Plant Circular RNA Database

Detail information of Zm00001d004118_circ_g.12

			
						 General Information
					
						CircRNA Name
						Zm00001d004118_circ_g.12
					
						ID in PlantcircBase
						zma_circ_007217
					
						Alias
						zma_circ_0001102, GRMZM2G161087_C4
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 83773650-83778886  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d004118						
					
						Parent gene annotation
						
							Protein MICRORCHIDIA 7
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d004118_circ_g.2 Zm00001d004118_circ_g.3 Zm00001d004118_circ_g.4 Zm00001d004118_circ_g.5 Zm00001d004118_circ_g.6 Zm00001d004118_circ_g.7 Zm00001d004118_circ_g.8 Zm00001d004118_circ_g.9 Zm00001d004118_circ_g.10 Zm00001d004118_circ_g.11 						
					
						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  
						
							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
						Zm00001d004118_T003:4
Zm00001d004118_T004:4
Zm00001d004118_T002:4
Zm00001d004118_T006:4

General Information
CircRNA Name	Zm00001d004118_circ_g.12
ID in PlantcircBase	zma_circ_007217
Alias	zma_circ_0001102, GRMZM2G161087_C4
Organism	Zea mays
Position	chr2: 83773650-83778886 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d004118
Parent gene annotation	Protein MICRORCHIDIA 7
Parent gene strand	+
Alternative splicing	Zm00001d004118_circ_g.2 Zm00001d004118_circ_g.3 Zm00001d004118_circ_g.4 Zm00001d004118_circ_g.5 Zm00001d004118_circ_g.6 Zm00001d004118_circ_g.7 Zm00001d004118_circ_g.8 Zm00001d004118_circ_g.9 Zm00001d004118_circ_g.10 Zm00001d004118_circ_g.11
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	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	Zm00001d004118_T003:4 Zm00001d004118_T004:4 Zm00001d004118_T002:4 Zm00001d004118_T006:4

			
						 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  
						
							AAACCGAAAATTGTTTCAAAATGGCAGTACTGGTTTGATAACACCTCAATCCAGTGGACTGATA
GAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGcctttctggagagtgtggactgctgctg
gaagtggaggtcgtggtgtcataggtagtccctattccatgctttcgtttatttagtctttttt
attgtcta

						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: 597
Transcript exons: 83773650-83773701,83773788-83773899,83774058-83774128,83
778525-83778886
CCTTTCTGGAGAGTGTGGACTGCTGCTGGAAGTGGAGGTCGTGGTGTCATAGGTGTTCTTGAGG
CAAACTTCATTGAACCTGCTCATGATAAGCAAGACTTTGAGCGGACAACACTTCTAGCAAGACT
TGAAGCACGATTAGTTCAAATGCAGAAGGATTACTGGTCTGGGAATGCTCATCGAATAGGATAT
GTTGCACCACGATTTGGCAGGAATACTGAGGCAGGAGATGGAGAAGACTCTCCTGAAAACACAG
CAAGTGCACAACCATCACCTTATCATTCTGGTAAAGGGTACACACATGCAAAAGACTTGAGTAA
TAATATCAAAAAGGGTGGTAAGGCAAGCACATCATTTGGTATTCAGCAAAGAGCTGAGAAGTCC
GCAAGGACTAAACGATCTACGAAGTCAATACTGCACGGGCTGTCTGATAGTGATAATAGTGATT
CTGAGTTTATGGGCACCCTGTCGAGGTCAAGATCGCACACCCTGAAGACAAACCGAAAATTGTT
TCAAAATGGCAGTACTGGTTTGATAACACCTCAATCCAGTGGACTGATAGAAAGAGAGAGGGTC
AGAACTAAATCCCAGCCATTG
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AAACCGAAAATTGTTTCAAAATGGCAGTACTGGTTTGATAACACCTCAATCCAGTGGACTGATA GAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGcctttctggagagtgtggactgctgctg gaagtggaggtcgtggtgtcataggtagtccctattccatgctttcgtttatttagtctttttt attgtcta
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: 597 Transcript exons: 83773650-83773701,83773788-83773899,83774058-83774128,83 778525-83778886 CCTTTCTGGAGAGTGTGGACTGCTGCTGGAAGTGGAGGTCGTGGTGTCATAGGTGTTCTTGAGG CAAACTTCATTGAACCTGCTCATGATAAGCAAGACTTTGAGCGGACAACACTTCTAGCAAGACT TGAAGCACGATTAGTTCAAATGCAGAAGGATTACTGGTCTGGGAATGCTCATCGAATAGGATAT GTTGCACCACGATTTGGCAGGAATACTGAGGCAGGAGATGGAGAAGACTCTCCTGAAAACACAG CAAGTGCACAACCATCACCTTATCATTCTGGTAAAGGGTACACACATGCAAAAGACTTGAGTAA TAATATCAAAAAGGGTGGTAAGGCAAGCACATCATTTGGTATTCAGCAAAGAGCTGAGAAGTCC GCAAGGACTAAACGATCTACGAAGTCAATACTGCACGGGCTGTCTGATAGTGATAATAGTGATT CTGAGTTTATGGGCACCCTGTCGAGGTCAAGATCGCACACCCTGAAGACAAACCGAAAATTGTT TCAAAATGGCAGTACTGGTTTGATAACACCTCAATCCAGTGGACTGATAGAAAGAGAGAGGGTC AGAACTAAATCCCAGCCATTG
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.064931657

