Plant Circular RNA Database

Detail information of Zm00001d053935_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d053935_circ_g.1
					
						ID in PlantcircBase
						zma_circ_008323
					
						Alias
						zma_circ_0001752
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 243879047-243881999  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d053935						
					
						Parent gene annotation
						
							Probable phosphoinositide phosphatase SAC9
							
						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  
						
							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
						Zm00001d053935_T047:4
Zm00001d053935_T020:4
Zm00001d053935_T013:4
Zm00001d053935_T036:3
Zm00001d053935_T006:4
Zm00001d053935_T040:3
Zm00001d053935_T004:4
Zm00001d053935_T005:4
Zm00001d053935_T056:4
Zm00001d053935_T045:4
Zm00001d053935_T022:2
Zm00001d053935_T048:3
Zm00001d053935_T015:4
Zm00001d053935_T014:4
Zm00001d053935_T026:4
Zm00001d053935_T035:4
Zm00001d053935_T052:4
Zm00001d053935_T010:4
Zm00001d053935_T009:4
Zm00001d053935_T024:3
Zm00001d053935_T055:3
Zm00001d053935_T037:4
Zm00001d053935_T028:4
Zm00001d053935_T041:4
Zm00001d053935_T039:4
Zm00001d053935_T043:4
Zm00001d053935_T017:2
Zm00001d053935_T050:4
Zm00001d053935_T033:3
Zm00001d053935_T019:3
Zm00001d053935_T003:4
Zm00001d053935_T030:3
Zm00001d053935_T001:4
Zm00001d053935_T054:4
Zm00001d053935_T002:3
Zm00001d053935_T011:4

General Information
CircRNA Name	Zm00001d053935_circ_g.1
ID in PlantcircBase	zma_circ_008323
Alias	zma_circ_0001752
Organism	Zea mays
Position	chr4: 243879047-243881999 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d053935
Parent gene annotation	Probable phosphoinositide phosphatase SAC9
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	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	Zm00001d053935_T047:4 Zm00001d053935_T020:4 Zm00001d053935_T013:4 Zm00001d053935_T036:3 Zm00001d053935_T006:4 Zm00001d053935_T040:3 Zm00001d053935_T004:4 Zm00001d053935_T005:4 Zm00001d053935_T056:4 Zm00001d053935_T045:4 Zm00001d053935_T022:2 Zm00001d053935_T048:3 Zm00001d053935_T015:4 Zm00001d053935_T014:4 Zm00001d053935_T026:4 Zm00001d053935_T035:4 Zm00001d053935_T052:4 Zm00001d053935_T010:4 Zm00001d053935_T009:4 Zm00001d053935_T024:3 Zm00001d053935_T055:3 Zm00001d053935_T037:4 Zm00001d053935_T028:4 Zm00001d053935_T041:4 Zm00001d053935_T039:4 Zm00001d053935_T043:4 Zm00001d053935_T017:2 Zm00001d053935_T050:4 Zm00001d053935_T033:3 Zm00001d053935_T019:3 Zm00001d053935_T003:4 Zm00001d053935_T030:3 Zm00001d053935_T001:4 Zm00001d053935_T054:4 Zm00001d053935_T002:3 Zm00001d053935_T011:4

			
						 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  
						
							TCGGGACTGTCTTTGTCAAATAAGATCAAGTTGTACTACTATGCTGATACATATGAGATGGGAA
AGATCGGCAGTCTCTCAGCTGTATAATGTATGTGAGgttgaaactgccaatgactctgaaccac
tgctttcattactggcgccttttggtactggagagtatacgtcttactggaaagctccacaagg
tatcactt

									
								

					

