Plant Circular RNA Database

Detail information of Zm00001d028952_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d028952_circ_g.1
					
						ID in PlantcircBase
						zma_circ_006507
					
						Alias
						zma_circ_0000660
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 52675280-52678801  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d028952						
					
						Parent gene annotation
						
							Alpha-L-arabinofuranosidase 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  
						
							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
						Zm00001d028952_T008:4
Zm00001d028952_T007:5
Zm00001d028952_T005:5
Zm00001d028952_T002:5
Zm00001d028952_T001:5
Zm00001d028952_T003:5
Zm00001d028952_T004:5
Zm00001d028952_T006:5

General Information
CircRNA Name	Zm00001d028952_circ_g.1
ID in PlantcircBase	zma_circ_006507
Alias	zma_circ_0000660
Organism	Zea mays
Position	chr1: 52675280-52678801 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d028952
Parent gene annotation	Alpha-L-arabinofuranosidase 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	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	Zm00001d028952_T008:4 Zm00001d028952_T007:5 Zm00001d028952_T005:5 Zm00001d028952_T002:5 Zm00001d028952_T001:5 Zm00001d028952_T003:5 Zm00001d028952_T004:5 Zm00001d028952_T006:5

			
						 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  
						
							CATGATGACCGATCTGTTGCCACAATAATATTTGATTCATCCCCAATGATCAACCATGGGTCAA
TGTTTGAAGGAGTATTAGAACCACCAGCTTCAAAACttgaagaaattcaaaaaacccaagtcca
tcatcagtccaataggcccaagcatcattgaagtggccaggtctctcttcccatggtccaacag
tttcactc

									
								

					

