Plant Circular RNA Database

Detail information of AT5G17020_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G17020_circ_g.4
					
						ID in PlantcircBase
						ath_circ_038726
					
						Alias
						At_ciR1909
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 5595534-5596252  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI-full
					
						Parent gene
						
							AT5G17020						
					
						Parent gene annotation
						
							XPO1A
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G17020_circ_g.1 AT5G17020_circ_g.2 AT5G17020_circ_g.3 AT5G17020_circ_g.5 AT5G17020_circ_g.6 AT5G17020_circ_g.7 AT5G17020_circ_g.8 AT5G17020_circ_g.9 AT5G17020_circ_g.10 AT5G17020_circ_g.11 AT5G17020_circ_g.12 AT5G17020_circ_g.13 AT5G17020_circ_g.14 AT5G17020_circ_g.15 AT5G17020_circ_g.16 AT5G17020_circ_g.17 AT5G17020_circ_g.18 AT5G17020_circ_g.19 AT5G17020_circ_g.20 AT5G17020_circ_g.21 AT5G17020_circ_g.22 AT5G17020_circ_g.23 AT5G17020_circ_g.24 AT5G17020_circ_g.25 AT5G17020_circ_g.26 AT5G17020_circ_g.27 AT5G17020_circ_g.28 AT5G17020_circ_g.29 AT5G17020_circ_g.30 AT5G17020_circ_g.31 AT5G17020_circ_g.32 AT5G17020_circ_g.33 AT5G17020_circ_g.34 AT5G17020_circ_g.35 AT5G17020_circ_g.36 AT5G17020_circ_g.37 AT5G17020_circ_g.38 AT5G17020_circ_g.39 AT5G17020_circ_g.40 AT5G17020_circ_g.41 						
					
						Support reads
						4/3/10
					
						Tissues
						leaf/whole_plant/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  
						
							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
						AT5G17020.2:4
AT5G17020.1:4

General Information
CircRNA Name	AT5G17020_circ_g.4
ID in PlantcircBase	ath_circ_038726
Alias	At_ciR1909
Organism	Arabidpsis thaliana
Position	chr5: 5595534-5596252 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI-full
Parent gene	AT5G17020
Parent gene annotation	XPO1A
Parent gene strand	+
Alternative splicing	AT5G17020_circ_g.1 AT5G17020_circ_g.2 AT5G17020_circ_g.3 AT5G17020_circ_g.5 AT5G17020_circ_g.6 AT5G17020_circ_g.7 AT5G17020_circ_g.8 AT5G17020_circ_g.9 AT5G17020_circ_g.10 AT5G17020_circ_g.11 AT5G17020_circ_g.12 AT5G17020_circ_g.13 AT5G17020_circ_g.14 AT5G17020_circ_g.15 AT5G17020_circ_g.16 AT5G17020_circ_g.17 AT5G17020_circ_g.18 AT5G17020_circ_g.19 AT5G17020_circ_g.20 AT5G17020_circ_g.21 AT5G17020_circ_g.22 AT5G17020_circ_g.23 AT5G17020_circ_g.24 AT5G17020_circ_g.25 AT5G17020_circ_g.26 AT5G17020_circ_g.27 AT5G17020_circ_g.28 AT5G17020_circ_g.29 AT5G17020_circ_g.30 AT5G17020_circ_g.31 AT5G17020_circ_g.32 AT5G17020_circ_g.33 AT5G17020_circ_g.34 AT5G17020_circ_g.35 AT5G17020_circ_g.36 AT5G17020_circ_g.37 AT5G17020_circ_g.38 AT5G17020_circ_g.39 AT5G17020_circ_g.40 AT5G17020_circ_g.41
Support reads	4/3/10
Tissues	leaf/whole_plant/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	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	AT5G17020.2:4 AT5G17020.1:4

			
						 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  
						
							ACATGATTGGCCGGCAAAGTGGACAAGCTTCATTCCTGATCTAGTTGCAGCTGCTAAAACTAGC
GAAACTATCTGCGAAAATTGCATGGCCATTTTGAAAagagctgctgcggaccagattttgcggg
atttgcaggctaatccagatatgtggcttcaagttgtccacattctacaaaatacaaacagctt
ggatacca

