Plant Circular RNA Database

Detail information of Zm00001d005257_circ_g.6

			
						 General Information
					
						CircRNA Name
						Zm00001d005257_circ_g.6
					
						ID in PlantcircBase
						zma_circ_007301
					
						Alias
						Zm02circ00084, zma_circ_0000859, GRMZM2G068212_C4
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 166030398-166031414  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d005257						
					
						Parent gene annotation
						
							Sulfate transporter 4.1 chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d005257_circ_g.1 Zm00001d005257_circ_g.2 Zm00001d005257_circ_g.3 Zm00001d005257_circ_g.4 Zm00001d005257_circ_g.5 Zm00001d005257_circ_g.7 Zm00001d005257_circ_g.8 Zm00001d005257_circ_g.9 Zm00001d005257_circ_g.10 Zm00001d005257_circ_g.11 Zm00001d005257_circ_g.12 						
					
						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
						Zm00001d005257_T002:4
Zm00001d005257_T003:2
Zm00001d005257_T004:2
Zm00001d005257_T001:3

General Information
CircRNA Name	Zm00001d005257_circ_g.6
ID in PlantcircBase	zma_circ_007301
Alias	Zm02circ00084, zma_circ_0000859, GRMZM2G068212_C4
Organism	Zea mays
Position	chr2: 166030398-166031414 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d005257
Parent gene annotation	Sulfate transporter 4.1 chloroplastic
Parent gene strand	-
Alternative splicing	Zm00001d005257_circ_g.1 Zm00001d005257_circ_g.2 Zm00001d005257_circ_g.3 Zm00001d005257_circ_g.4 Zm00001d005257_circ_g.5 Zm00001d005257_circ_g.7 Zm00001d005257_circ_g.8 Zm00001d005257_circ_g.9 Zm00001d005257_circ_g.10 Zm00001d005257_circ_g.11 Zm00001d005257_circ_g.12
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	Zm00001d005257_T002:4 Zm00001d005257_T003:2 Zm00001d005257_T004:2 Zm00001d005257_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  
						
							CAACACCAGTGATTAGTACAGCAGTTGGCACAAGTGACATTAGATGCTCAAATCCTTGAGGAAT
GGAGAACCTGGGAAGACCCTGTGGTATTTCACCAACctggggtatatcagtaaataatggggtc
ataaataagagagcaccaccaatgattatgcccattatgattccagataacccagtttttgccc
cactttca

						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: 363
Transcript exons: 166030398-166030525,166030640-166030700,166031157-166031
222,166031307-166031414
CTGGGGTATATCAGTAAATAATGGGGTCATAAATAAGAGAGCACCACCAATGATTATGCCCATT
ATGATTCCAGATAACCCAGTTTTTGCCCCACTTTCATGATTCACTGCTGACCTAGAAAAGGAGC
CTGTGGCAGGATATGCAGAGAAGAATGAACCACAGATATTTGCTATTCCCAGACCAAATAACTC
TTTGTTAGAGTCCAACTCATACCCATTCTTCGCTGCCAAAGCTTTAGCAATACCAACAGATTCC
AAAATAGCAACACCAGTGATTAGTACAGCAGTTGGCACAAGTGACATTAGATGCTCAAATCCTT
GAGGAATGGAGAACCTGGGAAGACCCTGTGGTATTTCACCAAC
						
