Plant Circular RNA Database

Detail information of Zm00001d042615_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d042615_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007710
					
						Alias
						Zm03circ00062, zma_circ_0001168
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 173793468-173795786  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d042615						
					
						Parent gene annotation
						
							wound-responsive family protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d042615_circ_g.1 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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
						Zm00001d042615_T005:3
Zm00001d042615_T020:2
Zm00001d042615_T009:2
Zm00001d042615_T007:2
Zm00001d042615_T001:2
Zm00001d042615_T024:2
Zm00001d042615_T003:3
Zm00001d042615_T014:1
Zm00001d042615_T006:3
Zm00001d042615_T002:2
Zm00001d042615_T022:3
Zm00001d042615_T004:3
Zm00001d042615_T008:3
Zm00001d042615_T026:1
Zm00001d042615_T016:1
Zm00001d042615_T018:2
Zm00001d042615_T017:2

General Information
CircRNA Name	Zm00001d042615_circ_g.2
ID in PlantcircBase	zma_circ_007710
Alias	Zm03circ00062, zma_circ_0001168
Organism	Zea mays
Position	chr3: 173793468-173795786 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d042615
Parent gene annotation	wound-responsive family protein
Parent gene strand	-
Alternative splicing	Zm00001d042615_circ_g.1
Support reads	NA
Tissues	leaf, endosperm, 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	Zm00001d042615_T005:3 Zm00001d042615_T020:2 Zm00001d042615_T009:2 Zm00001d042615_T007:2 Zm00001d042615_T001:2 Zm00001d042615_T024:2 Zm00001d042615_T003:3 Zm00001d042615_T014:1 Zm00001d042615_T006:3 Zm00001d042615_T002:2 Zm00001d042615_T022:3 Zm00001d042615_T004:3 Zm00001d042615_T008:3 Zm00001d042615_T026:1 Zm00001d042615_T016:1 Zm00001d042615_T018:2 Zm00001d042615_T017:2

			
						 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  
						
							TTCCATTCCTAACCTTCAGTGTCCTGCGCTGAACAAGGTGTCCAACTATGCCCATGAGGCGATT
CATTAGCTCATGTTCTTGGATCTTTCCGTTATTTGCctcaacatacatatcatacagatcacac
atcttgtcctccaatgcagtatccattgtatactttgtttttaaagctcttctttcatcattag
caacctga

									
								

					

						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: 342
Transcript exons: 173793468-173793599,173793730-173793852,173795700-173795
786
CTCAACATACATATCATACAGATCACACATCTTGTCCTCCAATGCAGTATCCATTGTATACTTT
GTTTTTAAAGCTCTTCTTTCATCATTAGCAACCTGAAAATCATCAGCTGAACCATCCTGTTCAT
TGACCTTGGACTTTGTAGCCATACGCTCTTTAATCATCTCATTGATCTCCAATTTTACACGCTG
AAACCTGTCAGCCTTCTCCAGTTTAGCAGATATACCAGATTCTACCATTTCTTTCATGTTTCTC
TTCAGTGTCCTGCGCTGAACAAGGTGTCCAACTATGCCCATGAGGCGATTCATTAGCTCATGTT
CTTGGATCTTTCCGTTATTTGC
						
					

