Plant Circular RNA Database

Detail information of Zm00001d052943_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d052943_circ_g.2
					
						ID in PlantcircBase
						zma_circ_008233
					
						Alias
						Zm04circ00086, zma_circ_0001573, ZmciR182
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 205714860-205715767  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d052943						
					
						Parent gene annotation
						
							Ubiquitin carboxyl-terminal hydrolase 13
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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
						Zm00001d052943_T012:5
Zm00001d052943_T028:2
Zm00001d052943_T009:5
Zm00001d052943_T021:3
Zm00001d052943_T003:2
Zm00001d052943_T018:5
Zm00001d052943_T016:4
Zm00001d052943_T001:4
Zm00001d052943_T011:5
Zm00001d052943_T002:5
Zm00001d052943_T026:4
Zm00001d052943_T022:5
Zm00001d052943_T004:2
Zm00001d052943_T015:3
Zm00001d052943_T024:5
Zm00001d052943_T023:2

General Information
CircRNA Name	Zm00001d052943_circ_g.2
ID in PlantcircBase	zma_circ_008233
Alias	Zm04circ00086, zma_circ_0001573, ZmciR182
Organism	Zea mays
Position	chr4: 205714860-205715767 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d052943
Parent gene annotation	Ubiquitin carboxyl-terminal hydrolase 13
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
Tissues	leaf, endosperm, 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	Zm00001d052943_T012:5 Zm00001d052943_T028:2 Zm00001d052943_T009:5 Zm00001d052943_T021:3 Zm00001d052943_T003:2 Zm00001d052943_T018:5 Zm00001d052943_T016:4 Zm00001d052943_T001:4 Zm00001d052943_T011:5 Zm00001d052943_T002:5 Zm00001d052943_T026:4 Zm00001d052943_T022:5 Zm00001d052943_T004:2 Zm00001d052943_T015:3 Zm00001d052943_T024:5 Zm00001d052943_T023:2

			
						 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  
						
							GGACATTATTTGTTTCCAAAAATCACCAGGAGCAGAATATGATGCACCCGTGCGATATCCGGAT
GTTCCTTCATTTTTGGAGTATGTCCATAATAGGCAGgtggggcaactgagagaaatatcaaata
aggcacacaatgttgagttgaagctgtttttggaagtagaacttgggctggtagtgatacacct
gatttgtg

						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: 456
Transcript exons: 205714860-205714937,205715046-205715134,205715251-205715
359,205715498-205715566,205715657-205715767
GTGGGGCAACTGAGAGAAATATCAAATAAGGCACACAATGTTGAGTTGAAGCTGTTTTTGGAAG
TAGAACTTGGGCTGGATTTGCGGCCTCTCCCTCCTCCTGAGAAGGGCAAGGAAGATATTCTTCT
TTTCTTCAAATTCTACAACCCAGAAAAGGAAGAACTCTGTTTCATGGGGAGGCTCTTTGTGAAG
GCCTTGGGAAAACCTTCAGAAATCCTGGCAAAACTAAACGAAATGGCTGGATTTCCCCCTGATC
AAGAAATTGAGCTTTTTGAGGAAATTAAGTTTGAGCCAAACGTGATGTGTGAAACTATAGACAA
GAAACTCACTTTTCATTATAGTCAGCTTGAAGATGGGGACATTATTTGTTTCCAAAAATCACCA
GGAGCAGAATATGATGCACCCGTGCGATATCCGGATGTTCCTTCATTTTTGGAGTATGTCCATA
ATAGGCAG
						
