Plant Circular RNA Database

Detail information of Zm00001d005785_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d005785_circ_g.1
					
						ID in PlantcircBase
						zma_circ_001156
					
						Alias
						circ494
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 188382252-188385851  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Zm00001d005785						
					
						Parent gene annotation
						
							Pentatricopeptide repeat-containing protein 
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d005785_circ_g.2 Zm00001d005785_circ_g.3 Zm00001d005785_circ_g.4 Zm00001d005785_circ_g.5 						
					
						Support reads
						3
					
						Tissues
						seedling leaves
					
						Exon boundary  
						
							No-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-AA							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
						Zm00001d005785_T019:6
Zm00001d005785_T012:6
Zm00001d005785_T016:5
Zm00001d005785_T001:6
Zm00001d005785_T004:6
Zm00001d005785_T003:3
Zm00001d005785_T005:6
Zm00001d005785_T006:6
Zm00001d005785_T002:5
Zm00001d005785_T020:6
Zm00001d005785_T013:4
Zm00001d005785_T021:7
Zm00001d005785_T015:5
Zm00001d005785_T011:6
Zm00001d005785_T018:5
Zm00001d005785_T008:5
Zm00001d005785_T014:5

General Information
CircRNA Name	Zm00001d005785_circ_g.1
ID in PlantcircBase	zma_circ_001156
Alias	circ494
Organism	Zea mays
Position	chr2: 188382252-188385851 JBrowse»
Reference genome	AGPv4.38
Type	ui-circRNA
Identification method	CIRI
Parent gene	Zm00001d005785
Parent gene annotation	Pentatricopeptide repeat-containing protein
Parent gene strand	+
Alternative splicing	Zm00001d005785_circ_g.2 Zm00001d005785_circ_g.3 Zm00001d005785_circ_g.4 Zm00001d005785_circ_g.5
Support reads	3
Tissues	seedling leaves
Exon boundary	No-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-AA 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	Zm00001d005785_T019:6 Zm00001d005785_T012:6 Zm00001d005785_T016:5 Zm00001d005785_T001:6 Zm00001d005785_T004:6 Zm00001d005785_T003:3 Zm00001d005785_T005:6 Zm00001d005785_T006:6 Zm00001d005785_T002:5 Zm00001d005785_T020:6 Zm00001d005785_T013:4 Zm00001d005785_T021:7 Zm00001d005785_T015:5 Zm00001d005785_T011:6 Zm00001d005785_T018:5 Zm00001d005785_T008:5 Zm00001d005785_T014:5

			
						 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  
						
							TAACAAGCGCATGTGGCTGGATTCAGTTGGATCAATTAGCCGTGCCGCCAAAGAAGAGACACAT
GAGCTATTAATGGAAGCTGCCATAAATAATAATCAGgggcctgggtatagcaagaaggattgat
gaagcattcgaaatactggaatcaattgagaaagattcttctattggggggcccaggctctctc
ctcatctc

									
								

					

