Plant Circular RNA Database

Detail information of Zm00001d027392_circ_g.9

			
						 General Information
					
						CircRNA Name
						Zm00001d027392_circ_g.9
					
						ID in PlantcircBase
						zma_circ_006362
					
						Alias
						Zm01circ00013
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 4274335-4275535  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d027392						
					
						Parent gene annotation
						
							Callose synthase 9
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d027392_circ_g.3 Zm00001d027392_circ_g.4 Zm00001d027392_circ_g.5 Zm00001d027392_circ_g.6 Zm00001d027392_circ_g.7 Zm00001d027392_circ_g.8 Zm00001d027392_circ_g.10 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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  
						
							GT-AG							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
						Zm00001d027392_T027:4
Zm00001d027392_T023:4
Zm00001d027392_T060:4
Zm00001d027392_T062:4
Zm00001d027392_T064:4
Zm00001d027392_T067:4
Zm00001d027392_T055:4
Zm00001d027392_T012:4
Zm00001d027392_T042:4
Zm00001d027392_T052:4
Zm00001d027392_T015:4
Zm00001d027392_T019:4
Zm00001d027392_T070:4
Zm00001d027392_T046:4
Zm00001d027392_T071:4
Zm00001d027392_T006:4
Zm00001d027392_T051:4
Zm00001d027392_T030:4
Zm00001d027392_T029:4
Zm00001d027392_T011:4
Zm00001d027392_T007:4
Zm00001d027392_T025:4
Zm00001d027392_T036:4
Zm00001d027392_T002:4
Zm00001d027392_T056:4
Zm00001d027392_T004:4
Zm00001d027392_T033:4
Zm00001d027392_T016:4
Zm00001d027392_T003:4
Zm00001d027392_T065:4
Zm00001d027392_T020:4
Zm00001d027392_T050:4
Zm00001d027392_T034:4
Zm00001d027392_T049:4
Zm00001d027392_T038:4
Zm00001d027392_T069:4
Zm00001d027392_T045:4
Zm00001d027392_T059:4
Zm00001d027392_T068:4
Zm00001d027392_T041:4
Zm00001d027392_T054:4

General Information
CircRNA Name	Zm00001d027392_circ_g.9
ID in PlantcircBase	zma_circ_006362
Alias	Zm01circ00013
Organism	Zea mays
Position	chr1: 4274335-4275535 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d027392
Parent gene annotation	Callose synthase 9
Parent gene strand	+
Alternative splicing	Zm00001d027392_circ_g.3 Zm00001d027392_circ_g.4 Zm00001d027392_circ_g.5 Zm00001d027392_circ_g.6 Zm00001d027392_circ_g.7 Zm00001d027392_circ_g.8 Zm00001d027392_circ_g.10
Support reads	NA
Tissues	leaf, endosperm
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	GT-AG 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	Zm00001d027392_T027:4 Zm00001d027392_T023:4 Zm00001d027392_T060:4 Zm00001d027392_T062:4 Zm00001d027392_T064:4 Zm00001d027392_T067:4 Zm00001d027392_T055:4 Zm00001d027392_T012:4 Zm00001d027392_T042:4 Zm00001d027392_T052:4 Zm00001d027392_T015:4 Zm00001d027392_T019:4 Zm00001d027392_T070:4 Zm00001d027392_T046:4 Zm00001d027392_T071:4 Zm00001d027392_T006:4 Zm00001d027392_T051:4 Zm00001d027392_T030:4 Zm00001d027392_T029:4 Zm00001d027392_T011:4 Zm00001d027392_T007:4 Zm00001d027392_T025:4 Zm00001d027392_T036:4 Zm00001d027392_T002:4 Zm00001d027392_T056:4 Zm00001d027392_T004:4 Zm00001d027392_T033:4 Zm00001d027392_T016:4 Zm00001d027392_T003:4 Zm00001d027392_T065:4 Zm00001d027392_T020:4 Zm00001d027392_T050:4 Zm00001d027392_T034:4 Zm00001d027392_T049:4 Zm00001d027392_T038:4 Zm00001d027392_T069:4 Zm00001d027392_T045:4 Zm00001d027392_T059:4 Zm00001d027392_T068:4 Zm00001d027392_T041:4 Zm00001d027392_T054:4

			
						 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  
						
							AGTTGCTTACATTGACGAAGTTGAGAATGCTAAGAACGGAAAACCCATCACCGAGTATTACTCA
AAGCTTGTCAAAGCTGATATTCATGGAAAGGACAAGatgaatggaagaacttccttactcgtat
caacagggatgaaaatgcagcagactctgagctttttggcaacccaaatgacatacttgaacta
cgtctatg

									
								

					

