Plant Circular RNA Database

Detail information of AT2G47860_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT2G47860_circ_g.4
					
						ID in PlantcircBase
						ath_circ_018939
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 19600273-19601439  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT2G47860						
					
						Parent gene annotation
						
							Phototropic-responsive NPH3 family protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G47860_circ_g.1 AT2G47860_circ_g.2 AT2G47860_circ_g.3 						
					
						Support reads
						3
					
						Tissues
						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  
						
							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
						AT2G47860.3:1
AT2G47860.5:1
AT2G47860.6:1
AT2G47860.1:1
AT2G47860.2:1
AT2G47860.4:1

General Information
CircRNA Name	AT2G47860_circ_g.4
ID in PlantcircBase	ath_circ_018939
Alias	NA
Organism	Arabidpsis thaliana
Position	chr2: 19600273-19601439 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	PcircRNA_finder
Parent gene	AT2G47860
Parent gene annotation	Phototropic-responsive NPH3 family protein
Parent gene strand	+
Alternative splicing	AT2G47860_circ_g.1 AT2G47860_circ_g.2 AT2G47860_circ_g.3
Support reads	3
Tissues	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	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	AT2G47860.3:1 AT2G47860.5:1 AT2G47860.6:1 AT2G47860.1:1 AT2G47860.2:1 AT2G47860.4:1

			
						 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  
						
							CCTTCCTCCCTCCAAGTTTATAGCACTCGCAGAGCTTCTCCCTGACCATGCTCGCGTCGTCTGC
GATGGCCTCTACCGAGCCGTTGATATCTTCCTCAAGtttcctctcgtctctcggagtggaagaa
tccggaaacttgttctggaatcaaaagacacgaacctgaacctagccgctgttccaggcggctc
agaatcgt

									
								

					

						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: 1167
Transcript exons: 19600273-19601439
TTTCCTCTCGTCTCTCGGAGTGGAAGAATCCGGAAACTTGTTCTGGAATCAAAAGACACGAACC
TGAACCTAGCCGCTGTTCCAGGCGGCTCAGAATCGTTCGAGCTTGCTGCAAAGTTCTGCTACGG
CGTTGGCGTCCAATATAACTCGTCCAACATTGCGGCGCTGCGATGCGTGGCTCATTACCTGGAG
ATGACAGAAGACTTGTCAGAGAAGAACCTCGAGGCGAGAACAGAGGCCTACCTGAAAGACTCCA
TTTTCAATGACATATCGAATTCGATCACTGTTCTTCACTCCTGCGAGAGGCTACTGCCTGTAGC
TGAAGAGATCAACCTCGTCGGGAGGCTGGTCAACGCAATCGCTGTAAACGCCTGCAAAGAACAG
CTAGCCTCTGGTTTGCTCAAGCTTGATCAGAGTTTCAGCTGCGGCGTCCCGGAGACTGCGAAAC
CTTGTGACTGGTGGGGTCGCTCTCTTCCCATCCTCAAGCTTGATTTCTTCCAGAGAGTTCTCTC
CGCCATGAAATCCAAAGGTCTCAATCACGACATTATCAGTGACATCCTTATGAGCTACGCTCGC
AAATCACTGCAGATCATCAGAGAACCGAATCTCGTCAAATCAGATTCCGATCTTCAGAGGAAAC
AGCGAATCGTCCTTGAAGCGGTCGTCGGGCTCCTCCCAACGCAAGCGAACAAAAGCTCGATTCC
GATCTCGTTCCTCTCTAGCTTGTTGAAGACCGCTATAGGATCTGGCACCTCCGTCTCTTGCAGA
TCCGATCTGGAGAGACGGATCAGCCACCTGCTCGACCAGGCCATCCTTGAAGACATCCTTATTC
CGGCGAACATCGGCGCCATGTACGACACCGACTCGGTGCAGAGGATTTTCTCAATGTTCTTGAA
CCTTGACGAGTGCGAGTACAGAGATGATGATGACGACGAGGAGGACGCGGTGGACGAGAGCGAG
ATGGCCATGTACGATTTCGAGGGGGCTGAGTCACCGAAACAGAGCTCCATCTTCAAGGTGTCGA
AGCTGATGGATAGTTATCTCGCTGAGGTGGCTCTGGACTCGAGCCTTCCTCCCTCCAAGTTTAT
AGCACTCGCAGAGCTTCTCCCTGACCATGCTCGCGTCGTCTGCGATGGCCTCTACCGAGCCGTT
GATATCTTCCTCAAG
						
