Plant Circular RNA Database

Detail information of Zm00001d051187_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d051187_circ_g.1
					
						ID in PlantcircBase
						zma_circ_008109
					
						Alias
						Zm04circ00056
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 147817317-147819832  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d051187						
					
						Parent gene annotation
						
							ADP-ribosylation factor GTPase-activating protein AGD2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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  
						
							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
						Zm00001d051187_T001:4
Zm00001d051187_T009:4
Zm00001d051187_T005:4
Zm00001d051187_T006:4
Zm00001d051187_T004:4
Zm00001d051187_T007:4
Zm00001d051187_T003:4
Zm00001d051187_T008:4
Zm00001d051187_T002:4

General Information
CircRNA Name	Zm00001d051187_circ_g.1
ID in PlantcircBase	zma_circ_008109
Alias	Zm04circ00056
Organism	Zea mays
Position	chr4: 147817317-147819832 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d051187
Parent gene annotation	ADP-ribosylation factor GTPase-activating protein AGD2
Parent gene strand	+
Alternative splicing	NA
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	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	Zm00001d051187_T001:4 Zm00001d051187_T009:4 Zm00001d051187_T005:4 Zm00001d051187_T006:4 Zm00001d051187_T004:4 Zm00001d051187_T007:4 Zm00001d051187_T003:4 Zm00001d051187_T008:4 Zm00001d051187_T002:4

			
						 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  
						
							TGAAAGTCTGGGAGCCAGTAATTATGGATCTCTTCCATGCACTAGGAAATGATTACGCTAATTC
CATTTGGGAAGCCCTGCTTCCAAAAGAAGATCAAGGcaaggagtgtcatcacaacaaacaactg
aaggtactggtgtttttggtcgattcagattcttgaaccaaagagtttcatctcagagtgaaga
ttcattat

									
								

					

						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: 668
Transcript exons: 147817317-147817526,147817685-147817771,147818923-147819
171,147819711-147819832
CAAGGAGTGTCATCACAACAAACAACTGAAGGTACTGGTGTTTTTGGTCGATTCAGATTCTTGA
ACCAAAGAGTTTCATCTCAGAGTGAAGATTCATTATCATGTCATAGAATTGATCTCAGAACTTC
AACAATTAAGATTGATGCAGATGAAAATGATTTAAGATTTTGCTTCAGAATAATCTCACCTGTT
AAGGCATACACATTACAGGCAGAATCAGGGGCTGATCAAAAGGACTGGATCCAGAAAATTACTG
GAGTTATCGCATCGCTACTAAATTCACCATTCCCACAGCAGTTGTCATATGGTAATGTAGCAGC
AGAGAGTAACAGATCCACAAGTTCTGTTGATTCTTTGTCTATTGAAGATAACAAGAGTTCAGAG
GGACATGATGATATATTCAACCTTCTGAGGAATATCCCTGGAAATGACAGTTGTGCAGAATGTC
GTTCCCCTGATCCTGATTGGGCATCTCTAAACTTGGGTATTCTGATTTGCATTGAGTGCTCTGG
GGCTCATAGGAATCTTGGAGTGCACATTTCAAAGGTTCGATCCTTGAGACTAGATGTGAAAGTC
TGGGAGCCAGTAATTATGGATCTCTTCCATGCACTAGGAAATGATTACGCTAATTCCATTTGGG
AAGCCCTGCTTCCAAAAGAAGATCAAGG
						
					

