Plant Circular RNA Database

Detail information of Zm00001d034766_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d034766_circ_g.1
					
						ID in PlantcircBase
						zma_circ_006977
					
						Alias
						Zm01circ00192
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 301669254-301672663  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d034766						
					
						Parent gene annotation
						
							Lysine--tRNA ligase chloroplastic/mitochondrial
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d034764_circ_g.1 Zm00001d034764_circ_ag.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  
						
							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
						Zm00001d034766_T001:3

General Information
CircRNA Name	Zm00001d034766_circ_g.1
ID in PlantcircBase	zma_circ_006977
Alias	Zm01circ00192
Organism	Zea mays
Position	chr1: 301669254-301672663 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d034766
Parent gene annotation	Lysine--tRNA ligase chloroplastic/mitochondrial
Parent gene strand	-
Alternative splicing	Zm00001d034764_circ_g.1 Zm00001d034764_circ_ag.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	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	Zm00001d034766_T001:3

			
						 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  
						
							TAACGTTTGTCCACATCAGTTAATCCATGATACTTATCTGGTAGTGGGAGTAATGATTTTGTGA
GAATTTCGAAATTTTTCACATAAACAGATAGCTCCCctgtagaactggagtttcgacttcaata
aaaccaaatgattccattgtcttgcggatttcagaaaccacctatcaaaaatgcaatatcgaag
ttcaaagt

									
								

					

						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: 236
Transcript exons: 301669254-301669322,301670190-301670247,301672555-301672
663
CTGTAGAACTGGAGTTTCGACTTCAATAAAACCAAATGATTCCATTGTCTTGCGGATTTCAGAA
ACCACCTTTGCCCTAGTTCGGAATACATCAGCGACCTTAGGGTTTGCAATCATGTCAACATACC
TTTGACGATAACGTTTGTCCACATCAGTTAATCCATGATACTTATCTGGTAGTGGGAGTAATGA
TTTTGTGAGAATTTCGAAATTTTTCACATAAACAGATAGCTCCC
						
					

