Plant Circular RNA Database

Detail information of AT5G06140_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G06140_circ_g.1
					
						ID in PlantcircBase
						ath_circ_036666
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 1856508-1858386  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, circRNA_finder
					
						Parent gene
						
							AT5G06140						
					
						Parent gene annotation
						
							Sorting nexin 1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G06140_circ_g.2 AT5G06140_circ_g.3 AT5G06140_circ_g.4 AT5G06140_circ_g.5 AT5G06140_circ_g.6 AT5G06140_circ_g.7 AT5G06140_circ_g.8 AT5G06140_circ_g.9 AT5G06140_circ_g.10 						
					
						Support reads
						16
					
						Tissues
						aerial, 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
						AT5G06140.1:8

General Information
CircRNA Name	AT5G06140_circ_g.1
ID in PlantcircBase	ath_circ_036666
Alias	NA
Organism	Arabidpsis thaliana
Position	chr5: 1856508-1858386 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, circRNA_finder
Parent gene	AT5G06140
Parent gene annotation	Sorting nexin 1
Parent gene strand	-
Alternative splicing	AT5G06140_circ_g.2 AT5G06140_circ_g.3 AT5G06140_circ_g.4 AT5G06140_circ_g.5 AT5G06140_circ_g.6 AT5G06140_circ_g.7 AT5G06140_circ_g.8 AT5G06140_circ_g.9 AT5G06140_circ_g.10
Support reads	16
Tissues	aerial, 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	AT5G06140.1:8

			
						 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  
						
							TGCCCTTGTACTTTTCAAAAAGCCGATCCCGTAACCAGACGAAATCACTGTATCGTCTAATAAC
AATCTTCTCGGGTCCTTGGTACTCCGGCAAGTTAGTctctctgtattcgatctcagcttctcct
actttgtctgaacgtgtgagcatgagtttgtcactacaataacagacgagaatttctataatgt
tctacgac

									
								

					

						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: 846
Transcript exons: 1856508-1856568,1856651-1856730,1856834-1856902,1857039-
1857172,1857293-1857452,1857553-1857624,1857771-1857904,
1858251-1858386
CTCTCTGTATTCGATCTCAGCTTCTCCTACTTTGTCTGAACGTGTGAGCATGAGTTTGTCAAGA
TTTATTTCTTTTAACTTTGTTGTTTCTGACAATTCACAATGTTGTTTGAAAGCAGTGCCTCGTT
CTGCTATTGTTGCCTTAATCGATTGTACATAACGAACATAGTCCTTCAAGGGTTCCTCGAAGTT
CATCAGGACTTGTTGAGCCTCTTTCTGGAGCTTAATCGATAACAGTTCAGATTTAGTTCCAAGA
TCGGAAAATGCTTTTCCTGTAGGTTCACCCTCACAAGCCCCAAGAAGTTTTACAGCCTTGCCAA
AATCCAACAGTGATTGACCCAACTCTCTATGCCTCTTGACTAGGCGATACGCATGCTTCTGAGC
CTCAGTCAAGTGGTTCTCAAGCTCGAAAATGTAATGTTTAAGCTTCTCGTAGTCAGCAGTAGTT
TCTTCAACAGGTTTTTCTTTTCCAAGGACAGCATCACTAACTTTTGACTGGACATCCCTAAACA
TTTGCATTAGATCTGCAGGCTTCTTGAATATACTAGTTTCCTGAAACCTGAATCTGTCCATTGT
CTCTTCATCTGCTTGCAAAAAGGTCCTAAGATCCTCACTCTGCTGAAGCTCAGGGTGTAATGCT
ATTCGATTAACAAATATATCCAATGCTGCTCGCCTCATTTCAATAAATTCGGCACTAAAGCGGA
ATTTTTCTACAGCACTCTTCTCTGGAAGAGGAGGAATGAAAATGCCCTTGTACTTTTCAAAAAG
CCGATCCCGTAACCAGACGAAATCACTGTATCGTCTAATAACAATCTTCTCGGGTCCTTGGTAC
TCCGGCAAGTTAGT
						
