACAGTGAATGGCTCAAACGGGT
TGAACGAGTGCGACGAGTTGACGGGTTTGAGAAATCTCGAGTACCAACCATTTCCTGAAACCTG
ATGAGGGATGCGTAAGCACCGGATTTGGCAATGAGTTCTTCATGTGTTCCGGTTTCAACAACTT
GGCCTTGCTGTATCACGGCAATGGAATCAACATTTCTGATGGTGCAGAGACGATGAGCAACAAC
AACAGTGGTCCTCCCCACCATGACTCTGTCTAAAGCTTCCTGAACAATGCTCTCAGAGCTAGCA
TCAAGAGCGCTTGTAGCTTCATCTAGTAACAGAATCTTTGGGTCTTTCAACATCGCCCTAGCAA
TTGCAATTCTCTGCTTCTGTCCACCTGAGAGTTGAACACCACGTTCTCCAACCTGTGTGTCGTA
GCCTTTAGGAAGTAATGTAATGAAACTATGCGCATTCGCAGCGGAAGCAGCAGCTTCAACTTCA
ACCATTGTTGCATCAGGCTTTCCATAGAGTATGTTCTCTAGTATAGTAGTGGCAAAGAGCGCAG
GTTCTTGATTCACAAGCCCGATTTGTTCACGCAAAAACTTCAACTGAAGCGTCTTTATCTCAAC
ACCATCCAACAGAATTTGCC
						
					

						Genomic sequence
						
							CTGAGAGCATCATTCTTCTTACTCTTGTTGTGAGGTTTTCTCCCATGATGCTAAAGAAGTAATG
TTGGATCAAATAAGCACCCACAGCATAGAGACCAGCACCAATGTAGATGAAGACATACTCTTTT
GTTTTCCTTTCCATTGAATCATAGTCTGTGTAGTAGAAGACTTCGATCATGTTGCTCATCACAA
TAGCAAATGTAGGACCAATGAAACCAGAAAGAATTGAGCCTACTGCTCCCATGATTGAGTAAGG
CCATTCCGGTGAATTAAGCTTGAGAAGCCTGTAGAAGTAATTTTCAGGGGCACGAGTCTTTCGG
TCAGTCTCTGCATTTGAAATCATCTCTATCCGACCATCAGCTCCAGTGCTGTAAGAATAGCTCA
GATTCCTCAAACTTCCTGATCTTAAACTGAGTGATTTCGTTGACAGTGAATGGCTCAAACGGGT
TGAACGAGTGCGACGAGTTGACGGGTTTGAGAAATCTCGAGTACCAACCATTTCCTGAAACCTG
ATGAGGGATGCGTAAGCACCGGATTTGGCAATGAGTTCTTCATGTGTTCCGGTTTCAACAACTT
GGCCTTGCTGTATCACGGCAATGGAATCAACATTTCTGATGGTGCAGAGACGATGAGCAACAAC
AACAGTGGTCCTCCCCACCATGACTCTGTCTAAAGCTTCCTGAACAATGCTCTCAGAGCTAGCA
TCAAGAGCGCTTGTAGCTTCATCTAGTAACAGAATCTTTGGGTCTTTCAACATCGCCCTAGCAA
TTGCAATTCTCTGCTTCTGTCCACCTGAGAGTTGAACACCACGTTCTCCAACCTAATTGTATTG
ACATTCAACAAAAAATTAAGCAAAAGGCCATGACATTAACTAGACATATAATCAAATATTTGAT
TTATACCTGTGTGTCGTAGCCTTTAGGAAGTAATGTAATGAAACTATGCGCATTCGCAGCGGAA
GCAGCAGCTTCAACTTCAACCATTGTTGCATCAGGCTTTCCATAGAGTATGTTCTCTAGTATAG
TAGTGGCAAAGAGCGCAGGTTCTTGATTCACAAGCCCGATTTGTTCACGCAAAAACTTCAACTG
AAGCGTCTTTATCTCAACACCATCCAACAGAATTTGCC
						