						Genomic sequence
						
							CAAGGAGTGTCATCACAACAAACAACTGAAGGTACTGGTGTTTTTGGTCGATTCAGATTCTTGA
ACCAAAGAGTTTCATCTCAGAGTGAAGATTCATTATCATGTCATAGAATTGATCTCAGAACTTC
AACAATTAAGATTGATGCAGATGAAAATGATTTAAGATTTTGCTTCAGAATAATCTCACCTGTT
AAGGCATACACATTACAGGTAACTGCATAGTCCTCAGATATCGAACTTTCTTTGTGCAATTCAT
GTTTTTGCTATTTCCTGAACAAGTGAATAACACATTTTATGATTTTTTAATTCTTCTATGATAC
ACCAATGGGCTGATGCCACATGAATGCTTTTCGCTTTGTTTATGGCAGGCAGAATCAGGGGCTG
ATCAAAAGGACTGGATCCAGAAAATTACTGGAGTTATCGCATCGCTACTAAATTCACCATTCCC
ACAGCAGGTTTGCTGCATCATCATATAACTAGTCTTGGTTTACCTTTTTGGTTGAAACAAAGGA
TAGATCTATTAAACTCTATGCATCAACTCTGGATAATCATGAAGTAATAATGCTTAGCCTTCCT
ACTTTGGTTCCATTTTAGGCCCCCTTTGGCATAACTTTAGCTTTTAAAAAAATAGCTTTAGCTC
TGGCTTCTCCGTGTAAGTAACTTTTCTAAAGGAGCCGAAGCCATTAAAAAAACTATTTGGTAAC
ATGGCTTTTAGACTGTTTTCCAAAATAAACCCTGACTACTTGACGGAAGATGGAATGTGAACCA
GAAGTCCAAGGGCGTCGTCGGAACCGTGGATGGTGAGGACGGCGAGTACAAGGATGAGCAGCCC
CACGGAAGCAGGAGGCGCTCCTTCTGCTTCTATGTCTCCAAAAATGGGAATCCACGTAGGAACA
AGGGAGAGAAGACGCCCTGGCTCATGGAGGACTTCACTGTTGTGGAGTACGGACACGATGAAGG
CGACGGGACCTTTGTCGTGTTTTGCAGAATCTACCTCACGCCAGCGCCACACTTTCTTGGGTAT
CAACAAGGTCAGCCCACGTCTGCCGCCGCTGCCCTTCCATGGACAGCAACACGGGCAGGCCGCT
GCGACACCAGTCGTTCTTGGAGATCACCATGGCCGCGCCATGCTGCTGCAGCTGCTGTTCCCAA
CGTGCCCGAGCGTCTGTCTTGTTGGTCACCAGCAAGGCGAGGCGATGACCCATATGGAGAAGAA
GCCGCAGCAGGCGTATGGTTTGCCGGCGTGATAGACGAAACGATGCAGCACATACTGATTGGTG
GGGAGGAGATTAGATCCTGATGCATCTGGTGGGAGCTGGTTTTCGCAAAAAGACCATAAGCCAA
AGTTGGTTAAGCCACTTTTTTTTGGCTTCACCTATCTTATAGAAAAGGGAGAAGTGTTTTTTTG
CCAAAAGCTATGTATCAAAATACCGTTTGGTACGGCTTATGGAAATAAACGCGAAGCTGCAGCA
GAAGCTGCTGGAGAGGAGCCTTGCCAAAGAGGGCCTTAATGCATTACATGCATATGTATATGTT
CAATCTATTGAAATTTGATGTATTCAAGATATGGTACTAATTTCGTTATTCTGATTTCATTTCA
TTTCAGTTGTCATATGGTAATGTAGCAGCAGAGAGTAACAGATCCACAAGTTCTGTTGATTCTT
TGTCTATTGAAGATAACAAGAGTTCAGAGGGACATGATGATATATTCAACCTTCTGAGGAATAT
CCCTGGAAATGACAGTTGTGCAGAATGTCGTTCCCCTGATCCTGATTGGGCATCTCTAAACTTG
GGTATTCTGATTTGCATTGAGTGCTCTGGGGCTCATAGGAATCTTGGAGTGCACATTTCAAAGG
TGCAATAACTAGTTTCCTTATACCATGATATATGCTAATTGGTGATACTGTTTGGTTGGAGATA
TCTTTTGTAGAAAAAAGTTCAGATTCTTGGATTTATTCACTTAGTAATGATAGATACTAGATAC
AGTAAATATATTACTGGATATCTTACTATAGTGCAATACTGCTTTTGTTCTCATTAGTTGTCAT
TTTTGACATTGGCATCTCCAATACAAAGCTTTAGTGGTTATGCGATCTATTATCATATAATATA
AAATTTATTTCCATGTGGTAAATTTAAGTACTTCTATGGGGTAGTGAACCATGCATAAGTTTTA
AAGACTTGGTATGAAAGGAAAACTTCGATTTAATACATTTGCTTGTTTTTTATTTGTTATGTCT
TTCAATTTTATCTGGTAATCAATGTGTGACTTCCAGAACTAGTAAATTTTGTAAAAACTATGCT
TTTAAAATTTTATCAGTCAGATTAAAAAAAAGAAAGCTATTAGCTTGTTCCATATGTCATTGTC
ACAGCTAATGTTTTTACTTGATGCAGGTTCGATCCTTGAGACTAGATGTGAAAGTCTGGGAGCC
AGTAATTATGGATCTCTTCCATGCACTAGGAAATGATTACGCTAATTCCATTTGGGAAGCCCTG
CTTCCAAAAGAAGATCAAGG
						
