Plant Circular RNA Database

Detail information of Zm00001d004396_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d004396_circ_g.4
					
						ID in PlantcircBase
						zma_circ_007242
					
						Alias
						zma_circ_0000765, GRMZM2G137984_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 108746786-108748280  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d004396						
					
						Parent gene annotation
						
							Vacuolar protein sorting-associated protein 54 chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d004396_circ_g.1 Zm00001d004396_circ_g.2 Zm00001d004396_circ_g.3 Zm00001d004396_circ_g.5 Zm00001d004396_circ_g.6 						
					
						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
						Zm00001d004396_T018:4
Zm00001d004396_T029:4
Zm00001d004396_T031:4
Zm00001d004396_T039:4
Zm00001d004396_T036:3
Zm00001d004396_T012:4
Zm00001d004396_T003:4
Zm00001d004396_T033:4
Zm00001d004396_T004:4
Zm00001d004396_T038:4
Zm00001d004396_T040:4
Zm00001d004396_T014:4
Zm00001d004396_T028:4
Zm00001d004396_T021:4
Zm00001d004396_T002:4
Zm00001d004396_T023:4
Zm00001d004396_T048:4
Zm00001d004396_T025:4
Zm00001d004396_T006:4
Zm00001d004396_T049:4
Zm00001d004396_T034:4
Zm00001d004396_T009:4
Zm00001d004396_T019:4
Zm00001d004396_T047:4
Zm00001d004396_T043:4
Zm00001d004396_T041:4
Zm00001d004396_T027:4
Zm00001d004396_T007:4
Zm00001d004396_T016:4
Zm00001d004396_T045:4

General Information
CircRNA Name	Zm00001d004396_circ_g.4
ID in PlantcircBase	zma_circ_007242
Alias	zma_circ_0000765, GRMZM2G137984_C1
Organism	Zea mays
Position	chr2: 108746786-108748280 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d004396
Parent gene annotation	Vacuolar protein sorting-associated protein 54 chloroplastic
Parent gene strand	-
Alternative splicing	Zm00001d004396_circ_g.1 Zm00001d004396_circ_g.2 Zm00001d004396_circ_g.3 Zm00001d004396_circ_g.5 Zm00001d004396_circ_g.6
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	Zm00001d004396_T018:4 Zm00001d004396_T029:4 Zm00001d004396_T031:4 Zm00001d004396_T039:4 Zm00001d004396_T036:3 Zm00001d004396_T012:4 Zm00001d004396_T003:4 Zm00001d004396_T033:4 Zm00001d004396_T004:4 Zm00001d004396_T038:4 Zm00001d004396_T040:4 Zm00001d004396_T014:4 Zm00001d004396_T028:4 Zm00001d004396_T021:4 Zm00001d004396_T002:4 Zm00001d004396_T023:4 Zm00001d004396_T048:4 Zm00001d004396_T025:4 Zm00001d004396_T006:4 Zm00001d004396_T049:4 Zm00001d004396_T034:4 Zm00001d004396_T009:4 Zm00001d004396_T019:4 Zm00001d004396_T047:4 Zm00001d004396_T043:4 Zm00001d004396_T041:4 Zm00001d004396_T027:4 Zm00001d004396_T007:4 Zm00001d004396_T016:4 Zm00001d004396_T045:4

			
						 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  
						
							TAATATTTCCACAACACGTTGGACCACCTCCAAAGATAGTGATGGTAAACATTTACTGATGTCA
ACGTATTCGGATAACATCTTCAACAGTATTAAACCActttgtaacagctttagcaaattgactc
ggctgcacgtcattatcctctgggccattccagccttccacaatttggggtaattttctaagat
ttgcaagc

									
								

					