Conservation Information
Conserved circRNAs	NA
PMCS	0.064931657

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							83773884-83778883(+)
83773824-83778766(-)
83773811-83778834(-)
						
						Potential amino acid sequence
						
							MQKDYWSGNAHRIGYVAPRFGRNTEAGDGEDSPENTASAQPSPYHSGKGYTHAKDLSNNIKKGG
KASTSFGIQQRAEKSARTKRSTKSILHGLSDSDNSDSEFMGTLSRSRSHTLKTNRKLFQNGSTG
LITPQSSGLIERERVRTKSQPLPFWRVWTAAGSGGRGVIGVLEANFIEPAHDKQDFERTTLLAR
LEARLVQMQKDYWSGNAHRIGYVAPRFGRNTEAGDGEDSPENTASAQPSPYHSGKGYTHAKDLS
NNIKKGGKASTSFGIQQRAEKSARTKRSTKSILHGLSDSDNSDSEFMGTLSRSRSHTLKTNRKL
FQNGSTGLITPQSSGLIERERVRTKSQPLPFWRVWTAAGSGGRGVIGVLEANFIEPAHDKQDFE
RTTLLARLEARLVQMQKDYWSGNAHRIGYVAPRFGRNTEAGDGEDSPENTASAQPSPYHSGKGY
THAKDLSNNIKKGGKASTSFGIQQRAEKSARTKRSTKSILHGLSDSDNSDSEFMGTLSRSRSHT
LKTNRKLFQNGSTGLITPQSSGLIERERVRTKSQPLPFWRVWTAAGSGGRGVIGVLEANFIEPA
HDKQDFERTTLLARLEARLVQMQKDYWSGNAHRIGYVAPRFGRNTEAGDGEDSPENTASAQPSP
YHSGKGYTHAKDLSNNIKKGGKASTSFGIQQRAEKSARTKRSTKSILHGLSDSDNSDSEFMGTL
SRSRSHTLKTNRKLFQNGSTGLITPQSSGLIERERVRTKSQPL(+)
MSRFNEVCLKNTYDTTTSTSSSSPHSPERQWLGFSSDPLSFYQSTGLRCYQTSTAILKQFSVCL
QGVRS*(-)
MKFASRTPMTPRPPLPAAVHTLQKGNGWDLVLTLSLSISPLD*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	83773884-83778883(+) 83773824-83778766(-) 83773811-83778834(-)
Potential amino acid sequence	MQKDYWSGNAHRIGYVAPRFGRNTEAGDGEDSPENTASAQPSPYHSGKGYTHAKDLSNNIKKGG KASTSFGIQQRAEKSARTKRSTKSILHGLSDSDNSDSEFMGTLSRSRSHTLKTNRKLFQNGSTG LITPQSSGLIERERVRTKSQPLPFWRVWTAAGSGGRGVIGVLEANFIEPAHDKQDFERTTLLAR LEARLVQMQKDYWSGNAHRIGYVAPRFGRNTEAGDGEDSPENTASAQPSPYHSGKGYTHAKDLS NNIKKGGKASTSFGIQQRAEKSARTKRSTKSILHGLSDSDNSDSEFMGTLSRSRSHTLKTNRKL FQNGSTGLITPQSSGLIERERVRTKSQPLPFWRVWTAAGSGGRGVIGVLEANFIEPAHDKQDFE RTTLLARLEARLVQMQKDYWSGNAHRIGYVAPRFGRNTEAGDGEDSPENTASAQPSPYHSGKGY THAKDLSNNIKKGGKASTSFGIQQRAEKSARTKRSTKSILHGLSDSDNSDSEFMGTLSRSRSHT LKTNRKLFQNGSTGLITPQSSGLIERERVRTKSQPLPFWRVWTAAGSGGRGVIGVLEANFIEPA HDKQDFERTTLLARLEARLVQMQKDYWSGNAHRIGYVAPRFGRNTEAGDGEDSPENTASAQPSP YHSGKGYTHAKDLSNNIKKGGKASTSFGIQQRAEKSARTKRSTKSILHGLSDSDNSDSEFMGTL SRSRSHTLKTNRKLFQNGSTGLITPQSSGLIERERVRTKSQPL(+) MSRFNEVCLKNTYDTTTSTSSSSPHSPERQWLGFSSDPLSFYQSTGLRCYQTSTAILKQFSVCL QGVRS(-) MKFASRTPMTPRPPLPAAVHTLQKGNGWDLVLTLSLSISPLD(-)
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 Zm00001d004118_circ_g.12

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