					

						Genomic sequence
						
							CTCTCTGTATTCGATCTCAGCTTCTCCTACTTTGTCTGAACGTGTGAGCATGAGTTTGTCACTA
CAATAACAGACGAGAATTTCTATAATGTTCTACGACGATTGTTGACAGAGAAGACAAAAAGGGA
GAGAAGCCATCATACAGATTTATTTCTTTTAACTTTGTTGTTTCTGACAATTCACAATGTTGTT
TGAAAGCAGTGCCTCGTTCTGCTATTGTTGCCTGGAAAAGCAAAATATGGAAACAAAAAGGTAA
GAGTTTAGTACCAGCAAAACGAAACCATGAAAGAGAAATCAATCCCACAGGCAAAGGCTAGAGA
ACTCACCTTAATCGATTGTACATAACGAACATAGTCCTTCAAGGGTTCCTCGAAGTTCATCAGG
ACTTGTTGAGCCTACAAATAGTGCAAGATAGGTCAATAAAAGCATCTAGGAATATAGAATAGAT
GAATTTCGCCAAGATATATACATTTCTTACTATAATGATTTAGAAAAAAAGAAGAAGATGATCT
AGTCTTACAAACTTAATACCTCTTTCTGGAGCTTAATCGATAACAGTTCAGATTTAGTTCCAAG
ATCGGAAAATGCTTTTCCTGTAGGTTCACCCTCACAAGCCCCAAGAAGTTTTACAGCCTTGCCA
AAATCCAACAGTGATTGACCCAACTCTGCCAATAGGTTGATACAGCATTAAAACTGAAGATCCA
TTCATGCGGTTGGGAAAGAGAAAACAGAAAACATAACAGAATTTATATAGACTAAATTCTGATT
TGTGATATTTTTATTACCTCTATGCCTCTTGACTAGGCGATACGCATGCTTCTGAGCCTCAGTC
AAGTGGTTCTCAAGCTCGAAAATGTAATGTTTAAGCTTCTCGTAGTCAGCAGTAGTTTCTTCAA
CAGGTTTTTCTTTTCCAAGGACAGCATCACTAACTTTTGACTGGACATCCTGTCAATAGTGCAG
ATATGGCAGTAAGATGATGGCGCACCACAAAGGTCAATAAAGAGCAGAAAAATAATATTTACAT
GGTCAGAAAAAACATTCTTACCCTAAACATTTGCATTAGATCTGCAGGCTTCTTGAATATACTA
GTTTCCTGAAACCTGAATCTGTCCATTGTCTGACGAGAAAAGTAAACTGTCATTAGAGACAAGA
ACCTTCTAATATGCAAATTGCAGTCCTTCCAGTAGGAAAAAAGAAGAAGCATTCTACGAGCATT
TTTATGTGAAGATGATGTAGTAGCAATGTGAAGTCCAGATATCCTACCTCTTCATCTGCTTGCA
AAAAGGTCCTAAGATCCTCACTCTGCTGAAGCTCAGGGTGTAATGCTATTCGATTAACAAATAT
ATCCAATGCTGCTCGCCTCATTTCAATAAATTCGGCACTAAAGCGGAATTTTTCTGCCAAAAAG
AGTATTAATAAACATGAATCCAATATACTAATCTCCATCAGATAACAATTACAAGAGGAAGGCA
CTCATAAGTAATAACTTTATCAAAGCTGTACATTACCCTCGTGCACTTTCCAAAGTCTCAACAC
CTAATCAGAGACCTCTACTAACAACATCTAACCTAACTAAATGGAACAAGGATAGCTGGATTGA
CTGACATAAAACTATAGAGATGCACAATTCGTATCTTTGACTCAATCAGATAATGTGTTCAACT
AGATAGAGAGCAATAGAATAGATGCCGACTACAAAAGATTCAAATTAATAGCTAGAAAGGGAAA
AGCTAGCTAATTTACCTACAGCACTCTTCTCTGGAAGAGGAGGAATGAAAATGCCCTTGTACTT
TTCAAAAAGCCGATCCCGTAACCAGACGAAATCACTGTATCGTCTAATAACAATCTTCTCGGGT
CCTTGGTACTCCGGCAAGTTAGT
						
