Plant Circular RNA Database

Detail information of Zm00001d026127_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d026127_circ_g.2
					
						ID in PlantcircBase
						zma_circ_010341
					
						Alias
						Zm10circ00063, GRMZM2G084491_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 139197995-139199265  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d026127						
					
						Parent gene annotation
						
							Patched family protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d026127_circ_igg.1 Zm00001d026127_circ_ag.1 Zm00001d026127_circ_ag.2 Zm00001d026127_circ_igg.3 Zm00001d026127_circ_igg.4 Zm00001d026127_circ_igg.5 Zm00001d026127_circ_igg.6 						
					
						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  
						
							GT-AG							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
						Zm00001d026127_T001:4

General Information
CircRNA Name	Zm00001d026127_circ_g.2
ID in PlantcircBase	zma_circ_010341
Alias	Zm10circ00063, GRMZM2G084491_C1
Organism	Zea mays
Position	chr10: 139197995-139199265 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d026127
Parent gene annotation	Patched family protein
Parent gene strand	+
Alternative splicing	Zm00001d026127_circ_igg.1 Zm00001d026127_circ_ag.1 Zm00001d026127_circ_ag.2 Zm00001d026127_circ_igg.3 Zm00001d026127_circ_igg.4 Zm00001d026127_circ_igg.5 Zm00001d026127_circ_igg.6
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	GT-AG 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	Zm00001d026127_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  
						
							TGCTTCATGGCTTGATGACTTCCTAATTTGGATGTCCCCTGAAGCATTTGGATGCTGTAGAAAA
TTTGTGAATGGAAGTTACTGCCCTCCAGACGATCAGgcattatctactagactgcaaccaggat
tggagcagcaaattgttctgccacgaaattcctatttacaggtttccccctaaagagttttgag
ttcttctt

									
								

					

						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: 366
Transcript exons: 139197995-139198063,139198137-139198213,139198746-139198
815,139199116-139199265
GCATTATCTACTAGACTGCAACCAGGATTGGAGCAGCAAATTGTTCTGCCACGAAATTCCTATT
TACAGGATTATTTTGATGACCTTGCAAAGTACATGAAAGTAGGTCCACCATTATACTTTGTTGT
GAAGGACTTCAATTACAGCTCTGCGTCGGTGGATACAAATCAAATATGTTCAATCAGCCAGTGT
AATTCAAATTCTCTTTTGAATGAGATATCACGACAATCATTATCCCCTGAGACTAGTTACATTG
CTAAACCTGCTGCTTCATGGCTTGATGACTTCCTAATTTGGATGTCCCCTGAAGCATTTGGATG
CTGTAGAAAATTTGTGAATGGAAGTTACTGCCCTCCAGACGATCAG
						
					

						Genomic sequence
						
							GCATTATCTACTAGACTGCAACCAGGATTGGAGCAGCAAATTGTTCTGCCACGAAATTCCTATT
TACAGGTTTCCCCCTAAAGAGTTTTGAGTTCTTCTTGAGGTGCCTTCCTTCAGATCACTCTGAT
CATTGTATTTCCAGGATTATTTTGATGACCTTGCAAAGTACATGAAAGTAGGTCCACCATTATA
CTTTGTTGTGAAGGACTTCAATTACAGGTATTTATGTATAAAAATAGTGCTCCCAAAGTTTATC
AAAGAAAAGAGTCACACTACGTGCAAATATACAAAATGTAATATTGACTCTTCCATCTTGCTTA
GTTCTTCAAATATGGTCAAGTCACTGTCATTTGTTGTTGGTGTGACAAATGTCACAAATGTTGC
ATATGATATATGCTTTCTTTCTTATGGAGAAAAAATAACATGCTGAATAACTGAACTTTCAGGT
TTCGATCATTCCTGATATGGTCATATAATAACAATAATAGCAAATCTTTTTGTTCCTGATATGC
AAAAAAGTTTTATAAAACAAAGTTTCTTATGTTGATTGACATGGTACAATTTAGTTTCTCTGTT
TGGTATACAAGTACAATGTGTTGAACTAAATAGGGACGGTGGAGATCCTTAAGGTCGCCGAATT
GCACCCAGAACATTATTTTCTCAAGCACACCCTGAAGCTCTTTTTTAAGTTGCATGCTTAAACA
GTGGTAGCCATGCTTGATTTATGATTTATTTTTATATTGTTTTCCAGCTCTGCGTCGGTGGATA
CAAATCAAATATGTTCAATCAGCCAGTGTAATTCAAATTCTCTTTTGAATGAGGTATATTATAT
TATCTTACTATGTTTTAACAAAGTTATGTTCCAGAATATCTTCAGTAGTAAATTACTCTTAGCT
CAGTTTACCAGTGCAATATATATCAGAGATGTGTTTGTTTATTACTCCCTCCATTCTTTTTTAT
TTGTCGTGTTTTAGTTAAAAAATAAGCTAGCGGGTGACAAATATTCGAGAATGGAGGGTAGTAT
AAGGTTACCCAGTGCAGGGTGCACACTGCAAACTGAGTATCCGGTACAACAGTTCATTTTGTTG
TGAAGATTGCATAACATGGTTTCAATCATGCAGATATCACGACAATCATTATCCCCTGAGACTA
GTTACATTGCTAAACCTGCTGCTTCATGGCTTGATGACTTCCTAATTTGGATGTCCCCTGAAGC
ATTTGGATGCTGTAGAAAATTTGTGAATGGAAGTTACTGCCCTCCAGACGATCAG
						
