Plant Circular RNA Database

Detail information of AT1G10870_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT1G10870_circ_g.9
					
						ID in PlantcircBase
						ath_circ_002013
					
						Alias
						At_ciR4403
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 3618873-3621042  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT1G10870						
					
						Parent gene annotation
						
							ARF-GAP domain 4
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G10870_circ_g.1 AT1G10870_circ_g.2 AT1G10870_circ_g.3 AT1G10870_circ_g.4 AT1G10870_circ_g.5 AT1G10870_circ_g.6 AT1G10870_circ_g.7 AT1G10870_circ_g.8 AT1G10870_circ_g.10 AT1G10870_circ_g.11 						
					
						Support reads
						3
					
						Tissues
						leaf
					
						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
						AT1G10870.1:5
AT1G10870.2:5

General Information
CircRNA Name	AT1G10870_circ_g.9
ID in PlantcircBase	ath_circ_002013
Alias	At_ciR4403
Organism	Arabidpsis thaliana
Position	chr1: 3618873-3621042 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ
Parent gene	AT1G10870
Parent gene annotation	ARF-GAP domain 4
Parent gene strand	-
Alternative splicing	AT1G10870_circ_g.1 AT1G10870_circ_g.2 AT1G10870_circ_g.3 AT1G10870_circ_g.4 AT1G10870_circ_g.5 AT1G10870_circ_g.6 AT1G10870_circ_g.7 AT1G10870_circ_g.8 AT1G10870_circ_g.10 AT1G10870_circ_g.11
Support reads	3
Tissues	leaf
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	AT1G10870.1:5 AT1G10870.2:5

			
						 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  
						
							TCATATTTGTTTTGCACATCTAAAATATTGAGACATCAAGTTGACTACAAGTTTGTACCTGATG
GATAAATGGTTCCAGTTGATTCAACAAGTCATATCCctgttgcagaaaatgagaattgagaagc
gtccctatagcttttgtgatcttatttacccagtccatcctatctgctccattttcagcctggt
aaggtagc

