Plant Circular RNA Database

Detail information of AT5G38880_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G38880_circ_g.3
					
						ID in PlantcircBase
						ath_circ_041562
					
						Alias
						5:15564244-15566506
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 15564244-15566506  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G38880						
					
						Parent gene annotation
						
							AUGMIN subunit 5
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G38880_circ_g.1 AT5G38880_circ_g.2 AT5G38880_circ_g.4 AT5G38880_circ_g.5 AT5G38880_circ_g.6 						
					
						Support reads
						2
					
						Tissues
						root
					
						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
						AT5G38880.1:6

General Information
CircRNA Name	AT5G38880_circ_g.3
ID in PlantcircBase	ath_circ_041562
Alias	5:15564244-15566506
Organism	Arabidpsis thaliana
Position	chr5: 15564244-15566506 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G38880
Parent gene annotation	AUGMIN subunit 5
Parent gene strand	-
Alternative splicing	AT5G38880_circ_g.1 AT5G38880_circ_g.2 AT5G38880_circ_g.4 AT5G38880_circ_g.5 AT5G38880_circ_g.6
Support reads	2
Tissues	root
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	AT5G38880.1:6

			
						 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  
						
							TTCCATGCAAACGGTTAATAAACTTGTGGCATAAATCACGAGCTTCAGCTGCTTTGTTTAGTGC
ATCTTCAGTAGCCAAAAATTGTTGAACATGGGCTTTcaaacccctaacgtatttgcagtgttcc
gaggaagcttgcgcattctgaactgcagtcctaagttcaggtaaccactggtccgatattgtat
tctcttgt

									
								

					

						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: 1056
Transcript exons: 15564244-15564376,15564485-15564680,15565103-15565262,15
565628-15565813,15565903-15566112,15566336-15566506
CAAACCCCTAACGTATTTGCAGTGTTCCGAGGAAGCTTGCGCATTCTGAACTGCAGTCCTAAGT
TCAGGTAACCACTGGTCCGATATTGTATTCTCTTGTTCAGAAGCTAGATCTAGGCAGTAGTTAG
TTGTTCTTTCATATTTTTGCTGGGCACGGAAAGCATGATCTAACAGAGAATGGCCACTTTCAAC
TAGATCCTGCCGAATATGGACCAAATCGATTGCCTTTGCTAAGTCTTCTAAAACACATGCTTCA
GAACCACGAACTCTTAAGCAGAACTCAAGAGACTCTAACACTGAGGCCAAACTTGCATCTGAAC
CCTCAAGACCTGCAGGATATTGAAGGGCAGCAGAAATGCGACATATAGATGGTATTGCCGATGG
ATCTCTTGCACCAGCTCTAGCCGTTAATAGAGCAGCATTCTTCTCTGCATATGCAACAGCTTCA
GGTCCCGTCGATCCATTAGCTCCCATAGATTCCAGAAGTCCCTGGGGAGTTGCTGGAAGCATAT
AAAGACTGTTATCAGGACTTTGAAAGAAAGCAGACACTTCTTTCTCAATGAAATCTTTTGCGCT
GTTTGAAATGTCCACAACAACTTCACTGGCTGGAATTACAGTGGCTGATGCATATTCCCTTGCA
GCTAGTGGTTGTTGATTCCAGAATGCAACAGCATCCATGTTGGCCTTGAGAAGAGTTGTATATA
TGGTTTCAAGTTCGGATCTGCGAGCATCAAATTCCTCAATTTTCTTCCACTTCTTTTTCAAGGA
ATCTTCGGCTTCTTTTCTTTCTGCACATAATTTATTCAGCCGTTGTATTTCAGATAACAATGTG
TTTAAGCTAGCCCTCAAACCAGCAGCTTCTCTTTCCTTTCCCCATACATCCAACTCAAATTGCC
TAAGATTGCTACCACTCTGTGTTGTGCCTCCAACAAACGAATGAGTAGCTGTATCAGCACTTCC
ATGCAAACGGTTAATAAACTTGTGGCATAAATCACGAGCTTCAGCTGCTTTGTTTAGTGCATCT
TCAGTAGCCAAAAATTGTTGAACATGGGCTTT
						
					

