Plant Circular RNA Database

Detail information of Zm00001d014640_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d014640_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008492
					
						Alias
						zma_circ_0002123
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 56934467-56935661  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d014640						
					
						Parent gene annotation
						
							E3 ubiquitin-protein ligase BRE1-like 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf, 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  
						
							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
						Zm00001d014640_T027:4
Zm00001d014640_T013:2
Zm00001d014640_T011:4
Zm00001d014640_T009:4
Zm00001d014640_T035:4
Zm00001d014640_T007:4
Zm00001d014640_T008:3
Zm00001d014640_T005:4
Zm00001d014640_T030:4
Zm00001d014640_T012:3
Zm00001d014640_T020:4
Zm00001d014640_T019:4
Zm00001d014640_T018:4
Zm00001d014640_T038:4
Zm00001d014640_T006:4
Zm00001d014640_T014:4
Zm00001d014640_T003:3
Zm00001d014640_T036:4
Zm00001d014640_T034:4
Zm00001d014640_T029:4
Zm00001d014640_T004:4
Zm00001d014640_T002:4
Zm00001d014640_T033:4
Zm00001d014640_T010:4

General Information
CircRNA Name	Zm00001d014640_circ_g.3
ID in PlantcircBase	zma_circ_008492
Alias	zma_circ_0002123
Organism	Zea mays
Position	chr5: 56934467-56935661 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d014640
Parent gene annotation	E3 ubiquitin-protein ligase BRE1-like 1
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
Tissues	leaf, 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	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	Zm00001d014640_T027:4 Zm00001d014640_T013:2 Zm00001d014640_T011:4 Zm00001d014640_T009:4 Zm00001d014640_T035:4 Zm00001d014640_T007:4 Zm00001d014640_T008:3 Zm00001d014640_T005:4 Zm00001d014640_T030:4 Zm00001d014640_T012:3 Zm00001d014640_T020:4 Zm00001d014640_T019:4 Zm00001d014640_T018:4 Zm00001d014640_T038:4 Zm00001d014640_T006:4 Zm00001d014640_T014:4 Zm00001d014640_T003:3 Zm00001d014640_T036:4 Zm00001d014640_T034:4 Zm00001d014640_T029:4 Zm00001d014640_T004:4 Zm00001d014640_T002:4 Zm00001d014640_T033:4 Zm00001d014640_T010:4

			
						 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  
						
							GTAGATAATCTTCACTTGAAACACAGGCAGTTAGCAGCGAACTATCAAAAACAAAGAGATTCGA
GTGCCTGGAACAGAGCTGAACAGAAACGTCTGAAAGcttgattttgctgtgcttaaatacaaaa
accaaaagcttgcggaacaactggaagtccacaaatttgagttctgtgctcttgagagtagatt
taatgatc

						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
						
							CTTGATTTTGCTGTGCTTAAATACAAAAACCAAAAGCTTGCGGAACAACTGGAAGTCCACAAAT
TTGAGTTCTGTGCTCTTGAGAGTAGATTTAATGATCTAAAAGAGAAACAAAGGACACATAATAA
GACACTTGTTCTAGTCAAAAGTTATTGGGAGCGAGTAAGTTGTTCTAACCTTGCTTATGTTACT
GTAACATACACACACACATCATATAAGCTCTCTGCTGAAATTCCCTTATCCAAACAGCTCATAG
CAGATCTGGGTATAGTTTCTGTTTGCAAAAATGAATCTTCACGTTCAAGCTGCAGTACAGGGAA
CAACAATATACGAAAGGGTATGTGATTATACTTTATGCATTATGAATATATTGGATATTGCATT
GTTCTAGAGTCATACATGGAAGGATTCTATGATGTCTCTGGCTGCTGTTGGCTTATACTTCTTT
CTACTAATGGAATGAAGTAGTAGTATTTTGAAACATTTTCTATTTGAGGTGTTTGTAGTTCTTC
GCTCTTTCAAAAGTAAATTTATGACAAGGGATCTATATGCATGCCTTCAGAACTAGCGTTACCA
ATTAATGATTGTTAACAGATATTTTTTTTATTCGAATAGCAAGCTACTATAGCCTTTGCTGATT
TATGCTGTCTACTTTAGATGTGTCTTATTTTTTCATTTTATCCTTCATACACATGCACATCTTA
TTTTTCGGATGGTATATGCTTTCACCTAGAAACAGACTTTTTAAATGGACTTTTGGAGGCTGGT
GCCACAGAAAGTTCAGGTTCTCCCAATTGCCAACTAGGAAATGACGTCTCTTCAGAACAATCAA
CAACAATTGATATTCTGCAGAAGCTATTCCTTCCATCAAGTGGTCCATGGCATGTGAATAACGA
GTTTGTTTCTGCTGCTCTCATGAAGTTGCCAGAAAATGGTTTGTTCTACTCTATATTTTCTGTT
GTAGAATAGCTTTTATGCGTCATTCAAAGTATGCTAAATTTTTCCTTAATTTTCTCATGTTCTC
TAGAACACAGCAGGCAATTGCACAATGCTACCAGCGATGTGTTATCCAAGCTTCATGTGGTGAT
GCGTACAGTAGATAATCTTCACTTGAAACACAGGCAGTTAGCAGCGAACTATCAAAAACAAAGA
GATTCGAGTGCCTGGAACAGAGCTGAACAGAAACGTCTGAAAG

