Plant Circular RNA Database

Detail information of Zm00001d012146_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d012146_circ_g.1
					
						ID in PlantcircBase
						zma_circ_002860
					
						Alias
						circ2795
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 168884647-168886796  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d012146						
					
						Parent gene annotation
						
							U-box domain-containing protein 7
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						3
					
						Tissues
						seedling leaves
					
						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-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
						Zm00001d012146_T008:4
Zm00001d012146_T002:4
Zm00001d012146_T003:4
Zm00001d012146_T012:4
Zm00001d012146_T001:4
Zm00001d012146_T011:4
Zm00001d012146_T004:3

General Information
CircRNA Name	Zm00001d012146_circ_g.1
ID in PlantcircBase	zma_circ_002860
Alias	circ2795
Organism	Zea mays
Position	chr8: 168884647-168886796 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d012146
Parent gene annotation	U-box domain-containing protein 7
Parent gene strand	+
Alternative splicing	NA
Support reads	3
Tissues	seedling leaves
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-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	Zm00001d012146_T008:4 Zm00001d012146_T002:4 Zm00001d012146_T003:4 Zm00001d012146_T012:4 Zm00001d012146_T001:4 Zm00001d012146_T011:4 Zm00001d012146_T004:3

			
						 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  
						
							CACTGGTTGAGTTCTTGAGGAATGCTGTGGATGATGGAAATGAGAAGGCACAGGAAGTCGGTGC
AATGGCTCTTTTCAATCTCGCAGTCAACAATAACAGgtcagatgttggagctcaggtaatagcc
acccatggaagcaatggaggccgaagaaggtccttttctggctaatgatgccaaggtatcatct
ttacagtg

									
								

					

						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
						
							GTCAGATGTTGGAGCTCAGGTAATAGCCACCCATGGAAGCAATGGAGGCCGAAGAAGGTCCTTT
TCTGGCTAATGATGCCAAGGTATCATCTTTACAGTGAATTTGTCTGGTAGTCCTGTTAATCTGT
TGTTCTCCTACCTTTTGCAAGTACATCTTAAAAGCCTGTTCATGTTTAGTTGATCAATGAGAGT
TACCTTTTCTTTTCCATATTGTTTAGGTAGTATTTGTTTCAATGGTTAGTACTATCACAATGCT
TTGGTTTCTTTAAGGTTCCTTTTTCTTTAAATACTACTTTGTACTGTGATAAGTTACTGGAACC
TTATAGCTTTCCGTTTGGTGGTTTTGCTTAATTTCGCAGCGAATCTGAAGAAATTTTGGTTTTT
TGCAGTTGCACGCAGGAATTTGTAGAGCATTTCATCCTTCTGTATCTAAACTTTCCACCATTTT
CCCCTTTATCGAAGCATCAAGACCCAGAAGCAAGTCTGGTATACAGGCATTGTGTTCACTACAT
GTGGCTCTTGATAAAGCCAAGGGGCTTCTTCAACATTGTGCAGACTGCAGCAGACTCTACTTGG
TAACTTCTTATTCCTCTTGCCCTACTACTACTGCTGTGACACACTTATTTCATCTTGGGCATTT
ATTTTGGATTTTTTTGCAATTGGAACAATTTTTTAATAGATATTATATTTCACTTAGGCAATCA
CTTCGGAAACTGTGCTTTTAAAGTTTGAGAAGTCTAGAAGCCAGCTTCAGGAGAGTCTAAGGCG
CATTGAAAGCATAGTAACTGAAGATATCGGCTGTAAGGTATATTGTGCACGAAGCTCATCTAGT
CAATATTTTTGTTTCACCAATCTTTGTCTTTTTCTTTTATGACTTTATAGTTTTGCGATTATTA
CAGTGTGTAATATGAACTGACATCCTGAACGTGTCAGATTGTGGAGATTGTTGGTGAACTGGAG
CAAATTGTTTTTACATTGGATAGATCAGAGAAGGAAGCTGGTGATGAGCTGATCAATTTGCTAC
AGAGAAACAATAAAACAAATGGTTCTAGTGATAATGGGGAACTTGAGGTCTTCCATATTTCTGC
TCTTAAATTGGGAATTACATCTTCTAGGGCAGCACTCACCGAAAGAAGAGCCCTTAAGAAGCTA
ATTGAGAAGGCTCGTTCTGATGAAGACAAGCGTAAGGAGCTTGTTGTGTCATACTTGTACAATC
TCATGAGGAAGTACTCAAAGTTCTTCAGAAGTGAGACTGGTGATGATACAGATTCTCAGGGATC
GTCTCCATGCTCGCCAACAGTATTAGGCGTGGATGATATGTGTAGTCCATACATCAATGGCCGT
GCATTTGGTAGACAGATTTTGAGCAGTCAGTCGTTCAATTCAAGGTTTGGATCTTTCAATTCTA
GGCTCGGATCATTCAATTGCAGACGTGCTGCTGGTGGTGGTCCAAGGTCTGGGAATATCTCAGT
CCCTCCTGAAGAACTTAGGTGCCCTATTTCCTTACAACTCATGTATGATCCAGTCATCATTTCA
TCCGGGCAGACTTATGAGCGTATTTGCATCGAGAAATGGTTCAATGATGGTCACAGCACATGTC
CTAAAACTCAGCAGCAGCTTGCCCACCTGTCATTGACTCCAAACTACTGTGTTAAGGCCCTGAT
TGCCAGCTGGTGCGAGTCGAACGATTTTCCACTTCCTGATGGTCCACCAGGAACTTTTGATGTA
AACTGGAGACTTGCTTCCTCTGACACTGAGGCTACAGGTTGTGTGTCTGTTGAAAGCTTTGATT
GTACCAGTGCAAAGAGCGTCAAGATTGTCCTGATGGAGGATGCTAGAAAAGAGGAGCCAGCAAA
CAGCGTATCTGGAACGCTGGATGACGGTTCTTGTAACGATTTCGATCTGAACGAAGGCTATGGG
AGCCTGCTGCTCTTGCTTCATGAAAGAAGTAACATGGACAAGCAGTGCAGGCTGGTGGAGCAGA
TAAGGTATCTTCTGAAAGACGACGAGGAAGCAAGGATCCAGCTAGGCTCAAATGGCTTTGCCGA
GGCACTGGTTGAGTTCTTGAGGAATGCTGTGGATGATGGAAATGAGAAGGCACAGGAAGTCGGT
GCAATGGCTCTTTTCAATCTCGCAGTCAACAATAACAG
						