						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
						
							GGGCCTGGGTATAGCAAGAAGGATTGATGAAGCATTCGAAATACTGGAATCAATTGAGAAAGAT
TCTTCTATTGGGGGGCCCAGGCTCTCTCCTCATCTCATTTGTGGTTTTCTAAATGCCCTTATCG
AAGCAGGTTGGTGCATGATCATTTAATCTTCCACAATACTAGAGTTGGTTTACATTCGTGCTGC
CAAATAAATTTACCTCTATCAAAAAGTTAAAAAAATCCCTTCGTCTACCCAACAGCAAAGCATA
GGTCTAAGGGCCGGCTCTGGTCGTGGTCGTTCTCACATAGGCTACGATGCCACTGTGTATAGGT
GGGGCAGGGATTCGGGAGTTTCTTGACCTGTGTAAAGTCTTCTTAATTCAATGCTTGAGGTTGT
CTTACCCCCGTAGATCGAGTTTTTTTGTTTACTTATTCCCTTGATATGGTTGTTTTCATCATTA
CCAATTTATCTAGTGCAGCTGGGACCAAGCTTGACAGGAATTGGACAATTATGCTCATTTGTAT
ATTACTACATTTGCTCTCTTGAATGAGCAGGAGAGCTATGCATCATTATATTAAGAAGAAAAAA
GGAGTCAAAGAGACTCGTAAAGACAAATAGGACTGGGTTTACATGTAAGAACTCTCTCACCAAT
GAATACTAAAAGGTGAACAACAAACTACCTACACACCCAGGTTATGGCCAAATGCACTGAGGCC
TTTGGTCCCTGCCGTACAACACATTTTTGCTGCATCACTGGCGTCCTGCACTAAAGCATCGGGA
CTAGGAGCCCCCCCCACCCCCCCCTCCAAAAAAAACACATCTATTCCTAGGATTCCAAATCCAC
CAACACAACTAAGGAATTGAATCTCTTTGGACCTTTGGACATTATTTTCCCAATGGTGCAGAAC
TTGGCACTATTAACCTGGTGCTTTGTGCTGCATGCCAACTAAAGAGAAAACTGAGAACCACTCT
GTTAATCTTCGCTCATGTTTCTGCAACCTCATTTACTGATGGAATTGAACTTCAACTTATCCAG
GAGATATGAGGCGTGCCAATGCTCTTGTCGCCCGTTTCCGCATGGTCCTTTACGAGGATCACTC
TGTCTTACTATACAACTTACTGATGAAGGTACACGTATTGCTAGTTTTCATTTGCAGTAAATCA
CCATGGTAGGTACATAATTTTTTCAACTGAATATACTCCAGGGGTATATTAAGAGCAACTTCCC
TCTCGGAGCTTTGACTGTTAAAGACGAGATATTGCGTCAAGGGTTGAAGCCTGATAGATTGACC
TACAATACCATCATTTCTGCCTGTGTAAAATCAGCAGAGAATGATAAAGCTATCCAATTTCTTG
AAGATATGAAGGTGTCACACAAGTGTTGGAAAGGCCAGTTTTAGCCACAAAATTGTTTTGGTAT
ACAAATAATTGTATCATGTAATTAAAATGAATTGATTATATTACAATGCAGGAAGAAGCTAATA
CAGAAAGTAACCCTGAACTTCTTCCAGATGCTGTTACCTACACAACATTACTCAAGGTGTGCCT
CCTGCTAGCGCACATCAGTTAGTGATAACAACTGCTGCCTTCTGGCTACACCTTTAATTTTACA
TTGTCAAGCAGTGATATTGTAGTGTTCTTACACTGCATAATTTATTTTTCTTTTCACGATAGAT
AATGTGGAGACTACACTCTACTTCTTTTGTTGACAACTTGACATGATCATACAATGATATTTGA
GTGTCTGTTACACAACATTCTTTTTTATGAGAATGCTTCATAATTGTTGAAAAAGAAGATGCTG
CCTACTGAAAAATGTGTTACACCTTAAAATTGATAATCATGATAGGGTTTCTGAAGGATGCCTT
TGAGACCTCTTTGAACAAGTAGTTTGATCACTGTTGTGTTCGCTATCATTTTTGGTTACTTCTT
AATTTTACAATTTGTGGAAGCATCCTGCAGGGTTTAGGAAATAGCCGTGACCTTTATTCAGTCG
TGAAGATTGTTGTGGAGATGAAATCTTCACTAATTTCAATCGACAGGACTGCATACACTGCTAT
GGTAGATGCTTTGCTAGCTTGTGGGTCCATCGACGGTAAGTTCTATACCATCTTTTTAGTCACT
ACAGTGAATTTTCCTAAAAAACAATACAATGAATTTGCAAGTTGGAAAACAACGTTGGTGTTTG
ACTAAGAACTAACAAGTGGCCTAGCACCCACTTTTCATCCTCACATTTGATTTATTTTCAAACT
GACACTTCTCTTTTCACTTTACAGTGGTTCAGCATTTAGCGTTCCATTTGACGCTAACAAGTGA
CATATCACATTCTTATCTGTACCCTTTTATGTCCCAGTTGCCCAAGCAGCATATCCAGTCTAAA
GTATCTAAAATGGTGAAACTGTTCTTCGTCAGTTGTGTTTGCATAATTTTTTATAATTACATCA
CCGATGTGTATAACCTAGTTGTACTTCTCAAATCATCACATGCAGTGACTATAAGTTACACCAA
AATCATTTTCTGAGGTATAGACTATAGATCACTTGTTAGTATGGTTCATTTAACCTTACTGTTG
TGCACAAGCAAATTGCTTGACAAATGACGATACTTGATGCCTCTCGCAACCTATTAGGATCATG
CCTGGTTTTAAATATTATGGTCCATGCAGGCGAATGTTTTTCATATTTTAAGTTATCATTTCCT
CACTTGCATAGTAAATGAGAATGTCAACTTTAGCACTATTTGCTTAGCATGACCCTCTGTTTTG
TATCCTAGATATCTGCCTCTGGGTCTATTCTAATGTTTTGACAATTTATCGCATGTCTTGATTA
CTCTCTAGCAATTCAGCATTATCCATAATTCTTAATCTAGTTGGTCCTGAGATGATAATGTTAC
CAGTTTACCTAAATTTAGTTTCTTCATTACATTTGTTCAAAATATCTTCAAATAATTTACACAT
ATCCTTCATTGTAATGTAATATGTGTGCCCCTAGCCCCAACAAATATTTGTGACAACAAATGTG
TTCACATTTGGACTTTGTAGAAGAAATAAAAATGGATAATAACTATGCATATGTTAACATGAGT
ATTGTGTTAAATTTGAGAATCTTTCAGTGTTCATGAATATACAGAACTACAGACTAACTTATTT
TTACTTTCCATCTTAGTGTATAAACTCTTTGTCCTTGTTTAAGTGAATATAAATGTGGATGAGG
CAATCAAATTACCTTGTTGCGAGAATGGCAATGCTGTTTCATGTGTTCTTGAGATCATGGGTTA
TGAGAGTGAAAGCTGTTATTCAGACAAAAAAAAACCTCTTGTTTATGATGTGTACTAGATTTCT
GTACTGATATGCTTTGAACCTTATTGGTGCTTATCGTAGGGGCCCTTTGCATTTTTGGTGATAT
AATAAAGCATGCTGGCAAGAACAATGATTTGAGACCTAAACCTCATCTTTATCTTTCAATCATG
AGAGCTTTTGCTACCAGAGGTGATGTTGATATGGTCATGAGATTTAACAAGCGCATGTGGCTGG
ATTCAGTTGGATCAATTAGCCGTGCCGCCAAAGAAGAGACACATGAGCTATTAATGGAAGCTGC
CATAAATAATAATCAG
						
