Plant Circular RNA Database

Detail information of AT3G13560_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G13560_circ_g.1
					
						ID in PlantcircBase
						ath_circ_021510
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 4425741-4427324  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT3G13560						
					
						Parent gene annotation
						
							Glucan endo-1,3-beta-glucosidase 4
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						3
					
						Tissues
						seedlings
					
						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
						AT3G13560.4:3
AT3G13560.5:3
AT3G13560.3:3
AT3G13560.2:3
AT3G13560.1:3

General Information
CircRNA Name	AT3G13560_circ_g.1
ID in PlantcircBase	ath_circ_021510
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 4425741-4427324 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	AT3G13560
Parent gene annotation	Glucan endo-1,3-beta-glucosidase 4
Parent gene strand	-
Alternative splicing	NA
Support reads	3
Tissues	seedlings
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	AT3G13560.4:3 AT3G13560.5:3 AT3G13560.3:3 AT3G13560.2:3 AT3G13560.1:3

			
						 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  
						
							ACAGGCAAGAATTGAAAGTAGGAGCAACAACGCTTCTGCAAACCATCTCGGAAGCAGCATTGGA
AACAGAGTGCTTGAAAACCTTAAACCTACAAAAACTcttcccgtatatgcacatgttctatagc
ctgcaaacacacaagccatcgaatttgagatttactctgaggaaacaacttgaaaacatagaat
tattgcaa

									
								

					

						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
						
							CTTCCCGTATATGCACATGTTCTATAGCCTGCAAACACACAAGCCATCGAATTTGAGATTTACT
CTGAGGAAACAACTTGAAAACATAGAATTATTGCAACACATAGATCAGAGGAAATGAGAAAAAC
TTACTAGGATCTCTAGTCGTAGTGATAGCCGTACCATCAAAGTCACAAGTTCCACCTGCACTTT
TCATCTTCTGGTAATAGTCATTGAAAGCAAAAGAAGCATGGCTCTTAACATCGTTAGGGAGGTA
GCAAGGTTGGCCCGGTTGAATGGCAGCGCAGTTAGCTCGGCCTTGACCACACGCCCAATTCAAA
CCGTCAACCAACTTATCATCATCAGCATCTGCTTTAGCCACGCAGAACATCGATGAACCGTTTA
GAGCTGCGGAGCTAGAGCCACCACTCAAACTCAGAGGGTAAACCGAGGTCCCATTTGGAAACAA
AATCCCCCAGTTTCTTTCAGAGACTGGTCCTGACCGCTTGTCTTCATTGTACAGCTCGTAGATG
TAAGTGTTTATCGGTATGTCTGGTTGACTAGGAGGACCTGAGTTGTTCAGCACTCTCTTGATCA
AGTTAGTGTTGAATGTCTCCGCATTAGCGACTGTTGCAGCCGCTTCATCGCTTCCACCAGACGA
AGGCCAGCCTGTTTCCGTGACTACAACAGGAATCTTGGAGAAATTCAAAGCTTCCATGGAGTAG
TAAGCAGCATCAACCATAGCATCAAACATGCTGTTGTAATGTAAAAGCGTGTTGGGATCAACAA
TCTGCTTCACCGGAGAAAGCTGCTTGAACAAAGCGTAATCAAGCGGGAAAATCCCATTAGCGGT
TGTGTAACCGTAGTAAGGATACGCGTTTAACATGAAAAAGGAACCAGTGTTCTTCAAAAACTGA
AGAAGCTGGTAAACCGTGGTGTTCCACGACGGGCTAAAGGTAGATGTAGATGGAGGAAACGGTT
TAGGCATTATATCCATAGACATAGGGCTGGAGACTTTGACCTTAAAGTTGAGATTGGAAGCCAC
AAGAGCCTTGTGAATGTTGTTAAGAGCAGAGGCGAGAATCGGCGCCACGTGAGGAATCGTGGTG
AGAACCTCACTACCAACAGCAATGGCGGTTATATTAGTTGAAGGAATATAAGCAGCGACGTTTT
TGTTAACCCAAGCAGCTGCAGCTGAAGGAAACCGTCCGATTTTGAGGATTTCTTCATTGGTTAC
ACCGACCATAACTTCGATGCTAGTGTTGGCAAATGCTTTGAGCATATGGCTATTAGCATCATAG
AGACGGACGTGTGTGATTTGTTGTGATTTGAGAAGTGTTACAATGTCTGAAGGCGGTGGCATGT
TGGTGAGATCAGTGCCAATGTTTACACCGATAAATGCAGCTGTATAAAGAATCAGATTAACATT
GAGAGTCTATGAACTTCACCAAGTAATAAAAAAGTAAACTTAGAGATAGATATAACATGTGAAA
TTTACCGTTTGAACAGGCAAGAATTGAAAGTAGGAGCAACAACGCTTCTGCAAACCATCTCGGA
AGCAGCATTGGAAACAGAGTGCTTGAAAACCTTAAACCTACAAAAACT
						