						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: 478
Transcript exons: 108746786-108746947,108747071-108747150,108747715-108747
796,108748127-108748280
CTTTGTAACAGCTTTAGCAAATTGACTCGGCTGCACGTCATTATCCTCTGGGCCATTCCAGCCT
TCCACAATTTGGGGTAATTTTCTAAGATTTGCAAGCAACCTCTCTCTCATTATCTGGACAAGTT
TGTTGTGAATTTCATCTCGATGGATCTTGTAGTCCTGAGCTACTCTATCCAGCTCAGACATTAA
CAGATGTTTGCGCGCTTCAGGTATTTTCAGGAAAAGTACTCGCCTGATATCTGGAATTAAAGAA
TGCATAAAACTAATGATTTGACTCGCCAAAGCTAAATGTTTGGACGTAATTGATTTAAGTCCAG
ACACCTGCATGGCTCCTGCACCGAGAACAAGTTGGCAAGTCCTAGTGTTGAAAAGCTTTAATAT
TTCCACAACACGTTGGACCACCTCCAAAGATAGTGATGGTAAACATTTACTGATGTCAACGTAT
TCGGATAACATCTTCAACAGTATTAAACCA
						
					

						Genomic sequence
						
							CTTTGTAACAGCTTTAGCAAATTGACTCGGCTGCACGTCATTATCCTCTGGGCCATTCCAGCCT
TCCACAATTTGGGGTAATTTTCTAAGATTTGCAAGCAACCTCTCTCTCATTATCTGGACAAGTT
TGTTGTGAATTTCATCTCGATGGATCTTGTAGTCCTGTTATTTCATTTAAAAAACTTCTATGAA
AATGCATTCGTGAAAGGACAAGAAAGGATAGTTGCACTCAAGACTCATGAATCGCTGTGACTCA
AATGCCAATATAAAAAATTGGAATTGCACCTGAGCTACTCTATCCAGCTCAGACATTAACAGAT
GTTTGCGCGCTTCAGGTATTTTCAGGAAAAGTACTCGCCTGATATCTGCAGTTTCAAGGAAAAC
TTATAAAAACTGGAAAGAAAATATATCATGGTCACTCACTGCATTTCACAGCATATATCCCATC
ACTCGAGTTGGCCTGCCATCATTTTTGTATACAAGATTGTAGCTAGTACTAGTTATTAGTGTTT
GAACTCTTTAATATGTAAGAGACTCAATTGTACCATGTGATTAATATGAAGCTATGAGCACGTG
TGGTCATTTCTCAGTTTTGTATGAGACTTAGTTCTCCTTGGGTCTGTGTCTTGTAGCTATAGAG
TATGGACATTAGTACTTCAAAATTTTATGGAAGTAGGATCCAAAAATAGCAAATCAATACAGTG
CATGTTTGGTTCCTAGCATCAGCAATTCAGTGCAGCAAAAGAAAAATCATGACAAACTCGTGGG
GTAATTACAGTTTGGACATACTGTGCTAAAAAAATTTAATTGGTTAGGCAGTAGACTTGTATGA
AAAACACATGGTCTTTAGAACTCCAGTAGCTAAGCATCCTGAAGTACTCCAAGAATGTAGAAAT
GGTAATTTGTAGAAGATTAAAATAAATGGTTACCTGGAATTAAAGAATGCATAAAACTAATGAT
TTGACTCGCCAAAGCTAAATGTTTGGACGTAATTGATTTAAGTCCAGACACCTGAGAAGCAAAA
CAGAAATAAAAAGGTCAGTAAATTAGGAGTATTGCAAGGAAGAAAACTGAGCTTCTAAATCAAA
AAGCTCTTGAGGTTGGTATTGGCTGTACTGAAAAATAAATAAAAATTGATTAAAATAGTGTCCA
AATAGGAACAGCTTATTTTGCAACTAGTTGTTCCATGCAGTGATGCATGTGATTCAGTGTATGC
ACCTCAGGTTGTTTAAAAAATGCAGACATTACTCACGTCAAGTGAAAATCACATTAAACATTTG
TATACAGTTGCCAATGAAATAAAGAGGCATTCTTAATAACTGAAATGGCATGCTGATATACCTG
CATGGCTCCTGCACCGAGAACAAGTTGGCAAGTCCTAGTGTTGAAAAGCTTTAATATTTCCACA
ACACGTTGGACCACCTCCAAAGATAGTGATGGTAAACATTTACTGATGTCAACGTATTCGGATA
ACATCTTCAACAGTATTAAACCA
						
