Plant Circular RNA Database

Detail information of Zm00001d003198_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d003198_circ_g.4
					
						ID in PlantcircBase
						zma_circ_007143
					
						Alias
						zma_circ_0001029
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 35374558-35377177  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						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.5 Zm00001d003198_circ_g.6 Zm00001d003198_circ_g.7 						
					
						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_T008:3
Zm00001d003198_T029:3
Zm00001d003198_T002:3
Zm00001d003198_T001:3
Zm00001d003198_T017:1
Zm00001d003198_T003:3
Zm00001d003198_T021:3
Zm00001d003198_T033:3
Zm00001d003198_T014:3
Zm00001d003198_T018:3
Zm00001d003198_T011:3
Zm00001d003198_T013:3
Zm00001d003198_T010:3
Zm00001d003198_T004:3
Zm00001d003198_T031:3
Zm00001d003198_T036:3
Zm00001d003198_T012:3
Zm00001d003198_T035:3
Zm00001d003198_T030:3
Zm00001d003198_T025:3
Zm00001d003198_T027:3
Zm00001d003198_T022:3
Zm00001d003198_T034:3

General Information
CircRNA Name	Zm00001d003198_circ_g.4
ID in PlantcircBase	zma_circ_007143
Alias	zma_circ_0001029
Organism	Zea mays
Position	chr2: 35374558-35377177 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
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.5 Zm00001d003198_circ_g.6 Zm00001d003198_circ_g.7
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_T008:3 Zm00001d003198_T029:3 Zm00001d003198_T002:3 Zm00001d003198_T001:3 Zm00001d003198_T017:1 Zm00001d003198_T003:3 Zm00001d003198_T021:3 Zm00001d003198_T033:3 Zm00001d003198_T014:3 Zm00001d003198_T018:3 Zm00001d003198_T011:3 Zm00001d003198_T013:3 Zm00001d003198_T010:3 Zm00001d003198_T004:3 Zm00001d003198_T031:3 Zm00001d003198_T036:3 Zm00001d003198_T012:3 Zm00001d003198_T035:3 Zm00001d003198_T030:3 Zm00001d003198_T025:3 Zm00001d003198_T027:3 Zm00001d003198_T022:3 Zm00001d003198_T034:3

			
						 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  
						
							ATGGACATGAGCTAGACCTTCCACAATTTGTCGAAACAGGTGCCAGGCATGGTCAACATCAAAA
GACGAGATGTATGTCTCAAAATCCTGCCGCAAAGTCcatttagccactcatcttccatccgagg
aggcagttcattttgcaagacctcgacagcagatggacggttagacgggcttggtgacagcaag
cttcttaa

									
								

					