						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
						
							GTTGAAACTGCCAATGACTCTGAACCACTGCTTTCATTACTGGCGCCTTTTGGTACTGGAGAGT
ATACGTCTTACTGGAAAGCTCCACAAGGTATCACTTCAGTGGAATTCTCAATTGTTCTTGGTGG
TTTATCAGATATTGCAGGAGTTTCCATAATTGTCAGTTCTTGCGGTTACTCAGCATCTGACTGC
CCAATTGTAAGATAGCATATCTTACTTTCTCTTCCTTCATCATGCTATCCTTATTTTTATCTAT
AAAATCAGTACTGACAATTTTAGCTAGGCATACTTAATATTGTATACACAGTATCCTAGCTATA
TGGAACTATGGGCATATCTTTCATTTCTGTTTTCTTAATGATTGAGAACAAAGAAGGATATTTA
CTAGAGTTACTGAAATCATCCTTTTTAATCATAAAATCACGAAGCTTGATTGAATATATGTTCT
TCCTGAGCAAGAGGAGGAAAACATTTCAGTACGGATGTACCATTAACAAGTTGAGCATGATACA
TGTTAACAAGGGAAGCAATATGAAAAATACTATCTTCATGTACATAATTGTATGTCACATTGTC
TTGAAAGACGCCTCTTGCTTTAGTCCACTTATTTCCAAGAAAGAAAAGAGCTCATGTTGGAAAT
CACTCCCTAGCCTTTCTTCAGTGTTTATCACAGACACACTAGGAAATCACTCCCTCTGTCTTCA
GTGTTTATCACAAACACACTAGGATTTCACACTTTCTTTATCTTCAGTGTTTATCATAAACACA
CACTAGGAAATCACTCCAATGTTTATCACAAACACACGAGGAAATCACTCCCTTTATCTCTTTT
GATTGATGCGGCTCTCTCAGCCCTCGCCATGTTCTCATATATATAGCTGATAAACCTGCCCATG
ATATCATCCTATTTACTGCAGTCGTAACTCCTATGTTTGCCTATTAGTCTCCTTAGAACTAGCT
GAAAATCTGCTAGTACTAAAGACTGCACCTAGACAGAGTGAACCTGGACACATGCATGGACACA
CAGGATTATAGCTAACAACTTATGTCCTTTGTAATTCGGCAATAACTTGTTTTAACAACCATAT
GATGCTTGTGGCTTCGTAATTTTGTGTCGATCACCTATCTTTCTGTACATACCATTAGTGTTGC
TATGAAAAGCAAATATATCTAATTTGTTGACATAATCTTTGTCTGGAGTTAGTGCAATGTGCAA
GAACTGCAAGATGTCCTTTTCATGTACTGCAGAGTTAGCTATCTATGCACAACCAGCGGATTAT
TTTAACTAGCCTGCTGAGCTATCTCATCTCTCTTTTTTTTGTGCATTTTCCTGCAAAACAGTGT
TTCCATATTCTGTGATAGCTAGCTATTTGTATATAACAAGCTAGCCTGTTGAGCTGTTTTCATT
TTTTTCCATTCCTTTGATTTATTTTTTCCTTTTAATGTTCATAATCATGCTGCTTGTGCAGGTA
GAGATATGGGCGAGTAATAAAATACACCGAGAAGATCGTACATTTATAGGAAAGTGGGATGTAC
AGGATATAATATCTTCATCTCCACAGCTTCGTGGACCTGAAAAATCTAGTAGATTGAGTGAAGA
ACCAAGACACATTAAATTTCACTTCCCAAATCCTATCCGTTGTCGTATAATTTCAATAAAAATG
ACACTTTCCCATAGAGGTTCTCATTCAACCAAGTTTAGTGAGGAGTTTGATCTTCTATCATTGA
ATGATAGCTCATCTTATGAATCGAAGCCAACCAATTTACATAATTCATTTATCCATGCAAAAAG
AATTGTAGTTTTTGGCAGTTTGTTGAGAAAGGAGATGGAGCCTGACACATCAGGGGGGATAATG
AGAATGAAAAGTTATTTAGACAGATCACCGGCCTTGGGGAGATTTAGGGTAAACCCTATGTCTT
TTGCTGACAGTTTTGAGCTTTGCATTCTAGCAGTGGCTGAAACTTCTCTTCTTTATTTTCCAGA
TCCCAGTTGAAGCTGAGAGGCTGAGAGATAATGATCTTGTTCTTGAGCAATATCTCTTAGCTAA
TTCACCTGGAATAGCTGGATTCCGGCTTGATTCTTTCAGTGTTATAAGACCTCGTGTGACCCAT
TCACCTTCTTCATCAGAGTTGGACATGAGGGAGTTTTCATTGACACGAATGGAAGATAGATTTA
TAAACCCAGCAATTCTGTATATACAGGTCACAGTTGTTAAGGTAATAGGCCACTGTCACTCTTC
AAAATTCACTTCGGTAGCTATGGTTTGGTTATTTTATGCTTCTTGAAATCTCCTTCAATGCTTG
TCCCTGAACGGTTCAAATAGCCATGGCATGGGTCCAGATGGTCATGTGAACTAGTTTTGTCGAG
TAAGGCCTGTGTCAGCAGACAGTTCTAATATACTAATTAGTGGAATGTCCAACTGATCTGTCTT
CGAAACTTCATTTACATATACTGGTGGAAGTCAATGTTGTCTGAACGAATGACTACAACAAAAT
ATTGTTCACCTATGCCATGATGGTTTTTTGAGGTTTGCTGCAAACTATGATAATTCTAGACGAG
CTGTTAATTGAGGGTTGAACCTTTTGCTACTTGTAGTTTTGTGAGGGCCTATTTTGTATGTGTG
CATAAAACATTTCTGCTGTGCTTGTGATTTTGTACAGGAGTCCGGCAAGTTGGTTGTAGAGGAA
TACCGTTTACCAGAAGTAAAAGCAAACACGCCACTATATTTTGATTTCCCAGATCTACAACAGG
ATGCGCGCTGTGTTATCTTTAGATTGCTTGGTGACGTCACTGCCTTTGTCGACGACATTTCTGA
GCTTGAGAACTTAAACTTGCGGAATCTTCCTTTGGCGTCGGGACTGTCTTTGTCAAATAAGATC
AAGTTGTACTACTATGCTGATACATATGAGATGGGAAAGATCGGCAGTCTCTCAGCTGTATAAT
GTATGTGAG
						
