Plant Circular RNA Database

Detail information of Zm00001d053316_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d053316_circ_g.1
					
						ID in PlantcircBase
						zma_circ_001823
					
						Alias
						circ2309
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 225861975-225864447  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d053316						
					
						Parent gene annotation
						
							Casein kinase I isoform delta-like; Putative casein kinase famil
y protein  
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d053316_circ_g.2 						
					
						Support reads
						33
					
						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  
						
							CT-TA							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
						Zm00001d053316_T004:8
Zm00001d053316_T005:8
Zm00001d053316_T009:8
Zm00001d053316_T016:5
Zm00001d053316_T011:8
Zm00001d053316_T017:8
Zm00001d053316_T006:7
Zm00001d053316_T014:8
Zm00001d053316_T010:8
Zm00001d053316_T003:8
Zm00001d053316_T001:8
Zm00001d053316_T007:5
Zm00001d053316_T012:8
Zm00001d053316_T002:8
Zm00001d053316_T008:8
Zm00001d053316_T013:8
Zm00001d053316_T015:8

General Information
CircRNA Name	Zm00001d053316_circ_g.1
ID in PlantcircBase	zma_circ_001823
Alias	circ2309
Organism	Zea mays
Position	chr4: 225861975-225864447 JBrowse»
Reference genome	AGPv4.38
Type	ui-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d053316
Parent gene annotation	Casein kinase I isoform delta-like; Putative casein kinase famil y protein
Parent gene strand	-
Alternative splicing	Zm00001d053316_circ_g.2
Support reads	33
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	CT-TA 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	Zm00001d053316_T004:8 Zm00001d053316_T005:8 Zm00001d053316_T009:8 Zm00001d053316_T016:5 Zm00001d053316_T011:8 Zm00001d053316_T017:8 Zm00001d053316_T006:7 Zm00001d053316_T014:8 Zm00001d053316_T010:8 Zm00001d053316_T003:8 Zm00001d053316_T001:8 Zm00001d053316_T007:5 Zm00001d053316_T012:8 Zm00001d053316_T002:8 Zm00001d053316_T008:8 Zm00001d053316_T013:8 Zm00001d053316_T015:8

			
						 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  
						
							AGCAATGGGTTTTAAAATCATTAGCTCACCTATAAGGTATATGGCGGTTGGTGGCTGAATCACG
ATATCTCTTTGCAAGCCCGAAGTCAATTACATAAACccaatctctcaggatgcagattattgga
acggctgtttaattgcattctgattgccgggcgttgttctgcttcaagcagacctgaagcatta
attgggcg

									
								

					