						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
						
							TTGAAGAAATTCAAAAAACCCAAGTCCATCATCAGTCCAATAGGCCCAAGCATCATTGAAGTGG
CCAGGTCTCTCTTCCCATGGTCCAACAGTTTCACTCCAGCGGAATGCATTTATAAGGTAATTTC
CCATTACATAGTTGCCACCTAAAAGTGACAAATATACTGTCAATTCTCAGCAACCTCACTGTTT
AACTACAACCCTATAAAAAGACATAATTTATTTTCTTAGTTAAACATTCTTGATTCATCTGTGT
AACAGAAACACGGACATAAAATATATCAGGTGGGTAAAAATTGATGCATCATGTATTCAGTAAG
AGCGATACTAGACCTTTTGAGGTTTTGGCAGACTACTTAAAGCTTTGGGTCATGTAAATGGCAA
GTACTTGTGCACTATTCACATATTGTGTAACTTCTACATCTGAAGAACCTCAGAAGTAGAATAA
AAATGCTAAGCGACAAACCTGGAAATTTTAGAAATCGAGGCTTCAGATTTGCCAGCATAGAGGC
AAGATCTTTACGGAAACCATGCCCCTGAAAAATAAAGTGGTGAATAAATGTCACTGACAAATCG
AGAAATGGAAGGTCCTTGGAAGTTGACACCTGGGTTGACTATGGATCAGATATTTTTCCTTTGT
TCTGGTGTTAATTAGGATTAATTTTTCAATCATACAAGAGCTGTGTATAGAAACTTATAATTTA
GCAGGTGCTGAAGTGGTAATGCATCACCACACAATGCAATTTTGATTATGATGGCTGCACGTTG
CAGCTTGTATTTAGAAACATTATGATGCAAACTATTATAACTACATGGTGGCTATCCATGGATG
GCATAGTTTGATCAAGATCAGTTAGTGTTCTCTGAACCAAGAATAATTCTTTCCGGCATATAGA
AATTTAAGTTACTTAAACTTATAGTTCAGGCTATGATGTATGGATATGTGATGAGGCAATTTGC
ATATAAATTTTGATTTTTCTTCTAACATACTATTTTAGGTTGCAAGGGAATGTATGGAGGAAAT
ATAAAATATGTATCACCTTCCTACCAAGTATCAAACATCAAAAGGATAAAAGAGTATTTGGAAA
TTAAATTACCATATAAGTATCTGATGGCATAAGTGATACTTGATCAAACCAAATTATGCCACTT
TTGGTGGTTGTAAGCTGAAGTCTTGAATTAGTATTTATATAATTTGATTGCAAATCAAATTCAA
CCTTCGTCCACTCAACGAAATCTTCTTTGTCTCCCCTACAATTTATATTGCATATTCGCATATC
TATTACTTCACGGAAATGGGCACAATAGTAGCACATGAAGTATTCTTCATAAGTCGAACCATGA
GATATCGCTTACATGATTGTATGAGAGGCTAGATTTTGAAGACCATCTGAACTTGTTAAAGAAA
CCATTAGCTCCACCGATTCTGATGACCTGATGTATATGGTAACTCTATAGACATTTGTTCTTTC
AATGTTCTGCAACAATTGTAGCAAATACTTACGGAGATGAGCTTACCTTAGAAATTTATCAAAT
CTAGAAGGAACAAGAAATGTGCATGTATAGTACTCTGATACTCTTATTGGTTCAGATATTAGTG
TAGAATAGTGTAATTGCTTGATGTATTGCATAGAGGAGGACTACAATATATAGAGAGGGAAACC
CTAACCCTAATGGGCCGGCAGCCCAACAGTGGTGCCGGCCCACACACACTCACACACACAGTCT
AACATTCCCCCGCAGTCGCAACGGGGGCACCACACACAATGAGACTGGAGTAGAGTCCGAAGGT
ACGAGCCGACGGGTTGAAATCCTCCCGCAGTCGCAGCGTCGTGATGGTGCGAATGTTGCGGCTG
GAGTAGAGACCGGTGTGTGCTCCAAGAAGACGATAGCCCCTGGATGCCGAGGTAGCCGAAGTCG
AGGTGGTCGCGGTCGGAAGACGCGCAGCAAAAGCCTGATCTTTGGGAGGGGTCGACGTTCGAGC
GTTAACGATCGGCAGGGCGACACAACAAAAGGGCACCGGCAGGCCGACCTTCCTGCTTCTTCGA
TCATCCAGGCGTCAAGGAGCCCCGCCAGGGAGCCGACGGCAGCGCACGCGTCTGCACCGGTCAT
GGTGTCCGCGCCCGCGGCAGAATAGAAGGGGAAACGACAGATTCAGCCGGGAAGGCCACGGCAG
CGACGGATCCAGTCGGGAAGACACGATCCAGCCAAAGGGACGGCGGATCGAACCGGAAAGGTCG
TAGCAACGTGGATCCGGCCGGGAAGGCCGCGACAGCGACGGATCCAGCGAAGGCGAAGAAGGGG
GTGGGCGGCGGGGCGTGTCCAGCCGGGCAGGGGCCTGCGCCGGACCTGGAAAATGGTGTTGACG
GCACCGGCGACGGGAGAAGCTCGAAGTGGGAGACGTTGCTGGGGCGTCAGCATGGACAGCACGT
GCGAGGACACAACGAAGAGGAGGGTGCACGTGCGGGTGACTCAGCGAAGAGGAGGACGCCGACC
AAGGGAGGCAGCCATGGGGAACAGGGAACCGAGCAGAGGGGCTGCTCGCGTCGGGGCCGGCGTG
GGCGCGCCCGCGCAAGGGGCCACTTGGGGCTGGGCTCGGCCGGGGCGCGCGCGTCCAGGCTGGT
GCAGAATAGTGTAATTGCTTGATGTATTGCATAGAGGAGGACTACAATATATAGAGAGGGAAAC
CCTAACCCTAATGGGCCGGCAGCCCAACAGTGGTGCCGGCCCACACACACTCACACACACAGTC
TAACAATTAGTACTTAGTACAGAGAACTTTAAGGGCCTGTTTGAGAATGTAGTTTTAAAATACT
ATAGTTTTGAGATACTATAGTTTACAATTGTACATGACATAAATACTACGGTATTGCTTTACCA
TAATAAAACTACAGTATTGTTCAAAACCGAGATCTGTTTGGTTCTATTGTAAAAACAAAGTATA
TGTAGAGAGAAGAGAAGAAAACTGAGGTCCTGAGTGGAGTTTCGAAAACTCCAAAAATACCGCA
GTTTTGGGTAAACCATGGTATTTAAAACTGAGTTTTGACTCTACAAACCAAACAACTTTTGAGC
TCCAATACTATAGTATCATCAAATACCATAGTATTGTTTCAAAACTGCAAAAATACTACAATTC
CAAACAAGGCCTAAGCCATCAAAGAAAAAAAATGGTAAGAAGAGCTCAGTAAGTAGTCTAAAAA
TACCCAAGTGAAAATTTCTAAAAAAATATATTCAACAGGCAGATGAAAATTTATGGAAGATTCC
ACAGGGAGAAAAACTACAAATTGTGTTAAATACATAAAGGTCATACCATGCCCCAGTAACCAGG
ATTGTAGATTCCAACTCCTCCTGATGGGCAAGCATTAGTTTCACTAGCTCCACAAAGTACTTCC
ATTCGAAGTGCAATTGGGTTACTAGCAAAACATGATGACCGATCTGTTGCCACAATAATATTTG
ATTCATCCCCAATGATCAACCATGGGTCAATGTTTGAAGGAGTATTAGAACCACCAGCTTCAAA
AC
						
