Plant Circular RNA Database

Detail information of Zm00001d003198_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d003198_circ_g.1
					
						ID in PlantcircBase
						zma_circ_001027
					
						Alias
						circ428
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 35358382-35361124  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Zm00001d003198						
					
						Parent gene annotation
						
							eIF-2-alpha kinase GCN2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						3
					
						Tissues
						seedling leaves
					
						Exon boundary  
						
							No-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-TA							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_T011:8
Zm00001d003198_T003:8
Zm00001d003198_T008:8
Zm00001d003198_T022:8
Zm00001d003198_T029:8
Zm00001d003198_T017:7
Zm00001d003198_T018:7
Zm00001d003198_T030:7
Zm00001d003198_T027:8
Zm00001d003198_T002:7
Zm00001d003198_T012:7
Zm00001d003198_T001:8
Zm00001d003198_T014:7
Zm00001d003198_T024:8
Zm00001d003198_T013:8
Zm00001d003198_T010:8
Zm00001d003198_T004:8
Zm00001d003198_T021:8
Zm00001d003198_T025:8
Zm00001d003198_T031:8

General Information
CircRNA Name	Zm00001d003198_circ_g.1
ID in PlantcircBase	zma_circ_001027
Alias	circ428
Organism	Zea mays
Position	chr2: 35358382-35361124 JBrowse»
Reference genome	AGPv4.38
Type	ei-circRNA
Identification method	CIRI
Parent gene	Zm00001d003198
Parent gene annotation	eIF-2-alpha kinase GCN2
Parent gene strand	-
Alternative splicing	NA
Support reads	3
Tissues	seedling leaves
Exon boundary	No-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-TA 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_T011:8 Zm00001d003198_T003:8 Zm00001d003198_T008:8 Zm00001d003198_T022:8 Zm00001d003198_T029:8 Zm00001d003198_T017:7 Zm00001d003198_T018:7 Zm00001d003198_T030:7 Zm00001d003198_T027:8 Zm00001d003198_T002:7 Zm00001d003198_T012:7 Zm00001d003198_T001:8 Zm00001d003198_T014:7 Zm00001d003198_T024:8 Zm00001d003198_T013:8 Zm00001d003198_T010:8 Zm00001d003198_T004:8 Zm00001d003198_T021:8 Zm00001d003198_T025:8 Zm00001d003198_T031:8

			
						 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  
						
							GACCTGATTAGAAGCAATTGACATAACAAATGGTGTTCGCAGTTCATAGCAAAGTTCTAGCATC
TCTCCTCCTTGAGTTAAGATTTTCACTGTGTTTCCCcagatgtctcatcccaagcttgttccac
caaccaatcatatcgtccaccaactgccagcaacttttcatggaaacccggtccatgattacct
tcttttga

									
								

					

