Plant Circular RNA Database

Detail information of Zm00001d010109_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d010109_circ_g.2
					
						ID in PlantcircBase
						zma_circ_009657
					
						Alias
						Zm08circ00043
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 99415303-99417969  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d010109						
					
						Parent gene annotation
						
							LETM1-like protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d010109_circ_g.1 Zm00001d010109_circ_g.3 						
					
						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
						Zm00001d010109_T005:5
Zm00001d010109_T010:6
Zm00001d010109_T008:6
Zm00001d010109_T002:6
Zm00001d010109_T001:6
Zm00001d010109_T007:5
Zm00001d010109_T009:5
Zm00001d010109_T012:2
Zm00001d010109_T011:2
Zm00001d010109_T003:6
Zm00001d010109_T004:6

General Information
CircRNA Name	Zm00001d010109_circ_g.2
ID in PlantcircBase	zma_circ_009657
Alias	Zm08circ00043
Organism	Zea mays
Position	chr8: 99415303-99417969 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d010109
Parent gene annotation	LETM1-like protein
Parent gene strand	-
Alternative splicing	Zm00001d010109_circ_g.1 Zm00001d010109_circ_g.3
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	Zm00001d010109_T005:5 Zm00001d010109_T010:6 Zm00001d010109_T008:6 Zm00001d010109_T002:6 Zm00001d010109_T001:6 Zm00001d010109_T007:5 Zm00001d010109_T009:5 Zm00001d010109_T012:2 Zm00001d010109_T011:2 Zm00001d010109_T003:6 Zm00001d010109_T004:6

			
						 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  
						
							AACACAAGAAGTCAGGAAATATCAACCGAACTTACCTTGAAAGTATGAGAAGTGAAGATGGCAC
AGCATGATTAAGTGATAGGTCCAACCAGTCTCGGAGctatcaagcagctgccaacggtttccaa
tttgtgcatccacatcatcaatctccttttctaattcttgaagcatagcatcaacctgaatgcg
gtacaata

									
								

					

