Plant Circular RNA Database

Detail information of Zm00001d019501_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d019501_circ_g.1
					
						ID in PlantcircBase
						zma_circ_009258
					
						Alias
						Zm07circ00027, zma_circ_0002354, ZmciR309
					
						Organism
						
							Zea mays						
					
						Position
						
							chr7: 37901734-37902920  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d019501						
					
						Parent gene annotation
						
							Tetratricopeptide repeat (TPR)-like superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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
						Zm00001d019501_T002:4
Zm00001d019501_T005:4
Zm00001d019501_T004:4
Zm00001d019501_T003:4

General Information
CircRNA Name	Zm00001d019501_circ_g.1
ID in PlantcircBase	zma_circ_009258
Alias	Zm07circ00027, zma_circ_0002354, ZmciR309
Organism	Zea mays
Position	chr7: 37901734-37902920 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d019501
Parent gene annotation	Tetratricopeptide repeat (TPR)-like superfamily protein
Parent gene strand	+
Alternative splicing	NA
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	Zm00001d019501_T002:4 Zm00001d019501_T005:4 Zm00001d019501_T004:4 Zm00001d019501_T003:4

			
						 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  
						
							CGTCTTATTTAATTTGCTTGCTTGCAGATGCGTGATGGTGCGTTGAAGGATGCCGCTGACATTG
CTACACTAAAACCCTGCACTCTCACATTGGTCGAAGctgcagctgggctgctagcttgagctga
gcttgccgttgggcgcgcgcgtgcatggcgcccaagagcaggcgtgggaaggccaagggcgaga
agaagaag

									
								

					

						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: 341
Transcript exons: 37901734-37901846,37901964-37902025,37902187-37902279,37
902848-37902920
CTGCAGCTGGGCTGCTAGCTTGAGCTGAGCTTGCCGTTGGGCGCGCGCGTGCATGGCGCCCAAG
AGCAGGCGTGGGAAGGCCAAGGGCGAGAAGAAGAAGAAAGATGAGAAAGTTCTCCCTGTGGCCA
TTGACATCACTGTCAACCTCCCGGACCAGTCTCATGTCATTCTGAAGGGTATTTCAACGGACAG
GATCATCGATGTGAGGCGGCTGCTCTGCGTCAACACCGCCACGTGTGCCATCACAAATTATTCT
CTCACACATGAGATGCGTGATGGTGCGTTGAAGGATGCCGCTGACATTGCTACACTAAAACCCT
GCACTCTCACATTGGTCGAAG
						
					

						Genomic sequence
						
							CTGCAGCTGGGCTGCTAGCTTGAGCTGAGCTTGCCGTTGGGCGCGCGCGTGCATGGCGCCCAAG
AGCAGGCGTGGGAAGGCCAAGGGCGAGAAGAAGAAGAAAGATGAGAAAGGTGAGTGCATGCCTT
TGTGATCTTCATCACTTGCTTGCTTTAGTTTCCTCTCGACCATTTGCATTGTTTAGTTTCCAGC
TTACCAATCTGATTCCGTCTTGTACGTGGTTATTGTAGTTCTCCCTGTGGCCATTGACATCACT
GTCAACCTCCCGGACCAGTCTCATGTCATTCTGAAGGTATGGTTTTCTGAGTCCTTGCCACACC
GTTCTAGCTGTGCTCAACCTCTCGTTTCGGTTCTCTCATCTGTCCCATGAACTGAAACGCATAG
CGAGAATAGAGTTATGTTCTCTATTGCAAGTCATAGGTTTGCTCAATATTTGCGTGCTTCTTTG
TCCAGGGTATTTCAACGGACAGGATCATCGATGTGAGGCGGCTGCTCTGCGTCAACACCGCCAC
GTGTGCCATCACAAATTATTCTCTCACACATGAGGTACTACTATATGCCAATTAGTCATGGGCG
CGGCAGACAGCAGCCTAACATGAAATAAATGTCTGTTTTTTTTTCAACTTGTGTTACTGTGCTA
AATTAAGGGATCTCTTCATTTTTCAAGGAATTGGAATTTACTTAATAGAGTAAGTTATTTGATT
TAGAATTTAACATTTCATCACTTTCCAAAGATTTGATTTAAGCCTATCCTAAATTCGGGGGTGA
GAATTAATTTCATGTATCACTAATAGTTATGTTTCCTAATCTATAACTTAGAACATGTTTTTCG
TATCGCTCTCCTATAATAAAAATATAGTACATAAATATCTCTTATATATGGCCAACAATAATAT
ATAAATATATTCGGTATAAAATTATATTAGCTTAATTAATCTATGTCTAAATTATAATTACTAA
AATAGAATTCAATTCTAAGGATCAAAACGGGTCTTAAGGGTAAAATGGTGTGTGAGTCACGTGT
ACTCTTCGCTTTCAGTCATTTTGTATATTTCTGAAATTTCTAAAATTGCGTGCAGTAATTATCC
GTCTTATTTAATTTGCTTGCTTGCAGATGCGTGATGGTGCGTTGAAGGATGCCGCTGACATTGC
TACACTAAAACCCTGCACTCTCACATTGGTCGAAG
						
					

			
		

