Plant Circular RNA Database

Detail information of Zm00001d003198_circ_g.7

			
						 General Information
					
						CircRNA Name
						Zm00001d003198_circ_g.7
					
						ID in PlantcircBase
						zma_circ_007145
					
						Alias
						zma_circ_0001031, GRMZM2G052142_C6
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 35376990-35377987  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d003198						
					
						Parent gene annotation
						
							eIF-2-alpha kinase GCN2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d003198_circ_g.2 Zm00001d003198_circ_g.3 Zm00001d003198_circ_g.4 Zm00001d003198_circ_g.5 Zm00001d003198_circ_g.6 						
					
						Support reads
						NA
					
						Tissues
						leaf, 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
						Zm00001d003198_T034:3
Zm00001d003198_T021:3
Zm00001d003198_T029:3
Zm00001d003198_T003:3
Zm00001d003198_T030:1
Zm00001d003198_T013:3
Zm00001d003198_T008:3
Zm00001d003198_T027:3
Zm00001d003198_T011:3
Zm00001d003198_T025:3
Zm00001d003198_T002:1
Zm00001d003198_T033:3
Zm00001d003198_T001:3
Zm00001d003198_T031:3
Zm00001d003198_T035:3
Zm00001d003198_T036:3
Zm00001d003198_T022:3
Zm00001d003198_T014:3
Zm00001d003198_T012:1
Zm00001d003198_T018:3
Zm00001d003198_T004:3
Zm00001d003198_T010:3

General Information
CircRNA Name	Zm00001d003198_circ_g.7
ID in PlantcircBase	zma_circ_007145
Alias	zma_circ_0001031, GRMZM2G052142_C6
Organism	Zea mays
Position	chr2: 35376990-35377987 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d003198
Parent gene annotation	eIF-2-alpha kinase GCN2
Parent gene strand	-
Alternative splicing	Zm00001d003198_circ_g.2 Zm00001d003198_circ_g.3 Zm00001d003198_circ_g.4 Zm00001d003198_circ_g.5 Zm00001d003198_circ_g.6
Support reads	NA
Tissues	leaf, 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	Zm00001d003198_T034:3 Zm00001d003198_T021:3 Zm00001d003198_T029:3 Zm00001d003198_T003:3 Zm00001d003198_T030:1 Zm00001d003198_T013:3 Zm00001d003198_T008:3 Zm00001d003198_T027:3 Zm00001d003198_T011:3 Zm00001d003198_T025:3 Zm00001d003198_T002:1 Zm00001d003198_T033:3 Zm00001d003198_T001:3 Zm00001d003198_T031:3 Zm00001d003198_T035:3 Zm00001d003198_T036:3 Zm00001d003198_T022:3 Zm00001d003198_T014:3 Zm00001d003198_T012:1 Zm00001d003198_T018:3 Zm00001d003198_T004:3 Zm00001d003198_T010:3

			
						 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  
						
							TTTGCGAAGAAAATAAGCATATCTGCGGAGTTATCACCTGGTAATAACGGACAACATGTTGATG
TTGCAATCTTGAAAGTGTGGCTACCTCTCTGAGTACctaaaccaaaatctccaattttaatatc
attgcggacatcaaaaaatatgttgctgggtgtcaggtctctgtgtaggattccttgactatgg
acatgagc

						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: 418
Transcript exons: 35376990-35377177,35377658-35377824,35377925-35377987
CTAAACCAAAATCTCCAATTTTAATATCATTGCGGACATCAAAAAATATGTTGCTGGGTGTCAG
GTCTCTGTGTAGGATTCCTTGACTATGGACATGAGCTAGACCTTCCACAATTTGTCGAAACAGG
TGCCAGGCATGGTCAACATCAAAAGACGAGATGTATGTCTCAAAATCCTGCCGCAAAGTCCTAG
GACAATACTCCATTTGAATGTACAAGTACGTGGATTCCTGCTTATTCCCACCACCTGCATCCGA
TAGGCTGACTTCATCATAACTAAAGATAGAGCTCTCAGCAGTGCAGGACCCGCCAGCATTCAAA
ATATTATGATGACCGTATTCAGTTTCAATCCATGCCTGGTAATAACGGACAACATGTTGATGTT
GCAATCTTGAAAGTGTGGCTACCTCTCTGAGTAC
						
