Plant Circular RNA Database

Detail information of Zm00001d023238_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d023238_circ_g.2
					
						ID in PlantcircBase
						zma_circ_010131
					
						Alias
						Zm10circ00001, GRMZM2G176546_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 1112079-1112358  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d023238						
					
						Parent gene annotation
						
							Long chain acyl-CoA synthetase 6 peroxisomal
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d023238_circ_g.1 						
					
						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
						Zm00001d023238_T004:2
Zm00001d023238_T003:2
Zm00001d023238_T001:2
Zm00001d023238_T008:1
Zm00001d023238_T006:2
Zm00001d023238_T010:2
Zm00001d023238_T005:1
Zm00001d023238_T002:2

General Information
CircRNA Name	Zm00001d023238_circ_g.2
ID in PlantcircBase	zma_circ_010131
Alias	Zm10circ00001, GRMZM2G176546_C1
Organism	Zea mays
Position	chr10: 1112079-1112358 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d023238
Parent gene annotation	Long chain acyl-CoA synthetase 6 peroxisomal
Parent gene strand	+
Alternative splicing	Zm00001d023238_circ_g.1
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	Zm00001d023238_T004:2 Zm00001d023238_T003:2 Zm00001d023238_T001:2 Zm00001d023238_T008:1 Zm00001d023238_T006:2 Zm00001d023238_T010:2 Zm00001d023238_T005:1 Zm00001d023238_T002:2

			
						 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  
						
							TCGATCTGTAGGATTACAAATGCTGTGAAGGAGTCTGGTGGGCTGAAAGAAAAATTGTTTCATA
CTGCATACAATGCCAAGAGACAAGCAATCCTTAAAGgataatttgaagctcatggatgatctgg
ctgctttgagaccgacaatattcgcaagtgttccccggttatataacagaatttatactgcgta
ataaaact

						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: 178
Transcript exons: 1112079-1112167,1112270-1112358
GATAATTTGAAGCTCATGGATGATCTGGCTGCTTTGAGACCGACAATATTCGCAAGTGTTCCCC
GGTTATATAACAGAATTTATACTGCGATTACAAATGCTGTGAAGGAGTCTGGTGGGCTGAAAGA
AAAATTGTTTCATACTGCATACAATGCCAAGAGACAAGCAATCCTTAAAG
Transcript length: 280
Transcript exons: 1112079-1112358
GATAATTTGAAGCTCATGGATGATCTGGCTGCTTTGAGACCGACAATATTCGCAAGTGTTCCCC
GGTTATATAACAGAATTTATACTGCGTAATAAAACTGTATCAATAACTTCTATGTTTGGTATAA
ATTCTTGAAGTGATATGATCTGTTCATAATGCTAACAATACTAGTTGCTTATTCGATCTGTAGG
ATTACAAATGCTGTGAAGGAGTCTGGTGGGCTGAAAGAAAAATTGTTTCATACTGCATACAATG
CCAAGAGACAAGCAATCCTTAAAG
						
						Genomic sequence
						
							GATAATTTGAAGCTCATGGATGATCTGGCTGCTTTGAGACCGACAATATTCGCAAGTGTTCCCC
GGTTATATAACAGAATTTATACTGCGTAATAAAACTGTATCAATAACTTCTATGTTTGGTATAA
ATTCTTGAAGTGATATGATCTGTTCATAATGCTAACAATACTAGTTGCTTATTCGATCTGTAGG
ATTACAAATGCTGTGAAGGAGTCTGGTGGGCTGAAAGAAAAATTGTTTCATACTGCATACAATG
CCAAGAGACAAGCAATCCTTAAAG

Sequences
Splice junction sequence	TCGATCTGTAGGATTACAAATGCTGTGAAGGAGTCTGGTGGGCTGAAAGAAAAATTGTTTCATA CTGCATACAATGCCAAGAGACAAGCAATCCTTAAAGgataatttgaagctcatggatgatctgg ctgctttgagaccgacaatattcgcaagtgttccccggttatataacagaatttatactgcgta ataaaact
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: 178 Transcript exons: 1112079-1112167,1112270-1112358 GATAATTTGAAGCTCATGGATGATCTGGCTGCTTTGAGACCGACAATATTCGCAAGTGTTCCCC GGTTATATAACAGAATTTATACTGCGATTACAAATGCTGTGAAGGAGTCTGGTGGGCTGAAAGA AAAATTGTTTCATACTGCATACAATGCCAAGAGACAAGCAATCCTTAAAG Transcript length: 280 Transcript exons: 1112079-1112358 GATAATTTGAAGCTCATGGATGATCTGGCTGCTTTGAGACCGACAATATTCGCAAGTGTTCCCC GGTTATATAACAGAATTTATACTGCGTAATAAAACTGTATCAATAACTTCTATGTTTGGTATAA ATTCTTGAAGTGATATGATCTGTTCATAATGCTAACAATACTAGTTGCTTATTCGATCTGTAGG ATTACAAATGCTGTGAAGGAGTCTGGTGGGCTGAAAGAAAAATTGTTTCATACTGCATACAATG CCAAGAGACAAGCAATCCTTAAAG
Genomic sequence	GATAATTTGAAGCTCATGGATGATCTGGCTGCTTTGAGACCGACAATATTCGCAAGTGTTCCCC GGTTATATAACAGAATTTATACTGCGTAATAAAACTGTATCAATAACTTCTATGTTTGGTATAA ATTCTTGAAGTGATATGATCTGTTCATAATGCTAACAATACTAGTTGCTTATTCGATCTGTAGG ATTACAAATGCTGTGAAGGAGTCTGGTGGGCTGAAAGAAAAATTGTTTCATACTGCATACAATG CCAAGAGACAAGCAATCCTTAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.278027124

Conservation Information
Conserved circRNAs	NA
PMCS	0.278027124

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1112095-1112080(+)
1112333-1112080(+)
1112097-1112147(-)
						
						Potential amino acid sequence
						
							MDDLAALRPTIFASVPRLYNRIYTAITNAVKESGGLKEKLFHTAYNAKRQAILKG*(+)
MPRDKQSLKDNLKLMDDLAALRPTIFASVPRLYNRIYTAITNAVKESGGLKEKLFHTAYNAKRQ
AILKG*(+)
MSFKLSFKDCLSLGIVCSMKQFFFQPTRLLHSICNRSINSVI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	1112095-1112080(+) 1112333-1112080(+) 1112097-1112147(-)
Potential amino acid sequence	MDDLAALRPTIFASVPRLYNRIYTAITNAVKESGGLKEKLFHTAYNAKRQAILKG(+) MPRDKQSLKDNLKLMDDLAALRPTIFASVPRLYNRIYTAITNAVKESGGLKEKLFHTAYNAKRQ AILKG(+) MSFKLSFKDCLSLGIVCSMKQFFFQPTRLLHSICNRSINSVI*(-)
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 Zm00001d023238_circ_g.2

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