					

						Genomic sequence
						
							TTTCCTCTCGTCTCTCGGAGTGGAAGAATCCGGAAACTTGTTCTGGAATCAAAAGACACGAACC
TGAACCTAGCCGCTGTTCCAGGCGGCTCAGAATCGTTCGAGCTTGCTGCAAAGTTCTGCTACGG
CGTTGGCGTCCAATATAACTCGTCCAACATTGCGGCGCTGCGATGCGTGGCTCATTACCTGGAG
ATGACAGAAGACTTGTCAGAGAAGAACCTCGAGGCGAGAACAGAGGCCTACCTGAAAGACTCCA
TTTTCAATGACATATCGAATTCGATCACTGTTCTTCACTCCTGCGAGAGGCTACTGCCTGTAGC
TGAAGAGATCAACCTCGTCGGGAGGCTGGTCAACGCAATCGCTGTAAACGCCTGCAAAGAACAG
CTAGCCTCTGGTTTGCTCAAGCTTGATCAGAGTTTCAGCTGCGGCGTCCCGGAGACTGCGAAAC
CTTGTGACTGGTGGGGTCGCTCTCTTCCCATCCTCAAGCTTGATTTCTTCCAGAGAGTTCTCTC
CGCCATGAAATCCAAAGGTCTCAATCACGACATTATCAGTGACATCCTTATGAGCTACGCTCGC
AAATCACTGCAGATCATCAGAGAACCGAATCTCGTCAAATCAGATTCCGATCTTCAGAGGAAAC
AGCGAATCGTCCTTGAAGCGGTCGTCGGGCTCCTCCCAACGCAAGCGAACAAAAGCTCGATTCC
GATCTCGTTCCTCTCTAGCTTGTTGAAGACCGCTATAGGATCTGGCACCTCCGTCTCTTGCAGA
TCCGATCTGGAGAGACGGATCAGCCACCTGCTCGACCAGGCCATCCTTGAAGACATCCTTATTC
CGGCGAACATCGGCGCCATGTACGACACCGACTCGGTGCAGAGGATTTTCTCAATGTTCTTGAA
CCTTGACGAGTGCGAGTACAGAGATGATGATGACGACGAGGAGGACGCGGTGGACGAGAGCGAG
ATGGCCATGTACGATTTCGAGGGGGCTGAGTCACCGAAACAGAGCTCCATCTTCAAGGTGTCGA
AGCTGATGGATAGTTATCTCGCTGAGGTGGCTCTGGACTCGAGCCTTCCTCCCTCCAAGTTTAT
AGCACTCGCAGAGCTTCTCCCTGACCATGCTCGCGTCGTCTGCGATGGCCTCTACCGAGCCGTT
GATATCTTCCTCAAG
						
					

			
		

