Plant Circular RNA Database

Detail information of Zm00001d052098_circ_g.6

			
						 General Information
					
						CircRNA Name
						Zm00001d052098_circ_g.6
					
						ID in PlantcircBase
						zma_circ_008165
					
						Alias
						Zm04circ00074, GRMZM2G091143_C3
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 179511396-179512497  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d052098						
					
						Parent gene annotation
						
							Probable NOT transcription complex subunit VIP2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d052098_circ_g.5 Zm00001d052098_circ_g.7 						
					
						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  
						
							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
						Zm00001d052098_T007:5
Zm00001d052098_T006:5
Zm00001d052098_T013:5
Zm00001d052098_T010:5
Zm00001d052098_T011:5
Zm00001d052098_T004:5
Zm00001d052098_T001:5
Zm00001d052098_T016:4
Zm00001d052098_T012:4
Zm00001d052098_T015:5
Zm00001d052098_T002:5
Zm00001d052098_T014:5
Zm00001d052098_T003:5
Zm00001d052098_T008:5
Zm00001d052098_T005:5

General Information
CircRNA Name	Zm00001d052098_circ_g.6
ID in PlantcircBase	zma_circ_008165
Alias	Zm04circ00074, GRMZM2G091143_C3
Organism	Zea mays
Position	chr4: 179511396-179512497 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d052098
Parent gene annotation	Probable NOT transcription complex subunit VIP2
Parent gene strand	+
Alternative splicing	Zm00001d052098_circ_g.5 Zm00001d052098_circ_g.7
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	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	Zm00001d052098_T007:5 Zm00001d052098_T006:5 Zm00001d052098_T013:5 Zm00001d052098_T010:5 Zm00001d052098_T011:5 Zm00001d052098_T004:5 Zm00001d052098_T001:5 Zm00001d052098_T016:4 Zm00001d052098_T012:4 Zm00001d052098_T015:5 Zm00001d052098_T002:5 Zm00001d052098_T014:5 Zm00001d052098_T003:5 Zm00001d052098_T008:5 Zm00001d052098_T005:5

			
						 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  
						
							CTTTATTAAGCTTGTCATTTACTCCCCATAGTTTAATCTGACTATAATTTTCTTACAGCATGCC
AAAAGATGAAGCTCAGCTGTACTCTGCCAATGAACTgtaacccttcggattataatgctataga
gttgcatcacaaggaacaactccacgataatgtacctgtaattcaagcacagcagtatcctgtg
ggttaatt

						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
						
							GTAACCCTTCGGATTATAATGCTATAGAGTTGCATCACAAGGAACAACTCCACGATAATGTACC
TGTAATTCAAGCACAGCAGTATCCTGTGGGTTAATTTTTCTCTATTTTGAATAATCATCCCCTT
GAATTGTCTTTTTTTTTTTGACATAATATGCACACATACACAGATGGCAAGGTCAGGCTTAGGA
AGTAGCTACCTACCCAATCGACAACAACACCAGCAAGGTGCTAATTCAGTAAGTATCCCACGAT
TTTCCCAAACAACCATCTTATTAATGTTTCCAGAGGGATGTATCACTTTGATGTTTATATTTCC
TCTTAGATTGAACGATGGTAGTAATCTCAATTATGTTCTATCAGGTCCAGAATGGCGGATCCCA
CAATATTTTACTGAGACCACCCAGTCAAACTTCTAGTTTGGGATCATATGATCCATTTCTGCAG
CAATACCAGCAGCCTCAGCCTCAAAATCATTTCAGATTGCAGCAGATGTCTTCAGCTGCACATT
CATATCGGGATCAGATTCAAAAGATTCAGGCGGGACCGACACCACCTGATCCATATGGCTTGTT
AGGATTTTTGGGTGTTATAAGGATGAATGATGCTGATTTAGCATCTCTTGCTTTAGGAATAGAT
TTGACAGCATTGGGTTTGAACTTGAACTCGCCAGATAATCTATACAAGACATTTGGCTCACCCT
GGTCGAATGACCCAGCAAAAGGAGATACTGATTTTCGAATTCCAGCTTGTTACCTCTTTGACAA
AACTCCTCCACTACAGGTAAGCACCCAGTAACTGTTGGCTACTTTCAATAATGAGATTTTTTTA
AAACCACATTATCTGATATAAGCACCCGAATTTTATGCCGTTGTGTCTGGTTCGTATTACATTT
TAACAAATTCTGTGTTGTTGCAGACCTTACTTTTTCAGAGGTTTCACATAGTAACACTATTTTT
CGTCTTCTATAGGTACTTCCACAGTTCTGCCATAATATTTTACTTTATTAAGCTTGTCATTTAC
TCCCCATAGTTTAATCTGACTATAATTTTCTTACAGCATGCCAAAAGATGAAGCTCAGCTGTAC
TCTGCCAATGAACT