					

			
		

Sequences
Splice junction sequence	GTGGCAAAGAGCGCAGGTTCTTGATTCACAAGCCCGATTTGTTCACGCAAAAACTTCAACTGAA GCGTCTTTATCTCAACACCATCCAACAGAATTTGCCctgagagcatcattcttcttactcttgt tgtgaggttttctcccatgatgctaaagaagtaatgttggatcaaataagcacccacagcatag agaccagc
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: 1044 Transcript exons: 10872910-10873729,10873812-10874035 CTGAGAGCATCATTCTTCTTACTCTTGTTGTGAGGTTTTCTCCCATGATGCTAAAGAAGTAATG TTGGATCAAATAAGCACCCACAGCATAGAGACCAGCACCAATGTAGATGAAGACATACTCTTTT GTTTTCCTTTCCATTGAATCATAGTCTGTGTAGTAGAAGACTTCGATCATGTTGCTCATCACAA TAGCAAATGTAGGACCAATGAAACCAGAAAGAATTGAGCCTACTGCTCCCATGATTGAGTAAGG CCATTCCGGTGAATTAAGCTTGAGAAGCCTGTAGAAGTAATTTTCAGGGGCACGAGTCTTTCGG TCAGTCTCTGCATTTGAAATCATCTCTATCCGACCATCAGCTCCAGTGCTGTAAGAATAGCTCA GATTCCTCAAACTTCCTGATCTTAAACTGAGTGATTTCGTTGACAGTGAATGGCTCAAACGGGT TGAACGAGTGCGACGAGTTGACGGGTTTGAGAAATCTCGAGTACCAACCATTTCCTGAAACCTG ATGAGGGATGCGTAAGCACCGGATTTGGCAATGAGTTCTTCATGTGTTCCGGTTTCAACAACTT GGCCTTGCTGTATCACGGCAATGGAATCAACATTTCTGATGGTGCAGAGACGATGAGCAACAAC AACAGTGGTCCTCCCCACCATGACTCTGTCTAAAGCTTCCTGAACAATGCTCTCAGAGCTAGCA TCAAGAGCGCTTGTAGCTTCATCTAGTAACAGAATCTTTGGGTCTTTCAACATCGCCCTAGCAA TTGCAATTCTCTGCTTCTGTCCACCTGAGAGTTGAACACCACGTTCTCCAACCTGTGTGTCGTA GCCTTTAGGAAGTAATGTAATGAAACTATGCGCATTCGCAGCGGAAGCAGCAGCTTCAACTTCA ACCATTGTTGCATCAGGCTTTCCATAGAGTATGTTCTCTAGTATAGTAGTGGCAAAGAGCGCAG GTTCTTGATTCACAAGCCCGATTTGTTCACGCAAAAACTTCAACTGAAGCGTCTTTATCTCAAC ACCATCCAACAGAATTTGCC
Genomic sequence	CTGAGAGCATCATTCTTCTTACTCTTGTTGTGAGGTTTTCTCCCATGATGCTAAAGAAGTAATG TTGGATCAAATAAGCACCCACAGCATAGAGACCAGCACCAATGTAGATGAAGACATACTCTTTT GTTTTCCTTTCCATTGAATCATAGTCTGTGTAGTAGAAGACTTCGATCATGTTGCTCATCACAA TAGCAAATGTAGGACCAATGAAACCAGAAAGAATTGAGCCTACTGCTCCCATGATTGAGTAAGG CCATTCCGGTGAATTAAGCTTGAGAAGCCTGTAGAAGTAATTTTCAGGGGCACGAGTCTTTCGG TCAGTCTCTGCATTTGAAATCATCTCTATCCGACCATCAGCTCCAGTGCTGTAAGAATAGCTCA GATTCCTCAAACTTCCTGATCTTAAACTGAGTGATTTCGTTGACAGTGAATGGCTCAAACGGGT TGAACGAGTGCGACGAGTTGACGGGTTTGAGAAATCTCGAGTACCAACCATTTCCTGAAACCTG ATGAGGGATGCGTAAGCACCGGATTTGGCAATGAGTTCTTCATGTGTTCCGGTTTCAACAACTT GGCCTTGCTGTATCACGGCAATGGAATCAACATTTCTGATGGTGCAGAGACGATGAGCAACAAC AACAGTGGTCCTCCCCACCATGACTCTGTCTAAAGCTTCCTGAACAATGCTCTCAGAGCTAGCA TCAAGAGCGCTTGTAGCTTCATCTAGTAACAGAATCTTTGGGTCTTTCAACATCGCCCTAGCAA TTGCAATTCTCTGCTTCTGTCCACCTGAGAGTTGAACACCACGTTCTCCAACCTAATTGTATTG ACATTCAACAAAAAATTAAGCAAAAGGCCATGACATTAACTAGACATATAATCAAATATTTGAT TTATACCTGTGTGTCGTAGCCTTTAGGAAGTAATGTAATGAAACTATGCGCATTCGCAGCGGAA GCAGCAGCTTCAACTTCAACCATTGTTGCATCAGGCTTTCCATAGAGTATGTTCTCTAGTATAG TAGTGGCAAAGAGCGCAGGTTCTTGATTCACAAGCCCGATTTGTTCACGCAAAAACTTCAACTG AAGCGTCTTTATCTCAACACCATCCAACAGAATTTGCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.497464079

