Plant Circular RNA Database

Detail information of Zm00001d041880_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d041880_circ_g.3
					
						ID in PlantcircBase
						zma_circ_001405
					
						Alias
						circ1730, leafdr_test_circ_002820
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 142140827-142142879  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRCexplor2, find_circ
					
						Parent gene
						
							Zm00001d041880						
					
						Parent gene annotation
						
							Beta-galactosidase 9
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d041880_circ_g.2 Zm00001d041880_circ_g.4 Zm00001d041880_circ_g.5 						
					
						Support reads
						113
					
						Tissues
						seedling leaves, leaf
					
						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  
						
							GT-CA							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
						Zm00001d041880_T006:5
Zm00001d041880_T010:4
Zm00001d041880_T009:4
Zm00001d041880_T005:4
Zm00001d041880_T004:4
Zm00001d041880_T001:4
Zm00001d041880_T002:5

General Information
CircRNA Name	Zm00001d041880_circ_g.3
ID in PlantcircBase	zma_circ_001405
Alias	circ1730, leafdr_test_circ_002820
Organism	Zea mays
Position	chr3: 142140827-142142879 JBrowse»
Reference genome	AGPv4.38
Type	ui-circRNA
Identification method	CIRCexplor2, find_circ
Parent gene	Zm00001d041880
Parent gene annotation	Beta-galactosidase 9
Parent gene strand	+
Alternative splicing	Zm00001d041880_circ_g.2 Zm00001d041880_circ_g.4 Zm00001d041880_circ_g.5
Support reads	113
Tissues	seedling leaves, leaf
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	GT-CA 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	Zm00001d041880_T006:5 Zm00001d041880_T010:4 Zm00001d041880_T009:4 Zm00001d041880_T005:4 Zm00001d041880_T004:4 Zm00001d041880_T001:4 Zm00001d041880_T002:5

			
						 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  
						
							CTTTTTGGCAGCTCAATACTTGCAATGCCTTTTACTGTGATGGGTTCAAACCAAATTCCTACAA
CAAGCCAACAATATGGACTGAGGATTGGGATGGATGgtggtttcccagtttggttgcgcgatgt
ccctgggatagaattccgcactgacaatgaaccctacaaggtagatgaaccactaagcatagat
tttgtctt

									
								

					