					

			
		

Sequences
Splice junction sequence	ACAGGCAAGAATTGAAAGTAGGAGCAACAACGCTTCTGCAAACCATCTCGGAAGCAGCATTGGA AACAGAGTGCTTGAAAACCTTAAACCTACAAAAACTcttcccgtatatgcacatgttctatagc ctgcaaacacacaagccatcgaatttgagatttactctgaggaaacaacttgaaaacatagaat tattgcaa
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	CTTCCCGTATATGCACATGTTCTATAGCCTGCAAACACACAAGCCATCGAATTTGAGATTTACT CTGAGGAAACAACTTGAAAACATAGAATTATTGCAACACATAGATCAGAGGAAATGAGAAAAAC TTACTAGGATCTCTAGTCGTAGTGATAGCCGTACCATCAAAGTCACAAGTTCCACCTGCACTTT TCATCTTCTGGTAATAGTCATTGAAAGCAAAAGAAGCATGGCTCTTAACATCGTTAGGGAGGTA GCAAGGTTGGCCCGGTTGAATGGCAGCGCAGTTAGCTCGGCCTTGACCACACGCCCAATTCAAA CCGTCAACCAACTTATCATCATCAGCATCTGCTTTAGCCACGCAGAACATCGATGAACCGTTTA GAGCTGCGGAGCTAGAGCCACCACTCAAACTCAGAGGGTAAACCGAGGTCCCATTTGGAAACAA AATCCCCCAGTTTCTTTCAGAGACTGGTCCTGACCGCTTGTCTTCATTGTACAGCTCGTAGATG TAAGTGTTTATCGGTATGTCTGGTTGACTAGGAGGACCTGAGTTGTTCAGCACTCTCTTGATCA AGTTAGTGTTGAATGTCTCCGCATTAGCGACTGTTGCAGCCGCTTCATCGCTTCCACCAGACGA AGGCCAGCCTGTTTCCGTGACTACAACAGGAATCTTGGAGAAATTCAAAGCTTCCATGGAGTAG TAAGCAGCATCAACCATAGCATCAAACATGCTGTTGTAATGTAAAAGCGTGTTGGGATCAACAA TCTGCTTCACCGGAGAAAGCTGCTTGAACAAAGCGTAATCAAGCGGGAAAATCCCATTAGCGGT TGTGTAACCGTAGTAAGGATACGCGTTTAACATGAAAAAGGAACCAGTGTTCTTCAAAAACTGA AGAAGCTGGTAAACCGTGGTGTTCCACGACGGGCTAAAGGTAGATGTAGATGGAGGAAACGGTT TAGGCATTATATCCATAGACATAGGGCTGGAGACTTTGACCTTAAAGTTGAGATTGGAAGCCAC AAGAGCCTTGTGAATGTTGTTAAGAGCAGAGGCGAGAATCGGCGCCACGTGAGGAATCGTGGTG AGAACCTCACTACCAACAGCAATGGCGGTTATATTAGTTGAAGGAATATAAGCAGCGACGTTTT TGTTAACCCAAGCAGCTGCAGCTGAAGGAAACCGTCCGATTTTGAGGATTTCTTCATTGGTTAC ACCGACCATAACTTCGATGCTAGTGTTGGCAAATGCTTTGAGCATATGGCTATTAGCATCATAG AGACGGACGTGTGTGATTTGTTGTGATTTGAGAAGTGTTACAATGTCTGAAGGCGGTGGCATGT TGGTGAGATCAGTGCCAATGTTTACACCGATAAATGCAGCTGTATAAAGAATCAGATTAACATT GAGAGTCTATGAACTTCACCAAGTAATAAAAAAGTAAACTTAGAGATAGATATAACATGTGAAA TTTACCGTTTGAACAGGCAAGAATTGAAAGTAGGAGCAACAACGCTTCTGCAAACCATCTCGGA AGCAGCATTGGAAACAGAGTGCTTGAAAACCTTAAACCTACAAAAACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.208107617