						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
						
							CTATCAAGCAGCTGCCAACGGTTTCCAATTTGTGCATCCACATCATCAATCTCCTTTTCTAATT
CTTGAAGCATAGCATCAACCTGAATGCGGTACAATACATGTGCAAGTGAATAACCAATTCCTTA
TCACAAATAACCAATACCACTGGTAGTTTGCACCTCCTCCTTGTGAAGCTTAAATGCAGAAATC
ATTCATGAAACAAGATATCTTTTAATGCTTCAGCTTTGCTAGTGAGATTAGATACCCGTACTCC
CTCCACTTTAGTTTGTTATAGCCTTATTTAGGTGAGCAGATAGATTAAGTTATAAAGCCTACGA
AAAGACAAGAGCAAATGACCAAGCTTAAATCTTATTTGATGGCTTGATGCAAGTCAGGATTTTC
CTCTAGCATGAAGATGACGGCAGTATATGGAGAATATGCAGATAGTATCATTGATAACTACACT
AGAGCATAATTTTTTTTGTGAAGTGGATTCAGGTTTAAACCATTTATATTATTATATACCTCGT
CGTCAGTGGTTTGCAGTATAAATTAATTGGCTCACATCACCCGAATCAAGTGGTGCAAGATTCT
TTTGTAGCATTCTAGAATGTCAGGGCAGCCAGCGAGTTTGGTATACTTACCAACTAGATCCATT
TAATATGATTATTAACTCTAAGTAGCTACCAACTAAATATTAAAAAAATAACAGCTTTATTGGG
AAAATTTTATCAGCCTTTTTAATATGCACAGACGTTCGGCATCCTTGAAATTAAAAAACAAAGG
CTAGTAACTGTTAAGTATCATCAATAAAATATTTGGTTATTGGTTGAACTGTCCGTACCTCAAG
TAAAAGTTTACAGTTATATCTCTAAACTTTTCGGACATCTCTTTATAATTTTTATGGGAAATAT
CAAAAACACTTACCTTAGAAAACACATCACAGGTAATATTTACAAATTTTAACTATGGCTATAA
CACGCATTAAGAGGATTTCTTACCTTCTCAATCAACGCCGACGAGACCTTTTCTTCTGCAGCAG
CCTCAGCATCATTGTCTGGGTCTTCCCTAGCGGCTATATATGCTTTTTTAGCTGCTTCTTCACC
TTCAGTACCCTCTTTTTTGAGCATGGAGTTATATAGCTCTATCTGCATTGGGACATTTGGACAG
CTCAATCCTATCAAACCTCCACGATGTATTATGTATTATAAACTGAAAGGTGAATGCATGAATA
ATTGTTGCTTTAATCCCACTTCACATTATACCTCTTTATTGACGAGGCTCAGAAACTCTTGACG
CTCCTTGCTAACAGACTGCAATGCAGATATGAAAGTTGGAAAAAGGTCAGACAGACAATCGTTC
TAGAATAATGGTGCTATTAGTGTCCATATGTACATTTACTGATAAAAGAATACAGATAGACTAG
GATCATACAGATGCAGATGCGAGCACAGCCAAGGCACGGCTGATATTACAGAGCTTCTCTTTGT
CATGTTCTTTTGCTTTTCTCAGTTCTTCCCTAGCAGTAGCATCAGTCATTTCCTTCAAAGCTAA
ATCTTCTTCAGCAGTTTCTGGTTCCTTCATCTTTGCCTCTTCTTTCTTTTGTTTTGCCTTTTCT
TCTTTCTCTTTCTTTTTCTCTTCCTCCTGAATGTGTTTTATATGCAAAACATCAACGACACAGA
TTTGCAACATGATAAAAATGATAAACAAATATGGATCTGTATACTGAATTTTTTAAAGCAAACT
GCATTAGCAGACCCCCCCCCCCCCCCCCACACACACACACAGAAGCAGACAGACATCAAAACTG
AGTTCTATTATAAAAATGTTTTCAAATTAAGTTCCACTTGACCGTGAAATAGCATAAACCATGG
ACTGAGCCATATTAATGGCTTGTTTAGATATAGTGGGATTAGGCTAATCCCTTCAAATAAGCTT
TAGTTCATTTGCCAATCAGAAGGGATTGGGCCAATGGTAAGTCCATTGGAATCTACCTTTGTAA
TTTTGTCACATGACAAAATATAAACAGGAAAGTAATTCAAGCATGAGATTCAGCAAGGTTACAG
GTTACAGAAAAACACCACCATATGAGTTGGCATATCAAAATATCTGAATATCCAGGGTGCATAG
AATTATATAAAGTTGGATTGTTAGAAAATACTAAACTATGGCTTAACTACTTAAGATGAATGTG
TCTTTCTGGATGGAATCAATCTTAAATAACAAAACTAGGAGGTGGCGAGGTGCACATTCAGTGG
ATGGAAGTTCTCTATCAGATACACAGCACTAATCCCACAGAAGACCTACCCAAATATGATAACA
AAAAGCTAAGAAAAAGAACAGCGTTTCAGTCTACAGTTCTATATCACCTTGATAAGTTCTTCCT
GCATCTCAAGGAATTCTAATTTTCTCCTCCTTTCAGAAACTGAATCTTCAGATGGCAATACTGT
CCCAATTGTATCCACAACTTCGTCTGGTAAAGAAGATAGTGTTGCTACAACAGCCTCCTCTGGC
TTCATTCTCCCAGACACAGTAAAGGCTCTAAAAGCATTATCAAATATAAGAATGCAAGCATGAG
CGGTAATAACACAAGAAGTCAGGAAATATCAACCGAACTTACCTTGAAAGTATGAGAAGTGAAG
ATGGCACAGCATGATTAAGTGATAGGTCCAACCAGTCTCGGAG
						
					

			
		