Sequences
Splice junction sequence	CTTTATTAAGCTTGTCATTTACTCCCCATAGTTTAATCTGACTATAATTTTCTTACAGCATGCC AAAAGATGAAGCTCAGCTGTACTCTGCCAATGAACTgtaacccttcggattataatgctataga gttgcatcacaaggaacaactccacgataatgtacctgtaattcaagcacagcagtatcctgtg ggttaatt
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	GTAACCCTTCGGATTATAATGCTATAGAGTTGCATCACAAGGAACAACTCCACGATAATGTACC TGTAATTCAAGCACAGCAGTATCCTGTGGGTTAATTTTTCTCTATTTTGAATAATCATCCCCTT GAATTGTCTTTTTTTTTTTGACATAATATGCACACATACACAGATGGCAAGGTCAGGCTTAGGA AGTAGCTACCTACCCAATCGACAACAACACCAGCAAGGTGCTAATTCAGTAAGTATCCCACGAT TTTCCCAAACAACCATCTTATTAATGTTTCCAGAGGGATGTATCACTTTGATGTTTATATTTCC TCTTAGATTGAACGATGGTAGTAATCTCAATTATGTTCTATCAGGTCCAGAATGGCGGATCCCA CAATATTTTACTGAGACCACCCAGTCAAACTTCTAGTTTGGGATCATATGATCCATTTCTGCAG CAATACCAGCAGCCTCAGCCTCAAAATCATTTCAGATTGCAGCAGATGTCTTCAGCTGCACATT CATATCGGGATCAGATTCAAAAGATTCAGGCGGGACCGACACCACCTGATCCATATGGCTTGTT AGGATTTTTGGGTGTTATAAGGATGAATGATGCTGATTTAGCATCTCTTGCTTTAGGAATAGAT TTGACAGCATTGGGTTTGAACTTGAACTCGCCAGATAATCTATACAAGACATTTGGCTCACCCT GGTCGAATGACCCAGCAAAAGGAGATACTGATTTTCGAATTCCAGCTTGTTACCTCTTTGACAA AACTCCTCCACTACAGGTAAGCACCCAGTAACTGTTGGCTACTTTCAATAATGAGATTTTTTTA AAACCACATTATCTGATATAAGCACCCGAATTTTATGCCGTTGTGTCTGGTTCGTATTACATTT TAACAAATTCTGTGTTGTTGCAGACCTTACTTTTTCAGAGGTTTCACATAGTAACACTATTTTT CGTCTTCTATAGGTACTTCCACAGTTCTGCCATAATATTTTACTTTATTAAGCTTGTCATTTAC TCCCCATAGTTTAATCTGACTATAATTTTCTTACAGCATGCCAAAAGATGAAGCTCAGCTGTAC TCTGCCAATGAACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.101630309

Conservation Information
Conserved circRNAs	NA
PMCS	0.101630309

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							179512468-179511396(+)
179511568-179511396(+)
179511432-179511988(-)
						
						Potential amino acid sequence
						
							MKLSCTLPMNCNPSDYNAIELHHKEQLHDNVPVIQAQQYPMARSGLGSSYLPNRQQHQQGANSV
QNGGSHNILLRPPSQTSSLGSYDPFLQQYQQPQPQNHFRLQQMSSAAHSYRDQIQKIQAGPTPP
DPYGLLGFLGVIRMNDADLASLALGIDLTALGLNLNSPDNLYKTFGSPWSNDPAKGDTDFRIPA
CYLFDKTPPLQTLLFQRFHIVTLFFVFYSMPKDEAQLYSANEL*(+)
MARSGLGSSYLPNRQQHQQGANSVQNGGSHNILLRPPSQTSSLGSYDPFLQQYQQPQPQNHFRL
QQMSSAAHSYRDQIQKIQAGPTPPDPYGLLGFLGVIRMNDADLASLALGIDLTALGLNLNSPDN
LYKTFGSPWSNDPAKGDTDFRIPACYLFDKTPPLQTLLFQRFHIVTLFFVFYSMPKDEAQLYSA
NEL*(+)
MQLYSIIIRRVTVHWQSTAELHLLACYRRRKIVLLCETSEKVRSVVEEFCQRGNKLEFENQYLL
LLGHSTRVSQMSCIDYLASSSSNPMLSNLFLKQEMLNQHHSSL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	179512468-179511396(+) 179511568-179511396(+) 179511432-179511988(-)
Potential amino acid sequence	MKLSCTLPMNCNPSDYNAIELHHKEQLHDNVPVIQAQQYPMARSGLGSSYLPNRQQHQQGANSV QNGGSHNILLRPPSQTSSLGSYDPFLQQYQQPQPQNHFRLQQMSSAAHSYRDQIQKIQAGPTPP DPYGLLGFLGVIRMNDADLASLALGIDLTALGLNLNSPDNLYKTFGSPWSNDPAKGDTDFRIPA CYLFDKTPPLQTLLFQRFHIVTLFFVFYSMPKDEAQLYSANEL(+) MARSGLGSSYLPNRQQHQQGANSVQNGGSHNILLRPPSQTSSLGSYDPFLQQYQQPQPQNHFRL QQMSSAAHSYRDQIQKIQAGPTPPDPYGLLGFLGVIRMNDADLASLALGIDLTALGLNLNSPDN LYKTFGSPWSNDPAKGDTDFRIPACYLFDKTPPLQTLLFQRFHIVTLFFVFYSMPKDEAQLYSA NEL(+) MQLYSIIIRRVTVHWQSTAELHLLACYRRRKIVLLCETSEKVRSVVEEFCQRGNKLEFENQYLL LLGHSTRVSQMSCIDYLASSSSNPMLSNLFLKQEMLNQHHSSL*(-)
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 Zm00001d052098_circ_g.6

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