					

			
		

Sequences
Splice junction sequence	TAATATTTCCACAACACGTTGGACCACCTCCAAAGATAGTGATGGTAAACATTTACTGATGTCA ACGTATTCGGATAACATCTTCAACAGTATTAAACCActttgtaacagctttagcaaattgactc ggctgcacgtcattatcctctgggccattccagccttccacaatttggggtaattttctaagat ttgcaagc
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: 478 Transcript exons: 108746786-108746947,108747071-108747150,108747715-108747 796,108748127-108748280 CTTTGTAACAGCTTTAGCAAATTGACTCGGCTGCACGTCATTATCCTCTGGGCCATTCCAGCCT TCCACAATTTGGGGTAATTTTCTAAGATTTGCAAGCAACCTCTCTCTCATTATCTGGACAAGTT TGTTGTGAATTTCATCTCGATGGATCTTGTAGTCCTGAGCTACTCTATCCAGCTCAGACATTAA CAGATGTTTGCGCGCTTCAGGTATTTTCAGGAAAAGTACTCGCCTGATATCTGGAATTAAAGAA TGCATAAAACTAATGATTTGACTCGCCAAAGCTAAATGTTTGGACGTAATTGATTTAAGTCCAG ACACCTGCATGGCTCCTGCACCGAGAACAAGTTGGCAAGTCCTAGTGTTGAAAAGCTTTAATAT TTCCACAACACGTTGGACCACCTCCAAAGATAGTGATGGTAAACATTTACTGATGTCAACGTAT TCGGATAACATCTTCAACAGTATTAAACCA
Genomic sequence	CTTTGTAACAGCTTTAGCAAATTGACTCGGCTGCACGTCATTATCCTCTGGGCCATTCCAGCCT TCCACAATTTGGGGTAATTTTCTAAGATTTGCAAGCAACCTCTCTCTCATTATCTGGACAAGTT TGTTGTGAATTTCATCTCGATGGATCTTGTAGTCCTGTTATTTCATTTAAAAAACTTCTATGAA AATGCATTCGTGAAAGGACAAGAAAGGATAGTTGCACTCAAGACTCATGAATCGCTGTGACTCA AATGCCAATATAAAAAATTGGAATTGCACCTGAGCTACTCTATCCAGCTCAGACATTAACAGAT GTTTGCGCGCTTCAGGTATTTTCAGGAAAAGTACTCGCCTGATATCTGCAGTTTCAAGGAAAAC TTATAAAAACTGGAAAGAAAATATATCATGGTCACTCACTGCATTTCACAGCATATATCCCATC ACTCGAGTTGGCCTGCCATCATTTTTGTATACAAGATTGTAGCTAGTACTAGTTATTAGTGTTT GAACTCTTTAATATGTAAGAGACTCAATTGTACCATGTGATTAATATGAAGCTATGAGCACGTG TGGTCATTTCTCAGTTTTGTATGAGACTTAGTTCTCCTTGGGTCTGTGTCTTGTAGCTATAGAG TATGGACATTAGTACTTCAAAATTTTATGGAAGTAGGATCCAAAAATAGCAAATCAATACAGTG CATGTTTGGTTCCTAGCATCAGCAATTCAGTGCAGCAAAAGAAAAATCATGACAAACTCGTGGG GTAATTACAGTTTGGACATACTGTGCTAAAAAAATTTAATTGGTTAGGCAGTAGACTTGTATGA AAAACACATGGTCTTTAGAACTCCAGTAGCTAAGCATCCTGAAGTACTCCAAGAATGTAGAAAT GGTAATTTGTAGAAGATTAAAATAAATGGTTACCTGGAATTAAAGAATGCATAAAACTAATGAT TTGACTCGCCAAAGCTAAATGTTTGGACGTAATTGATTTAAGTCCAGACACCTGAGAAGCAAAA CAGAAATAAAAAGGTCAGTAAATTAGGAGTATTGCAAGGAAGAAAACTGAGCTTCTAAATCAAA AAGCTCTTGAGGTTGGTATTGGCTGTACTGAAAAATAAATAAAAATTGATTAAAATAGTGTCCA AATAGGAACAGCTTATTTTGCAACTAGTTGTTCCATGCAGTGATGCATGTGATTCAGTGTATGC ACCTCAGGTTGTTTAAAAAATGCAGACATTACTCACGTCAAGTGAAAATCACATTAAACATTTG TATACAGTTGCCAATGAAATAAAGAGGCATTCTTAATAACTGAAATGGCATGCTGATATACCTG CATGGCTCCTGCACCGAGAACAAGTTGGCAAGTCCTAGTGTTGAAAAGCTTTAATATTTCCACA ACACGTTGGACCACCTCCAAAGATAGTGATGGTAAACATTTACTGATGTCAACGTATTCGGATA ACATCTTCAACAGTATTAAACCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.106621514