					

			
		

Sequences
Splice junction sequence	TCGGGACTGTCTTTGTCAAATAAGATCAAGTTGTACTACTATGCTGATACATATGAGATGGGAA AGATCGGCAGTCTCTCAGCTGTATAATGTATGTGAGgttgaaactgccaatgactctgaaccac tgctttcattactggcgccttttggtactggagagtatacgtcttactggaaagctccacaagg tatcactt
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	GTTGAAACTGCCAATGACTCTGAACCACTGCTTTCATTACTGGCGCCTTTTGGTACTGGAGAGT ATACGTCTTACTGGAAAGCTCCACAAGGTATCACTTCAGTGGAATTCTCAATTGTTCTTGGTGG TTTATCAGATATTGCAGGAGTTTCCATAATTGTCAGTTCTTGCGGTTACTCAGCATCTGACTGC CCAATTGTAAGATAGCATATCTTACTTTCTCTTCCTTCATCATGCTATCCTTATTTTTATCTAT AAAATCAGTACTGACAATTTTAGCTAGGCATACTTAATATTGTATACACAGTATCCTAGCTATA TGGAACTATGGGCATATCTTTCATTTCTGTTTTCTTAATGATTGAGAACAAAGAAGGATATTTA CTAGAGTTACTGAAATCATCCTTTTTAATCATAAAATCACGAAGCTTGATTGAATATATGTTCT TCCTGAGCAAGAGGAGGAAAACATTTCAGTACGGATGTACCATTAACAAGTTGAGCATGATACA TGTTAACAAGGGAAGCAATATGAAAAATACTATCTTCATGTACATAATTGTATGTCACATTGTC TTGAAAGACGCCTCTTGCTTTAGTCCACTTATTTCCAAGAAAGAAAAGAGCTCATGTTGGAAAT CACTCCCTAGCCTTTCTTCAGTGTTTATCACAGACACACTAGGAAATCACTCCCTCTGTCTTCA GTGTTTATCACAAACACACTAGGATTTCACACTTTCTTTATCTTCAGTGTTTATCATAAACACA CACTAGGAAATCACTCCAATGTTTATCACAAACACACGAGGAAATCACTCCCTTTATCTCTTTT GATTGATGCGGCTCTCTCAGCCCTCGCCATGTTCTCATATATATAGCTGATAAACCTGCCCATG ATATCATCCTATTTACTGCAGTCGTAACTCCTATGTTTGCCTATTAGTCTCCTTAGAACTAGCT GAAAATCTGCTAGTACTAAAGACTGCACCTAGACAGAGTGAACCTGGACACATGCATGGACACA CAGGATTATAGCTAACAACTTATGTCCTTTGTAATTCGGCAATAACTTGTTTTAACAACCATAT GATGCTTGTGGCTTCGTAATTTTGTGTCGATCACCTATCTTTCTGTACATACCATTAGTGTTGC TATGAAAAGCAAATATATCTAATTTGTTGACATAATCTTTGTCTGGAGTTAGTGCAATGTGCAA GAACTGCAAGATGTCCTTTTCATGTACTGCAGAGTTAGCTATCTATGCACAACCAGCGGATTAT TTTAACTAGCCTGCTGAGCTATCTCATCTCTCTTTTTTTTGTGCATTTTCCTGCAAAACAGTGT