Sequences
Splice junction sequence	AACACAAGAAGTCAGGAAATATCAACCGAACTTACCTTGAAAGTATGAGAAGTGAAGATGGCAC AGCATGATTAAGTGATAGGTCCAACCAGTCTCGGAGctatcaagcagctgccaacggtttccaa tttgtgcatccacatcatcaatctccttttctaattcttgaagcatagcatcaacctgaatgcg gtacaata
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	CTATCAAGCAGCTGCCAACGGTTTCCAATTTGTGCATCCACATCATCAATCTCCTTTTCTAATT CTTGAAGCATAGCATCAACCTGAATGCGGTACAATACATGTGCAAGTGAATAACCAATTCCTTA TCACAAATAACCAATACCACTGGTAGTTTGCACCTCCTCCTTGTGAAGCTTAAATGCAGAAATC ATTCATGAAACAAGATATCTTTTAATGCTTCAGCTTTGCTAGTGAGATTAGATACCCGTACTCC CTCCACTTTAGTTTGTTATAGCCTTATTTAGGTGAGCAGATAGATTAAGTTATAAAGCCTACGA AAAGACAAGAGCAAATGACCAAGCTTAAATCTTATTTGATGGCTTGATGCAAGTCAGGATTTTC CTCTAGCATGAAGATGACGGCAGTATATGGAGAATATGCAGATAGTATCATTGATAACTACACT AGAGCATAATTTTTTTTGTGAAGTGGATTCAGGTTTAAACCATTTATATTATTATATACCTCGT CGTCAGTGGTTTGCAGTATAAATTAATTGGCTCACATCACCCGAATCAAGTGGTGCAAGATTCT TTTGTAGCATTCTAGAATGTCAGGGCAGCCAGCGAGTTTGGTATACTTACCAACTAGATCCATT TAATATGATTATTAACTCTAAGTAGCTACCAACTAAATATTAAAAAAATAACAGCTTTATTGGG AAAATTTTATCAGCCTTTTTAATATGCACAGACGTTCGGCATCCTTGAAATTAAAAAACAAAGG CTAGTAACTGTTAAGTATCATCAATAAAATATTTGGTTATTGGTTGAACTGTCCGTACCTCAAG TAAAAGTTTACAGTTATATCTCTAAACTTTTCGGACATCTCTTTATAATTTTTATGGGAAATAT CAAAAACACTTACCTTAGAAAACACATCACAGGTAATATTTACAAATTTTAACTATGGCTATAA CACGCATTAAGAGGATTTCTTACCTTCTCAATCAACGCCGACGAGACCTTTTCTTCTGCAGCAG CCTCAGCATCATTGTCTGGGTCTTCCCTAGCGGCTATATATGCTTTTTTAGCTGCTTCTTCACC TTCAGTACCCTCTTTTTTGAGCATGGAGTTATATAGCTCTATCTGCATTGGGACATTTGGACAG CTCAATCCTATCAAACCTCCACGATGTATTATGTATTATAAACTGAAAGGTGAATGCATGAATA ATTGTTGCTTTAATCCCACTTCACATTATACCTCTTTATTGACGAGGCTCAGAAACTCTTGACG CTCCTTGCTAACAGACTGCAATGCAGATATGAAAGTTGGAAAAAGGTCAGACAGACAATCGTTC TAGAATAATGGTGCTATTAGTGTCCATATGTACATTTACTGATAAAAGAATACAGATAGACTAG GATCATACAGATGCAGATGCGAGCACAGCCAAGGCACGGCTGATATTACAGAGCTTCTCTTTGT CATGTTCTTTTGCTTTTCTCAGTTCTTCCCTAGCAGTAGCATCAGTCATTTCCTTCAAAGCTAA ATCTTCTTCAGCAGTTTCTGGTTCCTTCATCTTTGCCTCTTCTTTCTTTTGTTTTGCCTTTTCT TCTTTCTCTTTCTTTTTCTCTTCCTCCTGAATGTGTTTTATATGCAAAACATCAACGACACAGA TTTGCAACATGATAAAAATGATAAACAAATATGGATCTGTATACTGAATTTTTTAAAGCAAACT GCATTAGCAGACCCCCCCCCCCCCCCCCACACACACACACAGAAGCAGACAGACATCAAAACTG AGTTCTATTATAAAAATGTTTTCAAATTAAGTTCCACTTGACCGTGAAATAGCATAAACCATGG ACTGAGCCATATTAATGGCTTGTTTAGATATAGTGGGATTAGGCTAATCCCTTCAAATAAGCTT TAGTTCATTTGCCAATCAGAAGGGATTGGGCCAATGGTAAGTCCATTGGAATCTACCTTTGTAA TTTTGTCACATGACAAAATATAAACAGGAAAGTAATTCAAGCATGAGATTCAGCAAGGTTACAG GTTACAGAAAAACACCACCATATGAGTTGGCATATCAAAATATCTGAATATCCAGGGTGCATAG AATTATATAAAGTTGGATTGTTAGAAAATACTAAACTATGGCTTAACTACTTAAGATGAATGTG TCTTTCTGGATGGAATCAATCTTAAATAACAAAACTAGGAGGTGGCGAGGTGCACATTCAGTGG ATGGAAGTTCTCTATCAGATACACAGCACTAATCCCACAGAAGACCTACCCAAATATGATAACA AAAAGCTAAGAAAAAGAACAGCGTTTCAGTCTACAGTTCTATATCACCTTGATAAGTTCTTCCT GCATCTCAAGGAATTCTAATTTTCTCCTCCTTTCAGAAACTGAATCTTCAGATGGCAATACTGT CCCAATTGTATCCACAACTTCGTCTGGTAAAGAAGATAGTGTTGCTACAACAGCCTCCTCTGGC TTCATTCTCCCAGACACAGTAAAGGCTCTAAAAGCATTATCAAATATAAGAATGCAAGCATGAG CGGTAATAACACAAGAAGTCAGGAAATATCAACCGAACTTACCTTGAAAGTATGAGAAGTGAAG ATGGCACAGCATGATTAAGTGATAGGTCCAACCAGTCTCGGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.133345966

