Plant Circular RNA Database

Detail information of Zm00001d019907_circ_g.7

			
						 General Information
					
						CircRNA Name
						Zm00001d019907_circ_g.7
					
						ID in PlantcircBase
						zma_circ_009289
					
						Alias
						Zm07circ00039, zma_circ_0002385, GRMZM2G013794_C5
					
						Organism
						
							Zea mays						
					
						Position
						
							chr7: 74638485-74639437  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d019907						
					
						Parent gene annotation
						
							Histone-lysine N-methyltransferase ATX2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d019907_circ_g.1 Zm00001d019907_circ_g.2 Zm00001d019907_circ_g.3 Zm00001d019907_circ_g.4 Zm00001d019907_circ_g.5 Zm00001d019907_circ_g.6 Zm00001d019907_circ_g.8 						
					
						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
						Zm00001d019907_T035:2
Zm00001d019907_T001:2
Zm00001d019907_T028:2
Zm00001d019907_T009:2
Zm00001d019907_T002:2
Zm00001d019907_T019:2
Zm00001d019907_T015:2
Zm00001d019907_T036:2
Zm00001d019907_T013:2
Zm00001d019907_T044:2
Zm00001d019907_T034:2
Zm00001d019907_T024:2
Zm00001d019907_T033:2
Zm00001d019907_T042:2
Zm00001d019907_T005:2
Zm00001d019907_T020:2
Zm00001d019907_T043:2
Zm00001d019907_T006:2
Zm00001d019907_T003:2
Zm00001d019907_T047:2
Zm00001d019907_T012:2
Zm00001d019907_T022:2
Zm00001d019907_T039:2
Zm00001d019907_T025:2
Zm00001d019907_T046:2
Zm00001d019907_T032:2
Zm00001d019907_T041:2
Zm00001d019907_T029:2
Zm00001d019907_T031:2
Zm00001d019907_T016:2
Zm00001d019907_T004:2
Zm00001d019907_T018:2

General Information
CircRNA Name	Zm00001d019907_circ_g.7
ID in PlantcircBase	zma_circ_009289
Alias	Zm07circ00039, zma_circ_0002385, GRMZM2G013794_C5
Organism	Zea mays
Position	chr7: 74638485-74639437 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d019907
Parent gene annotation	Histone-lysine N-methyltransferase ATX2
Parent gene strand	-
Alternative splicing	Zm00001d019907_circ_g.1 Zm00001d019907_circ_g.2 Zm00001d019907_circ_g.3 Zm00001d019907_circ_g.4 Zm00001d019907_circ_g.5 Zm00001d019907_circ_g.6 Zm00001d019907_circ_g.8
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	Zm00001d019907_T035:2 Zm00001d019907_T001:2 Zm00001d019907_T028:2 Zm00001d019907_T009:2 Zm00001d019907_T002:2 Zm00001d019907_T019:2 Zm00001d019907_T015:2 Zm00001d019907_T036:2 Zm00001d019907_T013:2 Zm00001d019907_T044:2 Zm00001d019907_T034:2 Zm00001d019907_T024:2 Zm00001d019907_T033:2 Zm00001d019907_T042:2 Zm00001d019907_T005:2 Zm00001d019907_T020:2 Zm00001d019907_T043:2 Zm00001d019907_T006:2 Zm00001d019907_T003:2 Zm00001d019907_T047:2 Zm00001d019907_T012:2 Zm00001d019907_T022:2 Zm00001d019907_T039:2 Zm00001d019907_T025:2 Zm00001d019907_T046:2 Zm00001d019907_T032:2 Zm00001d019907_T041:2 Zm00001d019907_T029:2 Zm00001d019907_T031:2 Zm00001d019907_T016:2 Zm00001d019907_T004:2 Zm00001d019907_T018:2

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: CAGTTGGAGATGATAGGATG
 R: ATCTTCAGTGGTTATACTACC
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	Yes 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	F: CAGTTGGAGATGATAGGATG R: ATCTTCAGTGGTTATACTACC 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  
						
							ACAATATGAGGTCTATTCTCCACATATAAACGTTTCAGAGAAGCAGTAGCGACAACTTGTGGCT
GCTTTTGGCCCCTTCTCCTGTGTAAATTATAGGGTTcatatctccggccttgtgtgcaaccttg
gcaaagacaccatatccatgaatttttgattttcctatcaaaagacaatacaatcaatatatga
tgaacatt

						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: 323
Transcript exons: 74638485-74638546,74639177-74639437
CATATCTCCGGCCTTGTGTGCAACCTTGGCAAAGACACCATATCCATGAATTTTTGATTTTCCA
AAAGTTAGTCTCTTCCTAAATGTAGCCTTCACGATTGTATATTTTTCAACCATAGAAGACACAT
TGCCAATAGCTTCTTGCTGCACAGCATCTGACAAACCAAACGGTTGAATTGATTCTCCGCATGT
ATTGCCTACTCTGTTTTGGCAGTAGCCACTGACAATATGAGGTCTATTCTCCACATATAAACGT
TTCAGAGAAGCAGTAGCGACAACTTGTGGCTGCTTTTGGCCCCTTCTCCTGTGTAAATTATAGG
GTT
						
