Plant Circular RNA Database

Detail information of Zm00001d028038_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d028038_circ_g.3
					
						ID in PlantcircBase
						zma_circ_006425
					
						Alias
						zma_circ_0000386
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 21188147-21191416  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d028038						
					
						Parent gene annotation
						
							Methionine--tRNA ligase chloroplastic/mitochondrial
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d028038_circ_g.1 Zm00001d028038_circ_g.2 						
					
						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
						Zm00001d028038_T006:4
Zm00001d028038_T002:4
Zm00001d028038_T008:4
Zm00001d028038_T004:4
Zm00001d028038_T007:4
Zm00001d028038_T001:1
Zm00001d028038_T005:4
Zm00001d028038_T003:4

General Information
CircRNA Name	Zm00001d028038_circ_g.3
ID in PlantcircBase	zma_circ_006425
Alias	zma_circ_0000386
Organism	Zea mays
Position	chr1: 21188147-21191416 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d028038
Parent gene annotation	Methionine--tRNA ligase chloroplastic/mitochondrial
Parent gene strand	+
Alternative splicing	Zm00001d028038_circ_g.1 Zm00001d028038_circ_g.2
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	Zm00001d028038_T006:4 Zm00001d028038_T002:4 Zm00001d028038_T008:4 Zm00001d028038_T004:4 Zm00001d028038_T007:4 Zm00001d028038_T001:1 Zm00001d028038_T005:4 Zm00001d028038_T003:4

			
						 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  
						
							TAAGGGACTTTTCTATTTCTCGTGCATCTGTAGAATGGGGCATTCCGGTGCCAAACGATACCAA
GCAGACAATATATGTGTGGTTTGATGCTCTATTAGGaggttgctagagaagaatgttatattta
ttaccggaacagatgaacacggtgagaaaatatctgcttccgcagaggccagtggtagaaaccc
aaaggagc

									
								

					

						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: 594
Transcript exons: 21188147-21188290,21188391-21188540,21189437-21189604,21
191285-21191416
AGGTTGCTAGAGAAGAATGTTATATTTATTACCGGAACAGATGAACACGGTGAGAAAATATCTG
CTTCCGCAGAGGCCAGTGGTAGAAACCCAAAGGAGCATTGTGATGCAATTTCAAGTTCATATAG
GACGCTCTGGGCTGACTTAGACATAGAATATGACAAGTTTATTCGCACAACGGATCGTAAGCAT
GAGGCTGTTGTGAACGAATTCTATTCCAGAGTGTTAAACAATGGCGACATATATAGAGCTGATT
ATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGGATGAAAAAGAGCTATTGGAGAACAA
TTGTTGCCCTGTGCATCTGAAGCCTTGTGTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTG
TCAAAGTACCAACATAAATTGGAAGAGCTACTGACAAGAAATCCTGATTTTGTAAGGCCATCAT
ATCGCTTGAACGAGCTTGTAGGTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTT
CTCGTGCATCTGTAGAATGGGGCATTCCGGTGCCAAACGATACCAAGCAGACAATATATGTGTG
GTTTGATGCTCTATTAGG
						
					