					

			
		

Sequences
Splice junction sequence	TGAAAGTCTGGGAGCCAGTAATTATGGATCTCTTCCATGCACTAGGAAATGATTACGCTAATTC CATTTGGGAAGCCCTGCTTCCAAAAGAAGATCAAGGcaaggagtgtcatcacaacaaacaactg aaggtactggtgtttttggtcgattcagattcttgaaccaaagagtttcatctcagagtgaaga ttcattat
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: 668 Transcript exons: 147817317-147817526,147817685-147817771,147818923-147819 171,147819711-147819832 CAAGGAGTGTCATCACAACAAACAACTGAAGGTACTGGTGTTTTTGGTCGATTCAGATTCTTGA ACCAAAGAGTTTCATCTCAGAGTGAAGATTCATTATCATGTCATAGAATTGATCTCAGAACTTC AACAATTAAGATTGATGCAGATGAAAATGATTTAAGATTTTGCTTCAGAATAATCTCACCTGTT AAGGCATACACATTACAGGCAGAATCAGGGGCTGATCAAAAGGACTGGATCCAGAAAATTACTG GAGTTATCGCATCGCTACTAAATTCACCATTCCCACAGCAGTTGTCATATGGTAATGTAGCAGC AGAGAGTAACAGATCCACAAGTTCTGTTGATTCTTTGTCTATTGAAGATAACAAGAGTTCAGAG GGACATGATGATATATTCAACCTTCTGAGGAATATCCCTGGAAATGACAGTTGTGCAGAATGTC GTTCCCCTGATCCTGATTGGGCATCTCTAAACTTGGGTATTCTGATTTGCATTGAGTGCTCTGG GGCTCATAGGAATCTTGGAGTGCACATTTCAAAGGTTCGATCCTTGAGACTAGATGTGAAAGTC TGGGAGCCAGTAATTATGGATCTCTTCCATGCACTAGGAAATGATTACGCTAATTCCATTTGGG AAGCCCTGCTTCCAAAAGAAGATCAAGG
Genomic sequence	CAAGGAGTGTCATCACAACAAACAACTGAAGGTACTGGTGTTTTTGGTCGATTCAGATTCTTGA ACCAAAGAGTTTCATCTCAGAGTGAAGATTCATTATCATGTCATAGAATTGATCTCAGAACTTC AACAATTAAGATTGATGCAGATGAAAATGATTTAAGATTTTGCTTCAGAATAATCTCACCTGTT AAGGCATACACATTACAGGTAACTGCATAGTCCTCAGATATCGAACTTTCTTTGTGCAATTCAT GTTTTTGCTATTTCCTGAACAAGTGAATAACACATTTTATGATTTTTTAATTCTTCTATGATAC ACCAATGGGCTGATGCCACATGAATGCTTTTCGCTTTGTTTATGGCAGGCAGAATCAGGGGCTG ATCAAAAGGACTGGATCCAGAAAATTACTGGAGTTATCGCATCGCTACTAAATTCACCATTCCC ACAGCAGGTTTGCTGCATCATCATATAACTAGTCTTGGTTTACCTTTTTGGTTGAAACAAAGGA TAGATCTATTAAACTCTATGCATCAACTCTGGATAATCATGAAGTAATAATGCTTAGCCTTCCT ACTTTGGTTCCATTTTAGGCCCCCTTTGGCATAACTTTAGCTTTTAAAAAAATAGCTTTAGCTC TGGCTTCTCCGTGTAAGTAACTTTTCTAAAGGAGCCGAAGCCATTAAAAAAACTATTTGGTAAC ATGGCTTTTAGACTGTTTTCCAAAATAAACCCTGACTACTTGACGGAAGATGGAATGTGAACCA GAAGTCCAAGGGCGTCGTCGGAACCGTGGATGGTGAGGACGGCGAGTACAAGGATGAGCAGCCC CACGGAAGCAGGAGGCGCTCCTTCTGCTTCTATGTCTCCAAAAATGGGAATCCACGTAGGAACA AGGGAGAGAAGACGCCCTGGCTCATGGAGGACTTCACTGTTGTGGAGTACGGACACGATGAAGG CGACGGGACCTTTGTCGTGTTTTGCAGAATCTACCTCACGCCAGCGCCACACTTTCTTGGGTAT CAACAAGGTCAGCCCACGTCTGCCGCCGCTGCCCTTCCATGGACAGCAACACGGGCAGGCCGCT