						Genomic sequence
						
							CATATCTCCGGCCTTGTGTGCAACCTTGGCAAAGACACCATATCCATGAATTTTTGATTTTCCT
ATCAAAAGACAATACAATCAATATATGATGAACATTTCACTGAAGTACAAGTGAATATCATAAC
ATTGCCAAATTGTTTCATTCAAATCCAACAATTCAACAAAATAGAATACCATAGTTCTGATATT
CCTATGCAGGGGCAATACAGATCACATCCTCAAAATCATAAAACAATCCCTACCCCGATCTGTA
ATACTCACAGCTGGTACAAACTAAATCCAATTCCACTACAGACTATCACCCAATTTAACATTAG
ACTTTAAGCAACAAAAAAGTGAAAGATTTGTATCAATAAAATTTTCAATCTATTGCTATAAACT
CCACTGCTACTGCAGACAAAAAATGTGTCCATCATTGACAAAGCACAGATATTGATAAATGGTA
TAGAAGAAGCAATGTGTGAAATAGGACAAAAGCTTCCTCCCTTGAAACAACACAACATATTCAG
GAAAAAGATATGTTTTTCTAGTAAAAATAAATTGGAGACAGGAAAAACACAAGTGATTAAGATT
ACAAAACTAGTATCTTATCTTGGCTCAGAACGTATTTCCTGGAAAATGGTATGAAGACTTGACC
AACTCCAGAAGATATGGAAATACAAAAGGATAAGAAACCGAATAGAACTCACCAAAAGTTAGTC
TCTTCCTAAATGTAGCCTTCACGATTGTATATTTTTCAACCATAGAAGACACATTGCCAATAGC
TTCTTGCTGCACAGCATCTGACAAACCAAACGGTTGAATTGATTCTCCGCATGTATTGCCTACT
CTGTTTTGGCAGTAGCCACTGACAATATGAGGTCTATTCTCCACATATAAACGTTTCAGAGAAG
CAGTAGCGACAACTTGTGGCTGCTTTTGGCCCCTTCTCCTGTGTAAATTATAGGGTT

Sequences
Splice junction sequence	ACAATATGAGGTCTATTCTCCACATATAAACGTTTCAGAGAAGCAGTAGCGACAACTTGTGGCT GCTTTTGGCCCCTTCTCCTGTGTAAATTATAGGGTTcatatctccggccttgtgtgcaaccttg gcaaagacaccatatccatgaatttttgattttcctatcaaaagacaatacaatcaatatatga tgaacatt
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: 323 Transcript exons: 74638485-74638546,74639177-74639437 CATATCTCCGGCCTTGTGTGCAACCTTGGCAAAGACACCATATCCATGAATTTTTGATTTTCCA AAAGTTAGTCTCTTCCTAAATGTAGCCTTCACGATTGTATATTTTTCAACCATAGAAGACACAT TGCCAATAGCTTCTTGCTGCACAGCATCTGACAAACCAAACGGTTGAATTGATTCTCCGCATGT ATTGCCTACTCTGTTTTGGCAGTAGCCACTGACAATATGAGGTCTATTCTCCACATATAAACGT TTCAGAGAAGCAGTAGCGACAACTTGTGGCTGCTTTTGGCCCCTTCTCCTGTGTAAATTATAGG GTT
Genomic sequence	CATATCTCCGGCCTTGTGTGCAACCTTGGCAAAGACACCATATCCATGAATTTTTGATTTTCCT ATCAAAAGACAATACAATCAATATATGATGAACATTTCACTGAAGTACAAGTGAATATCATAAC ATTGCCAAATTGTTTCATTCAAATCCAACAATTCAACAAAATAGAATACCATAGTTCTGATATT CCTATGCAGGGGCAATACAGATCACATCCTCAAAATCATAAAACAATCCCTACCCCGATCTGTA ATACTCACAGCTGGTACAAACTAAATCCAATTCCACTACAGACTATCACCCAATTTAACATTAG ACTTTAAGCAACAAAAAAGTGAAAGATTTGTATCAATAAAATTTTCAATCTATTGCTATAAACT CCACTGCTACTGCAGACAAAAAATGTGTCCATCATTGACAAAGCACAGATATTGATAAATGGTA TAGAAGAAGCAATGTGTGAAATAGGACAAAAGCTTCCTCCCTTGAAACAACACAACATATTCAG GAAAAAGATATGTTTTTCTAGTAAAAATAAATTGGAGACAGGAAAAACACAAGTGATTAAGATT ACAAAACTAGTATCTTATCTTGGCTCAGAACGTATTTCCTGGAAAATGGTATGAAGACTTGACC AACTCCAGAAGATATGGAAATACAAAAGGATAAGAAACCGAATAGAACTCACCAAAAGTTAGTC TCTTCCTAAATGTAGCCTTCACGATTGTATATTTTTCAACCATAGAAGACACATTGCCAATAGC TTCTTGCTGCACAGCATCTGACAAACCAAACGGTTGAATTGATTCTCCGCATGTATTGCCTACT CTGTTTTGGCAGTAGCCACTGACAATATGAGGTCTATTCTCCACATATAAACGTTTCAGAGAAG CAGTAGCGACAACTTGTGGCTGCTTTTGGCCCCTTCTCCTGTGTAAATTATAGGGTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.219137655

Conservation Information
Conserved circRNAs	NA
PMCS	0.219137655

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							74639233-74639374(-)
						
						Potential amino acid sequence
						
							MVEKYTIVKATFRKRLTFGKSKIHGYGVFAKVAHKAGDMNPIIYTGEGAKSSHKLSLLLL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress; regulating the response to N deficiency  (validated)

Functional Information
Coding potential	Y
Potential coding position	74639233-74639374(-)
Potential amino acid sequence	MVEKYTIVKATFRKRLTFGKSKIHGYGVFAKVAHKAGDMNPIIYTGEGAKSSHKLSLLLL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress; regulating the response to N deficiency (validated)

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

circRNA

Detail information of Zm00001d019907_circ_g.7

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