						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: 494
Transcript exons: 4274335-4274469,4274898-4274966,4275049-4275223,4275421-
4275535
ATGAATGGAAGAACTTCCTTACTCGTATCAACAGGGATGAAAATGCAGCAGACTCTGAGCTTTT
TGGCAACCCAAATGACATACTTGAACTACGTCTATGGGCTTCTTATCGTGGGCAGACCTTAGCT
CGAACTGTCCGTGGTATGATGTACTATAGGAAAGCCCTTATGCTGCAGAGTTATTTGGAGAGGA
TACAATCTGAAGATTTGGAATCTACATTAGGGTTGGCTGGTTCAGCTGATAGGCATTTTGAGTT
GTCACCTGAGGCGCGTGCTCAGGCTGATTTGAAGTTTACATATGTGGTTACCTGCCAAATTTAT
GGAAAACAGAAGGGGGAAGGGAAGGCTGAAGCTGCAGACATAGCCTTACTAATGCAAAGGAATG
AAGCTCTTAGAGTTGCTTACATTGACGAAGTTGAGAATGCTAAGAACGGAAAACCCATCACCGA
GTATTACTCAAAGCTTGTCAAAGCTGATATTCATGGAAAGGACAAG
						
					

						Genomic sequence
						
							ATGAATGGAAGAACTTCCTTACTCGTATCAACAGGGATGAAAATGCAGCAGACTCTGAGCTTTT
TGGCAACCCAAATGACATACTTGAACTACGTCTATGGGCTTCTTATCGTGGGCAGACCTTAGCT
CGAACTGGTCAGTTATCCTCTGTAAACTTAATAACTTATACATTTATAGTATATTTATTGACAG
GCTCACGTTTGCTTTTACTCAATCCTGTTTTTCAATTTGTAAACCTTTTGTCCAACATGGTGAA
AACTTGTATTTTCAGCAAGTTTTTATTTCATTATTGACTCATGAACCACACTCTGTTTACTATT
TGGGTATGGAATAATTTACTCCAGTAGCAAAATTTGCGATTAATCTGTGAATGTTGAATGATAT
ACCTGTACTTTTGTATTTATAATTTTTACTCTAGTTCATCAAGTCACGTGTGCTTTTCTGATGG
CATCACAAAAGATTAATCTGTTTGTCCTCCTTGAACTTCTAAGTGGAACTCATTCGCTCAATAT
ATTTGATTATAATCAGTTCACGTCAACAATATTTTTTGTTTTACTCTGCAGTCCGTGGTATGAT
GTACTATAGGAAAGCCCTTATGCTGCAGAGTTATTTGGAGAGGATACAATCTGAAGGTATTGCA
CTGCTCAGCATGTGAGATGCATATATGCTACTTTATCTGAATGTATATCCTCTTTTCTTGTTTT
CCTTCACTAGATTTGGAATCTACATTAGGGTTGGCTGGTTCAGCTGATAGGCATTTTGAGTTGT
CACCTGAGGCGCGTGCTCAGGCTGATTTGAAGTTTACATATGTGGTTACCTGCCAAATTTATGG
AAAACAGAAGGGGGAAGGGAAGGCTGAAGCTGCAGACATAGCCTTACTAATGCAAAGGTACATT
TAATTTATTTATGCTAGAGATGTCTTTGCTTGTTAGCTCTCTTTGTAAAGACCTAACGGGCCTG
GTTAGTTCTCTGTATCTCACTTAAAGCATTTGAGCACATGCACATAAACTATTACACTCCAAGG
CCTATTTTGGTTTGTTATTTGTTGTGTACACAACCTATAACTTTTTGTACTATCTTTTGTAGGA
ATGAAGCTCTTAGAGTTGCTTACATTGACGAAGTTGAGAATGCTAAGAACGGAAAACCCATCAC
CGAGTATTACTCAAAGCTTGTCAAAGCTGATATTCATGGAAAGGACAAG
						
					

			
		

