Plant Circular RNA Database

Detail information of Zm00001d050851_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d050851_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008093
					
						Alias
						Zm04circ00053, GRMZM2G403915_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 126973352-126975137  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d050851						
					
						Parent gene annotation
						
							CMP-sialic acid transporter 5
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d050851_circ_g.2 						
					
						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
						Zm00001d050851_T008:4
Zm00001d050851_T004:4
Zm00001d050851_T006:4
Zm00001d050851_T005:4
Zm00001d050851_T009:4
Zm00001d050851_T002:4
Zm00001d050851_T007:4
Zm00001d050851_T001:4

General Information
CircRNA Name	Zm00001d050851_circ_g.3
ID in PlantcircBase	zma_circ_008093
Alias	Zm04circ00053, GRMZM2G403915_C1
Organism	Zea mays
Position	chr4: 126973352-126975137 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d050851
Parent gene annotation	CMP-sialic acid transporter 5
Parent gene strand	-
Alternative splicing	Zm00001d050851_circ_g.2
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	Zm00001d050851_T008:4 Zm00001d050851_T004:4 Zm00001d050851_T006:4 Zm00001d050851_T005:4 Zm00001d050851_T009:4 Zm00001d050851_T002:4 Zm00001d050851_T007:4 Zm00001d050851_T001:4

			
						 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  
						
							ACCCAGGTGAAAAACATGTCATAATGATCATACTAAAAACTAGTGCCAGACCTTTGCTGCTTCC
GTTGCAAGAACGAGTGAAGTCACTATAGTATCTTGGcatggtccagaaagtccattcatggaaa
accccatatttccttatggcttctccatctggtgaccgataggtacttgctaacaagcacacac
ttccaata

									
								

					

						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: 619
Transcript exons: 126973352-126973495,126973570-126973768,126974783-126975
009,126975089-126975137
CATGGTCCAGAAAGTCCATTCATGGAAAACCCCATATTTCCTTATGGCTTCTCCATCTGGTGAC
CGATAGGTACTTGCTAACAAGCACACACTTCCAATAAATGACATTTCTATAGTCATCATGTAAG
AGGTATGCTTTTTAACCTGAGATGCCCACTGACATAATGAAGAGGCCAAACCAGACAGCATAGA
AGCGACTGTAACCGGAATGATCCCATATAGCAAGATATAGTCAGAGCCACCACCATTTGAACCT
TTGCTAGTACTCTCCCCAACACTTAAAAGAACAGCGGCACTAATTAAGAGGGCCAATGCTAAAA
TTTGCTTGGATGATTGCTTTTGCCCCAAAATAAGAAATGTGAAAAATGATGTCCACAAAAGCTT
AGTCTGGTTAAGGATTGAAAAGGTCAAGGAATCCAGATTCTTGAATGATACTTGCAGCAGACTA
TTCTGAAGGGCATAGATAGCAGCAGGCAGTCCAGACGCAGTCAGTGATCCAATGAGGGTCCAAT
TACTGAACTGTTTTTTCAGACTACCGTCTGCAATCAATAAAATGATTGCACAAATAACCTTTGC
TGCTTCCGTTGCAAGAACGAGTGAAGTCACTATAGTATCTTGG
						
					

