Plant Circular RNA Database

Detail information of Zm00001d029608_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d029608_circ_g.4
					
						ID in PlantcircBase
						zma_circ_006563
					
						Alias
						Zm01circ00079, zma_circ_0000218, GRMZM2G028914_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 79104922-79105810  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d029608						
					
						Parent gene annotation
						
							Mechanosensitive ion channel protein 3 chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d029608_circ_g.1 Zm00001d029608_circ_g.2 Zm00001d029608_circ_g.3 Zm00001d029608_circ_g.5 Zm00001d029608_circ_g.6 Zm00001d029608_circ_g.7 Zm00001d029608_circ_g.8 Zm00001d029608_circ_g.9 Zm00001d029608_circ_g.10 Zm00001d029608_circ_g.11 						
					
						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  
						
							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
						Zm00001d029608_T015:4
Zm00001d029608_T006:4
Zm00001d029608_T007:4
Zm00001d029608_T001:4
Zm00001d029608_T014:4
Zm00001d029608_T004:4
Zm00001d029608_T002:4
Zm00001d029608_T005:4
Zm00001d029608_T011:4
Zm00001d029608_T003:4
Zm00001d029608_T009:4
Zm00001d029608_T013:4
Zm00001d029608_T008:4

General Information
CircRNA Name	Zm00001d029608_circ_g.4
ID in PlantcircBase	zma_circ_006563
Alias	Zm01circ00079, zma_circ_0000218, GRMZM2G028914_C1
Organism	Zea mays
Position	chr1: 79104922-79105810 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d029608
Parent gene annotation	Mechanosensitive ion channel protein 3 chloroplastic
Parent gene strand	-
Alternative splicing	Zm00001d029608_circ_g.1 Zm00001d029608_circ_g.2 Zm00001d029608_circ_g.3 Zm00001d029608_circ_g.5 Zm00001d029608_circ_g.6 Zm00001d029608_circ_g.7 Zm00001d029608_circ_g.8 Zm00001d029608_circ_g.9 Zm00001d029608_circ_g.10 Zm00001d029608_circ_g.11
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	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	Zm00001d029608_T015:4 Zm00001d029608_T006:4 Zm00001d029608_T007:4 Zm00001d029608_T001:4 Zm00001d029608_T014:4 Zm00001d029608_T004:4 Zm00001d029608_T002:4 Zm00001d029608_T005:4 Zm00001d029608_T011:4 Zm00001d029608_T003:4 Zm00001d029608_T009:4 Zm00001d029608_T013:4 Zm00001d029608_T008:4

			
						 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  
						
							TCCACTTCTGGGTATTGAAACCCAGCAACTCCATAAAGAGAGAAACAGAAGCAATCCAAACACC
AGTATAAAGAGCTTTCATGGTAAAATCAAACCCCATcataagtgcttgattttttggatcaatt
ttctcaaagaatactctcctgtgcagcttttgttgttctatatgcggattttttgccaaaactt
tcctcatg

						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: 543
Transcript exons: 79104922-79105035,79105152-79105319,79105479-79105589,79
105661-79105810
CATAAGTGCTTGATTTTTTGGATCAATTTTCTCAAAGAATACTCTCCTGTGCAGCTTTTGTTGT
TCTATATGCGGATTTTTTGCCAAAACTTTCCTCATGTCAGCAACTATAGTCCCAATTTTTCCAG
CATCCATGTGGCTAATAGCAAGATAGGTCTTAATACGCCAATGGGTCCTCTGAGTGTTATTCCT
TAATATAGAAACTGTAAACTTATGGTTAGGAATGTATATCGCTTCTCGATCAACACCTCTAATG
AGTGTTGGAGACCACAAACCAACATGCTCAACAATGCCAGAGACATCAACACCATCTATCTTTG
CATCGATCCATTCATTGACTACAAATGGGCGTGTTGCATTGATCATGACACTTGAGAGGAAGTT
AGTAAAAATCTCTCGACCAGCAAGTGTAAGCAACACTGTCCCAAACCCTCCAGCAGTTATCCAC
TTCTGGGTATTGAAACCCAGCAACTCCATAAAGAGAGAAACAGAAGCAATCCAAACACCAGTAT
AAAGAGCTTTCATGGTAAAATCAAACCCCAT
						