GCGACACCAGTCGTTCTTGGAGATCACCATGGCCGCGCCATGCTGCTGCAGCTGCTGTTCCCAA CGTGCCCGAGCGTCTGTCTTGTTGGTCACCAGCAAGGCGAGGCGATGACCCATATGGAGAAGAA GCCGCAGCAGGCGTATGGTTTGCCGGCGTGATAGACGAAACGATGCAGCACATACTGATTGGTG GGGAGGAGATTAGATCCTGATGCATCTGGTGGGAGCTGGTTTTCGCAAAAAGACCATAAGCCAA AGTTGGTTAAGCCACTTTTTTTTGGCTTCACCTATCTTATAGAAAAGGGAGAAGTGTTTTTTTG CCAAAAGCTATGTATCAAAATACCGTTTGGTACGGCTTATGGAAATAAACGCGAAGCTGCAGCA GAAGCTGCTGGAGAGGAGCCTTGCCAAAGAGGGCCTTAATGCATTACATGCATATGTATATGTT CAATCTATTGAAATTTGATGTATTCAAGATATGGTACTAATTTCGTTATTCTGATTTCATTTCA TTTCAGTTGTCATATGGTAATGTAGCAGCAGAGAGTAACAGATCCACAAGTTCTGTTGATTCTT TGTCTATTGAAGATAACAAGAGTTCAGAGGGACATGATGATATATTCAACCTTCTGAGGAATAT CCCTGGAAATGACAGTTGTGCAGAATGTCGTTCCCCTGATCCTGATTGGGCATCTCTAAACTTG GGTATTCTGATTTGCATTGAGTGCTCTGGGGCTCATAGGAATCTTGGAGTGCACATTTCAAAGG TGCAATAACTAGTTTCCTTATACCATGATATATGCTAATTGGTGATACTGTTTGGTTGGAGATA TCTTTTGTAGAAAAAAGTTCAGATTCTTGGATTTATTCACTTAGTAATGATAGATACTAGATAC AGTAAATATATTACTGGATATCTTACTATAGTGCAATACTGCTTTTGTTCTCATTAGTTGTCAT TTTTGACATTGGCATCTCCAATACAAAGCTTTAGTGGTTATGCGATCTATTATCATATAATATA AAATTTATTTCCATGTGGTAAATTTAAGTACTTCTATGGGGTAGTGAACCATGCATAAGTTTTA AAGACTTGGTATGAAAGGAAAACTTCGATTTAATACATTTGCTTGTTTTTTATTTGTTATGTCT TTCAATTTTATCTGGTAATCAATGTGTGACTTCCAGAACTAGTAAATTTTGTAAAAACTATGCT TTTAAAATTTTATCAGTCAGATTAAAAAAAAGAAAGCTATTAGCTTGTTCCATATGTCATTGTC ACAGCTAATGTTTTTACTTGATGCAGGTTCGATCCTTGAGACTAGATGTGAAAGTCTGGGAGCC AGTAATTATGGATCTCTTCCATGCACTAGGAAATGATTACGCTAATTCCATTTGGGAAGCCCTG CTTCCAAAAGAAGATCAAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.069139186

Conservation Information
Conserved circRNAs	NA
PMCS	0.069139186

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							147819757-147817377(+)
147819782-147817342(+)
147817331-147819776(-)
						
						Potential amino acid sequence
						
							MDLFHALGNDYANSIWEALLPKEDQGKECHHNKQLKVLVFLVDSDS*(+)
MITLIPFGKPCFQKKIKARSVITTNN*(+)
MTLLALIFFWKQGFPNGISVIIS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	147819757-147817377(+) 147819782-147817342(+) 147817331-147819776(-)
Potential amino acid sequence	MDLFHALGNDYANSIWEALLPKEDQGKECHHNKQLKVLVFLVDSDS(+) MITLIPFGKPCFQKKIKARSVITTNN(+) MTLLALIFFWKQGFPNGISVIIS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d051187_circ_g.1

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