Plant Circular RNA Database

Detail information of Zm00001d020046_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d020046_circ_g.3
					
						ID in PlantcircBase
						zma_circ_009314
					
						Alias
						Zm07circ00043, GRMZM2G126170_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr7: 88539431-88544453  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d020046						
					
						Parent gene annotation
						
							Protein SAWADEE HOMEODOMAIN HOMOLOG 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d020046_circ_g.1 Zm00001d020046_circ_g.2 Zm00001d020046_circ_g.4 Zm00001d020046_circ_g.5 						
					
						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
						Zm00001d020046_T013:1
Zm00001d020046_T005:4
Zm00001d020046_T004:4
Zm00001d020046_T010:4
Zm00001d020046_T001:1
Zm00001d020046_T002:4
Zm00001d020046_T012:2
Zm00001d020046_T006:4
Zm00001d020046_T003:3
Zm00001d020046_T007:4
Zm00001d020046_T011:3
Zm00001d020046_T009:4
Zm00001d020046_T008:4

General Information
CircRNA Name	Zm00001d020046_circ_g.3
ID in PlantcircBase	zma_circ_009314
Alias	Zm07circ00043, GRMZM2G126170_C2
Organism	Zea mays
Position	chr7: 88539431-88544453 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d020046
Parent gene annotation	Protein SAWADEE HOMEODOMAIN HOMOLOG 2
Parent gene strand	-
Alternative splicing	Zm00001d020046_circ_g.1 Zm00001d020046_circ_g.2 Zm00001d020046_circ_g.4 Zm00001d020046_circ_g.5
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	Zm00001d020046_T013:1 Zm00001d020046_T005:4 Zm00001d020046_T004:4 Zm00001d020046_T010:4 Zm00001d020046_T001:1 Zm00001d020046_T002:4 Zm00001d020046_T012:2 Zm00001d020046_T006:4 Zm00001d020046_T003:3 Zm00001d020046_T007:4 Zm00001d020046_T011:3 Zm00001d020046_T009:4 Zm00001d020046_T008:4

			
						 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  
						
							AATAAAAAAGTATGAGATATGATAATATTTTGGTACCATGCACCATCACGAGCTGACTTGGCCT
CAAACTCAACTGAGACACCTTCCATAGGGTTCTTCCctcagaagagtcatgatcatagcgaaca
agaaatctacaacggcaacctctaacatcatgccttctcctttgagcatcaaggacacgagcat
caaaatag

						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: 380
Transcript exons: 88539431-88539550,88540612-88540755,88543641-88543692,88
544390-88544453
CTCAGAAGAGTCATGATCATAGCGAACAAGAAATCTACAACGGCAACCTCTAACATCATGCCTT
CTCCTTTGAGCATCAAGGACACGAGCATCAAAATAGAGAGCCTGCTCTTTATCTTCCTGAAAAC
AAAGAATGAGGTCCCCAGGAAGCACAGCAACGCATTCTGTGGCCTCGCATGGAAGAGAACGTTG
TCGCACACATTTGCGAACATTGATCCATTCATCCTCCTCTGCCCCAAATCCAGAAAAACGAACC
CGCACTTCCGGGTCACCGGATTCAAACAACCTATGTGACAGAAAGGCAGCAACATCATACCATG
CACCATCACGAGCTGACTTGGCCTCAAACTCAACTGAGACACCTTCCATAGGGTTCTTCC
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AATAAAAAAGTATGAGATATGATAATATTTTGGTACCATGCACCATCACGAGCTGACTTGGCCT CAAACTCAACTGAGACACCTTCCATAGGGTTCTTCCctcagaagagtcatgatcatagcgaaca agaaatctacaacggcaacctctaacatcatgccttctcctttgagcatcaaggacacgagcat caaaatag
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: 380 Transcript exons: 88539431-88539550,88540612-88540755,88543641-88543692,88 544390-88544453 CTCAGAAGAGTCATGATCATAGCGAACAAGAAATCTACAACGGCAACCTCTAACATCATGCCTT CTCCTTTGAGCATCAAGGACACGAGCATCAAAATAGAGAGCCTGCTCTTTATCTTCCTGAAAAC AAAGAATGAGGTCCCCAGGAAGCACAGCAACGCATTCTGTGGCCTCGCATGGAAGAGAACGTTG TCGCACACATTTGCGAACATTGATCCATTCATCCTCCTCTGCCCCAAATCCAGAAAAACGAACC CGCACTTCCGGGTCACCGGATTCAAACAACCTATGTGACAGAAAGGCAGCAACATCATACCATG CACCATCACGAGCTGACTTGGCCTCAAACTCAACTGAGACACCTTCCATAGGGTTCTTCC
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.128839683

Conservation Information
Conserved circRNAs	NA
PMCS	0.128839683

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							88540626-88539480(+)
88544401-88544425(-)
88544444-88544425(-)
						
						Potential amino acid sequence
						
							MRSPGSTATHSVASHGRERCRTHLRTLIHSSSSAPNPEKRTRTSGSPDSNNLCDRKAATSYHAP
SRADLASNSTETPSIGFFPQKSHDHSEQEIYNGNL*(+)
MVHGMMLLPFCHIGCLNPVTRKCGFVFLDLGQRRMNGSMFANVCDNVLFHARPQNALLCFLGTS
FFVFRKIKSRLSILMLVSLMLKGEGMMLEVAVVDFLFAMIMTLLREEPYGRCLS*(-)
MEGVSVEFEAKSARDGAWYDVAAFLSHRLFESGDPEVRVRFSGFGAEEDEWINVRKCVRQRSLP
CEATECVAVLPGDLILCFQEDKEQALYFDARVLDAQRRRHDVRGCRCRFLVRYDHDSSEGRTLW
KVSQLSLRPSQLVMVHGMMLLPFCHIGCLNPVTRKCGFVFLDLGQRRMNGSMFANVCDNVLFHA
RPQNALLCFLGTSFFVFRKIKSRLSILMLVSLMLKGEGMMLEVAVVDFLFAMIMTLLREEPYGR
CLS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	88540626-88539480(+) 88544401-88544425(-) 88544444-88544425(-)
Potential amino acid sequence	MRSPGSTATHSVASHGRERCRTHLRTLIHSSSSAPNPEKRTRTSGSPDSNNLCDRKAATSYHAP SRADLASNSTETPSIGFFPQKSHDHSEQEIYNGNL(+) MVHGMMLLPFCHIGCLNPVTRKCGFVFLDLGQRRMNGSMFANVCDNVLFHARPQNALLCFLGTS FFVFRKIKSRLSILMLVSLMLKGEGMMLEVAVVDFLFAMIMTLLREEPYGRCLS(-) MEGVSVEFEAKSARDGAWYDVAAFLSHRLFESGDPEVRVRFSGFGAEEDEWINVRKCVRQRSLP CEATECVAVLPGDLILCFQEDKEQALYFDARVLDAQRRRHDVRGCRCRFLVRYDHDSSEGRTLW KVSQLSLRPSQLVMVHGMMLLPFCHIGCLNPVTRKCGFVFLDLGQRRMNGSMFANVCDNVLFHA RPQNALLCFLGTSFFVFRKIKSRLSILMLVSLMLKGEGMMLEVAVVDFLFAMIMTLLREEPYGR CLS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020;Zhang et al., 2019

circRNA

Detail information of Zm00001d020046_circ_g.3

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