Plant Circular RNA Database

Detail information of AT1G28420_circ_g.14

			
						 General Information
					
						CircRNA Name
						AT1G28420_circ_g.14
					
						ID in PlantcircBase
						ath_circ_004699
					
						Alias
						Ath_circ_FC0540
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 9983817-9985373  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT1G28420						
					
						Parent gene annotation
						
							Homeobox-DDT domain protein RLT1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G28420_circ_g.1 AT1G28420_circ_g.2 AT1G28420_circ_g.3 AT1G28420_circ_g.4 AT1G28420_circ_g.5 AT1G28420_circ_g.6 AT1G28420_circ_g.7 AT1G28420_circ_g.8 AT1G28420_circ_g.9 AT1G28420_circ_g.10 AT1G28420_circ_g.11 AT1G28420_circ_g.12 AT1G28420_circ_g.13 AT1G28420_circ_g.15 						
					
						Support reads
						1
					
						Tissues
						root
					
						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
						AT1G28420.1:3

General Information
CircRNA Name	AT1G28420_circ_g.14
ID in PlantcircBase	ath_circ_004699
Alias	Ath_circ_FC0540
Organism	Arabidpsis thaliana
Position	chr1: 9983817-9985373 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT1G28420
Parent gene annotation	Homeobox-DDT domain protein RLT1
Parent gene strand	+
Alternative splicing	AT1G28420_circ_g.1 AT1G28420_circ_g.2 AT1G28420_circ_g.3 AT1G28420_circ_g.4 AT1G28420_circ_g.5 AT1G28420_circ_g.6 AT1G28420_circ_g.7 AT1G28420_circ_g.8 AT1G28420_circ_g.9 AT1G28420_circ_g.10 AT1G28420_circ_g.11 AT1G28420_circ_g.12 AT1G28420_circ_g.13 AT1G28420_circ_g.15
Support reads	1
Tissues	root
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	AT1G28420.1:3

			
						 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  
						
							CTGGCATTTTGCTGTATCAGTGTCTAAGAGTGATCCTTGTTCGAGGCTCTTATTTGTTGAGCTA
CATGATGGCAAGTGGCTCCTCATTGATTCAGAAGAGgctaaaggttgtgaagatgtcatttcta
ctatccgaaatggtacagcagctgaaagtgcttttgcatcgatgcgggagaaagggttgctcgc
tcctcgca

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							GCTAAAGGTTGTGAAGATGTCATTTCTACTATCCGAAATGGTACAGCAGCTGAAAGTGCTTTTG
CATCGATGCGGGAGAAAGGGTTGCTCGCTCCTCGCAAGTCGAGGCACCGGTTGACACCTGGAAC
CGTCAAATTTGCAGCCTTTCATGTTCTATCTCTTGAAGGAAGCAAGGGACTGACAGTATTAGAA
CTTGCTGACAAGATTCAGGTAAATCTATAATCTATATTTGCTATGCTGTTTTCATCGTATTTGA
ATTTTTTTCATTTACATAGTCTTTATGTTTTCCATTGAAAGAAATCTGGACTTCGGGACTTGAC
CACAAGCAAGACACCAGAGGCTTCTATTTCTGTTGCATTGACAAGAGATGTGAAACTCTTTGAA
AGAATAGCTCCTTCGACTTATTGTGTACGAGCTCCTTATGTGAAGGATCCTAAGGATGGAGAGG
CAATACTCGCAGATGCCAGGAAGAAGATACGGGCTTTTGAAAATGGATTTACAGGTCCAGAAGA
TGTGAATGATCTTGAAAGGGATGAAGACTTCGAAATTGATATTGATGAGGATCCCGAGGTTGAT
GATTTAGCTACACTGGCAAGTGCATCAAAAAGTGCCGTTCTTGGAGAAGCGAATGTTTTGTCAG
GAAAGGGGGTAGATACAATGTTCTGTGATGTTAAAGCAGATGTAAAGAGTGAGCTTGAGAAGGA
GTTTTCATCTCCTCCTCCAAGCACTATGAAGAGCATTGTTCCACAACATAGTGAGCGGCATAAA
AATACAGTGGTTGGCGGCGTGGATGCCGTAATTGATGAAAGCAACCAGGGCCAATCATGGATTC
AAGGTCTTACGGAAGGGGATTACTGTCATCTAAGTGTTGAAGAGCGCCTTAATGCCCTTGTTGC
TTTAGTCGGCATTGCCAATGAAGGAAACTCCATCAGAACAGGTCTTGAGGTAAAGTCTGGGTTT
TCTTTTATCAGCTTTCCTGTTGAACAGAGTAGAAATTGACCTTTTGAGTCTATTATTTGTTATC
TGATTGAAATTTATTCACAGGATCGTATGGAAGCAGCAAATGCTCTTAAAAAGCAAATGTGGGC
TGAAGCACAGTTAGATAACAGCTGTATGAGAGATGTACTTAAGCTTGATCTTCAAAACTTAGCA
AGCAGCAAAACTGAATCAACGATAGGCCTACCAATCATTCAAAGCTCTACTCGTGAGAGGGATA
GTTTTGATAGAGACCCTTCTCAACTTCTAGATGAAACAAAGCCCCTGGAAGATCTTTCGAACGA
TCTTCATAAATCATCTGCTGAGAGAGCACTTATTAATCAGGATGCCAATATAAGTCAAGAAAAT
TATGCTTCAAAGAGATCACGCTCCCAATTAAAGTCATATATAGGCCACAAAGCAGAAGAGGTGT
ATCCATACCGATCTTTGCCGCTTGGACAAGATCGGCGCCACAATCGTTACTGGCATTTTGCTGT
ATCAGTGTCTAAGAGTGATCCTTGTTCGAGGCTCTTATTTGTTGAGCTACATGATGGCAAGTGG
CTCCTCATTGATTCAGAAGAG
						
