Plant Circular RNA Database

Detail information of Zm00001d011854_circ_g.3

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d011854_circ_g.3
					

						ID in PlantcircBase
						zma_circ_009769
					

						Alias
						Zm08circ00072, GRMZM2G180988_C2
					

						Organism
						
							Zea mays						
					

						Position
						
							chr8: 162916951-162918861  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						CIRI2
					

						Parent gene
						
							Zm00001d011854						
					

						Parent gene annotation
						
							Villin-2
							
					

						Parent gene strand
						-
					

						Alternative splicing
						
							Zm00001d011854_circ_g.2 						
					

						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  
						
							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
						Zm00001d011854_T039:6
Zm00001d011854_T006:4
Zm00001d011854_T041:6
Zm00001d011854_T025:6
Zm00001d011854_T067:6
Zm00001d011854_T065:6
Zm00001d011854_T043:6
Zm00001d011854_T079:5
Zm00001d011854_T038:6
Zm00001d011854_T040:6
Zm00001d011854_T014:6
Zm00001d011854_T083:6
Zm00001d011854_T068:2
Zm00001d011854_T077:6
Zm00001d011854_T013:4
Zm00001d011854_T046:6
Zm00001d011854_T063:6
Zm00001d011854_T089:6
Zm00001d011854_T064:5
Zm00001d011854_T021:6
Zm00001d011854_T036:6
Zm00001d011854_T010:6
Zm00001d011854_T056:5
Zm00001d011854_T070:5
Zm00001d011854_T092:1
Zm00001d011854_T069:6
Zm00001d011854_T054:6
Zm00001d011854_T018:6
Zm00001d011854_T002:6
Zm00001d011854_T015:6
Zm00001d011854_T075:5
Zm00001d011854_T030:5
Zm00001d011854_T088:6
Zm00001d011854_T005:4
Zm00001d011854_T008:6
Zm00001d011854_T033:6
Zm00001d011854_T051:6
Zm00001d011854_T028:6
Zm00001d011854_T080:6
Zm00001d011854_T091:6
Zm00001d011854_T055:6
Zm00001d011854_T001:4
Zm00001d011854_T031:6
Zm00001d011854_T022:6
Zm00001d011854_T087:6
Zm00001d011854_T072:3
Zm00001d011854_T037:6
Zm00001d011854_T004:4
Zm00001d011854_T024:6
Zm00001d011854_T017:6
Zm00001d011854_T011:6
Zm00001d011854_T047:6
Zm00001d011854_T050:4

					

			
		

General Information
CircRNA Name	Zm00001d011854_circ_g.3
ID in PlantcircBase	zma_circ_009769
Alias	Zm08circ00072, GRMZM2G180988_C2
Organism	Zea mays
Position	chr8: 162916951-162918861 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d011854
Parent gene annotation	Villin-2
Parent gene strand	-
Alternative splicing	Zm00001d011854_circ_g.2
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	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	Zm00001d011854_T039:6 Zm00001d011854_T006:4 Zm00001d011854_T041:6 Zm00001d011854_T025:6 Zm00001d011854_T067:6 Zm00001d011854_T065:6 Zm00001d011854_T043:6 Zm00001d011854_T079:5 Zm00001d011854_T038:6 Zm00001d011854_T040:6 Zm00001d011854_T014:6 Zm00001d011854_T083:6 Zm00001d011854_T068:2 Zm00001d011854_T077:6 Zm00001d011854_T013:4 Zm00001d011854_T046:6 Zm00001d011854_T063:6 Zm00001d011854_T089:6 Zm00001d011854_T064:5 Zm00001d011854_T021:6 Zm00001d011854_T036:6 Zm00001d011854_T010:6 Zm00001d011854_T056:5 Zm00001d011854_T070:5 Zm00001d011854_T092:1 Zm00001d011854_T069:6 Zm00001d011854_T054:6 Zm00001d011854_T018:6 Zm00001d011854_T002:6 Zm00001d011854_T015:6 Zm00001d011854_T075:5 Zm00001d011854_T030:5 Zm00001d011854_T088:6 Zm00001d011854_T005:4 Zm00001d011854_T008:6 Zm00001d011854_T033:6 Zm00001d011854_T051:6 Zm00001d011854_T028:6 Zm00001d011854_T080:6 Zm00001d011854_T091:6 Zm00001d011854_T055:6 Zm00001d011854_T001:4 Zm00001d011854_T031:6 Zm00001d011854_T022:6 Zm00001d011854_T087:6 Zm00001d011854_T072:3 Zm00001d011854_T037:6 Zm00001d011854_T004:4 Zm00001d011854_T024:6 Zm00001d011854_T017:6 Zm00001d011854_T011:6 Zm00001d011854_T047:6 Zm00001d011854_T050:4

