Plant Circular RNA Database

Detail information of AT4G38552_circ_g.11

			
						 General Information
					
						CircRNA Name
						AT4G38552_circ_g.11
					
						ID in PlantcircBase
						ath_circ_035431
					
						Alias
						At_ciR3104, Ath_circ_FC3058, AT4G38550_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 18027239-18027708  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, CIRI-full, MapSplice, find_circ, CIRI2
					
						Parent gene
						
							AT4G38550						
					
						Parent gene annotation
						
							Arabidopsis phospholipase-like protein (PEARLI 4) family
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G38552_circ_g.7 AT4G38552_circ_g.8 AT4G38552_circ_g.9 AT4G38552_circ_g.10 AT4G38552_circ_g.12 						
					
						Support reads
						2/3
					
						Tissues
						leaf/root, aerial
					
						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
						AT4G38550.4:2
AT4G38550.5:2
AT4G38550.3:2
AT4G38550.1:2
AT4G38550.2:2

General Information
CircRNA Name	AT4G38552_circ_g.11
ID in PlantcircBase	ath_circ_035431
Alias	At_ciR3104, Ath_circ_FC3058, AT4G38550_C1
Organism	Arabidpsis thaliana
Position	chr4: 18027239-18027708 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, CIRI-full, MapSplice, find_circ, CIRI2
Parent gene	AT4G38550
Parent gene annotation	Arabidopsis phospholipase-like protein (PEARLI 4) family
Parent gene strand	+
Alternative splicing	AT4G38552_circ_g.7 AT4G38552_circ_g.8 AT4G38552_circ_g.9 AT4G38552_circ_g.10 AT4G38552_circ_g.12
Support reads	2/3
Tissues	leaf/root, aerial
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	AT4G38550.4:2 AT4G38550.5:2 AT4G38550.3:2 AT4G38550.1:2 AT4G38550.2:2

			
						 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  
						
							ACCATACTATTCATCCAGCGACGACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGC
CCACTTCGTTCCAGGATCGTATCCGAGAACAGCACGtctgatcaacgtagtaaccatggtaaag
agcaaattgaggacttttatgagcaagatgacgatgtaacaccacgaaacagctctccacctag
cccattgc

									
								

					

						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: 223
Transcript exons: 18027239-18027384,18027632-18027708
TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG
TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC
ACCACAACCATACAGAACACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGCCCACT
TCGTTCCAGGATCGTATCCGAGAACAGCACG
Transcript length: 228
Transcript exons: 18027239-18027385,18027628-18027708
TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG
TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC
ACCACAACCATACAGAACGGACGACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGC
CCACTTCGTTCCAGGATCGTATCCGAGAACAGCACG
Transcript length: 251
Transcript exons: 18027239-18027385,18027605-18027708
TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG
TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC
ACCACAACCATACAGAACGATGGACCATACTATTCATCCAGCGACGACGATAATCACTCCACCT
ACCTCTATCCAGAAATCCGCAGCCCACTTCGTTCCAGGATCGTATCCGAGAACAGCACG
Transcript length: 269
Transcript exons: 18027239-18027385,18027587-18027708
TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG
TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC
ACCACAACCATACAGAACGCTCCTCCGAGTCCCGTTCATGGACCATACTATTCATCCAGCGACG
ACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGCCCACTTCGTTCCAGGATCGTATC
CGAGAACAGCACG
Transcript length: 277
Transcript exons: 18027239-18027385,18027579-18027708
TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG
TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC
ACCACAACCATACAGAACGGAAGAGCGCTCCTCCGAGTCCCGTTCATGGACCATACTATTCATC
CAGCGACGACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGCCCACTTCGTTCCAGG
ATCGTATCCGAGAACAGCACG
Transcript length: 305
Transcript exons: 18027239-18027385,18027551-18027708
TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG
TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC
ACCACAACCATACAGAACGATGAGCTAGATGGCGACTTAATACACCAGAAGAGCGCTCCTCCGA
GTCCCGTTCATGGACCATACTATTCATCCAGCGACGACGATAATCACTCCACCTACCTCTATCC
AGAAATCCGCAGCCCACTTCGTTCCAGGATCGTATCCGAGAACAGCACG
Transcript length: 325
Transcript exons: 18027239-18027385,18027531-18027708
TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG
TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC
ACCACAACCATACAGAACGCGAGGATTTCGAGGCAATGTATGAGCTAGATGGCGACTTAATACA
CCAGAAGAGCGCTCCTCCGAGTCCCGTTCATGGACCATACTATTCATCCAGCGACGACGATAAT
CACTCCACCTACCTCTATCCAGAAATCCGCAGCCCACTTCGTTCCAGGATCGTATCCGAGAACA
GCACG
Transcript length: 347
Transcript exons: 18027239-18027385,18027501-18027577,18027586-18027708
TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG
TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC
ACCACAACCATACAGAACGGCCTGACCATCGTAGAAGCCACCAGGATAACGAGGATTTCGAGGC
AATGTATGAGCTAGATGGCGACTTAATACACCGCTCCTCCGAGTCCCGTTCATGGACCATACTA
TTCATCCAGCGACGACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGCCCACTTCGT
TCCAGGATCGTATCCGAGAACAGCACG
Transcript length: 354
Transcript exons: 18027239-18027385,18027502-18027708
TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG
TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC
ACCACAACCATACAGAACGCCTGACCATCGTAGAAGCCACCAGGATAACGAGGATTTCGAGGCA
ATGTATGAGCTAGATGGCGACTTAATACACCAGAAGAGCGCTCCTCCGAGTCCCGTTCATGGAC
CATACTATTCATCCAGCGACGACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGCCC
ACTTCGTTCCAGGATCGTATCCGAGAACAGCACG
						
