Plant Circular RNA Database

Detail information of Zm00001d047074_circ_g.5

			
						 General Information
					
						CircRNA Name
						Zm00001d047074_circ_g.5
					
						ID in PlantcircBase
						zma_circ_010019
					
						Alias
						Zm09circ00057, zma_circ_0003012
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 117447976-117448630  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d047074						
					
						Parent gene annotation
						
							pleckstrin homology (PH) domain-containing protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d047074_circ_g.4 Zm00001d047074_circ_g.6 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, root
					
						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-AG							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
						Zm00001d047074_T002:2
Zm00001d047074_T014:2
Zm00001d047074_T020:2
Zm00001d047074_T022:2
Zm00001d047074_T025:2
Zm00001d047074_T023:2
Zm00001d047074_T018:2
Zm00001d047074_T017:2
Zm00001d047074_T016:2
Zm00001d047074_T012:2
Zm00001d047074_T010:2

General Information
CircRNA Name	Zm00001d047074_circ_g.5
ID in PlantcircBase	zma_circ_010019
Alias	Zm09circ00057, zma_circ_0003012
Organism	Zea mays
Position	chr9: 117447976-117448630 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d047074
Parent gene annotation	pleckstrin homology (PH) domain-containing protein
Parent gene strand	+
Alternative splicing	Zm00001d047074_circ_g.4 Zm00001d047074_circ_g.6
Support reads	NA
Tissues	leaf, endosperm, root
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-AG 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	Zm00001d047074_T002:2 Zm00001d047074_T014:2 Zm00001d047074_T020:2 Zm00001d047074_T022:2 Zm00001d047074_T025:2 Zm00001d047074_T023:2 Zm00001d047074_T018:2 Zm00001d047074_T017:2 Zm00001d047074_T016:2 Zm00001d047074_T012:2 Zm00001d047074_T010:2

			
						 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  
						
							TTTAAGTAACAAATCTGTTCCGCAGAGGATAAGAGATCCTCGTGCTATACATCGTGATGGTATA
GTAAGAGACTATGACAAATTTGAAGCTGCTGGCCAGgtgcatctgaggaaggtcatgcacagaa
gccggtttatgcggaagagctccatcatccctgctatcacgaaccgaatcaagagagatctgat
tcacaatc

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 582
Transcript exons: 117447976-117448197,117448271-117448630
GTGCATCTGAGGAAGGTCATGCACAGAAGCCGGTTTATGCGGAAGAGCTCCATCATCCCTGCTA
TCACGAACCGAATCAAGAGAGATCTGATTCACAATCCGCTACATCTAATCTTTTCTGTGGATTT
TCTTGGAGTAACAAAATCAACTTTATCATCACTTAGTAAAGGATTTGCAGAGCTCTCTACTGAT
GGGCAATTTCTTCAGCTGAGATCAAAGCAGGTTTGGTCAAGGAGAATCACTGGTGTTGGTGATG
GGCTAGTTCAAGGGACTGAAGCATTTGCTCAGGGTTTGGCTTTCGGGGTTTCTGGTGTTTTAAG
AAAGCCAGTTGAGAGTGCCAGACAGTATGGTGTTATAGGTATTGCACCTGGCATTGGCCGTGCT
TTTGTGGGTTTCATTGTCCAACCTTTAAGTGGGGCTCTGGATTTTTTTTCACTGACGGTTGATG
GAATCAGTGCTAGTTTTATGAGATGTGTTAACATTTTAAGTAACAAATCTGTTCCGCAGAGGAT
AAGAGATCCTCGTGCTATACATCGTGATGGTATAGTAAGAGACTATGACAAATTTGAAGCTGCT
GGCCAG
						
