Plant Circular RNA Database

Detail information of Zm00001d033502_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d033502_circ_g.4
					
						ID in PlantcircBase
						zma_circ_006878
					
						Alias
						Zm01circ00162, GRMZM2G093855_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 264627201-264629009  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d033502						
					
						Parent gene annotation
						
							Rhomboid-like protein 15
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d033502_circ_g.1 Zm00001d033502_circ_g.2 Zm00001d033502_circ_g.3 Zm00001d033502_circ_g.5 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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  
						
							GC-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
						Zm00001d033502_T007:5
Zm00001d033502_T004:6
Zm00001d033502_T001:6
Zm00001d033502_T005:6
Zm00001d033502_T008:6
Zm00001d033502_T006:6
Zm00001d033502_T003:6
Zm00001d033502_T002:6

General Information
CircRNA Name	Zm00001d033502_circ_g.4
ID in PlantcircBase	zma_circ_006878
Alias	Zm01circ00162, GRMZM2G093855_C2
Organism	Zea mays
Position	chr1: 264627201-264629009 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d033502
Parent gene annotation	Rhomboid-like protein 15
Parent gene strand	+
Alternative splicing	Zm00001d033502_circ_g.1 Zm00001d033502_circ_g.2 Zm00001d033502_circ_g.3 Zm00001d033502_circ_g.5
Support reads	NA
Tissues	leaf, endosperm
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	GC-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	Zm00001d033502_T007:5 Zm00001d033502_T004:6 Zm00001d033502_T001:6 Zm00001d033502_T005:6 Zm00001d033502_T008:6 Zm00001d033502_T006:6 Zm00001d033502_T003:6 Zm00001d033502_T002:6

			
						 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  
						
							GAATCTGCTGATTTTTATCCTTCAGGAAGGAGAAGACCCAAGGTTTCCTGGGAGAGCACGAACA
CTTGGTTCTGTAGGAACTGAACCCACTGCAAGGGAGtgtcttcggcctcttcaatgttcctgca
aaatggtactcttttttttttgcatgtgttgatggtattcagtattcacttctggttactagat
gatatcgg

									
								

					

						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
						
							TGTCTTCGGCCTCTTCAATGTTCCTGCAAAATGGTACTCTTTTTTTTTTGCATGTGTTGATGGT
ATTCAGTATTCACTTCTGGTTACTAGATGATATCGGAGACCCATATCTTATGTAAAAAAACTTA
AATTTGTACAATGCCAGGTACGCATGGATTTTGCTAGTGCTATTTCAGTTTCTCGCAAGCAATG
TTTCATTGCTGGGACACCTTTGTGGCATCTTGTCAGGATTTGCATGTTTGTCCTTTATATCCTT
CTTATTTGTTAATTCTTCACGAGCTATATTTTATTTTTAATCATATTCCTTGCTAAGCCTATTT
ATTTGGCACCAGACACTTATGGGCTGTTCAACTACTTGCTTCCTGGGCCATCATTTTATTCTAA
AATCGAAGGCTTGTCAGCACTAGTAAGTTTTGCTTAGATGGTTTAAGTTATCCTGACCAATGAC
CATATCATCTTCTGTATGAGATGTTTCTTATATCTGTATTTATTGTCTGATGTATTGGATGTCA
GTCTGTTTGTGTGAGGCGTCCTGGCTTTATTATGTGTACTGGAGGCACTACTTATGGTCAGCTT
CCTACATACTCTAACACGTCTGCTGCACCAAGGTACTGTTTTCAGATTCATTCCTTTTATGTAA
TGCTCACAGAAGTAACATGTTATTCGTTTAATTTACAGTGCTCTCATAAATGGAAATTTCTTGA
GAAATATATCTTCATGGATGCCTAGCAGACACACATCAACTGCTCAGGTATTGAAAAATCGACA
ATGCCATATACTCAAATATGCTCATACTTGCAATGGTTTTCTGTTGGTGATGTTAATCATCTGC
TTAGGGTTTAAGCAACCATTGTAGAAATTTACTGTAACCCAAGGCTTTTGGGGCTTCTCCAATC
TGATTTTATTTTTCACCTATTCTGTGGTGGCCTAAGTATCAAGCCATGGCTTATGGTAGGAGTT
CTAGAATGTGTGCTAAAAGTTTTGATCTACTGAGAAATCATTAGATATATCTCTCTGTTTCACA
TATATTTTCCTGGAAGCTGTTTGTTAAAGCTTCTGAGGAGCCTGAATCAAAACTGAATCCGTCC
ATGGAAGAATACAACATATTAGCATTTTTTACGTGACCTTTTTGCAATTTGCCAATTTGATCAT
CCAACTAATAGAAACATATTCCAAACATTCCTCTAAGTAAAACAAAAGGTTGTCCTTTGCTGGT
ATTTGCATTTAAAAGAGCACTGCGCTTTTTTAACACCTTGCTGTTAGTTTTTTTTTAAAAGAAA
CCAAAAGCTTCATTAACAGAAAGCTATGTTGGACAGGTACACAGTAAAAGCTATGGCCTGCTAG
GTTCCTGGTTATGGCAGTTAATTTCAAGATTAATACCACTTGATACATATTAGGTCACATATTG
TTCTTCTGTGTCGATTAATACATTACAAATTCATAAACTATCTTTCTGAAATATGTGTTACCTA
ACTATCTTGCTTGGAGTTAAAAGTTTTGTTGTCATTAGCTAGTTACTTAAAGTATATCCCCTCC
TTCCAAAAAGAATCTCATTCTAGTTTTCTCCTAAGTCAAACTATTTTTGTAGTGCACCTATTTG
GTGTTATAAATGTTGATAATCTTCTTTATAAGCTCGGTCAAGCCTAAGATAGTTTGACTTGCCA
AACTAAAGCCGTATTCTTTTCGGAACAGGGGTAGTATGAGCTTATGAATCTGCTGATTTTTATC
CTTCAGGAAGGAGAAGACCCAAGGTTTCCTGGGAGAGCACGAACACTTGGTTCTGTAGGAACTG
AACCCACTGCAAGGGAG
						