					

			
		

Sequences
Splice junction sequence	CATGATGACCGATCTGTTGCCACAATAATATTTGATTCATCCCCAATGATCAACCATGGGTCAA TGTTTGAAGGAGTATTAGAACCACCAGCTTCAAAACttgaagaaattcaaaaaacccaagtcca tcatcagtccaataggcccaagcatcattgaagtggccaggtctctcttcccatggtccaacag tttcactc
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	TTGAAGAAATTCAAAAAACCCAAGTCCATCATCAGTCCAATAGGCCCAAGCATCATTGAAGTGG CCAGGTCTCTCTTCCCATGGTCCAACAGTTTCACTCCAGCGGAATGCATTTATAAGGTAATTTC CCATTACATAGTTGCCACCTAAAAGTGACAAATATACTGTCAATTCTCAGCAACCTCACTGTTT AACTACAACCCTATAAAAAGACATAATTTATTTTCTTAGTTAAACATTCTTGATTCATCTGTGT AACAGAAACACGGACATAAAATATATCAGGTGGGTAAAAATTGATGCATCATGTATTCAGTAAG AGCGATACTAGACCTTTTGAGGTTTTGGCAGACTACTTAAAGCTTTGGGTCATGTAAATGGCAA GTACTTGTGCACTATTCACATATTGTGTAACTTCTACATCTGAAGAACCTCAGAAGTAGAATAA AAATGCTAAGCGACAAACCTGGAAATTTTAGAAATCGAGGCTTCAGATTTGCCAGCATAGAGGC AAGATCTTTACGGAAACCATGCCCCTGAAAAATAAAGTGGTGAATAAATGTCACTGACAAATCG AGAAATGGAAGGTCCTTGGAAGTTGACACCTGGGTTGACTATGGATCAGATATTTTTCCTTTGT TCTGGTGTTAATTAGGATTAATTTTTCAATCATACAAGAGCTGTGTATAGAAACTTATAATTTA GCAGGTGCTGAAGTGGTAATGCATCACCACACAATGCAATTTTGATTATGATGGCTGCACGTTG CAGCTTGTATTTAGAAACATTATGATGCAAACTATTATAACTACATGGTGGCTATCCATGGATG GCATAGTTTGATCAAGATCAGTTAGTGTTCTCTGAACCAAGAATAATTCTTTCCGGCATATAGA AATTTAAGTTACTTAAACTTATAGTTCAGGCTATGATGTATGGATATGTGATGAGGCAATTTGC ATATAAATTTTGATTTTTCTTCTAACATACTATTTTAGGTTGCAAGGGAATGTATGGAGGAAAT ATAAAATATGTATCACCTTCCTACCAAGTATCAAACATCAAAAGGATAAAAGAGTATTTGGAAA TTAAATTACCATATAAGTATCTGATGGCATAAGTGATACTTGATCAAACCAAATTATGCCACTT TTGGTGGTTGTAAGCTGAAGTCTTGAATTAGTATTTATATAATTTGATTGCAAATCAAATTCAA CCTTCGTCCACTCAACGAAATCTTCTTTGTCTCCCCTACAATTTATATTGCATATTCGCATATC TATTACTTCACGGAAATGGGCACAATAGTAGCACATGAAGTATTCTTCATAAGTCGAACCATGA GATATCGCTTACATGATTGTATGAGAGGCTAGATTTTGAAGACCATCTGAACTTGTTAAAGAAA CCATTAGCTCCACCGATTCTGATGACCTGATGTATATGGTAACTCTATAGACATTTGTTCTTTC AATGTTCTGCAACAATTGTAGCAAATACTTACGGAGATGAGCTTACCTTAGAAATTTATCAAAT CTAGAAGGAACAAGAAATGTGCATGTATAGTACTCTGATACTCTTATTGGTTCAGATATTAGTG TAGAATAGTGTAATTGCTTGATGTATTGCATAGAGGAGGACTACAATATATAGAGAGGGAAACC