Sequences
Splice junction sequence	AGTTGCTTACATTGACGAAGTTGAGAATGCTAAGAACGGAAAACCCATCACCGAGTATTACTCA AAGCTTGTCAAAGCTGATATTCATGGAAAGGACAAGatgaatggaagaacttccttactcgtat caacagggatgaaaatgcagcagactctgagctttttggcaacccaaatgacatacttgaacta cgtctatg
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: 494 Transcript exons: 4274335-4274469,4274898-4274966,4275049-4275223,4275421- 4275535 ATGAATGGAAGAACTTCCTTACTCGTATCAACAGGGATGAAAATGCAGCAGACTCTGAGCTTTT TGGCAACCCAAATGACATACTTGAACTACGTCTATGGGCTTCTTATCGTGGGCAGACCTTAGCT CGAACTGTCCGTGGTATGATGTACTATAGGAAAGCCCTTATGCTGCAGAGTTATTTGGAGAGGA TACAATCTGAAGATTTGGAATCTACATTAGGGTTGGCTGGTTCAGCTGATAGGCATTTTGAGTT GTCACCTGAGGCGCGTGCTCAGGCTGATTTGAAGTTTACATATGTGGTTACCTGCCAAATTTAT GGAAAACAGAAGGGGGAAGGGAAGGCTGAAGCTGCAGACATAGCCTTACTAATGCAAAGGAATG AAGCTCTTAGAGTTGCTTACATTGACGAAGTTGAGAATGCTAAGAACGGAAAACCCATCACCGA GTATTACTCAAAGCTTGTCAAAGCTGATATTCATGGAAAGGACAAG
Genomic sequence	ATGAATGGAAGAACTTCCTTACTCGTATCAACAGGGATGAAAATGCAGCAGACTCTGAGCTTTT TGGCAACCCAAATGACATACTTGAACTACGTCTATGGGCTTCTTATCGTGGGCAGACCTTAGCT CGAACTGGTCAGTTATCCTCTGTAAACTTAATAACTTATACATTTATAGTATATTTATTGACAG GCTCACGTTTGCTTTTACTCAATCCTGTTTTTCAATTTGTAAACCTTTTGTCCAACATGGTGAA AACTTGTATTTTCAGCAAGTTTTTATTTCATTATTGACTCATGAACCACACTCTGTTTACTATT TGGGTATGGAATAATTTACTCCAGTAGCAAAATTTGCGATTAATCTGTGAATGTTGAATGATAT ACCTGTACTTTTGTATTTATAATTTTTACTCTAGTTCATCAAGTCACGTGTGCTTTTCTGATGG CATCACAAAAGATTAATCTGTTTGTCCTCCTTGAACTTCTAAGTGGAACTCATTCGCTCAATAT ATTTGATTATAATCAGTTCACGTCAACAATATTTTTTGTTTTACTCTGCAGTCCGTGGTATGAT GTACTATAGGAAAGCCCTTATGCTGCAGAGTTATTTGGAGAGGATACAATCTGAAGGTATTGCA CTGCTCAGCATGTGAGATGCATATATGCTACTTTATCTGAATGTATATCCTCTTTTCTTGTTTT CCTTCACTAGATTTGGAATCTACATTAGGGTTGGCTGGTTCAGCTGATAGGCATTTTGAGTTGT CACCTGAGGCGCGTGCTCAGGCTGATTTGAAGTTTACATATGTGGTTACCTGCCAAATTTATGG AAAACAGAAGGGGGAAGGGAAGGCTGAAGCTGCAGACATAGCCTTACTAATGCAAAGGTACATT TAATTTATTTATGCTAGAGATGTCTTTGCTTGTTAGCTCTCTTTGTAAAGACCTAACGGGCCTG GTTAGTTCTCTGTATCTCACTTAAAGCATTTGAGCACATGCACATAAACTATTACACTCCAAGG CCTATTTTGGTTTGTTATTTGTTGTGTACACAACCTATAACTTTTTGTACTATCTTTTGTAGGA ATGAAGCTCTTAGAGTTGCTTACATTGACGAAGTTGAGAATGCTAAGAACGGAAAACCCATCAC CGAGTATTACTCAAAGCTTGTCAAAGCTGATATTCATGGAAAGGACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.082395853

Conservation Information
Conserved circRNAs	NA
PMCS	0.082395853

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4275424-4274335(+)
4274907-4274457(+)
4274418-4275509(-)
						
						Potential amino acid sequence
						
							MKLLELLTLTKLRMLRTENPSPSITQSLSKLIFMERTR*(+)
MMYYRKALMLQSYLERIQSEDLESTLGLAGSADRHFELSPEARAQADLKFTYVVTCQIYGKQKG
EGKAEAADIALLMQRNEALRVAYIDEVENAKNGKPITEYYSKLVKADIHGKDKMNGRTSLLVST
GMKMQQTLSFLATQMTYLNYVYGLLIVGRP*(+)
MSFGLPKSSESAAFSSLLIRVRKFFHSSCPFHEYQL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4275424-4274335(+) 4274907-4274457(+) 4274418-4275509(-)
Potential amino acid sequence	MKLLELLTLTKLRMLRTENPSPSITQSLSKLIFMERTR(+) MMYYRKALMLQSYLERIQSEDLESTLGLAGSADRHFELSPEARAQADLKFTYVVTCQIYGKQKG EGKAEAADIALLMQRNEALRVAYIDEVENAKNGKPITEYYSKLVKADIHGKDKMNGRTSLLVST GMKMQQTLSFLATQMTYLNYVYGLLIVGRP(+) MSFGLPKSSESAAFSSLLIRVRKFFHSSCPFHEYQL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d027392_circ_g.9

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