Conservation Information
Conserved circRNAs	NA
PMCS	0.497464079

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10873893-10872912(-)
						
						Potential amino acid sequence
						
							MVEVEAAASAANAHSFITLLPKGYDTQVGERGVQLSGGQKQRIAIARAMLKDPKILLLDEATSA
LDASSESIVQEALDRVMVGRTTVVVAHRLCTIRNVDSIAVIQQGQVVETGTHEELIAKSGAYAS
LIRFQEMVGTRDFSNPSTRRTRSTRLSHSLSTKSLSLRSGSLRNLSYSYSTGADGRIEMISNAE
TDRKTRAPENYFYRLLKLNSPEWPYSIMGAVGSILSGFIGPTFAIVMSNMIEVFYYTDYDSMER
KTKEYVFIYIGAGLYAVGAYLIQHYFFSIMGENLTTRVRRMMLSGQILLDGVEIKTLQLKFLRE
QIGLVNQEPALFATTILENILYGKPDATMVEVEAAASAANAHSFITLLPKGYDTQVGERGVQLS
GGQKQRIAIARAMLKDPKILLLDEATSALDASSESIVQEALDRVMVGRTTVVVAHRLCTIRNVD
SIAVIQQGQVVETGTHEELIAKSGAYASLIRFQEMVGTRDFSNPSTRRTRSTRLSHSLSTKSLS
LRSGSLRNLSYSYSTGADGRIEMISNAETDRKTRAPENYFYRLLKLNSPEWPYSIMGAVGSILS
GFIGPTFAIVMSNMIEVFYYTDYDSMERKTKEYVFIYIGAGLYAVGAYLIQHYFFSIMGENLTT
RVRRMMLSGQILLDGVEIKTLQLKFLREQIGLVNQEPALFATTILENILYGKPDATMVEVEAAA
SAANAHSFITLLPKGYDTQVGERGVQLSGGQKQRIAIARAMLKDPKILLLDEATSALDASSESI
VQEALDRVMVGRTTVVVAHRLCTIRNVDSIAVIQQGQVVETGTHEELIAKSGAYASLIRFQEMV
GTRDFSNPSTRRTRSTRLSHSLSTKSLSLRSGSLRNLSYSYSTGADGRIEMISNAETDRKTRAP
ENYFYRLLKLNSPEWPYSIMGAVGSILSGFIGPTFAIVMSNMIEVFYYTDYDSMERKTKEYVFI
YIGAGLYAVGAYLIQHYFFSIMGENLTTRVRRMMLSGQILLDGVEIKTLQLKFLREQIGLVNQE
PALFATTILENILYGKPDATMVEVEAAASAANAHSFITLLPKGYDTQVGERGVQLSGGQKQRIA
IARAMLKDPKILLLDEATSALDASSESIVQEALDRVMVGRTTVVVAHRLCTIRNVDSIAVIQQG
QVVETGTHEELIAKSGAYASLIRFQEMVGTRDFSNPSTRRTRSTRLSHSLSTKSLSLRSGSLRN
LSYSYSTGADGRIEMISNAETDRKTRAPENYFYRLLKLNSPEWPYSIMGAVGSILSGFIGPTFA
IVMSNMIEVFYYTDYDSMERKTKEYVFIYIGAGLYAVGAYLIQHYFFSIMGENLTTRVRRMMLS