					

			
		

Sequences
Splice junction sequence	CTGGCATTTTGCTGTATCAGTGTCTAAGAGTGATCCTTGTTCGAGGCTCTTATTTGTTGAGCTA CATGATGGCAAGTGGCTCCTCATTGATTCAGAAGAGgctaaaggttgtgaagatgtcatttcta ctatccgaaatggtacagcagctgaaagtgcttttgcatcgatgcgggagaaagggttgctcgc tcctcgca
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GCTAAAGGTTGTGAAGATGTCATTTCTACTATCCGAAATGGTACAGCAGCTGAAAGTGCTTTTG CATCGATGCGGGAGAAAGGGTTGCTCGCTCCTCGCAAGTCGAGGCACCGGTTGACACCTGGAAC CGTCAAATTTGCAGCCTTTCATGTTCTATCTCTTGAAGGAAGCAAGGGACTGACAGTATTAGAA CTTGCTGACAAGATTCAGGTAAATCTATAATCTATATTTGCTATGCTGTTTTCATCGTATTTGA ATTTTTTTCATTTACATAGTCTTTATGTTTTCCATTGAAAGAAATCTGGACTTCGGGACTTGAC CACAAGCAAGACACCAGAGGCTTCTATTTCTGTTGCATTGACAAGAGATGTGAAACTCTTTGAA AGAATAGCTCCTTCGACTTATTGTGTACGAGCTCCTTATGTGAAGGATCCTAAGGATGGAGAGG CAATACTCGCAGATGCCAGGAAGAAGATACGGGCTTTTGAAAATGGATTTACAGGTCCAGAAGA TGTGAATGATCTTGAAAGGGATGAAGACTTCGAAATTGATATTGATGAGGATCCCGAGGTTGAT GATTTAGCTACACTGGCAAGTGCATCAAAAAGTGCCGTTCTTGGAGAAGCGAATGTTTTGTCAG GAAAGGGGGTAGATACAATGTTCTGTGATGTTAAAGCAGATGTAAAGAGTGAGCTTGAGAAGGA GTTTTCATCTCCTCCTCCAAGCACTATGAAGAGCATTGTTCCACAACATAGTGAGCGGCATAAA AATACAGTGGTTGGCGGCGTGGATGCCGTAATTGATGAAAGCAACCAGGGCCAATCATGGATTC AAGGTCTTACGGAAGGGGATTACTGTCATCTAAGTGTTGAAGAGCGCCTTAATGCCCTTGTTGC TTTAGTCGGCATTGCCAATGAAGGAAACTCCATCAGAACAGGTCTTGAGGTAAAGTCTGGGTTT TCTTTTATCAGCTTTCCTGTTGAACAGAGTAGAAATTGACCTTTTGAGTCTATTATTTGTTATC TGATTGAAATTTATTCACAGGATCGTATGGAAGCAGCAAATGCTCTTAAAAAGCAAATGTGGGC TGAAGCACAGTTAGATAACAGCTGTATGAGAGATGTACTTAAGCTTGATCTTCAAAACTTAGCA AGCAGCAAAACTGAATCAACGATAGGCCTACCAATCATTCAAAGCTCTACTCGTGAGAGGGATA GTTTTGATAGAGACCCTTCTCAACTTCTAGATGAAACAAAGCCCCTGGAAGATCTTTCGAACGA TCTTCATAAATCATCTGCTGAGAGAGCACTTATTAATCAGGATGCCAATATAAGTCAAGAAAAT TATGCTTCAAAGAGATCACGCTCCCAATTAAAGTCATATATAGGCCACAAAGCAGAAGAGGTGT ATCCATACCGATCTTTGCCGCTTGGACAAGATCGGCGCCACAATCGTTACTGGCATTTTGCTGT ATCAGTGTCTAAGAGTGATCCTTGTTCGAGGCTCTTATTTGTTGAGCTACATGATGGCAAGTGG CTCCTCATTGATTCAGAAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.178956263

