Plant Circular RNA Database

Detail information of Zm00001d046039_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d046039_circ_g.4
					
						ID in PlantcircBase
						zma_circ_009943
					
						Alias
						Zm09circ00036, zma_circ_0002964, ZmciR405
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 58129434-58130092  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.1 Zm00001d046039_circ_g.2 Zm00001d046039_circ_g.3 						
					
						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_T035:3
Zm00001d046039_T025:3
Zm00001d046039_T066:3
Zm00001d046039_T037:3
Zm00001d046039_T030:3
Zm00001d046039_T001:3
Zm00001d046039_T039:3
Zm00001d046039_T031:3
Zm00001d046039_T029:3
Zm00001d046039_T024:3
Zm00001d046039_T005:3
Zm00001d046039_T015:3
Zm00001d046039_T013:3
Zm00001d046039_T006:3
Zm00001d046039_T038:3
Zm00001d046039_T008:3
Zm00001d046039_T052:3
Zm00001d046039_T007:3
Zm00001d046039_T014:3
Zm00001d046039_T032:3
Zm00001d046039_T040:3
Zm00001d046039_T011:3
Zm00001d046039_T018:3
Zm00001d046039_T023:3
Zm00001d046039_T003:3
Zm00001d046039_T017:3
Zm00001d046039_T027:3
Zm00001d046039_T022:3
Zm00001d046039_T012:3
Zm00001d046039_T010:3
Zm00001d046039_T004:2
Zm00001d046039_T021:3
Zm00001d046039_T002:3
Zm00001d046039_T033:3

General Information
CircRNA Name	Zm00001d046039_circ_g.4
ID in PlantcircBase	zma_circ_009943
Alias	Zm09circ00036, zma_circ_0002964, ZmciR405
Organism	Zea mays
Position	chr9: 58129434-58130092 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.1 Zm00001d046039_circ_g.2 Zm00001d046039_circ_g.3
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_T035:3 Zm00001d046039_T025:3 Zm00001d046039_T066:3 Zm00001d046039_T037:3 Zm00001d046039_T030:3 Zm00001d046039_T001:3 Zm00001d046039_T039:3 Zm00001d046039_T031:3 Zm00001d046039_T029:3 Zm00001d046039_T024:3 Zm00001d046039_T005:3 Zm00001d046039_T015:3 Zm00001d046039_T013:3 Zm00001d046039_T006:3 Zm00001d046039_T038:3 Zm00001d046039_T008:3 Zm00001d046039_T052:3 Zm00001d046039_T007:3 Zm00001d046039_T014:3 Zm00001d046039_T032:3 Zm00001d046039_T040:3 Zm00001d046039_T011:3 Zm00001d046039_T018:3 Zm00001d046039_T023:3 Zm00001d046039_T003:3 Zm00001d046039_T017:3 Zm00001d046039_T027:3 Zm00001d046039_T022:3 Zm00001d046039_T012:3 Zm00001d046039_T010:3 Zm00001d046039_T004:2 Zm00001d046039_T021:3 Zm00001d046039_T002:3 Zm00001d046039_T033:3

			
						 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  
						
							CTCCATAGTACACATCATTCTCAGATGTACTATCAGGAGGATTATGCCCAAAACATGACAGAAC
TTCACCTGTGTTTCTTCTAATTGACGTAGCAAGAACcttgtccattatcaaacacaaaagcttc
acacctattggttgcattccttcaaattgcccagtactaatctgccacccaaaggtagaatgtc
atccataa