			
						 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  
						
							GAGGAGCATTTTTATTTGTATAACTCTGTTTTCCTCCAAGAGCAAACCAGAAACCTGAACTCTC
TGTCCCCTCCTTGCAGTGCTTCACTGCAACGCCAGGcagtcttatctcctgtgctgctagcttt
ggctcgtagattttctgaagatccagattgctcagcagtcagcacagaggatagtgcagctacg
gcagctgc

									
								

					

						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: 823
Transcript exons: 162916951-162917188,162917356-162917454,162917873-162917
929,162918079-162918204,162918307-162918458,162918711-16
2918861
CAGTCTTATCTCCTGTGCTGCTAGCTTTGGCTCGTAGATTTTCTGAAGATCCAGATTGCTCAGC
AGTCAGCACAGAGGATAGTGCAGCTACGGCAGCTGCTCTTTGGGAACCTTGACCTGAGCGAGAT
GGAGGTGGTGTTTTGGGTTTTAAGGATGAATTGAATGCATTAGATAGGGCAGCCAGTGCTGAGG
CGCGTTGAGTGGGTCCATCGCCTGTGCTTTTAGGCCTCTCATTAGAGAGCCTTTGTTGAGACGA
TGGATTGAATGCAGATGATAGAGCTGCTAATGCAGATGCCCTTTGAGTTGGTCCACCATTACCA
GAGCTCCTAGATGCACCCTCAGAACGCAATCCAAAAAGCAGTGAGAGTTTCTTCTGGAAGGAAT
TTCCATGAACCAAAGATTTTGTGTTATCCCAAGAGAAATATGTCTTGAAGAAGCATGGCTCATT
CCCTTCCATAACTTTATATAGTGGTGCATATGGAGAAAGATCATCAATAGAATTTGCATGCTCC
ACGTATTTCTGGCCAATATCAAATGCCTTCTGTTTCTCTTTTGATTCCACGCACTGACCAATCC
AAATGAAAACCTCACCATGTGTGTCAAGTATCATCATGTCTTCAGTTAACAAATCATCTTGGGA
AAAGTTGAAGATCTCAGTTACCTGAATAAGCCCGTTCTTGAATGAGAATGCATACAAGTGAGGC
TCTCTAGTAATAATATCCTGAGGAGCATTTTTATTTGTATAACTCTGTTTTCCTCCAAGAGCAA
ACCAGAAACCTGAACTCTCTGTCCCCTCCTTGCAGTGCTTCACTGCAACGCCAGG
						
					