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CTGTTGCAGAAAATGAGAATTGAGAAGCGTCCCTATAGCTTTTGTGATCTTATTTACCCAGTCC
ATCCTATCTGCTCCATTTTCAGCCTGGTAAGGTAGCATAATTGTTGTCAGCATTCTGAAGTACT
TGGATCAGGGGAAGAAGGAATTAGTATAGAGATACTTAAGTATCAATTGCTAAGAGGGTCCATG
CAGGTTGTCTACAAGGCACAGCTCTCTTTTTCATATAATGAATTTGGAAAAACCCAACAGGAAA
AATTCAGACTAAGTAAGCCCGGTGACTTGCAACCTAGTCTATAGCGAGTAAACTGGGTACCTGA
AGTGTGTAAGTTTTTTGAGGAGAAATAATTCTGAAACAGAGACGAAGATCCATGTCTTCTGCGT
CTAGTTTTATCAAAGAAGTGCGAAGATCAATAGTATTATAGCCTAAGCTGCCCTCAGTGAGCGA
ACCTGATCGATTATGTCTTGCCCGAAATCGACCAAAAACTCCAGTATTATGGTCAGATGATCCA
CTATAGTGATGATGAGATCCCTGAGAACACGAATAGCAGATAAAGTCAACCATTATAAACAAAC
ATAAACTATAAATATAAAGAAAGATAAAGGATCTGCTAAACTGCTAAATAGATGGTTAGTTCCA
GAATCTATACTTCTATAGATAAAAACAACAGCATGAGGAAGTGCCAGGTAAATTTTACGTGCAA
CTACTCATTAAAGGCTTAATATTCCTGGACCTGATAGGCTTATATCAAAATCCACTATAATTTT
AGAAATTTCCTATCACAAGATATCACAGAGTTAAATCTGAAAGCTGATACAGCAATCTCATCAT
TTACTTATCTATTTCTTCACATATATTTTCCCGTTATTTCATAACAAATCTATTATTCATTTCA
GGGGAAAAGAAGGACTTATGAAACGATTAATGAGATTTAAGAAATTGTACCAATTGGCATGTTG
AACTATAACGCAAATTTGAAAGAACTAATGGAGGTCTCTCATGGAAATGAGGCAGGAAAAAGAG
GTTTGCACGCGTACCATTGATTTATTACCATTAGTTCTGTAATAGTACATGGAGCCATGACTAT
CAAGGACAAAAAACTTTCTTTTCCAATCAGTTCTCAAACTTGACGAACGCTTTAATAGATACCC
CTGTTTAATTACCTGCATCAGTACAAAGGAACTCTGTAAAACAATAAGAATTCAGCCTGTTCTG
AAAACTAAGTGTAAAATGATTACAAAACGAGTCTCTATATGTTGCATAATCGCATTGGCGCACA
AGATGCTAGGAGTAATTTTGTAGGGGCTATCAGGAAATTGACATAATCTAAAATGTATCAACAG
ATGTACAACAATGAGTGGCTTAAAATAATTGTGTTGCAGGTAGTAAAAAACAGTAATAAGCCAG
ATTTAAGAGCTACGGAACCAAAAGGTAAAACGTGAATTGCTCGCAATTCTTGCAAGAATGAAAT
CAGAAACGCTTACTTCCTTGTCTGCTGTTAAACTTGTTTCGGTATTTTTGTAAGGGATATTCCC
ACCAACACGGTTCCCGTTAGCACCAGACGACTCTGCATTAGCGACCAGCTGTTGGCTGTCTAAT
TCAGACTGGGTCCTGAATTCTTGAATGCGTCTTGCTAGTCGATCTTGTTCAATCTTAGACTGTT
CTTTTGATTGCTGAGCATATGTTAATATCTATAAGAAGAACAATCACAAGTCAGCATCAGTGGA
TTTCATTAGAGATCATGAAACTTTGGCTATTTCACATCACATTTTACTAGAGCAAAAACTAAAT
CTTGGACAGGAGAGGCTTTTACCTATGGGTGTTCTTTTTAAATCCAGATAAACCAAGTTTTTGG
AACTAAAAGATTGGGAAAGTCTTCTTTGATTTTAAACAAAAAGTTATCTTTCAAATTTTATGTA
AGGAAATGTAAACATTAAAACTTAAATCGATGAATTAGATGACTTTGGGCTTCCAAAAGCCTAA
AAAGTCTCTTCAAGACCTCAGTCCTTCTAACCTAATTATTACTTCCCCATTTGCACGTTTAAAG
TCCCTGTGGGAACTATAGAAGCTCATATTTGTTTTGCACATCTAAAATATTGAGACATCAAGTT
GACTACAAGTTTGTACCTGATGGATAAATGGTTCCAGTTGATTCAACAAGTCATATCC
						
					

			
		

