Plant Circular RNA Database

Detail information of Zm00001d014640_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d014640_circ_g.4
					
						ID in PlantcircBase
						zma_circ_008493
					
						Alias
						zma_circ_0002124
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 56935985-56938681  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_T038:10
Zm00001d014640_T035:10
Zm00001d014640_T007:10
Zm00001d014640_T030:10
Zm00001d014640_T018:10
Zm00001d014640_T020:10
Zm00001d014640_T033:10
Zm00001d014640_T034:8
Zm00001d014640_T019:10
Zm00001d014640_T004:10
Zm00001d014640_T014:10
Zm00001d014640_T012:10
Zm00001d014640_T010:10
Zm00001d014640_T002:10
Zm00001d014640_T006:10
Zm00001d014640_T003:10
Zm00001d014640_T027:10
Zm00001d014640_T013:10
Zm00001d014640_T005:10
Zm00001d014640_T009:10
Zm00001d014640_T036:10
Zm00001d014640_T029:10
Zm00001d014640_T008:10
Zm00001d014640_T011:10

General Information
CircRNA Name	Zm00001d014640_circ_g.4
ID in PlantcircBase	zma_circ_008493
Alias	zma_circ_0002124
Organism	Zea mays
Position	chr5: 56935985-56938681 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_T038:10 Zm00001d014640_T035:10 Zm00001d014640_T007:10 Zm00001d014640_T030:10 Zm00001d014640_T018:10 Zm00001d014640_T020:10 Zm00001d014640_T033:10 Zm00001d014640_T034:8 Zm00001d014640_T019:10 Zm00001d014640_T004:10 Zm00001d014640_T014:10 Zm00001d014640_T012:10 Zm00001d014640_T010:10 Zm00001d014640_T002:10 Zm00001d014640_T006:10 Zm00001d014640_T003:10 Zm00001d014640_T027:10 Zm00001d014640_T013:10 Zm00001d014640_T005:10 Zm00001d014640_T009:10 Zm00001d014640_T036:10 Zm00001d014640_T029:10 Zm00001d014640_T008:10 Zm00001d014640_T011:10

			
						 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  
						
							TTTTCTATGACAGAGCATTGGCCATGCCTATGAAGATATAATGTCACAAAATCAACAATTGCTA
CAGCAGATTATTGAAAGAGATGATCATAATACCAAGaggagttgactagtgttgttgccaagtt
ggaaggaagcaaacaaaaactggcagtactgaaagcacagggagacaataaacaagcaacaccg
atcctggt

									
								

					