						Genomic sequence
						
							CAGTCTTATCTCCTGTGCTGCTAGCTTTGGCTCGTAGATTTTCTGAAGATCCAGATTGCTCAGC
AGTCAGCACAGAGGATAGTGCAGCTACGGCAGCTGCTCTTTGGGAACCTTGACCTGAGCGAGAT
GGAGGTGGTGTTTTGGGTTTTAAGGATGAATTGAATGCATTAGATAGGGCAGCCAGTGCTGAGG
CGCGTTGAGTGGGTCCATCGCCTGTGCTTTTAGGCCTCTCATTAGACTGAAAAGAAGGATAAAA
AAGGTAGTTACATTTATGTTTTCTTTTATACAAAATGTAGACATTTTTGTGAGGATAGTTGCAA
CAATGTTTTCATATAGAATGTATCATTCTTTTAGACAAAATGTAGACATTTCTGTGAGAAGTCA
AATCAATGGTTTCAAACTTACGAGCCTTTGTTGAGACGATGGATTGAATGCAGATGATAGAGCT
GCTAATGCAGATGCCCTTTGAGTTGGTCCACCATTACCAGAGCTCCTAGATGCACCCTACAAAA
GGACTGATGTAAAGATTGTACTAGCTTAACATCTATTTGCATTTCCAAACAATGGTTCAATGTA
ACCTTTCTACAGTTCAAGAAATAGTTATTCATGCAAATACCGAATGCATCTCATAATAACAACT
TAGCAACTGACTTGAGAACATCCAAAAAAACTCATAGAAAACCATGCATATGTTTTTTCAATAT
GTAACTAAAACATAAACTCAAGAAGGGTAAGCATGGTCCAGCAGTGAAAGCTGTCTCACTAAGT
CACCGGATCATAGATCATAGGTTCGAAGCAGCCTCTCCGCATTTGCGGGGAGAAGGCTTGCCTC
GGTTTTCCCCTTCCCCAAACTCCACTCATGTGGGAGCCCCGGCACTGGGTCTGTCCCCTTTTTA
ACTAAAACCTAAAATCTCAGGTTTACCTCAGAACGCAATCCAAAAAGCAGTGAGAGTTTCTTCT
GGAAGGAATTTCCATGAACCTGTGCAAAGTATGAAACTTATTAGTAAACATGATGCAGATTATA
ACAAAAAAAAACTTGCAGAAAAAATTGGCTAATATTTTTTATGAGTAATATCAGATATAACAAC
AAAAGCATAATAATATAGAATAAGATAACCAAGCTCATACCAAAGATTTTGTGTTATCCCAAGA
GAAATATGTCTTGAAGAAGCATGGCTCATTCCCTTCCATAACTTTATATAGTGGTGCATATGGA
GAAAGATCATCAATAGAATTTGCATGCTCCACGTATTTCTGGTTGAGAAGTAGTCGTTATGCAT
ACAGAATAACAGTAATATAACAGCAAACAGGAACTGAGATTGACCACTTGAATAAGGTCAGGGC
TTCAATCAATACCTGGCCAATATCAAATGCCTTCTGTTTCTCTTTTGATTCCACGCACTGACCA
ATCCAAATGAAAACCTCACCATGTGTGTCAAGTATCATCATGTCTTCAGTTAACAAATCATCTT
GGGAAAAGTTGAAGATCTCAGTTACCTGAATAAGCCCATAAAATCAGATACCCTGAATTTTGCA
AAACAAAATATAGATCTAAGAAGAGCAAGTGTAACAGGACCGACCTCCAGTCTCCCTGGTTAAC
AACGATGATCGTAGCATAAACAAAACCGAGCAATAAAATGATAATTAGGTCAAAAACTTGGATA
GTATAGATATCTCAAAAATGAACGAAAGAAAACAGAAACTTCATACGGATATACAAATGTCAAA
TGCATGAATGTACAAAATTTACAGCAACTGACCGTTCTTGAATGAGAATGCATACAAGTGAGGC
TCTCTAGTAATAATATCCTGAGGAGCATTTTTATTTGTATAACTCTGTTTTCCTCCAAGAGCAA
ACCAGAAACCTGAACTCTCTGTCCCCTCCTTGCAGTGCTTCACTGCAACGCCAGG
						
					

			
		

