Plant Circular RNA Database

Detail information of Zm00001d002332_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d002332_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007055
					
						Alias
						zma_circ_0000758, GRMZM2G005107_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 10493318-10494988  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d002332						
					
						Parent gene annotation
						
							NAD(P)-binding Rossmann-fold superfamily protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d002332_circ_g.1 Zm00001d002332_circ_g.2 Zm00001d002332_circ_g.4 Zm00001d002332_circ_g.5 						
					
						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
						Zm00001d002332_T001:4
Zm00001d002332_T016:4
Zm00001d002332_T018:4
Zm00001d002332_T026:4
Zm00001d002332_T024:4
Zm00001d002332_T007:4
Zm00001d002332_T004:4
Zm00001d002332_T005:4
Zm00001d002332_T020:4
Zm00001d002332_T022:4
Zm00001d002332_T006:4
Zm00001d002332_T011:4
Zm00001d002332_T025:4
Zm00001d002332_T012:4
Zm00001d002332_T015:4

General Information
CircRNA Name	Zm00001d002332_circ_g.3
ID in PlantcircBase	zma_circ_007055
Alias	zma_circ_0000758, GRMZM2G005107_C1
Organism	Zea mays
Position	chr2: 10493318-10494988 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d002332
Parent gene annotation	NAD(P)-binding Rossmann-fold superfamily protein
Parent gene strand	-
Alternative splicing	Zm00001d002332_circ_g.1 Zm00001d002332_circ_g.2 Zm00001d002332_circ_g.4 Zm00001d002332_circ_g.5
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	Zm00001d002332_T001:4 Zm00001d002332_T016:4 Zm00001d002332_T018:4 Zm00001d002332_T026:4 Zm00001d002332_T024:4 Zm00001d002332_T007:4 Zm00001d002332_T004:4 Zm00001d002332_T005:4 Zm00001d002332_T020:4 Zm00001d002332_T022:4 Zm00001d002332_T006:4 Zm00001d002332_T011:4 Zm00001d002332_T025:4 Zm00001d002332_T012:4 Zm00001d002332_T015:4

			
						 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  
						
							CGTTCACAAGAATGTCGAGCTTGCCAAAATGTGCAACTGTTGCAGCAAGCACTCTGGCCGCGTC
CTCCTGGTTGCGGACATCTCCATCGAAACCAACAGCcttcttctcaaccaccttcgacagctcc
ctaacttcctccttgggaatatggcgagggtgacttaaccaaagacctccatcgaccaccagtg
ttgtccca

									
								

					

						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: 666
Transcript exons: 10493318-10493430,10494206-10494428,10494500-10494669,10
494829-10494988
CTTCTTCTCAACCACCTTCGACAGCTCCCTAACTTCCTCCTTGGGAATATGGCGAGGGTGACTT
AACCAAAGACCTCCATCGACCACCAGTGTTGTCCCATTTACATATTTGCCTGCATCAGAAGCAA
GGTAGAGCGCAGCCATTGCTATGTCCCGCTTCTCCCCAAATTTGAACAATGGCATCATTTCTCG
AAGCCCCTTGCTCATTTCTTCAGGTGCAAGCTTCCTCAGCCCCGGGGTGTCTTGAATTGGTCCA
GGTGCAATCCCGTTGACTCTAATGTCATAATCTGTTCCCCACTCCAGAGCCAGTGATCTTGTGA
TGCTATCAACCCCAGCCTTAGCAGCAGAGACATGGATTTGGTACCAAGAAGCACTGTAATGCAG
TGTTGCACTTATGTTAATGATTAGTCCACCAGTGGACGGGCCTTTTCCTGGCCCACCCTTTTTC
AGATACTTGAGGGCTTCATAGCACATTGTGTATGTACCCAAAGTGTCGATCTCAAGAACAGTTC
TGAATCCCTTGGGCGTCAAATCCTCCGGGGAAGCAAGGAAGTTGCCAGCTGCACCGTTCACAAG
AATGTCGAGCTTGCCAAAATGTGCAACTGTTGCAGCAAGCACTCTGGCCGCGTCCTCCTGGTTG
CGGACATCTCCATCGAAACCAACAGC
						
					