						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: 441
Transcript exons: 58129434-58129502,58129602-58129749,58129869-58130092
CTTGTCCATTATCAAACACAAAAGCTTCACACCTATTGGTTGCATTCCTTCAAATTGCCCAGTA
CTAATCTGGTATGAAAGTGAGACCAGTTCCTGTAGTTTAAGCACTAGCCAATCATTTGACAAAT
AAGTGCCTTGAGATATTGCGCTCCTTGCCAACAAGAGGTCAAAATGAGCAGGTTCTGCTCCAAC
TGCAATTGGTACATGGCTAACGCATTCTGCAGCAAAAACCCTGGTACGATATCTGAGGTGTTTA
TTCCTTGGAGGAAACTGGCTGGATATAGAACCAGCACAGCGGATTTGCTGCTGCTTTGAGCTGG
AAATCATGTTGTCTTCATCTTCTCCATAGTACACATCATTCTCAGATGTACTATCAGGAGGATT
ATGCCCAAAACATGACAGAACTTCACCTGTGTTTCTTCTAATTGACGTAGCAAGAAC
						
						Genomic sequence
						
							CTTGTCCATTATCAAACACAAAAGCTTCACACCTATTGGTTGCATTCCTTCAAATTGCCCAGTA
CTAATCTGCCACCCAAAGGTAGAATGTCATCCATAAGTTACTTAAATTTAACACAAATTTTCAC
CCACTAGTTTCAGCATCTAGAATCTGATTTATGTAAAAACCTGGTATGAAAGTGAGACCAGTTC
CTGTAGTTTAAGCACTAGCCAATCATTTGACAAATAAGTGCCTTGAGATATTGCGCTCCTTGCC
AACAAGAGGTCAAAATGAGCAGGTTCTGCTCCAACTGCAATTGGTACATGGCTAACGCATCTGT
TTTAACACAAAAGGAAAACATTTGCAATAATAATAAGAAATTAATGGACATCTTAACAAATTGG
TCTTGACCCATGCAAAAAAAAAGAGTGCATAAAATAAAAAAGCAAACATACTCTGCAGCAAAAA
CCCTGGTACGATATCTGAGGTGTTTATTCCTTGGAGGAAACTGGCTGGATATAGAACCAGCACA
GCGGATTTGCTGCTGCTTTGAGCTGGAAATCATGTTGTCTTCATCTTCTCCATAGTACACATCA
TTCTCAGATGTACTATCAGGAGGATTATGCCCAAAACATGACAGAACTTCACCTGTGTTTCTTC
TAATTGACGTAGCAAGAAC

Sequences
Splice junction sequence	CTCCATAGTACACATCATTCTCAGATGTACTATCAGGAGGATTATGCCCAAAACATGACAGAAC TTCACCTGTGTTTCTTCTAATTGACGTAGCAAGAACcttgtccattatcaaacacaaaagcttc acacctattggttgcattccttcaaattgcccagtactaatctgccacccaaaggtagaatgtc atccataa
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: 441 Transcript exons: 58129434-58129502,58129602-58129749,58129869-58130092 CTTGTCCATTATCAAACACAAAAGCTTCACACCTATTGGTTGCATTCCTTCAAATTGCCCAGTA CTAATCTGGTATGAAAGTGAGACCAGTTCCTGTAGTTTAAGCACTAGCCAATCATTTGACAAAT AAGTGCCTTGAGATATTGCGCTCCTTGCCAACAAGAGGTCAAAATGAGCAGGTTCTGCTCCAAC TGCAATTGGTACATGGCTAACGCATTCTGCAGCAAAAACCCTGGTACGATATCTGAGGTGTTTA TTCCTTGGAGGAAACTGGCTGGATATAGAACCAGCACAGCGGATTTGCTGCTGCTTTGAGCTGG AAATCATGTTGTCTTCATCTTCTCCATAGTACACATCATTCTCAGATGTACTATCAGGAGGATT ATGCCCAAAACATGACAGAACTTCACCTGTGTTTCTTCTAATTGACGTAGCAAGAAC
Genomic sequence	CTTGTCCATTATCAAACACAAAAGCTTCACACCTATTGGTTGCATTCCTTCAAATTGCCCAGTA CTAATCTGCCACCCAAAGGTAGAATGTCATCCATAAGTTACTTAAATTTAACACAAATTTTCAC CCACTAGTTTCAGCATCTAGAATCTGATTTATGTAAAAACCTGGTATGAAAGTGAGACCAGTTC CTGTAGTTTAAGCACTAGCCAATCATTTGACAAATAAGTGCCTTGAGATATTGCGCTCCTTGCC AACAAGAGGTCAAAATGAGCAGGTTCTGCTCCAACTGCAATTGGTACATGGCTAACGCATCTGT TTTAACACAAAAGGAAAACATTTGCAATAATAATAAGAAATTAATGGACATCTTAACAAATTGG TCTTGACCCATGCAAAAAAAAAGAGTGCATAAAATAAAAAAGCAAACATACTCTGCAGCAAAAA CCCTGGTACGATATCTGAGGTGTTTATTCCTTGGAGGAAACTGGCTGGATATAGAACCAGCACA GCGGATTTGCTGCTGCTTTGAGCTGGAAATCATGTTGTCTTCATCTTCTCCATAGTACACATCA TTCTCAGATGTACTATCAGGAGGATTATGCCCAAAACATGACAGAACTTCACCTGTGTTTCTTC TAATTGACGTAGCAAGAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.144604721