						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
						
							AGGAGTTGACTAGTGTTGTTGCCAAGTTGGAAGGAAGCAAACAAAAACTGGCAGTACTGAAAGC
ACAGGGAGACAATAAACAAGCAACACCGATCCTGGTTCCTACGCTGGGAAACAAAAATATGACT
GCAGAAAAGGTGAGAGATAAACAAACAGAACTGCAAGATCTTGAAGCTACTCACAAGGAGTTAA
TGGTAATGTCAAGTTCTTGTTTTAGAGCTCCAAACTATTGGCTAGGATGCTAGATGTGTATGGA
CTTTTAAGATTGACACATACAAATATGAGCAGGAATTGATTTCAAAGCGTCTGGAGGAAATTAG
AAGGCTGCATACAGAGAGAATTGAAATTTTGAACAAGTTAGCAACTTTTCAGGTTCGTTGAACC
AAATATACACGATCAAGCCCAGAACAAATTGCTTCATAGTTTTTGGACTCCCATACCTAATTTT
TATTATGTGGTTGAAAGTTAGATTTTGTAATGTCAGACTTAATATGCCCTTTTTAATCTTGTTT
TGTTGCTCCCAGAATATACTAACGGATTTCAAAAGCATTCACTCTTCCAAAGCTTTTCAACTTG
TCAATGACCAACTTCAGAAGTCACAAGCAGAACTGGATGATCACCAAACGTTGTTAGAGAAATT
ACAGGTGGTTACTGGTCAGTGCATTTGCATGTCTGTGTAGCAGATTTGTTTCCCTAAAAAATTT
CTGATTTTGGTTAAACTTCTATTTTTCATGTTTCAGGTTGAGATGGATACCTTTGTTTGGCGAG
AAAGGCAATTTAATCAAAAAGTTGATTTGGCTGAAATCCCCCAGAAGGTTTCTGCATACTGTGT
GTCTAGAATTGCTGACCTTGAAAAGGATGTCCAGAAACTGTGTAATGAAAAGAATATGCTTGTG
CTGAAACTTGAAGAGGCTTCGAGAGAACCTGGTGCTGTAATTACAACACATCAAGTTTGAAATA
CTTTTCTATCGGATCACTGTTCAAAGCAGGAAATAATATTATTTTTCTTCATCTGTCAGGTCGG
AACCAGGTTATCTCAGAGTTTAAAGCTCTGGTGTCATCACTACCGAGGGAAATGGGTGCCGTGC
AAAGTGAACTGTCCAAACACAAGGATGCTTCCTTACAGTTGCATTCTTTGCGAGCAGAAGTTCA
TTCACTTTCTAGTATCCAAACCAGAAAGGTTAGTTCCATTTTATTAGTTTGCACGATCAGTGGG
CAAGTGGAGTTGATTTGCTGATGTGTCAATTTTACATTCTGTTTTTTAGGAACAAGAAATTGAA
GAAATGTCATTTAGATCTGCCCATGCTGGATCTGATATAAGCCAACTTCAATCTCTGGTAAGCA
TCTTACTTTGGGATCTTCTTTGTATCTCGAAAACTTTTAATATTTTCTGTACTGGCTACTGAAA
GCAGATGAACTAGTATATTTGATGAATAGATGAGAGAGCTGAGGTTACATATATGTAGGGATGA
GATCTATGTGGTTTATAGAAACAGAACCAATCAGATGTCCTCATATCTCTAGCTATCCTTATAA
CTATCAATCAGACTCAATCAGGATCAATCAGGAGCTAGCTAGCCATATATGACTGATTGGGGGC
CCAAGATGACGGCAGTGAATCTGATCTGCTAACAGCTACAAATGTGCAATGCACCTACTGCATG
ATTTGTTCATGCCATTGTTTTATCTATTAACATATTTGACATATCGTAGGTCCGTGAGCTGAGG
GAAAATACACAGGAGCTTAAGCTATTTGTGGAGTTGTATAAGCATGAGTCCACTGATTCCAGGT
AGGTTCTTCTTATGTCTTAATCAAACCTTGGAATAACTTCTAGAGTGACATTTCTGGGGGTGGG
TTGCATGCTACTCGTTTATGGCAATGTTATATCTTGTAGCTCATCCTTAGTCCCAGTAGCCTGT
GTCTATCATGCTAGCTATTGCAATTCTTTTTTTTTTTTGTAATTCTTAGTGATGAAATACTTAC
TGAGCATTTAAACTTGTCTACTGTCCAGTTCATTTATTTCATGGGTACAAGTTTCTGCTATATT
CACATGTCTTACTCTCTTATGGCAGACAGCTGATGGAATCGAGAGATAGGGAACTCGCTGAATG
GGCTCGAGTTCACATTCTCAAATATTCTCTTAGTGAAAGTAAATTAGAGCAACGTGTAATTTCA
GCCAATGAAGCTGAAGCAATCTCTCAGCAGAGGTTGGCAACTGCTGAAGCTGAGATTGCTGAAT
TAGGGCAGAAGCTAGAAACTTCTAGGAGGTATTCATGCATTTTCACTCTTCCTGCTATCATTTA
GAATTTAGAAACACAATCAGAAAAGACAATTTGTTACCACTTTTTATACTGGGTGGTTCAAGAC
TGTTGCTATAGTACAGGAGGCATATTTTCTTTTTATAAAAATTTCAAGTAAAGTGATATCAGGC
GCTGGGTTTCTATGTCTCAGAGATCTAGTGAAACAATCTGATATACTGAAGTCTAAACATGAAG
AATGTGAAGCGTATGTTGTGGAGATCGAGGTGTGGACAATCTTCCATCTATACCTTCCAACCAT
GTTTATCGATGTTATATTTTCAGGCCTCAAAATGTTATTTTCTATGACAGAGCATTGGCCATGC
CTATGAAGATATAATGTCACAAAATCAACAATTGCTACAGCAGATTATTGAAAGAGATGATCAT
AATACCAAG
						