						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
						
							GTGGTTTCCCAGTTTGGTTGCGCGATGTCCCTGGGATAGAATTCCGCACTGACAATGAACCCTA
CAAGGTAGATGAACCACTAAGCATAGATTTTGTCTTCCTATGATGAACATTTTTCATTTATTTG
AATTCACTAATCCTTAAAATTGTCGTACAGGCTGAAATGCAGATTTTTGTGACAAAAATTGTAG
ATATCATGAAAGAGGAGAAGCTTTATTCTTGGCAAGGTGGTCCCATTATACTGCAGCAGGTCTG
AAAACTTTTCTCGAAGTTCACTTATTGGTGTTTCTTTTCTCCTCCCTCCCTCCCTCCTAGGAGA
CCCCTTGCATAAAGCACTCTATCTTGTTGAGGAGACGAGAGAGGTTCAGGTTTGGACAATTGGA
CAAATAAAGAAACCATCTGAAAAGAGGAAAAAACCCGGACTCAACCAGGGCTGGTTATTAAACC
CTCAACAAGACCTAGACCATGTTCTTGAAGTTTACGTAATGTATACATGTCTTAGGGGTGTCTT
TAGTACAACTTCGTCTTCCGTCATCCCCTTAGCGTCATCTTTCATCATGCGTAGGCGTATGCCT
TGTACGGTGTATTGCCCTGCCCCCTCCGGCGTATGGGTCACTGTAGAGACCCTGATGCTGAGGT
CTCTATGGCTGGAGCCTTCTGGTCCCACTAGTCAGCGGGGATACGTATCCGGCGTCGTGCTTTG
ACAGAGACCTCTCGGTACCGCTTCCACAGTCTGGGCATGGCTCGGTGATGTCCCATCGTGTCGA
CGTGGCTTGATAGTACTAGGTGGGCTCTTCTTGAGAGCCGGCTGTCGTTTTGCTGGGTTGCTCG
GCAGCCTCGCCTCGTTGGGTTGCTCAGCGGGCAGGTTGCTCGGCAGCCTCGTCTCGTTGGGTTG
CTTCGCGGGCAGGTTGCTCGGTAGCCCCGCCTCGCTGGGTTGCTCGGCGGACATTAGTTCGTTG
GGCCGATCGGCTTGGTAGGCCGTCCCTGGGCGGCCTTTTGGTCTTTCCCGCCGATTTGTTTGGC
AGGCGGGCTGCTCGGTTCGTGGGTTGTCTTTGGGAGGCCTTCGGGCCTTCTTTGGGTACCCTGT
TTCCAGGTACCCAACAGTTAGCTAAGCTATCACCCATTAATCAGTACACAGAGATCTGAAAAAT
ATCAATGACAAGTGGATATTATGTTATATGTGGCTTAAGTAATTTTTGGTTGGTGCCATTTGGT
GACAACATTGCTTAGTATCTTTGATGTTCAGTTAATTCCTTTGTTTAATAAAACTGTTAGATGG
CGTTCTATATATGGATGGTGCTCATGATAGAGTTAAACATTGAACCATAATGTGGTAAAGGATA
CAATTCTGAAGTATGTTATGTAGCCAAAAGCTAGATGCTGGCTGTTTTACCTTCTGAAGTAGCA
ATACTTATGGTGTTGGCTCTGTGCTCTAGTTAATTCAGCACAAACACCTGAAATTTGGTGGATG
TAAGAGGCTCATATTAATAAAAACTTGACCAATCTAGGAGGAACTAGGCATCTTTTACTTTTAG
TAAGAAGAAAAAGGCACTGAAATTTGACTGGGAAAGGACTTGAACATGAGTGGTCAACCAAATG
AGCAGGTCTCAGTTTCTTAAGAGTTAAGAGGCTTATATTCATGCTTAATGTGTCAGTTGAATTA
TGTATTACATTAAAATGCGTATAATTGTTTTGTCTGAAAAATGTTTGACAGATTGAAAATGAAT
ACGGTAACATTCAAGGCCATTATGGTCAAGCAGGGAAGAGATACATGCTATGGGCAGCTCAGAT
GGCACTTGCACTTGATACTGGTGTTCCTTGGGTAATGTGTAGGCAAACAGATGCTCCAGAACAA
ATTGTAGGTTGCCTCAAAATCTATTGAGATCGACTTCACATTACATTAGAGATTGTCAAATGTG
CTTACTGCAAAGTAAATAGATTACTGCCTTGTCCTTTTTGGCAGCTCAATACTTGCAATGCCTT
TTACTGTGATGGGTTCAAACCAAATTCCTACAACAAGCCAACAATATGGACTGAGGATTGGGAT
GGATG
						
					

			
		