						Genomic sequence
						
							CTCAACATACATATCATACAGATCACACATCTTGTCCTCCAATGCAGTATCCATTGTATACTTT
GTTTTTAAAGCTCTTCTTTCATCATTAGCAACCTGAAAATCATCAGCTGAACCATCCTGTTCAT
TGACCTGGTAGCATGTTGACAACAGAACATCTATCATCAGCCACAATGCTATAAGAAAAAAGTA
TTAATAACAAGAGTTCATATATCAATAGACTAGAGGGAAGTCTAACACTTGTAACCAATTATAT
CTTTACCTTGGACTTTGTAGCCATACGCTCTTTAATCATCTCATTGATCTCCAATTTTACACGC
TGAAACCTGTCAGCCTTCTCCAGTTTAGCAGATATACCAGATTCTACCATTTCTTTCATGTTTC
TCTGTTAAAGATAGGAATGATTAGAAATGGAAGCAAGCATACTAAGTTAAAATAATTGTCCTGG
ACGTGTAGCTTGAGTGAATGGTCATCACACGGGATCAATATACTACAAAATAGATAGGGATGAC
AATCTTACCCGCGGGTGTGTGTATCCACGAGTTTCCTACCCGATGGGTGTTGGCATGGGTATGA
AATCTCACCCGCATGTACATGAGGGTCGGGTACCCGCAAATATACAGGTAGAGTACACATATCA
AATTTTACCTGCGGGTACCCGCAATTTGAGAATATATATGAATATATATCACATGTCGTTCGCA
TATCATGTGGACTAGCTCATTTAGGATATCTACAGTAGCTTACCCATTCACATACCCATATTCA
AACTCCACTCTGCGAACAATGCAGTCTACAGTGCAAAACAGTGTTTTAGGTAACCATATGGGTG
AACTGCTGGACAGTCTTAACATGTAATGTGTAGCATATGCAATTATGCATAACAATGTCGAACT
ATAGAGATGATATTTTTTGGATGGCTAAATAAAGTGATTGCGTGAGCTACTAACTTGTTATGTT
AGTTCTTGTGTAAGTTTTTTGTGTTATTTGTACGAGCATGAATGACCGAATTATTGTTCTAGTT
ATGTATTGTGACTTGTGAGCTACTGTATATTGTCCTAGTGAACTCTACACAAGTGACATTGATA
TATTTACATGATGTTTAACTATGAATTTATTATATCATACCACTATGACTATTATTTGTCTTAA
TATACCTAGCAGGTATATTTACATGTTGTTTAGCAATGAATTTATTATTTCATACCACTATGAC
TTCATTATTTGATCACTCTTAATATACCCGATAGGTACAAGATACCCGTCGGGTGCGGGCACAG
GTACAATATCTTACCCGCAGCCCGCAGGTATGCTCGCGGGCACGGGTAAAAATTAGGATCACAG
GTATACTCATGTGCGGATAATACCTGACCCGCTGCCATCCCTAAACATAAACCTAGACTATAAC
ATAATGGTCAAATCGACAACTAGATATTCTGCGCAACAGCACTAGACTTTCAAAACGAACTAGG
CTATAGGAAAAGTCAGGCTCCCACTGTTGCCAAGGCACCACACGTAGGCTGATCTAGGAGTCCC
CTTTTTAAAGATAGCAGATTTCTTTTTTTACACCAAATCAAATATCAAAATATTATATCTGTTG
CTCAGTTGGTCTTCATGTTGCACTCTGTTTTATATTTACCTCATAGATCAGCATTGCCAGTGCT
ATTTGAGTACATTGAATAGCCAAATTATGATAGTTTTTCTATGATTGCCATTACTTTTGCAACA
TAAACCTACTACAGACAAAGAGACAAGGACCTGAGTTGGCATGCTAAAAAAATCATTATTCATA
TCTGTCTAGCCTAGCCAAACTTGCTTGGGATTAAAAGAATTTGTTGTTTTTGTTGTACTCTATT
CATATTTGATGAAAAATAACAAACTGGGAAGTTTTGCCATAGCTTAATTGACGCACTACCCCAA
TATGACATTTTGAAAATGCATTGGCTCTCAAAGTCTTCTAACTGAACCCGTAATATGATGCAAC
ATTTGGAAGTGATAGGTTCTAAAATGATATTGCTAGTTTAGACAAGAAAGATGCTTTTCTTACA
CAACAATATATTGTATTTTTTGCTAACATAGATTTAGATGAACATAGGCCAACATTACAAGTTC
AAGATCGCGTCAGTATCTAACTTTTCAATCAATAAAAACAAAGACAAAACCAACCAGTTACCAG
TGCTCTACAATAGCAAATACATATCCAAGATAAGCCAATTAGCTTCCATTCCTAACCTTCAGTG
TCCTGCGCTGAACAAGGTGTCCAACTATGCCCATGAGGCGATTCATTAGCTCATGTTCTTGGAT
CTTTCCGTTATTTGC
						
					

			
		