Sequences
Splice junction sequence	GAGGAGCATTTTTATTTGTATAACTCTGTTTTCCTCCAAGAGCAAACCAGAAACCTGAACTCTC TGTCCCCTCCTTGCAGTGCTTCACTGCAACGCCAGGcagtcttatctcctgtgctgctagcttt ggctcgtagattttctgaagatccagattgctcagcagtcagcacagaggatagtgcagctacg gcagctgc
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: 823 Transcript exons: 162916951-162917188,162917356-162917454,162917873-162917 929,162918079-162918204,162918307-162918458,162918711-16 2918861 CAGTCTTATCTCCTGTGCTGCTAGCTTTGGCTCGTAGATTTTCTGAAGATCCAGATTGCTCAGC AGTCAGCACAGAGGATAGTGCAGCTACGGCAGCTGCTCTTTGGGAACCTTGACCTGAGCGAGAT GGAGGTGGTGTTTTGGGTTTTAAGGATGAATTGAATGCATTAGATAGGGCAGCCAGTGCTGAGG CGCGTTGAGTGGGTCCATCGCCTGTGCTTTTAGGCCTCTCATTAGAGAGCCTTTGTTGAGACGA TGGATTGAATGCAGATGATAGAGCTGCTAATGCAGATGCCCTTTGAGTTGGTCCACCATTACCA GAGCTCCTAGATGCACCCTCAGAACGCAATCCAAAAAGCAGTGAGAGTTTCTTCTGGAAGGAAT TTCCATGAACCAAAGATTTTGTGTTATCCCAAGAGAAATATGTCTTGAAGAAGCATGGCTCATT CCCTTCCATAACTTTATATAGTGGTGCATATGGAGAAAGATCATCAATAGAATTTGCATGCTCC ACGTATTTCTGGCCAATATCAAATGCCTTCTGTTTCTCTTTTGATTCCACGCACTGACCAATCC AAATGAAAACCTCACCATGTGTGTCAAGTATCATCATGTCTTCAGTTAACAAATCATCTTGGGA AAAGTTGAAGATCTCAGTTACCTGAATAAGCCCGTTCTTGAATGAGAATGCATACAAGTGAGGC TCTCTAGTAATAATATCCTGAGGAGCATTTTTATTTGTATAACTCTGTTTTCCTCCAAGAGCAA ACCAGAAACCTGAACTCTCTGTCCCCTCCTTGCAGTGCTTCACTGCAACGCCAGG
Genomic sequence	CAGTCTTATCTCCTGTGCTGCTAGCTTTGGCTCGTAGATTTTCTGAAGATCCAGATTGCTCAGC AGTCAGCACAGAGGATAGTGCAGCTACGGCAGCTGCTCTTTGGGAACCTTGACCTGAGCGAGAT GGAGGTGGTGTTTTGGGTTTTAAGGATGAATTGAATGCATTAGATAGGGCAGCCAGTGCTGAGG CGCGTTGAGTGGGTCCATCGCCTGTGCTTTTAGGCCTCTCATTAGACTGAAAAGAAGGATAAAA AAGGTAGTTACATTTATGTTTTCTTTTATACAAAATGTAGACATTTTTGTGAGGATAGTTGCAA CAATGTTTTCATATAGAATGTATCATTCTTTTAGACAAAATGTAGACATTTCTGTGAGAAGTCA AATCAATGGTTTCAAACTTACGAGCCTTTGTTGAGACGATGGATTGAATGCAGATGATAGAGCT GCTAATGCAGATGCCCTTTGAGTTGGTCCACCATTACCAGAGCTCCTAGATGCACCCTACAAAA GGACTGATGTAAAGATTGTACTAGCTTAACATCTATTTGCATTTCCAAACAATGGTTCAATGTA ACCTTTCTACAGTTCAAGAAATAGTTATTCATGCAAATACCGAATGCATCTCATAATAACAACT TAGCAACTGACTTGAGAACATCCAAAAAAACTCATAGAAAACCATGCATATGTTTTTTCAATAT GTAACTAAAACATAAACTCAAGAAGGGTAAGCATGGTCCAGCAGTGAAAGCTGTCTCACTAAGT CACCGGATCATAGATCATAGGTTCGAAGCAGCCTCTCCGCATTTGCGGGGAGAAGGCTTGCCTC GGTTTTCCCCTTCCCCAAACTCCACTCATGTGGGAGCCCCGGCACTGGGTCTGTCCCCTTTTTA ACTAAAACCTAAAATCTCAGGTTTACCTCAGAACGCAATCCAAAAAGCAGTGAGAGTTTCTTCT GGAAGGAATTTCCATGAACCTGTGCAAAGTATGAAACTTATTAGTAAACATGATGCAGATTATA ACAAAAAAAAACTTGCAGAAAAAATTGGCTAATATTTTTTATGAGTAATATCAGATATAACAAC AAAAGCATAATAATATAGAATAAGATAACCAAGCTCATACCAAAGATTTTGTGTTATCCCAAGA GAAATATGTCTTGAAGAAGCATGGCTCATTCCCTTCCATAACTTTATATAGTGGTGCATATGGA GAAAGATCATCAATAGAATTTGCATGCTCCACGTATTTCTGGTTGAGAAGTAGTCGTTATGCAT ACAGAATAACAGTAATATAACAGCAAACAGGAACTGAGATTGACCACTTGAATAAGGTCAGGGC TTCAATCAATACCTGGCCAATATCAAATGCCTTCTGTTTCTCTTTTGATTCCACGCACTGACCA ATCCAAATGAAAACCTCACCATGTGTGTCAAGTATCATCATGTCTTCAGTTAACAAATCATCTT GGGAAAAGTTGAAGATCTCAGTTACCTGAATAAGCCCATAAAATCAGATACCCTGAATTTTGCA AAACAAAATATAGATCTAAGAAGAGCAAGTGTAACAGGACCGACCTCCAGTCTCCCTGGTTAAC AACGATGATCGTAGCATAAACAAAACCGAGCAATAAAATGATAATTAGGTCAAAAACTTGGATA GTATAGATATCTCAAAAATGAACGAAAGAAAACAGAAACTTCATACGGATATACAAATGTCAAA TGCATGAATGTACAAAATTTACAGCAACTGACCGTTCTTGAATGAGAATGCATACAAGTGAGGC TCTCTAGTAATAATATCCTGAGGAGCATTTTTATTTGTATAACTCTGTTTTCCTCCAAGAGCAA ACCAGAAACCTGAACTCTCTGTCCCCTCCTTGCAGTGCTTCACTGCAACGCCAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.158974871