						Genomic sequence
						
							GTGCATCTGAGGAAGGTCATGCACAGAAGCCGGTTTATGCGGAAGAGCTCCATCATCCCTGCTA
TCACGAACCGAATCAAGAGAGATCTGATTCACAATCCGCTACATCTAATCTTTTCTGTGGATTT
TCTTGGAGTAACAAAATCAACTTTATCATCACTTAGTAAAGGATTTGCAGAGCTCTCTACTGAT
GGGCAATTTCTTCAGCTGAGATCAAAGCAGGTGCAATAGCTTGTGGTTTTTTTTGTCCTTGTTT
ATGTCACTTTTTTAAACATTTACGCTTCATGTGATTCAGGTTTGGTCAAGGAGAATCACTGGTG
TTGGTGATGGGCTAGTTCAAGGGACTGAAGCATTTGCTCAGGGTTTGGCTTTCGGGGTTTCTGG
TGTTTTAAGAAAGCCAGTTGAGAGTGCCAGACAGTATGGTGTTATAGGTATTGCACCTGGCATT
GGCCGTGCTTTTGTGGGTTTCATTGTCCAACCTTTAAGTGGGGCTCTGGATTTTTTTTCACTGA
CGGTTGATGGAATCAGTGCTAGTTTTATGAGATGTGTTAACATTTTAAGTAACAAATCTGTTCC
GCAGAGGATAAGAGATCCTCGTGCTATACATCGTGATGGTATAGTAAGAGACTATGACAAATTT
GAAGCTGCTGGCCAG

Sequences
Splice junction sequence	TTTAAGTAACAAATCTGTTCCGCAGAGGATAAGAGATCCTCGTGCTATACATCGTGATGGTATA GTAAGAGACTATGACAAATTTGAAGCTGCTGGCCAGgtgcatctgaggaaggtcatgcacagaa gccggtttatgcggaagagctccatcatccctgctatcacgaaccgaatcaagagagatctgat tcacaatc
Assembled circRNA sequence	Yes 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	Transcript length: 582 Transcript exons: 117447976-117448197,117448271-117448630 GTGCATCTGAGGAAGGTCATGCACAGAAGCCGGTTTATGCGGAAGAGCTCCATCATCCCTGCTA TCACGAACCGAATCAAGAGAGATCTGATTCACAATCCGCTACATCTAATCTTTTCTGTGGATTT TCTTGGAGTAACAAAATCAACTTTATCATCACTTAGTAAAGGATTTGCAGAGCTCTCTACTGAT GGGCAATTTCTTCAGCTGAGATCAAAGCAGGTTTGGTCAAGGAGAATCACTGGTGTTGGTGATG GGCTAGTTCAAGGGACTGAAGCATTTGCTCAGGGTTTGGCTTTCGGGGTTTCTGGTGTTTTAAG AAAGCCAGTTGAGAGTGCCAGACAGTATGGTGTTATAGGTATTGCACCTGGCATTGGCCGTGCT TTTGTGGGTTTCATTGTCCAACCTTTAAGTGGGGCTCTGGATTTTTTTTCACTGACGGTTGATG GAATCAGTGCTAGTTTTATGAGATGTGTTAACATTTTAAGTAACAAATCTGTTCCGCAGAGGAT AAGAGATCCTCGTGCTATACATCGTGATGGTATAGTAAGAGACTATGACAAATTTGAAGCTGCT GGCCAG
Genomic sequence	GTGCATCTGAGGAAGGTCATGCACAGAAGCCGGTTTATGCGGAAGAGCTCCATCATCCCTGCTA TCACGAACCGAATCAAGAGAGATCTGATTCACAATCCGCTACATCTAATCTTTTCTGTGGATTT TCTTGGAGTAACAAAATCAACTTTATCATCACTTAGTAAAGGATTTGCAGAGCTCTCTACTGAT GGGCAATTTCTTCAGCTGAGATCAAAGCAGGTGCAATAGCTTGTGGTTTTTTTTGTCCTTGTTT ATGTCACTTTTTTAAACATTTACGCTTCATGTGATTCAGGTTTGGTCAAGGAGAATCACTGGTG TTGGTGATGGGCTAGTTCAAGGGACTGAAGCATTTGCTCAGGGTTTGGCTTTCGGGGTTTCTGG TGTTTTAAGAAAGCCAGTTGAGAGTGCCAGACAGTATGGTGTTATAGGTATTGCACCTGGCATT GGCCGTGCTTTTGTGGGTTTCATTGTCCAACCTTTAAGTGGGGCTCTGGATTTTTTTTCACTGA CGGTTGATGGAATCAGTGCTAGTTTTATGAGATGTGTTAACATTTTAAGTAACAAATCTGTTCC GCAGAGGATAAGAGATCCTCGTGCTATACATCGTGATGGTATAGTAAGAGACTATGACAAATTT GAAGCTGCTGGCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.3713053

Conservation Information
Conserved circRNAs	NA
PMCS	0.3713053

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							117447995-117448627(+)
117447983-117448534(-)
117448033-117448605(-)
						