						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
						
							CATTTAGCCACTCATCTTCCATCCGAGGAGGCAGTTCATTTTGCAAGACCTCGACAGCAGATGG
ACGGTTAGACGGGCTTGGTGACAGCAAGCTTCTTAACAGGACTGACTGACGAGGAAATTTTGAT
TCCCATGACAATGGCGGGTCTCCCTTCTGCTTAAGATCGGAAAGAACAAGATGCCTTTCCATCG
CTGTGGCAAATGGATGCCAAAGCTCAAAAAATATTACTCCCAAACTGTACATGTCAACCTGACA
AAAGACGTAAATAAGAGCAAGGTAAACTTGAAATTTTAGAGTCTGTCTAGTTGCCATATTAAAA
AAAATAACGTCATGTTTCACCAAATTATTAAACCATTGGTAGGAACTCTTCATTCATTTCGAGA
ATAAGAAAATAGTTCTGCATTCATTTTGAGAATAAGAGAAACACTATCTGCAGTGATAAAGGAA
AAATAAATACGAAAACATAGGCAGTAGGCCAGATCAACATTTCATAAAAAAATCATTTGTTAAG
TAAAAGTCCAAGTAATTTGTTCTGACCTTTTCATTAATCTGTGGCCATTTCTGCTCTACCTCTG
GTGCAGTATAAAAATATGTACCAACTTGACCTGTTCCATCCATTGATACACCCAGTGCTTCAGT
AGGAAGATATTGGTCATGATCTAGCTGCTCCAGCTTCAGAAATTTGGCTGACAACAATGATAAC
ATATATTTTAGCTGAGATTTTCTTCAACCAATTTTGGAGAAGAGGAAGCAGCCATTATTACAAA
GTCAAACACTGAGTGAACCATACACTACCACTGACCCACTCATGTTTTTGTCCTCGCTTCACAT
AAAAGAGTTAACAGTTAACCCAGGGATTTTGGTACAACCAAGGTGGGACTACCCACACCACCCC
CACCCCCCAAAAAAAACTCACATGACCATACACAGGGACCACTATGGGCCAAACCCAGACTAGG
CCAGATGTCACACACACACCCTCTCAAAGGCTCAACCGTCATCGTCAACCTACCTAACATACCC
ACAATTGGACAAACGATAACTAGGAACGGGAATTTCTAACACCCCAAAGTACAAATAGTTCTGA
TCCACTAGCACCAACTCATTTAGGCTTTCGTCCTCGCTTCACGTAAAAAGGTTAACCTATGGAT
GGTGATATGAACTCTAAAAGCCATGTTGGTCGAATCTGCTCTGACGCTCTCAATATCCAAGGTT
GGACTAAGACCCCCCACAATCTCACATCAACATACACATGGGCCACTATGTGACAAATCCAAAC
TGAGCCAGATGTCACATAAACTTCACATGATCACACTTGCCAAAAAATGAGTTCTTCCTCATCC
CCAAAATAATTGCACATCTCGCTTTTCCAGAAGTCAAAAAAATAAGTTTGACAAACTATACACA
AAAATATACTCTACTATTTATGACGTGTAATAAGTATCATTAGATTAATAGTCGAATATATTTT
CATAACGAACATATTAGGAGATACAAATGTTGATAATGTTTTGTCAAACTTTTGGAAAAGCGAG
ATGTGCAATTATTTTGGAAAATAGCTCAGAAGCCACATGCCCCACTTCTGGAAAACTTTTGCTC
TTTTCCAAGGCTGAGGAAGCGGGGTTGCTGCAGCATTTCTGTAGGAGAAAGAAGCTCCACAGAA
TATCTATTTATGTTGATGATGTGGCCTTATTTCTGCATCCTACTTAGGCTGATATTTCTATCAC
TCTTGATATCCTTAAGCTCTTTGGGGATGCCTCTGGTCTTCACAACAATGCACAGAAGTCCAAT
ATTTTCCCTGTTAGATGTTCTGAGGAATCCATCCTGGAAATTCAGAGCAGTCTACCTTGTGAAA
TTGCCTCCTTTCCAAGCAAATATTTAGGCCTTGTTCTTTCTTTGCACAAATTAACCACGTCAAC
ATTAACATCAACATAGCCTTTTAGTCCCAAGCAAGTTGGGGTAGGCTAGAGTTGAAACCCAACA
AGATGTCACCAAAAGGAGAAAGAGAGAGAAAGGGGAGGGGAAAAGCTTTTGAGAGCACTAAAAG
GAAAAATGCCTAATCATGGTTCGGACACGTGGATAGCTTCTTTCCAAACACTTCTAACCTCAAT
CTGAAATTCACTCCCACTGGAATTCGAACTCAGGACCTGAGGAGTGCTCCTCAGATCATCTAAC
CAACTCAGCTAGAGACCCACACATACAACCCCAAAAGGGAAGAAAACTAGCCCATAAAATCATA
TAATCGCATTTTAAAGCTTCATGTTTAAAGAACAATTTCCAAACAATCAGGCAAAGGATACTAC
ATGCAGATATCAGCAATAGTTGCATCCTATTCGACACTATGCTTTAGTAATTAGTAGTACATAA
TGATAAATATTATAATAAAAAATGAAACTAGATTGAAAATATATGACAGTTCTGGACACCGTAC
CTAAACCAAAATCTCCAATTTTAATATCATTGCGGACATCAAAAAATATGTTGCTGGGTGTCAG
GTCTCTGTGTAGGATTCCTTGACTATGGACATGAGCTAGACCTTCCACAATTTGTCGAAACAGG
TGCCAGGCATGGTCAACATCAAAAGACGAGATGTATGTCTCAAAATCCTGCCGCAAAGTC
						