						Genomic sequence
						
							CTGTAGAACTGGAGTTTCGACTTCAATAAAACCAAATGATTCCATTGTCTTGCGGATTTCAGAA
ACCACCTATCAAAAATGCAATATCGAAGTTCAAAGTAAAAGAAGCTATAGCGAATTATGTCAGT
GATGCAACTACTGGTTAAGGTAGTTATTTTTCGAGGACCAACAATATGATAATGTATGCCTTAG
TTTCTTTTTTCATACCAAAACTCCCTCAATCCATTAAGAAAAATATGCTCCTGTGCTACATGAT
ATTTAGGGCCCGTTTGGCACAGCTCCAGCTCCTGATTCTAAGCGAGGATCTGGAGGAGCCGTGC
CAAACAGGTATTTTTTTAAACTGATTCTCGTGTGGAGCCGAAAGATCAGGAGTCGTTTTTGTGA
AGAAAGGTGGGATCTAAAAAAACCTGCTCCACCCTCCCTTAAAACAGCTCCTCAACCAACCAAA
TATGGATCTCCTCTTAAAATTTGATCGAAATTACCCGCAATTGCCATTGGACAAAAACATAACG
AGCCAATTTATGGATTAAACATTTGAGACCATTTTATGCACTACTATGATTGGAATATTTTATA
TGTTATTGTTTCATATTTTTTTCCCGTATATGCATCCTACTTATTGGTTTGTAATAAAGTTGAA
CTGCAAAGAGTAAAACAGACAATCGCCACATACCACCAACTCTCAGAAGACAAGAATCAGTTTA
CTTGTCAAACGGTTTTAAAAATGATTCTGATTTTCTAGGAGAATCAGGAGGATCAACTCCTCAC
GAGGATCAGGATCTAGAGCTAAAGAAGCAGGAGCTGGAGCTTTGCCAAACGGGCCCTTAAAATG
ATATAAGAGTTTCCAAACTAAACTATAATAGTAAATTAGTAATAGGTGTAGTTAATTGCCCAAC
AGTTTCAAAATACAGATTTAGCATCACATGTAGTCAATACCTTTGCCCTAGTTCGGAATACATC
AGCGACCTTAGGGTTTGCAATCATGTCAACATACCTATCATTAATCAAAGGTAGCACACATGGT
CAATGCACTATGCAGAACACGGTTGCAATCATTTAAAGTAGGACTAGGAATGAAGGAATAGCAA
CAAAGGTTCTTTAATAATAATCCTGAAAGGGAAAATGATGCCTTTTTAACCATTTTTCAAGCTT
GAAAGAAACTCGAATTCAAACACGTTGGTAGTATAATAAATGGTTTGCACATCAAAACCATATA
TGATATATCAAGATAGTAGAGCCCGGGGTCAAGCCTATGACGACCTTTATCAACGGCTGGACAC
AAAGCAGGGAGAAAAGGATATCTATAGGATGGCCAAGATTCGTGAAAGGAAGACAAGGGATGTC
AACCAAGTCAAATGCATCAAGGACGAAGCAAACCAACTATTAGTGAAGAGTGAAGAGATCAAGA
ACAGATGGAAGGAGTACTTCAACAAATTGTTCAATGGAGGGAATGAGAGTGCTACAATAGAATT
GGACGAACCATTCGATGACAACAACAGGGGTTTTGTACGAAGGATACAAGAATATGAAGTTAAG
GAGGCGCTAAAAAGGATGAAGGTAGGAAAGGCGATGGGCCCTGATGGTATCCCTATCGAGGTAT
GGAGATGTCTTGGAGACATAGCGATAGTATGGCTGACTAAGCTTTTCAACACCATCTTTCGGGC
AAACAGAATGCCCGACGAGTGGCGGCGGAGTACATTAGTACCAATCTTCAAGAACAAAGGAGAT
GTTCAAAGTTGTACTAATTACCGTGGAATTAAGCTCATGAGCCATACAATGAAGCTATGGGAGA
GAGTCATTGAACACCGCCTGCGAAAGATGACGAGCGTGACCCAAAATCAGTTTGGTTTCATGCC
CGGGAGATCAACTATGGAGGCCATTTTCTTACTAAGACAACTTATGGAGAGATTCAGAGAACAA
AAGAAAGACCTGCATATGGTCTTCATAGACTTGGAGAAGGCTTATGACAAAGTACCTAGGAGTG
TAATGTGGTGGGCCTTGGAAAAACACAAAGTAGCAACAAAGTACATTAATCTTATGAAAGATAT
GTACACTAATGTTGTGACAAGTGTCCGAACAAGTGATGGAGACACCGATGACTTTCCAATTAAC
ATAGGACTACATCAAGGGTCGGCTTTGAGCCCTTATCTTTTCGCTTTGGTGATAGATGAGGTCA
CAAGGGACATACAAGGAGTTTTACCGTGGTGTATGCTTTTTGCCGATGATGTGGTACTTATTGA
GGAGAGTAGGAGTGGTGTTTCTCAAAAGTTGGAATTGTGGAGGCAGACGCTGGAAGCAAAAGGT
TTTAGGCTTAGTAGGTCTAAAACAGAGTATATGAAGTGTGATTTCAGTGCCATGGGGTATGAGG
ATGGCGATGTTAGTCTTGATGGGCAAGTGGTACCCAAGAAAGACACTTTTCGTTACTTAGGATC
AATGCTTCAAAAGGAGGGAGACATCGATGAGGATGTCAGTCATAGAATTAAAGCCGGATGGTTG
AAGTGGCGACAAGCTGCGGGTGTCTTATGCGACCACCGGGTGCCACGCAAACTAAAAGGCAAAT
TCTACAGGACAGCAATCCGGCCGGCTATGTTGTATGGAGCAGAATGTTGGCCCACTAAAAGACG
ACATGTCCAACAACTAAGTGTGGCAGAGATGCGTATGTTGCGCTGGATATGTGGCCACACAAGG
AGAGATCGAGTCCGGAATGATGATATACGAGAGAGAGTAGGAGTGGCGCCAATTGAGGAGAAGC
TTATGCAACATCGCTTGAGATGGTTTGGACATATCCAACGAAGACCTGAAGAGGCACCAGTGCA
TATCGGAATAATTAGGCGTCCCGAAAATGTGAAGAGAGGTAGAGGCCGACCAACTTTGACGTGG
ACAGAGGCTGTGAAGAGAGACCTGAAGGAGTGGAATATTGATAAAGAGCTCGCCGCAGATAGGA
AGGGGTGGAAGTGTGCAATTCACGTGCCAGAACCCTGATTGATAGTTTCGCTTTTCCTCCTTAA
TCGTTTGACCTTTTCTTGTGTCCATTTTAGATCTTGCTGGTCCTTGTGGGTTTTATCTCTTTTA
TGTGTTTCCCCGTTTCGTTGTTTTCGGTTCTCCTTTGCCTTTGTTTCCCTTTTCTGTTCTTTGG
GGGTTGAGCTCTGAGGTTTTCATACGGGGTTTCATCTCTAGCCTACCCCAACGTGCTTGGGACA
AAAAGGCTTTGTTGTTGTTGTTGTTGTTGTATTAGATGGGTTCTAATTTTGAACAGATAGGATA
TGACTTAGCAGGTACAAGAAGCAAGATGAAAGCCAACCTTTGACGATAACGTTTGTCCACATCA
GTTAATCCATGATACTTATCTGGTAGTGGGAGTAATGATTTTGTGAGAATTTCGAAATTTTTCA
CATAAACAGATAGCTCCC
						