						Genomic sequence
						
							GTGGGGCAACTGAGAGAAATATCAAATAAGGCACACAATGTTGAGTTGAAGCTGTTTTTGGAAG
TAGAACTTGGGCTGGTAGTGATACACCTGATTTGTGCTTCCTTCTTGTTCTGCATGTTGCTTAT
AGTATCTGCTGTGGCACTCAGCTGTGGATCCCTTACCTATCTTTATTTACTCATTTAGGATTTG
CGGCCTCTCCCTCCTCCTGAGAAGGGCAAGGAAGATATTCTTCTTTTCTTCAAATTCTACAACC
CAGAAAAGGAAGAACTCTGGTACATCTTCTGTTTTAAGTGATAACATTGACATCTTGTCCTAAG
TACTGCTTCTTTATTCTTCATTAAAATAATGATATTATCATGTGACTCATGGAGCTGTTTCATG
CATGTAGTTTCATGGGGAGGCTCTTTGTGAAGGCCTTGGGAAAACCTTCAGAAATCCTGGCAAA
ACTAAACGAAATGGCTGGATTTCCCCCTGATCAAGAAATTGAGCTTTTTGAGGCAATATTGATT
TTTTTGATAAATTTATTGTCCCGATGATTTGTCCACTAGTGCATTGTTATACAGATGCATTAAT
TCTGTCTGTGATGGCCTTATGATGGATACTGTGCTTAAATTGTTCCATTGGTACATATGCAGGA
AATTAAGTTTGAGCCAAACGTGATGTGTGAAACTATAGACAAGAAACTCACTTTTCATTATAGT
CAGGTTTGTCAATACACTTCTATTCAAAGGGATGCACAACTCAAATTAAAGGGTCATTTATTGA
ATTGTTTCCAAAATCTTTCAATATTCTAGCTTGAAGATGGGGACATTATTTGTTTCCAAAAATC
ACCAGGAGCAGAATATGATGCACCCGTGCGATATCCGGATGTTCCTTCATTTTTGGAGTATGTC
CATAATAGGCAG

Sequences
Splice junction sequence	GGACATTATTTGTTTCCAAAAATCACCAGGAGCAGAATATGATGCACCCGTGCGATATCCGGAT GTTCCTTCATTTTTGGAGTATGTCCATAATAGGCAGgtggggcaactgagagaaatatcaaata aggcacacaatgttgagttgaagctgtttttggaagtagaacttgggctggtagtgatacacct gatttgtg
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: 456 Transcript exons: 205714860-205714937,205715046-205715134,205715251-205715 359,205715498-205715566,205715657-205715767 GTGGGGCAACTGAGAGAAATATCAAATAAGGCACACAATGTTGAGTTGAAGCTGTTTTTGGAAG TAGAACTTGGGCTGGATTTGCGGCCTCTCCCTCCTCCTGAGAAGGGCAAGGAAGATATTCTTCT TTTCTTCAAATTCTACAACCCAGAAAAGGAAGAACTCTGTTTCATGGGGAGGCTCTTTGTGAAG GCCTTGGGAAAACCTTCAGAAATCCTGGCAAAACTAAACGAAATGGCTGGATTTCCCCCTGATC AAGAAATTGAGCTTTTTGAGGAAATTAAGTTTGAGCCAAACGTGATGTGTGAAACTATAGACAA GAAACTCACTTTTCATTATAGTCAGCTTGAAGATGGGGACATTATTTGTTTCCAAAAATCACCA GGAGCAGAATATGATGCACCCGTGCGATATCCGGATGTTCCTTCATTTTTGGAGTATGTCCATA ATAGGCAG
Genomic sequence	GTGGGGCAACTGAGAGAAATATCAAATAAGGCACACAATGTTGAGTTGAAGCTGTTTTTGGAAG TAGAACTTGGGCTGGTAGTGATACACCTGATTTGTGCTTCCTTCTTGTTCTGCATGTTGCTTAT AGTATCTGCTGTGGCACTCAGCTGTGGATCCCTTACCTATCTTTATTTACTCATTTAGGATTTG CGGCCTCTCCCTCCTCCTGAGAAGGGCAAGGAAGATATTCTTCTTTTCTTCAAATTCTACAACC CAGAAAAGGAAGAACTCTGGTACATCTTCTGTTTTAAGTGATAACATTGACATCTTGTCCTAAG TACTGCTTCTTTATTCTTCATTAAAATAATGATATTATCATGTGACTCATGGAGCTGTTTCATG CATGTAGTTTCATGGGGAGGCTCTTTGTGAAGGCCTTGGGAAAACCTTCAGAAATCCTGGCAAA ACTAAACGAAATGGCTGGATTTCCCCCTGATCAAGAAATTGAGCTTTTTGAGGCAATATTGATT TTTTTGATAAATTTATTGTCCCGATGATTTGTCCACTAGTGCATTGTTATACAGATGCATTAAT TCTGTCTGTGATGGCCTTATGATGGATACTGTGCTTAAATTGTTCCATTGGTACATATGCAGGA AATTAAGTTTGAGCCAAACGTGATGTGTGAAACTATAGACAAGAAACTCACTTTTCATTATAGT CAGGTTTGTCAATACACTTCTATTCAAAGGGATGCACAACTCAAATTAAAGGGTCATTTATTGA ATTGTTTCCAAAATCTTTCAATATTCTAGCTTGAAGATGGGGACATTATTTGTTTCCAAAAATC ACCAGGAGCAGAATATGATGCACCCGTGCGATATCCGGATGTTCCTTCATTTTTGGAGTATGTC CATAATAGGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.139614879

