Plant Circular RNA Database

Detail information of Zm00001d003590_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d003590_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007170
					
						Alias
						zma_circ_0001058
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 49124383-49127320  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d003590						
					
						Parent gene annotation
						
							Protein phosphatase methylesterase 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
						Zm00001d003590_T003:8
Zm00001d003590_T001:8
Zm00001d003590_T002:8

General Information
CircRNA Name	Zm00001d003590_circ_g.1
ID in PlantcircBase	zma_circ_007170
Alias	zma_circ_0001058
Organism	Zea mays
Position	chr2: 49124383-49127320 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Zm00001d003590
Parent gene annotation	Protein phosphatase methylesterase 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	Zm00001d003590_T003:8 Zm00001d003590_T001:8 Zm00001d003590_T002:8

			
						 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  
						
							AACGCATGCTGCTGACTCACCTATGCCCAACAAGTATAATTGCTGGTGGCAAATCTCCATACAT
TGTACGTATAACAGCTATGACATCATTGGTAAGAGTctcgacaccattaggccctattttgttg
cgggatatgaacttcagtatgtgcgatgcaaattcttcaggtacatcttcctgaaataaataac
ggtttgat

									
								

					

						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
						
							CTCGACACCATTAGGCCCTATTTTGTTGCGGGATATGAACTTCAGTATGTGCGATGCAAATTCT
TCAGGTACATCTTCCTGAAATAAATAACGGTTTGATGACATGGCAAAAGCAGTAAAGGTTTGTA
ATTCGTTGGCTAAAACTATATTCCTAAACCAATGCTTCCAAAAGAAAAAGTTCACAGACTATAA
CAGAACACAATCAGCACTCGGAGAATAAATCTTTCATTGTCAATTCCTGCTATTGCTACGTGAG
TGCAAATTAGTGAAAAATTGAAGTAGCCCTAGAGCATTCAGGCACAGCACGATCATCACAAGCT
CTAGAAATGACTACTGAACGAATCTAGAAGAATGGTACAAAAGCTCCTAGCCTTGCAAGAATTA
TGCAATGGACTCATATATTAACATAACTCAAACATACTATAAGAACCAACCTGTATAGCATGTC
CAGTGTGCCGAATCACCACCATTTGAAATTTTCCTTGCATTTGACCGATTGTTAAAGCTCTGCA
AATTGTAAACCAACTAACCGATACATTACACAATTTATCTTCGATAGTGGATCATCGGCATGAG
TGATTGAAGGTGTTTGATATTTCAGAACACTTAATTATGATGGCAATATGATTCCACATCCAAC
AAAATCAACAATTCAGAACACAACAAACAATTTTACAAGAGGTTTCACTTCAATAAACAGCATT
TTGATAATCGATTATCACCCATCCGATTTGTCATTCAAAAGCTCTAGCAACAAAGCCTGGCAAA
AATTTCCATATTTTGCGAACCATAATCATGACAAGCAACTGACTTTGCTACCTTTTGATTTATA
