Plant Circular RNA Database

Detail information of AT1G79280_circ_g.11

			
						 General Information
					
						CircRNA Name
						AT1G79280_circ_g.11
					
						ID in PlantcircBase
						ath_circ_010963
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 29823942-29825328  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT1G79280						
					
						Parent gene annotation
						
							nuclear pore anchor
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G79280_circ_g.7 AT1G79280_circ_g.8 AT1G79280_circ_g.9 AT1G79280_circ_g.10 AT1G79280_circ_g.12 AT1G79280_circ_g.13 AT1G79280_circ_g.14 AT1G79280_circ_g.15 						
					
						Support reads
						2
					
						Tissues
						seed, whole_plant
					
						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
						AT1G79280.3:6
AT1G79280.2:6
AT1G79280.1:6

General Information
CircRNA Name	AT1G79280_circ_g.11
ID in PlantcircBase	ath_circ_010963
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 29823942-29825328 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT1G79280
Parent gene annotation	nuclear pore anchor
Parent gene strand	-
Alternative splicing	AT1G79280_circ_g.7 AT1G79280_circ_g.8 AT1G79280_circ_g.9 AT1G79280_circ_g.10 AT1G79280_circ_g.12 AT1G79280_circ_g.13 AT1G79280_circ_g.14 AT1G79280_circ_g.15
Support reads	2
Tissues	seed, whole_plant
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	AT1G79280.3:6 AT1G79280.2:6 AT1G79280.1:6

			
						 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  
						
							CCAATTCAGGAAGTACCTGGAGCATGTGGCTTTTACTAGATTCTACTTCTCCCCTCAATTTTTC
AATTTCTTCCTTTGCGGTACGCAGTTCGATGGACATctgttcattaagttcatgatactttttc
tcagccagattcttttgctgctctagcatcaatttctcttcactccacttggcattaagctcag
actgataa

									
								

					

						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: 657
Transcript exons: 29823942-29824034,29824133-29824249,29824597-29824699,29
824795-29824979,29825097-29825171,29825245-29825328
CTGTTCATTAAGTTCATGATACTTTTTCTCAGCCAGATTCTTTTGCTGCTCTAGCATCAATTTC
TCTTCACTCCACTTGGCATTAAGCTCAGAATTTTCAATTCCCCGTGCATCAGCCAATTTACGTA
GTTCAGATGCCTCCTCTTGAAGGGCTGCTAAGGCTTGTGATGTTTTCGTAAGCTCCTGAATAGT
TTCAGACAGCAGAATAACCTGTCTTTCATAATTTCTCTGAGCAACACGCCATTTCTCATGTTCA
GTCTCCAGGTCATTCTTCAAAGTGGACATTTGGATATTCATTGCTTCAATTTGGGACTTTTTAA
CTAAGTTTTCTTCTCTCAGACTTGCAATTTCAGCCGATGCTGATAGAAGAGCATCTTCTTTTCC
TGCAGCAGCAGTGGCTAGTTGCTCGGATTTCTGAATACAGTCGTTTTCAAGTTCTGACACCCTC
TCCCTAAGAGAAACAAGTTCTGCTTCCAATGATCGTTGTCTCTTTTCAGCCTCAAGTCTGAAGT
TCTCATGAGCAGACTCCATCTGCTTTAATGCAGTTTCATTCACCTGAGCTATACTCTTGTACTG
GAGCATGTGGCTTTTACTAGATTCTACTTCTCCCCTCAATTTTTCAATTTCTTCCTTTGCGGTA
CGCAGTTCGATGGACAT
						
					