						Genomic sequence
						
							CTTCTTCTCAACCACCTTCGACAGCTCCCTAACTTCCTCCTTGGGAATATGGCGAGGGTGACTT
AACCAAAGACCTCCATCGACCACCAGTGTTGTCCCATTTACATATTTGCCTGCAAACATGATTA
TGTCAAATGTCTGTGTTTCAGCTGAATTCAAACTGTTTCACCGCTCTATGGATTCCTTTAGATT
ACACCTAAAACAGTGTTAGACTGTTAGGGCTTGTTTGGGATAAATGGTAATGGAGGGGATTGAG
GGGGCTATAATCCCTCACTATTCAAAATTGAGTAGTGAGGGATTCTAGCCCACTTAACCCACTT
CATTACCTTTGATCCCAAACAAACCCTTGGTGTCTGTCTAAGTGCTATGGGCCTAGAGCCCAGT
TCATATAATCCACTACCATTGGGTATATCAGTATATGTAGTAATTTTCTCTTCCCCTCTCCTCC
CTTAGCTGCCGCCGCCACCTAGGCAGCATGACCCGCACTCCTACCCCTCCTCTCCTCTCCTCTC
CCCTCTCCCTCGAGGCTGGGTGTCAGTGGTCGCGGCACCTCCACCTCTCCCCGCCACCGCCCCC
TCCACCCTAGCCACCGCCGCCGTTCCCCGAGCAAAAATCACAATATAGAGTCGGCTAAGGCCTT
GTTCGGTAATTACTATTCCATATAGATGGAATGAAATTGGAAAACAATATGAAAGATTTTAAAT
TGTTTGGGATTTAAACCCACTCAATCCAATACATTGAGAGCAAAACGAACAAGCCCTTCTATTA
GCTCTGTGGACAATATCTTTCGTAATGACCTTCAGGTAAGTGGTGCACATCTATTGTTGAAATT
ATGTGAGTATCTGACTTACGATAATCTCGTTAGGAAATATGCAGAACAGAACCAACCTGCATCA
GAAGCAAGGTAGAGCGCAGCCATTGCTATGTCCCGCTTCTCCCCAAATTTGAACAATGGCATCA
TTTCTCGAAGCCCCTTGCTCATTTCTTCAGGTGCAAGCTTCCTCAGCCCCGGGGTGTCTTGAAT
TGGTCCAGGTGCAATCCCGTTGACTCTAATGTCATAATCTGTTCCCCACTCCAGAGCCAGTGAT
CTTGTGATGCTATCAACCCCAGCCTATACAAACGAATCTGCTTACTCCAATTATTTTCTGTTAT
TAAGGAGTGATTCAGAGAAGAACCAGGTACCTTAGCAGCAGAGACATGGATTTGGTACCAAGAA
GCACTGTAATGCAGTGTTGCACTTATGTTAATGATTAGTCCACCAGTGGACGGGCCTTTTCCTG
GCCCACCCTTTTTCAGATACTTGAGGGCTTCATAGCACATTGTGTATGTACCCAAAGTGTCGAT
CTCAAGAACTGCAGAGAGAAATTCAGTCATTACAAACTTGTCTGAAAAAAGCGTAATAACAAAC
AAAGTAAAATAAACAAGTTTTTGATCTAGCAGGCAATCACAATTGCCCAAACCAAAGACTCAGT
GAATCTGAATGGAAACAAGAGCACATTTTGATGAAGTACCAGTTCTGAATCCCTTGGGCGTCAA
ATCCTCCGGGGAAGCAAGGAAGTTGCCAGCTGCACCGTTCACAAGAATGTCGAGCTTGCCAAAA
TGTGCAACTGTTGCAGCAAGCACTCTGGCCGCGTCCTCCTGGTTGCGGACATCTCCATCGAAAC
CAACAGC
						
					

			
		