ATTTATAAGCCATAATCAACAGCTGATAAACCATAATAAAATATGCTAAAGACTGACTTTGCAA
GCCCATTCCGTTGAAACTGACAAGCAGCAAAACATTGAATGACACCGAGTTAAGTCACTAGCCA
AAGTTGATGAAATTAAATGTGGAGTAAACATCATGAACATGGACTAGAAAATAGATAATTTCTC
ATACTCGAACATAACAAACCTGTCCAGTCTGTCGGTACCAGCTAACAACAGGATCTTTTGCACT
GGGCAAGATAGGAACTTGTCTGAAAGACCTTCATACCTAACAAAGAAACACATGCACTTTAGTA
TCGACTAACACAGAAGAGAAAAAAGGACATGAGAAGACAAACGATTTTACAAAACATAGATTTT
TTTTTTTTTTAAAAAAAGAAGGAAATGTCAGACTGAAAGCATACCATCCTTTCCAGTACTTTTC
TGTTTGCTCAAGAGGAGTGCGATATGTATAGCTGAAACAAAGTATGACAGCATACTTAGTTTCA
AAATAATAACAATACTACATCTGCAATGGTGGCCAACAGGCCACCATGATTCTTTATGTGCATA
GGCCTGTGAGATACAATACGAAAAACATACACTTCTCAAACTACTCACCATTCTCGTGATTCAT
CGTATTTCAGGGTAGATGGAATGGACACACGAGCAGACTCGATGTTCCTTAATGGCCCACCTTT
GACACTCCATTCAATCTGCATAATTCCAAAATTGATTGAACAAGAAATAAGGTGAAGAGAAAAA
TTTAACAATATAAACTGCTGCCTTAGCAAGAATGGTTTACTAAGCATGATGCTAATTCAAAATT
GAATTAGTTTCATTGTATAGTTGTTCTTCCATTCTATTATCAACCTTTGCATGTTTGTGTCCAT
GCCGTACATACACAACTCAAATACATATGTGACTGACAGGTACTCATTTCATCTTGAAGTGATG
AACACGATATCTTTTAAGATAATGAGGGAAATGGATAATTACACATATTCAAAGCTGATTTGAG
GTATCAAAAACAAGGTAGGCCGAAATCAACATACTGCTTTTTCAATGCTAGGAAAATGCTGTGC
CCGGTTTGCTAAGATCTTCTGCATATGAACTAATGAAGCCATTGCTGTTCCCTGTTTAGAATAA
AGATATGCCAGAATCAGTGATGGTTAATATTGTACAACCACAAAGTAAGATGCCAATAGGGAAA
AATTCTTGCTGACCTCGACAACATCAACGACAACAAGCCCATGAAGATTTCTAATTTCTTTTCT
TGCAGCCACATGTATAGCCACTGAACCGCCCATGCTAAAAAAGGAAGTTCAACCACTCTATTAA
TAAGGTTTTTTCAATGATTTAAGCTATAGACAGAAATAGAAATATTCTATACAAACAGGCTGGC
TGAACTTAAAAGAGAAAAGAAGAAATTTTATAAAGAGAAGTGATAATATATATGTCATCATTCG
TGTAGCAACACCAGGGTACAAAGATTATCAAAAGGAGAGAATTAGGAGGGAGTGTGGCGCAAGT
CGGCTGTCGCACTGAATTTGGGCACGAGTGCGAGCCAGCATGGGTGCAGTTATTGAGGTTCGAT
TGATGAACACAAAGGTAGAAAAGATTATAAGCTCAAACACCCGTGAGTATCAAGACATTCTAGC
TCCCCGTCACCTCTTTGTTGTGGTGGGAAGTCTGGCTTAATGGTTCTAAATCCACCTTTATGCC
TGCCCACTGACCACTGTGAAGAGTGCATTCTACACTAGGGGAGTGTATATTCTCAGATCCCCTA
GGTATACCCGGAATGGTTCTGTCCTACTCAGCTTGTTCTATCGGAATCGAGTCTGGTCTCCAAC
GCGGAATCGATCCTTTTCCCTTCCTTTTATAGTGCAAGGGACGAGATAGAGGTTACATGAACCT
CGGATTCCACTAGCTAAGCCCAAGCCCAACTACCATGTTCTTATCATGATTCAGATAATGTGGC
AACAGAAGAAAACAGAAGGGAAAACGCATGCTGCTGACTCACCTATGCCCAACAAGTATAATTG
CTGGTGGCAAATCTCCATACATTGTACGTATAACAGCTATGACATCATTGGTAAGAGT
						
					

			
		