					

			
		

Sequences
Splice junction sequence	TGCCCTTGTACTTTTCAAAAAGCCGATCCCGTAACCAGACGAAATCACTGTATCGTCTAATAAC AATCTTCTCGGGTCCTTGGTACTCCGGCAAGTTAGTctctctgtattcgatctcagcttctcct actttgtctgaacgtgtgagcatgagtttgtcactacaataacagacgagaatttctataatgt tctacgac
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: 846 Transcript exons: 1856508-1856568,1856651-1856730,1856834-1856902,1857039- 1857172,1857293-1857452,1857553-1857624,1857771-1857904, 1858251-1858386 CTCTCTGTATTCGATCTCAGCTTCTCCTACTTTGTCTGAACGTGTGAGCATGAGTTTGTCAAGA TTTATTTCTTTTAACTTTGTTGTTTCTGACAATTCACAATGTTGTTTGAAAGCAGTGCCTCGTT CTGCTATTGTTGCCTTAATCGATTGTACATAACGAACATAGTCCTTCAAGGGTTCCTCGAAGTT CATCAGGACTTGTTGAGCCTCTTTCTGGAGCTTAATCGATAACAGTTCAGATTTAGTTCCAAGA TCGGAAAATGCTTTTCCTGTAGGTTCACCCTCACAAGCCCCAAGAAGTTTTACAGCCTTGCCAA AATCCAACAGTGATTGACCCAACTCTCTATGCCTCTTGACTAGGCGATACGCATGCTTCTGAGC CTCAGTCAAGTGGTTCTCAAGCTCGAAAATGTAATGTTTAAGCTTCTCGTAGTCAGCAGTAGTT TCTTCAACAGGTTTTTCTTTTCCAAGGACAGCATCACTAACTTTTGACTGGACATCCCTAAACA TTTGCATTAGATCTGCAGGCTTCTTGAATATACTAGTTTCCTGAAACCTGAATCTGTCCATTGT CTCTTCATCTGCTTGCAAAAAGGTCCTAAGATCCTCACTCTGCTGAAGCTCAGGGTGTAATGCT ATTCGATTAACAAATATATCCAATGCTGCTCGCCTCATTTCAATAAATTCGGCACTAAAGCGGA ATTTTTCTACAGCACTCTTCTCTGGAAGAGGAGGAATGAAAATGCCCTTGTACTTTTCAAAAAG CCGATCCCGTAACCAGACGAAATCACTGTATCGTCTAATAACAATCTTCTCGGGTCCTTGGTAC TCCGGCAAGTTAGT
Genomic sequence	CTCTCTGTATTCGATCTCAGCTTCTCCTACTTTGTCTGAACGTGTGAGCATGAGTTTGTCACTA CAATAACAGACGAGAATTTCTATAATGTTCTACGACGATTGTTGACAGAGAAGACAAAAAGGGA GAGAAGCCATCATACAGATTTATTTCTTTTAACTTTGTTGTTTCTGACAATTCACAATGTTGTT TGAAAGCAGTGCCTCGTTCTGCTATTGTTGCCTGGAAAAGCAAAATATGGAAACAAAAAGGTAA GAGTTTAGTACCAGCAAAACGAAACCATGAAAGAGAAATCAATCCCACAGGCAAAGGCTAGAGA