						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: 390
Transcript exons: 5595534-5595650,5595731-5595823,5595918-5595989,5596145-
5596252
AGAGCTGCTGCGGACCAGATTTTGCGGGATTTGCAGGCTAATCCAGATATGTGGCTTCAAGTTG
TCCACATTCTACAAAATACAAACAGCTTGGATACCAAGTTCTTTGCTCTGCAGGTTCTAGAAGG
TGTTATAAAGTATAGATGGAATGCACTGCCTGTTGAACAACGAGATGGAATGAAAAATTACATC
TCAGAGGTTATTGTACAGCTCTCGAGTAATGAAGCATCTTTCAGATCAGAAAGGCTCTATGTCA
ACAAGCTAAATGTCATTTTGGTCCAGATCGTGAAACATGATTGGCCGGCAAAGTGGACAAGCTT
CATTCCTGATCTAGTTGCAGCTGCTAAAACTAGCGAAACTATCTGCGAAAATTGCATGGCCATT
TTGAAA
						
						Genomic sequence
						
							AGAGCTGCTGCGGACCAGATTTTGCGGGATTTGCAGGCTAATCCAGATATGTGGCTTCAAGTTG
TCCACATTCTACAAAATACAAACAGCTTGGATACCAAGTTCTTTGCTCTGCAGGTCAGTTTTAG
TTCCTTATGCAGTTGTAAATTAAAACTGTTCTGTTGAGATACTTTACTCTTTTTGGCATCCACT
CTCAGGTTCTAGAAGGTGTTATAAAGTATAGATGGAATGCACTGCCTGTTGAACAACGAGATGG
AATGAAAAATTACATCTCAGAGGTTATTGTACAGGTATATACTTTTGGAGGCTTTATTACCTTG
TTCTCTGGATATAACTGGGAAGCTTAGTTAACAGAACTGTTTTGATAATGAGTTTACCTTGTAG
CTCTCGAGTAATGAAGCATCTTTCAGATCAGAAAGGCTCTATGTCAACAAGCTAAATGTCATTT
TGGTCCAGGTATATTCAGCACTCCCTGATAATAATATTCAATGCGTTTATTAGTTGCACTTCTC
TTGTCTCTTTGGTTTCAGTAGCTGATACTTACAAACTTCATTCCAACCCGTAGACTTATTTTAT
CTTCTGGCATAACATATGTTGTGATAAATGCACAGATCGTGAAACATGATTGGCCGGCAAAGTG
GACAAGCTTCATTCCTGATCTAGTTGCAGCTGCTAAAACTAGCGAAACTATCTGCGAAAATTGC
ATGGCCATTTTGAAA

Sequences
Splice junction sequence	ACATGATTGGCCGGCAAAGTGGACAAGCTTCATTCCTGATCTAGTTGCAGCTGCTAAAACTAGC GAAACTATCTGCGAAAATTGCATGGCCATTTTGAAAagagctgctgcggaccagattttgcggg atttgcaggctaatccagatatgtggcttcaagttgtccacattctacaaaatacaaacagctt ggatacca
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: 390 Transcript exons: 5595534-5595650,5595731-5595823,5595918-5595989,5596145- 5596252 AGAGCTGCTGCGGACCAGATTTTGCGGGATTTGCAGGCTAATCCAGATATGTGGCTTCAAGTTG TCCACATTCTACAAAATACAAACAGCTTGGATACCAAGTTCTTTGCTCTGCAGGTTCTAGAAGG TGTTATAAAGTATAGATGGAATGCACTGCCTGTTGAACAACGAGATGGAATGAAAAATTACATC TCAGAGGTTATTGTACAGCTCTCGAGTAATGAAGCATCTTTCAGATCAGAAAGGCTCTATGTCA ACAAGCTAAATGTCATTTTGGTCCAGATCGTGAAACATGATTGGCCGGCAAAGTGGACAAGCTT CATTCCTGATCTAGTTGCAGCTGCTAAAACTAGCGAAACTATCTGCGAAAATTGCATGGCCATT TTGAAA
Genomic sequence	AGAGCTGCTGCGGACCAGATTTTGCGGGATTTGCAGGCTAATCCAGATATGTGGCTTCAAGTTG TCCACATTCTACAAAATACAAACAGCTTGGATACCAAGTTCTTTGCTCTGCAGGTCAGTTTTAG TTCCTTATGCAGTTGTAAATTAAAACTGTTCTGTTGAGATACTTTACTCTTTTTGGCATCCACT CTCAGGTTCTAGAAGGTGTTATAAAGTATAGATGGAATGCACTGCCTGTTGAACAACGAGATGG AATGAAAAATTACATCTCAGAGGTTATTGTACAGGTATATACTTTTGGAGGCTTTATTACCTTG TTCTCTGGATATAACTGGGAAGCTTAGTTAACAGAACTGTTTTGATAATGAGTTTACCTTGTAG CTCTCGAGTAATGAAGCATCTTTCAGATCAGAAAGGCTCTATGTCAACAAGCTAAATGTCATTT TGGTCCAGGTATATTCAGCACTCCCTGATAATAATATTCAATGCGTTTATTAGTTGCACTTCTC TTGTCTCTTTGGTTTCAGTAGCTGATACTTACAAACTTCATTCCAACCCGTAGACTTATTTTAT CTTCTGGCATAACATATGTTGTGATAAATGCACAGATCGTGAAACATGATTGGCCGGCAAAGTG GACAAGCTTCATTCCTGATCTAGTTGCAGCTGCTAAAACTAGCGAAACTATCTGCGAAAATTGC ATGGCCATTTTGAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.36538065