						Genomic sequence
						
							CATAAGTGCTTGATTTTTTGGATCAATTTTCTCAAAGAATACTCTCCTGTGCAGCTTTTGTTGT
TCTATATGCGGATTTTTTGCCAAAACTTTCCTCATGTCAGCAACTATAGTCTGCCAAGAAAAAC
AAAGATGCAACGCTAAGACAGTTTTAATACACTGGGGAAAAAATCGAACAGCTAAGAGAAGAGG
ATTATCAATTATGTTAAGTAATTCCTTGTGGTACTTACCCCAATTTTTCCAGCATCCATGTGGC
TAATAGCAAGATAGGTCTTAATACGCCAATGGGTCCTCTGAGTGTTATTCCTTAATATAGAAAC
TGTAAACTTATGGTTAGGAATGTATATCGCTTCTCGATCAACACCTCTAATGAGTGTTGGAGAC
CACAAACCAACATGCTGAAAATAAAATAGCTTTAAGTTAGAAATGATTCAAAGTATTGACCAAA
TCTTCCATGGGAAAAAACTGATAGTAAATAGAAATAAAACCTAAGCATGGTACAGATAATATCA
TAACTAGATGGTGTAGTTTTAGCTCAAAGTTAAATTAAGGCATACCTCAACAATGCCAGAGACA
TCAACACCATCTATCTTTGCATCGATCCATTCATTGACTACAAATGGGCGTGTTGCATTGATCA
TGACACTTGAGAGGAAGTTAGTAAAAATCTGCAACAAATTATGATAGATATTAGCACCACAGCA
CAAATGAATCATATCAGCAACATGCTTTGTAGTACCTCTCGACCAGCAAGTGTAAGCAACACTG
TCCCAAACCCTCCAGCAGTTATCCACTTCTGGGTATTGAAACCCAGCAACTCCATAAAGAGAGA
AACAGAAGCAATCCAAACACCAGTATAAAGAGCTTTCATGGTAAAATCAAACCCCAT

Sequences
Splice junction sequence	TCCACTTCTGGGTATTGAAACCCAGCAACTCCATAAAGAGAGAAACAGAAGCAATCCAAACACC AGTATAAAGAGCTTTCATGGTAAAATCAAACCCCATcataagtgcttgattttttggatcaatt ttctcaaagaatactctcctgtgcagcttttgttgttctatatgcggattttttgccaaaactt tcctcatg
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: 543 Transcript exons: 79104922-79105035,79105152-79105319,79105479-79105589,79 105661-79105810 CATAAGTGCTTGATTTTTTGGATCAATTTTCTCAAAGAATACTCTCCTGTGCAGCTTTTGTTGT TCTATATGCGGATTTTTTGCCAAAACTTTCCTCATGTCAGCAACTATAGTCCCAATTTTTCCAG CATCCATGTGGCTAATAGCAAGATAGGTCTTAATACGCCAATGGGTCCTCTGAGTGTTATTCCT TAATATAGAAACTGTAAACTTATGGTTAGGAATGTATATCGCTTCTCGATCAACACCTCTAATG AGTGTTGGAGACCACAAACCAACATGCTCAACAATGCCAGAGACATCAACACCATCTATCTTTG CATCGATCCATTCATTGACTACAAATGGGCGTGTTGCATTGATCATGACACTTGAGAGGAAGTT AGTAAAAATCTCTCGACCAGCAAGTGTAAGCAACACTGTCCCAAACCCTCCAGCAGTTATCCAC TTCTGGGTATTGAAACCCAGCAACTCCATAAAGAGAGAAACAGAAGCAATCCAAACACCAGTAT AAAGAGCTTTCATGGTAAAATCAAACCCCAT
Genomic sequence	CATAAGTGCTTGATTTTTTGGATCAATTTTCTCAAAGAATACTCTCCTGTGCAGCTTTTGTTGT TCTATATGCGGATTTTTTGCCAAAACTTTCCTCATGTCAGCAACTATAGTCTGCCAAGAAAAAC AAAGATGCAACGCTAAGACAGTTTTAATACACTGGGGAAAAAATCGAACAGCTAAGAGAAGAGG ATTATCAATTATGTTAAGTAATTCCTTGTGGTACTTACCCCAATTTTTCCAGCATCCATGTGGC TAATAGCAAGATAGGTCTTAATACGCCAATGGGTCCTCTGAGTGTTATTCCTTAATATAGAAAC TGTAAACTTATGGTTAGGAATGTATATCGCTTCTCGATCAACACCTCTAATGAGTGTTGGAGAC CACAAACCAACATGCTGAAAATAAAATAGCTTTAAGTTAGAAATGATTCAAAGTATTGACCAAA TCTTCCATGGGAAAAAACTGATAGTAAATAGAAATAAAACCTAAGCATGGTACAGATAATATCA TAACTAGATGGTGTAGTTTTAGCTCAAAGTTAAATTAAGGCATACCTCAACAATGCCAGAGACA TCAACACCATCTATCTTTGCATCGATCCATTCATTGACTACAAATGGGCGTGTTGCATTGATCA TGACACTTGAGAGGAAGTTAGTAAAAATCTGCAACAAATTATGATAGATATTAGCACCACAGCA CAAATGAATCATATCAGCAACATGCTTTGTAGTACCTCTCGACCAGCAAGTGTAAGCAACACTG TCCCAAACCCTCCAGCAGTTATCCACTTCTGGGTATTGAAACCCAGCAACTCCATAAAGAGAGA AACAGAAGCAATCCAAACACCAGTATAAAGAGCTTTCATGGTAAAATCAAACCCCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_020425 						
					