					

			
		

Sequences
Splice junction sequence	TAACGTTTGTCCACATCAGTTAATCCATGATACTTATCTGGTAGTGGGAGTAATGATTTTGTGA GAATTTCGAAATTTTTCACATAAACAGATAGCTCCCctgtagaactggagtttcgacttcaata aaaccaaatgattccattgtcttgcggatttcagaaaccacctatcaaaaatgcaatatcgaag ttcaaagt
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: 236 Transcript exons: 301669254-301669322,301670190-301670247,301672555-301672 663 CTGTAGAACTGGAGTTTCGACTTCAATAAAACCAAATGATTCCATTGTCTTGCGGATTTCAGAA ACCACCTTTGCCCTAGTTCGGAATACATCAGCGACCTTAGGGTTTGCAATCATGTCAACATACC TTTGACGATAACGTTTGTCCACATCAGTTAATCCATGATACTTATCTGGTAGTGGGAGTAATGA TTTTGTGAGAATTTCGAAATTTTTCACATAAACAGATAGCTCCC
Genomic sequence	CTGTAGAACTGGAGTTTCGACTTCAATAAAACCAAATGATTCCATTGTCTTGCGGATTTCAGAA ACCACCTATCAAAAATGCAATATCGAAGTTCAAAGTAAAAGAAGCTATAGCGAATTATGTCAGT GATGCAACTACTGGTTAAGGTAGTTATTTTTCGAGGACCAACAATATGATAATGTATGCCTTAG TTTCTTTTTTCATACCAAAACTCCCTCAATCCATTAAGAAAAATATGCTCCTGTGCTACATGAT ATTTAGGGCCCGTTTGGCACAGCTCCAGCTCCTGATTCTAAGCGAGGATCTGGAGGAGCCGTGC CAAACAGGTATTTTTTTAAACTGATTCTCGTGTGGAGCCGAAAGATCAGGAGTCGTTTTTGTGA AGAAAGGTGGGATCTAAAAAAACCTGCTCCACCCTCCCTTAAAACAGCTCCTCAACCAACCAAA TATGGATCTCCTCTTAAAATTTGATCGAAATTACCCGCAATTGCCATTGGACAAAAACATAACG AGCCAATTTATGGATTAAACATTTGAGACCATTTTATGCACTACTATGATTGGAATATTTTATA TGTTATTGTTTCATATTTTTTTCCCGTATATGCATCCTACTTATTGGTTTGTAATAAAGTTGAA CTGCAAAGAGTAAAACAGACAATCGCCACATACCACCAACTCTCAGAAGACAAGAATCAGTTTA CTTGTCAAACGGTTTTAAAAATGATTCTGATTTTCTAGGAGAATCAGGAGGATCAACTCCTCAC GAGGATCAGGATCTAGAGCTAAAGAAGCAGGAGCTGGAGCTTTGCCAAACGGGCCCTTAAAATG ATATAAGAGTTTCCAAACTAAACTATAATAGTAAATTAGTAATAGGTGTAGTTAATTGCCCAAC AGTTTCAAAATACAGATTTAGCATCACATGTAGTCAATACCTTTGCCCTAGTTCGGAATACATC AGCGACCTTAGGGTTTGCAATCATGTCAACATACCTATCATTAATCAAAGGTAGCACACATGGT CAATGCACTATGCAGAACACGGTTGCAATCATTTAAAGTAGGACTAGGAATGAAGGAATAGCAA CAAAGGTTCTTTAATAATAATCCTGAAAGGGAAAATGATGCCTTTTTAACCATTTTTCAAGCTT GAAAGAAACTCGAATTCAAACACGTTGGTAGTATAATAAATGGTTTGCACATCAAAACCATATA TGATATATCAAGATAGTAGAGCCCGGGGTCAAGCCTATGACGACCTTTATCAACGGCTGGACAC AAAGCAGGGAGAAAAGGATATCTATAGGATGGCCAAGATTCGTGAAAGGAAGACAAGGGATGTC AACCAAGTCAAATGCATCAAGGACGAAGCAAACCAACTATTAGTGAAGAGTGAAGAGATCAAGA ACAGATGGAAGGAGTACTTCAACAAATTGTTCAATGGAGGGAATGAGAGTGCTACAATAGAATT GGACGAACCATTCGATGACAACAACAGGGGTTTTGTACGAAGGATACAAGAATATGAAGTTAAG GAGGCGCTAAAAAGGATGAAGGTAGGAAAGGCGATGGGCCCTGATGGTATCCCTATCGAGGTAT GGAGATGTCTTGGAGACATAGCGATAGTATGGCTGACTAAGCTTTTCAACACCATCTTTCGGGC AAACAGAATGCCCGACGAGTGGCGGCGGAGTACATTAGTACCAATCTTCAAGAACAAAGGAGAT