					

						Genomic sequence
						
							TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG
TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC
ACCACAACCATACAGAACGGTACTCAAAAAATCTTAAGTCTGGCTCATTGTTTTTGTTTCAGCT
TCTTCCTAGTGATAAAAAACGTCCTCTTGACAGTGAGTCACATATATTGAATTTTCTCTCTAAT
TGTGCAGCCTGACCATCGTAGAAGCCACCAGGATAACGAGGATTTCGAGGCAATGTATGAGCTA
GATGGCGACTTAATACACCAGAAGAGCGCTCCTCCGAGTCCCGTTCATGGACCATACTATTCAT
CCAGCGACGACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGCCCACTTCGTTCCAG
GATCGTATCCGAGAACAGCACG
						
					

			
		

Sequences
Splice junction sequence	ACCATACTATTCATCCAGCGACGACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGC CCACTTCGTTCCAGGATCGTATCCGAGAACAGCACGtctgatcaacgtagtaaccatggtaaag agcaaattgaggacttttatgagcaagatgacgatgtaacaccacgaaacagctctccacctag cccattgc
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: 223 Transcript exons: 18027239-18027384,18027632-18027708 TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC ACCACAACCATACAGAACACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGCCCACT TCGTTCCAGGATCGTATCCGAGAACAGCACG Transcript length: 228 Transcript exons: 18027239-18027385,18027628-18027708 TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC ACCACAACCATACAGAACGGACGACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGC CCACTTCGTTCCAGGATCGTATCCGAGAACAGCACG Transcript length: 251 Transcript exons: 18027239-18027385,18027605-18027708 TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC ACCACAACCATACAGAACGATGGACCATACTATTCATCCAGCGACGACGATAATCACTCCACCT ACCTCTATCCAGAAATCCGCAGCCCACTTCGTTCCAGGATCGTATCCGAGAACAGCACG Transcript length: 269 Transcript exons: 18027239-18027385,18027587-18027708 TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC ACCACAACCATACAGAACGCTCCTCCGAGTCCCGTTCATGGACCATACTATTCATCCAGCGACG ACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGCCCACTTCGTTCCAGGATCGTATC CGAGAACAGCACG Transcript length: 277 Transcript exons: 18027239-18027385,18027579-18027708 TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC ACCACAACCATACAGAACGGAAGAGCGCTCCTCCGAGTCCCGTTCATGGACCATACTATTCATC CAGCGACGACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGCCCACTTCGTTCCAGG ATCGTATCCGAGAACAGCACG Transcript length: 305 Transcript exons: 18027239-18027385,18027551-18027708 TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC ACCACAACCATACAGAACGATGAGCTAGATGGCGACTTAATACACCAGAAGAGCGCTCCTCCGA GTCCCGTTCATGGACCATACTATTCATCCAGCGACGACGATAATCACTCCACCTACCTCTATCC AGAAATCCGCAGCCCACTTCGTTCCAGGATCGTATCCGAGAACAGCACG Transcript length: 325 Transcript exons: 18027239-18027385,18027531-18027708 TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC ACCACAACCATACAGAACGCGAGGATTTCGAGGCAATGTATGAGCTAGATGGCGACTTAATACA CCAGAAGAGCGCTCCTCCGAGTCCCGTTCATGGACCATACTATTCATCCAGCGACGACGATAAT CACTCCACCTACCTCTATCCAGAAATCCGCAGCCCACTTCGTTCCAGGATCGTATCCGAGAACA GCACG Transcript length: 347 Transcript exons: 18027239-18027385,18027501-18027577,18027586-18027708 TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC ACCACAACCATACAGAACGGCCTGACCATCGTAGAAGCCACCAGGATAACGAGGATTTCGAGGC AATGTATGAGCTAGATGGCGACTTAATACACCGCTCCTCCGAGTCCCGTTCATGGACCATACTA TTCATCCAGCGACGACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGCCCACTTCGT TCCAGGATCGTATCCGAGAACAGCACG Transcript length: 354 Transcript exons: 18027239-18027385,18027502-18027708 TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC ACCACAACCATACAGAACGCCTGACCATCGTAGAAGCCACCAGGATAACGAGGATTTCGAGGCA ATGTATGAGCTAGATGGCGACTTAATACACCAGAAGAGCGCTCCTCCGAGTCCCGTTCATGGAC CATACTATTCATCCAGCGACGACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGCCC ACTTCGTTCCAGGATCGTATCCGAGAACAGCACG
Genomic sequence	TCTGATCAACGTAGTAACCATGGTAAAGAGCAAATTGAGGACTTTTATGAGCAAGATGACGATG TAACACCACGAAACAGCTCTCCACCTAGCCCATTGCATCCAGCAGCAAGCCATTCACCACCACC ACCACAACCATACAGAACGGTACTCAAAAAATCTTAAGTCTGGCTCATTGTTTTTGTTTCAGCT TCTTCCTAGTGATAAAAAACGTCCTCTTGACAGTGAGTCACATATATTGAATTTTCTCTCTAAT TGTGCAGCCTGACCATCGTAGAAGCCACCAGGATAACGAGGATTTCGAGGCAATGTATGAGCTA GATGGCGACTTAATACACCAGAAGAGCGCTCCTCCGAGTCCCGTTCATGGACCATACTATTCAT CCAGCGACGACGATAATCACTCCACCTACCTCTATCCAGAAATCCGCAGCCCACTTCGTTCCAG GATCGTATCCGAGAACAGCACG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.565712198