						Genomic sequence
						
							CTGTTCATTAAGTTCATGATACTTTTTCTCAGCCAGATTCTTTTGCTGCTCTAGCATCAATTTC
TCTTCACTCCACTTGGCATTAAGCTCAGACTGATAAACACCAAGAAAATAGAAATTGATGTTTC
ACGAATCAACTATAATTGTAGGAAGAATTGAATCACAAAAAGTTGTGTACAAGTAGAAGTTACA
TTTTCAATTCCCCGTGCATCAGCCAATTTACGTAGTTCAGATGCCTCCTCTTGAAGGGCTGCTA
AGGCTTGTGATGTTTTCGTAAGCTCCTGAATAGTTTCAGACAGCAGAATAACCTGCACTCCAAA
AAGAAGTAGGAAACAAAAAGAGTGATAGTTGTAATATCTATGGAAAGAGAGAAGAACAGAATTA
GCTGATGGCAGTAAGACCTTAAGTTATGAAAAACCTAACAATGATTTAATGTAATGTAAAACAC
AATTCAGAAAATATTTGAAGATATCCTCGGATATATGACAAAGGTGCAGTAAAATAGAGTATTC
AGAAAACAACAGTTTCATGAAATGGATCAACAGGATGGGTAATAAAATCTAGTCAGTTTCTAGC
ATCATATAATAAAAACCAACGTCAACGTGAATATGCATGATGGTCAAAATGTTTCTTGAAATAG
AGAGCTTTAACCAACCTGTCTTTCATAATTTCTCTGAGCAACACGCCATTTCTCATGTTCAGTC
TCCAGGTCATTCTTCAAAGTGGACATTTGGATATTCATTGCTTCAATTTGGGACCTGCAGTCAA
TTGCAAAATATCAATTAAGGGACAAACATGTGTTTGTCCACGAGAAAGAAAAAAAGATACTTCT
GTTACATGATAGAACATTTACTTTTTAACTAAGTTTTCTTCTCTCAGACTTGCAATTTCAGCCG
ATGCTGATAGAAGAGCATCTTCTTTTCCTGCAGCAGCAGTGGCTAGTTGCTCGGATTTCTGAAT
ACAGTCGTTTTCAAGTTCTGACACCCTCTCCCTAAGAGAAACAAGTTCTGCTTCCAATGATCGT
TGTCTCTTTTCAGCCTACAAACAGCCATCAGATTTAAAATATAAACCAACAGCAGATCTAGTTC
TATCACAGTGGACATAGCAGCATATCCAGATGTGATCATTGTTTCATCCAAACATAATCACAAA
TACCTCAAGTCTGAAGTTCTCATGAGCAGACTCCATCTGCTTTAATGCAGTTTCATTCACCTGA
GCTATACTCTTGTACTGCATGATGGTTCACAAGGTCAATTAATAGTCATGTTGAAATCGAAACT
AACTTAGCCAATTCAGGAAGTACCTGGAGCATGTGGCTTTTACTAGATTCTACTTCTCCCCTCA
ATTTTTCAATTTCTTCCTTTGCGGTACGCAGTTCGATGGACAT
						
					

			
		