Sequences
Splice junction sequence	CCTTCCTCCCTCCAAGTTTATAGCACTCGCAGAGCTTCTCCCTGACCATGCTCGCGTCGTCTGC GATGGCCTCTACCGAGCCGTTGATATCTTCCTCAAGtttcctctcgtctctcggagtggaagaa tccggaaacttgttctggaatcaaaagacacgaacctgaacctagccgctgttccaggcggctc agaatcgt
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: 1167 Transcript exons: 19600273-19601439 TTTCCTCTCGTCTCTCGGAGTGGAAGAATCCGGAAACTTGTTCTGGAATCAAAAGACACGAACC TGAACCTAGCCGCTGTTCCAGGCGGCTCAGAATCGTTCGAGCTTGCTGCAAAGTTCTGCTACGG CGTTGGCGTCCAATATAACTCGTCCAACATTGCGGCGCTGCGATGCGTGGCTCATTACCTGGAG ATGACAGAAGACTTGTCAGAGAAGAACCTCGAGGCGAGAACAGAGGCCTACCTGAAAGACTCCA TTTTCAATGACATATCGAATTCGATCACTGTTCTTCACTCCTGCGAGAGGCTACTGCCTGTAGC TGAAGAGATCAACCTCGTCGGGAGGCTGGTCAACGCAATCGCTGTAAACGCCTGCAAAGAACAG CTAGCCTCTGGTTTGCTCAAGCTTGATCAGAGTTTCAGCTGCGGCGTCCCGGAGACTGCGAAAC CTTGTGACTGGTGGGGTCGCTCTCTTCCCATCCTCAAGCTTGATTTCTTCCAGAGAGTTCTCTC CGCCATGAAATCCAAAGGTCTCAATCACGACATTATCAGTGACATCCTTATGAGCTACGCTCGC AAATCACTGCAGATCATCAGAGAACCGAATCTCGTCAAATCAGATTCCGATCTTCAGAGGAAAC AGCGAATCGTCCTTGAAGCGGTCGTCGGGCTCCTCCCAACGCAAGCGAACAAAAGCTCGATTCC GATCTCGTTCCTCTCTAGCTTGTTGAAGACCGCTATAGGATCTGGCACCTCCGTCTCTTGCAGA TCCGATCTGGAGAGACGGATCAGCCACCTGCTCGACCAGGCCATCCTTGAAGACATCCTTATTC CGGCGAACATCGGCGCCATGTACGACACCGACTCGGTGCAGAGGATTTTCTCAATGTTCTTGAA CCTTGACGAGTGCGAGTACAGAGATGATGATGACGACGAGGAGGACGCGGTGGACGAGAGCGAG ATGGCCATGTACGATTTCGAGGGGGCTGAGTCACCGAAACAGAGCTCCATCTTCAAGGTGTCGA AGCTGATGGATAGTTATCTCGCTGAGGTGGCTCTGGACTCGAGCCTTCCTCCCTCCAAGTTTAT AGCACTCGCAGAGCTTCTCCCTGACCATGCTCGCGTCGTCTGCGATGGCCTCTACCGAGCCGTT GATATCTTCCTCAAG
Genomic sequence	TTTCCTCTCGTCTCTCGGAGTGGAAGAATCCGGAAACTTGTTCTGGAATCAAAAGACACGAACC TGAACCTAGCCGCTGTTCCAGGCGGCTCAGAATCGTTCGAGCTTGCTGCAAAGTTCTGCTACGG CGTTGGCGTCCAATATAACTCGTCCAACATTGCGGCGCTGCGATGCGTGGCTCATTACCTGGAG ATGACAGAAGACTTGTCAGAGAAGAACCTCGAGGCGAGAACAGAGGCCTACCTGAAAGACTCCA TTTTCAATGACATATCGAATTCGATCACTGTTCTTCACTCCTGCGAGAGGCTACTGCCTGTAGC TGAAGAGATCAACCTCGTCGGGAGGCTGGTCAACGCAATCGCTGTAAACGCCTGCAAAGAACAG CTAGCCTCTGGTTTGCTCAAGCTTGATCAGAGTTTCAGCTGCGGCGTCCCGGAGACTGCGAAAC CTTGTGACTGGTGGGGTCGCTCTCTTCCCATCCTCAAGCTTGATTTCTTCCAGAGAGTTCTCTC CGCCATGAAATCCAAAGGTCTCAATCACGACATTATCAGTGACATCCTTATGAGCTACGCTCGC AAATCACTGCAGATCATCAGAGAACCGAATCTCGTCAAATCAGATTCCGATCTTCAGAGGAAAC AGCGAATCGTCCTTGAAGCGGTCGTCGGGCTCCTCCCAACGCAAGCGAACAAAAGCTCGATTCC GATCTCGTTCCTCTCTAGCTTGTTGAAGACCGCTATAGGATCTGGCACCTCCGTCTCTTGCAGA TCCGATCTGGAGAGACGGATCAGCCACCTGCTCGACCAGGCCATCCTTGAAGACATCCTTATTC CGGCGAACATCGGCGCCATGTACGACACCGACTCGGTGCAGAGGATTTTCTCAATGTTCTTGAA CCTTGACGAGTGCGAGTACAGAGATGATGATGACGACGAGGAGGACGCGGTGGACGAGAGCGAG ATGGCCATGTACGATTTCGAGGGGGCTGAGTCACCGAAACAGAGCTCCATCTTCAAGGTGTCGA AGCTGATGGATAGTTATCTCGCTGAGGTGGCTCTGGACTCGAGCCTTCCTCCCTCCAAGTTTAT AGCACTCGCAGAGCTTCTCCCTGACCATGCTCGCGTCGTCTGCGATGGCCTCTACCGAGCCGTT GATATCTTCCTCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.223543779

