Plant Circular RNA Database

Detail information of Zm00001d025134_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d025134_circ_g.3
					
						ID in PlantcircBase
						zma_circ_010285
					
						Alias
						Zm10circ00039, zma_circ_0003204, GRMZM2G323754_C3
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 105955563-105956369  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d025134						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d025134_circ_g.2 						
					
						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  
						
							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
						Zm00001d025134_T003:3
Zm00001d025134_T002:3
Zm00001d025134_T008:3
Zm00001d025134_T005:3
Zm00001d025134_T007:3
Zm00001d025134_T006:3
Zm00001d025134_T004:3
Zm00001d025134_T001:3

General Information
CircRNA Name	Zm00001d025134_circ_g.3
ID in PlantcircBase	zma_circ_010285
Alias	Zm10circ00039, zma_circ_0003204, GRMZM2G323754_C3
Organism	Zea mays
Position	chr10: 105955563-105956369 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d025134
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Zm00001d025134_circ_g.2
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	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	Zm00001d025134_T003:3 Zm00001d025134_T002:3 Zm00001d025134_T008:3 Zm00001d025134_T005:3 Zm00001d025134_T007:3 Zm00001d025134_T006:3 Zm00001d025134_T004:3 Zm00001d025134_T001:3

			
						 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  
						
							AGGTGAAGACCTTGCTGAAACACAATTATTTTCGTCAAGCAGCAGTCTAACTGATGACAGCATT
TGTAGTGATTTTGATATTTATGTAAGGAAGCTTCAGggaacacttgctgtcctatatcacagaa
ggagatgattcacaagctttgggttcattgtgcttattcgctacattattgcagacgaaaggtg
tgtttgac

						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: 271
Transcript exons: 105955563-105955651,105955736-105955806,105956259-105956
369
GGAACACTTGCTGTCCTATATCACAGAAGGAGATGATTCACAAGCTTTGGGTTCATTGTGCTTA
TTCGCTACATTATTGCAGACGAAAGAACTTGATGAATCAATGCTGGATGCCCTTGGAATCCTCC
CTCAAAGAAAGCAGCATAAGAAACTTCTATTACAAGCTTTAGTAGGTGAAGACCTTGCTGAAAC
ACAATTATTTTCGTCAAGCAGCAGTCTAACTGATGACAGCATTTGTAGTGATTTTGATATTTAT
GTAAGGAAGCTTCAG
						
						Genomic sequence
						
							GGAACACTTGCTGTCCTATATCACAGAAGGAGATGATTCACAAGCTTTGGGTTCATTGTGCTTA
TTCGCTACATTATTGCAGACGAAAGGTGTGTTTGACATTTTCTCATATACTTATCCTTTTCACT
GTGGCTTTCCCAGAAAATGATTGCAAGTAATTGTTTGCTTTATAGAACTTGATGAATCAATGCT
GGATGCCCTTGGAATCCTCCCTCAAAGAAAGCAGCATAAGAAACTTCTATTAGTAAGTACTTTC
ACCTTCCCACTTTGAGAGAAAAAACAGTTATATTACTTGTTTACTTACTATAATGTGGTCAACT
GTAGAATGCACCCATGTTTTCCTCAACATTAGTTGACTATGTTGTTAGCATCCTAAAATTCTGA
CACCTTGTTTGTTGATGTCTATGTGAATGGTTATTGTGCTATGTTTTTTTTTCAGTAGTTACAG
TTCTATCATATGCAGGCTTTCTCTTCCCATTAAAAATCACATAAGGCAGCTAGTATAATATTTT
ATGGGTAGTCGTGATTAGGGTTAAATGAACAAGATTTGACAGGTTTGTTGGCCCTTCATCGTTT
TGCAGTCCCCTGTTCCTTGGTTCTAGTTATGTCTTTGTATTACCTCCTTTGTATTTGGAAACAT
GATCATAGTACTTTATTTTGCTTTAATTTTCTGACACCTGTCTTCTCTTTCTGCAGCAAGCTTT
AGTAGGTGAAGACCTTGCTGAAACACAATTATTTTCGTCAAGCAGCAGTCTAACTGATGACAGC
ATTTGTAGTGATTTTGATATTTATGTAAGGAAGCTTCAG