						Genomic sequence
						
							AGGTTGCTAGAGAAGAATGTTATATTTATTACCGGAACAGATGAACACGGTGAGAAAATATCTG
CTTCCGCAGAGGCCAGTGGTAGAAACCCAAAGGAGCATTGTGATGCAATTTCAAGTTCATATAG
GACGCTCTGGGCTGACGTATGTCTACAACACCAAGTTTCAGTTTACAATACTTTTTACTACAGA
GTAAACCATGAGCTCAGCTTTGCCCTCCAAATTTGTTTCACATTTCTTGCAGTTAGACATAGAA
TATGACAAGTTTATTCGCACAACGGATCGTAAGCATGAGGCTGTTGTGAACGAATTCTATTCCA
GAGTGTTAAACAATGGCGACATATATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGA
AGAGTACAAGGTAAGCTTTCATGTCAACTTCCTCACATCGTACTGAGCTGTTTCCAATCCATTA
TGGAAGTACCATTAAACATATTAATCCTTACACATATTTGATTTAATGCTGTCATATGGTTAAT
AGAATTGTCTACTAAGTGGTTTTCTGAGCAACATTTTTTTTTCTGGATTTACATGGATAAATAT
CTTGGCTATCTGTCCATTTTAGGTGAGGGAACTGGTACCTATGTCGATTGCCATGCCTAACCTC
TCTTAAGTATGAATTTGGATTAATGGTGTGGTTTAATTTTTTGGCTCTTCAATTTTTTTATTAA
CAATCAATATTGTGGAACTGCAAAACTTGATATTTTTATGCAGCAGAGATGAGTACTATACTAT
TATGTGCTCTATTTTAGTTTTCTACTTCCTCTGATACATCATATTAGTCCATTAGGAATTTAGG
ACATCGACATTGTCTCCAATATAACACTTTGACTAACAATATGTATTAGGAAAATGTTACTATA
AATAAAAAATATAATGCAACAGTATTTTCATGATCAATCTATTTATGTCAATAAGAAGGACAAG
CCTGACGCAGTGGTGAGAAGCCTTTCCACTGAGCCAAACGTCCTGGGTTAGATGCAGCCTCTCT
GCAAAAATGCAGGGTAAGGCTTGGTTCGGTTATTCTTACTCCTTCCCCAGACCCCACTCATGTG
GGAGCCGCTAGCACCAAGTCTGTCCTTTTTAAATCTATTTATGTCAATCTTGTGTTGTCAATAA
ATACTCCTTTTTAGAAATTGTTGGCTAAAGTAAGAAAATGTTCGAAGTACTTTTTTGTGTGCCA
TGTGCACCTATATATATCAACCCTCTTTTTAATACTACTACAAATACTGATGCTTTAGTATTGA
CTGAACAAAGGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCTTGT
GTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTGTCAAAGTACCAACATAAATTGGAAGAGC
TACTGACAAGAAATCCTGATTTTGTAAGGCCATCATATCGCTTGAACGAGGTGAGGTTTTAGTC
CTATTTTTATATGCTATTGTTCAATGTTTTTGTTATTGTTGAGTTACTATAAACCATCACAAAT
TGTGGTGGGAAATGTAAAACTGTTTTTTTTTTGTTAGAATGTATGCCAGGTGACTCAAGCATAG
ACACTAGAAACAAGTCCAAAAAACAAAGTTGACATATGTCTTCATGAAGCTTTGACACAATTTT
CGTGATCATGCCTGTGTTGTCAAGCATTTACTAACCAAACAACGCGATTTCATTTGATCATTGC
TTTTCTGAAGTACTTTGGCATATTCAACAAAAATACATGCAATACATTTTCTTATGCATATCAT
GTCTGGTAGTGACCTAGATGACACCGCGACAAGGTTAAAGATAGAGACCATGATGACAGTACTT
ATCAGTTCTGGACAAAGAGAACTGCCAGCATTGCTCTATATAGGGGATAGGGGAAAGCAAACTC
ATTAGTTAATAGACAGAGAGAGCAACTTCAGGTGTTTCTTATAATTAACTTGCTAAACCAATAA
GGGTGTGTTTGGTTTGACTTTTGGCTTTGGCTTTTGCCCCCTAAAAGCCAAAAGCCAACCAAAG
GGCTGGATCCAGGAAGCAGGTTTTTCTAAAAGCCGACTTTCTTGTAGTGCAAATCTGAAAGCAC
CCCTGGACCTGCTTTTAGTGGCTTTTCGGATGGAACTATGAAAACATATATTGGAGAATTTTTA
ACGACTTTTAGTGGTTTCCACCAAACGGTTTTTAGCTTTTTAACAGCTTACAGCCTACAACAGC
TTTTTCCACAGCTCACAGCTCACAGCAACTTTTTTTCACAGCCACAGCCCAACCAAAATAAGTA
GCAACCTCAATTTATTTTCTCTCCATTAGGTTCCTGTATTAGCTTCCTAAACGATTTTGCATTG
GGAACCCAAACTATTTCTAAACAACCAAACCTCTTTTAATAGTTTTTGTCTTTTACTGTTTCCT
CACCTGGAACCCTTTATTTTCTTAATTTACTCATGTGTCCAATTTACTCCGATTTCCCAAGGCA
AACGCCGGATGGCTAGCGGATATAGGAGTTCCTCTTGACTGAAACTTATGAGTTGGAGAGAATA
TTTGGTAACCTTTATTTTAAGGAGTTCTTTTACCAAACTGTTGGAGGGGACTTTTCCCTTTTTG
CTAAAAAAATCAAATTAGGAAGCTGTTTCATAAAACTCCTGGAGATGCTCTGAAGAGGCTATGA
GGAACAAACTGTTCCTTTTTATTCTTAGTTTGTGCAGTTGTACCAGTATATTACTGATTGTGAT
TGTAAACCAAGCTAGTAAGTTTTTGGTGCCTGAAATTTTTTCCTTTGCTGTTGCAAGGTAAGCT
TGCCTTGACTCCTCAAATCACATATGCTCATAGGTGCATGTGCATGTTGAGAGCAAGGTCTGGC
AATAGTTGTAACGTTTTTGTGTAGTGAACTGGCATCTTACTAAGTTTGCAGTGTTGGCATCACC
ATTTTATTTGTATTGGATTCAATTTTCAATAGGGGACTCACTATCATTATCGTTTATCGAATAA
AATATTCATATTTTAGCTTCTAAGGGCAACATAACCTGGGTTGCTTCATTTCTTGTCAATCTTT
CTGTTTGTATGTGCTTATTTTCATAGTTTTACAATGTACCTATTTCTTAGTCTCACGAAGGCAC
AGCTTGTAGGTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTTCTCGTGCATCTG
TAGAATGGGGCATTCCGGTGCCAAACGATACCAAGCAGACAATATATGTGTGGTTTGATGCTCT
ATTAGG
						