						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
						
							CCAATCTCTCAGGATGCAGATTATTGGAACGGCTGTTTAATTGCATTCTGATTGCCGGGCGTTG
TTCTGCTTCAAGCAGACCTGAAGCATTAATTGGGCGTGCAACACCAACTGAAAAAGGTTGTTAT
AAACATGCCACTGTGAATTGACATCCTATAGAAGTTACAACTAAAGAAGTACATTTTTTGACAA
AAAAAAAACTAACACCACAAAGAAGCATTATGCACGAAAACTTGAAATCCAGAAAGCAAAATGC
ACTGTACAAATAGAGAAAAATGACTACAAACAGCACTAGTTTTATACTACATCACCTAGTTTTA
TACTACATAGACTACCTTGGTGCTTGTCCACGTTTGTTGCAACTGGACGGCTGCTTACGCCTGC
ATCATGCTGCCACGGCGGGAGAACAATCAGCAAAACCGCTAAAACAATTGGGGAAGATACACTC
GTTTATTTGTTGCATCAAATCCATATTAGAAAGTATCACTTTCTGGAAACCTCCAACATATTTA
AAATGAAATACTGAGGGAAGTTATAACTCCAAAAACAAGCAGTACTTACAGAGCATCCTTGCTG
AACCTTAGCCTTCTGGGATTGCTTACACTTCAACAAAGTCCAGTCATACACATAATCAAATTGA
TAGCCTAGAGAAGATCAAATAATAAACAAGTTATCAAGCTTTTCATAATTAATAAGATATGATG
GGAGATTGCACACCAGAATTCCAAATGTTTACCTTCGCGCTCAAACAATTCTCGAAAGACATGC
CTCAAGAAACTATAATCGGGACGCTGATCAAATGTCAGAGAATGGCAGTAGTGGAAATAGGAAG
CAAATTCCACAGGATGGGATTTACATAGAGCCTATAATGACAAAAGTCATGAGTACTCTTCCTG
TCAACGATATCAAAGGAGTTAACATTCGTAAATGCAAAGCAAGTTACTCAAACAACCTCAATAG
GAGTCGAAAGCTTCTTCTCACTTATTTTGTCATACTTCTGTTTCTTTGTGGCTGCTTTCAAGCC
CTGCCAAGGAAGACTGGACAGAACAGATAGTTAGTTAGTTACACTTACACCAAGTCCATAAAAT
GTTTCATACACAACAAATTACGATCAAAATGTTTCATACACAAGAAATCACAATCAAAGATAGC
TGGCATATTGAGTTATTGACCACTGGTTTTCAGGACAGATTTGAGAAAAATGTACTAGTTGTTT
TGCTTCAGGCATAACCACATAATATATTGGGGGAAAGTGTTTTTGCCCTGTCCAAAATTTCAAT
TGTGATTTACTGAGCCATTTGCCATTTGCATGTCCATTATTTGGACGGAGATTAAACGATCTAA
AAAATAAAACACATAAAACCAGATGCAAAATGACCGAATTGCCCTTATCCAAGCTATCCAACCA
GGCCCATCCCAACCGTCTCGATAGCCCAAACTTAGGGAAGACGGCGCACGGGTGCAGACACGAG
CAGCACACAGGCAGGACCCGCGTGGGTCGGTCATTGCCAGTGCGGCGTGTAGGCACTAGCCAGT
ACTCTTATCTGTTTCGTTTCGCACAGGGCAGCCTCGGCGAGCTGATTTCATTTCGCTTTTGTGT
GAGTGTCTTCTAATCTGTTTCGGCAACGTTTTTTCCTGTCTGTGCCCAGACCTGTGTGCTCAAG
GTGAATATTCACTGTGATGGCTGCACAAAGAAGGTGAAGAAGGTCCTTCACAAGATTGATGATA
AGTTGCGGGAGCAAGAAAGATCTTTTTTAAAATGCAAATTGCTTGCTTTTTTCCATTCTTGTGT
GTGCGTCTTACTGCTACTGTGATGCCGCCAGGGTGAGAGGGTCTATTCAGTTCGGTTCAGCTGT
GCTATTTTGTTTTTCTCTGTAACATGGTTTTCATTAATGACTGCTACACATGCAGCATTATTCT
AGGACAATGGTGAAAGAAATAAACTATCGAGATCTTTAGCACAAAATAATACCTTCCCCTAAGG
AAATACAGAAGAACGTATCCGATCGATTCCAAATCATCTCTGCGGCTTTGCTCTGGCAACAAAA
CTTAGTGATAGTGAACCAAAGGAAAAATAAATGGCTATAATTTTGTCCGATAATCTATAGAACC
AGTGCTATTTTAGTGTTATAATAATATACATGTGCACAATACAAGCATTCAAAGTAATGACACA
AGAGATAAATGCAAAATAGAACGGCCATATTACTCACCAATCCCAAGATGAGTATTACGGCTAG
CATAGCGAGCTGTGCCAGTCAAGTTTTTATTTTCTCTGTAAAAACAATTATGTTAACTGGTCAA
AAAAATAAACAGGTATTACCACAATTGCAAAAATAAGAATAAAATGAAACAAAAACTGATAGTT
CCGGAAGCAATGGGTTTTAAAATCATTAGCTCACCTATAAGGTATATGGCGGTTGGTGGCTGAA
TCACGATATCTCTTTGCAAGCCCGAAGTCAATTACATAAAC
						
					

			
		

