Plant Circular RNA Database

Detail information of Zm00001d010974_circ_g.3

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d010974_circ_g.3
					

						ID in PlantcircBase
						zma_circ_009702
					

						Alias
						Zm08circ00049, GRMZM2G155123_C1
					

						Organism
						
							Zea mays						
					

						Position
						
							chr8: 135536486-135537465  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						CIRI2
					

						Parent gene
						
							Zm00001d010974						
					

						Parent gene annotation
						
							E3 SUMO-protein ligase SIZ1
							
					

						Parent gene strand
						-
					

						Alternative splicing
						
							Zm00001d010974_circ_g.1 Zm00001d010974_circ_g.2 Zm00001d010974_circ_g.4 						
					

						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  
						
							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
						Zm00001d010974_T005:3
Zm00001d010974_T028:3
Zm00001d010974_T046:3
Zm00001d010974_T051:3
Zm00001d010974_T065:3
Zm00001d010974_T025:3
Zm00001d010974_T037:3
Zm00001d010974_T075:3
Zm00001d010974_T020:3
Zm00001d010974_T021:3
Zm00001d010974_T040:3
Zm00001d010974_T030:3
Zm00001d010974_T039:3
Zm00001d010974_T014:3
Zm00001d010974_T061:3
Zm00001d010974_T002:3
Zm00001d010974_T044:3
Zm00001d010974_T053:3
Zm00001d010974_T007:3
Zm00001d010974_T059:3
Zm00001d010974_T004:3
Zm00001d010974_T001:3
Zm00001d010974_T013:3
Zm00001d010974_T056:4
Zm00001d010974_T049:3
Zm00001d010974_T016:3
Zm00001d010974_T057:3
Zm00001d010974_T022:3
Zm00001d010974_T063:3
Zm00001d010974_T052:3
Zm00001d010974_T062:3
Zm00001d010974_T011:3
Zm00001d010974_T047:3
Zm00001d010974_T038:3
Zm00001d010974_T008:3
Zm00001d010974_T023:3
Zm00001d010974_T009:3
Zm00001d010974_T043:3
Zm00001d010974_T017:3
Zm00001d010974_T064:3
Zm00001d010974_T048:3
Zm00001d010974_T041:3
Zm00001d010974_T060:3
Zm00001d010974_T027:3
Zm00001d010974_T026:3
Zm00001d010974_T015:3
Zm00001d010974_T033:3
Zm00001d010974_T034:3
Zm00001d010974_T010:3
Zm00001d010974_T055:3
Zm00001d010974_T036:3
Zm00001d010974_T032:3
Zm00001d010974_T035:3
Zm00001d010974_T018:3
Zm00001d010974_T024:3
Zm00001d010974_T012:3
Zm00001d010974_T029:3
Zm00001d010974_T072:3
Zm00001d010974_T050:3
Zm00001d010974_T058:3
Zm00001d010974_T045:3
Zm00001d010974_T042:3
Zm00001d010974_T019:3
Zm00001d010974_T054:3
Zm00001d010974_T031:3
Zm00001d010974_T003:3
Zm00001d010974_T006:3

					

			
		

General Information
CircRNA Name	Zm00001d010974_circ_g.3
ID in PlantcircBase	zma_circ_009702
Alias	Zm08circ00049, GRMZM2G155123_C1
Organism	Zea mays
Position	chr8: 135536486-135537465 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d010974
Parent gene annotation	E3 SUMO-protein ligase SIZ1
Parent gene strand	-
Alternative splicing	Zm00001d010974_circ_g.1 Zm00001d010974_circ_g.2 Zm00001d010974_circ_g.4
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	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	Zm00001d010974_T005:3 Zm00001d010974_T028:3 Zm00001d010974_T046:3 Zm00001d010974_T051:3 Zm00001d010974_T065:3 Zm00001d010974_T025:3 Zm00001d010974_T037:3 Zm00001d010974_T075:3 Zm00001d010974_T020:3 Zm00001d010974_T021:3 Zm00001d010974_T040:3 Zm00001d010974_T030:3 Zm00001d010974_T039:3 Zm00001d010974_T014:3 Zm00001d010974_T061:3 Zm00001d010974_T002:3 Zm00001d010974_T044:3 Zm00001d010974_T053:3 Zm00001d010974_T007:3 Zm00001d010974_T059:3 Zm00001d010974_T004:3 Zm00001d010974_T001:3 Zm00001d010974_T013:3 Zm00001d010974_T056:4 Zm00001d010974_T049:3 Zm00001d010974_T016:3 Zm00001d010974_T057:3 Zm00001d010974_T022:3 Zm00001d010974_T063:3 Zm00001d010974_T052:3 Zm00001d010974_T062:3 Zm00001d010974_T011:3 Zm00001d010974_T047:3 Zm00001d010974_T038:3 Zm00001d010974_T008:3 Zm00001d010974_T023:3 Zm00001d010974_T009:3 Zm00001d010974_T043:3 Zm00001d010974_T017:3 Zm00001d010974_T064:3 Zm00001d010974_T048:3 Zm00001d010974_T041:3 Zm00001d010974_T060:3 Zm00001d010974_T027:3 Zm00001d010974_T026:3 Zm00001d010974_T015:3 Zm00001d010974_T033:3 Zm00001d010974_T034:3 Zm00001d010974_T010:3 Zm00001d010974_T055:3 Zm00001d010974_T036:3 Zm00001d010974_T032:3 Zm00001d010974_T035:3 Zm00001d010974_T018:3 Zm00001d010974_T024:3 Zm00001d010974_T012:3 Zm00001d010974_T029:3 Zm00001d010974_T072:3 Zm00001d010974_T050:3 Zm00001d010974_T058:3 Zm00001d010974_T045:3 Zm00001d010974_T042:3 Zm00001d010974_T019:3 Zm00001d010974_T054:3 Zm00001d010974_T031:3 Zm00001d010974_T003:3 Zm00001d010974_T006:3

