Plant Circular RNA Database

Detail information of Zm00001d014340_circ_g.7

			
						 General Information
					
						CircRNA Name
						Zm00001d014340_circ_g.7
					
						ID in PlantcircBase
						zma_circ_008466
					
						Alias
						Zm05circ00039, zma_circ_0001814, GRMZM2G151195_C3
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 41564347-41565107  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d014340						
					
						Parent gene annotation
						
							Whole genome shotgun sequence of line PN40024 scaffold_7.assembl
y12x (Fragment)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d014340_circ_g.1 Zm00001d014340_circ_g.2 Zm00001d014340_circ_g.3 Zm00001d014340_circ_g.4 Zm00001d014340_circ_g.5 Zm00001d014340_circ_g.6 						
					
						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
						Zm00001d014340_T001:2
Zm00001d014340_T009:2
Zm00001d014340_T012:2
Zm00001d014340_T005:2
Zm00001d014340_T004:2
Zm00001d014340_T007:2
Zm00001d014340_T010:3
Zm00001d014340_T014:2
Zm00001d014340_T002:2
Zm00001d014340_T013:2

General Information
CircRNA Name	Zm00001d014340_circ_g.7
ID in PlantcircBase	zma_circ_008466
Alias	Zm05circ00039, zma_circ_0001814, GRMZM2G151195_C3
Organism	Zea mays
Position	chr5: 41564347-41565107 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d014340
Parent gene annotation	Whole genome shotgun sequence of line PN40024 scaffold_7.assembl y12x (Fragment)
Parent gene strand	-
Alternative splicing	Zm00001d014340_circ_g.1 Zm00001d014340_circ_g.2 Zm00001d014340_circ_g.3 Zm00001d014340_circ_g.4 Zm00001d014340_circ_g.5 Zm00001d014340_circ_g.6
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	Zm00001d014340_T001:2 Zm00001d014340_T009:2 Zm00001d014340_T012:2 Zm00001d014340_T005:2 Zm00001d014340_T004:2 Zm00001d014340_T007:2 Zm00001d014340_T010:3 Zm00001d014340_T014:2 Zm00001d014340_T002:2 Zm00001d014340_T013:2

			
						 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  
						
							ACCTTGAACAGTACAAATTCTTGCGAGCATGCTCAATAAGGGTCTGTTTATCAAGTCTTAACAG
CTCATGTCGTGCATGAGGTGACAGGGCACTCCAAAActgtgcataagtctttcaatgaagtcct
cttctttcatccttaaaagagatgatctagtttcttcacccagagccgaccaaaaatccaccag
agtatcac

						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: 575
Transcript exons: 41564347-41564606,41564793-41565107
CTGTGCATAAGTCTTTCAATGAAGTCCTCTTCTTTCATCCTTAAAAGAGATGATCTAGTTTCTT
CACCCAGAGCCGACCAAAAATCCACCAGAGTATCACAAGAAAGGTGTGCAGTGTGCAAAGCACA
GGTATCTCGTGTTCCATGGCCCCTGCCATAGTTAGGTATCACTGGGCTAATCCATCCTCTGCCA
CCGCCACCACATGCATCAGGGTAAAGCATCTCACGTTCACGTTCTCTCGCACGTGCATTGTCAA
ATACATTCTGGATCACATGAAGAGATTTTGCATTTATGAAGCAATCAAGAAGAGTTAGGATGCC
ATCCTTTGTTGTCGAAAGACCTCCCCAAGGATGAACTGAAGGTTCCTGAACTTCTGCTTCAACT
TCCTGAATCCTTGGCTCACATGAACCTTCATGAAGCAGAGACTTCCCATACATGACTATTTGTG
TGAAACTTTCCAAAAGCAACCCATTACACCTTGAACAGTACAAATTCTTGCGAGCATGCTCAAT
AAGGGTCTGTTTATCAAGTCTTAACAGCTCATGTCGTGCATGAGGTGACAGGGCACTCCAAAA
						
						Genomic sequence
						
							CTGTGCATAAGTCTTTCAATGAAGTCCTCTTCTTTCATCCTTAAAAGAGATGATCTAGTTTCTT
CACCCAGAGCCGACCAAAAATCCACCAGAGTATCACAAGAAAGGTGTGCAGTGTGCAAAGCACA
GGTATCTCGTGTTCCATGGCCCCTGCCATAGTTAGGTATCACTGGGCTAATCCATCCTCTGCCA
CCGCCACCACATGCATCAGGGTAAAGCATCTCACGTTCACGTTCTCTCGCACGTGCATTGTCAA
ATACCTAGTCACAACAATATGGATTACATCATAGTAAGAAATCTAGAATCATCATGGAACAACT
TCATAGAAGGAATGCCACAGAAAGATGCCAAAACAGACAATTGGAAAGCACATAAAAAATCAAG
GAAGAAGTTCATGAACCAGATAAGGGAGATAAAGAAAGCAAAGGCAACTGTTTCAGGCGTACAT
TCTGGATCACATGAAGAGATTTTGCATTTATGAAGCAATCAAGAAGAGTTAGGATGCCATCCTT
TGTTGTCGAAAGACCTCCCCAAGGATGAACTGAAGGTTCCTGAACTTCTGCTTCAACTTCCTGA
ATCCTTGGCTCACATGAACCTTCATGAAGCAGAGACTTCCCATACATGACTATTTGTGTGAAAC
TTTCCAAAAGCAACCCATTACACCTTGAACAGTACAAATTCTTGCGAGCATGCTCAATAAGGGT
CTGTTTATCAAGTCTTAACAGCTCATGTCGTGCATGAGGTGACAGGGCACTCCAAAA