					

			
		

Sequences
Splice junction sequence	TTTTCTATGACAGAGCATTGGCCATGCCTATGAAGATATAATGTCACAAAATCAACAATTGCTA CAGCAGATTATTGAAAGAGATGATCATAATACCAAGaggagttgactagtgttgttgccaagtt ggaaggaagcaaacaaaaactggcagtactgaaagcacagggagacaataaacaagcaacaccg atcctggt
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	AGGAGTTGACTAGTGTTGTTGCCAAGTTGGAAGGAAGCAAACAAAAACTGGCAGTACTGAAAGC ACAGGGAGACAATAAACAAGCAACACCGATCCTGGTTCCTACGCTGGGAAACAAAAATATGACT GCAGAAAAGGTGAGAGATAAACAAACAGAACTGCAAGATCTTGAAGCTACTCACAAGGAGTTAA TGGTAATGTCAAGTTCTTGTTTTAGAGCTCCAAACTATTGGCTAGGATGCTAGATGTGTATGGA CTTTTAAGATTGACACATACAAATATGAGCAGGAATTGATTTCAAAGCGTCTGGAGGAAATTAG AAGGCTGCATACAGAGAGAATTGAAATTTTGAACAAGTTAGCAACTTTTCAGGTTCGTTGAACC AAATATACACGATCAAGCCCAGAACAAATTGCTTCATAGTTTTTGGACTCCCATACCTAATTTT TATTATGTGGTTGAAAGTTAGATTTTGTAATGTCAGACTTAATATGCCCTTTTTAATCTTGTTT TGTTGCTCCCAGAATATACTAACGGATTTCAAAAGCATTCACTCTTCCAAAGCTTTTCAACTTG TCAATGACCAACTTCAGAAGTCACAAGCAGAACTGGATGATCACCAAACGTTGTTAGAGAAATT ACAGGTGGTTACTGGTCAGTGCATTTGCATGTCTGTGTAGCAGATTTGTTTCCCTAAAAAATTT CTGATTTTGGTTAAACTTCTATTTTTCATGTTTCAGGTTGAGATGGATACCTTTGTTTGGCGAG AAAGGCAATTTAATCAAAAAGTTGATTTGGCTGAAATCCCCCAGAAGGTTTCTGCATACTGTGT GTCTAGAATTGCTGACCTTGAAAAGGATGTCCAGAAACTGTGTAATGAAAAGAATATGCTTGTG CTGAAACTTGAAGAGGCTTCGAGAGAACCTGGTGCTGTAATTACAACACATCAAGTTTGAAATA CTTTTCTATCGGATCACTGTTCAAAGCAGGAAATAATATTATTTTTCTTCATCTGTCAGGTCGG AACCAGGTTATCTCAGAGTTTAAAGCTCTGGTGTCATCACTACCGAGGGAAATGGGTGCCGTGC AAAGTGAACTGTCCAAACACAAGGATGCTTCCTTACAGTTGCATTCTTTGCGAGCAGAAGTTCA TTCACTTTCTAGTATCCAAACCAGAAAGGTTAGTTCCATTTTATTAGTTTGCACGATCAGTGGG CAAGTGGAGTTGATTTGCTGATGTGTCAATTTTACATTCTGTTTTTTAGGAACAAGAAATTGAA GAAATGTCATTTAGATCTGCCCATGCTGGATCTGATATAAGCCAACTTCAATCTCTGGTAAGCA TCTTACTTTGGGATCTTCTTTGTATCTCGAAAACTTTTAATATTTTCTGTACTGGCTACTGAAA GCAGATGAACTAGTATATTTGATGAATAGATGAGAGAGCTGAGGTTACATATATGTAGGGATGA GATCTATGTGGTTTATAGAAACAGAACCAATCAGATGTCCTCATATCTCTAGCTATCCTTATAA CTATCAATCAGACTCAATCAGGATCAATCAGGAGCTAGCTAGCCATATATGACTGATTGGGGGC CCAAGATGACGGCAGTGAATCTGATCTGCTAACAGCTACAAATGTGCAATGCACCTACTGCATG ATTTGTTCATGCCATTGTTTTATCTATTAACATATTTGACATATCGTAGGTCCGTGAGCTGAGG GAAAATACACAGGAGCTTAAGCTATTTGTGGAGTTGTATAAGCATGAGTCCACTGATTCCAGGT AGGTTCTTCTTATGTCTTAATCAAACCTTGGAATAACTTCTAGAGTGACATTTCTGGGGGTGGG TTGCATGCTACTCGTTTATGGCAATGTTATATCTTGTAGCTCATCCTTAGTCCCAGTAGCCTGT GTCTATCATGCTAGCTATTGCAATTCTTTTTTTTTTTTGTAATTCTTAGTGATGAAATACTTAC TGAGCATTTAAACTTGTCTACTGTCCAGTTCATTTATTTCATGGGTACAAGTTTCTGCTATATT CACATGTCTTACTCTCTTATGGCAGACAGCTGATGGAATCGAGAGATAGGGAACTCGCTGAATG GGCTCGAGTTCACATTCTCAAATATTCTCTTAGTGAAAGTAAATTAGAGCAACGTGTAATTTCA GCCAATGAAGCTGAAGCAATCTCTCAGCAGAGGTTGGCAACTGCTGAAGCTGAGATTGCTGAAT TAGGGCAGAAGCTAGAAACTTCTAGGAGGTATTCATGCATTTTCACTCTTCCTGCTATCATTTA GAATTTAGAAACACAATCAGAAAAGACAATTTGTTACCACTTTTTATACTGGGTGGTTCAAGAC TGTTGCTATAGTACAGGAGGCATATTTTCTTTTTATAAAAATTTCAAGTAAAGTGATATCAGGC GCTGGGTTTCTATGTCTCAGAGATCTAGTGAAACAATCTGATATACTGAAGTCTAAACATGAAG AATGTGAAGCGTATGTTGTGGAGATCGAGGTGTGGACAATCTTCCATCTATACCTTCCAACCAT GTTTATCGATGTTATATTTTCAGGCCTCAAAATGTTATTTTCTATGACAGAGCATTGGCCATGC CTATGAAGATATAATGTCACAAAATCAACAATTGCTACAGCAGATTATTGAAAGAGATGATCAT AATACCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.058429938