						Genomic sequence
						
							CTGGGGTATATCAGTAAATAATGGGGTCATAAATAAGAGAGCACCACCAATGATTATGCCCATT
ATGATTCCAGATAACCCAGTTTTTGCCCCACTTTCATGATTCACTGCTGACCTAGAAAAGGAGC
CTGCATGAACCAGTAGTTTAGGCTTGTAATATTTTGATCTAGCAACTAAGACAATATGCAAAAG
ACTAACAAAGGACTGGGTTATTTATCACTATATAATGTTAAATATTTTACCTGTGGCAGGATAT
GCAGAGAAGAATGAACCACAGATATTTGCTATTCCCAGACCAAATAACTATAACAAAGAAAACA
TGAGCGGAACAGTTAAACAAGCTATATTACAAGACAAAACATGCAATCCTCAATACAGAAGTAC
ATATTCCATGTCCTTCCCTAAACCTATTTATTATCCAATCATGGTACCTAACTTTATATAGGCT
AAAATTCTTAGTTAACAATTGAGACAAGTGTGTGTTGTCAAGTGAACAAGATGCATAGAAGCTA
ACATTTGATTCATTAGATCTTGGCATATTAACTATTGCAACCTACTAAGTTAAAATCTTCCTGA
TGATACATTGACTACCACTGCGGAAGAGCTTCATCCCACAACACAAAAAAATGTGCCTGAAAAT
TTCATTGTTTTGTCGCATACCATGCAGTGATACAAATAAAATTACATGTGTACGAACAATGTTT
ATCAACTTGTAACAACTGCAAAGAAACACTAATTAGGCTAGTAAATGATGCTTGCCTCTTTGTT
AGAGTCCAACTCATACCCATTCTTCGCTGCCAAAGCTTTAGCAATACCAACAGATTCCTGGAAT
GGTATGGTAAAATACTTAATGGAGAACCTGGGAAGACCCTGTGGTATTTCTCACCAAAATAGCA
ACAAATTTCTCACCAAAATAGCAACACCAGTGATTAGTACAGCAGTTGGCACAAGTGACATTAG
ATGCTCAAATCCTTGAGGAATGGAGAACCTGGGAAGACCCTGTGGTATTTCACCAAC

Sequences
Splice junction sequence	CAACACCAGTGATTAGTACAGCAGTTGGCACAAGTGACATTAGATGCTCAAATCCTTGAGGAAT GGAGAACCTGGGAAGACCCTGTGGTATTTCACCAACctggggtatatcagtaaataatggggtc ataaataagagagcaccaccaatgattatgcccattatgattccagataacccagtttttgccc cactttca
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: 363 Transcript exons: 166030398-166030525,166030640-166030700,166031157-166031 222,166031307-166031414 CTGGGGTATATCAGTAAATAATGGGGTCATAAATAAGAGAGCACCACCAATGATTATGCCCATT ATGATTCCAGATAACCCAGTTTTTGCCCCACTTTCATGATTCACTGCTGACCTAGAAAAGGAGC CTGTGGCAGGATATGCAGAGAAGAATGAACCACAGATATTTGCTATTCCCAGACCAAATAACTC TTTGTTAGAGTCCAACTCATACCCATTCTTCGCTGCCAAAGCTTTAGCAATACCAACAGATTCC AAAATAGCAACACCAGTGATTAGTACAGCAGTTGGCACAAGTGACATTAGATGCTCAAATCCTT GAGGAATGGAGAACCTGGGAAGACCCTGTGGTATTTCACCAAC
Genomic sequence	CTGGGGTATATCAGTAAATAATGGGGTCATAAATAAGAGAGCACCACCAATGATTATGCCCATT ATGATTCCAGATAACCCAGTTTTTGCCCCACTTTCATGATTCACTGCTGACCTAGAAAAGGAGC CTGCATGAACCAGTAGTTTAGGCTTGTAATATTTTGATCTAGCAACTAAGACAATATGCAAAAG ACTAACAAAGGACTGGGTTATTTATCACTATATAATGTTAAATATTTTACCTGTGGCAGGATAT GCAGAGAAGAATGAACCACAGATATTTGCTATTCCCAGACCAAATAACTATAACAAAGAAAACA TGAGCGGAACAGTTAAACAAGCTATATTACAAGACAAAACATGCAATCCTCAATACAGAAGTAC ATATTCCATGTCCTTCCCTAAACCTATTTATTATCCAATCATGGTACCTAACTTTATATAGGCT AAAATTCTTAGTTAACAATTGAGACAAGTGTGTGTTGTCAAGTGAACAAGATGCATAGAAGCTA ACATTTGATTCATTAGATCTTGGCATATTAACTATTGCAACCTACTAAGTTAAAATCTTCCTGA TGATACATTGACTACCACTGCGGAAGAGCTTCATCCCACAACACAAAAAAATGTGCCTGAAAAT TTCATTGTTTTGTCGCATACCATGCAGTGATACAAATAAAATTACATGTGTACGAACAATGTTT ATCAACTTGTAACAACTGCAAAGAAACACTAATTAGGCTAGTAAATGATGCTTGCCTCTTTGTT AGAGTCCAACTCATACCCATTCTTCGCTGCCAAAGCTTTAGCAATACCAACAGATTCCTGGAAT GGTATGGTAAAATACTTAATGGAGAACCTGGGAAGACCCTGTGGTATTTCTCACCAAAATAGCA ACAAATTTCTCACCAAAATAGCAACACCAGTGATTAGTACAGCAGTTGGCACAAGTGACATTAG ATGCTCAAATCCTTGAGGAATGGAGAACCTGGGAAGACCCTGTGGTATTTCACCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.084216116