Conservation Information
Conserved circRNAs	NA
PMCS	0.178956263

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							9983886-9985370(+)
						
					

						Potential amino acid sequence
						
							MREKGLLAPRKSRHRLTPGTVKFAAFHVLSLEGSKGLTVLELADKIQKSGLRDLTTSKTPEASI
SVALTRDVKLFERIAPSTYCVRAPYVKDPKDGEAILADARKKIRAFENGFTGPEDVNDLERDED
FEIDIDEDPEVDDLATLASASKSAVLGEANVLSGKGVDTMFCDVKADVKSELEKEFSSPPPSTM
KSIVPQHSERHKNTVVGGVDAVIDESNQGQSWIQGLTEGDYCHLSVEERLNALVALVGIANEGN
SIRTGLEDRMEAANALKKQMWAEAQLDNSCMRDVLKLDLQNLASSKTESTIGLPIIQSSTRERD
SFDRDPSQLLDETKPLEDLSNDLHKSSAERALINQDANISQENYASKRSRSQLKSYIGHKAEEV
YPYRSLPLGQDRRHNRYWHFAVSVSKSDPCSRLLFVELHDGKWLLIDSEEAKGCEDVISTIRNG
TAAESAFASMREKGLLAPRKSRHRLTPGTVKFAAFHVLSLEGSKGLTVLELADKIQKSGLRDLT
TSKTPEASISVALTRDVKLFERIAPSTYCVRAPYVKDPKDGEAILADARKKIRAFENGFTGPED
VNDLERDEDFEIDIDEDPEVDDLATLASASKSAVLGEANVLSGKGVDTMFCDVKADVKSELEKE
FSSPPPSTMKSIVPQHSERHKNTVVGGVDAVIDESNQGQSWIQGLTEGDYCHLSVEERLNALVA
LVGIANEGNSIRTGLEDRMEAANALKKQMWAEAQLDNSCMRDVLKLDLQNLASSKTESTIGLPI
IQSSTRERDSFDRDPSQLLDETKPLEDLSNDLHKSSAERALINQDANISQENYASKRSRSQLKS
YIGHKAEEVYPYRSLPLGQDRRHNRYWHFAVSVSKSDPCSRLLFVELHDGKWLLIDSEEAKGCE
DVISTIRNGTAAESAFASMREKGLLAPRKSRHRLTPGTVKFAAFHVLSLEGSKGLTVLELADKI
QKSGLRDLTTSKTPEASISVALTRDVKLFERIAPSTYCVRAPYVKDPKDGEAILADARKKIRAF
ENGFTGPEDVNDLERDEDFEIDIDEDPEVDDLATLASASKSAVLGEANVLSGKGVDTMFCDVKA
DVKSELEKEFSSPPPSTMKSIVPQHSERHKNTVVGGVDAVIDESNQGQSWIQGLTEGDYCHLSV
EERLNALVALVGIANEGNSIRTGLEDRMEAANALKKQMWAEAQLDNSCMRDVLKLDLQNLASSK
TESTIGLPIIQSSTRERDSFDRDPSQLLDETKPLEDLSNDLHKSSAERALINQDANISQENYAS
KRSRSQLKSYIGHKAEEVYPYRSLPLGQDRRHNRYWHFAVSVSKSDPCSRLLFVELHDGKWLLI
DSEEAKGCEDVISTIRNGTAAESAFASMREKGLLAPRKSRHRLTPGTVKFAAFHVLSLEGSKGL
TVLELADKIQKSGLRDLTTSKTPEASISVALTRDVKLFERIAPSTYCVRAPYVKDPKDGEAILA
DARKKIRAFENGFTGPEDVNDLERDEDFEIDIDEDPEVDDLATLASASKSAVLGEANVLSGKGV
DTMFCDVKADVKSELEKEFSSPPPSTMKSIVPQHSERHKNTVVGGVDAVIDESNQGQSWIQGLT
EGDYCHLSVEERLNALVALVGIANEGNSIRTGLEDRMEAANALKKQMWAEAQLDNSCMRDVLKL
DLQNLASSKTESTIGLPIIQSSTRERDSFDRDPSQLLDETKPLEDLSNDLHKSSAERALINQDA
NISQENYASKRSRSQLKSYIGHKAEEVYPYRSLPLGQDRRHNRYWHFAVSVSKSDPCSRLLFVE