CTAACCCTAATGGGCCGGCAGCCCAACAGTGGTGCCGGCCCACACACACTCACACACACAGTCT AACATTCCCCCGCAGTCGCAACGGGGGCACCACACACAATGAGACTGGAGTAGAGTCCGAAGGT ACGAGCCGACGGGTTGAAATCCTCCCGCAGTCGCAGCGTCGTGATGGTGCGAATGTTGCGGCTG GAGTAGAGACCGGTGTGTGCTCCAAGAAGACGATAGCCCCTGGATGCCGAGGTAGCCGAAGTCG AGGTGGTCGCGGTCGGAAGACGCGCAGCAAAAGCCTGATCTTTGGGAGGGGTCGACGTTCGAGC GTTAACGATCGGCAGGGCGACACAACAAAAGGGCACCGGCAGGCCGACCTTCCTGCTTCTTCGA TCATCCAGGCGTCAAGGAGCCCCGCCAGGGAGCCGACGGCAGCGCACGCGTCTGCACCGGTCAT GGTGTCCGCGCCCGCGGCAGAATAGAAGGGGAAACGACAGATTCAGCCGGGAAGGCCACGGCAG CGACGGATCCAGTCGGGAAGACACGATCCAGCCAAAGGGACGGCGGATCGAACCGGAAAGGTCG TAGCAACGTGGATCCGGCCGGGAAGGCCGCGACAGCGACGGATCCAGCGAAGGCGAAGAAGGGG GTGGGCGGCGGGGCGTGTCCAGCCGGGCAGGGGCCTGCGCCGGACCTGGAAAATGGTGTTGACG GCACCGGCGACGGGAGAAGCTCGAAGTGGGAGACGTTGCTGGGGCGTCAGCATGGACAGCACGT GCGAGGACACAACGAAGAGGAGGGTGCACGTGCGGGTGACTCAGCGAAGAGGAGGACGCCGACC AAGGGAGGCAGCCATGGGGAACAGGGAACCGAGCAGAGGGGCTGCTCGCGTCGGGGCCGGCGTG GGCGCGCCCGCGCAAGGGGCCACTTGGGGCTGGGCTCGGCCGGGGCGCGCGCGTCCAGGCTGGT GCAGAATAGTGTAATTGCTTGATGTATTGCATAGAGGAGGACTACAATATATAGAGAGGGAAAC CCTAACCCTAATGGGCCGGCAGCCCAACAGTGGTGCCGGCCCACACACACTCACACACACAGTC TAACAATTAGTACTTAGTACAGAGAACTTTAAGGGCCTGTTTGAGAATGTAGTTTTAAAATACT ATAGTTTTGAGATACTATAGTTTACAATTGTACATGACATAAATACTACGGTATTGCTTTACCA TAATAAAACTACAGTATTGTTCAAAACCGAGATCTGTTTGGTTCTATTGTAAAAACAAAGTATA TGTAGAGAGAAGAGAAGAAAACTGAGGTCCTGAGTGGAGTTTCGAAAACTCCAAAAATACCGCA GTTTTGGGTAAACCATGGTATTTAAAACTGAGTTTTGACTCTACAAACCAAACAACTTTTGAGC TCCAATACTATAGTATCATCAAATACCATAGTATTGTTTCAAAACTGCAAAAATACTACAATTC CAAACAAGGCCTAAGCCATCAAAGAAAAAAAATGGTAAGAAGAGCTCAGTAAGTAGTCTAAAAA TACCCAAGTGAAAATTTCTAAAAAAATATATTCAACAGGCAGATGAAAATTTATGGAAGATTCC ACAGGGAGAAAAACTACAAATTGTGTTAAATACATAAAGGTCATACCATGCCCCAGTAACCAGG ATTGTAGATTCCAACTCCTCCTGATGGGCAAGCATTAGTTTCACTAGCTCCACAAAGTACTTCC ATTCGAAGTGCAATTGGGTTACTAGCAAAACATGATGACCGATCTGTTGCCACAATAATATTTG ATTCATCCCCAATGATCAACCATGGGTCAATGTTTGAAGGAGTATTAGAACCACCAGCTTCAAA AC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.053592249