GTTCAAAGTTGTACTAATTACCGTGGAATTAAGCTCATGAGCCATACAATGAAGCTATGGGAGA GAGTCATTGAACACCGCCTGCGAAAGATGACGAGCGTGACCCAAAATCAGTTTGGTTTCATGCC CGGGAGATCAACTATGGAGGCCATTTTCTTACTAAGACAACTTATGGAGAGATTCAGAGAACAA AAGAAAGACCTGCATATGGTCTTCATAGACTTGGAGAAGGCTTATGACAAAGTACCTAGGAGTG TAATGTGGTGGGCCTTGGAAAAACACAAAGTAGCAACAAAGTACATTAATCTTATGAAAGATAT GTACACTAATGTTGTGACAAGTGTCCGAACAAGTGATGGAGACACCGATGACTTTCCAATTAAC ATAGGACTACATCAAGGGTCGGCTTTGAGCCCTTATCTTTTCGCTTTGGTGATAGATGAGGTCA CAAGGGACATACAAGGAGTTTTACCGTGGTGTATGCTTTTTGCCGATGATGTGGTACTTATTGA GGAGAGTAGGAGTGGTGTTTCTCAAAAGTTGGAATTGTGGAGGCAGACGCTGGAAGCAAAAGGT TTTAGGCTTAGTAGGTCTAAAACAGAGTATATGAAGTGTGATTTCAGTGCCATGGGGTATGAGG ATGGCGATGTTAGTCTTGATGGGCAAGTGGTACCCAAGAAAGACACTTTTCGTTACTTAGGATC AATGCTTCAAAAGGAGGGAGACATCGATGAGGATGTCAGTCATAGAATTAAAGCCGGATGGTTG AAGTGGCGACAAGCTGCGGGTGTCTTATGCGACCACCGGGTGCCACGCAAACTAAAAGGCAAAT TCTACAGGACAGCAATCCGGCCGGCTATGTTGTATGGAGCAGAATGTTGGCCCACTAAAAGACG ACATGTCCAACAACTAAGTGTGGCAGAGATGCGTATGTTGCGCTGGATATGTGGCCACACAAGG AGAGATCGAGTCCGGAATGATGATATACGAGAGAGAGTAGGAGTGGCGCCAATTGAGGAGAAGC TTATGCAACATCGCTTGAGATGGTTTGGACATATCCAACGAAGACCTGAAGAGGCACCAGTGCA TATCGGAATAATTAGGCGTCCCGAAAATGTGAAGAGAGGTAGAGGCCGACCAACTTTGACGTGG ACAGAGGCTGTGAAGAGAGACCTGAAGGAGTGGAATATTGATAAAGAGCTCGCCGCAGATAGGA AGGGGTGGAAGTGTGCAATTCACGTGCCAGAACCCTGATTGATAGTTTCGCTTTTCCTCCTTAA TCGTTTGACCTTTTCTTGTGTCCATTTTAGATCTTGCTGGTCCTTGTGGGTTTTATCTCTTTTA TGTGTTTCCCCGTTTCGTTGTTTTCGGTTCTCCTTTGCCTTTGTTTCCCTTTTCTGTTCTTTGG GGGTTGAGCTCTGAGGTTTTCATACGGGGTTTCATCTCTAGCCTACCCCAACGTGCTTGGGACA AAAAGGCTTTGTTGTTGTTGTTGTTGTTGTATTAGATGGGTTCTAATTTTGAACAGATAGGATA TGACTTAGCAGGTACAAGAAGCAAGATGAAAGCCAACCTTTGACGATAACGTTTGTCCACATCA GTTAATCCATGATACTTATCTGGTAGTGGGAGTAATGATTTTGTGAGAATTTCGAAATTTTTCA CATAAACAGATAGCTCCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.156080072

Conservation Information
Conserved circRNAs	NA
PMCS	0.156080072

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							301670214-301672599(-)
301670239-301672645(-)
						
						Potential amino acid sequence
						
							MYSELGQRWFLKSARQWNHLVLLKSKLQFYRGAICLCEKFRNSHKIITPTTR*(-)
MIANPKVADVFRTRAKVVSEIRKTMESFGFIEVETPVLQGSYLFM*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	301670214-301672599(-) 301670239-301672645(-)
Potential amino acid sequence	MYSELGQRWFLKSARQWNHLVLLKSKLQFYRGAICLCEKFRNSHKIITPTTR(-) MIANPKVADVFRTRAKVVSEIRKTMESFGFIEVETPVLQGSYLFM(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d034766_circ_g.1

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