Conservation Information
Conserved circRNAs	NA
PMCS	0.084216116

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							166031359-166030415(+)
166031378-166030497(+)
166031356-166030400(-)
						
						Potential amino acid sequence
						
							MLKSLRNGEPGKTLWYFTNLGYISK*(+)
MENLGRPCGISPTWGISVNNGVINKRAPPMIMPIMIPDNPVFAPLS*(+)
MSLVPTAVLITGVAILESVGIAKALAAKNGYELDSNKELFGLGIANICGSFFSAYPATGSFSRS
AVNHESGAKTGLSGIIMGIIIGGALLFMTPLFTDIPQVGEIPQGLPRFSIPQGFEHLMSLVPTA
VLITGVAILESVGIAKALAAKNGYELDSNKELFGLGIANICGSFFSAYPATGSFSRSAVNHESG
AKTGLSGIIMGIIIGGALLFMTPLFTDIPQVGEIPQGLPRFSIPQGFEHLMSLVPTAVLITGVA
ILESVGIAKALAAKNGYELDSNKELFGLGIANICGSFFSAYPATGSFSRSAVNHESGAKTGLSG
IIMGIIIGGALLFMTPLFTDIPQVGEIPQGLPRFSIPQGFEHLMSLVPTAVLITGVAILESVGI
AKALAAKNGYELDSNKELFGLGIANICGSFFSAYPATGSFSRSAVNHESGAKTGLSGIIMGIII
GGALLFMTPLFTDIPQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	166031359-166030415(+) 166031378-166030497(+) 166031356-166030400(-)
Potential amino acid sequence	MLKSLRNGEPGKTLWYFTNLGYISK(+) MENLGRPCGISPTWGISVNNGVINKRAPPMIMPIMIPDNPVFAPLS(+) MSLVPTAVLITGVAILESVGIAKALAAKNGYELDSNKELFGLGIANICGSFFSAYPATGSFSRS AVNHESGAKTGLSGIIMGIIIGGALLFMTPLFTDIPQVGEIPQGLPRFSIPQGFEHLMSLVPTA VLITGVAILESVGIAKALAAKNGYELDSNKELFGLGIANICGSFFSAYPATGSFSRSAVNHESG AKTGLSGIIMGIIIGGALLFMTPLFTDIPQVGEIPQGLPRFSIPQGFEHLMSLVPTAVLITGVA ILESVGIAKALAAKNGYELDSNKELFGLGIANICGSFFSAYPATGSFSRSAVNHESGAKTGLSG IIMGIIIGGALLFMTPLFTDIPQVGEIPQGLPRFSIPQGFEHLMSLVPTAVLITGVAILESVGI AKALAAKNGYELDSNKELFGLGIANICGSFFSAYPATGSFSRSAVNHESGAKTGLSGIIMGIII GGALLFMTPLFTDIPQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d005257_circ_g.6

Address

Any questions?

Supported by