					

			
		

Sequences
Splice junction sequence	GAATCTGCTGATTTTTATCCTTCAGGAAGGAGAAGACCCAAGGTTTCCTGGGAGAGCACGAACA CTTGGTTCTGTAGGAACTGAACCCACTGCAAGGGAGtgtcttcggcctcttcaatgttcctgca aaatggtactcttttttttttgcatgtgttgatggtattcagtattcacttctggttactagat gatatcgg
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	TGTCTTCGGCCTCTTCAATGTTCCTGCAAAATGGTACTCTTTTTTTTTTGCATGTGTTGATGGT ATTCAGTATTCACTTCTGGTTACTAGATGATATCGGAGACCCATATCTTATGTAAAAAAACTTA AATTTGTACAATGCCAGGTACGCATGGATTTTGCTAGTGCTATTTCAGTTTCTCGCAAGCAATG TTTCATTGCTGGGACACCTTTGTGGCATCTTGTCAGGATTTGCATGTTTGTCCTTTATATCCTT CTTATTTGTTAATTCTTCACGAGCTATATTTTATTTTTAATCATATTCCTTGCTAAGCCTATTT ATTTGGCACCAGACACTTATGGGCTGTTCAACTACTTGCTTCCTGGGCCATCATTTTATTCTAA AATCGAAGGCTTGTCAGCACTAGTAAGTTTTGCTTAGATGGTTTAAGTTATCCTGACCAATGAC CATATCATCTTCTGTATGAGATGTTTCTTATATCTGTATTTATTGTCTGATGTATTGGATGTCA GTCTGTTTGTGTGAGGCGTCCTGGCTTTATTATGTGTACTGGAGGCACTACTTATGGTCAGCTT CCTACATACTCTAACACGTCTGCTGCACCAAGGTACTGTTTTCAGATTCATTCCTTTTATGTAA TGCTCACAGAAGTAACATGTTATTCGTTTAATTTACAGTGCTCTCATAAATGGAAATTTCTTGA GAAATATATCTTCATGGATGCCTAGCAGACACACATCAACTGCTCAGGTATTGAAAAATCGACA ATGCCATATACTCAAATATGCTCATACTTGCAATGGTTTTCTGTTGGTGATGTTAATCATCTGC TTAGGGTTTAAGCAACCATTGTAGAAATTTACTGTAACCCAAGGCTTTTGGGGCTTCTCCAATC TGATTTTATTTTTCACCTATTCTGTGGTGGCCTAAGTATCAAGCCATGGCTTATGGTAGGAGTT CTAGAATGTGTGCTAAAAGTTTTGATCTACTGAGAAATCATTAGATATATCTCTCTGTTTCACA TATATTTTCCTGGAAGCTGTTTGTTAAAGCTTCTGAGGAGCCTGAATCAAAACTGAATCCGTCC ATGGAAGAATACAACATATTAGCATTTTTTACGTGACCTTTTTGCAATTTGCCAATTTGATCAT CCAACTAATAGAAACATATTCCAAACATTCCTCTAAGTAAAACAAAAGGTTGTCCTTTGCTGGT ATTTGCATTTAAAAGAGCACTGCGCTTTTTTAACACCTTGCTGTTAGTTTTTTTTTAAAAGAAA CCAAAAGCTTCATTAACAGAAAGCTATGTTGGACAGGTACACAGTAAAAGCTATGGCCTGCTAG GTTCCTGGTTATGGCAGTTAATTTCAAGATTAATACCACTTGATACATATTAGGTCACATATTG TTCTTCTGTGTCGATTAATACATTACAAATTCATAAACTATCTTTCTGAAATATGTGTTACCTA ACTATCTTGCTTGGAGTTAAAAGTTTTGTTGTCATTAGCTAGTTACTTAAAGTATATCCCCTCC TTCCAAAAAGAATCTCATTCTAGTTTTCTCCTAAGTCAAACTATTTTTGTAGTGCACCTATTTG GTGTTATAAATGTTGATAATCTTCTTTATAAGCTCGGTCAAGCCTAAGATAGTTTGACTTGCCA AACTAAAGCCGTATTCTTTTCGGAACAGGGGTAGTATGAGCTTATGAATCTGCTGATTTTTATC CTTCAGGAAGGAGAAGACCCAAGGTTTCCTGGGAGAGCACGAACACTTGGTTCTGTAGGAACTG AACCCACTGCAAGGGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.032059365

Conservation Information
Conserved circRNAs	NA
PMCS	0.032059365

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							264627745-264627581(+)
						
						Potential amino acid sequence
						
							MCTGGTTYGQLPTYSNTSAAPSALINGNFLRNISSWMPSRHTSTAQEGEDPRFPGRARTLGSVG
TEPTARECLRPLQCSCKMVRMDFASAISVSRKQCFIAGTPLWHLVRICIHLWAVQLLASWAIIL
F*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	264627745-264627581(+)
Potential amino acid sequence	MCTGGTTYGQLPTYSNTSAAPSALINGNFLRNISSWMPSRHTSTAQEGEDPRFPGRARTLGSVG TEPTARECLRPLQCSCKMVRMDFASAISVSRKQCFIAGTPLWHLVRICIHLWAVQLLASWAIIL F*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d033502_circ_g.4

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