Sequences
Splice junction sequence	AGCAATGGGTTTTAAAATCATTAGCTCACCTATAAGGTATATGGCGGTTGGTGGCTGAATCACG ATATCTCTTTGCAAGCCCGAAGTCAATTACATAAACccaatctctcaggatgcagattattgga acggctgtttaattgcattctgattgccgggcgttgttctgcttcaagcagacctgaagcatta attgggcg
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	CCAATCTCTCAGGATGCAGATTATTGGAACGGCTGTTTAATTGCATTCTGATTGCCGGGCGTTG TTCTGCTTCAAGCAGACCTGAAGCATTAATTGGGCGTGCAACACCAACTGAAAAAGGTTGTTAT AAACATGCCACTGTGAATTGACATCCTATAGAAGTTACAACTAAAGAAGTACATTTTTTGACAA AAAAAAAACTAACACCACAAAGAAGCATTATGCACGAAAACTTGAAATCCAGAAAGCAAAATGC ACTGTACAAATAGAGAAAAATGACTACAAACAGCACTAGTTTTATACTACATCACCTAGTTTTA TACTACATAGACTACCTTGGTGCTTGTCCACGTTTGTTGCAACTGGACGGCTGCTTACGCCTGC ATCATGCTGCCACGGCGGGAGAACAATCAGCAAAACCGCTAAAACAATTGGGGAAGATACACTC GTTTATTTGTTGCATCAAATCCATATTAGAAAGTATCACTTTCTGGAAACCTCCAACATATTTA AAATGAAATACTGAGGGAAGTTATAACTCCAAAAACAAGCAGTACTTACAGAGCATCCTTGCTG AACCTTAGCCTTCTGGGATTGCTTACACTTCAACAAAGTCCAGTCATACACATAATCAAATTGA TAGCCTAGAGAAGATCAAATAATAAACAAGTTATCAAGCTTTTCATAATTAATAAGATATGATG GGAGATTGCACACCAGAATTCCAAATGTTTACCTTCGCGCTCAAACAATTCTCGAAAGACATGC CTCAAGAAACTATAATCGGGACGCTGATCAAATGTCAGAGAATGGCAGTAGTGGAAATAGGAAG CAAATTCCACAGGATGGGATTTACATAGAGCCTATAATGACAAAAGTCATGAGTACTCTTCCTG TCAACGATATCAAAGGAGTTAACATTCGTAAATGCAAAGCAAGTTACTCAAACAACCTCAATAG GAGTCGAAAGCTTCTTCTCACTTATTTTGTCATACTTCTGTTTCTTTGTGGCTGCTTTCAAGCC CTGCCAAGGAAGACTGGACAGAACAGATAGTTAGTTAGTTACACTTACACCAAGTCCATAAAAT GTTTCATACACAACAAATTACGATCAAAATGTTTCATACACAAGAAATCACAATCAAAGATAGC TGGCATATTGAGTTATTGACCACTGGTTTTCAGGACAGATTTGAGAAAAATGTACTAGTTGTTT TGCTTCAGGCATAACCACATAATATATTGGGGGAAAGTGTTTTTGCCCTGTCCAAAATTTCAAT TGTGATTTACTGAGCCATTTGCCATTTGCATGTCCATTATTTGGACGGAGATTAAACGATCTAA AAAATAAAACACATAAAACCAGATGCAAAATGACCGAATTGCCCTTATCCAAGCTATCCAACCA GGCCCATCCCAACCGTCTCGATAGCCCAAACTTAGGGAAGACGGCGCACGGGTGCAGACACGAG CAGCACACAGGCAGGACCCGCGTGGGTCGGTCATTGCCAGTGCGGCGTGTAGGCACTAGCCAGT ACTCTTATCTGTTTCGTTTCGCACAGGGCAGCCTCGGCGAGCTGATTTCATTTCGCTTTTGTGT GAGTGTCTTCTAATCTGTTTCGGCAACGTTTTTTCCTGTCTGTGCCCAGACCTGTGTGCTCAAG GTGAATATTCACTGTGATGGCTGCACAAAGAAGGTGAAGAAGGTCCTTCACAAGATTGATGATA AGTTGCGGGAGCAAGAAAGATCTTTTTTAAAATGCAAATTGCTTGCTTTTTTCCATTCTTGTGT GTGCGTCTTACTGCTACTGTGATGCCGCCAGGGTGAGAGGGTCTATTCAGTTCGGTTCAGCTGT GCTATTTTGTTTTTCTCTGTAACATGGTTTTCATTAATGACTGCTACACATGCAGCATTATTCT AGGACAATGGTGAAAGAAATAAACTATCGAGATCTTTAGCACAAAATAATACCTTCCCCTAAGG AAATACAGAAGAACGTATCCGATCGATTCCAAATCATCTCTGCGGCTTTGCTCTGGCAACAAAA CTTAGTGATAGTGAACCAAAGGAAAAATAAATGGCTATAATTTTGTCCGATAATCTATAGAACC AGTGCTATTTTAGTGTTATAATAATATACATGTGCACAATACAAGCATTCAAAGTAATGACACA AGAGATAAATGCAAAATAGAACGGCCATATTACTCACCAATCCCAAGATGAGTATTACGGCTAG CATAGCGAGCTGTGCCAGTCAAGTTTTTATTTTCTCTGTAAAAACAATTATGTTAACTGGTCAA AAAAATAAACAGGTATTACCACAATTGCAAAAATAAGAATAAAATGAAACAAAAACTGATAGTT CCGGAAGCAATGGGTTTTAAAATCATTAGCTCACCTATAAGGTATATGGCGGTTGGTGGCTGAA TCACGATATCTCTTTGCAAGCCCGAAGTCAATTACATAAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.006975334

Conservation Information
Conserved circRNAs	NA
PMCS	0.006975334

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

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d053316_circ_g.1

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