Sequences
Splice junction sequence	AACGCATGCTGCTGACTCACCTATGCCCAACAAGTATAATTGCTGGTGGCAAATCTCCATACAT TGTACGTATAACAGCTATGACATCATTGGTAAGAGTctcgacaccattaggccctattttgttg cgggatatgaacttcagtatgtgcgatgcaaattcttcaggtacatcttcctgaaataaataac ggtttgat
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	CTCGACACCATTAGGCCCTATTTTGTTGCGGGATATGAACTTCAGTATGTGCGATGCAAATTCT TCAGGTACATCTTCCTGAAATAAATAACGGTTTGATGACATGGCAAAAGCAGTAAAGGTTTGTA ATTCGTTGGCTAAAACTATATTCCTAAACCAATGCTTCCAAAAGAAAAAGTTCACAGACTATAA CAGAACACAATCAGCACTCGGAGAATAAATCTTTCATTGTCAATTCCTGCTATTGCTACGTGAG TGCAAATTAGTGAAAAATTGAAGTAGCCCTAGAGCATTCAGGCACAGCACGATCATCACAAGCT CTAGAAATGACTACTGAACGAATCTAGAAGAATGGTACAAAAGCTCCTAGCCTTGCAAGAATTA TGCAATGGACTCATATATTAACATAACTCAAACATACTATAAGAACCAACCTGTATAGCATGTC CAGTGTGCCGAATCACCACCATTTGAAATTTTCCTTGCATTTGACCGATTGTTAAAGCTCTGCA AATTGTAAACCAACTAACCGATACATTACACAATTTATCTTCGATAGTGGATCATCGGCATGAG TGATTGAAGGTGTTTGATATTTCAGAACACTTAATTATGATGGCAATATGATTCCACATCCAAC AAAATCAACAATTCAGAACACAACAAACAATTTTACAAGAGGTTTCACTTCAATAAACAGCATT TTGATAATCGATTATCACCCATCCGATTTGTCATTCAAAAGCTCTAGCAACAAAGCCTGGCAAA AATTTCCATATTTTGCGAACCATAATCATGACAAGCAACTGACTTTGCTACCTTTTGATTTATA ATTTATAAGCCATAATCAACAGCTGATAAACCATAATAAAATATGCTAAAGACTGACTTTGCAA GCCCATTCCGTTGAAACTGACAAGCAGCAAAACATTGAATGACACCGAGTTAAGTCACTAGCCA AAGTTGATGAAATTAAATGTGGAGTAAACATCATGAACATGGACTAGAAAATAGATAATTTCTC ATACTCGAACATAACAAACCTGTCCAGTCTGTCGGTACCAGCTAACAACAGGATCTTTTGCACT GGGCAAGATAGGAACTTGTCTGAAAGACCTTCATACCTAACAAAGAAACACATGCACTTTAGTA TCGACTAACACAGAAGAGAAAAAAGGACATGAGAAGACAAACGATTTTACAAAACATAGATTTT TTTTTTTTTTAAAAAAAGAAGGAAATGTCAGACTGAAAGCATACCATCCTTTCCAGTACTTTTC TGTTTGCTCAAGAGGAGTGCGATATGTATAGCTGAAACAAAGTATGACAGCATACTTAGTTTCA