Sequences
Splice junction sequence	CGTCTTATTTAATTTGCTTGCTTGCAGATGCGTGATGGTGCGTTGAAGGATGCCGCTGACATTG CTACACTAAAACCCTGCACTCTCACATTGGTCGAAGctgcagctgggctgctagcttgagctga gcttgccgttgggcgcgcgcgtgcatggcgcccaagagcaggcgtgggaaggccaagggcgaga agaagaag
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: 341 Transcript exons: 37901734-37901846,37901964-37902025,37902187-37902279,37 902848-37902920 CTGCAGCTGGGCTGCTAGCTTGAGCTGAGCTTGCCGTTGGGCGCGCGCGTGCATGGCGCCCAAG AGCAGGCGTGGGAAGGCCAAGGGCGAGAAGAAGAAGAAAGATGAGAAAGTTCTCCCTGTGGCCA TTGACATCACTGTCAACCTCCCGGACCAGTCTCATGTCATTCTGAAGGGTATTTCAACGGACAG GATCATCGATGTGAGGCGGCTGCTCTGCGTCAACACCGCCACGTGTGCCATCACAAATTATTCT CTCACACATGAGATGCGTGATGGTGCGTTGAAGGATGCCGCTGACATTGCTACACTAAAACCCT GCACTCTCACATTGGTCGAAG
Genomic sequence	CTGCAGCTGGGCTGCTAGCTTGAGCTGAGCTTGCCGTTGGGCGCGCGCGTGCATGGCGCCCAAG AGCAGGCGTGGGAAGGCCAAGGGCGAGAAGAAGAAGAAAGATGAGAAAGGTGAGTGCATGCCTT TGTGATCTTCATCACTTGCTTGCTTTAGTTTCCTCTCGACCATTTGCATTGTTTAGTTTCCAGC TTACCAATCTGATTCCGTCTTGTACGTGGTTATTGTAGTTCTCCCTGTGGCCATTGACATCACT GTCAACCTCCCGGACCAGTCTCATGTCATTCTGAAGGTATGGTTTTCTGAGTCCTTGCCACACC GTTCTAGCTGTGCTCAACCTCTCGTTTCGGTTCTCTCATCTGTCCCATGAACTGAAACGCATAG CGAGAATAGAGTTATGTTCTCTATTGCAAGTCATAGGTTTGCTCAATATTTGCGTGCTTCTTTG TCCAGGGTATTTCAACGGACAGGATCATCGATGTGAGGCGGCTGCTCTGCGTCAACACCGCCAC GTGTGCCATCACAAATTATTCTCTCACACATGAGGTACTACTATATGCCAATTAGTCATGGGCG CGGCAGACAGCAGCCTAACATGAAATAAATGTCTGTTTTTTTTTCAACTTGTGTTACTGTGCTA AATTAAGGGATCTCTTCATTTTTCAAGGAATTGGAATTTACTTAATAGAGTAAGTTATTTGATT TAGAATTTAACATTTCATCACTTTCCAAAGATTTGATTTAAGCCTATCCTAAATTCGGGGGTGA GAATTAATTTCATGTATCACTAATAGTTATGTTTCCTAATCTATAACTTAGAACATGTTTTTCG TATCGCTCTCCTATAATAAAAATATAGTACATAAATATCTCTTATATATGGCCAACAATAATAT ATAAATATATTCGGTATAAAATTATATTAGCTTAATTAATCTATGTCTAAATTATAATTACTAA AATAGAATTCAATTCTAAGGATCAAAACGGGTCTTAAGGGTAAAATGGTGTGTGAGTCACGTGT ACTCTTCGCTTTCAGTCATTTTGTATATTTCTGAAATTTCTAAAATTGCGTGCAGTAATTATCC GTCTTATTTAATTTGCTTGCTTGCAGATGCGTGATGGTGCGTTGAAGGATGCCGCTGACATTGC TACACTAAAACCCTGCACTCTCACATTGGTCGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.157533953

Conservation Information
Conserved circRNAs	NA
PMCS	0.157533953

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							37901787-37901753(+)
37902015-37902263(-)
37901987-37902908(-)
						
						Potential amino acid sequence
						
							MAPKSRRGKAKGEKKKKDEKVLPVAIDITVNLPDQSHVILKGISTDRIIDVRRLLCVNTATCAI
TNYSLTHEMRDGALKDAADIATLKPCTLTLVEAAAGLLA*(+)
MRLVREVDSDVNGHRENFLIFLLLLALGLPTPALGRHARARPTASSAQASSPAAASTNVRVQGF
SVAMSAASFNAPSRISCVRE*(-)
MSMATGRTFSSFFFFSPLAFPRLLLGAMHARAQRQAQLKLAAQLQLRPM*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	37901787-37901753(+) 37902015-37902263(-) 37901987-37902908(-)
Potential amino acid sequence	MAPKSRRGKAKGEKKKKDEKVLPVAIDITVNLPDQSHVILKGISTDRIIDVRRLLCVNTATCAI TNYSLTHEMRDGALKDAADIATLKPCTLTLVEAAAGLLA(+) MRLVREVDSDVNGHRENFLIFLLLLALGLPTPALGRHARARPTASSAQASSPAAASTNVRVQGF SVAMSAASFNAPSRISCVRE(-) MSMATGRTFSSFFFFSPLAFPRLLLGAMHARAQRQAQLKLAAQLQLRPM*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d019501_circ_g.1

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