						Genomic sequence
						
							CATGGTCCAGAAAGTCCATTCATGGAAAACCCCATATTTCCTTATGGCTTCTCCATCTGGTGAC
CGATAGGTACTTGCTAACAAGCACACACTTCCAATAAATGACATTTCTATAGTCATCATGTAAG
AGGTATGCTTTTTAACCTGAAGCATTAGTGAACATGTTAGTACTAGCCATAAACTGCATCCTGG
AAAATAACAAGGTACGAAAGTCCAACCTGAGATGCCCACTGACATAATGAAGAGGCCAAACCAG
ACAGCATAGAAGCGACTGTAACCGGAATGATCCCATATAGCAAGATATAGTCAGAGCCACCACC
ATTTGAACCTTTGCTAGTACTCTCCCCAACACTTAAAAGAACAGCGGCACTAATTAAGAGGGCC
AATGCTAAAATTTGCTTGGATGATTGCTTTTGCCTGCACAATGTTGCAAAAGGAAATCAAACTA
ATGAGTGCTGGAATTACTAGTCCAGATCTGCATGATGTTGCAAAAGGAAATCAAACTACTGAGT
GCTGGTAGTTGTTTGTTTAATCAGAGAGTTAATGACGTGATATTGTGGATGGAGAAGTTTCAAA
ATGAACATAAGAGTCCCAAGTTACATGTAGTAAGTGATCAGTAGTAAACTATAAACCCAAGTGC
TGATTACTAAGACAATCTACCCAAAAATAACTTCAAACCAAATTCTTCGAAAACAGTCTAAATA
GACCACAAAATTGACTAATTCCCTAACATGCTAATTCTATATCATCCAGGGTTGAGGATGAAAC
TCCATGTTGAGATTTCATTTTTCATAATCCATTAACCACTATTTGTTCTGCACAACCTTGAGGC
CTCCCGCCCCTCACCCCTTCATTTTTTTTATGAAAACTATGCTACCAACCTTGAGCTAAAAAGG
CATGAACGACTAGGCTCATTGAATTATTAGCTTGTGACTTATTTAGGGGGTGTTTGGGATGGCT
CCAGTGTGGAGCTGTAGTTTATAATATCAATTTAAATAGTTTTAAAAATGATTTTAATCTAAAT
AATAAACAAAATGGTTTATCTAAATGTCTTCTAAAGGCTTACAACTCCAGCTCCACGATTTTTT
AGAGCAACTAATGACTTGCTCCACCAACTACACCAAATTTCCTCGAGCTAGAGCTATCCCAAAC
AGAGACTTAATATGTATAGTTTGCATATGGACTTCCAGATAATCAACATTTTGCAGTTAAACTT
TAGAGCACCAGACAAGTTTTAAGAACTGCCACTTTTCATTAGGTGAACATCTTCTGGTCTCAGG
CACGGCGTCGACAGGATCAAATGACTCTGCAAGTATTCAATACTAAGGAAGTTCGAACTATAAT
GCTTGCATGCATGTTTTGGTAGTTACTTCTTCAGATGTTCTTCAACCTGAGTATTTTTTTGAAA
TTGAAATGCAAATAGGGACATACCCCAAAATAAGAAATGTGAAAAATGATGTCCACAAAAGCTT
AGTCTGGTTAAGGATTGAAAAGGTCAAGGAATCCAGATTCTTGAATGATACTTGCAGCAGACTA
TTCTGAAGGGCATAGATAGCAGCAGGCAGTCCAGACGCAGTCAGTGATCCAATGAGGGTCCAAT
TACTGAACTGTTTTTTCAGACTACCGTCTGCAATCAATAAAATGATTGCACAAATAACCTATAC
AGATGAAAAGGAAATCAGAAACACCCAGGTGAAAAACATGTCATAATGATCATACTAAAAACTA
GTGCCAGACCTTTGCTGCTTCCGTTGCAAGAACGAGTGAAGTCACTATAGTATCTTGG
						
					

			
		

Sequences
Splice junction sequence	ACCCAGGTGAAAAACATGTCATAATGATCATACTAAAAACTAGTGCCAGACCTTTGCTGCTTCC GTTGCAAGAACGAGTGAAGTCACTATAGTATCTTGGcatggtccagaaagtccattcatggaaa accccatatttccttatggcttctccatctggtgaccgataggtacttgctaacaagcacacac ttccaata
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: 619 Transcript exons: 126973352-126973495,126973570-126973768,126974783-126975 009,126975089-126975137 CATGGTCCAGAAAGTCCATTCATGGAAAACCCCATATTTCCTTATGGCTTCTCCATCTGGTGAC CGATAGGTACTTGCTAACAAGCACACACTTCCAATAAATGACATTTCTATAGTCATCATGTAAG AGGTATGCTTTTTAACCTGAGATGCCCACTGACATAATGAAGAGGCCAAACCAGACAGCATAGA AGCGACTGTAACCGGAATGATCCCATATAGCAAGATATAGTCAGAGCCACCACCATTTGAACCT TTGCTAGTACTCTCCCCAACACTTAAAAGAACAGCGGCACTAATTAAGAGGGCCAATGCTAAAA TTTGCTTGGATGATTGCTTTTGCCCCAAAATAAGAAATGTGAAAAATGATGTCCACAAAAGCTT AGTCTGGTTAAGGATTGAAAAGGTCAAGGAATCCAGATTCTTGAATGATACTTGCAGCAGACTA TTCTGAAGGGCATAGATAGCAGCAGGCAGTCCAGACGCAGTCAGTGATCCAATGAGGGTCCAAT TACTGAACTGTTTTTTCAGACTACCGTCTGCAATCAATAAAATGATTGCACAAATAACCTTTGC TGCTTCCGTTGCAAGAACGAGTGAAGTCACTATAGTATCTTGG
Genomic sequence	CATGGTCCAGAAAGTCCATTCATGGAAAACCCCATATTTCCTTATGGCTTCTCCATCTGGTGAC CGATAGGTACTTGCTAACAAGCACACACTTCCAATAAATGACATTTCTATAGTCATCATGTAAG AGGTATGCTTTTTAACCTGAAGCATTAGTGAACATGTTAGTACTAGCCATAAACTGCATCCTGG AAAATAACAAGGTACGAAAGTCCAACCTGAGATGCCCACTGACATAATGAAGAGGCCAAACCAG ACAGCATAGAAGCGACTGTAACCGGAATGATCCCATATAGCAAGATATAGTCAGAGCCACCACC ATTTGAACCTTTGCTAGTACTCTCCCCAACACTTAAAAGAACAGCGGCACTAATTAAGAGGGCC AATGCTAAAATTTGCTTGGATGATTGCTTTTGCCTGCACAATGTTGCAAAAGGAAATCAAACTA ATGAGTGCTGGAATTACTAGTCCAGATCTGCATGATGTTGCAAAAGGAAATCAAACTACTGAGT GCTGGTAGTTGTTTGTTTAATCAGAGAGTTAATGACGTGATATTGTGGATGGAGAAGTTTCAAA ATGAACATAAGAGTCCCAAGTTACATGTAGTAAGTGATCAGTAGTAAACTATAAACCCAAGTGC TGATTACTAAGACAATCTACCCAAAAATAACTTCAAACCAAATTCTTCGAAAACAGTCTAAATA GACCACAAAATTGACTAATTCCCTAACATGCTAATTCTATATCATCCAGGGTTGAGGATGAAAC TCCATGTTGAGATTTCATTTTTCATAATCCATTAACCACTATTTGTTCTGCACAACCTTGAGGC CTCCCGCCCCTCACCCCTTCATTTTTTTTATGAAAACTATGCTACCAACCTTGAGCTAAAAAGG CATGAACGACTAGGCTCATTGAATTATTAGCTTGTGACTTATTTAGGGGGTGTTTGGGATGGCT CCAGTGTGGAGCTGTAGTTTATAATATCAATTTAAATAGTTTTAAAAATGATTTTAATCTAAAT AATAAACAAAATGGTTTATCTAAATGTCTTCTAAAGGCTTACAACTCCAGCTCCACGATTTTTT AGAGCAACTAATGACTTGCTCCACCAACTACACCAAATTTCCTCGAGCTAGAGCTATCCCAAAC AGAGACTTAATATGTATAGTTTGCATATGGACTTCCAGATAATCAACATTTTGCAGTTAAACTT TAGAGCACCAGACAAGTTTTAAGAACTGCCACTTTTCATTAGGTGAACATCTTCTGGTCTCAGG CACGGCGTCGACAGGATCAAATGACTCTGCAAGTATTCAATACTAAGGAAGTTCGAACTATAAT GCTTGCATGCATGTTTTGGTAGTTACTTCTTCAGATGTTCTTCAACCTGAGTATTTTTTTGAAA TTGAAATGCAAATAGGGACATACCCCAAAATAAGAAATGTGAAAAATGATGTCCACAAAAGCTT AGTCTGGTTAAGGATTGAAAAGGTCAAGGAATCCAGATTCTTGAATGATACTTGCAGCAGACTA TTCTGAAGGGCATAGATAGCAGCAGGCAGTCCAGACGCAGTCAGTGATCCAATGAGGGTCCAAT TACTGAACTGTTTTTTCAGACTACCGTCTGCAATCAATAAAATGATTGCACAAATAACCTATAC AGATGAAAAGGAAATCAGAAACACCCAGGTGAAAAACATGTCATAATGATCATACTAAAAACTA GTGCCAGACCTTTGCTGCTTCCGTTGCAAGAACGAGTGAAGTCACTATAGTATCTTGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.173774637

