Plant Circular RNA Database

Detail information of Zm00001d046039_circ_g.11

			
						 General Information
					
						CircRNA Name
						Zm00001d046039_circ_g.11
					
						ID in PlantcircBase
						zma_circ_009945
					
						Alias
						Zm09circ00037, zma_circ_0002967, GRMZM2G356423_C4
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 58165199-58166450  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d046039						
					
						Parent gene annotation
						
							HEAT repeat-containing protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d046039_circ_g.8 Zm00001d046039_circ_g.9 Zm00001d046039_circ_g.10 Zm00001d046039_circ_g.12 Zm00001d046039_circ_g.13 Zm00001d046039_circ_g.14 Zm00001d046039_circ_g.15 						
					
						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
						Zm00001d046039_T024:4
Zm00001d046039_T003:4
Zm00001d046039_T029:4
Zm00001d046039_T035:4
Zm00001d046039_T006:4
Zm00001d046039_T001:4
Zm00001d046039_T052:4
Zm00001d046039_T033:4
Zm00001d046039_T017:4
Zm00001d046039_T014:4
Zm00001d046039_T007:4
Zm00001d046039_T004:4
Zm00001d046039_T039:4
Zm00001d046039_T031:4
Zm00001d046039_T030:4
Zm00001d046039_T015:4
Zm00001d046039_T040:4
Zm00001d046039_T010:4
Zm00001d046039_T021:4
Zm00001d046039_T037:4
Zm00001d046039_T011:4
Zm00001d046039_T027:4

General Information
CircRNA Name	Zm00001d046039_circ_g.11
ID in PlantcircBase	zma_circ_009945
Alias	Zm09circ00037, zma_circ_0002967, GRMZM2G356423_C4
Organism	Zea mays
Position	chr9: 58165199-58166450 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d046039
Parent gene annotation	HEAT repeat-containing protein
Parent gene strand	-
Alternative splicing	Zm00001d046039_circ_g.8 Zm00001d046039_circ_g.9 Zm00001d046039_circ_g.10 Zm00001d046039_circ_g.12 Zm00001d046039_circ_g.13 Zm00001d046039_circ_g.14 Zm00001d046039_circ_g.15
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	Zm00001d046039_T024:4 Zm00001d046039_T003:4 Zm00001d046039_T029:4 Zm00001d046039_T035:4 Zm00001d046039_T006:4 Zm00001d046039_T001:4 Zm00001d046039_T052:4 Zm00001d046039_T033:4 Zm00001d046039_T017:4 Zm00001d046039_T014:4 Zm00001d046039_T007:4 Zm00001d046039_T004:4 Zm00001d046039_T039:4 Zm00001d046039_T031:4 Zm00001d046039_T030:4 Zm00001d046039_T015:4 Zm00001d046039_T040:4 Zm00001d046039_T010:4 Zm00001d046039_T021:4 Zm00001d046039_T037:4 Zm00001d046039_T011:4 Zm00001d046039_T027:4

			
						 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  
						
							TAGCAACCAACCAGCTTCACGCTCTGCAATAGCAGCCACTGGATTTCGACTGAAACCATTCAGC
ATTTTTTTGGATAATTCAAGTACAGACTTGGGCAGCctgaacggacttgagcatagctgaagta
tctgctggtgctcagttttatataccactggattcgaaagggaccaataagccatcaatgttct
agttgtga

									
								

					