					

			
		

Sequences
Splice junction sequence	ATGGACATGAGCTAGACCTTCCACAATTTGTCGAAACAGGTGCCAGGCATGGTCAACATCAAAA GACGAGATGTATGTCTCAAAATCCTGCCGCAAAGTCcatttagccactcatcttccatccgagg aggcagttcattttgcaagacctcgacagcagatggacggttagacgggcttggtgacagcaag cttcttaa
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	CATTTAGCCACTCATCTTCCATCCGAGGAGGCAGTTCATTTTGCAAGACCTCGACAGCAGATGG ACGGTTAGACGGGCTTGGTGACAGCAAGCTTCTTAACAGGACTGACTGACGAGGAAATTTTGAT TCCCATGACAATGGCGGGTCTCCCTTCTGCTTAAGATCGGAAAGAACAAGATGCCTTTCCATCG CTGTGGCAAATGGATGCCAAAGCTCAAAAAATATTACTCCCAAACTGTACATGTCAACCTGACA AAAGACGTAAATAAGAGCAAGGTAAACTTGAAATTTTAGAGTCTGTCTAGTTGCCATATTAAAA AAAATAACGTCATGTTTCACCAAATTATTAAACCATTGGTAGGAACTCTTCATTCATTTCGAGA ATAAGAAAATAGTTCTGCATTCATTTTGAGAATAAGAGAAACACTATCTGCAGTGATAAAGGAA AAATAAATACGAAAACATAGGCAGTAGGCCAGATCAACATTTCATAAAAAAATCATTTGTTAAG TAAAAGTCCAAGTAATTTGTTCTGACCTTTTCATTAATCTGTGGCCATTTCTGCTCTACCTCTG GTGCAGTATAAAAATATGTACCAACTTGACCTGTTCCATCCATTGATACACCCAGTGCTTCAGT AGGAAGATATTGGTCATGATCTAGCTGCTCCAGCTTCAGAAATTTGGCTGACAACAATGATAAC ATATATTTTAGCTGAGATTTTCTTCAACCAATTTTGGAGAAGAGGAAGCAGCCATTATTACAAA GTCAAACACTGAGTGAACCATACACTACCACTGACCCACTCATGTTTTTGTCCTCGCTTCACAT AAAAGAGTTAACAGTTAACCCAGGGATTTTGGTACAACCAAGGTGGGACTACCCACACCACCCC CACCCCCCAAAAAAAACTCACATGACCATACACAGGGACCACTATGGGCCAAACCCAGACTAGG CCAGATGTCACACACACACCCTCTCAAAGGCTCAACCGTCATCGTCAACCTACCTAACATACCC ACAATTGGACAAACGATAACTAGGAACGGGAATTTCTAACACCCCAAAGTACAAATAGTTCTGA TCCACTAGCACCAACTCATTTAGGCTTTCGTCCTCGCTTCACGTAAAAAGGTTAACCTATGGAT GGTGATATGAACTCTAAAAGCCATGTTGGTCGAATCTGCTCTGACGCTCTCAATATCCAAGGTT GGACTAAGACCCCCCACAATCTCACATCAACATACACATGGGCCACTATGTGACAAATCCAAAC TGAGCCAGATGTCACATAAACTTCACATGATCACACTTGCCAAAAAATGAGTTCTTCCTCATCC CCAAAATAATTGCACATCTCGCTTTTCCAGAAGTCAAAAAAATAAGTTTGACAAACTATACACA AAAATATACTCTACTATTTATGACGTGTAATAAGTATCATTAGATTAATAGTCGAATATATTTT CATAACGAACATATTAGGAGATACAAATGTTGATAATGTTTTGTCAAACTTTTGGAAAAGCGAG ATGTGCAATTATTTTGGAAAATAGCTCAGAAGCCACATGCCCCACTTCTGGAAAACTTTTGCTC TTTTCCAAGGCTGAGGAAGCGGGGTTGCTGCAGCATTTCTGTAGGAGAAAGAAGCTCCACAGAA TATCTATTTATGTTGATGATGTGGCCTTATTTCTGCATCCTACTTAGGCTGATATTTCTATCAC TCTTGATATCCTTAAGCTCTTTGGGGATGCCTCTGGTCTTCACAACAATGCACAGAAGTCCAAT ATTTTCCCTGTTAGATGTTCTGAGGAATCCATCCTGGAAATTCAGAGCAGTCTACCTTGTGAAA TTGCCTCCTTTCCAAGCAAATATTTAGGCCTTGTTCTTTCTTTGCACAAATTAACCACGTCAAC ATTAACATCAACATAGCCTTTTAGTCCCAAGCAAGTTGGGGTAGGCTAGAGTTGAAACCCAACA AGATGTCACCAAAAGGAGAAAGAGAGAGAAAGGGGAGGGGAAAAGCTTTTGAGAGCACTAAAAG GAAAAATGCCTAATCATGGTTCGGACACGTGGATAGCTTCTTTCCAAACACTTCTAACCTCAAT CTGAAATTCACTCCCACTGGAATTCGAACTCAGGACCTGAGGAGTGCTCCTCAGATCATCTAAC CAACTCAGCTAGAGACCCACACATACAACCCCAAAAGGGAAGAAAACTAGCCCATAAAATCATA TAATCGCATTTTAAAGCTTCATGTTTAAAGAACAATTTCCAAACAATCAGGCAAAGGATACTAC ATGCAGATATCAGCAATAGTTGCATCCTATTCGACACTATGCTTTAGTAATTAGTAGTACATAA TGATAAATATTATAATAAAAAATGAAACTAGATTGAAAATATATGACAGTTCTGGACACCGTAC CTAAACCAAAATCTCCAATTTTAATATCATTGCGGACATCAAAAAATATGTTGCTGGGTGTCAG GTCTCTGTGTAGGATTCCTTGACTATGGACATGAGCTAGACCTTCCACAATTTGTCGAAACAGG TGCCAGGCATGGTCAACATCAAAAGACGAGATGTATGTCTCAAAATCCTGCCGCAAAGTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.04439291