						Genomic sequence
						
							CAAACCCCTAACGTATTTGCAGTGTTCCGAGGAAGCTTGCGCATTCTGAACTGCAGTCCTAAGT
TCAGGTAACCACTGGTCCGATATTGTATTCTCTTGTTCAGAAGCTAGATCTAGGCAGTAGTTAG
TTGTTCTGCATACAAGATACACAGTATAGTGGAAGTTTACATAAGATAGTGTGGGGCAATAAAT
AAGATAATTGTGGCCTGTGTAGACCAGAGCACTGAGGAACACGCTTTACCTTTCATATTTTTGC
TGGGCACGGAAAGCATGATCTAACAGAGAATGGCCACTTTCAACTAGATCCTGCCGAATATGGA
CCAAATCGATTGCCTTTGCTAAGTCTTCTAAAACACATGCTTCAGAACCACGAACTCTTAAGCA
GAACTCAAGAGACTCTAACACTGAGGCCAAACTTGCATCTGAACCCTCAAGACCTATTCAAGCA
GCAGAATATAGATGATAAGCAAGTCCTACTAAGAAGCCACTAAGAATTTTGATCTATGAAGATT
TCTAAGTATTTTATATAAAAGGTGTTCCACTTTTTATGGTTGAAAACAACAGCAGATCCAAAGC
GTGGTAATGATATGCAACTAGTGGCCATCATTAAACCTTTTGGTTATTATAGCATTCCTCAATC
GACGTAATAGGTAGATGAACTAACAATGCTAGGAACTTTTTTTTATTTTTAAAATGTTTGTTTT
ATGATTTTGCACTGCATTGAGAAAGATTGTCATTCATGAAGCAGTGAGCAATAGTTTCATTAAA
AAGCTCCTTGTCAATGCAAATAATTTTTGTCCAGAGAGATGAACTATACGTCCTTGGATTTTTG
AAAAAAAAACGAAGAAAAAAATCTTACCTGCAGGATATTGAAGGGCAGCAGAAATGCGACATAT
AGATGGTATTGCCGATGGATCTCTTGCACCAGCTCTAGCCGTTAATAGAGCAGCATTCTTCTCT
GCATATGCAACAGCTTCAGGTCCCGTCGATCCATTAGCTCCCATAGATTCCAGAAGTCCCTGAT
TAAAAAAATGTTCATATAAATGAACAGAAACGAGGTATTTACATGCAAGTTTGCCAAGTTGAAA
GAAAATGATCTTCTAATTGCAAGTTCTGTTACACCTATGAGAGCAACAAATTTTAACTTGAACC
ATAAACTCCAAATTTTTCTTATGCTGCATGATTATTTGATTTACAGACCAAAAGAACCTTGAAG
ATATACCACACTTTTCTATATGCAACTTCTATTGTTTATATATTATTCAACAAATATCAGTCTA
CGATTATGAGTGAAATATATCCTACAAATTAACTGAAATACAATTGTATCACGCAGAAATGGAT
AGATAAAATACATCAGAATGTCATCTGACAACTTACACACCTGGGGAGTTGCTGGAAGCATATA
AAGACTGTTATCAGGACTTTGAAAGAAAGCAGACACTTCTTTCTCAATGAAATCTTTTGCGCTG
TTTGAAATGTCCACAACAACTTCACTGGCTGGAATTACAGTGGCTGATGCATATTCCCTTGCAG
CTAGTGGTTGTTGATTCCAGAATGCAACAGCATCCTATATAAAAAGGAAGGTCATGATACAGAG
TATTACTCATGGTATTTATCACTTAATCAATTTAATGAATGAATCACTTGGGATATTACCATGT
TGGCCTTGAGAAGAGTTGTATATATGGTTTCAAGTTCGGATCTGCGAGCATCAAATTCCTCAAT
TTTCTTCCACTTCTTTTTCAAGGAATCTTCGGCTTCTTTTCTTTCTGCACATAATTTATTCAGC
CGTTGTATTTCAGATAACAATGTGTTTAAGCTAGCCCTCAAACCAGCAGCTTCTCTTTCCTTTC
CCCATACATCCAACTGCAAAGATAAAATCGGATCGTTTGTTCAAGCAAGTAAATCAGCATATAT
ATTAAACATAAAATGAACTTTAATGATAACTGAGAATCAGTCATGCAGTGCCTGCTACATAACA
AGTATAAGAGTGTTTGGATTGTAAGATTTGTACAGGAACATGATTTTGTCTTTTTAGATTCAAG
TGAAGGGAAAAAAACTAAAGAAACCAAGGGAGTCTGGCATCTACCTCAAATTGCCTAAGATTGC
TACCACTCTGTGTTGTGCCTCCAACAAACGAATGAGTAGCTGTATCAGCACTTCCATGCAAACG
GTTAATAAACTTGTGGCATAAATCACGAGCTTCAGCTGCTTTGTTTAGTGCATCTTCAGTAGCC
AAAAATTGTTGAACATGGGCTTT
						