TTCCATATTCTGTGATAGCTAGCTATTTGTATATAACAAGCTAGCCTGTTGAGCTGTTTTCATT TTTTTCCATTCCTTTGATTTATTTTTTCCTTTTAATGTTCATAATCATGCTGCTTGTGCAGGTA GAGATATGGGCGAGTAATAAAATACACCGAGAAGATCGTACATTTATAGGAAAGTGGGATGTAC AGGATATAATATCTTCATCTCCACAGCTTCGTGGACCTGAAAAATCTAGTAGATTGAGTGAAGA ACCAAGACACATTAAATTTCACTTCCCAAATCCTATCCGTTGTCGTATAATTTCAATAAAAATG ACACTTTCCCATAGAGGTTCTCATTCAACCAAGTTTAGTGAGGAGTTTGATCTTCTATCATTGA ATGATAGCTCATCTTATGAATCGAAGCCAACCAATTTACATAATTCATTTATCCATGCAAAAAG AATTGTAGTTTTTGGCAGTTTGTTGAGAAAGGAGATGGAGCCTGACACATCAGGGGGGATAATG AGAATGAAAAGTTATTTAGACAGATCACCGGCCTTGGGGAGATTTAGGGTAAACCCTATGTCTT TTGCTGACAGTTTTGAGCTTTGCATTCTAGCAGTGGCTGAAACTTCTCTTCTTTATTTTCCAGA TCCCAGTTGAAGCTGAGAGGCTGAGAGATAATGATCTTGTTCTTGAGCAATATCTCTTAGCTAA TTCACCTGGAATAGCTGGATTCCGGCTTGATTCTTTCAGTGTTATAAGACCTCGTGTGACCCAT TCACCTTCTTCATCAGAGTTGGACATGAGGGAGTTTTCATTGACACGAATGGAAGATAGATTTA TAAACCCAGCAATTCTGTATATACAGGTCACAGTTGTTAAGGTAATAGGCCACTGTCACTCTTC AAAATTCACTTCGGTAGCTATGGTTTGGTTATTTTATGCTTCTTGAAATCTCCTTCAATGCTTG TCCCTGAACGGTTCAAATAGCCATGGCATGGGTCCAGATGGTCATGTGAACTAGTTTTGTCGAG TAAGGCCTGTGTCAGCAGACAGTTCTAATATACTAATTAGTGGAATGTCCAACTGATCTGTCTT CGAAACTTCATTTACATATACTGGTGGAAGTCAATGTTGTCTGAACGAATGACTACAACAAAAT ATTGTTCACCTATGCCATGATGGTTTTTTGAGGTTTGCTGCAAACTATGATAATTCTAGACGAG CTGTTAATTGAGGGTTGAACCTTTTGCTACTTGTAGTTTTGTGAGGGCCTATTTTGTATGTGTG CATAAAACATTTCTGCTGTGCTTGTGATTTTGTACAGGAGTCCGGCAAGTTGGTTGTAGAGGAA TACCGTTTACCAGAAGTAAAAGCAAACACGCCACTATATTTTGATTTCCCAGATCTACAACAGG ATGCGCGCTGTGTTATCTTTAGATTGCTTGGTGACGTCACTGCCTTTGTCGACGACATTTCTGA GCTTGAGAACTTAAACTTGCGGAATCTTCCTTTGGCGTCGGGACTGTCTTTGTCAAATAAGATC AAGTTGTACTACTATGCTGATACATATGAGATGGGAAAGATCGGCAGTCTCTCAGCTGTATAAT GTATGTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.061904253