Conservation Information
Conserved circRNAs	NA
PMCS	0.133345966

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							99417805-99417802(-)
99415350-99417943(-)
						
						Potential amino acid sequence
						
							MKPEEAVVATLSSLPDEVVDTIGTVLPSEDSVSERRRKLEFLEMQEELIKEEEKKKEKEEKAKQ
KKEEAKMKEPETAEEDLALKEMTDATAREELRKAKEHDKEKLCNISRALAVLASASSVSKERQE
FLSLVNKEIELYNSMLKKEGTEGEEAAKKAYIAAREDPDNDAEAAAEEKVSSALIEKVRNPLNA
CYSHRIGYSLAHVLYRIQVDAMLQELEKEIDDVDAQIGNRWQLLDSSETGWTYHLIMLCHLHFS
YFQEPLLCLGE*(-)
MMWMHKLETVGSCLIAPRLVGPIT*(-)
						
						Sponge-miRNAs
						
							zma-miR167h-3p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	99417805-99417802(-) 99415350-99417943(-)
Potential amino acid sequence	MKPEEAVVATLSSLPDEVVDTIGTVLPSEDSVSERRRKLEFLEMQEELIKEEEKKKEKEEKAKQ KKEEAKMKEPETAEEDLALKEMTDATAREELRKAKEHDKEKLCNISRALAVLASASSVSKERQE FLSLVNKEIELYNSMLKKEGTEGEEAAKKAYIAAREDPDNDAEAAAEEKVSSALIEKVRNPLNA CYSHRIGYSLAHVLYRIQVDAMLQELEKEIDDVDAQIGNRWQLLDSSETGWTYHLIMLCHLHFS YFQEPLLCLGE(-) MMWMHKLETVGSCLIAPRLVGPIT(-)
Sponge-miRNAs	zma-miR167h-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d010109_circ_g.2

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