					

			
		

Sequences
Splice junction sequence	TAAGGGACTTTTCTATTTCTCGTGCATCTGTAGAATGGGGCATTCCGGTGCCAAACGATACCAA GCAGACAATATATGTGTGGTTTGATGCTCTATTAGGaggttgctagagaagaatgttatattta ttaccggaacagatgaacacggtgagaaaatatctgcttccgcagaggccagtggtagaaaccc aaaggagc
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: 594 Transcript exons: 21188147-21188290,21188391-21188540,21189437-21189604,21 191285-21191416 AGGTTGCTAGAGAAGAATGTTATATTTATTACCGGAACAGATGAACACGGTGAGAAAATATCTG CTTCCGCAGAGGCCAGTGGTAGAAACCCAAAGGAGCATTGTGATGCAATTTCAAGTTCATATAG GACGCTCTGGGCTGACTTAGACATAGAATATGACAAGTTTATTCGCACAACGGATCGTAAGCAT GAGGCTGTTGTGAACGAATTCTATTCCAGAGTGTTAAACAATGGCGACATATATAGAGCTGATT ATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGGATGAAAAAGAGCTATTGGAGAACAA TTGTTGCCCTGTGCATCTGAAGCCTTGTGTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTG TCAAAGTACCAACATAAATTGGAAGAGCTACTGACAAGAAATCCTGATTTTGTAAGGCCATCAT ATCGCTTGAACGAGCTTGTAGGTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTT CTCGTGCATCTGTAGAATGGGGCATTCCGGTGCCAAACGATACCAAGCAGACAATATATGTGTG GTTTGATGCTCTATTAGG
Genomic sequence	AGGTTGCTAGAGAAGAATGTTATATTTATTACCGGAACAGATGAACACGGTGAGAAAATATCTG CTTCCGCAGAGGCCAGTGGTAGAAACCCAAAGGAGCATTGTGATGCAATTTCAAGTTCATATAG GACGCTCTGGGCTGACGTATGTCTACAACACCAAGTTTCAGTTTACAATACTTTTTACTACAGA GTAAACCATGAGCTCAGCTTTGCCCTCCAAATTTGTTTCACATTTCTTGCAGTTAGACATAGAA TATGACAAGTTTATTCGCACAACGGATCGTAAGCATGAGGCTGTTGTGAACGAATTCTATTCCA GAGTGTTAAACAATGGCGACATATATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGA AGAGTACAAGGTAAGCTTTCATGTCAACTTCCTCACATCGTACTGAGCTGTTTCCAATCCATTA TGGAAGTACCATTAAACATATTAATCCTTACACATATTTGATTTAATGCTGTCATATGGTTAAT AGAATTGTCTACTAAGTGGTTTTCTGAGCAACATTTTTTTTTCTGGATTTACATGGATAAATAT CTTGGCTATCTGTCCATTTTAGGTGAGGGAACTGGTACCTATGTCGATTGCCATGCCTAACCTC TCTTAAGTATGAATTTGGATTAATGGTGTGGTTTAATTTTTTGGCTCTTCAATTTTTTTATTAA CAATCAATATTGTGGAACTGCAAAACTTGATATTTTTATGCAGCAGAGATGAGTACTATACTAT TATGTGCTCTATTTTAGTTTTCTACTTCCTCTGATACATCATATTAGTCCATTAGGAATTTAGG ACATCGACATTGTCTCCAATATAACACTTTGACTAACAATATGTATTAGGAAAATGTTACTATA AATAAAAAATATAATGCAACAGTATTTTCATGATCAATCTATTTATGTCAATAAGAAGGACAAG CCTGACGCAGTGGTGAGAAGCCTTTCCACTGAGCCAAACGTCCTGGGTTAGATGCAGCCTCTCT GCAAAAATGCAGGGTAAGGCTTGGTTCGGTTATTCTTACTCCTTCCCCAGACCCCACTCATGTG GGAGCCGCTAGCACCAAGTCTGTCCTTTTTAAATCTATTTATGTCAATCTTGTGTTGTCAATAA ATACTCCTTTTTAGAAATTGTTGGCTAAAGTAAGAAAATGTTCGAAGTACTTTTTTGTGTGCCA TGTGCACCTATATATATCAACCCTCTTTTTAATACTACTACAAATACTGATGCTTTAGTATTGA CTGAACAAAGGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCTTGT GTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTGTCAAAGTACCAACATAAATTGGAAGAGC