ACTCACCTTAATCGATTGTACATAACGAACATAGTCCTTCAAGGGTTCCTCGAAGTTCATCAGG ACTTGTTGAGCCTACAAATAGTGCAAGATAGGTCAATAAAAGCATCTAGGAATATAGAATAGAT GAATTTCGCCAAGATATATACATTTCTTACTATAATGATTTAGAAAAAAAGAAGAAGATGATCT AGTCTTACAAACTTAATACCTCTTTCTGGAGCTTAATCGATAACAGTTCAGATTTAGTTCCAAG ATCGGAAAATGCTTTTCCTGTAGGTTCACCCTCACAAGCCCCAAGAAGTTTTACAGCCTTGCCA AAATCCAACAGTGATTGACCCAACTCTGCCAATAGGTTGATACAGCATTAAAACTGAAGATCCA TTCATGCGGTTGGGAAAGAGAAAACAGAAAACATAACAGAATTTATATAGACTAAATTCTGATT TGTGATATTTTTATTACCTCTATGCCTCTTGACTAGGCGATACGCATGCTTCTGAGCCTCAGTC AAGTGGTTCTCAAGCTCGAAAATGTAATGTTTAAGCTTCTCGTAGTCAGCAGTAGTTTCTTCAA CAGGTTTTTCTTTTCCAAGGACAGCATCACTAACTTTTGACTGGACATCCTGTCAATAGTGCAG ATATGGCAGTAAGATGATGGCGCACCACAAAGGTCAATAAAGAGCAGAAAAATAATATTTACAT GGTCAGAAAAAACATTCTTACCCTAAACATTTGCATTAGATCTGCAGGCTTCTTGAATATACTA GTTTCCTGAAACCTGAATCTGTCCATTGTCTGACGAGAAAAGTAAACTGTCATTAGAGACAAGA ACCTTCTAATATGCAAATTGCAGTCCTTCCAGTAGGAAAAAAGAAGAAGCATTCTACGAGCATT TTTATGTGAAGATGATGTAGTAGCAATGTGAAGTCCAGATATCCTACCTCTTCATCTGCTTGCA AAAAGGTCCTAAGATCCTCACTCTGCTGAAGCTCAGGGTGTAATGCTATTCGATTAACAAATAT ATCCAATGCTGCTCGCCTCATTTCAATAAATTCGGCACTAAAGCGGAATTTTTCTGCCAAAAAG AGTATTAATAAACATGAATCCAATATACTAATCTCCATCAGATAACAATTACAAGAGGAAGGCA CTCATAAGTAATAACTTTATCAAAGCTGTACATTACCCTCGTGCACTTTCCAAAGTCTCAACAC CTAATCAGAGACCTCTACTAACAACATCTAACCTAACTAAATGGAACAAGGATAGCTGGATTGA CTGACATAAAACTATAGAGATGCACAATTCGTATCTTTGACTCAATCAGATAATGTGTTCAACT AGATAGAGAGCAATAGAATAGATGCCGACTACAAAAGATTCAAATTAATAGCTAGAAAGGGAAA AGCTAGCTAATTTACCTACAGCACTCTTCTCTGGAAGAGGAGGAATGAAAATGCCCTTGTACTT TTCAAAAAGCCGATCCCGTAACCAGACGAAATCACTGTATCGTCTAATAACAATCTTCTCGGGT CCTTGGTACTCCGGCAAGTTAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.208321258