Sequences
Splice junction sequence	TCATATTTGTTTTGCACATCTAAAATATTGAGACATCAAGTTGACTACAAGTTTGTACCTGATG GATAAATGGTTCCAGTTGATTCAACAAGTCATATCCctgttgcagaaaatgagaattgagaagc gtccctatagcttttgtgatcttatttacccagtccatcctatctgctccattttcagcctggt aaggtagc
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CTGTTGCAGAAAATGAGAATTGAGAAGCGTCCCTATAGCTTTTGTGATCTTATTTACCCAGTCC ATCCTATCTGCTCCATTTTCAGCCTGGTAAGGTAGCATAATTGTTGTCAGCATTCTGAAGTACT TGGATCAGGGGAAGAAGGAATTAGTATAGAGATACTTAAGTATCAATTGCTAAGAGGGTCCATG CAGGTTGTCTACAAGGCACAGCTCTCTTTTTCATATAATGAATTTGGAAAAACCCAACAGGAAA AATTCAGACTAAGTAAGCCCGGTGACTTGCAACCTAGTCTATAGCGAGTAAACTGGGTACCTGA AGTGTGTAAGTTTTTTGAGGAGAAATAATTCTGAAACAGAGACGAAGATCCATGTCTTCTGCGT CTAGTTTTATCAAAGAAGTGCGAAGATCAATAGTATTATAGCCTAAGCTGCCCTCAGTGAGCGA ACCTGATCGATTATGTCTTGCCCGAAATCGACCAAAAACTCCAGTATTATGGTCAGATGATCCA CTATAGTGATGATGAGATCCCTGAGAACACGAATAGCAGATAAAGTCAACCATTATAAACAAAC ATAAACTATAAATATAAAGAAAGATAAAGGATCTGCTAAACTGCTAAATAGATGGTTAGTTCCA GAATCTATACTTCTATAGATAAAAACAACAGCATGAGGAAGTGCCAGGTAAATTTTACGTGCAA CTACTCATTAAAGGCTTAATATTCCTGGACCTGATAGGCTTATATCAAAATCCACTATAATTTT AGAAATTTCCTATCACAAGATATCACAGAGTTAAATCTGAAAGCTGATACAGCAATCTCATCAT TTACTTATCTATTTCTTCACATATATTTTCCCGTTATTTCATAACAAATCTATTATTCATTTCA GGGGAAAAGAAGGACTTATGAAACGATTAATGAGATTTAAGAAATTGTACCAATTGGCATGTTG AACTATAACGCAAATTTGAAAGAACTAATGGAGGTCTCTCATGGAAATGAGGCAGGAAAAAGAG GTTTGCACGCGTACCATTGATTTATTACCATTAGTTCTGTAATAGTACATGGAGCCATGACTAT CAAGGACAAAAAACTTTCTTTTCCAATCAGTTCTCAAACTTGACGAACGCTTTAATAGATACCC CTGTTTAATTACCTGCATCAGTACAAAGGAACTCTGTAAAACAATAAGAATTCAGCCTGTTCTG AAAACTAAGTGTAAAATGATTACAAAACGAGTCTCTATATGTTGCATAATCGCATTGGCGCACA AGATGCTAGGAGTAATTTTGTAGGGGCTATCAGGAAATTGACATAATCTAAAATGTATCAACAG ATGTACAACAATGAGTGGCTTAAAATAATTGTGTTGCAGGTAGTAAAAAACAGTAATAAGCCAG ATTTAAGAGCTACGGAACCAAAAGGTAAAACGTGAATTGCTCGCAATTCTTGCAAGAATGAAAT CAGAAACGCTTACTTCCTTGTCTGCTGTTAAACTTGTTTCGGTATTTTTGTAAGGGATATTCCC ACCAACACGGTTCCCGTTAGCACCAGACGACTCTGCATTAGCGACCAGCTGTTGGCTGTCTAAT TCAGACTGGGTCCTGAATTCTTGAATGCGTCTTGCTAGTCGATCTTGTTCAATCTTAGACTGTT CTTTTGATTGCTGAGCATATGTTAATATCTATAAGAAGAACAATCACAAGTCAGCATCAGTGGA TTTCATTAGAGATCATGAAACTTTGGCTATTTCACATCACATTTTACTAGAGCAAAAACTAAAT CTTGGACAGGAGAGGCTTTTACCTATGGGTGTTCTTTTTAAATCCAGATAAACCAAGTTTTTGG AACTAAAAGATTGGGAAAGTCTTCTTTGATTTTAAACAAAAAGTTATCTTTCAAATTTTATGTA AGGAAATGTAAACATTAAAACTTAAATCGATGAATTAGATGACTTTGGGCTTCCAAAAGCCTAA AAAGTCTCTTCAAGACCTCAGTCCTTCTAACCTAATTATTACTTCCCCATTTGCACGTTTAAAG TCCCTGTGGGAACTATAGAAGCTCATATTTGTTTTGCACATCTAAAATATTGAGACATCAAGTT GACTACAAGTTTGTACCTGATGGATAAATGGTTCCAGTTGATTCAACAAGTCATATCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.104790015