AAATAATAACAATACTACATCTGCAATGGTGGCCAACAGGCCACCATGATTCTTTATGTGCATA GGCCTGTGAGATACAATACGAAAAACATACACTTCTCAAACTACTCACCATTCTCGTGATTCAT CGTATTTCAGGGTAGATGGAATGGACACACGAGCAGACTCGATGTTCCTTAATGGCCCACCTTT GACACTCCATTCAATCTGCATAATTCCAAAATTGATTGAACAAGAAATAAGGTGAAGAGAAAAA TTTAACAATATAAACTGCTGCCTTAGCAAGAATGGTTTACTAAGCATGATGCTAATTCAAAATT GAATTAGTTTCATTGTATAGTTGTTCTTCCATTCTATTATCAACCTTTGCATGTTTGTGTCCAT GCCGTACATACACAACTCAAATACATATGTGACTGACAGGTACTCATTTCATCTTGAAGTGATG AACACGATATCTTTTAAGATAATGAGGGAAATGGATAATTACACATATTCAAAGCTGATTTGAG GTATCAAAAACAAGGTAGGCCGAAATCAACATACTGCTTTTTCAATGCTAGGAAAATGCTGTGC CCGGTTTGCTAAGATCTTCTGCATATGAACTAATGAAGCCATTGCTGTTCCCTGTTTAGAATAA AGATATGCCAGAATCAGTGATGGTTAATATTGTACAACCACAAAGTAAGATGCCAATAGGGAAA AATTCTTGCTGACCTCGACAACATCAACGACAACAAGCCCATGAAGATTTCTAATTTCTTTTCT TGCAGCCACATGTATAGCCACTGAACCGCCCATGCTAAAAAAGGAAGTTCAACCACTCTATTAA TAAGGTTTTTTCAATGATTTAAGCTATAGACAGAAATAGAAATATTCTATACAAACAGGCTGGC TGAACTTAAAAGAGAAAAGAAGAAATTTTATAAAGAGAAGTGATAATATATATGTCATCATTCG TGTAGCAACACCAGGGTACAAAGATTATCAAAAGGAGAGAATTAGGAGGGAGTGTGGCGCAAGT CGGCTGTCGCACTGAATTTGGGCACGAGTGCGAGCCAGCATGGGTGCAGTTATTGAGGTTCGAT TGATGAACACAAAGGTAGAAAAGATTATAAGCTCAAACACCCGTGAGTATCAAGACATTCTAGC TCCCCGTCACCTCTTTGTTGTGGTGGGAAGTCTGGCTTAATGGTTCTAAATCCACCTTTATGCC TGCCCACTGACCACTGTGAAGAGTGCATTCTACACTAGGGGAGTGTATATTCTCAGATCCCCTA GGTATACCCGGAATGGTTCTGTCCTACTCAGCTTGTTCTATCGGAATCGAGTCTGGTCTCCAAC GCGGAATCGATCCTTTTCCCTTCCTTTTATAGTGCAAGGGACGAGATAGAGGTTACATGAACCT CGGATTCCACTAGCTAAGCCCAAGCCCAACTACCATGTTCTTATCATGATTCAGATAATGTGGC AACAGAAGAAAACAGAAGGGAAAACGCATGCTGCTGACTCACCTATGCCCAACAAGTATAATTG CTGGTGGCAAATCTCCATACATTGTACGTATAACAGCTATGACATCATTGGTAAGAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.020959323