Conservation Information
Conserved circRNAs	NA
PMCS	0.139614879

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							205715256-205715764(+)
205715665-205714869(+)
						
						Potential amino acid sequence
						
							MGRLFVKALGKPSEILAKLNEMAGFPPDQEIELFEEIKFEPNVMCETIDKKLTFHYSQLEDGDI
ICFQKSPGAEYDAPVRYPDVPSFLEYVHNRQVGQLREISNKAHNVELKLFLEVELGLDLRPLPP
PEKGKEDILLFFKFYNPEKEELCFMGRLFVKALGKPSEILAKLNEMAGFPPDQEIELFEEIKFE
PNVMCETIDKKLTFHYSQLEDGDIICFQKSPGAEYDAPVRYPDVPSFLEYVHNRQVGQLREISN
KAHNVELKLFLEVELGLDLRPLPPPEKGKEDILLFFKFYNPEKEELCFMGRLFVKALGKPSEIL
AKLNEMAGFPPDQEIELFEEIKFEPNVMCETIDKKLTFHYSQLEDGDIICFQKSPGAEYDAPVR
YPDVPSFLEYVHNRQVGQLREISNKAHNVELKLFLEVELGLDLRPLPPPEKGKEDILLFFKFYN
PEKEELCFMGRLFVKALGKPSEILAKLNEMAGFPPDQEIELFEEIKFEPNVMCETIDKKLTFHY
SQLEDGDIICFQKSPGAEYDAPVRYPDVPSFLEYVHNRQ(+)
MGTLFVSKNHQEQNMMHPCDIRMFLHFWSMSIIGRWGN*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	205715256-205715764(+) 205715665-205714869(+)
Potential amino acid sequence	MGRLFVKALGKPSEILAKLNEMAGFPPDQEIELFEEIKFEPNVMCETIDKKLTFHYSQLEDGDI ICFQKSPGAEYDAPVRYPDVPSFLEYVHNRQVGQLREISNKAHNVELKLFLEVELGLDLRPLPP PEKGKEDILLFFKFYNPEKEELCFMGRLFVKALGKPSEILAKLNEMAGFPPDQEIELFEEIKFE PNVMCETIDKKLTFHYSQLEDGDIICFQKSPGAEYDAPVRYPDVPSFLEYVHNRQVGQLREISN KAHNVELKLFLEVELGLDLRPLPPPEKGKEDILLFFKFYNPEKEELCFMGRLFVKALGKPSEIL AKLNEMAGFPPDQEIELFEEIKFEPNVMCETIDKKLTFHYSQLEDGDIICFQKSPGAEYDAPVR YPDVPSFLEYVHNRQVGQLREISNKAHNVELKLFLEVELGLDLRPLPPPEKGKEDILLFFKFYN PEKEELCFMGRLFVKALGKPSEILAKLNEMAGFPPDQEIELFEEIKFEPNVMCETIDKKLTFHY SQLEDGDIICFQKSPGAEYDAPVRYPDVPSFLEYVHNRQ(+) MGTLFVSKNHQEQNMMHPCDIRMFLHFWSMSIIGRWGN*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d052943_circ_g.2

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