						PMCS
						0.138885111

Conservation Information
Conserved circRNAs	osa_circ_020425
PMCS	0.138885111

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							79105812-79104924(-)
						
						Potential amino acid sequence
						
							MGFDFTMKALYTGVWIASVSLFMELLGFNTQKWITAGGFGTVLLTLAGREIFTNFLSSVMINAT
RPFVVNEWIDAKIDGVDVSGIVEHVGLWSPTLIRGVDREAIYIPNHKFTVSILRNNTQRTHWRI
KTYLAISHMDAGKIGTIVADMRKVLAKNPHIEQQKLHRRVFFEKIDPKNQALMMGFDFTMKALY
TGVWIASVSLFMELLGFNTQKWITAGGFGTVLLTLAGREIFTNFLSSVMINATRPFVVNEWIDA
KIDGVDVSGIVEHVGLWSPTLIRGVDREAIYIPNHKFTVSILRNNTQRTHWRIKTYLAISHMDA
GKIGTIVADMRKVLAKNPHIEQQKLHRRVFFEKIDPKNQALMMGFDFTMKALYTGVWIASVSLF
MELLGFNTQKWITAGGFGTVLLTLAGREIFTNFLSSVMINATRPFVVNEWIDAKIDGVDVSGIV
EHVGLWSPTLIRGVDREAIYIPNHKFTVSILRNNTQRTHWRIKTYLAISHMDAGKIGTIVADMR
KVLAKNPHIEQQKLHRRVFFEKIDPKNQALMMGFDFTMKALYTGVWIASVSLFMELLGFNTQKW
ITAGGFGTVLLTLAGREIFTNFLSSVMINATRPFVVNEWIDAKIDGVDVSGIVEHVGLWSPTLI
RGVDREAIYIPNHKFTVSILRNNTQRTHWRIKTYLAISHMDAGKIGTIVADMRKVLAKNPHIEQ
QKLHRRVFFEKIDPKNQALM(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	79105812-79104924(-)
Potential amino acid sequence	MGFDFTMKALYTGVWIASVSLFMELLGFNTQKWITAGGFGTVLLTLAGREIFTNFLSSVMINAT RPFVVNEWIDAKIDGVDVSGIVEHVGLWSPTLIRGVDREAIYIPNHKFTVSILRNNTQRTHWRI KTYLAISHMDAGKIGTIVADMRKVLAKNPHIEQQKLHRRVFFEKIDPKNQALMMGFDFTMKALY TGVWIASVSLFMELLGFNTQKWITAGGFGTVLLTLAGREIFTNFLSSVMINATRPFVVNEWIDA KIDGVDVSGIVEHVGLWSPTLIRGVDREAIYIPNHKFTVSILRNNTQRTHWRIKTYLAISHMDA GKIGTIVADMRKVLAKNPHIEQQKLHRRVFFEKIDPKNQALMMGFDFTMKALYTGVWIASVSLF MELLGFNTQKWITAGGFGTVLLTLAGREIFTNFLSSVMINATRPFVVNEWIDAKIDGVDVSGIV EHVGLWSPTLIRGVDREAIYIPNHKFTVSILRNNTQRTHWRIKTYLAISHMDAGKIGTIVADMR KVLAKNPHIEQQKLHRRVFFEKIDPKNQALMMGFDFTMKALYTGVWIASVSLFMELLGFNTQKW ITAGGFGTVLLTLAGREIFTNFLSSVMINATRPFVVNEWIDAKIDGVDVSGIVEHVGLWSPTLI RGVDREAIYIPNHKFTVSILRNNTQRTHWRIKTYLAISHMDAGKIGTIVADMRKVLAKNPHIEQ QKLHRRVFFEKIDPKNQALM(-)
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 Zm00001d029608_circ_g.4

Address

Any questions?

Supported by