Conservation Information
Conserved circRNAs	NA
PMCS	0.36538065

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5595582-5596249(+)
						
						Potential amino acid sequence
						
							MWLQVVHILQNTNSLDTKFFALQVLEGVIKYRWNALPVEQRDGMKNYISEVIVQLSSNEASFRS
ERLYVNKLNVILVQIVKHDWPAKWTSFIPDLVAAAKTSETICENCMAILKRAAADQILRDLQAN
PDMWLQVVHILQNTNSLDTKFFALQVLEGVIKYRWNALPVEQRDGMKNYISEVIVQLSSNEASF
RSERLYVNKLNVILVQIVKHDWPAKWTSFIPDLVAAAKTSETICENCMAILKRAAADQILRDLQ
ANPDMWLQVVHILQNTNSLDTKFFALQVLEGVIKYRWNALPVEQRDGMKNYISEVIVQLSSNEA
SFRSERLYVNKLNVILVQIVKHDWPAKWTSFIPDLVAAAKTSETICENCMAILKRAAADQILRD
LQANPDMWLQVVHILQNTNSLDTKFFALQVLEGVIKYRWNALPVEQRDGMKNYISEVIVQLSSN
EASFRSERLYVNKLNVILVQIVKHDWPAKWTSFIPDLVAAAKTSETICENCMAILK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to heat stress

Functional Information
Coding potential	Y
Potential coding position	5595582-5596249(+)
Potential amino acid sequence	MWLQVVHILQNTNSLDTKFFALQVLEGVIKYRWNALPVEQRDGMKNYISEVIVQLSSNEASFRS ERLYVNKLNVILVQIVKHDWPAKWTSFIPDLVAAAKTSETICENCMAILKRAAADQILRDLQAN PDMWLQVVHILQNTNSLDTKFFALQVLEGVIKYRWNALPVEQRDGMKNYISEVIVQLSSNEASF RSERLYVNKLNVILVQIVKHDWPAKWTSFIPDLVAAAKTSETICENCMAILKRAAADQILRDLQ ANPDMWLQVVHILQNTNSLDTKFFALQVLEGVIKYRWNALPVEQRDGMKNYISEVIVQLSSNEA SFRSERLYVNKLNVILVQIVKHDWPAKWTSFIPDLVAAAKTSETICENCMAILKRAAADQILRD LQANPDMWLQVVHILQNTNSLDTKFFALQVLEGVIKYRWNALPVEQRDGMKNYISEVIVQLSSN EASFRSERLYVNKLNVILVQIVKHDWPAKWTSFIPDLVAAAKTSETICENCMAILK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to heat stress

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

circRNA

Detail information of AT5G17020_circ_g.4

Address

Any questions?

Supported by