Sequences
Splice junction sequence	TTCCATTCCTAACCTTCAGTGTCCTGCGCTGAACAAGGTGTCCAACTATGCCCATGAGGCGATT CATTAGCTCATGTTCTTGGATCTTTCCGTTATTTGCctcaacatacatatcatacagatcacac atcttgtcctccaatgcagtatccattgtatactttgtttttaaagctcttctttcatcattag caacctga
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: 342 Transcript exons: 173793468-173793599,173793730-173793852,173795700-173795 786 CTCAACATACATATCATACAGATCACACATCTTGTCCTCCAATGCAGTATCCATTGTATACTTT GTTTTTAAAGCTCTTCTTTCATCATTAGCAACCTGAAAATCATCAGCTGAACCATCCTGTTCAT TGACCTTGGACTTTGTAGCCATACGCTCTTTAATCATCTCATTGATCTCCAATTTTACACGCTG AAACCTGTCAGCCTTCTCCAGTTTAGCAGATATACCAGATTCTACCATTTCTTTCATGTTTCTC TTCAGTGTCCTGCGCTGAACAAGGTGTCCAACTATGCCCATGAGGCGATTCATTAGCTCATGTT CTTGGATCTTTCCGTTATTTGC
Genomic sequence	CTCAACATACATATCATACAGATCACACATCTTGTCCTCCAATGCAGTATCCATTGTATACTTT GTTTTTAAAGCTCTTCTTTCATCATTAGCAACCTGAAAATCATCAGCTGAACCATCCTGTTCAT TGACCTGGTAGCATGTTGACAACAGAACATCTATCATCAGCCACAATGCTATAAGAAAAAAGTA TTAATAACAAGAGTTCATATATCAATAGACTAGAGGGAAGTCTAACACTTGTAACCAATTATAT CTTTACCTTGGACTTTGTAGCCATACGCTCTTTAATCATCTCATTGATCTCCAATTTTACACGC TGAAACCTGTCAGCCTTCTCCAGTTTAGCAGATATACCAGATTCTACCATTTCTTTCATGTTTC TCTGTTAAAGATAGGAATGATTAGAAATGGAAGCAAGCATACTAAGTTAAAATAATTGTCCTGG ACGTGTAGCTTGAGTGAATGGTCATCACACGGGATCAATATACTACAAAATAGATAGGGATGAC AATCTTACCCGCGGGTGTGTGTATCCACGAGTTTCCTACCCGATGGGTGTTGGCATGGGTATGA AATCTCACCCGCATGTACATGAGGGTCGGGTACCCGCAAATATACAGGTAGAGTACACATATCA AATTTTACCTGCGGGTACCCGCAATTTGAGAATATATATGAATATATATCACATGTCGTTCGCA TATCATGTGGACTAGCTCATTTAGGATATCTACAGTAGCTTACCCATTCACATACCCATATTCA AACTCCACTCTGCGAACAATGCAGTCTACAGTGCAAAACAGTGTTTTAGGTAACCATATGGGTG AACTGCTGGACAGTCTTAACATGTAATGTGTAGCATATGCAATTATGCATAACAATGTCGAACT ATAGAGATGATATTTTTTGGATGGCTAAATAAAGTGATTGCGTGAGCTACTAACTTGTTATGTT AGTTCTTGTGTAAGTTTTTTGTGTTATTTGTACGAGCATGAATGACCGAATTATTGTTCTAGTT ATGTATTGTGACTTGTGAGCTACTGTATATTGTCCTAGTGAACTCTACACAAGTGACATTGATA TATTTACATGATGTTTAACTATGAATTTATTATATCATACCACTATGACTATTATTTGTCTTAA TATACCTAGCAGGTATATTTACATGTTGTTTAGCAATGAATTTATTATTTCATACCACTATGAC TTCATTATTTGATCACTCTTAATATACCCGATAGGTACAAGATACCCGTCGGGTGCGGGCACAG GTACAATATCTTACCCGCAGCCCGCAGGTATGCTCGCGGGCACGGGTAAAAATTAGGATCACAG GTATACTCATGTGCGGATAATACCTGACCCGCTGCCATCCCTAAACATAAACCTAGACTATAAC ATAATGGTCAAATCGACAACTAGATATTCTGCGCAACAGCACTAGACTTTCAAAACGAACTAGG CTATAGGAAAAGTCAGGCTCCCACTGTTGCCAAGGCACCACACGTAGGCTGATCTAGGAGTCCC CTTTTTAAAGATAGCAGATTTCTTTTTTTACACCAAATCAAATATCAAAATATTATATCTGTTG CTCAGTTGGTCTTCATGTTGCACTCTGTTTTATATTTACCTCATAGATCAGCATTGCCAGTGCT ATTTGAGTACATTGAATAGCCAAATTATGATAGTTTTTCTATGATTGCCATTACTTTTGCAACA TAAACCTACTACAGACAAAGAGACAAGGACCTGAGTTGGCATGCTAAAAAAATCATTATTCATA TCTGTCTAGCCTAGCCAAACTTGCTTGGGATTAAAAGAATTTGTTGTTTTTGTTGTACTCTATT CATATTTGATGAAAAATAACAAACTGGGAAGTTTTGCCATAGCTTAATTGACGCACTACCCCAA TATGACATTTTGAAAATGCATTGGCTCTCAAAGTCTTCTAACTGAACCCGTAATATGATGCAAC ATTTGGAAGTGATAGGTTCTAAAATGATATTGCTAGTTTAGACAAGAAAGATGCTTTTCTTACA CAACAATATATTGTATTTTTTGCTAACATAGATTTAGATGAACATAGGCCAACATTACAAGTTC AAGATCGCGTCAGTATCTAACTTTTCAATCAATAAAAACAAAGACAAAACCAACCAGTTACCAG TGCTCTACAATAGCAAATACATATCCAAGATAAGCCAATTAGCTTCCATTCCTAACCTTCAGTG TCCTGCGCTGAACAAGGTGTCCAACTATGCCCATGAGGCGATTCATTAGCTCATGTTCTTGGAT CTTTCCGTTATTTGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.057493843

