Plant Circular RNA Database

Detail information of AT5G61140_circ_g.11

			
						 General Information
					
						CircRNA Name
						AT5G61140_circ_g.11
					
						ID in PlantcircBase
						ath_circ_045127
					
						Alias
						At_ciR179, AT5G61140_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 24598413-24599125  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT5G61140						
					
						Parent gene annotation
						
							DExH-box ATP-dependent RNA helicase DExH14
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G61140_circ_g.7 AT5G61140_circ_g.8 AT5G61140_circ_g.9 AT5G61140_circ_g.10 AT5G61140_circ_g.12 AT5G61140_circ_g.13 AT5G61140_circ_g.14 AT5G61140_circ_g.15 AT5G61140_circ_g.16 AT5G61140_circ_g.17 AT5G61140_circ_g.18 						
					
						Support reads
						50/2
					
						Tissues
						leaf/root, aerial, whole_plant
					
						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
						AT5G61140.2:3
AT5G61140.1:3

General Information
CircRNA Name	AT5G61140_circ_g.11
ID in PlantcircBase	ath_circ_045127
Alias	At_ciR179, AT5G61140_C1
Organism	Arabidpsis thaliana
Position	chr5: 24598413-24599125 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ, CIRI-full, CIRI2
Parent gene	AT5G61140
Parent gene annotation	DExH-box ATP-dependent RNA helicase DExH14
Parent gene strand	+
Alternative splicing	AT5G61140_circ_g.7 AT5G61140_circ_g.8 AT5G61140_circ_g.9 AT5G61140_circ_g.10 AT5G61140_circ_g.12 AT5G61140_circ_g.13 AT5G61140_circ_g.14 AT5G61140_circ_g.15 AT5G61140_circ_g.16 AT5G61140_circ_g.17 AT5G61140_circ_g.18
Support reads	50/2
Tissues	leaf/root, aerial, whole_plant
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	AT5G61140.2:3 AT5G61140.1:3

			
						 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  
						
							CCTTTTCAGTGATTTGGCTGACTGGTTGGGTGTTGGGGAGATCGGACTTTTCAATTTTAAACCA
AGCGTCAGGCCTGTACCAATTGAAGTTCATATTCAGgtcggccttgttattttggatgagattc
acttgcttggagccgacagaggaccgattcttgaggtagaagcttaataactattatatcccat
tttctaag

									
								

					

						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: 243
Transcript exons: 24598413-24598475,24598675-24598763,24599035-24599125
GTCGGCCTTGTTATTTTGGATGAGATTCACTTGCTTGGAGCCGACAGAGGACCGATTCTTGAGG
TTATTGTATCTAGGATGAGATATATATCATCACAGACAGAGCGCTCCGTCCGGTTTGTTGGGCT
TTCTACAGCTCTGGCAAATGCAGGTGATTTGGCTGACTGGTTGGGTGTTGGGGAGATCGGACTT
TTCAATTTTAAACCAAGCGTCAGGCCTGTACCAATTGAAGTTCATATTCAG
Transcript length: 442
Transcript exons: 24598413-24599125
GTCGGCCTTGTTATTTTGGATGAGATTCACTTGCTTGGAGCCGACAGAGGACCGATTCTTGAGG
TAGAAGCTTAATAACTATTATATCCCATTTTCTAAGTACTTACGCTAAGCTCCATCTATTGGTT
AGAAGTTTCCAGTTATATCATGACACATGCAATGTATCTATGGTCTTGGTGAAGAGCTTATATC
TTTTCGGCTCAGGTTTTTTCAAAGTTATGTGTTCCACCAGATTTATTTTTGATCTACATTTGGT
TTCCAGGTTATTGTATCTAGGATGAGATATATATCATCACAGACAGAGCGCTCCGTCCGGTTTG
TTGGGCTTTCTACAGCTCTGGCAAATGCAGGTGATTTGGCTGACTGGTTGGGTGTTGGGGAGAT
CGGACTTTTCAATTTTAAACCAAGCGTCAGGCCTGTACCAATTGAAGTTCATATTCAG
						
					

						Genomic sequence
						
							GTCGGCCTTGTTATTTTGGATGAGATTCACTTGCTTGGAGCCGACAGAGGACCGATTCTTGAGG
TAGAAGCTTAATAACTATTATATCCCATTTTCTAAGTACTTACGCTAAGCTCCATCTATTGGTT
AGAAGTTTCCAGTTATATCATGACACATGCAATGTATCTATGGTCTTGGTGAAGAGCTTATATC
TTTTCGGCTCAGGTTTTTTCAAAGTTATGTGTTCCACCAGATTTATTTTTGATCTACATTTGGT
TTCCAGGTTATTGTATCTAGGATGAGATATATATCATCACAGACAGAGCGCTCCGTCCGGTTTG
TTGGGCTTTCTACAGCTCTGGCAAATGCAGGGTTCGTATTTTAACTTCTCAGACTCTTTGAATA
TGCTCTTTTCTATGTATTATCATTAAACACGCAACTGAATGTTCGAGCTGGTAGACTGTTATTC
GTGTCTTTTCTGTGCTGATGACATTGTGCTTATAGTGTGATTTGTGAGTGAAAGACTTTCAACT
TTAGTCTTATTTACTAGAAAATGTTAATGTGGAAGATGGCTTAAGATATACCTTACTCCCAATT
TTTCTGGTAGCCAGTTTTACTTATTCTCTCAAGTCTCCCTTTTCAGTGATTTGGCTGACTGGTT
GGGTGTTGGGGAGATCGGACTTTTCAATTTTAAACCAAGCGTCAGGCCTGTACCAATTGAAGTT
CATATTCAG
						
