Plant Circular RNA Database

Detail information of AT5G61140_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G61140_circ_g.3
					
						ID in PlantcircBase
						ath_circ_045119
					
						Alias
						At_ciR2842
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 24593853-24594654  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder, circRNA_finder, find_circ
					
						Parent gene
						
							AT5G61140						
					
						Parent gene annotation
						
							DExH-box ATP-dependent RNA helicase DExH14
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G61140_circ_g.4 AT5G61140_circ_g.5 AT5G61140_circ_g.6 						
					
						Support reads
						3/15
					
						Tissues
						leaf/inflorescences
					
						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
						AT5G61140.1:4
AT5G61140.2:4

General Information
CircRNA Name	AT5G61140_circ_g.3
ID in PlantcircBase	ath_circ_045119
Alias	At_ciR2842
Organism	Arabidpsis thaliana
Position	chr5: 24593853-24594654 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, PcircRNA_finder, circRNA_finder, find_circ
Parent gene	AT5G61140
Parent gene annotation	DExH-box ATP-dependent RNA helicase DExH14
Parent gene strand	+
Alternative splicing	AT5G61140_circ_g.4 AT5G61140_circ_g.5 AT5G61140_circ_g.6
Support reads	3/15
Tissues	leaf/inflorescences
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	AT5G61140.1:4 AT5G61140.2:4

			
						 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  
						
							TGTCAAATTCTTTGAAGCTGGCTTCGGAATTCATCATGCTGGGATGTTGAGATCTGATAGAACA
CTTACGGAGAGGCTGTTTTCTGATGGTCTCTTGAAGgttgctcagtttctacgagtgaatacag
acactggcctattctattttgattcaagttatcgcccagttcccttagctcaacaatacatagg
catcactg

						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: 444
Transcript exons: 24593853-24594005,24594089-24594172,24594368-24594442,24
594523-24594654
GTTGCTCAGTTTCTACGAGTGAATACAGACACTGGCCTATTCTATTTTGATTCAAGTTATCGCC
CAGTTCCCTTAGCTCAACAATACATAGGCATCACTGAGCATAACTTTGCTGCTAGAAACGAATT
ATTAAATGAGATATGCTACAAAAAGGTTGTTGATTCAATTAAACAAGGTCATCAAGCAATGATA
TTTGTTCATTCCCGAAAAGACACTTCAAAAACAGCTGAGAAACTGGTTGATCTTGCCCGGCAAT
ATGAAACTCTGGATTTGTTCACGAATGAGACTCATCCTCAATTTCAACTGATGAAGAAAGACGT
TATGAAGTCCAGAAATAAGGATCTTGTCAAATTCTTTGAAGCTGGCTTCGGAATTCATCATGCT
GGGATGTTGAGATCTGATAGAACACTTACGGAGAGGCTGTTTTCTGATGGTCTCTTGAAG
						
						Genomic sequence
						
							GTTGCTCAGTTTCTACGAGTGAATACAGACACTGGCCTATTCTATTTTGATTCAAGTTATCGCC
CAGTTCCCTTAGCTCAACAATACATAGGCATCACTGAGCATAACTTTGCTGCTAGAAACGAATT
ATTAAATGAGATATGCTACAAAAAGGTCTCTATCTCGAGCAAAGACTCTTTTTCATTTATGTGA
AAATGGATAGGTCACTTATCTATCTGGTAATGCTTTCATGTTAGGTTGTTGATTCAATTAAACA
AGGTCATCAAGCAATGATATTTGTTCATTCCCGAAAAGACACTTCAAAAACAGCTGAGAAACTG
GTACATGATATTTTACCTTTTTATATTCAGCTTCTACTTTTTACCTGATGTCTTCCAAAACGCA
TGCATTTGTGGTTTTCCTGAAATCTTAATTATTGCATATGAGAATGATCTCGCCGCCGAAAACA
TGGTTTCTCAAACGATTTTGGAATCCAGATCTAGAAGTACATGACTTTTATATTTTCACTTTGG
CAGGTTGATCTTGCCCGGCAATATGAAACTCTGGATTTGTTCACGAATGAGACTCATCCTCAAT
TTCAACTGATGAAGGTAAAAAATGGAATATATATTATCTTTTTTAACATCATTGTTGGTGTTAA
TTTCTCAAGATTGTTTCTGATGTATCTCAGAAAGACGTTATGAAGTCCAGAAATAAGGATCTTG
TCAAATTCTTTGAAGCTGGCTTCGGAATTCATCATGCTGGGATGTTGAGATCTGATAGAACACT
TACGGAGAGGCTGTTTTCTGATGGTCTCTTGAAG