Conservation Information
Conserved circRNAs	NA
PMCS	0.565712198

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18027547-18027705(+)
						
						Potential amino acid sequence
						
							MYELDGDLIHQKSAPPSPVHGPYYSSSDDDNHSTYLYPEIRSPLRSRIVSENSTSDQRSNHGKE
QIEDFYEQDDDVTPRNSSPPSPLHPAASHSPPPPQPYRTPDHRRSHQDNEDFEAMYELDGDLIH
QKSAPPSPVHGPYYSSSDDDNHSTYLYPEIRSPLRSRIVSENSTSDQRSNHGKEQIEDFYEQDD
DVTPRNSSPPSPLHPAASHSPPPPQPYRTPDHRRSHQDNEDFEAMYELDGDLIHQKSAPPSPVH
GPYYSSSDDDNHSTYLYPEIRSPLRSRIVSENSTSDQRSNHGKEQIEDFYEQDDDVTPRNSSPP
SPLHPAASHSPPPPQPYRTPDHRRSHQDNEDFEAMYELDGDLIHQKSAPPSPVHGPYYSSSDDD
NHSTYLYPEIRSPLRSRIVSENST(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	18027547-18027705(+)
Potential amino acid sequence	MYELDGDLIHQKSAPPSPVHGPYYSSSDDDNHSTYLYPEIRSPLRSRIVSENSTSDQRSNHGKE QIEDFYEQDDDVTPRNSSPPSPLHPAASHSPPPPQPYRTPDHRRSHQDNEDFEAMYELDGDLIH QKSAPPSPVHGPYYSSSDDDNHSTYLYPEIRSPLRSRIVSENSTSDQRSNHGKEQIEDFYEQDD DVTPRNSSPPSPLHPAASHSPPPPQPYRTPDHRRSHQDNEDFEAMYELDGDLIHQKSAPPSPVH GPYYSSSDDDNHSTYLYPEIRSPLRSRIVSENSTSDQRSNHGKEQIEDFYEQDDDVTPRNSSPP SPLHPAASHSPPPPQPYRTPDHRRSHQDNEDFEAMYELDGDLIHQKSAPPSPVHGPYYSSSDDD NHSTYLYPEIRSPLRSRIVSENST(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Chen et al., 2017a;Liu et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT4G38552_circ_g.11

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