					

			
		

Sequences
Splice junction sequence	TTCCATGCAAACGGTTAATAAACTTGTGGCATAAATCACGAGCTTCAGCTGCTTTGTTTAGTGC ATCTTCAGTAGCCAAAAATTGTTGAACATGGGCTTTcaaacccctaacgtatttgcagtgttcc gaggaagcttgcgcattctgaactgcagtcctaagttcaggtaaccactggtccgatattgtat tctcttgt
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: 1056 Transcript exons: 15564244-15564376,15564485-15564680,15565103-15565262,15 565628-15565813,15565903-15566112,15566336-15566506 CAAACCCCTAACGTATTTGCAGTGTTCCGAGGAAGCTTGCGCATTCTGAACTGCAGTCCTAAGT TCAGGTAACCACTGGTCCGATATTGTATTCTCTTGTTCAGAAGCTAGATCTAGGCAGTAGTTAG TTGTTCTTTCATATTTTTGCTGGGCACGGAAAGCATGATCTAACAGAGAATGGCCACTTTCAAC TAGATCCTGCCGAATATGGACCAAATCGATTGCCTTTGCTAAGTCTTCTAAAACACATGCTTCA GAACCACGAACTCTTAAGCAGAACTCAAGAGACTCTAACACTGAGGCCAAACTTGCATCTGAAC CCTCAAGACCTGCAGGATATTGAAGGGCAGCAGAAATGCGACATATAGATGGTATTGCCGATGG ATCTCTTGCACCAGCTCTAGCCGTTAATAGAGCAGCATTCTTCTCTGCATATGCAACAGCTTCA GGTCCCGTCGATCCATTAGCTCCCATAGATTCCAGAAGTCCCTGGGGAGTTGCTGGAAGCATAT AAAGACTGTTATCAGGACTTTGAAAGAAAGCAGACACTTCTTTCTCAATGAAATCTTTTGCGCT GTTTGAAATGTCCACAACAACTTCACTGGCTGGAATTACAGTGGCTGATGCATATTCCCTTGCA GCTAGTGGTTGTTGATTCCAGAATGCAACAGCATCCATGTTGGCCTTGAGAAGAGTTGTATATA TGGTTTCAAGTTCGGATCTGCGAGCATCAAATTCCTCAATTTTCTTCCACTTCTTTTTCAAGGA ATCTTCGGCTTCTTTTCTTTCTGCACATAATTTATTCAGCCGTTGTATTTCAGATAACAATGTG TTTAAGCTAGCCCTCAAACCAGCAGCTTCTCTTTCCTTTCCCCATACATCCAACTCAAATTGCC TAAGATTGCTACCACTCTGTGTTGTGCCTCCAACAAACGAATGAGTAGCTGTATCAGCACTTCC ATGCAAACGGTTAATAAACTTGTGGCATAAATCACGAGCTTCAGCTGCTTTGTTTAGTGCATCT TCAGTAGCCAAAAATTGTTGAACATGGGCTTT
Genomic sequence	CAAACCCCTAACGTATTTGCAGTGTTCCGAGGAAGCTTGCGCATTCTGAACTGCAGTCCTAAGT TCAGGTAACCACTGGTCCGATATTGTATTCTCTTGTTCAGAAGCTAGATCTAGGCAGTAGTTAG TTGTTCTGCATACAAGATACACAGTATAGTGGAAGTTTACATAAGATAGTGTGGGGCAATAAAT AAGATAATTGTGGCCTGTGTAGACCAGAGCACTGAGGAACACGCTTTACCTTTCATATTTTTGC TGGGCACGGAAAGCATGATCTAACAGAGAATGGCCACTTTCAACTAGATCCTGCCGAATATGGA CCAAATCGATTGCCTTTGCTAAGTCTTCTAAAACACATGCTTCAGAACCACGAACTCTTAAGCA GAACTCAAGAGACTCTAACACTGAGGCCAAACTTGCATCTGAACCCTCAAGACCTATTCAAGCA GCAGAATATAGATGATAAGCAAGTCCTACTAAGAAGCCACTAAGAATTTTGATCTATGAAGATT TCTAAGTATTTTATATAAAAGGTGTTCCACTTTTTATGGTTGAAAACAACAGCAGATCCAAAGC