						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
						
							CAGATGTCTCATCCCAAGCTTGTTCCACCAACCAATCATATCGTCCACCAACTGCCAGCAACTT
TTCATGGAAACCCGGTCCATGATTACCTTCTTTTGAGTATACCTGTGTTGTGTTGAGATGAAAT
AATTTGCAGCGCAATATCAAGAAATATGTAAATTTCAAAGGAGCAAAGCATCAACACTAATAAA
AGGGAAGCATAGAAAATGCGAAGAACATTGCAAAATATCTCCTAATAAAATGCTTTGCATATAT
TGACACATCACCTATTATTTCATATGACTGAAGACTGAACTAGGAAAGCCTAGAGAATGCAAAG
AACATTTCCATATGTTGTTTCTTAATCTTATCCAACTACATTTTTCCCAAATAACTAAAATAAG
GAATAGATATGACATTAGAATGCTATGGTTAACTTTCATAATGAGGATCAAAATAGAGTTCTCT
CCCAAGGTTGCTCTATGAAAATTTTCTCGAAGGTGCAGGGGAACTGCACCTTAAATATATTAAG
AAGATAAAAAAGGTATATAGAAGACCAGAGGTTATAGCAAAGAACTCCTTAAGGAGGCTAGCAA
CGCACATAAATGAAAGGATCCATGGAAACCAGACTCAAAAAACTACTAAAGAACTCCTTTCTCG
AAGTGTGATCTATGAAATGTTCCAAAACAATTTAGGAGATGTAAGGTTACAGTATTCACCTGGA
AAAACAAATTTGTATAGTAACATTCTGACGGAGGCATGAGTACATCAATAGTAGTAATTGGTTG
TTCTACCGACCATACTCTCAAACATCTCAGAAGCGCGGATAGATCATCAAGAGCCTTGCAAGCA
GATTCATCTGCAACAAGAAACCCACAGTAGCAACAATTAAATATTCCCAGCTTTAACAGCTAAA
AGAACGAAGATTAAGAACCACTACCATAAAACAGGGTCCCTCTTAATCTAGCAAGTACTAGATC
TGCAGAGCCACAAAACCGCTGATCTGCTTTATGTAGCTTCTCAACAACTTCTTCAGAAAGACGA
AGATCCTGGAACATTTGATAAACCAGCCAATGTCATCAAAGCTTAGGTGAAATTCTAAATTTTC
ACTAAATGATGTTCATATGCTGATATGCATAATAATCTAGCACAACCACTTTCATAAAAACAAA
AAAGATTCCCACGAAAAAGCATTTAAATTGCGAAAAGCACACTTCTACATGTCTAAATCGAATC
TTTTAGTTGGCCATTGGTAAACAAGACAGGTTGGGCATGAAGAAGCAAGCACCTTTATCTAACG
AGAAACACAAAAAGAACACATTTACGACTCATCCAAGTTTGTTAACTGCAATTTCCATGTTGTA
GCACTACCAAGGATGCTCTTACAAAAAAAAAGCTACAAAAGTACTCATTTGACCTGTACTGTAT
CACTATAATGCTTCTTTTACCTGTAAAAGTTGCCCCCTAATCAAACTCCACTGTGACTTGCGGT
CAGCTTCATTTGGCCAATACTGAACAATAGTTGAAGACAGAAACTGAAACAGTAAATAAAATAT
TTCAGTTAATTGAAGACAGAAATTGCAAAAGTTTCAGGAACAGTTAAGACAGAACATCACACCT
CAGCAACATTTTGTCTTTGATCCTGAGAAACCCCTGCCCAAGAGCAAATTGCTTCAGCAAGTTT
ACCGTGATTCAGACGTATGACTAGCGTCTTGGAATCATAAAAGCGGGTCCCCAGGTCCAAAGCC
ACCTATCATCACATGGATTCAGAGTTATTTATATGACAATACAAAACTATATTTTTAACATTAA
AATCGACCTTCCAAGATAATTGTCTCCTTACAAATGATTTTATTATAAAATGGAAGATAGACTA
TAACCAACATGGCAACATGATAGCAAGAATATAGTTGCAGAGTGAATGTACAAGATGAGCTGCT
ATGTGGAGATGAGCTACCTTGATGATTTCAGCCTCTGGAATCGGTGAAGTACCGCCAATAATGT
CAAAATCACCCTAACAGGATATCAACATTATGTTTCAGAAGTATTTCTTCAATTATTTCGAGAC
CAAAAGAGTAGAAAGTTGAGGTTGCAAAGTATAAAAATTGTTGAGTTTCAATGGAAATTCACTC
TATATAAAGAATATACCTGAAGAAAACGATAAGGAGTTGAATGGCCAACGGCTCTTCTATGAAC
CCATGATATTTCATAACGTTTGAATGATGATGTCTGCAGGTGAATTTATAAGCAAGTAGGGAGA
GACAAGAAAGAAATCAAACAGTGACAAGTTATTCCAGAAAATCCCAAAACAGTGGCTAGACGGC
TGGTAGAAGGTGAACTAGTAAATGCTATCAAACAGCATGCACATTCACATTAAAAAGTTTGCTA
ACATATTCTAACAAAATGTGCATATAATTAAAAAACAGTGATCTAAACATATAATGCAGACTGC
ATCATGGAAGTATGACCTATGTCCAAAATGACAAGTTAAAAGAAAAATGAAGGTAAATGACACA
TAAAAATTTAACAATTATTTTGTAATGAAGAAAAGCAATGATCCATATTAGTCTAAAAACTCAG
ACTATGCATAACACAAAATTAGGAACAAAAATAGAAGCATAAACATTCACACAAGATGAAAGAA
AAATAAACAACTTGTCACAGACCTGATTAGAAGCAATTGACATAACAAATGGTGTTCGCAGTTC
ATAGCAAAGTTCTAGCATCTCTCCTCCTTGAGTTAAGATTTTCACTGTGTTTCCC
						
					

			
		