					

			
		

Sequences
Splice junction sequence	TGCTTCATGGCTTGATGACTTCCTAATTTGGATGTCCCCTGAAGCATTTGGATGCTGTAGAAAA TTTGTGAATGGAAGTTACTGCCCTCCAGACGATCAGgcattatctactagactgcaaccaggat tggagcagcaaattgttctgccacgaaattcctatttacaggtttccccctaaagagttttgag ttcttctt
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: 366 Transcript exons: 139197995-139198063,139198137-139198213,139198746-139198 815,139199116-139199265 GCATTATCTACTAGACTGCAACCAGGATTGGAGCAGCAAATTGTTCTGCCACGAAATTCCTATT TACAGGATTATTTTGATGACCTTGCAAAGTACATGAAAGTAGGTCCACCATTATACTTTGTTGT GAAGGACTTCAATTACAGCTCTGCGTCGGTGGATACAAATCAAATATGTTCAATCAGCCAGTGT AATTCAAATTCTCTTTTGAATGAGATATCACGACAATCATTATCCCCTGAGACTAGTTACATTG CTAAACCTGCTGCTTCATGGCTTGATGACTTCCTAATTTGGATGTCCCCTGAAGCATTTGGATG CTGTAGAAAATTTGTGAATGGAAGTTACTGCCCTCCAGACGATCAG
Genomic sequence	GCATTATCTACTAGACTGCAACCAGGATTGGAGCAGCAAATTGTTCTGCCACGAAATTCCTATT TACAGGTTTCCCCCTAAAGAGTTTTGAGTTCTTCTTGAGGTGCCTTCCTTCAGATCACTCTGAT CATTGTATTTCCAGGATTATTTTGATGACCTTGCAAAGTACATGAAAGTAGGTCCACCATTATA CTTTGTTGTGAAGGACTTCAATTACAGGTATTTATGTATAAAAATAGTGCTCCCAAAGTTTATC AAAGAAAAGAGTCACACTACGTGCAAATATACAAAATGTAATATTGACTCTTCCATCTTGCTTA GTTCTTCAAATATGGTCAAGTCACTGTCATTTGTTGTTGGTGTGACAAATGTCACAAATGTTGC ATATGATATATGCTTTCTTTCTTATGGAGAAAAAATAACATGCTGAATAACTGAACTTTCAGGT TTCGATCATTCCTGATATGGTCATATAATAACAATAATAGCAAATCTTTTTGTTCCTGATATGC AAAAAAGTTTTATAAAACAAAGTTTCTTATGTTGATTGACATGGTACAATTTAGTTTCTCTGTT TGGTATACAAGTACAATGTGTTGAACTAAATAGGGACGGTGGAGATCCTTAAGGTCGCCGAATT GCACCCAGAACATTATTTTCTCAAGCACACCCTGAAGCTCTTTTTTAAGTTGCATGCTTAAACA GTGGTAGCCATGCTTGATTTATGATTTATTTTTATATTGTTTTCCAGCTCTGCGTCGGTGGATA CAAATCAAATATGTTCAATCAGCCAGTGTAATTCAAATTCTCTTTTGAATGAGGTATATTATAT TATCTTACTATGTTTTAACAAAGTTATGTTCCAGAATATCTTCAGTAGTAAATTACTCTTAGCT CAGTTTACCAGTGCAATATATATCAGAGATGTGTTTGTTTATTACTCCCTCCATTCTTTTTTAT TTGTCGTGTTTTAGTTAAAAAATAAGCTAGCGGGTGACAAATATTCGAGAATGGAGGGTAGTAT AAGGTTACCCAGTGCAGGGTGCACACTGCAAACTGAGTATCCGGTACAACAGTTCATTTTGTTG TGAAGATTGCATAACATGGTTTCAATCATGCAGATATCACGACAATCATTATCCCCTGAGACTA GTTACATTGCTAAACCTGCTGCTTCATGGCTTGATGACTTCCTAATTTGGATGTCCCCTGAAGC ATTTGGATGCTGTAGAAAATTTGTGAATGGAAGTTACTGCCCTCCAGACGATCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.178459716