Sequences
Splice junction sequence	CTTTTTGGCAGCTCAATACTTGCAATGCCTTTTACTGTGATGGGTTCAAACCAAATTCCTACAA CAAGCCAACAATATGGACTGAGGATTGGGATGGATGgtggtttcccagtttggttgcgcgatgt ccctgggatagaattccgcactgacaatgaaccctacaaggtagatgaaccactaagcatagat tttgtctt
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	GTGGTTTCCCAGTTTGGTTGCGCGATGTCCCTGGGATAGAATTCCGCACTGACAATGAACCCTA CAAGGTAGATGAACCACTAAGCATAGATTTTGTCTTCCTATGATGAACATTTTTCATTTATTTG AATTCACTAATCCTTAAAATTGTCGTACAGGCTGAAATGCAGATTTTTGTGACAAAAATTGTAG ATATCATGAAAGAGGAGAAGCTTTATTCTTGGCAAGGTGGTCCCATTATACTGCAGCAGGTCTG AAAACTTTTCTCGAAGTTCACTTATTGGTGTTTCTTTTCTCCTCCCTCCCTCCCTCCTAGGAGA CCCCTTGCATAAAGCACTCTATCTTGTTGAGGAGACGAGAGAGGTTCAGGTTTGGACAATTGGA CAAATAAAGAAACCATCTGAAAAGAGGAAAAAACCCGGACTCAACCAGGGCTGGTTATTAAACC CTCAACAAGACCTAGACCATGTTCTTGAAGTTTACGTAATGTATACATGTCTTAGGGGTGTCTT TAGTACAACTTCGTCTTCCGTCATCCCCTTAGCGTCATCTTTCATCATGCGTAGGCGTATGCCT TGTACGGTGTATTGCCCTGCCCCCTCCGGCGTATGGGTCACTGTAGAGACCCTGATGCTGAGGT CTCTATGGCTGGAGCCTTCTGGTCCCACTAGTCAGCGGGGATACGTATCCGGCGTCGTGCTTTG ACAGAGACCTCTCGGTACCGCTTCCACAGTCTGGGCATGGCTCGGTGATGTCCCATCGTGTCGA CGTGGCTTGATAGTACTAGGTGGGCTCTTCTTGAGAGCCGGCTGTCGTTTTGCTGGGTTGCTCG GCAGCCTCGCCTCGTTGGGTTGCTCAGCGGGCAGGTTGCTCGGCAGCCTCGTCTCGTTGGGTTG CTTCGCGGGCAGGTTGCTCGGTAGCCCCGCCTCGCTGGGTTGCTCGGCGGACATTAGTTCGTTG GGCCGATCGGCTTGGTAGGCCGTCCCTGGGCGGCCTTTTGGTCTTTCCCGCCGATTTGTTTGGC AGGCGGGCTGCTCGGTTCGTGGGTTGTCTTTGGGAGGCCTTCGGGCCTTCTTTGGGTACCCTGT TTCCAGGTACCCAACAGTTAGCTAAGCTATCACCCATTAATCAGTACACAGAGATCTGAAAAAT ATCAATGACAAGTGGATATTATGTTATATGTGGCTTAAGTAATTTTTGGTTGGTGCCATTTGGT GACAACATTGCTTAGTATCTTTGATGTTCAGTTAATTCCTTTGTTTAATAAAACTGTTAGATGG CGTTCTATATATGGATGGTGCTCATGATAGAGTTAAACATTGAACCATAATGTGGTAAAGGATA CAATTCTGAAGTATGTTATGTAGCCAAAAGCTAGATGCTGGCTGTTTTACCTTCTGAAGTAGCA ATACTTATGGTGTTGGCTCTGTGCTCTAGTTAATTCAGCACAAACACCTGAAATTTGGTGGATG TAAGAGGCTCATATTAATAAAAACTTGACCAATCTAGGAGGAACTAGGCATCTTTTACTTTTAG TAAGAAGAAAAAGGCACTGAAATTTGACTGGGAAAGGACTTGAACATGAGTGGTCAACCAAATG AGCAGGTCTCAGTTTCTTAAGAGTTAAGAGGCTTATATTCATGCTTAATGTGTCAGTTGAATTA TGTATTACATTAAAATGCGTATAATTGTTTTGTCTGAAAAATGTTTGACAGATTGAAAATGAAT ACGGTAACATTCAAGGCCATTATGGTCAAGCAGGGAAGAGATACATGCTATGGGCAGCTCAGAT GGCACTTGCACTTGATACTGGTGTTCCTTGGGTAATGTGTAGGCAAACAGATGCTCCAGAACAA ATTGTAGGTTGCCTCAAAATCTATTGAGATCGACTTCACATTACATTAGAGATTGTCAAATGTG CTTACTGCAAAGTAAATAGATTACTGCCTTGTCCTTTTTGGCAGCTCAATACTTGCAATGCCTT TTACTGTGATGGGTTCAAACCAAATTCCTACAACAAGCCAACAATATGGACTGAGGATTGGGAT GGATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_009687 						
					
						PMCS
						0.087797841

Conservation Information
Conserved circRNAs	osi_circ_009687
PMCS	0.087797841

			
						 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; Tang et al., 2018

circRNA

Detail information of Zm00001d041880_circ_g.3

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