Conservation Information
Conserved circRNAs	NA
PMCS	0.208107617

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							4427285-4425743(-)
						
					

						Potential amino acid sequence
						
							MLLPRWFAEALLLLLSILACSNAAFIGVNIGTDLTNMPPPSDIVTLLKSQQITHVRLYDANSHM
LKAFANTSIEVMVGVTNEEILKIGRFPSAAAAWVNKNVAAYIPSTNITAIAVGSEVLTTIPHVA
PILASALNNIHKALVASNLNFKVKVSSPMSMDIMPKPFPPSTSTFSPSWNTTVYQLLQFLKNTG
SFFMLNAYPYYGYTTANGIFPLDYALFKQLSPVKQIVDPNTLLHYNSMFDAMVDAAYYSMEALN
FSKIPVVVTETGWPSSGGSDEAAATVANAETFNTNLIKRVLNNSGPPSQPDIPINTYIYELYNE
DKRSGPVSERNWGILFPNGTSVYPLSLSGGSSSAALNGSSMFCVAKADADDDKLVDGLNWACGQ
GRANCAAIQPGQPCYLPNDVKSHASFAFNDYYQKMKSAGGTCDFDGTAITTTRDPSYRTCAYTG
RVFVGLRFSSTLFPMLLPRWFAEALLLLLSILACSNAAFIGVNIGTDLTNMPPPSDIVTLLKSQ
QITHVRLYDANSHMLKAFANTSIEVMVGVTNEEILKIGRFPSAAAAWVNKNVAAYIPSTNITAI
AVGSEVLTTIPHVAPILASALNNIHKALVASNLNFKVKVSSPMSMDIMPKPFPPSTSTFSPSWN
TTVYQLLQFLKNTGSFFMLNAYPYYGYTTANGIFPLDYALFKQLSPVKQIVDPNTLLHYNSMFD
AMVDAAYYSMEALNFSKIPVVVTETGWPSSGGSDEAAATVANAETFNTNLIKRVLNNSGPPSQP
DIPINTYIYELYNEDKRSGPVSERNWGILFPNGTSVYPLSLSGGSSSAALNGSSMFCVAKADAD
DDKLVDGLNWACGQGRANCAAIQPGQPCYLPNDVKSHASFAFNDYYQKMKSAGGTCDFDGTAIT
TTRDPSYRTCAYTGRVFVGLRFSSTLFPMLLPRWFAEALLLLLSILACSNAAFIGVNIGTDLTN
MPPPSDIVTLLKSQQITHVRLYDANSHMLKAFANTSIEVMVGVTNEEILKIGRFPSAAAAWVNK
NVAAYIPSTNITAIAVGSEVLTTIPHVAPILASALNNIHKALVASNLNFKVKVSSPMSMDIMPK
PFPPSTSTFSPSWNTTVYQLLQFLKNTGSFFMLNAYPYYGYTTANGIFPLDYALFKQLSPVKQI
VDPNTLLHYNSMFDAMVDAAYYSMEALNFSKIPVVVTETGWPSSGGSDEAAATVANAETFNTNL
IKRVLNNSGPPSQPDIPINTYIYELYNEDKRSGPVSERNWGILFPNGTSVYPLSLSGGSSSAAL
NGSSMFCVAKADADDDKLVDGLNWACGQGRANCAAIQPGQPCYLPNDVKSHASFAFNDYYQKMK
SAGGTCDFDGTAITTTRDPSYRTCAYTGRVFVGLRFSSTLFPMLLPRWFAEALLLLLSILACSN
AAFIGVNIGTDLTNMPPPSDIVTLLKSQQITHVRLYDANSHMLKAFANTSIEVMVGVTNEEILK
IGRFPSAAAAWVNKNVAAYIPSTNITAIAVGSEVLTTIPHVAPILASALNNIHKALVASNLNFK
VKVSSPMSMDIMPKPFPPSTSTFSPSWNTTVYQLLQFLKNTGSFFMLNAYPYYGYTTANGIFPL
DYALFKQLSPVKQIVDPNTLLHYNSMFDAMVDAAYYSMEALNFSKIPVVVTETGWPSSGGSDEA
AATVANAETFNTNLIKRVLNNSGPPSQPDIPINTYIYELYNEDKRSGPVSERNWGILFPNGTSV
YPLSLSGGSSSAALNGSSMFCVAKADADDDKLVDGLNWACGQGRANCAAIQPGQPCYLPNDVKS
HASFAFNDYYQKMKSAGGTCDFDGTAITTTRDPSYRTCAYTG(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	4427285-4425743(-)