Conservation Information
Conserved circRNAs	NA
PMCS	0.104790015

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3619947-3618875(-)
						
						Potential amino acid sequence
						
							MYYYRTNGNKSMGSHHHYSGSSDHNTGVFGRFRARHNRSGSLTEGSLGYNTIDLRTSLIKLDAE
DMDLRLCFRIISPQKTYTLQAENGADRMDWVNKITKAIGTLLNSHFLQQGYDLLNQLEPFIHQI
LTYAQQSKEQSKIEQDRLARRIQEFRTQSELDSQQLVANAESSGANGNRVGGNIPYKNTETSLT
ADKEVIKQGYLLKRSSSLRTDWKRKFFVLDSHGSMYYYRTNGNKSMGSHHHYSGSSDHNTGVFG
RFRARHNRSGSLTEGSLGYNTIDLRTSLIKLDAEDMDLRLCFRIISPQKTYTLQAENGADRMDW
VNKITKAIGTLLNSHFLQQGYDLLNQLEPFIHQILTYAQQSKEQSKIEQDRLARRIQEFRTQSE
LDSQQLVANAESSGANGNRVGGNIPYKNTETSLTADKEVIKQGYLLKRSSSLRTDWKRKFFVLD
SHGSMYYYRTNGNKSMGSHHHYSGSSDHNTGVFGRFRARHNRSGSLTEGSLGYNTIDLRTSLIK
LDAEDMDLRLCFRIISPQKTYTLQAENGADRMDWVNKITKAIGTLLNSHFLQQGYDLLNQLEPF
IHQILTYAQQSKEQSKIEQDRLARRIQEFRTQSELDSQQLVANAESSGANGNRVGGNIPYKNTE
TSLTADKEVIKQGYLLKRSSSLRTDWKRKFFVLDSHGSMYYYRTNGNKSMGSHHHYSGSSDHNT
GVFGRFRARHNRSGSLTEGSLGYNTIDLRTSLIKLDAEDMDLRLCFRIISPQKTYTLQAENGAD
RMDWVNKITKAIGTLLNSHFLQQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3619947-3618875(-)
Potential amino acid sequence	MYYYRTNGNKSMGSHHHYSGSSDHNTGVFGRFRARHNRSGSLTEGSLGYNTIDLRTSLIKLDAE DMDLRLCFRIISPQKTYTLQAENGADRMDWVNKITKAIGTLLNSHFLQQGYDLLNQLEPFIHQI LTYAQQSKEQSKIEQDRLARRIQEFRTQSELDSQQLVANAESSGANGNRVGGNIPYKNTETSLT ADKEVIKQGYLLKRSSSLRTDWKRKFFVLDSHGSMYYYRTNGNKSMGSHHHYSGSSDHNTGVFG RFRARHNRSGSLTEGSLGYNTIDLRTSLIKLDAEDMDLRLCFRIISPQKTYTLQAENGADRMDW VNKITKAIGTLLNSHFLQQGYDLLNQLEPFIHQILTYAQQSKEQSKIEQDRLARRIQEFRTQSE LDSQQLVANAESSGANGNRVGGNIPYKNTETSLTADKEVIKQGYLLKRSSSLRTDWKRKFFVLD SHGSMYYYRTNGNKSMGSHHHYSGSSDHNTGVFGRFRARHNRSGSLTEGSLGYNTIDLRTSLIK LDAEDMDLRLCFRIISPQKTYTLQAENGADRMDWVNKITKAIGTLLNSHFLQQGYDLLNQLEPF IHQILTYAQQSKEQSKIEQDRLARRIQEFRTQSELDSQQLVANAESSGANGNRVGGNIPYKNTE TSLTADKEVIKQGYLLKRSSSLRTDWKRKFFVLDSHGSMYYYRTNGNKSMGSHHHYSGSSDHNT GVFGRFRARHNRSGSLTEGSLGYNTIDLRTSLIKLDAEDMDLRLCFRIISPQKTYTLQAENGAD RMDWVNKITKAIGTLLNSHFLQQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT1G10870_circ_g.9

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