			
						 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  
						
							GAGAGAGTAAACCTGGAGATCATATTCTTGTCTCTGAACTGTTTCTCTATCTGCTCGGGAAAGT
TGGAAAGTCTTCTCCACAATTTGAGGTACACTTGCTcagtggcccatcatcccgcccatttatc
cctagtaactgagaaccgggcctggtcattactcgtacaggaatacctgaacaaacagaaataa
atatcaga

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							CAGTGGCCCATCATCCCGCCCATTTATCCCTAGTAACTGAGAACCGGGCCTGGTCATTACTCGT
ACAGGAATACCTGAACAAACAGAAATAAATATCAGACTGGCAATCCCTTAATTTCAAGTATGAA
TGTAAATTAAACTTGTATGGCTCAGATATATGTATCTATACAGCATATAAGCCAAGATTTGTGC
CACAATGCATTTTAATAAATCCAAGTTGTACAAGAAAATTTAAACATTACCGTTCACTTGCAAT
TCTGCATATTGAGGCCATTGCATCCTGAACTGGACTTTGTCATTTATAAGGATGCACCAAACCT
GTCCACAGACCCACAACACAATCGGTAGTTAACAGGACTGTGCAACAGAACCAGTGAGTGTATC
CAAGTGTTTTTCTTTGTTGAATAGGACATGATAAACCTTAATTCATCAAATCGATACCTTTTGA
CAGCACTTAATGTGCAATACTCACGTCTATATCGCACACACAATTTACAAATGATTTAAATAGA
TAACTCATAATTAAGGTAGACATGAAAAATCAAAGACATTTGATGTTAGACAAAGGTCATAATA
ATCCGTAGTTATTTTCCTTAAATGTACCATGCATGAACACTATGTTAAAGAGGTTGATTCAATG
ACAAAGTTCGGTGACTCCAAGTGACCTAATCTCACATACATCAATGTTATCCTAAGGTTTATTT
ATGGCATGATTTATGGCATAGCATAATCACCAATGTACTATACGTGAACTCTATATTAGAGAAA
AAAACATAATCATCTGCAGTTAAGATTTATTTATGGGTAGCAGCATCGTGACATTAATAAAGTG
TGCAAGATTTTTATCAGGATCTAGGCAAATGAAACTTAGGTTATGGAGGAGAGAGTAAACCTGG
AGATCATATTCTTGTCTCTGAACTGTTTCTCTATCTGCTCGGGAAAGTTGGAAAGTCTTCTCCA
CAATTTGAGGTACACTTGCT

Sequences
Splice junction sequence	GAGAGAGTAAACCTGGAGATCATATTCTTGTCTCTGAACTGTTTCTCTATCTGCTCGGGAAAGT TGGAAAGTCTTCTCCACAATTTGAGGTACACTTGCTcagtggcccatcatcccgcccatttatc cctagtaactgagaaccgggcctggtcattactcgtacaggaatacctgaacaaacagaaataa atatcaga
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CAGTGGCCCATCATCCCGCCCATTTATCCCTAGTAACTGAGAACCGGGCCTGGTCATTACTCGT ACAGGAATACCTGAACAAACAGAAATAAATATCAGACTGGCAATCCCTTAATTTCAAGTATGAA TGTAAATTAAACTTGTATGGCTCAGATATATGTATCTATACAGCATATAAGCCAAGATTTGTGC CACAATGCATTTTAATAAATCCAAGTTGTACAAGAAAATTTAAACATTACCGTTCACTTGCAAT TCTGCATATTGAGGCCATTGCATCCTGAACTGGACTTTGTCATTTATAAGGATGCACCAAACCT GTCCACAGACCCACAACACAATCGGTAGTTAACAGGACTGTGCAACAGAACCAGTGAGTGTATC CAAGTGTTTTTCTTTGTTGAATAGGACATGATAAACCTTAATTCATCAAATCGATACCTTTTGA CAGCACTTAATGTGCAATACTCACGTCTATATCGCACACACAATTTACAAATGATTTAAATAGA TAACTCATAATTAAGGTAGACATGAAAAATCAAAGACATTTGATGTTAGACAAAGGTCATAATA ATCCGTAGTTATTTTCCTTAAATGTACCATGCATGAACACTATGTTAAAGAGGTTGATTCAATG ACAAAGTTCGGTGACTCCAAGTGACCTAATCTCACATACATCAATGTTATCCTAAGGTTTATTT ATGGCATGATTTATGGCATAGCATAATCACCAATGTACTATACGTGAACTCTATATTAGAGAAA AAAACATAATCATCTGCAGTTAAGATTTATTTATGGGTAGCAGCATCGTGACATTAATAAAGTG TGCAAGATTTTTATCAGGATCTAGGCAAATGAAACTTAGGTTATGGAGGAGAGAGTAAACCTGG AGATCATATTCTTGTCTCTGAACTGTTTCTCTATCTGCTCGGGAAAGTTGGAAAGTCTTCTCCA CAATTTGAGGTACACTTGCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.109439048

Conservation Information
Conserved circRNAs	NA
PMCS	0.109439048

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							135536766-135537414(-)
						
						Potential amino acid sequence
						
							MQWPQYAELQVNGIPVRVMTRPGSQLLGINGRDDGPLSKCTSNCGEDFPTFPSR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	135536766-135537414(-)
Potential amino acid sequence	MQWPQYAELQVNGIPVRVMTRPGSQLLGINGRDDGPLSKCTSNCGEDFPTFPSR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d010974_circ_g.3

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