Sequences
Splice junction sequence	ACCTTGAACAGTACAAATTCTTGCGAGCATGCTCAATAAGGGTCTGTTTATCAAGTCTTAACAG CTCATGTCGTGCATGAGGTGACAGGGCACTCCAAAActgtgcataagtctttcaatgaagtcct cttctttcatccttaaaagagatgatctagtttcttcacccagagccgaccaaaaatccaccag agtatcac
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: 575 Transcript exons: 41564347-41564606,41564793-41565107 CTGTGCATAAGTCTTTCAATGAAGTCCTCTTCTTTCATCCTTAAAAGAGATGATCTAGTTTCTT CACCCAGAGCCGACCAAAAATCCACCAGAGTATCACAAGAAAGGTGTGCAGTGTGCAAAGCACA GGTATCTCGTGTTCCATGGCCCCTGCCATAGTTAGGTATCACTGGGCTAATCCATCCTCTGCCA CCGCCACCACATGCATCAGGGTAAAGCATCTCACGTTCACGTTCTCTCGCACGTGCATTGTCAA ATACATTCTGGATCACATGAAGAGATTTTGCATTTATGAAGCAATCAAGAAGAGTTAGGATGCC ATCCTTTGTTGTCGAAAGACCTCCCCAAGGATGAACTGAAGGTTCCTGAACTTCTGCTTCAACT TCCTGAATCCTTGGCTCACATGAACCTTCATGAAGCAGAGACTTCCCATACATGACTATTTGTG TGAAACTTTCCAAAAGCAACCCATTACACCTTGAACAGTACAAATTCTTGCGAGCATGCTCAAT AAGGGTCTGTTTATCAAGTCTTAACAGCTCATGTCGTGCATGAGGTGACAGGGCACTCCAAAA
Genomic sequence	CTGTGCATAAGTCTTTCAATGAAGTCCTCTTCTTTCATCCTTAAAAGAGATGATCTAGTTTCTT CACCCAGAGCCGACCAAAAATCCACCAGAGTATCACAAGAAAGGTGTGCAGTGTGCAAAGCACA GGTATCTCGTGTTCCATGGCCCCTGCCATAGTTAGGTATCACTGGGCTAATCCATCCTCTGCCA CCGCCACCACATGCATCAGGGTAAAGCATCTCACGTTCACGTTCTCTCGCACGTGCATTGTCAA ATACCTAGTCACAACAATATGGATTACATCATAGTAAGAAATCTAGAATCATCATGGAACAACT TCATAGAAGGAATGCCACAGAAAGATGCCAAAACAGACAATTGGAAAGCACATAAAAAATCAAG GAAGAAGTTCATGAACCAGATAAGGGAGATAAAGAAAGCAAAGGCAACTGTTTCAGGCGTACAT TCTGGATCACATGAAGAGATTTTGCATTTATGAAGCAATCAAGAAGAGTTAGGATGCCATCCTT TGTTGTCGAAAGACCTCCCCAAGGATGAACTGAAGGTTCCTGAACTTCTGCTTCAACTTCCTGA ATCCTTGGCTCACATGAACCTTCATGAAGCAGAGACTTCCCATACATGACTATTTGTGTGAAAC TTTCCAAAAGCAACCCATTACACCTTGAACAGTACAAATTCTTGCGAGCATGCTCAATAAGGGT CTGTTTATCAAGTCTTAACAGCTCATGTCGTGCATGAGGTGACAGGGCACTCCAAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.143292444

Conservation Information
Conserved circRNAs	NA
PMCS	0.143292444

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							41564971-41565067(-)
						
						Potential amino acid sequence
						
							MYGKSLLHEGSCEPRIQEVEAEVQEPSVHPWGGLSTTKDGILTLLDCFINAKSLHVIQNVFDNA
RAREREREMLYPDACGGGGRGWISPVIPNYGRGHGTRDTCALHTAHLSCDTLVDFWSALGEETR
SSLLRMKEEDFIERLMHSFGVPCHLMHDMSC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	41564971-41565067(-)
Potential amino acid sequence	MYGKSLLHEGSCEPRIQEVEAEVQEPSVHPWGGLSTTKDGILTLLDCFINAKSLHVIQNVFDNA RAREREREMLYPDACGGGGRGWISPVIPNYGRGHGTRDTCALHTAHLSCDTLVDFWSALGEETR SSLLRMKEEDFIERLMHSFGVPCHLMHDMSC*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d014340_circ_g.7

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