Conservation Information
Conserved circRNAs	NA
PMCS	0.061904253

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							243881941-243881986(+)
243881990-243879200(+)
243879085-243881940(-)
						
						Potential amino acid sequence
						
							MLIHMRWERSAVSQLYNVCEVETANDSEPLLSLLAPFGTGEYTSYWKAPQGITSVEFSIVLGGL
SDIAGVSIIVSSCGYSASDCPIVEIWASNKIHREDRTFIGKWDVQDIISSSPQLRGPEKSSRLS
EEPRHIKFHFPNPIRCRIISIKMTLSHRGSHSTKFSEEFDLLSLNDSSSYESKPTNLHNSFIHA
KRIVVFGSLLRKEMEPDTSGGIMRMKSYLDRSPALGRFRIPVEAERLRDNDLVLEQYLLANSPG
IAGFRLDSFSVIRPRVTHSPSSSELDMREFSLTRMEDRFINPAILYIQVTVVKESGKLVVEEYR
LPEVKANTPLYFDFPDLQQDARCVIFRLLGDVTAFVDDISELENLNLRNLPLASGLSLSNKIKL
YYYADTYEMGKIGSLSAV*(+)
MYVRLKLPMTLNHCFHYWRLLVLESIRLTGKLHKVSLQWNSQLFLVVYQILQEFP*(+)
MKAVVQSHWQFQPHIHYTAERLPIFPISYVSA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	243881941-243881986(+) 243881990-243879200(+) 243879085-243881940(-)
Potential amino acid sequence	MLIHMRWERSAVSQLYNVCEVETANDSEPLLSLLAPFGTGEYTSYWKAPQGITSVEFSIVLGGL SDIAGVSIIVSSCGYSASDCPIVEIWASNKIHREDRTFIGKWDVQDIISSSPQLRGPEKSSRLS EEPRHIKFHFPNPIRCRIISIKMTLSHRGSHSTKFSEEFDLLSLNDSSSYESKPTNLHNSFIHA KRIVVFGSLLRKEMEPDTSGGIMRMKSYLDRSPALGRFRIPVEAERLRDNDLVLEQYLLANSPG IAGFRLDSFSVIRPRVTHSPSSSELDMREFSLTRMEDRFINPAILYIQVTVVKESGKLVVEEYR LPEVKANTPLYFDFPDLQQDARCVIFRLLGDVTAFVDDISELENLNLRNLPLASGLSLSNKIKL YYYADTYEMGKIGSLSAV(+) MYVRLKLPMTLNHCFHYWRLLVLESIRLTGKLHKVSLQWNSQLFLVVYQILQEFP(+) MKAVVQSHWQFQPHIHYTAERLPIFPISYVSA*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d053935_circ_g.1

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