(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	10873893-10872912(-)
Potential amino acid sequence	MVEVEAAASAANAHSFITLLPKGYDTQVGERGVQLSGGQKQRIAIARAMLKDPKILLLDEATSA LDASSESIVQEALDRVMVGRTTVVVAHRLCTIRNVDSIAVIQQGQVVETGTHEELIAKSGAYAS LIRFQEMVGTRDFSNPSTRRTRSTRLSHSLSTKSLSLRSGSLRNLSYSYSTGADGRIEMISNAE TDRKTRAPENYFYRLLKLNSPEWPYSIMGAVGSILSGFIGPTFAIVMSNMIEVFYYTDYDSMER KTKEYVFIYIGAGLYAVGAYLIQHYFFSIMGENLTTRVRRMMLSGQILLDGVEIKTLQLKFLRE QIGLVNQEPALFATTILENILYGKPDATMVEVEAAASAANAHSFITLLPKGYDTQVGERGVQLS GGQKQRIAIARAMLKDPKILLLDEATSALDASSESIVQEALDRVMVGRTTVVVAHRLCTIRNVD SIAVIQQGQVVETGTHEELIAKSGAYASLIRFQEMVGTRDFSNPSTRRTRSTRLSHSLSTKSLS LRSGSLRNLSYSYSTGADGRIEMISNAETDRKTRAPENYFYRLLKLNSPEWPYSIMGAVGSILS GFIGPTFAIVMSNMIEVFYYTDYDSMERKTKEYVFIYIGAGLYAVGAYLIQHYFFSIMGENLTT RVRRMMLSGQILLDGVEIKTLQLKFLREQIGLVNQEPALFATTILENILYGKPDATMVEVEAAA SAANAHSFITLLPKGYDTQVGERGVQLSGGQKQRIAIARAMLKDPKILLLDEATSALDASSESI VQEALDRVMVGRTTVVVAHRLCTIRNVDSIAVIQQGQVVETGTHEELIAKSGAYASLIRFQEMV GTRDFSNPSTRRTRSTRLSHSLSTKSLSLRSGSLRNLSYSYSTGADGRIEMISNAETDRKTRAP ENYFYRLLKLNSPEWPYSIMGAVGSILSGFIGPTFAIVMSNMIEVFYYTDYDSMERKTKEYVFI YIGAGLYAVGAYLIQHYFFSIMGENLTTRVRRMMLSGQILLDGVEIKTLQLKFLREQIGLVNQE PALFATTILENILYGKPDATMVEVEAAASAANAHSFITLLPKGYDTQVGERGVQLSGGQKQRIA IARAMLKDPKILLLDEATSALDASSESIVQEALDRVMVGRTTVVVAHRLCTIRNVDSIAVIQQG QVVETGTHEELIAKSGAYASLIRFQEMVGTRDFSNPSTRRTRSTRLSHSLSTKSLSLRSGSLRN LSYSYSTGADGRIEMISNAETDRKTRAPENYFYRLLKLNSPEWPYSIMGAVGSILSGFIGPTFA IVMSNMIEVFYYTDYDSMERKTKEYVFIYIGAGLYAVGAYLIQHYFFSIMGENLTTRVRRMMLS (-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G28860_circ_g.3

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