LHDGKWLLIDSEE(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	9983886-9985370(+)
Potential amino acid sequence	MREKGLLAPRKSRHRLTPGTVKFAAFHVLSLEGSKGLTVLELADKIQKSGLRDLTTSKTPEASI SVALTRDVKLFERIAPSTYCVRAPYVKDPKDGEAILADARKKIRAFENGFTGPEDVNDLERDED FEIDIDEDPEVDDLATLASASKSAVLGEANVLSGKGVDTMFCDVKADVKSELEKEFSSPPPSTM KSIVPQHSERHKNTVVGGVDAVIDESNQGQSWIQGLTEGDYCHLSVEERLNALVALVGIANEGN SIRTGLEDRMEAANALKKQMWAEAQLDNSCMRDVLKLDLQNLASSKTESTIGLPIIQSSTRERD SFDRDPSQLLDETKPLEDLSNDLHKSSAERALINQDANISQENYASKRSRSQLKSYIGHKAEEV YPYRSLPLGQDRRHNRYWHFAVSVSKSDPCSRLLFVELHDGKWLLIDSEEAKGCEDVISTIRNG TAAESAFASMREKGLLAPRKSRHRLTPGTVKFAAFHVLSLEGSKGLTVLELADKIQKSGLRDLT TSKTPEASISVALTRDVKLFERIAPSTYCVRAPYVKDPKDGEAILADARKKIRAFENGFTGPED VNDLERDEDFEIDIDEDPEVDDLATLASASKSAVLGEANVLSGKGVDTMFCDVKADVKSELEKE FSSPPPSTMKSIVPQHSERHKNTVVGGVDAVIDESNQGQSWIQGLTEGDYCHLSVEERLNALVA LVGIANEGNSIRTGLEDRMEAANALKKQMWAEAQLDNSCMRDVLKLDLQNLASSKTESTIGLPI IQSSTRERDSFDRDPSQLLDETKPLEDLSNDLHKSSAERALINQDANISQENYASKRSRSQLKS YIGHKAEEVYPYRSLPLGQDRRHNRYWHFAVSVSKSDPCSRLLFVELHDGKWLLIDSEEAKGCE DVISTIRNGTAAESAFASMREKGLLAPRKSRHRLTPGTVKFAAFHVLSLEGSKGLTVLELADKI QKSGLRDLTTSKTPEASISVALTRDVKLFERIAPSTYCVRAPYVKDPKDGEAILADARKKIRAF ENGFTGPEDVNDLERDEDFEIDIDEDPEVDDLATLASASKSAVLGEANVLSGKGVDTMFCDVKA DVKSELEKEFSSPPPSTMKSIVPQHSERHKNTVVGGVDAVIDESNQGQSWIQGLTEGDYCHLSV EERLNALVALVGIANEGNSIRTGLEDRMEAANALKKQMWAEAQLDNSCMRDVLKLDLQNLASSK TESTIGLPIIQSSTRERDSFDRDPSQLLDETKPLEDLSNDLHKSSAERALINQDANISQENYAS KRSRSQLKSYIGHKAEEVYPYRSLPLGQDRRHNRYWHFAVSVSKSDPCSRLLFVELHDGKWLLI DSEEAKGCEDVISTIRNGTAAESAFASMREKGLLAPRKSRHRLTPGTVKFAAFHVLSLEGSKGL TVLELADKIQKSGLRDLTTSKTPEASISVALTRDVKLFERIAPSTYCVRAPYVKDPKDGEAILA DARKKIRAFENGFTGPEDVNDLERDEDFEIDIDEDPEVDDLATLASASKSAVLGEANVLSGKGV DTMFCDVKADVKSELEKEFSSPPPSTMKSIVPQHSERHKNTVVGGVDAVIDESNQGQSWIQGLT EGDYCHLSVEERLNALVALVGIANEGNSIRTGLEDRMEAANALKKQMWAEAQLDNSCMRDVLKL DLQNLASSKTESTIGLPIIQSSTRERDSFDRDPSQLLDETKPLEDLSNDLHKSSAERALINQDA NISQENYASKRSRSQLKSYIGHKAEEVYPYRSLPLGQDRRHNRYWHFAVSVSKSDPCSRLLFVE LHDGKWLLIDSEE(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT1G28420_circ_g.14

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