Conservation Information
Conserved circRNAs	NA
PMCS	0.020959323

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							49127244-49124882(+)
49126527-49124853(+)
49127286-49124385(-)
						
						Potential amino acid sequence
						
							MPNKYNCWWQISIHCTYNSYDIIGKSLDTIRPYFVAGYELQYVRCKFFRYIFLYSMSSVPNHHH
LKFSLHLTDC*(+)
MLCPTSIIAGGKSPYIVRITAMTSLVRVSTPLGPILLRDMNFSMCDANSSGTSSCIACPVCRIT
TI*(+)
MYGDLPPAIILVGHSMGGSVAIHVAARKEIRNLHGLVVVDVVEGTAMASLVHMQKILANRAQHF
PSIEKAIEWSVKGGPLRNIESARVSIPSTLKYDESRECYTYRTPLEQTEKYWKGWYEGLSDKFL
SCPVQKILLLAGTDRLDRFVMFDWFTICRALTIGQMQGKFQMVVIRHTGHAIQEDVPEEFASHI
LKFISRNKIGPNGVETLTNDVIAVIRTMYGDLPPAIILVGHSMGGSVAIHVAARKEIRNLHGLV
VVDVVEGTAMASLVHMQKILANRAQHFPSIEKAIEWSVKGGPLRNIESARVSIPSTLKYDESRE
CYTYRTPLEQTEKYWKGWYEGLSDKFLSCPVQKILLLAGTDRLDRFVMFDWFTICRALTIGQMQ
GKFQMVVIRHTGHAIQEDVPEEFASHILKFISRNKIGPNGVETLTNDVIAVIRTMYGDLPPAII
LVGHSMGGSVAIHVAARKEIRNLHGLVVVDVVEGTAMASLVHMQKILANRAQHFPSIEKAIEWS
VKGGPLRNIESARVSIPSTLKYDESRECYTYRTPLEQTEKYWKGWYEGLSDKFLSCPVQKILLL
AGTDRLDRFVMFDWFTICRALTIGQMQGKFQMVVIRHTGHAIQEDVPEEFASHILKFISRNKIG
PNGVETLTNDVIAVIRTMYGDLPPAIILVGHSMGGSVAIHVAARKEIRNLHGLVVVDVVEGTAM
ASLVHMQKILANRAQHFPSIEKAIEWSVKGGPLRNIESARVSIPSTLKYDESRECYTYRTPLEQ
TEKYWKGWYEGLSDKFLSCPVQKILLLAGTDRLDRFVMFDWFTICRALTIGQMQGKFQMVVIRH
TGHAIQEDVPEEFASHILKFISRNKIGPNGVE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	49127244-49124882(+) 49126527-49124853(+) 49127286-49124385(-)
Potential amino acid sequence	MPNKYNCWWQISIHCTYNSYDIIGKSLDTIRPYFVAGYELQYVRCKFFRYIFLYSMSSVPNHHH LKFSLHLTDC(+) MLCPTSIIAGGKSPYIVRITAMTSLVRVSTPLGPILLRDMNFSMCDANSSGTSSCIACPVCRIT TI(+) MYGDLPPAIILVGHSMGGSVAIHVAARKEIRNLHGLVVVDVVEGTAMASLVHMQKILANRAQHF PSIEKAIEWSVKGGPLRNIESARVSIPSTLKYDESRECYTYRTPLEQTEKYWKGWYEGLSDKFL SCPVQKILLLAGTDRLDRFVMFDWFTICRALTIGQMQGKFQMVVIRHTGHAIQEDVPEEFASHI LKFISRNKIGPNGVETLTNDVIAVIRTMYGDLPPAIILVGHSMGGSVAIHVAARKEIRNLHGLV VVDVVEGTAMASLVHMQKILANRAQHFPSIEKAIEWSVKGGPLRNIESARVSIPSTLKYDESRE CYTYRTPLEQTEKYWKGWYEGLSDKFLSCPVQKILLLAGTDRLDRFVMFDWFTICRALTIGQMQ GKFQMVVIRHTGHAIQEDVPEEFASHILKFISRNKIGPNGVETLTNDVIAVIRTMYGDLPPAII LVGHSMGGSVAIHVAARKEIRNLHGLVVVDVVEGTAMASLVHMQKILANRAQHFPSIEKAIEWS VKGGPLRNIESARVSIPSTLKYDESRECYTYRTPLEQTEKYWKGWYEGLSDKFLSCPVQKILLL AGTDRLDRFVMFDWFTICRALTIGQMQGKFQMVVIRHTGHAIQEDVPEEFASHILKFISRNKIG PNGVETLTNDVIAVIRTMYGDLPPAIILVGHSMGGSVAIHVAARKEIRNLHGLVVVDVVEGTAM ASLVHMQKILANRAQHFPSIEKAIEWSVKGGPLRNIESARVSIPSTLKYDESRECYTYRTPLEQ TEKYWKGWYEGLSDKFLSCPVQKILLLAGTDRLDRFVMFDWFTICRALTIGQMQGKFQMVVIRH TGHAIQEDVPEEFASHILKFISRNKIGPNGVE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d003590_circ_g.1

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