Sequences
Splice junction sequence	AGGTGAAGACCTTGCTGAAACACAATTATTTTCGTCAAGCAGCAGTCTAACTGATGACAGCATT TGTAGTGATTTTGATATTTATGTAAGGAAGCTTCAGggaacacttgctgtcctatatcacagaa ggagatgattcacaagctttgggttcattgtgcttattcgctacattattgcagacgaaaggtg tgtttgac
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: 271 Transcript exons: 105955563-105955651,105955736-105955806,105956259-105956 369 GGAACACTTGCTGTCCTATATCACAGAAGGAGATGATTCACAAGCTTTGGGTTCATTGTGCTTA TTCGCTACATTATTGCAGACGAAAGAACTTGATGAATCAATGCTGGATGCCCTTGGAATCCTCC CTCAAAGAAAGCAGCATAAGAAACTTCTATTACAAGCTTTAGTAGGTGAAGACCTTGCTGAAAC ACAATTATTTTCGTCAAGCAGCAGTCTAACTGATGACAGCATTTGTAGTGATTTTGATATTTAT GTAAGGAAGCTTCAG
Genomic sequence	GGAACACTTGCTGTCCTATATCACAGAAGGAGATGATTCACAAGCTTTGGGTTCATTGTGCTTA TTCGCTACATTATTGCAGACGAAAGGTGTGTTTGACATTTTCTCATATACTTATCCTTTTCACT GTGGCTTTCCCAGAAAATGATTGCAAGTAATTGTTTGCTTTATAGAACTTGATGAATCAATGCT GGATGCCCTTGGAATCCTCCCTCAAAGAAAGCAGCATAAGAAACTTCTATTAGTAAGTACTTTC ACCTTCCCACTTTGAGAGAAAAAACAGTTATATTACTTGTTTACTTACTATAATGTGGTCAACT GTAGAATGCACCCATGTTTTCCTCAACATTAGTTGACTATGTTGTTAGCATCCTAAAATTCTGA CACCTTGTTTGTTGATGTCTATGTGAATGGTTATTGTGCTATGTTTTTTTTTCAGTAGTTACAG TTCTATCATATGCAGGCTTTCTCTTCCCATTAAAAATCACATAAGGCAGCTAGTATAATATTTT ATGGGTAGTCGTGATTAGGGTTAAATGAACAAGATTTGACAGGTTTGTTGGCCCTTCATCGTTT TGCAGTCCCCTGTTCCTTGGTTCTAGTTATGTCTTTGTATTACCTCCTTTGTATTTGGAAACAT GATCATAGTACTTTATTTTGCTTTAATTTTCTGACACCTGTCTTCTCTTTCTGCAGCAAGCTTT AGTAGGTGAAGACCTTGCTGAAACACAATTATTTTCGTCAAGCAGCAGTCTAACTGATGACAGC ATTTGTAGTGATTTTGATATTTATGTAAGGAAGCTTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.190715478

Conservation Information
Conserved circRNAs	NA
PMCS	0.190715478

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							105955751-105955595(+)
						
						Potential amino acid sequence
						
							MLDALGILPQRKQHKKLLLQALVGEDLAETQLFSSSSSLTDDSICSDFDIYVRKLQGTLAVLYH
RRR*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	105955751-105955595(+)
Potential amino acid sequence	MLDALGILPQRKQHKKLLLQALVGEDLAETQLFSSSSSLTDDSICSDFDIYVRKLQGTLAVLYH RRR*(+)
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 Zm00001d025134_circ_g.3

Address

Any questions?

Supported by