Conservation Information
Conserved circRNAs	NA
PMCS	0.173774637

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							126974940-126973411(+)
126973616-126974974(-)
126973388-126974974(-)
						
						Potential amino acid sequence
						
							MRVQLLNCFFRLPSAINKMIAQITFAASVARTSEVTIVSWHGPESPFMENPIFPYGFSIW*(+)
MLSGLASSLCQWASQVKKHTSYMMTIEMSFIGSVCLLASTYRSPDGEAIRKYGVFHEWTFWTMP
RYYSDFTRSCNGSSKGYLCNHFIDCRR*(-)
MGFSMNGLSGPCQDTIVTSLVLATEAAKVICAIILLIADGSLKKQFSNWTLIGSLTASGLPAAI
YALQNSLLQVSFKNLDSLTFSILNQTKLLWTSFFTFLILGQKQSSKQILALALLISAAVLLSVG
ESTSKGSNGGGSDYILLYGIIPVTVASMLSGLASSLCQWASQVKKHTSYMMTIEMSFIGSVCLL
ASTYRSPDGEAIRKYGVFHEWTFWTMPRYYSDFTRSCNGSSKGYLCNHFIDCRR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	126974940-126973411(+) 126973616-126974974(-) 126973388-126974974(-)
Potential amino acid sequence	MRVQLLNCFFRLPSAINKMIAQITFAASVARTSEVTIVSWHGPESPFMENPIFPYGFSIW(+) MLSGLASSLCQWASQVKKHTSYMMTIEMSFIGSVCLLASTYRSPDGEAIRKYGVFHEWTFWTMP RYYSDFTRSCNGSSKGYLCNHFIDCRR(-) MGFSMNGLSGPCQDTIVTSLVLATEAAKVICAIILLIADGSLKKQFSNWTLIGSLTASGLPAAI YALQNSLLQVSFKNLDSLTFSILNQTKLLWTSFFTFLILGQKQSSKQILALALLISAAVLLSVG ESTSKGSNGGGSDYILLYGIIPVTVASMLSGLASSLCQWASQVKKHTSYMMTIEMSFIGSVCLL ASTYRSPDGEAIRKYGVFHEWTFWTMPRYYSDFTRSCNGSSKGYLCNHFIDCRR*(-)
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 Zm00001d050851_circ_g.3

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