Sequences
Splice junction sequence	CGTTCACAAGAATGTCGAGCTTGCCAAAATGTGCAACTGTTGCAGCAAGCACTCTGGCCGCGTC CTCCTGGTTGCGGACATCTCCATCGAAACCAACAGCcttcttctcaaccaccttcgacagctcc ctaacttcctccttgggaatatggcgagggtgacttaaccaaagacctccatcgaccaccagtg ttgtccca
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: 666 Transcript exons: 10493318-10493430,10494206-10494428,10494500-10494669,10 494829-10494988 CTTCTTCTCAACCACCTTCGACAGCTCCCTAACTTCCTCCTTGGGAATATGGCGAGGGTGACTT AACCAAAGACCTCCATCGACCACCAGTGTTGTCCCATTTACATATTTGCCTGCATCAGAAGCAA GGTAGAGCGCAGCCATTGCTATGTCCCGCTTCTCCCCAAATTTGAACAATGGCATCATTTCTCG AAGCCCCTTGCTCATTTCTTCAGGTGCAAGCTTCCTCAGCCCCGGGGTGTCTTGAATTGGTCCA GGTGCAATCCCGTTGACTCTAATGTCATAATCTGTTCCCCACTCCAGAGCCAGTGATCTTGTGA TGCTATCAACCCCAGCCTTAGCAGCAGAGACATGGATTTGGTACCAAGAAGCACTGTAATGCAG TGTTGCACTTATGTTAATGATTAGTCCACCAGTGGACGGGCCTTTTCCTGGCCCACCCTTTTTC AGATACTTGAGGGCTTCATAGCACATTGTGTATGTACCCAAAGTGTCGATCTCAAGAACAGTTC TGAATCCCTTGGGCGTCAAATCCTCCGGGGAAGCAAGGAAGTTGCCAGCTGCACCGTTCACAAG AATGTCGAGCTTGCCAAAATGTGCAACTGTTGCAGCAAGCACTCTGGCCGCGTCCTCCTGGTTG CGGACATCTCCATCGAAACCAACAGC
Genomic sequence	CTTCTTCTCAACCACCTTCGACAGCTCCCTAACTTCCTCCTTGGGAATATGGCGAGGGTGACTT AACCAAAGACCTCCATCGACCACCAGTGTTGTCCCATTTACATATTTGCCTGCAAACATGATTA TGTCAAATGTCTGTGTTTCAGCTGAATTCAAACTGTTTCACCGCTCTATGGATTCCTTTAGATT ACACCTAAAACAGTGTTAGACTGTTAGGGCTTGTTTGGGATAAATGGTAATGGAGGGGATTGAG GGGGCTATAATCCCTCACTATTCAAAATTGAGTAGTGAGGGATTCTAGCCCACTTAACCCACTT CATTACCTTTGATCCCAAACAAACCCTTGGTGTCTGTCTAAGTGCTATGGGCCTAGAGCCCAGT TCATATAATCCACTACCATTGGGTATATCAGTATATGTAGTAATTTTCTCTTCCCCTCTCCTCC CTTAGCTGCCGCCGCCACCTAGGCAGCATGACCCGCACTCCTACCCCTCCTCTCCTCTCCTCTC CCCTCTCCCTCGAGGCTGGGTGTCAGTGGTCGCGGCACCTCCACCTCTCCCCGCCACCGCCCCC TCCACCCTAGCCACCGCCGCCGTTCCCCGAGCAAAAATCACAATATAGAGTCGGCTAAGGCCTT GTTCGGTAATTACTATTCCATATAGATGGAATGAAATTGGAAAACAATATGAAAGATTTTAAAT TGTTTGGGATTTAAACCCACTCAATCCAATACATTGAGAGCAAAACGAACAAGCCCTTCTATTA GCTCTGTGGACAATATCTTTCGTAATGACCTTCAGGTAAGTGGTGCACATCTATTGTTGAAATT ATGTGAGTATCTGACTTACGATAATCTCGTTAGGAAATATGCAGAACAGAACCAACCTGCATCA GAAGCAAGGTAGAGCGCAGCCATTGCTATGTCCCGCTTCTCCCCAAATTTGAACAATGGCATCA TTTCTCGAAGCCCCTTGCTCATTTCTTCAGGTGCAAGCTTCCTCAGCCCCGGGGTGTCTTGAAT TGGTCCAGGTGCAATCCCGTTGACTCTAATGTCATAATCTGTTCCCCACTCCAGAGCCAGTGAT CTTGTGATGCTATCAACCCCAGCCTATACAAACGAATCTGCTTACTCCAATTATTTTCTGTTAT TAAGGAGTGATTCAGAGAAGAACCAGGTACCTTAGCAGCAGAGACATGGATTTGGTACCAAGAA GCACTGTAATGCAGTGTTGCACTTATGTTAATGATTAGTCCACCAGTGGACGGGCCTTTTCCTG GCCCACCCTTTTTCAGATACTTGAGGGCTTCATAGCACATTGTGTATGTACCCAAAGTGTCGAT CTCAAGAACTGCAGAGAGAAATTCAGTCATTACAAACTTGTCTGAAAAAAGCGTAATAACAAAC AAAGTAAAATAAACAAGTTTTTGATCTAGCAGGCAATCACAATTGCCCAAACCAAAGACTCAGT GAATCTGAATGGAAACAAGAGCACATTTTGATGAAGTACCAGTTCTGAATCCCTTGGGCGTCAA ATCCTCCGGGGAAGCAAGGAAGTTGCCAGCTGCACCGTTCACAAGAATGTCGAGCTTGCCAAAA TGTGCAACTGTTGCAGCAAGCACTCTGGCCGCGTCCTCCTGGTTGCGGACATCTCCATCGAAAC CAACAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.131318766

Conservation Information
Conserved circRNAs	NA
PMCS	0.131318766

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10494918-10493380(+)
10494901-10493375(+)
10494639-10493320(-)
						