						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: 525
Transcript exons: 58165199-58165366,58165446-58165562,58166112-58166218,58
166318-58166450
CTGAACGGACTTGAGCATAGCTGAAGTATCTGCTGGTGCTCAGTTTTATATACCACTGGATTCG
AAAGGGACCAATAAGCCATCAATGTTCTAGTTGTGAGTAGGTCCAGCGCAGACCTTACATTGGG
CACTTGTTTAGATCTCAACGAAGATATGAGGGATAGAGCTCCGCCAAGGTAGGCAAGTACAGGA
TTAAGCAAGATTCCACAATCAGTAGTTGTGATAGATGGATAAACAAAACTTCTTATGAAGGCAG
TAAGCGCCTCAACTGCAACTGACAGAACCCGCAATTCTGATGCCCAATCCTGTATATGACGAAG
GTAAGATTCAGGATTTCCAGTAAAAGGACCCGCCCATAGCAAAAGAACATCAAACACCTGGTCT
TCCAGCTCCTCTTTTGGCATGGATGCTAGAAGAGAAGCTAATAGCAACCAACCAGCTTCACGCT
CTGCAATAGCAGCCACTGGATTTCGACTGAAACCATTCAGCATTTTTTTGGATAATTCAAGTAC
AGACTTGGGCAGC
						
					

						Genomic sequence
						
							CTGAACGGACTTGAGCATAGCTGAAGTATCTGCTGGTGCTCAGTTTTATATACCACTGGATTCG
AAAGGGACCAATAAGCCATCAATGTTCTAGTTGTGAGTAGGTCCAGCGCAGACCTTACATTGGG
CACTTGTTTAGATCTCAACGAAGATATGAGGGATAGAGCTCTGAATGATATAGTTTCAGAATTA
AGCACCATAAACGATACAGATCAGAATAGAAATGCATCAGTAAATGTTTACGCACCCGCCAAGG
TAGGCAAGTACAGGATTAAGCAAGATTCCACAATCAGTAGTTGTGATAGATGGATAAACAAAAC
TTCTTATGAAGGCAGTAAGCGCCTCAACTGCAACTGACAGAACCCTGCAGCATATATATATATA
TACACACACACAATAAAACGTTAGTGAATAACATCAATTGGACGAAAACTAAGATTGTTAGAAT
GAGGCCATATATGTGATGTCCAATGCAATTTTGTCTTGTGAGATCATTCATTTGCCTTCTTGTG
CAACTTTTTTTTCTCGAACACGCAGGAGAGCTGTGTATTTTTGTGTTAAGAAGATGAAAAGGGT
AGAGAACCCCAAAAAACAGGTTGCAAAAGGAAAAGGAAAAAGGAAAACCAACACACTCACAAAC
CCTGACCAAAACAAACAAACATGACCCTGGCCAAGCTAGAGGATTACTCGCCAGCAAGCTGACC
AGTCAGCATCACTGCCTATTGTTTAAGCTGATTACGTAATATAGGGGTAAATAAAGTGGCATCA
AGAAACTAGACATTAGTATGGGCATCCAAAAAGATTAAAAAATTGCATTGCTCAAGAAAAAAAT
TAGGGCTAATACCCTATGAATTAGTAGAGTAAAAACATGTGATGGTGCTCCTGCAGTCCACATG
CACCCAATAAAACTCACCGCAATTCTGATGCCCAATCCTGTATATGACGAAGGTAAGATTCAGG
ATTTCCAGTAAAAGGACCCGCCCATAGCAAAAGAACATCAAACACCTGGTCTTCCAGCTCCTGC
ATACATGATCATGTATAATAGAAAGACACATCACTCTCAACGCTATCAAATACCAATAACTACT
TTACAAAAAAATTAGAAAGTATCTCTAATACCTCTTTTGGCATGGATGCTAGAAGAGAAGCTAA
TAGCAACCAACCAGCTTCACGCTCTGCAATAGCAGCCACTGGATTTCGACTGAAACCATTCAGC
ATTTTTTTGGATAATTCAAGTACAGACTTGGGCAGC
						
					

			
		