Conservation Information
Conserved circRNAs	NA
PMCS	0.057493843

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							173795761-173793536(+)
173795735-173793564(+)
173795755-173793470(-)
						
						Potential amino acid sequence
						
							MFLDLSVICLNIHIIQITHLVLQCSIHCILCF*(+)
MPMRRFISSCSWIFPLFASTYISYRSHILSSNAVSIVYFVFKALLSSLAT*(+)
MNRLMGIVGHLVQRRTLKRNMKEMVESGISAKLEKADRFQRVKLEINEMIKERMATKSKVNEQD
GSADDFQVANDERRALKTKYTMDTALEDKMCDLYDMYVEANNGKIQEHELMNRLMGIVGHLVQR
RTLKRNMKEMVESGISAKLEKADRFQRVKLEINEMIKERMATKSKVNEQDGSADDFQVANDERR
ALKTKYTMDTALEDKMCDLYDMYVEANNGKIQEHELMNRLMGIVGHLVQRRTLKRNMKEMVESG
ISAKLEKADRFQRVKLEINEMIKERMATKSKVNEQDGSADDFQVANDERRALKTKYTMDTALED
KMCDLYDMYVEANNGKIQEHELMNRLMGIVGHLVQRRTLKRNMKEMVESGISAKLEKADRFQRV
KLEINEMIKERMATKSKVNEQDGSADDFQVANDERRALKTKYTMDTALEDKMCDLYDMYVE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	173795761-173793536(+) 173795735-173793564(+) 173795755-173793470(-)
Potential amino acid sequence	MFLDLSVICLNIHIIQITHLVLQCSIHCILCF(+) MPMRRFISSCSWIFPLFASTYISYRSHILSSNAVSIVYFVFKALLSSLAT(+) MNRLMGIVGHLVQRRTLKRNMKEMVESGISAKLEKADRFQRVKLEINEMIKERMATKSKVNEQD GSADDFQVANDERRALKTKYTMDTALEDKMCDLYDMYVEANNGKIQEHELMNRLMGIVGHLVQR RTLKRNMKEMVESGISAKLEKADRFQRVKLEINEMIKERMATKSKVNEQDGSADDFQVANDERR ALKTKYTMDTALEDKMCDLYDMYVEANNGKIQEHELMNRLMGIVGHLVQRRTLKRNMKEMVESG ISAKLEKADRFQRVKLEINEMIKERMATKSKVNEQDGSADDFQVANDERRALKTKYTMDTALED KMCDLYDMYVEANNGKIQEHELMNRLMGIVGHLVQRRTLKRNMKEMVESGISAKLEKADRFQRV KLEINEMIKERMATKSKVNEQDGSADDFQVANDERRALKTKYTMDTALEDKMCDLYDMYVE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b

circRNA

Detail information of Zm00001d042615_circ_g.2

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