Conservation Information
Conserved circRNAs	NA
PMCS	0.058429938

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							56936108-56935990(+)
						
						Potential amino acid sequence
						
							MTAEKVRDKQTELQDLEATHKELMELISKRLEEIRRLHTERIEILNKLATFQNILTDFKSIHSS
KAFQLVNDQLQKSQAELDDHQTLLEKLQVEMDTFVWRERQFNQKVDLAEIPQKVSAYCVSRIAD
LEKDVQKLCNEKNMLVLKLEEASREPGRNQVISEFKALVSSLPREMGAVQSELSKHKDASLQLH
SLRAEVHSLSSIQTRKEQEIEEMSFRSAHAGSDISQLQSLVRELRENTQELKLFVELYKHESTD
SRQLMESRDRELAEWARVHILKYSLSESKLEQRVISANEAEAISQQRLATAEAEIAELGQKLET
SRRDLVKQSDILKSKHEECEAYVVEIESIGHAYEDIMSQNQQLLQQIIERDDHNTKRS*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	56936108-56935990(+)
Potential amino acid sequence	MTAEKVRDKQTELQDLEATHKELMELISKRLEEIRRLHTERIEILNKLATFQNILTDFKSIHSS KAFQLVNDQLQKSQAELDDHQTLLEKLQVEMDTFVWRERQFNQKVDLAEIPQKVSAYCVSRIAD LEKDVQKLCNEKNMLVLKLEEASREPGRNQVISEFKALVSSLPREMGAVQSELSKHKDASLQLH SLRAEVHSLSSIQTRKEQEIEEMSFRSAHAGSDISQLQSLVRELRENTQELKLFVELYKHESTD SRQLMESRDRELAEWARVHILKYSLSESKLEQRVISANEAEAISQQRLATAEAEIAELGQKLET SRRDLVKQSDILKSKHEECEAYVVEIESIGHAYEDIMSQNQQLLQQIIERDDHNTKRS*(+)
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.4

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