GTGGTAATGATATGCAACTAGTGGCCATCATTAAACCTTTTGGTTATTATAGCATTCCTCAATC GACGTAATAGGTAGATGAACTAACAATGCTAGGAACTTTTTTTTATTTTTAAAATGTTTGTTTT ATGATTTTGCACTGCATTGAGAAAGATTGTCATTCATGAAGCAGTGAGCAATAGTTTCATTAAA AAGCTCCTTGTCAATGCAAATAATTTTTGTCCAGAGAGATGAACTATACGTCCTTGGATTTTTG AAAAAAAAACGAAGAAAAAAATCTTACCTGCAGGATATTGAAGGGCAGCAGAAATGCGACATAT AGATGGTATTGCCGATGGATCTCTTGCACCAGCTCTAGCCGTTAATAGAGCAGCATTCTTCTCT GCATATGCAACAGCTTCAGGTCCCGTCGATCCATTAGCTCCCATAGATTCCAGAAGTCCCTGAT TAAAAAAATGTTCATATAAATGAACAGAAACGAGGTATTTACATGCAAGTTTGCCAAGTTGAAA GAAAATGATCTTCTAATTGCAAGTTCTGTTACACCTATGAGAGCAACAAATTTTAACTTGAACC ATAAACTCCAAATTTTTCTTATGCTGCATGATTATTTGATTTACAGACCAAAAGAACCTTGAAG ATATACCACACTTTTCTATATGCAACTTCTATTGTTTATATATTATTCAACAAATATCAGTCTA CGATTATGAGTGAAATATATCCTACAAATTAACTGAAATACAATTGTATCACGCAGAAATGGAT AGATAAAATACATCAGAATGTCATCTGACAACTTACACACCTGGGGAGTTGCTGGAAGCATATA AAGACTGTTATCAGGACTTTGAAAGAAAGCAGACACTTCTTTCTCAATGAAATCTTTTGCGCTG TTTGAAATGTCCACAACAACTTCACTGGCTGGAATTACAGTGGCTGATGCATATTCCCTTGCAG CTAGTGGTTGTTGATTCCAGAATGCAACAGCATCCTATATAAAAAGGAAGGTCATGATACAGAG TATTACTCATGGTATTTATCACTTAATCAATTTAATGAATGAATCACTTGGGATATTACCATGT TGGCCTTGAGAAGAGTTGTATATATGGTTTCAAGTTCGGATCTGCGAGCATCAAATTCCTCAAT TTTCTTCCACTTCTTTTTCAAGGAATCTTCGGCTTCTTTTCTTTCTGCACATAATTTATTCAGC CGTTGTATTTCAGATAACAATGTGTTTAAGCTAGCCCTCAAACCAGCAGCTTCTCTTTCCTTTC CCCATACATCCAACTGCAAAGATAAAATCGGATCGTTTGTTCAAGCAAGTAAATCAGCATATAT ATTAAACATAAAATGAACTTTAATGATAACTGAGAATCAGTCATGCAGTGCCTGCTACATAACA AGTATAAGAGTGTTTGGATTGTAAGATTTGTACAGGAACATGATTTTGTCTTTTTAGATTCAAG TGAAGGGAAAAAAACTAAAGAAACCAAGGGAGTCTGGCATCTACCTCAAATTGCCTAAGATTGC TACCACTCTGTGTTGTGCCTCCAACAAACGAATGAGTAGCTGTATCAGCACTTCCATGCAAACG GTTAATAAACTTGTGGCATAAATCACGAGCTTCAGCTGCTTTGTTTAGTGCATCTTCAGTAGCC AAAAATTGTTGAACATGGGCTTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.24468931

Conservation Information
Conserved circRNAs	NA
PMCS	0.24468931

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR5021 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	ath-miR5021
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT5G38880_circ_g.3

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