Plant Circular RNA Database

Detail information of Zm00001d047540_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d047540_circ_g.4
					
						ID in PlantcircBase
						zma_circ_010048
					
						Alias
						Zm09circ00061, GRMZM2G462803_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 134462255-134463246  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d047540						
					
						Parent gene annotation
						
							Guanine nucleotide exchange factor SPIKE 1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d047540_T025:2
Zm00001d047540_T003:4
Zm00001d047540_T029:4
Zm00001d047540_T034:4
Zm00001d047540_T033:4
Zm00001d047540_T002:4
Zm00001d047540_T009:4
Zm00001d047540_T004:4
Zm00001d047540_T006:4
Zm00001d047540_T036:4
Zm00001d047540_T024:1
Zm00001d047540_T031:4
Zm00001d047540_T001:4
Zm00001d047540_T008:4

General Information
CircRNA Name	Zm00001d047540_circ_g.4
ID in PlantcircBase	zma_circ_010048
Alias	Zm09circ00061, GRMZM2G462803_C2
Organism	Zea mays
Position	chr9: 134462255-134463246 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d047540
Parent gene annotation	Guanine nucleotide exchange factor SPIKE 1
Parent gene strand	-
Alternative splicing	NA
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d047540_T025:2 Zm00001d047540_T003:4 Zm00001d047540_T029:4 Zm00001d047540_T034:4 Zm00001d047540_T033:4 Zm00001d047540_T002:4 Zm00001d047540_T009:4 Zm00001d047540_T004:4 Zm00001d047540_T006:4 Zm00001d047540_T036:4 Zm00001d047540_T024:1 Zm00001d047540_T031:4 Zm00001d047540_T001:4 Zm00001d047540_T008:4

			
						 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  
						
							AACCGAGAAACAGATAATCAAGAAGCAGACCTTTCCACTTCCCTGCAGGTAATGTGGAACGAGC
TCTCTCAAAATTGGCAAGGATACATCTGAAAGTAACcgggttaaaatgttaaccatggctcgaa
acgcagcaacctgcaaaacaacaatgttgtagtcataaatacattagcatagaataccaagtgt
aaatatat

						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
						
							CGGGTTAAAATGTTAACCATGGCTCGAAACGCAGCAACCTGCAAAACAACAATGTTGTAGTCAT
AAATACATTAGCATAGAATACCAAGTGTAAATATATATGACAGAGTATATTCAGTTACAATATG
TAGGTTCAGAAAATTGTGTAAAATAATTATGCACAAGATGTAACGAACCAACAACCTGAAGGGT
CTCACCGCCATCGCCAATAAGATGAAGCAGCATGTTAAGTATTGGTTGCAGAAATTGTAATAAT
GCAGTAGATTCAACGTTTTTCAAACTATTTATGGCCTGCAAAAATCTCATCCCGAAATCAGTCA
GTGTATAGCACTGGTATCTACTGCAAAGTACTTTTAACATGGAAGGTTATGCAAAAGCAATGCA
AGGAAACAATTCTTTGAGGAAAATAAATTACAAAGAAAAATTACTAACCCTAAACCATCTTTCA
TAAAGAAAATTGGTGTTAGGAAAAGAAAGGAAAAATAGGTTCCGCTGCCTTCTAAAACTTGATT
ATATTTGGCTACTTCTAGACATATAAGCACAGAAGATAAAACATCTGCTAACCACAAAAGCAAA
ATCTCTAGCTTCTGTTTTAATTATGAAAGCAAAAACATCAACCCTCCACATTAAGTTGGCCAGA
AGCAGAATAGTTACCTCAAGAAGCTCAGAACCCCATGGGGGACTTGTATGTAGAGTATGGCGGT
CATATTCAACAAAAAAGTCTCTTATCCTTTCATTAACCGGGAACAATGAAGAACAGAGCCTTAA
ACGCAACTTGAAAACAGTTTTTCCATCTTCCAGATAGTCCATTCTCTCCTGTATAAAAAATGAA
AATTAGAGAAGAATCTAACCACAGATACTTACATAGATGGAATTTCTGTGATTAAGGTGGAACC
GAGAAACAGATAATCAAGAAGCAGACCTTTCCACTTCCCTGCAGGTAATGTGGAACGAGCTCTC
TCAAAATTGGCAAGGATACATCTGAAAGTAAC