Conservation Information
Conserved circRNAs	NA
PMCS	0.144604721

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							58129980-58129436(-)
						
						Potential amino acid sequence
						
							MISSSKQQQIRCAGSISSQFPPRNKHLRYRTRVFAAECVSHVPIAVGAEPAHFDLLLARSAISQ
GTYLSNDWLVLKLQELVSLSYQISTGQFEGMQPIGVKLLCLIMDKVLATSIRRNTGEVLSCFGH
NPPDSTSENDVYYGEDEDNMISSSKQQQIRCAGSISSQFPPRNKHLRYRTRVFAAECVSHVPIA
VGAEPAHFDLLLARSAISQGTYLSNDWLVLKLQELVSLSYQISTGQFEGMQPIGVKLLCLIMDK
VLATSIRRNTGEVLSCFGHNPPDSTSENDVYYGEDEDNMISSSKQQQIRCAGSISSQFPPRNKH
LRYRTRVFAAECVSHVPIAVGAEPAHFDLLLARSAISQGTYLSNDWLVLKLQELVSLSYQISTG
QFEGMQPIGVKLLCLIMDKVLATSIRRNTGEVLSCFGHNPPDSTSENDVYYGEDEDNMISSSKQ
QQIRCAGSISSQFPPRNKHLRYRTRVFAAECVSHVPIAVGAEPAHFDLLLARSAISQGTYLSND
WLVLKLQELVSLSYQISTGQFEGMQPIGVKLLCLIMDK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	58129980-58129436(-)
Potential amino acid sequence	MISSSKQQQIRCAGSISSQFPPRNKHLRYRTRVFAAECVSHVPIAVGAEPAHFDLLLARSAISQ GTYLSNDWLVLKLQELVSLSYQISTGQFEGMQPIGVKLLCLIMDKVLATSIRRNTGEVLSCFGH NPPDSTSENDVYYGEDEDNMISSSKQQQIRCAGSISSQFPPRNKHLRYRTRVFAAECVSHVPIA VGAEPAHFDLLLARSAISQGTYLSNDWLVLKLQELVSLSYQISTGQFEGMQPIGVKLLCLIMDK VLATSIRRNTGEVLSCFGHNPPDSTSENDVYYGEDEDNMISSSKQQQIRCAGSISSQFPPRNKH LRYRTRVFAAECVSHVPIAVGAEPAHFDLLLARSAISQGTYLSNDWLVLKLQELVSLSYQISTG QFEGMQPIGVKLLCLIMDKVLATSIRRNTGEVLSCFGHNPPDSTSENDVYYGEDEDNMISSSKQ QQIRCAGSISSQFPPRNKHLRYRTRVFAAECVSHVPIAVGAEPAHFDLLLARSAISQGTYLSND WLVLKLQELVSLSYQISTGQFEGMQPIGVKLLCLIMDK(-)
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.4

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