					

			
		

Sequences
Splice junction sequence	CCTTTTCAGTGATTTGGCTGACTGGTTGGGTGTTGGGGAGATCGGACTTTTCAATTTTAAACCA AGCGTCAGGCCTGTACCAATTGAAGTTCATATTCAGgtcggccttgttattttggatgagattc acttgcttggagccgacagaggaccgattcttgaggtagaagcttaataactattatatcccat tttctaag
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: 243 Transcript exons: 24598413-24598475,24598675-24598763,24599035-24599125 GTCGGCCTTGTTATTTTGGATGAGATTCACTTGCTTGGAGCCGACAGAGGACCGATTCTTGAGG TTATTGTATCTAGGATGAGATATATATCATCACAGACAGAGCGCTCCGTCCGGTTTGTTGGGCT TTCTACAGCTCTGGCAAATGCAGGTGATTTGGCTGACTGGTTGGGTGTTGGGGAGATCGGACTT TTCAATTTTAAACCAAGCGTCAGGCCTGTACCAATTGAAGTTCATATTCAG Transcript length: 442 Transcript exons: 24598413-24599125 GTCGGCCTTGTTATTTTGGATGAGATTCACTTGCTTGGAGCCGACAGAGGACCGATTCTTGAGG TAGAAGCTTAATAACTATTATATCCCATTTTCTAAGTACTTACGCTAAGCTCCATCTATTGGTT AGAAGTTTCCAGTTATATCATGACACATGCAATGTATCTATGGTCTTGGTGAAGAGCTTATATC TTTTCGGCTCAGGTTTTTTCAAAGTTATGTGTTCCACCAGATTTATTTTTGATCTACATTTGGT TTCCAGGTTATTGTATCTAGGATGAGATATATATCATCACAGACAGAGCGCTCCGTCCGGTTTG TTGGGCTTTCTACAGCTCTGGCAAATGCAGGTGATTTGGCTGACTGGTTGGGTGTTGGGGAGAT CGGACTTTTCAATTTTAAACCAAGCGTCAGGCCTGTACCAATTGAAGTTCATATTCAG
Genomic sequence	GTCGGCCTTGTTATTTTGGATGAGATTCACTTGCTTGGAGCCGACAGAGGACCGATTCTTGAGG TAGAAGCTTAATAACTATTATATCCCATTTTCTAAGTACTTACGCTAAGCTCCATCTATTGGTT AGAAGTTTCCAGTTATATCATGACACATGCAATGTATCTATGGTCTTGGTGAAGAGCTTATATC TTTTCGGCTCAGGTTTTTTCAAAGTTATGTGTTCCACCAGATTTATTTTTGATCTACATTTGGT TTCCAGGTTATTGTATCTAGGATGAGATATATATCATCACAGACAGAGCGCTCCGTCCGGTTTG TTGGGCTTTCTACAGCTCTGGCAAATGCAGGGTTCGTATTTTAACTTCTCAGACTCTTTGAATA TGCTCTTTTCTATGTATTATCATTAAACACGCAACTGAATGTTCGAGCTGGTAGACTGTTATTC GTGTCTTTTCTGTGCTGATGACATTGTGCTTATAGTGTGATTTGTGAGTGAAAGACTTTCAACT TTAGTCTTATTTACTAGAAAATGTTAATGTGGAAGATGGCTTAAGATATACCTTACTCCCAATT TTTCTGGTAGCCAGTTTTACTTATTCTCTCAAGTCTCCCTTTTCAGTGATTTGGCTGACTGGTT GGGTGTTGGGGAGATCGGACTTTTCAATTTTAAACCAAGCGTCAGGCCTGTACCAATTGAAGTT CATATTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.32769192

Conservation Information
Conserved circRNAs	NA
PMCS	0.32769192

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24598690-24599122(+)
						
						Potential amino acid sequence
						
							MRYISSQTERSVRFVGLSTALANAGDLADWLGVGEIGLFNFKPSVRPVPIEVHIQVGLVILDEI
HLLGADRGPILEVIVSRMRYISSQTERSVRFVGLSTALANAGDLADWLGVGEIGLFNFKPSVRP
VPIEVHIQVGLVILDEIHLLGADRGPILEVIVSRMRYISSQTERSVRFVGLSTALANAGDLADW
LGVGEIGLFNFKPSVRPVPIEVHIQVGLVILDEIHLLGADRGPILEVIVSRMRYISSQTERSVR
FVGLSTALANAGDLADWLGVGEIGLFNFKPSVRPVPIEVHIQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	24598690-24599122(+)
Potential amino acid sequence	MRYISSQTERSVRFVGLSTALANAGDLADWLGVGEIGLFNFKPSVRPVPIEVHIQVGLVILDEI HLLGADRGPILEVIVSRMRYISSQTERSVRFVGLSTALANAGDLADWLGVGEIGLFNFKPSVRP VPIEVHIQVGLVILDEIHLLGADRGPILEVIVSRMRYISSQTERSVRFVGLSTALANAGDLADW LGVGEIGLFNFKPSVRPVPIEVHIQVGLVILDEIHLLGADRGPILEVIVSRMRYISSQTERSVR FVGLSTALANAGDLADWLGVGEIGLFNFKPSVRPVPIEVHIQ(+)
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;Zhang et al., 2019

circRNA

Detail information of AT5G61140_circ_g.11

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