Sequences
Splice junction sequence	CCAATTCAGGAAGTACCTGGAGCATGTGGCTTTTACTAGATTCTACTTCTCCCCTCAATTTTTC AATTTCTTCCTTTGCGGTACGCAGTTCGATGGACATctgttcattaagttcatgatactttttc tcagccagattcttttgctgctctagcatcaatttctcttcactccacttggcattaagctcag actgataa
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: 657 Transcript exons: 29823942-29824034,29824133-29824249,29824597-29824699,29 824795-29824979,29825097-29825171,29825245-29825328 CTGTTCATTAAGTTCATGATACTTTTTCTCAGCCAGATTCTTTTGCTGCTCTAGCATCAATTTC TCTTCACTCCACTTGGCATTAAGCTCAGAATTTTCAATTCCCCGTGCATCAGCCAATTTACGTA GTTCAGATGCCTCCTCTTGAAGGGCTGCTAAGGCTTGTGATGTTTTCGTAAGCTCCTGAATAGT TTCAGACAGCAGAATAACCTGTCTTTCATAATTTCTCTGAGCAACACGCCATTTCTCATGTTCA GTCTCCAGGTCATTCTTCAAAGTGGACATTTGGATATTCATTGCTTCAATTTGGGACTTTTTAA CTAAGTTTTCTTCTCTCAGACTTGCAATTTCAGCCGATGCTGATAGAAGAGCATCTTCTTTTCC TGCAGCAGCAGTGGCTAGTTGCTCGGATTTCTGAATACAGTCGTTTTCAAGTTCTGACACCCTC TCCCTAAGAGAAACAAGTTCTGCTTCCAATGATCGTTGTCTCTTTTCAGCCTCAAGTCTGAAGT TCTCATGAGCAGACTCCATCTGCTTTAATGCAGTTTCATTCACCTGAGCTATACTCTTGTACTG GAGCATGTGGCTTTTACTAGATTCTACTTCTCCCCTCAATTTTTCAATTTCTTCCTTTGCGGTA CGCAGTTCGATGGACAT
Genomic sequence	CTGTTCATTAAGTTCATGATACTTTTTCTCAGCCAGATTCTTTTGCTGCTCTAGCATCAATTTC TCTTCACTCCACTTGGCATTAAGCTCAGACTGATAAACACCAAGAAAATAGAAATTGATGTTTC ACGAATCAACTATAATTGTAGGAAGAATTGAATCACAAAAAGTTGTGTACAAGTAGAAGTTACA TTTTCAATTCCCCGTGCATCAGCCAATTTACGTAGTTCAGATGCCTCCTCTTGAAGGGCTGCTA AGGCTTGTGATGTTTTCGTAAGCTCCTGAATAGTTTCAGACAGCAGAATAACCTGCACTCCAAA AAGAAGTAGGAAACAAAAAGAGTGATAGTTGTAATATCTATGGAAAGAGAGAAGAACAGAATTA GCTGATGGCAGTAAGACCTTAAGTTATGAAAAACCTAACAATGATTTAATGTAATGTAAAACAC AATTCAGAAAATATTTGAAGATATCCTCGGATATATGACAAAGGTGCAGTAAAATAGAGTATTC AGAAAACAACAGTTTCATGAAATGGATCAACAGGATGGGTAATAAAATCTAGTCAGTTTCTAGC ATCATATAATAAAAACCAACGTCAACGTGAATATGCATGATGGTCAAAATGTTTCTTGAAATAG AGAGCTTTAACCAACCTGTCTTTCATAATTTCTCTGAGCAACACGCCATTTCTCATGTTCAGTC TCCAGGTCATTCTTCAAAGTGGACATTTGGATATTCATTGCTTCAATTTGGGACCTGCAGTCAA TTGCAAAATATCAATTAAGGGACAAACATGTGTTTGTCCACGAGAAAGAAAAAAAGATACTTCT GTTACATGATAGAACATTTACTTTTTAACTAAGTTTTCTTCTCTCAGACTTGCAATTTCAGCCG ATGCTGATAGAAGAGCATCTTCTTTTCCTGCAGCAGCAGTGGCTAGTTGCTCGGATTTCTGAAT ACAGTCGTTTTCAAGTTCTGACACCCTCTCCCTAAGAGAAACAAGTTCTGCTTCCAATGATCGT TGTCTCTTTTCAGCCTACAAACAGCCATCAGATTTAAAATATAAACCAACAGCAGATCTAGTTC TATCACAGTGGACATAGCAGCATATCCAGATGTGATCATTGTTTCATCCAAACATAATCACAAA TACCTCAAGTCTGAAGTTCTCATGAGCAGACTCCATCTGCTTTAATGCAGTTTCATTCACCTGA GCTATACTCTTGTACTGCATGATGGTTCACAAGGTCAATTAATAGTCATGTTGAAATCGAAACT AACTTAGCCAATTCAGGAAGTACCTGGAGCATGTGGCTTTTACTAGATTCTACTTCTCCCCTCA ATTTTTCAATTTCTTCCTTTGCGGTACGCAGTTCGATGGACAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.198432452

Conservation Information
Conserved circRNAs	NA
PMCS	0.198432452

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							29825329-29823944(-)
						
