Plant Circular RNA Database

Detail information of Zm00001d025128_circ_g.5

			
						 General Information
					
						CircRNA Name
						Zm00001d025128_circ_g.5
					
						ID in PlantcircBase
						zma_circ_010280
					
						Alias
						zma_circ_0000019, GRMZM2G126545_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 105645703-105646366  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d025128						
					
						Parent gene annotation
						
							 methyl binding domain113
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d025128_circ_g.2 Zm00001d025128_circ_g.3 Zm00001d025128_circ_g.4 						
					
						Support reads
						NA
					
						Tissues
						leaf, 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
						Zm00001d025128_T012:3
Zm00001d025128_T011:3
Zm00001d025128_T003:3
Zm00001d025128_T017:3
Zm00001d025128_T009:3
Zm00001d025128_T001:3
Zm00001d025128_T006:3
Zm00001d025128_T007:3
Zm00001d025128_T016:3
Zm00001d025128_T015:3
Zm00001d025128_T004:3
Zm00001d025128_T014:3
Zm00001d025128_T013:3
Zm00001d025128_T010:3
Zm00001d025128_T008:3
Zm00001d025128_T002:3

General Information
CircRNA Name	Zm00001d025128_circ_g.5
ID in PlantcircBase	zma_circ_010280
Alias	zma_circ_0000019, GRMZM2G126545_C2
Organism	Zea mays
Position	chr10: 105645703-105646366 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d025128
Parent gene annotation	methyl binding domain113
Parent gene strand	-
Alternative splicing	Zm00001d025128_circ_g.2 Zm00001d025128_circ_g.3 Zm00001d025128_circ_g.4
Support reads	NA
Tissues	leaf, 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	Zm00001d025128_T012:3 Zm00001d025128_T011:3 Zm00001d025128_T003:3 Zm00001d025128_T017:3 Zm00001d025128_T009:3 Zm00001d025128_T001:3 Zm00001d025128_T006:3 Zm00001d025128_T007:3 Zm00001d025128_T016:3 Zm00001d025128_T015:3 Zm00001d025128_T004:3 Zm00001d025128_T014:3 Zm00001d025128_T013:3 Zm00001d025128_T010:3 Zm00001d025128_T008:3 Zm00001d025128_T002:3

			
						 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  
						
							ATGAACCACTAAGACCTCCTTACCTTGCCTCCCCTGTTTTTCTACCTCCACGGTCTGCTTCAAT
GTGTTGTCATTAGAGATAACCAGGCCATTATTCTCCcttgtacattttgtccattttcttccca
ccggctctgacttcaatcacccacccacgtggaagccatgtatgtgactcctgcatgcaacaat
caggaaag

						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: 415
Transcript exons: 105645703-105645780,105645863-105645988,105646156-105646
366
CTTGTACATTTTGTCCATTTTCTTCCCACCGGCTCTGACTTCAATCACCCACCCACGTGGAAGC
CATGTATGTGACTCATGAAGCTCGTTGTCCTCGGCGCTTGCCTGCAACTCCAACATGCGTTCTT
CCACCCCTGAGAAAAGATAATGCAATGTCTCCATCTTTGATGTGAACATGTATCCGGACATTGG
GGAAGTGTAGTACTTGTAGATGGAGCCATTGTCTTCTTGACAAACCTCCATAGTCCAACCGTCA
GGAAGCCAACCCGGCGGCTCATCCAATGACCCAGAATCCTCATTCGACTCATCCAATTCATGAA
CCACTAAGACCTCCTTACCTTGCCTCCCCTGTTTTTCTACCTCCACGGTCTGCTTCAATGTGTT
GTCATTAGAGATAACCAGGCCATTATTCTCC
						