Conservation Information
Conserved circRNAs	NA
PMCS	0.223543779

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							19600465-19601436(+)
						
					

						Potential amino acid sequence
						
							MTEDLSEKNLEARTEAYLKDSIFNDISNSITVLHSCERLLPVAEEINLVGRLVNAIAVNACKEQ
LASGLLKLDQSFSCGVPETAKPCDWWGRSLPILKLDFFQRVLSAMKSKGLNHDIISDILMSYAR
KSLQIIREPNLVKSDSDLQRKQRIVLEAVVGLLPTQANKSSIPISFLSSLLKTAIGSGTSVSCR
SDLERRISHLLDQAILEDILIPANIGAMYDTDSVQRIFSMFLNLDECEYRDDDDDEEDAVDESE
MAMYDFEGAESPKQSSIFKVSKLMDSYLAEVALDSSLPPSKFIALAELLPDHARVVCDGLYRAV
DIFLKFPLVSRSGRIRKLVLESKDTNLNLAAVPGGSESFELAAKFCYGVGVQYNSSNIAALRCV
AHYLEMTEDLSEKNLEARTEAYLKDSIFNDISNSITVLHSCERLLPVAEEINLVGRLVNAIAVN
ACKEQLASGLLKLDQSFSCGVPETAKPCDWWGRSLPILKLDFFQRVLSAMKSKGLNHDIISDIL
MSYARKSLQIIREPNLVKSDSDLQRKQRIVLEAVVGLLPTQANKSSIPISFLSSLLKTAIGSGT
SVSCRSDLERRISHLLDQAILEDILIPANIGAMYDTDSVQRIFSMFLNLDECEYRDDDDDEEDA
VDESEMAMYDFEGAESPKQSSIFKVSKLMDSYLAEVALDSSLPPSKFIALAELLPDHARVVCDG
LYRAVDIFLKFPLVSRSGRIRKLVLESKDTNLNLAAVPGGSESFELAAKFCYGVGVQYNSSNIA
ALRCVAHYLEMTEDLSEKNLEARTEAYLKDSIFNDISNSITVLHSCERLLPVAEEINLVGRLVN
AIAVNACKEQLASGLLKLDQSFSCGVPETAKPCDWWGRSLPILKLDFFQRVLSAMKSKGLNHDI
ISDILMSYARKSLQIIREPNLVKSDSDLQRKQRIVLEAVVGLLPTQANKSSIPISFLSSLLKTA
IGSGTSVSCRSDLERRISHLLDQAILEDILIPANIGAMYDTDSVQRIFSMFLNLDECEYRDDDD
DEEDAVDESEMAMYDFEGAESPKQSSIFKVSKLMDSYLAEVALDSSLPPSKFIALAELLPDHAR
VVCDGLYRAVDIFLKFPLVSRSGRIRKLVLESKDTNLNLAAVPGGSESFELAAKFCYGVGVQYN
SSNIAALRCVAHYLEMTEDLSEKNLEARTEAYLKDSIFNDISNSITVLHSCERLLPVAEEINLV
GRLVNAIAVNACKEQLASGLLKLDQSFSCGVPETAKPCDWWGRSLPILKLDFFQRVLSAMKSKG
LNHDIISDILMSYARKSLQIIREPNLVKSDSDLQRKQRIVLEAVVGLLPTQANKSSIPISFLSS
LLKTAIGSGTSVSCRSDLERRISHLLDQAILEDILIPANIGAMYDTDSVQRIFSMFLNLDECEY
RDDDDDEEDAVDESEMAMYDFEGAESPKQSSIFKVSKLMDSYLAEVALDSSLPPSKFIALAELL
PDHARVVCDGLYRAVDIFLK(+)
						