Sequences
Splice junction sequence	TGTCAAATTCTTTGAAGCTGGCTTCGGAATTCATCATGCTGGGATGTTGAGATCTGATAGAACA CTTACGGAGAGGCTGTTTTCTGATGGTCTCTTGAAGgttgctcagtttctacgagtgaatacag acactggcctattctattttgattcaagttatcgcccagttcccttagctcaacaatacatagg catcactg
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: 444 Transcript exons: 24593853-24594005,24594089-24594172,24594368-24594442,24 594523-24594654 GTTGCTCAGTTTCTACGAGTGAATACAGACACTGGCCTATTCTATTTTGATTCAAGTTATCGCC CAGTTCCCTTAGCTCAACAATACATAGGCATCACTGAGCATAACTTTGCTGCTAGAAACGAATT ATTAAATGAGATATGCTACAAAAAGGTTGTTGATTCAATTAAACAAGGTCATCAAGCAATGATA TTTGTTCATTCCCGAAAAGACACTTCAAAAACAGCTGAGAAACTGGTTGATCTTGCCCGGCAAT ATGAAACTCTGGATTTGTTCACGAATGAGACTCATCCTCAATTTCAACTGATGAAGAAAGACGT TATGAAGTCCAGAAATAAGGATCTTGTCAAATTCTTTGAAGCTGGCTTCGGAATTCATCATGCT GGGATGTTGAGATCTGATAGAACACTTACGGAGAGGCTGTTTTCTGATGGTCTCTTGAAG
Genomic sequence	GTTGCTCAGTTTCTACGAGTGAATACAGACACTGGCCTATTCTATTTTGATTCAAGTTATCGCC CAGTTCCCTTAGCTCAACAATACATAGGCATCACTGAGCATAACTTTGCTGCTAGAAACGAATT ATTAAATGAGATATGCTACAAAAAGGTCTCTATCTCGAGCAAAGACTCTTTTTCATTTATGTGA AAATGGATAGGTCACTTATCTATCTGGTAATGCTTTCATGTTAGGTTGTTGATTCAATTAAACA AGGTCATCAAGCAATGATATTTGTTCATTCCCGAAAAGACACTTCAAAAACAGCTGAGAAACTG GTACATGATATTTTACCTTTTTATATTCAGCTTCTACTTTTTACCTGATGTCTTCCAAAACGCA TGCATTTGTGGTTTTCCTGAAATCTTAATTATTGCATATGAGAATGATCTCGCCGCCGAAAACA TGGTTTCTCAAACGATTTTGGAATCCAGATCTAGAAGTACATGACTTTTATATTTTCACTTTGG CAGGTTGATCTTGCCCGGCAATATGAAACTCTGGATTTGTTCACGAATGAGACTCATCCTCAAT TTCAACTGATGAAGGTAAAAAATGGAATATATATTATCTTTTTTAACATCATTGTTGGTGTTAA TTTCTCAAGATTGTTTCTGATGTATCTCAGAAAGACGTTATGAAGTCCAGAAATAAGGATCTTG TCAAATTCTTTGAAGCTGGCTTCGGAATTCATCATGCTGGGATGTTGAGATCTGATAGAACACT TACGGAGAGGCTGTTTTCTGATGGTCTCTTGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.236208316

Conservation Information
Conserved circRNAs	NA
PMCS	0.236208316

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24594122-24594651(+)
						
						Potential amino acid sequence
						
							MIFVHSRKDTSKTAEKLVDLARQYETLDLFTNETHPQFQLMKKDVMKSRNKDLVKFFEAGFGIH
HAGMLRSDRTLTERLFSDGLLKVAQFLRVNTDTGLFYFDSSYRPVPLAQQYIGITEHNFAARNE
LLNEICYKKVVDSIKQGHQAMIFVHSRKDTSKTAEKLVDLARQYETLDLFTNETHPQFQLMKKD
VMKSRNKDLVKFFEAGFGIHHAGMLRSDRTLTERLFSDGLLKVAQFLRVNTDTGLFYFDSSYRP
VPLAQQYIGITEHNFAARNELLNEICYKKVVDSIKQGHQAMIFVHSRKDTSKTAEKLVDLARQY
ETLDLFTNETHPQFQLMKKDVMKSRNKDLVKFFEAGFGIHHAGMLRSDRTLTERLFSDGLLKVA
QFLRVNTDTGLFYFDSSYRPVPLAQQYIGITEHNFAARNELLNEICYKKVVDSIKQGHQAMIFV
HSRKDTSKTAEKLVDLARQYETLDLFTNETHPQFQLMKKDVMKSRNKDLVKFFEAGFGIHHAGM
LRSDRTLTERLFSDGLLK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24594122-24594651(+)
Potential amino acid sequence	MIFVHSRKDTSKTAEKLVDLARQYETLDLFTNETHPQFQLMKKDVMKSRNKDLVKFFEAGFGIH HAGMLRSDRTLTERLFSDGLLKVAQFLRVNTDTGLFYFDSSYRPVPLAQQYIGITEHNFAARNE LLNEICYKKVVDSIKQGHQAMIFVHSRKDTSKTAEKLVDLARQYETLDLFTNETHPQFQLMKKD VMKSRNKDLVKFFEAGFGIHHAGMLRSDRTLTERLFSDGLLKVAQFLRVNTDTGLFYFDSSYRP VPLAQQYIGITEHNFAARNELLNEICYKKVVDSIKQGHQAMIFVHSRKDTSKTAEKLVDLARQY ETLDLFTNETHPQFQLMKKDVMKSRNKDLVKFFEAGFGIHHAGMLRSDRTLTERLFSDGLLKVA QFLRVNTDTGLFYFDSSYRPVPLAQQYIGITEHNFAARNELLNEICYKKVVDSIKQGHQAMIFV HSRKDTSKTAEKLVDLARQYETLDLFTNETHPQFQLMKKDVMKSRNKDLVKFFEAGFGIHHAGM LRSDRTLTERLFSDGLLK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of AT5G61140_circ_g.3

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