Conservation Information
Conserved circRNAs	NA
PMCS	0.053592249

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							52678748-52675335(+)
52675394-52678797(-)
52678675-52678753(-)
						
						Potential amino acid sequence
						
							MINHGSMFEGVLEPPASKLEEIQKTQVHHQSNRPKHH*(+)
MHSAGVKLLDHGKRDLATSMMLGPIGLMMDLGFLNFFKF*(-)
MEVLCGASETNACPSGGVGIYNPGYWGMNIERTNVYRVTIYIRSSESVELMVSLTSSDGLQNLA
SHTIMGDKEDFVEWTKVEFDLQSNYINTNSRLQLTTTKSGIIWFDQVSLMPSDTYMGHGFRKDL
ASMLANLKPRFLKFPGGNYVMGNYLINAFRWSETVGPWEERPGHFNDAWAYWTDDGLGFFEFLQ
VLKLVVLILLQTLTHG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	52678748-52675335(+) 52675394-52678797(-) 52678675-52678753(-)
Potential amino acid sequence	MINHGSMFEGVLEPPASKLEEIQKTQVHHQSNRPKHH(+) MHSAGVKLLDHGKRDLATSMMLGPIGLMMDLGFLNFFKF(-) MEVLCGASETNACPSGGVGIYNPGYWGMNIERTNVYRVTIYIRSSESVELMVSLTSSDGLQNLA SHTIMGDKEDFVEWTKVEFDLQSNYINTNSRLQLTTTKSGIIWFDQVSLMPSDTYMGHGFRKDL ASMLANLKPRFLKFPGGNYVMGNYLINAFRWSETVGPWEERPGHFNDAWAYWTDDGLGFFEFLQ VLKLVVLILLQTLTHG*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d028952_circ_g.1

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