						Genomic sequence
						
							CTTGTACATTTTGTCCATTTTCTTCCCACCGGCTCTGACTTCAATCACCCACCCACGTGGAAGC
CATGTATGTGACTCCTGCATGCAACAATCAGGAAAGCACATCAGTTTAATCAGCAGTGTCATAC
AATATGGCATGACTGAATAAGAATTGACTAACATGAAGCTCGTTGTCCTCGGCGCTTGCCTGCA
ACTCCAACATGCGTTCTTCCACCCCTGAGAAAAGATAATGCAATGTCTCCATCTTTGATGTGAA
CATGTATCCGGACATTGGGGAAGTGTAGTACTGCAGAAAACAAGTAACAAATTTTTTCACAAAT
ATTAACAAATAAATGTTCTATAAACTCCAGAATCAGGTTTATAAGATCTACACAAACATATGTA
TGGTCAGCATTTGAAACATCACATGACATATATGTTCATATGCAAGGGCATATGTGGAAGCATG
CATACCTTGTAGATGGAGCCATTGTCTTCTTGACAAACCTCCATAGTCCAACCGTCAGGAAGCC
AACCCGGCGGCTCATCCAATGACCCAGAATCCTCATTCGACTCATCCAATTCATGAACCACTAA
GACCTCCTTACCTTGCCTCCCCTGTTTTTCTACCTCCACGGTCTGCTTCAATGTGTTGTCATTA
GAGATAACCAGGCCATTATTCTCC

Sequences
Splice junction sequence	ATGAACCACTAAGACCTCCTTACCTTGCCTCCCCTGTTTTTCTACCTCCACGGTCTGCTTCAAT GTGTTGTCATTAGAGATAACCAGGCCATTATTCTCCcttgtacattttgtccattttcttccca ccggctctgacttcaatcacccacccacgtggaagccatgtatgtgactcctgcatgcaacaat caggaaag
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: 415 Transcript exons: 105645703-105645780,105645863-105645988,105646156-105646 366 CTTGTACATTTTGTCCATTTTCTTCCCACCGGCTCTGACTTCAATCACCCACCCACGTGGAAGC CATGTATGTGACTCATGAAGCTCGTTGTCCTCGGCGCTTGCCTGCAACTCCAACATGCGTTCTT CCACCCCTGAGAAAAGATAATGCAATGTCTCCATCTTTGATGTGAACATGTATCCGGACATTGG GGAAGTGTAGTACTTGTAGATGGAGCCATTGTCTTCTTGACAAACCTCCATAGTCCAACCGTCA GGAAGCCAACCCGGCGGCTCATCCAATGACCCAGAATCCTCATTCGACTCATCCAATTCATGAA CCACTAAGACCTCCTTACCTTGCCTCCCCTGTTTTTCTACCTCCACGGTCTGCTTCAATGTGTT GTCATTAGAGATAACCAGGCCATTATTCTCC
Genomic sequence	CTTGTACATTTTGTCCATTTTCTTCCCACCGGCTCTGACTTCAATCACCCACCCACGTGGAAGC CATGTATGTGACTCCTGCATGCAACAATCAGGAAAGCACATCAGTTTAATCAGCAGTGTCATAC AATATGGCATGACTGAATAAGAATTGACTAACATGAAGCTCGTTGTCCTCGGCGCTTGCCTGCA ACTCCAACATGCGTTCTTCCACCCCTGAGAAAAGATAATGCAATGTCTCCATCTTTGATGTGAA CATGTATCCGGACATTGGGGAAGTGTAGTACTGCAGAAAACAAGTAACAAATTTTTTCACAAAT ATTAACAAATAAATGTTCTATAAACTCCAGAATCAGGTTTATAAGATCTACACAAACATATGTA TGGTCAGCATTTGAAACATCACATGACATATATGTTCATATGCAAGGGCATATGTGGAAGCATG CATACCTTGTAGATGGAGCCATTGTCTTCTTGACAAACCTCCATAGTCCAACCGTCAGGAAGCC AACCCGGCGGCTCATCCAATGACCCAGAATCCTCATTCGACTCATCCAATTCATGAACCACTAA GACCTCCTTACCTTGCCTCCCCTGTTTTTCTACCTCCACGGTCTGCTTCAATGTGTTGTCATTA GAGATAACCAGGCCATTATTCTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.166037158

Conservation Information
Conserved circRNAs	NA
PMCS	0.166037158

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							105646196-105646360(-)
						
						Potential amino acid sequence
						
							MEVCQEDNGSIYKYYTSPMSGYMFTSKMETLHYLFSGVEERMLELQASAEDNELHESHTWLPRG
WVIEVRAGGKKMDKMYKGE*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	105646196-105646360(-)
Potential amino acid sequence	MEVCQEDNGSIYKYYTSPMSGYMFTSKMETLHYLFSGVEERMLELQASAEDNELHESHTWLPRG WVIEVRAGGKKMDKMYKGE*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d025128_circ_g.5

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