Sequences
Splice junction sequence	GTAGATAATCTTCACTTGAAACACAGGCAGTTAGCAGCGAACTATCAAAAACAAAGAGATTCGA GTGCCTGGAACAGAGCTGAACAGAAACGTCTGAAAGcttgattttgctgtgcttaaatacaaaa accaaaagcttgcggaacaactggaagtccacaaatttgagttctgtgctcttgagagtagatt taatgatc
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	CTTGATTTTGCTGTGCTTAAATACAAAAACCAAAAGCTTGCGGAACAACTGGAAGTCCACAAAT TTGAGTTCTGTGCTCTTGAGAGTAGATTTAATGATCTAAAAGAGAAACAAAGGACACATAATAA GACACTTGTTCTAGTCAAAAGTTATTGGGAGCGAGTAAGTTGTTCTAACCTTGCTTATGTTACT GTAACATACACACACACATCATATAAGCTCTCTGCTGAAATTCCCTTATCCAAACAGCTCATAG CAGATCTGGGTATAGTTTCTGTTTGCAAAAATGAATCTTCACGTTCAAGCTGCAGTACAGGGAA CAACAATATACGAAAGGGTATGTGATTATACTTTATGCATTATGAATATATTGGATATTGCATT GTTCTAGAGTCATACATGGAAGGATTCTATGATGTCTCTGGCTGCTGTTGGCTTATACTTCTTT CTACTAATGGAATGAAGTAGTAGTATTTTGAAACATTTTCTATTTGAGGTGTTTGTAGTTCTTC GCTCTTTCAAAAGTAAATTTATGACAAGGGATCTATATGCATGCCTTCAGAACTAGCGTTACCA ATTAATGATTGTTAACAGATATTTTTTTTATTCGAATAGCAAGCTACTATAGCCTTTGCTGATT TATGCTGTCTACTTTAGATGTGTCTTATTTTTTCATTTTATCCTTCATACACATGCACATCTTA TTTTTCGGATGGTATATGCTTTCACCTAGAAACAGACTTTTTAAATGGACTTTTGGAGGCTGGT GCCACAGAAAGTTCAGGTTCTCCCAATTGCCAACTAGGAAATGACGTCTCTTCAGAACAATCAA CAACAATTGATATTCTGCAGAAGCTATTCCTTCCATCAAGTGGTCCATGGCATGTGAATAACGA GTTTGTTTCTGCTGCTCTCATGAAGTTGCCAGAAAATGGTTTGTTCTACTCTATATTTTCTGTT GTAGAATAGCTTTTATGCGTCATTCAAAGTATGCTAAATTTTTCCTTAATTTTCTCATGTTCTC TAGAACACAGCAGGCAATTGCACAATGCTACCAGCGATGTGTTATCCAAGCTTCATGTGGTGAT GCGTACAGTAGATAATCTTCACTTGAAACACAGGCAGTTAGCAGCGAACTATCAAAAACAAAGA GATTCGAGTGCCTGGAACAGAGCTGAACAGAAACGTCTGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.064145028

Conservation Information
Conserved circRNAs	NA
PMCS	0.064145028

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							56935383-56934468(+)
						
						Potential amino acid sequence
						
							MKLPENEHSRQLHNATSDVLSKLHVVMRTVDNLHLKHRQLAANYQKQRDSSAWNRAEQKRLKA*
(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	56935383-56934468(+)
Potential amino acid sequence	MKLPENEHSRQLHNATSDVLSKLHVVMRTVDNLHLKHRQLAANYQKQRDSSAWNRAEQKRLKA* (+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d014640_circ_g.3

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