Sequences
Splice junction sequence	GACCTGATTAGAAGCAATTGACATAACAAATGGTGTTCGCAGTTCATAGCAAAGTTCTAGCATC TCTCCTCCTTGAGTTAAGATTTTCACTGTGTTTCCCcagatgtctcatcccaagcttgttccac caaccaatcatatcgtccaccaactgccagcaacttttcatggaaacccggtccatgattacct tcttttga
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	CAGATGTCTCATCCCAAGCTTGTTCCACCAACCAATCATATCGTCCACCAACTGCCAGCAACTT TTCATGGAAACCCGGTCCATGATTACCTTCTTTTGAGTATACCTGTGTTGTGTTGAGATGAAAT AATTTGCAGCGCAATATCAAGAAATATGTAAATTTCAAAGGAGCAAAGCATCAACACTAATAAA AGGGAAGCATAGAAAATGCGAAGAACATTGCAAAATATCTCCTAATAAAATGCTTTGCATATAT TGACACATCACCTATTATTTCATATGACTGAAGACTGAACTAGGAAAGCCTAGAGAATGCAAAG AACATTTCCATATGTTGTTTCTTAATCTTATCCAACTACATTTTTCCCAAATAACTAAAATAAG GAATAGATATGACATTAGAATGCTATGGTTAACTTTCATAATGAGGATCAAAATAGAGTTCTCT CCCAAGGTTGCTCTATGAAAATTTTCTCGAAGGTGCAGGGGAACTGCACCTTAAATATATTAAG AAGATAAAAAAGGTATATAGAAGACCAGAGGTTATAGCAAAGAACTCCTTAAGGAGGCTAGCAA CGCACATAAATGAAAGGATCCATGGAAACCAGACTCAAAAAACTACTAAAGAACTCCTTTCTCG AAGTGTGATCTATGAAATGTTCCAAAACAATTTAGGAGATGTAAGGTTACAGTATTCACCTGGA AAAACAAATTTGTATAGTAACATTCTGACGGAGGCATGAGTACATCAATAGTAGTAATTGGTTG TTCTACCGACCATACTCTCAAACATCTCAGAAGCGCGGATAGATCATCAAGAGCCTTGCAAGCA GATTCATCTGCAACAAGAAACCCACAGTAGCAACAATTAAATATTCCCAGCTTTAACAGCTAAA AGAACGAAGATTAAGAACCACTACCATAAAACAGGGTCCCTCTTAATCTAGCAAGTACTAGATC TGCAGAGCCACAAAACCGCTGATCTGCTTTATGTAGCTTCTCAACAACTTCTTCAGAAAGACGA AGATCCTGGAACATTTGATAAACCAGCCAATGTCATCAAAGCTTAGGTGAAATTCTAAATTTTC ACTAAATGATGTTCATATGCTGATATGCATAATAATCTAGCACAACCACTTTCATAAAAACAAA AAAGATTCCCACGAAAAAGCATTTAAATTGCGAAAAGCACACTTCTACATGTCTAAATCGAATC TTTTAGTTGGCCATTGGTAAACAAGACAGGTTGGGCATGAAGAAGCAAGCACCTTTATCTAACG AGAAACACAAAAAGAACACATTTACGACTCATCCAAGTTTGTTAACTGCAATTTCCATGTTGTA GCACTACCAAGGATGCTCTTACAAAAAAAAAGCTACAAAAGTACTCATTTGACCTGTACTGTAT CACTATAATGCTTCTTTTACCTGTAAAAGTTGCCCCCTAATCAAACTCCACTGTGACTTGCGGT CAGCTTCATTTGGCCAATACTGAACAATAGTTGAAGACAGAAACTGAAACAGTAAATAAAATAT TTCAGTTAATTGAAGACAGAAATTGCAAAAGTTTCAGGAACAGTTAAGACAGAACATCACACCT CAGCAACATTTTGTCTTTGATCCTGAGAAACCCCTGCCCAAGAGCAAATTGCTTCAGCAAGTTT ACCGTGATTCAGACGTATGACTAGCGTCTTGGAATCATAAAAGCGGGTCCCCAGGTCCAAAGCC ACCTATCATCACATGGATTCAGAGTTATTTATATGACAATACAAAACTATATTTTTAACATTAA AATCGACCTTCCAAGATAATTGTCTCCTTACAAATGATTTTATTATAAAATGGAAGATAGACTA TAACCAACATGGCAACATGATAGCAAGAATATAGTTGCAGAGTGAATGTACAAGATGAGCTGCT ATGTGGAGATGAGCTACCTTGATGATTTCAGCCTCTGGAATCGGTGAAGTACCGCCAATAATGT CAAAATCACCCTAACAGGATATCAACATTATGTTTCAGAAGTATTTCTTCAATTATTTCGAGAC CAAAAGAGTAGAAAGTTGAGGTTGCAAAGTATAAAAATTGTTGAGTTTCAATGGAAATTCACTC TATATAAAGAATATACCTGAAGAAAACGATAAGGAGTTGAATGGCCAACGGCTCTTCTATGAAC CCATGATATTTCATAACGTTTGAATGATGATGTCTGCAGGTGAATTTATAAGCAAGTAGGGAGA GACAAGAAAGAAATCAAACAGTGACAAGTTATTCCAGAAAATCCCAAAACAGTGGCTAGACGGC TGGTAGAAGGTGAACTAGTAAATGCTATCAAACAGCATGCACATTCACATTAAAAAGTTTGCTA ACATATTCTAACAAAATGTGCATATAATTAAAAAACAGTGATCTAAACATATAATGCAGACTGC ATCATGGAAGTATGACCTATGTCCAAAATGACAAGTTAAAAGAAAAATGAAGGTAAATGACACA TAAAAATTTAACAATTATTTTGTAATGAAGAAAAGCAATGATCCATATTAGTCTAAAAACTCAG ACTATGCATAACACAAAATTAGGAACAAAAATAGAAGCATAAACATTCACACAAGATGAAAGAA AAATAAACAACTTGTCACAGACCTGATTAGAAGCAATTGACATAACAAATGGTGTTCGCAGTTC ATAGCAAAGTTCTAGCATCTCTCCTCCTTGAGTTAAGATTTTCACTGTGTTTCCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.109601355

Conservation Information
Conserved circRNAs	NA
PMCS	0.109601355

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

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

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d003198_circ_g.1

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