					

						Sponge-miRNAs
						
							ath-miR156i 						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	19600465-19601436(+)
Potential amino acid sequence	MTEDLSEKNLEARTEAYLKDSIFNDISNSITVLHSCERLLPVAEEINLVGRLVNAIAVNACKEQ LASGLLKLDQSFSCGVPETAKPCDWWGRSLPILKLDFFQRVLSAMKSKGLNHDIISDILMSYAR KSLQIIREPNLVKSDSDLQRKQRIVLEAVVGLLPTQANKSSIPISFLSSLLKTAIGSGTSVSCR SDLERRISHLLDQAILEDILIPANIGAMYDTDSVQRIFSMFLNLDECEYRDDDDDEEDAVDESE MAMYDFEGAESPKQSSIFKVSKLMDSYLAEVALDSSLPPSKFIALAELLPDHARVVCDGLYRAV DIFLKFPLVSRSGRIRKLVLESKDTNLNLAAVPGGSESFELAAKFCYGVGVQYNSSNIAALRCV AHYLEMTEDLSEKNLEARTEAYLKDSIFNDISNSITVLHSCERLLPVAEEINLVGRLVNAIAVN ACKEQLASGLLKLDQSFSCGVPETAKPCDWWGRSLPILKLDFFQRVLSAMKSKGLNHDIISDIL MSYARKSLQIIREPNLVKSDSDLQRKQRIVLEAVVGLLPTQANKSSIPISFLSSLLKTAIGSGT SVSCRSDLERRISHLLDQAILEDILIPANIGAMYDTDSVQRIFSMFLNLDECEYRDDDDDEEDA VDESEMAMYDFEGAESPKQSSIFKVSKLMDSYLAEVALDSSLPPSKFIALAELLPDHARVVCDG LYRAVDIFLKFPLVSRSGRIRKLVLESKDTNLNLAAVPGGSESFELAAKFCYGVGVQYNSSNIA ALRCVAHYLEMTEDLSEKNLEARTEAYLKDSIFNDISNSITVLHSCERLLPVAEEINLVGRLVN AIAVNACKEQLASGLLKLDQSFSCGVPETAKPCDWWGRSLPILKLDFFQRVLSAMKSKGLNHDI ISDILMSYARKSLQIIREPNLVKSDSDLQRKQRIVLEAVVGLLPTQANKSSIPISFLSSLLKTA IGSGTSVSCRSDLERRISHLLDQAILEDILIPANIGAMYDTDSVQRIFSMFLNLDECEYRDDDD DEEDAVDESEMAMYDFEGAESPKQSSIFKVSKLMDSYLAEVALDSSLPPSKFIALAELLPDHAR VVCDGLYRAVDIFLKFPLVSRSGRIRKLVLESKDTNLNLAAVPGGSESFELAAKFCYGVGVQYN SSNIAALRCVAHYLEMTEDLSEKNLEARTEAYLKDSIFNDISNSITVLHSCERLLPVAEEINLV GRLVNAIAVNACKEQLASGLLKLDQSFSCGVPETAKPCDWWGRSLPILKLDFFQRVLSAMKSKG LNHDIISDILMSYARKSLQIIREPNLVKSDSDLQRKQRIVLEAVVGLLPTQANKSSIPISFLSS LLKTAIGSGTSVSCRSDLERRISHLLDQAILEDILIPANIGAMYDTDSVQRIFSMFLNLDECEY RDDDDDEEDAVDESEMAMYDFEGAESPKQSSIFKVSKLMDSYLAEVALDSSLPPSKFIALAELL PDHARVVCDGLYRAVDIFLK(+)
Sponge-miRNAs	ath-miR156i
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT2G47860_circ_g.4

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