						Potential amino acid sequence
						
							MSIELRTAKEEIEKLRGEVESSKSHMLQYKSIAQVNETALKQMESAHENFRLEAEKRQRSLEAE
LVSLRERVSELENDCIQKSEQLATAAAGKEDALLSASAEIASLREENLVKKSQIEAMNIQMSTL
KNDLETEHEKWRVAQRNYERQVILLSETIQELTKTSQALAALQEEASELRKLADARGIENSELN
AKWSEEKLMLEQQKNLAEKKYHELNEQMSIELRTAKEEIEKLRGEVESSKSHMLQYKSIAQVNE
TALKQMESAHENFRLEAEKRQRSLEAELVSLRERVSELENDCIQKSEQLATAAAGKEDALLSAS
AEIASLREENLVKKSQIEAMNIQMSTLKNDLETEHEKWRVAQRNYERQVILLSETIQELTKTSQ
ALAALQEEASELRKLADARGIENSELNAKWSEEKLMLEQQKNLAEKKYHELNEQMSIELRTAKE
EIEKLRGEVESSKSHMLQYKSIAQVNETALKQMESAHENFRLEAEKRQRSLEAELVSLRERVSE
LENDCIQKSEQLATAAAGKEDALLSASAEIASLREENLVKKSQIEAMNIQMSTLKNDLETEHEK
WRVAQRNYERQVILLSETIQELTKTSQALAALQEEASELRKLADARGIENSELNAKWSEEKLML
EQQKNLAEKKYHELNEQMSIELRTAKEEIEKLRGEVESSKSHMLQYKSIAQVNETALKQMESAH
ENFRLEAEKRQRSLEAELVSLRERVSELENDCIQKSEQLATAAAGKEDALLSASAEIASLREEN
LVKKSQIEAMNIQMSTLKNDLETEHEKWRVAQRNYERQVILLSETIQELTKTSQALAALQEEAS
ELRKLADARGIENSELNAKWSEEKLMLEQQKNLAEKKYHELNEQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	29825329-29823944(-)
Potential amino acid sequence	MSIELRTAKEEIEKLRGEVESSKSHMLQYKSIAQVNETALKQMESAHENFRLEAEKRQRSLEAE LVSLRERVSELENDCIQKSEQLATAAAGKEDALLSASAEIASLREENLVKKSQIEAMNIQMSTL KNDLETEHEKWRVAQRNYERQVILLSETIQELTKTSQALAALQEEASELRKLADARGIENSELN AKWSEEKLMLEQQKNLAEKKYHELNEQMSIELRTAKEEIEKLRGEVESSKSHMLQYKSIAQVNE TALKQMESAHENFRLEAEKRQRSLEAELVSLRERVSELENDCIQKSEQLATAAAGKEDALLSAS AEIASLREENLVKKSQIEAMNIQMSTLKNDLETEHEKWRVAQRNYERQVILLSETIQELTKTSQ ALAALQEEASELRKLADARGIENSELNAKWSEEKLMLEQQKNLAEKKYHELNEQMSIELRTAKE EIEKLRGEVESSKSHMLQYKSIAQVNETALKQMESAHENFRLEAEKRQRSLEAELVSLRERVSE LENDCIQKSEQLATAAAGKEDALLSASAEIASLREENLVKKSQIEAMNIQMSTLKNDLETEHEK WRVAQRNYERQVILLSETIQELTKTSQALAALQEEASELRKLADARGIENSELNAKWSEEKLML EQQKNLAEKKYHELNEQMSIELRTAKEEIEKLRGEVESSKSHMLQYKSIAQVNETALKQMESAH ENFRLEAEKRQRSLEAELVSLRERVSELENDCIQKSEQLATAAAGKEDALLSASAEIASLREEN LVKKSQIEAMNIQMSTLKNDLETEHEKWRVAQRNYERQVILLSETIQELTKTSQALAALQEEAS ELRKLADARGIENSELNAKWSEEKLMLEQQKNLAEKKYHELNEQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G79280_circ_g.11

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