Sequences
Splice junction sequence	AACCGAGAAACAGATAATCAAGAAGCAGACCTTTCCACTTCCCTGCAGGTAATGTGGAACGAGC TCTCTCAAAATTGGCAAGGATACATCTGAAAGTAACcgggttaaaatgttaaccatggctcgaa acgcagcaacctgcaaaacaacaatgttgtagtcataaatacattagcatagaataccaagtgt aaatatat
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	CGGGTTAAAATGTTAACCATGGCTCGAAACGCAGCAACCTGCAAAACAACAATGTTGTAGTCAT AAATACATTAGCATAGAATACCAAGTGTAAATATATATGACAGAGTATATTCAGTTACAATATG TAGGTTCAGAAAATTGTGTAAAATAATTATGCACAAGATGTAACGAACCAACAACCTGAAGGGT CTCACCGCCATCGCCAATAAGATGAAGCAGCATGTTAAGTATTGGTTGCAGAAATTGTAATAAT GCAGTAGATTCAACGTTTTTCAAACTATTTATGGCCTGCAAAAATCTCATCCCGAAATCAGTCA GTGTATAGCACTGGTATCTACTGCAAAGTACTTTTAACATGGAAGGTTATGCAAAAGCAATGCA AGGAAACAATTCTTTGAGGAAAATAAATTACAAAGAAAAATTACTAACCCTAAACCATCTTTCA TAAAGAAAATTGGTGTTAGGAAAAGAAAGGAAAAATAGGTTCCGCTGCCTTCTAAAACTTGATT ATATTTGGCTACTTCTAGACATATAAGCACAGAAGATAAAACATCTGCTAACCACAAAAGCAAA ATCTCTAGCTTCTGTTTTAATTATGAAAGCAAAAACATCAACCCTCCACATTAAGTTGGCCAGA AGCAGAATAGTTACCTCAAGAAGCTCAGAACCCCATGGGGGACTTGTATGTAGAGTATGGCGGT CATATTCAACAAAAAAGTCTCTTATCCTTTCATTAACCGGGAACAATGAAGAACAGAGCCTTAA ACGCAACTTGAAAACAGTTTTTCCATCTTCCAGATAGTCCATTCTCTCCTGTATAAAAAATGAA AATTAGAGAAGAATCTAACCACAGATACTTACATAGATGGAATTTCTGTGATTAAGGTGGAACC GAGAAACAGATAATCAAGAAGCAGACCTTTCCACTTCCCTGCAGGTAATGTGGAACGAGCTCTC TCAAAATTGGCAAGGATACATCTGAAAGTAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.138123269

Conservation Information
Conserved circRNAs	NA
PMCS	0.138123269

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							134463066-134462257(-)
						
						Potential amino acid sequence
						
							MDYLEDGKTVFKLRLRLCSSLFPVNERIRDFFVEYDRHTLHTSPPWGSELLEAINSLKNVESTA
LLQFLQPILNMLLHLIGDGGETLQVAAFRAMVNILTRLLSDVSLPILRELVPHYLQGSGKERMD
YLEDGKTVFKLRLRLCSSLFPVNERIRDFFVEYDRHTLHTSPPWGSELLEAINSLKNVESTALL
QFLQPILNMLLHLIGDGGETLQVAAFRAMVNILTRLLSDVSLPILRELVPHYLQGSGKERMDYL
EDGKTVFKLRLRLCSSLFPVNERIRDFFVEYDRHTLHTSPPWGSELLEAINSLKNVESTALLQF
LQPILNMLLHLIGDGGETLQVAAFRAMVNILTRLLSDVSLPILRELVPHYLQGSGKERMDYLED
GKTVFKLRLRLCSSLFPVNERIRDFFVEYDRHTLHTSPPWGSELLEAINSLKNVESTALLQFLQ
PILNMLLHLIGDGGETLQVAAFRAMVNILT(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	134463066-134462257(-)
Potential amino acid sequence	MDYLEDGKTVFKLRLRLCSSLFPVNERIRDFFVEYDRHTLHTSPPWGSELLEAINSLKNVESTA LLQFLQPILNMLLHLIGDGGETLQVAAFRAMVNILTRLLSDVSLPILRELVPHYLQGSGKERMD YLEDGKTVFKLRLRLCSSLFPVNERIRDFFVEYDRHTLHTSPPWGSELLEAINSLKNVESTALL QFLQPILNMLLHLIGDGGETLQVAAFRAMVNILTRLLSDVSLPILRELVPHYLQGSGKERMDYL EDGKTVFKLRLRLCSSLFPVNERIRDFFVEYDRHTLHTSPPWGSELLEAINSLKNVESTALLQF LQPILNMLLHLIGDGGETLQVAAFRAMVNILTRLLSDVSLPILRELVPHYLQGSGKERMDYLED GKTVFKLRLRLCSSLFPVNERIRDFFVEYDRHTLHTSPPWGSELLEAINSLKNVESTALLQFLQ PILNMLLHLIGDGGETLQVAAFRAMVNILT(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020;Zhang et al., 2019

circRNA

Detail information of Zm00001d047540_circ_g.4

Address

Any questions?

Supported by