Sequences
Splice junction sequence	TAGCAACCAACCAGCTTCACGCTCTGCAATAGCAGCCACTGGATTTCGACTGAAACCATTCAGC ATTTTTTTGGATAATTCAAGTACAGACTTGGGCAGCctgaacggacttgagcatagctgaagta tctgctggtgctcagttttatataccactggattcgaaagggaccaataagccatcaatgttct agttgtga
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: 525 Transcript exons: 58165199-58165366,58165446-58165562,58166112-58166218,58 166318-58166450 CTGAACGGACTTGAGCATAGCTGAAGTATCTGCTGGTGCTCAGTTTTATATACCACTGGATTCG AAAGGGACCAATAAGCCATCAATGTTCTAGTTGTGAGTAGGTCCAGCGCAGACCTTACATTGGG CACTTGTTTAGATCTCAACGAAGATATGAGGGATAGAGCTCCGCCAAGGTAGGCAAGTACAGGA TTAAGCAAGATTCCACAATCAGTAGTTGTGATAGATGGATAAACAAAACTTCTTATGAAGGCAG TAAGCGCCTCAACTGCAACTGACAGAACCCGCAATTCTGATGCCCAATCCTGTATATGACGAAG GTAAGATTCAGGATTTCCAGTAAAAGGACCCGCCCATAGCAAAAGAACATCAAACACCTGGTCT TCCAGCTCCTCTTTTGGCATGGATGCTAGAAGAGAAGCTAATAGCAACCAACCAGCTTCACGCT CTGCAATAGCAGCCACTGGATTTCGACTGAAACCATTCAGCATTTTTTTGGATAATTCAAGTAC AGACTTGGGCAGC
Genomic sequence	CTGAACGGACTTGAGCATAGCTGAAGTATCTGCTGGTGCTCAGTTTTATATACCACTGGATTCG AAAGGGACCAATAAGCCATCAATGTTCTAGTTGTGAGTAGGTCCAGCGCAGACCTTACATTGGG CACTTGTTTAGATCTCAACGAAGATATGAGGGATAGAGCTCTGAATGATATAGTTTCAGAATTA AGCACCATAAACGATACAGATCAGAATAGAAATGCATCAGTAAATGTTTACGCACCCGCCAAGG TAGGCAAGTACAGGATTAAGCAAGATTCCACAATCAGTAGTTGTGATAGATGGATAAACAAAAC TTCTTATGAAGGCAGTAAGCGCCTCAACTGCAACTGACAGAACCCTGCAGCATATATATATATA TACACACACACAATAAAACGTTAGTGAATAACATCAATTGGACGAAAACTAAGATTGTTAGAAT GAGGCCATATATGTGATGTCCAATGCAATTTTGTCTTGTGAGATCATTCATTTGCCTTCTTGTG CAACTTTTTTTTCTCGAACACGCAGGAGAGCTGTGTATTTTTGTGTTAAGAAGATGAAAAGGGT AGAGAACCCCAAAAAACAGGTTGCAAAAGGAAAAGGAAAAAGGAAAACCAACACACTCACAAAC CCTGACCAAAACAAACAAACATGACCCTGGCCAAGCTAGAGGATTACTCGCCAGCAAGCTGACC AGTCAGCATCACTGCCTATTGTTTAAGCTGATTACGTAATATAGGGGTAAATAAAGTGGCATCA AGAAACTAGACATTAGTATGGGCATCCAAAAAGATTAAAAAATTGCATTGCTCAAGAAAAAAAT TAGGGCTAATACCCTATGAATTAGTAGAGTAAAAACATGTGATGGTGCTCCTGCAGTCCACATG CACCCAATAAAACTCACCGCAATTCTGATGCCCAATCCTGTATATGACGAAGGTAAGATTCAGG ATTTCCAGTAAAAGGACCCGCCCATAGCAAAAGAACATCAAACACCTGGTCTTCCAGCTCCTGC ATACATGATCATGTATAATAGAAAGACACATCACTCTCAACGCTATCAAATACCAATAACTACT TTACAAAAAAATTAGAAAGTATCTCTAATACCTCTTTTGGCATGGATGCTAGAAGAGAAGCTAA TAGCAACCAACCAGCTTCACGCTCTGCAATAGCAGCCACTGGATTTCGACTGAAACCATTCAGC ATTTTTTTGGATAATTCAAGTACAGACTTGGGCAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.190997147