Conservation Information
Conserved circRNAs	NA
PMCS	0.178459716

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							139198165-139199262(+)
139199238-139198164(+)
139198000-139199158(-)
						
						Potential amino acid sequence
						
							MKVGPPLYFVVKDFNYSSASVDTNQICSISQCNSNSLLNEISRQSLSPETSYIAKPAASWLDDF
LIWMSPEAFGCCRKFVNGSYCPPDDQALSTRLQPGLEQQIVLPRNSYLQDYFDDLAKYMKVGPP
LYFVVKDFNYSSASVDTNQICSISQCNSNSLLNEISRQSLSPETSYIAKPAASWLDDFLIWMSP
EAFGCCRKFVNGSYCPPDDQALSTRLQPGLEQQIVLPRNSYLQDYFDDLAKYMKVGPPLYFVVK
DFNYSSASVDTNQICSISQCNSNSLLNEISRQSLSPETSYIAKPAASWLDDFLIWMSPEAFGCC
RKFVNGSYCPPDDQALSTRLQPGLEQQIVLPRNSYLQDYFDDLAKYMKVGPPLYFVVKDFNYSS
ASVDTNQICSISQCNSNSLLNEISRQSLSPETSYIAKPAASWLDDFLIWMSPEAFGCCRKFVNG
SYCPPDDQ(+)
MEVTALQTIRHYLLDCNQDWSSKLFCHEIPIYRIILMTLQST*(+)
MPDRLEGSNFHSQIFYSIQMLQGTSKLGSHQAMKQQV*(-)
						
						Sponge-miRNAs
						
							zma-miR167h-3p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	139198165-139199262(+) 139199238-139198164(+) 139198000-139199158(-)
Potential amino acid sequence	MKVGPPLYFVVKDFNYSSASVDTNQICSISQCNSNSLLNEISRQSLSPETSYIAKPAASWLDDF LIWMSPEAFGCCRKFVNGSYCPPDDQALSTRLQPGLEQQIVLPRNSYLQDYFDDLAKYMKVGPP LYFVVKDFNYSSASVDTNQICSISQCNSNSLLNEISRQSLSPETSYIAKPAASWLDDFLIWMSP EAFGCCRKFVNGSYCPPDDQALSTRLQPGLEQQIVLPRNSYLQDYFDDLAKYMKVGPPLYFVVK DFNYSSASVDTNQICSISQCNSNSLLNEISRQSLSPETSYIAKPAASWLDDFLIWMSPEAFGCC RKFVNGSYCPPDDQALSTRLQPGLEQQIVLPRNSYLQDYFDDLAKYMKVGPPLYFVVKDFNYSS ASVDTNQICSISQCNSNSLLNEISRQSLSPETSYIAKPAASWLDDFLIWMSPEAFGCCRKFVNG SYCPPDDQ(+) MEVTALQTIRHYLLDCNQDWSSKLFCHEIPIYRIILMTLQST(+) MPDRLEGSNFHSQIFYSIQMLQGTSKLGSHQAMKQQV(-)
Sponge-miRNAs	zma-miR167h-3p
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 Zm00001d026127_circ_g.2

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