						Potential amino acid sequence
						
							MCNCCSKHSGRVLLVADISIETNSLLLNHLRQLPNFLLGNMARVT*(+)
MSSLPKCATVAASTLAASSWLRTSPSKPTAFFSTTFDSSLTSSLGIWRG*(+)
MCYEALKYLKKGGPGKGPSTGGLIINISATLHYSASWYQIHVSAAKAGVDSITRSLALEWGTDY
DIRVNGIAPGPIQDTPGLRKLAPEEMSKGLREMMPLFKFGEKRDIAMAALYLASDAGKYVNGTT
LVVDGGLWLSHPRHIPKEEVRELSKVVEKKAVGFDGDVRNQEDAARVLAATVAHFGKLDILVNG
AAGNFLASPEDLTPKGFRTVLEIDTLGTYTMCYEALKYLKKGGPGKGPSTGGLIINISATLHYS
ASWYQIHVSAAKAGVDSITRSLALEWGTDYDIRVNGIAPGPIQDTPGLRKLAPEEMSKGLREMM
PLFKFGEKRDIAMAALYLASDAGKYVNGTTLVVDGGLWLSHPRHIPKEEVRELSKVVEKKAVGF
DGDVRNQEDAARVLAATVAHFGKLDILVNGAAGNFLASPEDLTPKGFRTVLEIDTLGTYTMCYE
ALKYLKKGGPGKGPSTGGLIINISATLHYSASWYQIHVSAAKAGVDSITRSLALEWGTDYDIRV
NGIAPGPIQDTPGLRKLAPEEMSKGLREMMPLFKFGEKRDIAMAALYLASDAGKYVNGTTLVVD
GGLWLSHPRHIPKEEVRELSKVVEKKAVGFDGDVRNQEDAARVLAATVAHFGKLDILVNGAAGN
FLASPEDLTPKGFRTVLEIDTLGTYTMCYEALKYLKKGGPGKGPSTGGLIINISATLHYSASWY
QIHVSAAKAGVDSITRSLALEWGTDYDIRVNGIAPGPIQDTPGLRKLAPEEMSKGLREMMPLFK
FGEKRDIAMAALYLASDAGKYVNGTTLVVDGGLWLSHPRHIPKEEVRELSKVVEKK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	10494918-10493380(+) 10494901-10493375(+) 10494639-10493320(-)
Potential amino acid sequence	MCNCCSKHSGRVLLVADISIETNSLLLNHLRQLPNFLLGNMARVT(+) MSSLPKCATVAASTLAASSWLRTSPSKPTAFFSTTFDSSLTSSLGIWRG(+) MCYEALKYLKKGGPGKGPSTGGLIINISATLHYSASWYQIHVSAAKAGVDSITRSLALEWGTDY DIRVNGIAPGPIQDTPGLRKLAPEEMSKGLREMMPLFKFGEKRDIAMAALYLASDAGKYVNGTT LVVDGGLWLSHPRHIPKEEVRELSKVVEKKAVGFDGDVRNQEDAARVLAATVAHFGKLDILVNG AAGNFLASPEDLTPKGFRTVLEIDTLGTYTMCYEALKYLKKGGPGKGPSTGGLIINISATLHYS ASWYQIHVSAAKAGVDSITRSLALEWGTDYDIRVNGIAPGPIQDTPGLRKLAPEEMSKGLREMM PLFKFGEKRDIAMAALYLASDAGKYVNGTTLVVDGGLWLSHPRHIPKEEVRELSKVVEKKAVGF DGDVRNQEDAARVLAATVAHFGKLDILVNGAAGNFLASPEDLTPKGFRTVLEIDTLGTYTMCYE ALKYLKKGGPGKGPSTGGLIINISATLHYSASWYQIHVSAAKAGVDSITRSLALEWGTDYDIRV NGIAPGPIQDTPGLRKLAPEEMSKGLREMMPLFKFGEKRDIAMAALYLASDAGKYVNGTTLVVD GGLWLSHPRHIPKEEVRELSKVVEKKAVGFDGDVRNQEDAARVLAATVAHFGKLDILVNGAAGN FLASPEDLTPKGFRTVLEIDTLGTYTMCYEALKYLKKGGPGKGPSTGGLIINISATLHYSASWY QIHVSAAKAGVDSITRSLALEWGTDYDIRVNGIAPGPIQDTPGLRKLAPEEMSKGLREMMPLFK FGEKRDIAMAALYLASDAGKYVNGTTLVVDGGLWLSHPRHIPKEEVRELSKVVEKK(-)
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 Zm00001d002332_circ_g.3

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