Conservation Information
Conserved circRNAs	NA
PMCS	0.190997147

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							58166329-58165219(+)
58166418-58165201(-)
						
						Potential amino acid sequence
						
							MDARREANSNQPASRSAIAATGFRLKPFSIFLDNSSTDLGSLNGLEHS*(+)
MLNGFSRNPVAAIAEREAGWLLLASLLASMPKEELEDQVFDVLLLWAGPFTGNPESYLRHIQDW
ASELRVLSVAVEALTAFIRSFVYPSITTTDCGILLNPVLAYLGGALSLISSLRSKQVPNVRSAL
DLLTTRTLMAYWSLSNPVVYKTEHQQILQLCSSPFRLPKSVLELSKKMLNGFSRNPVAAIAERE
AGWLLLASLLASMPKEELEDQVFDVLLLWAGPFTGNPESYLRHIQDWASELRVLSVAVEALTAF
IRSFVYPSITTTDCGILLNPVLAYLGGALSLISSLRSKQVPNVRSALDLLTTRTLMAYWSLSNP
VVYKTEHQQILQLCSSPFRLPKSVLELSKKMLNGFSRNPVAAIAEREAGWLLLASLLASMPKEE
LEDQVFDVLLLWAGPFTGNPESYLRHIQDWASELRVLSVAVEALTAFIRSFVYPSITTTDCGIL
LNPVLAYLGGALSLISSLRSKQVPNVRSALDLLTTRTLMAYWSLSNPVVYKTEHQQILQLCSSP
FRLPKSVLELSKKMLNGFSRNPVAAIAEREAGWLLLASLLASMPKEELEDQVFDVLLLWAGPFT
GNPESYLRHIQDWASELRVLSVAVEALTAFIRSFVYPSITTTDCGILLNPVLAYLGGALSLISS
LRSKQVPNVRSALDLLTTRTLMAYWSLSNPVVYKTEHQQILQLCSSPF(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	58166329-58165219(+) 58166418-58165201(-)
Potential amino acid sequence	MDARREANSNQPASRSAIAATGFRLKPFSIFLDNSSTDLGSLNGLEHS*(+) MLNGFSRNPVAAIAEREAGWLLLASLLASMPKEELEDQVFDVLLLWAGPFTGNPESYLRHIQDW ASELRVLSVAVEALTAFIRSFVYPSITTTDCGILLNPVLAYLGGALSLISSLRSKQVPNVRSAL DLLTTRTLMAYWSLSNPVVYKTEHQQILQLCSSPFRLPKSVLELSKKMLNGFSRNPVAAIAERE AGWLLLASLLASMPKEELEDQVFDVLLLWAGPFTGNPESYLRHIQDWASELRVLSVAVEALTAF IRSFVYPSITTTDCGILLNPVLAYLGGALSLISSLRSKQVPNVRSALDLLTTRTLMAYWSLSNP VVYKTEHQQILQLCSSPFRLPKSVLELSKKMLNGFSRNPVAAIAEREAGWLLLASLLASMPKEE LEDQVFDVLLLWAGPFTGNPESYLRHIQDWASELRVLSVAVEALTAFIRSFVYPSITTTDCGIL LNPVLAYLGGALSLISSLRSKQVPNVRSALDLLTTRTLMAYWSLSNPVVYKTEHQQILQLCSSP FRLPKSVLELSKKMLNGFSRNPVAAIAEREAGWLLLASLLASMPKEELEDQVFDVLLLWAGPFT GNPESYLRHIQDWASELRVLSVAVEALTAFIRSFVYPSITTTDCGILLNPVLAYLGGALSLISS LRSKQVPNVRSALDLLTTRTLMAYWSLSNPVVYKTEHQQILQLCSSPF(-)
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 Zm00001d046039_circ_g.11

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