					

			
		

Sequences
Splice junction sequence	CACTGGTTGAGTTCTTGAGGAATGCTGTGGATGATGGAAATGAGAAGGCACAGGAAGTCGGTGC AATGGCTCTTTTCAATCTCGCAGTCAACAATAACAGgtcagatgttggagctcaggtaatagcc acccatggaagcaatggaggccgaagaaggtccttttctggctaatgatgccaaggtatcatct ttacagtg
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	GTCAGATGTTGGAGCTCAGGTAATAGCCACCCATGGAAGCAATGGAGGCCGAAGAAGGTCCTTT TCTGGCTAATGATGCCAAGGTATCATCTTTACAGTGAATTTGTCTGGTAGTCCTGTTAATCTGT TGTTCTCCTACCTTTTGCAAGTACATCTTAAAAGCCTGTTCATGTTTAGTTGATCAATGAGAGT TACCTTTTCTTTTCCATATTGTTTAGGTAGTATTTGTTTCAATGGTTAGTACTATCACAATGCT TTGGTTTCTTTAAGGTTCCTTTTTCTTTAAATACTACTTTGTACTGTGATAAGTTACTGGAACC TTATAGCTTTCCGTTTGGTGGTTTTGCTTAATTTCGCAGCGAATCTGAAGAAATTTTGGTTTTT TGCAGTTGCACGCAGGAATTTGTAGAGCATTTCATCCTTCTGTATCTAAACTTTCCACCATTTT CCCCTTTATCGAAGCATCAAGACCCAGAAGCAAGTCTGGTATACAGGCATTGTGTTCACTACAT GTGGCTCTTGATAAAGCCAAGGGGCTTCTTCAACATTGTGCAGACTGCAGCAGACTCTACTTGG TAACTTCTTATTCCTCTTGCCCTACTACTACTGCTGTGACACACTTATTTCATCTTGGGCATTT ATTTTGGATTTTTTTGCAATTGGAACAATTTTTTAATAGATATTATATTTCACTTAGGCAATCA CTTCGGAAACTGTGCTTTTAAAGTTTGAGAAGTCTAGAAGCCAGCTTCAGGAGAGTCTAAGGCG CATTGAAAGCATAGTAACTGAAGATATCGGCTGTAAGGTATATTGTGCACGAAGCTCATCTAGT CAATATTTTTGTTTCACCAATCTTTGTCTTTTTCTTTTATGACTTTATAGTTTTGCGATTATTA CAGTGTGTAATATGAACTGACATCCTGAACGTGTCAGATTGTGGAGATTGTTGGTGAACTGGAG CAAATTGTTTTTACATTGGATAGATCAGAGAAGGAAGCTGGTGATGAGCTGATCAATTTGCTAC AGAGAAACAATAAAACAAATGGTTCTAGTGATAATGGGGAACTTGAGGTCTTCCATATTTCTGC TCTTAAATTGGGAATTACATCTTCTAGGGCAGCACTCACCGAAAGAAGAGCCCTTAAGAAGCTA ATTGAGAAGGCTCGTTCTGATGAAGACAAGCGTAAGGAGCTTGTTGTGTCATACTTGTACAATC TCATGAGGAAGTACTCAAAGTTCTTCAGAAGTGAGACTGGTGATGATACAGATTCTCAGGGATC GTCTCCATGCTCGCCAACAGTATTAGGCGTGGATGATATGTGTAGTCCATACATCAATGGCCGT GCATTTGGTAGACAGATTTTGAGCAGTCAGTCGTTCAATTCAAGGTTTGGATCTTTCAATTCTA GGCTCGGATCATTCAATTGCAGACGTGCTGCTGGTGGTGGTCCAAGGTCTGGGAATATCTCAGT CCCTCCTGAAGAACTTAGGTGCCCTATTTCCTTACAACTCATGTATGATCCAGTCATCATTTCA TCCGGGCAGACTTATGAGCGTATTTGCATCGAGAAATGGTTCAATGATGGTCACAGCACATGTC CTAAAACTCAGCAGCAGCTTGCCCACCTGTCATTGACTCCAAACTACTGTGTTAAGGCCCTGAT TGCCAGCTGGTGCGAGTCGAACGATTTTCCACTTCCTGATGGTCCACCAGGAACTTTTGATGTA AACTGGAGACTTGCTTCCTCTGACACTGAGGCTACAGGTTGTGTGTCTGTTGAAAGCTTTGATT GTACCAGTGCAAAGAGCGTCAAGATTGTCCTGATGGAGGATGCTAGAAAAGAGGAGCCAGCAAA CAGCGTATCTGGAACGCTGGATGACGGTTCTTGTAACGATTTCGATCTGAACGAAGGCTATGGG AGCCTGCTGCTCTTGCTTCATGAAAGAAGTAACATGGACAAGCAGTGCAGGCTGGTGGAGCAGA TAAGGTATCTTCTGAAAGACGACGAGGAAGCAAGGATCCAGCTAGGCTCAAATGGCTTTGCCGA GGCACTGGTTGAGTTCTTGAGGAATGCTGTGGATGATGGAAATGAGAAGGCACAGGAAGTCGGT GCAATGGCTCTTTTCAATCTCGCAGTCAACAATAACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.006627907