Potential amino acid sequence	MLLPRWFAEALLLLLSILACSNAAFIGVNIGTDLTNMPPPSDIVTLLKSQQITHVRLYDANSHM LKAFANTSIEVMVGVTNEEILKIGRFPSAAAAWVNKNVAAYIPSTNITAIAVGSEVLTTIPHVA PILASALNNIHKALVASNLNFKVKVSSPMSMDIMPKPFPPSTSTFSPSWNTTVYQLLQFLKNTG SFFMLNAYPYYGYTTANGIFPLDYALFKQLSPVKQIVDPNTLLHYNSMFDAMVDAAYYSMEALN FSKIPVVVTETGWPSSGGSDEAAATVANAETFNTNLIKRVLNNSGPPSQPDIPINTYIYELYNE DKRSGPVSERNWGILFPNGTSVYPLSLSGGSSSAALNGSSMFCVAKADADDDKLVDGLNWACGQ GRANCAAIQPGQPCYLPNDVKSHASFAFNDYYQKMKSAGGTCDFDGTAITTTRDPSYRTCAYTG RVFVGLRFSSTLFPMLLPRWFAEALLLLLSILACSNAAFIGVNIGTDLTNMPPPSDIVTLLKSQ QITHVRLYDANSHMLKAFANTSIEVMVGVTNEEILKIGRFPSAAAAWVNKNVAAYIPSTNITAI AVGSEVLTTIPHVAPILASALNNIHKALVASNLNFKVKVSSPMSMDIMPKPFPPSTSTFSPSWN TTVYQLLQFLKNTGSFFMLNAYPYYGYTTANGIFPLDYALFKQLSPVKQIVDPNTLLHYNSMFD AMVDAAYYSMEALNFSKIPVVVTETGWPSSGGSDEAAATVANAETFNTNLIKRVLNNSGPPSQP DIPINTYIYELYNEDKRSGPVSERNWGILFPNGTSVYPLSLSGGSSSAALNGSSMFCVAKADAD DDKLVDGLNWACGQGRANCAAIQPGQPCYLPNDVKSHASFAFNDYYQKMKSAGGTCDFDGTAIT TTRDPSYRTCAYTGRVFVGLRFSSTLFPMLLPRWFAEALLLLLSILACSNAAFIGVNIGTDLTN MPPPSDIVTLLKSQQITHVRLYDANSHMLKAFANTSIEVMVGVTNEEILKIGRFPSAAAAWVNK NVAAYIPSTNITAIAVGSEVLTTIPHVAPILASALNNIHKALVASNLNFKVKVSSPMSMDIMPK PFPPSTSTFSPSWNTTVYQLLQFLKNTGSFFMLNAYPYYGYTTANGIFPLDYALFKQLSPVKQI VDPNTLLHYNSMFDAMVDAAYYSMEALNFSKIPVVVTETGWPSSGGSDEAAATVANAETFNTNL IKRVLNNSGPPSQPDIPINTYIYELYNEDKRSGPVSERNWGILFPNGTSVYPLSLSGGSSSAAL NGSSMFCVAKADADDDKLVDGLNWACGQGRANCAAIQPGQPCYLPNDVKSHASFAFNDYYQKMK SAGGTCDFDGTAITTTRDPSYRTCAYTGRVFVGLRFSSTLFPMLLPRWFAEALLLLLSILACSN AAFIGVNIGTDLTNMPPPSDIVTLLKSQQITHVRLYDANSHMLKAFANTSIEVMVGVTNEEILK IGRFPSAAAAWVNKNVAAYIPSTNITAIAVGSEVLTTIPHVAPILASALNNIHKALVASNLNFK VKVSSPMSMDIMPKPFPPSTSTFSPSWNTTVYQLLQFLKNTGSFFMLNAYPYYGYTTANGIFPL DYALFKQLSPVKQIVDPNTLLHYNSMFDAMVDAAYYSMEALNFSKIPVVVTETGWPSSGGSDEA AATVANAETFNTNLIKRVLNNSGPPSQPDIPINTYIYELYNEDKRSGPVSERNWGILFPNGTSV YPLSLSGGSSSAALNGSSMFCVAKADADDDKLVDGLNWACGQGRANCAAIQPGQPCYLPNDVKS HASFAFNDYYQKMKSAGGTCDFDGTAITTTRDPSYRTCAYTG(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Pan et al., 2017

circRNA

Detail information of AT3G13560_circ_g.1

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