Conservation Information
Conserved circRNAs	NA
PMCS	0.04439291

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							35377127-35374667(+)
35377149-35374626(+)
35375178-35377091(-)
						
						Potential amino acid sequence
						
							MVNIKRRDVCLKILPQSPFSHSSSIRGGSSFCKTSTADGRLDGLGDSKLLNRTD*(+)
MYVSKSCRKVHLATHLPSEEAVHFARPRQQMDG*(+)
MDGTGQVGTYFYTAPEVEQKWPQINEKVDMYSLGVIFFELWHPFATAMERHLVLSDLKQKGDPP
LSWESKFPRQSVLLRSLLSPSPSNRPSAVEVLQNELPPRMEDEWLNGLCGRILRHTSRLLMLTM
PGTCFDKLWKV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	35377127-35374667(+) 35377149-35374626(+) 35375178-35377091(-)
Potential amino acid sequence	MVNIKRRDVCLKILPQSPFSHSSSIRGGSSFCKTSTADGRLDGLGDSKLLNRTD(+) MYVSKSCRKVHLATHLPSEEAVHFARPRQQMDG(+) MDGTGQVGTYFYTAPEVEQKWPQINEKVDMYSLGVIFFELWHPFATAMERHLVLSDLKQKGDPP LSWESKFPRQSVLLRSLLSPSPSNRPSAVEVLQNELPPRMEDEWLNGLCGRILRHTSRLLMLTM PGTCFDKLWKV*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d003198_circ_g.4

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