Conservation Information
Conserved circRNAs	NA
PMCS	0.006627907

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							168886719-168884666(+)
168884680-168884716(+)
168885067-168886786(-)
						
						Potential amino acid sequence
						
							MLWMMEMRRHRKSVQWLFSISQSTITGQMLELR*(+)
MEAMEAEEGPFLANDAKLHAGICRAFHPSVSKLSTIFPFIEASRPRSKSGIQALCSLHVALDKA
KGLLQHCADCSRLYLAITSETVLLKFEKSRSQLQESLRRIESIVTEDIGCKIVEIVGELEQIVF
TLDRSEKEAGDELINLLQRNNKTNGSSDNGELEVFHISALKLGITSSRAALTERRALKKLIEKA
RSDEDKRKELVVSYLYNLMRKYSKFFRSETGDDTDSQGSSPCSPTVLGVDDMCSPYINGRAFGR
QILSSQSFNSRFGSFNSRLGSFNCRRAAGGGPRSGNISVPPEELRCPISLQLMYDPVIISSGQT
YERICIEKWFNDGHSTCPKTQQQLAHLSLTPNYCVKALIASWCESNDFPLPDGPPGTFDVNWRL
ASSDTEATGCVSVESFDCTSAKSVKIVLMEDARKEEPANSVSGTLDDGSCNDFDLNEGYGSLLL
LLHERSNMDKQCRLVEQIRYLLKDDEEARIQLGSNGFAEALVEFLRNAVDDGNEKAQEVGAMAL
FNLAVNNNRSDVGAQVIATHGSNGGRRRSFSG*(+)
MKCSTNSCVQLGIISQKRTFFGLHCFHGWLLPELQHLTCYC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	168886719-168884666(+) 168884680-168884716(+) 168885067-168886786(-)
Potential amino acid sequence	MLWMMEMRRHRKSVQWLFSISQSTITGQMLELR(+) MEAMEAEEGPFLANDAKLHAGICRAFHPSVSKLSTIFPFIEASRPRSKSGIQALCSLHVALDKA KGLLQHCADCSRLYLAITSETVLLKFEKSRSQLQESLRRIESIVTEDIGCKIVEIVGELEQIVF TLDRSEKEAGDELINLLQRNNKTNGSSDNGELEVFHISALKLGITSSRAALTERRALKKLIEKA RSDEDKRKELVVSYLYNLMRKYSKFFRSETGDDTDSQGSSPCSPTVLGVDDMCSPYINGRAFGR QILSSQSFNSRFGSFNSRLGSFNCRRAAGGGPRSGNISVPPEELRCPISLQLMYDPVIISSGQT YERICIEKWFNDGHSTCPKTQQQLAHLSLTPNYCVKALIASWCESNDFPLPDGPPGTFDVNWRL ASSDTEATGCVSVESFDCTSAKSVKIVLMEDARKEEPANSVSGTLDDGSCNDFDLNEGYGSLLL LLHERSNMDKQCRLVEQIRYLLKDDEEARIQLGSNGFAEALVEFLRNAVDDGNEKAQEVGAMAL FNLAVNNNRSDVGAQVIATHGSNGGRRRSFSG(+) MKCSTNSCVQLGIISQKRTFFGLHCFHGWLLPELQHLTCYC*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d012146_circ_g.1

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