TACTGACAAGAAATCCTGATTTTGTAAGGCCATCATATCGCTTGAACGAGGTGAGGTTTTAGTC CTATTTTTATATGCTATTGTTCAATGTTTTTGTTATTGTTGAGTTACTATAAACCATCACAAAT TGTGGTGGGAAATGTAAAACTGTTTTTTTTTTGTTAGAATGTATGCCAGGTGACTCAAGCATAG ACACTAGAAACAAGTCCAAAAAACAAAGTTGACATATGTCTTCATGAAGCTTTGACACAATTTT CGTGATCATGCCTGTGTTGTCAAGCATTTACTAACCAAACAACGCGATTTCATTTGATCATTGC TTTTCTGAAGTACTTTGGCATATTCAACAAAAATACATGCAATACATTTTCTTATGCATATCAT GTCTGGTAGTGACCTAGATGACACCGCGACAAGGTTAAAGATAGAGACCATGATGACAGTACTT ATCAGTTCTGGACAAAGAGAACTGCCAGCATTGCTCTATATAGGGGATAGGGGAAAGCAAACTC ATTAGTTAATAGACAGAGAGAGCAACTTCAGGTGTTTCTTATAATTAACTTGCTAAACCAATAA GGGTGTGTTTGGTTTGACTTTTGGCTTTGGCTTTTGCCCCCTAAAAGCCAAAAGCCAACCAAAG GGCTGGATCCAGGAAGCAGGTTTTTCTAAAAGCCGACTTTCTTGTAGTGCAAATCTGAAAGCAC CCCTGGACCTGCTTTTAGTGGCTTTTCGGATGGAACTATGAAAACATATATTGGAGAATTTTTA ACGACTTTTAGTGGTTTCCACCAAACGGTTTTTAGCTTTTTAACAGCTTACAGCCTACAACAGC TTTTTCCACAGCTCACAGCTCACAGCAACTTTTTTTCACAGCCACAGCCCAACCAAAATAAGTA GCAACCTCAATTTATTTTCTCTCCATTAGGTTCCTGTATTAGCTTCCTAAACGATTTTGCATTG GGAACCCAAACTATTTCTAAACAACCAAACCTCTTTTAATAGTTTTTGTCTTTTACTGTTTCCT CACCTGGAACCCTTTATTTTCTTAATTTACTCATGTGTCCAATTTACTCCGATTTCCCAAGGCA AACGCCGGATGGCTAGCGGATATAGGAGTTCCTCTTGACTGAAACTTATGAGTTGGAGAGAATA TTTGGTAACCTTTATTTTAAGGAGTTCTTTTACCAAACTGTTGGAGGGGACTTTTCCCTTTTTG CTAAAAAAATCAAATTAGGAAGCTGTTTCATAAAACTCCTGGAGATGCTCTGAAGAGGCTATGA GGAACAAACTGTTCCTTTTTATTCTTAGTTTGTGCAGTTGTACCAGTATATTACTGATTGTGAT TGTAAACCAAGCTAGTAAGTTTTTGGTGCCTGAAATTTTTTCCTTTGCTGTTGCAAGGTAAGCT TGCCTTGACTCCTCAAATCACATATGCTCATAGGTGCATGTGCATGTTGAGAGCAAGGTCTGGC AATAGTTGTAACGTTTTTGTGTAGTGAACTGGCATCTTACTAAGTTTGCAGTGTTGGCATCACC ATTTTATTTGTATTGGATTCAATTTTCAATAGGGGACTCACTATCATTATCGTTTATCGAATAA AATATTCATATTTTAGCTTCTAAGGGCAACATAACCTGGGTTGCTTCATTTCTTGTCAATCTTT CTGTTTGTATGTGCTTATTTTCATAGTTTTACAATGTACCTATTTCTTAGTCTCACGAAGGCAC AGCTTGTAGGTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTTCTCGTGCATCTG TAGAATGGGGCATTCCGGTGCCAAACGATACCAAGCAGACAATATATGTGTGGTTTGATGCTCT ATTAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.072025717

Conservation Information
Conserved circRNAs	NA
PMCS	0.072025717

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21188400-21191331(-)
						
						Potential amino acid sequence
						
							MSKSAQSVLYELEIASQCSFGFLPLASAEADIFSPCSSVPVINITFFSSNLLIEHQTTHILSAW
YRLAPECPILQMHEK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21188400-21191331(-)
Potential amino acid sequence	MSKSAQSVLYELEIASQCSFGFLPLASAEADIFSPCSSVPVINITFFSSNLLIEHQTTHILSAW YRLAPECPILQMHEK*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d028038_circ_g.3

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