						Genomic sequence
						
							CTAAACCAAAATCTCCAATTTTAATATCATTGCGGACATCAAAAAATATGTTGCTGGGTGTCAG
GTCTCTGTGTAGGATTCCTTGACTATGGACATGAGCTAGACCTTCCACAATTTGTCGAAACAGG
TGCCAGGCATGGTCAACATCAAAAGACGAGATGTATGTCTCAAAATCCTGCCGCAAAGTCCTTC
AAACAATAGACCAAAAGAACTTAGATACAGAATAGCTACAATCAATACACTAAATGACTGAAAA
TACATAAACAAAGATCACATGTTTAAATTCTAAAGTTCTAAAAGTCAAACTACCAGGTCCTCCA
GAACCTTTCAAGATTACAAATTAATATTTATACTCTGCAGTAACTTAAACCCTCCAATTTTTTT
TACAACACAGGGATCATGGAGCTCATAAAACCAAGAAAATAATTTAGGGGAATCATTATATATC
CCACATTAGTGTCTGAGTGCTTGGGGGAATAAAAGAATTCTTAGTAGTATCAAGAAGAGTGATT
TTTGCATGGTACAGGTGTAGTGTACCCTTGATTAACTATCACAAAATTTTATATGGCCCGAGCA
TCAATAGTTTGACTAGTTTCTCATGTAATAAAAAGCAGTGAAGAAATAGCAGCACAAATTTCCT
TAGTGCGTAACTGCAAAATGAAACACACCTAGGACAATACTCCATTTGAATGTACAAGTACGTG
GATTCCTGCTTATTCCCACCACCTGCATCCGATAGGCTGACTTCATCATAACTAAAGATAGAGC
TCTCAGCAGTGCAGGACCCGCCAGCATTCAAAATATTATGATGACCGTATTCAGTTTCAATCCA
TGCCTGGCATCTCAATGACAGTTGAGTTAGAATTGTCCAAAACAAATTGTGAGTGCAATGAGTG
TTTTTGCGAAGAAAATAAGCATATCTGCGGAGTTATCACCTGGTAATAACGGACAACATGTTGA
TGTTGCAATCTTGAAAGTGTGGCTACCTCTCTGAGTAC

Sequences
Splice junction sequence	TTTGCGAAGAAAATAAGCATATCTGCGGAGTTATCACCTGGTAATAACGGACAACATGTTGATG TTGCAATCTTGAAAGTGTGGCTACCTCTCTGAGTACctaaaccaaaatctccaattttaatatc attgcggacatcaaaaaatatgttgctgggtgtcaggtctctgtgtaggattccttgactatgg acatgagc
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: 418 Transcript exons: 35376990-35377177,35377658-35377824,35377925-35377987 CTAAACCAAAATCTCCAATTTTAATATCATTGCGGACATCAAAAAATATGTTGCTGGGTGTCAG GTCTCTGTGTAGGATTCCTTGACTATGGACATGAGCTAGACCTTCCACAATTTGTCGAAACAGG TGCCAGGCATGGTCAACATCAAAAGACGAGATGTATGTCTCAAAATCCTGCCGCAAAGTCCTAG GACAATACTCCATTTGAATGTACAAGTACGTGGATTCCTGCTTATTCCCACCACCTGCATCCGA TAGGCTGACTTCATCATAACTAAAGATAGAGCTCTCAGCAGTGCAGGACCCGCCAGCATTCAAA ATATTATGATGACCGTATTCAGTTTCAATCCATGCCTGGTAATAACGGACAACATGTTGATGTT GCAATCTTGAAAGTGTGGCTACCTCTCTGAGTAC
Genomic sequence	CTAAACCAAAATCTCCAATTTTAATATCATTGCGGACATCAAAAAATATGTTGCTGGGTGTCAG GTCTCTGTGTAGGATTCCTTGACTATGGACATGAGCTAGACCTTCCACAATTTGTCGAAACAGG TGCCAGGCATGGTCAACATCAAAAGACGAGATGTATGTCTCAAAATCCTGCCGCAAAGTCCTTC AAACAATAGACCAAAAGAACTTAGATACAGAATAGCTACAATCAATACACTAAATGACTGAAAA TACATAAACAAAGATCACATGTTTAAATTCTAAAGTTCTAAAAGTCAAACTACCAGGTCCTCCA GAACCTTTCAAGATTACAAATTAATATTTATACTCTGCAGTAACTTAAACCCTCCAATTTTTTT TACAACACAGGGATCATGGAGCTCATAAAACCAAGAAAATAATTTAGGGGAATCATTATATATC CCACATTAGTGTCTGAGTGCTTGGGGGAATAAAAGAATTCTTAGTAGTATCAAGAAGAGTGATT TTTGCATGGTACAGGTGTAGTGTACCCTTGATTAACTATCACAAAATTTTATATGGCCCGAGCA TCAATAGTTTGACTAGTTTCTCATGTAATAAAAAGCAGTGAAGAAATAGCAGCACAAATTTCCT TAGTGCGTAACTGCAAAATGAAACACACCTAGGACAATACTCCATTTGAATGTACAAGTACGTG GATTCCTGCTTATTCCCACCACCTGCATCCGATAGGCTGACTTCATCATAACTAAAGATAGAGC TCTCAGCAGTGCAGGACCCGCCAGCATTCAAAATATTATGATGACCGTATTCAGTTTCAATCCA TGCCTGGCATCTCAATGACAGTTGAGTTAGAATTGTCCAAAACAAATTGTGAGTGCAATGAGTG TTTTTGCGAAGAAAATAAGCATATCTGCGGAGTTATCACCTGGTAATAACGGACAACATGTTGA TGTTGCAATCTTGAAAGTGTGGCTACCTCTCTGAGTAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.201826308

Conservation Information
Conserved circRNAs	NA
PMCS	0.201826308

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							35377676-35377816(-)
						
						Potential amino acid sequence
						
							MEYCPRTLRQDFETYISSFDVDHAWHLFRQIVEGLAHVHSQGILHRDLTPSNIFFDVRNDIKIG
DFGLGTQRGSHTFKIATSTCCPLLPGMD*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	35377676-35377816(-)
Potential amino acid sequence	MEYCPRTLRQDFETYISSFDVDHAWHLFRQIVEGLAHVHSQGILHRDLTPSNIFFDVRNDIKIG DFGLGTQRGSHTFKIATSTCCPLLPGMD*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d003198_circ_g.7

Address

Any questions?

Supported by