Conservation Information
Conserved circRNAs	NA
PMCS	0.208321258

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1857873-1856510(-)
						
						Potential amino acid sequence
						
							MRRAALDIFVNRIALHPELQQSEDLRTFLQADEETMDRFRFQETSIFKKPADLMQMFRDVQSKV
SDAVLGKEKPVEETTADYEKLKHYIFELENHLTEAQKHAYRLVKRHRELGQSLLDFGKAVKLLG
ACEGEPTGKAFSDLGTKSELLSIKLQKEAQQVLMNFEEPLKDYVRYVQSIKATIAERGTAFKQH
CELSETTKLKEINLDKLMLTRSDKVGEAEIEYRETNLPEYQGPEKIVIRRYSDFVWLRDRLFEK
YKGIFIPPLPEKSAVEKFRFSAEFIEMRRAALDIFVNRIALHPELQQSEDLRTFLQADEETMDR
FRFQETSIFKKPADLMQMFRDVQSKVSDAVLGKEKPVEETTADYEKLKHYIFELENHLTEAQKH
AYRLVKRHRELGQSLLDFGKAVKLLGACEGEPTGKAFSDLGTKSELLSIKLQKEAQQVLMNFEE
PLKDYVRYVQSIKATIAERGTAFKQHCELSETTKLKEINLDKLMLTRSDKVGEAEIEYRETNLP
EYQGPEKIVIRRYSDFVWLRDRLFEKYKGIFIPPLPEKSAVEKFRFSAEFIEMRRAALDIFVNR
IALHPELQQSEDLRTFLQADEETMDRFRFQETSIFKKPADLMQMFRDVQSKVSDAVLGKEKPVE
ETTADYEKLKHYIFELENHLTEAQKHAYRLVKRHRELGQSLLDFGKAVKLLGACEGEPTGKAFS
DLGTKSELLSIKLQKEAQQVLMNFEEPLKDYVRYVQSIKATIAERGTAFKQHCELSETTKLKEI
NLDKLMLTRSDKVGEAEIEYRETNLPEYQGPEKIVIRRYSDFVWLRDRLFEKYKGIFIPPLPEK
SAVEKFRFSAEFIEMRRAALDIFVNRIALHPELQQSEDLRTFLQADEETMDRFRFQETSIFKKP
ADLMQMFRDVQSKVSDAVLGKEKPVEETTADYEKLKHYIFELENHLTEAQKHAYRLVKRHRELG
QSLLDFGKAVKLLGACEGEPTGKAFSDLGTKSELLSIKLQKEAQQVLMNFEEPLKDYVRYVQSI
KATIAERGTAFKQHCELSETTKLKEINLDKLMLTRSDKVGEAEIEYRE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1857873-1856510(-)
Potential amino acid sequence	MRRAALDIFVNRIALHPELQQSEDLRTFLQADEETMDRFRFQETSIFKKPADLMQMFRDVQSKV SDAVLGKEKPVEETTADYEKLKHYIFELENHLTEAQKHAYRLVKRHRELGQSLLDFGKAVKLLG ACEGEPTGKAFSDLGTKSELLSIKLQKEAQQVLMNFEEPLKDYVRYVQSIKATIAERGTAFKQH CELSETTKLKEINLDKLMLTRSDKVGEAEIEYRETNLPEYQGPEKIVIRRYSDFVWLRDRLFEK YKGIFIPPLPEKSAVEKFRFSAEFIEMRRAALDIFVNRIALHPELQQSEDLRTFLQADEETMDR FRFQETSIFKKPADLMQMFRDVQSKVSDAVLGKEKPVEETTADYEKLKHYIFELENHLTEAQKH AYRLVKRHRELGQSLLDFGKAVKLLGACEGEPTGKAFSDLGTKSELLSIKLQKEAQQVLMNFEE PLKDYVRYVQSIKATIAERGTAFKQHCELSETTKLKEINLDKLMLTRSDKVGEAEIEYRETNLP EYQGPEKIVIRRYSDFVWLRDRLFEKYKGIFIPPLPEKSAVEKFRFSAEFIEMRRAALDIFVNR IALHPELQQSEDLRTFLQADEETMDRFRFQETSIFKKPADLMQMFRDVQSKVSDAVLGKEKPVE ETTADYEKLKHYIFELENHLTEAQKHAYRLVKRHRELGQSLLDFGKAVKLLGACEGEPTGKAFS DLGTKSELLSIKLQKEAQQVLMNFEEPLKDYVRYVQSIKATIAERGTAFKQHCELSETTKLKEI NLDKLMLTRSDKVGEAEIEYRETNLPEYQGPEKIVIRRYSDFVWLRDRLFEKYKGIFIPPLPEK SAVEKFRFSAEFIEMRRAALDIFVNRIALHPELQQSEDLRTFLQADEETMDRFRFQETSIFKKP ADLMQMFRDVQSKVSDAVLGKEKPVEETTADYEKLKHYIFELENHLTEAQKHAYRLVKRHRELG QSLLDFGKAVKLLGACEGEPTGKAFSDLGTKSELLSIKLQKEAQQVLMNFEEPLKDYVRYVQSI KATIAERGTAFKQHCELSETTKLKEINLDKLMLTRSDKVGEAEIEYRE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT5G06140_circ_g.1

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