					

			
		

Sequences
Splice junction sequence	TAACAAGCGCATGTGGCTGGATTCAGTTGGATCAATTAGCCGTGCCGCCAAAGAAGAGACACAT GAGCTATTAATGGAAGCTGCCATAAATAATAATCAGgggcctgggtatagcaagaaggattgat gaagcattcgaaatactggaatcaattgagaaagattcttctattggggggcccaggctctctc ctcatctc
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	GGGCCTGGGTATAGCAAGAAGGATTGATGAAGCATTCGAAATACTGGAATCAATTGAGAAAGAT TCTTCTATTGGGGGGCCCAGGCTCTCTCCTCATCTCATTTGTGGTTTTCTAAATGCCCTTATCG AAGCAGGTTGGTGCATGATCATTTAATCTTCCACAATACTAGAGTTGGTTTACATTCGTGCTGC CAAATAAATTTACCTCTATCAAAAAGTTAAAAAAATCCCTTCGTCTACCCAACAGCAAAGCATA GGTCTAAGGGCCGGCTCTGGTCGTGGTCGTTCTCACATAGGCTACGATGCCACTGTGTATAGGT GGGGCAGGGATTCGGGAGTTTCTTGACCTGTGTAAAGTCTTCTTAATTCAATGCTTGAGGTTGT CTTACCCCCGTAGATCGAGTTTTTTTGTTTACTTATTCCCTTGATATGGTTGTTTTCATCATTA CCAATTTATCTAGTGCAGCTGGGACCAAGCTTGACAGGAATTGGACAATTATGCTCATTTGTAT ATTACTACATTTGCTCTCTTGAATGAGCAGGAGAGCTATGCATCATTATATTAAGAAGAAAAAA GGAGTCAAAGAGACTCGTAAAGACAAATAGGACTGGGTTTACATGTAAGAACTCTCTCACCAAT GAATACTAAAAGGTGAACAACAAACTACCTACACACCCAGGTTATGGCCAAATGCACTGAGGCC TTTGGTCCCTGCCGTACAACACATTTTTGCTGCATCACTGGCGTCCTGCACTAAAGCATCGGGA CTAGGAGCCCCCCCCACCCCCCCCTCCAAAAAAAACACATCTATTCCTAGGATTCCAAATCCAC CAACACAACTAAGGAATTGAATCTCTTTGGACCTTTGGACATTATTTTCCCAATGGTGCAGAAC TTGGCACTATTAACCTGGTGCTTTGTGCTGCATGCCAACTAAAGAGAAAACTGAGAACCACTCT GTTAATCTTCGCTCATGTTTCTGCAACCTCATTTACTGATGGAATTGAACTTCAACTTATCCAG GAGATATGAGGCGTGCCAATGCTCTTGTCGCCCGTTTCCGCATGGTCCTTTACGAGGATCACTC TGTCTTACTATACAACTTACTGATGAAGGTACACGTATTGCTAGTTTTCATTTGCAGTAAATCA CCATGGTAGGTACATAATTTTTTCAACTGAATATACTCCAGGGGTATATTAAGAGCAACTTCCC TCTCGGAGCTTTGACTGTTAAAGACGAGATATTGCGTCAAGGGTTGAAGCCTGATAGATTGACC TACAATACCATCATTTCTGCCTGTGTAAAATCAGCAGAGAATGATAAAGCTATCCAATTTCTTG AAGATATGAAGGTGTCACACAAGTGTTGGAAAGGCCAGTTTTAGCCACAAAATTGTTTTGGTAT ACAAATAATTGTATCATGTAATTAAAATGAATTGATTATATTACAATGCAGGAAGAAGCTAATA CAGAAAGTAACCCTGAACTTCTTCCAGATGCTGTTACCTACACAACATTACTCAAGGTGTGCCT CCTGCTAGCGCACATCAGTTAGTGATAACAACTGCTGCCTTCTGGCTACACCTTTAATTTTACA TTGTCAAGCAGTGATATTGTAGTGTTCTTACACTGCATAATTTATTTTTCTTTTCACGATAGAT AATGTGGAGACTACACTCTACTTCTTTTGTTGACAACTTGACATGATCATACAATGATATTTGA GTGTCTGTTACACAACATTCTTTTTTATGAGAATGCTTCATAATTGTTGAAAAAGAAGATGCTG CCTACTGAAAAATGTGTTACACCTTAAAATTGATAATCATGATAGGGTTTCTGAAGGATGCCTT