Conservation Information
Conserved circRNAs	NA
PMCS	0.106621514

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							108748132-108746863(+)
108748263-108748244(-)
108746843-108748244(-)
						
						Potential amino acid sequence
						
							MAPAPRTSWQVLVLKSFNISTTRWTTSKDSDGKHLLMSTYSDNIFNSIKPLCNSFSKLTRLHVI
ILWAIPAFHNLG*(+)
MLSEYVDISKCLPSLSLEVVQRVVEILKLFNTRTCQLVLGAGAMQVSGLKSITSKHLALASQII
SFMHSLIPDIRRVLFLKIPEARKHLLMSELDRVAQDYKIHRDEIHNKLVQIMRERLLANLRKLP
QIVEGWNGPEDNDVQPSQFAKAVTKWFNTVEDVIRIR*(-)
MAQRIMTCSRVNLLKLLQSGLILLKMLSEYVDISKCLPSLSLEVVQRVVEILKLFNTRTCQLVL
GAGAMQVSGLKSITSKHLALASQIISFMHSLIPDIRRVLFLKIPEARKHLLMSELDRVAQDYKI
HRDEIHNKLVQIMRERLLANLRKLPQIVEGWNGPEDNDVQPSQFAKAVTKWFNTVEDVIRIR*(
-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	108748132-108746863(+) 108748263-108748244(-) 108746843-108748244(-)
Potential amino acid sequence	MAPAPRTSWQVLVLKSFNISTTRWTTSKDSDGKHLLMSTYSDNIFNSIKPLCNSFSKLTRLHVI ILWAIPAFHNLG(+) MLSEYVDISKCLPSLSLEVVQRVVEILKLFNTRTCQLVLGAGAMQVSGLKSITSKHLALASQII SFMHSLIPDIRRVLFLKIPEARKHLLMSELDRVAQDYKIHRDEIHNKLVQIMRERLLANLRKLP QIVEGWNGPEDNDVQPSQFAKAVTKWFNTVEDVIRIR(-) MAQRIMTCSRVNLLKLLQSGLILLKMLSEYVDISKCLPSLSLEVVQRVVEILKLFNTRTCQLVL GAGAMQVSGLKSITSKHLALASQIISFMHSLIPDIRRVLFLKIPEARKHLLMSELDRVAQDYKI HRDEIHNKLVQIMRERLLANLRKLPQIVEGWNGPEDNDVQPSQFAKAVTKWFNTVEDVIRIR*( -)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d004396_circ_g.4

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