Conservation Information
Conserved circRNAs	NA
PMCS	0.158974871

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							162918401-162918775(-)
						
						Potential amino acid sequence
						
							MMILDTHGEVFIWIGQCVESKEKQKAFDIGQKYVEHANSIDDLSPYAPLYKVMEGNEPCFFKTY
FSWDNTKSLVHGNSFQKKLSLLFGLRSEGASRSSGNGGPTQRASALAALSSAFNPSSQQRLSNE
RPKSTGDGPTQRASALAALSNAFNSSLKPKTPPPSRSGQGSQRAAAVAALSSVLTAEQSGSSEN
LRAKASSTGDKTAWRCSEALQGGDREFRFLVCSWRKTELYK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	162918401-162918775(-)
Potential amino acid sequence	MMILDTHGEVFIWIGQCVESKEKQKAFDIGQKYVEHANSIDDLSPYAPLYKVMEGNEPCFFKTY FSWDNTKSLVHGNSFQKKLSLLFGLRSEGASRSSGNGGPTQRASALAALSSAFNPSSQQRLSNE RPKSTGDGPTQRASALAALSNAFNSSLKPKTPPPSRSGQGSQRAAAVAALSSVLTAEQSGSSEN LRAKASSTGDKTAWRCSEALQGGDREFRFLVCSWRKTELYK*(-)
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 Zm00001d011854_circ_g.3

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