TGAGACCTCTTTGAACAAGTAGTTTGATCACTGTTGTGTTCGCTATCATTTTTGGTTACTTCTT AATTTTACAATTTGTGGAAGCATCCTGCAGGGTTTAGGAAATAGCCGTGACCTTTATTCAGTCG TGAAGATTGTTGTGGAGATGAAATCTTCACTAATTTCAATCGACAGGACTGCATACACTGCTAT GGTAGATGCTTTGCTAGCTTGTGGGTCCATCGACGGTAAGTTCTATACCATCTTTTTAGTCACT ACAGTGAATTTTCCTAAAAAACAATACAATGAATTTGCAAGTTGGAAAACAACGTTGGTGTTTG ACTAAGAACTAACAAGTGGCCTAGCACCCACTTTTCATCCTCACATTTGATTTATTTTCAAACT GACACTTCTCTTTTCACTTTACAGTGGTTCAGCATTTAGCGTTCCATTTGACGCTAACAAGTGA CATATCACATTCTTATCTGTACCCTTTTATGTCCCAGTTGCCCAAGCAGCATATCCAGTCTAAA GTATCTAAAATGGTGAAACTGTTCTTCGTCAGTTGTGTTTGCATAATTTTTTATAATTACATCA CCGATGTGTATAACCTAGTTGTACTTCTCAAATCATCACATGCAGTGACTATAAGTTACACCAA AATCATTTTCTGAGGTATAGACTATAGATCACTTGTTAGTATGGTTCATTTAACCTTACTGTTG TGCACAAGCAAATTGCTTGACAAATGACGATACTTGATGCCTCTCGCAACCTATTAGGATCATG CCTGGTTTTAAATATTATGGTCCATGCAGGCGAATGTTTTTCATATTTTAAGTTATCATTTCCT CACTTGCATAGTAAATGAGAATGTCAACTTTAGCACTATTTGCTTAGCATGACCCTCTGTTTTG TATCCTAGATATCTGCCTCTGGGTCTATTCTAATGTTTTGACAATTTATCGCATGTCTTGATTA CTCTCTAGCAATTCAGCATTATCCATAATTCTTAATCTAGTTGGTCCTGAGATGATAATGTTAC CAGTTTACCTAAATTTAGTTTCTTCATTACATTTGTTCAAAATATCTTCAAATAATTTACACAT ATCCTTCATTGTAATGTAATATGTGTGCCCCTAGCCCCAACAAATATTTGTGACAACAAATGTG TTCACATTTGGACTTTGTAGAAGAAATAAAAATGGATAATAACTATGCATATGTTAACATGAGT ATTGTGTTAAATTTGAGAATCTTTCAGTGTTCATGAATATACAGAACTACAGACTAACTTATTT TTACTTTCCATCTTAGTGTATAAACTCTTTGTCCTTGTTTAAGTGAATATAAATGTGGATGAGG CAATCAAATTACCTTGTTGCGAGAATGGCAATGCTGTTTCATGTGTTCTTGAGATCATGGGTTA TGAGAGTGAAAGCTGTTATTCAGACAAAAAAAAACCTCTTGTTTATGATGTGTACTAGATTTCT GTACTGATATGCTTTGAACCTTATTGGTGCTTATCGTAGGGGCCCTTTGCATTTTTGGTGATAT AATAAAGCATGCTGGCAAGAACAATGATTTGAGACCTAAACCTCATCTTTATCTTTCAATCATG AGAGCTTTTGCTACCAGAGGTGATGTTGATATGGTCATGAGATTTAACAAGCGCATGTGGCTGG ATTCAGTTGGATCAATTAGCCGTGCCGCCAAAGAAGAGACACATGAGCTATTAATGGAAGCTGC CATAAATAATAATCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.021249678

Conservation Information
Conserved circRNAs	NA
PMCS	0.021249678

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							zma-miR827-5p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	zma-miR827-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d005785_circ_g.1

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