						Potential amino acid sequence
						
							MHRSRFMRKSSIIPAITNRIKRDLIHNPLHLIFSVDFLGVTKSTLSSLSKGFAELSTDGQFLQL
RSKQVWSRRITGVGDGLVQGTEAFAQGLAFGVSGVLRKPVESARQYGVIGIAPGIGRAFVGFIV
QPLSGALDFFSLTVDGISASFMRCVNILSNKSVPQRIRDPRAIHRDGIVRDYDKFEAAGQVHLR
KVMHRSRFMRKSSIIPAITNRIKRDLIHNPLHLIFSVDFLGVTKSTLSSLSKGFAELSTDGQFL
QLRSKQVWSRRITGVGDGLVQGTEAFAQGLAFGVSGVLRKPVESARQYGVIGIAPGIGRAFVGF
IVQPLSGALDFFSLTVDGISASFMRCVNILSNKSVPQRIRDPRAIHRDGIVRDYDKFEAAGQVH
LRKVMHRSRFMRKSSIIPAITNRIKRDLIHNPLHLIFSVDFLGVTKSTLSSLSKGFAELSTDGQ
FLQLRSKQVWSRRITGVGDGLVQGTEAFAQGLAFGVSGVLRKPVESARQYGVIGIAPGIGRAFV
GFIVQPLSGALDFFSLTVDGISASFMRCVNILSNKSVPQRIRDPRAIHRDGIVRDYDKFEAAGQ
VHLRKVMHRSRFMRKSSIIPAITNRIKRDLIHNPLHLIFSVDFLGVTKSTLSSLSKGFAELSTD
GQFLQLRSKQVWSRRITGVGDGLVQGTEAFAQGLAFGVSGVLRKPVESARQYGVIGIAPGIGRA
FVGFIVQPLSGALDFFSLTVDGISASFMRCVNILSNKSVPQRIRDPRAIHRDGIVRDYDKFEAA
GQ(+)
MHLASSFKFVIVSYYTITMYSTRISYPLRNRFVT*(-)
MMELFRINRLLCMTFLRCTWPAASNLS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	117447995-117448627(+) 117447983-117448534(-) 117448033-117448605(-)
Potential amino acid sequence	MHRSRFMRKSSIIPAITNRIKRDLIHNPLHLIFSVDFLGVTKSTLSSLSKGFAELSTDGQFLQL RSKQVWSRRITGVGDGLVQGTEAFAQGLAFGVSGVLRKPVESARQYGVIGIAPGIGRAFVGFIV QPLSGALDFFSLTVDGISASFMRCVNILSNKSVPQRIRDPRAIHRDGIVRDYDKFEAAGQVHLR KVMHRSRFMRKSSIIPAITNRIKRDLIHNPLHLIFSVDFLGVTKSTLSSLSKGFAELSTDGQFL QLRSKQVWSRRITGVGDGLVQGTEAFAQGLAFGVSGVLRKPVESARQYGVIGIAPGIGRAFVGF IVQPLSGALDFFSLTVDGISASFMRCVNILSNKSVPQRIRDPRAIHRDGIVRDYDKFEAAGQVH LRKVMHRSRFMRKSSIIPAITNRIKRDLIHNPLHLIFSVDFLGVTKSTLSSLSKGFAELSTDGQ FLQLRSKQVWSRRITGVGDGLVQGTEAFAQGLAFGVSGVLRKPVESARQYGVIGIAPGIGRAFV GFIVQPLSGALDFFSLTVDGISASFMRCVNILSNKSVPQRIRDPRAIHRDGIVRDYDKFEAAGQ VHLRKVMHRSRFMRKSSIIPAITNRIKRDLIHNPLHLIFSVDFLGVTKSTLSSLSKGFAELSTD GQFLQLRSKQVWSRRITGVGDGLVQGTEAFAQGLAFGVSGVLRKPVESARQYGVIGIAPGIGRA FVGFIVQPLSGALDFFSLTVDGISASFMRCVNILSNKSVPQRIRDPRAIHRDGIVRDYDKFEAA GQ(+) MHLASSFKFVIVSYYTITMYSTRISYPLRNRFVT(-) MMELFRINRLLCMTFLRCTWPAASNLS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b

circRNA

Detail information of Zm00001d047074_circ_g.5

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