Plant Circular RNA Database

Detail information of Zm00001d015890_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d015890_circ_g.2
					
						ID in PlantcircBase
						zma_circ_008651
					
						Alias
						Zm05circ00078, zma_circ_0001975
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 129471368-129474086  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d015890						
					
						Parent gene annotation
						
							SNARE-interacting protein KEULE
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d015890_circ_g.1 Zm00001d015890_circ_g.3 Zm00001d015890_circ_g.4 Zm00001d015890_circ_g.5 Zm00001d015890_circ_g.6 Zm00001d015890_circ_g.7 Zm00001d015890_circ_g.8 Zm00001d015890_circ_g.9 						
					
						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  
						
							CT-AC							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
						Zm00001d015890_T001:5
Zm00001d015890_T002:5

General Information
CircRNA Name	Zm00001d015890_circ_g.2
ID in PlantcircBase	zma_circ_008651
Alias	Zm05circ00078, zma_circ_0001975
Organism	Zea mays
Position	chr5: 129471368-129474086 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d015890
Parent gene annotation	SNARE-interacting protein KEULE
Parent gene strand	-
Alternative splicing	Zm00001d015890_circ_g.1 Zm00001d015890_circ_g.3 Zm00001d015890_circ_g.4 Zm00001d015890_circ_g.5 Zm00001d015890_circ_g.6 Zm00001d015890_circ_g.7 Zm00001d015890_circ_g.8 Zm00001d015890_circ_g.9
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	CT-AC 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	Zm00001d015890_T001:5 Zm00001d015890_T002:5

			
						 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  
						
							GTTCTTTGGTTCCAGCATCGCCAAACACAAGATCTTGCTCTAGCTGTCCAACATCCCGAAGACA
TTGTTCCCTTATTATGTTATTGAGTTTTCCTGCAATcttgaatatccatcatcagagccacgag
gtcttgcccatgtgccacctgttcgtctggatcgcattgagtgagcggggcttgttcgggcaga
gctactgg

									
								

					

						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: 623
Transcript exons: 129471368-129471558,129472738-129472815,129472902-129473
050,129473803-129473881,129473961-129474086
CTTGAATATCCATCATCAGAGCCACGAGGTCTTGCCCATGTGCCACCTGTTCGTCTGGATCGCA
TTGAGTGAGCGGGGCTTGTTCGGGCAGAGCTACTGGTTGGCAGTCCATGAACAGTAGGACTAGG
GTCATTCATACAGTTATATTCATCTTTTGGCAGCTCACCTTTGCTAAGATTTTCAATCAATTGC
TCCAAAATAGGGTAAAATCGAGAGAGTGCCCATGTTGATTCTTCCCCTGTTCGCTCTTTTCGAT
TTGTGTGTTTCTTCTTGTGAACATCAAATTTCAGTGTAAAACCCCCTACTGAAGACTTTTTGGT
ATCAGGCCCACATAAGCAACGCATATTATTTACAGCAATCATGTCATCAGCAGATAATCCTGCC
AACTGTAAAACAGCATTCCTCAGGTTCAATGTGGCCTTGTCGCTTTCAAACTTCTCTGGGTTAA
GTGCTGCATAAATCATCAGCAAGCGTAATTTATTTTCACGACTTACAACCAATTGTGTTCTCAA
AAAGTTGATTAGTTCTTTGGTTCCAGCATCGCCAAACACAAGATCTTGCTCTAGCTGTCCAACA
TCCCGAAGACATTGTTCCCTTATTATGTTATTGAGTTTTCCTGCAAT
						
					

						Genomic sequence
						
							CTTGAATATCCATCATCAGAGCCACGAGGTCTTGCCCATGTGCCACCTGTTCGTCTGGATCGCA
TTGAGTGAGCGGGGCTTGTTCGGGCAGAGCTACTGGTTGGCAGTCCATGAACAGTAGGACTAGG
GTCATTCATACAGTTATATTCATCTTTTGGCAGCTCACCTTTGCTAAGATTTTCAATCAATTGC
TGCAGGACAGGTGAGAACCTCATTCACATCATTATACCAATACAAACAAAAACTGGTAAAACCA
AGGAATAAAGGAATTCTATGGTGGCATTCACATAATTCTAGAGAAAAATAAAATTCTTTCATTG
CTTTCTGACAGGGAAGATGGTTTGACTGTAGAAAGGGCAGCCCTGCAGACTAGAATAGTGCTCA
AATCCAATTAGTACCCCCATAGGCCTTGTACTCTCCATAGCTTAATGGGATGAGGTATGATCAT
TCTGATATCCCAGATAGTAAAGTTTCTTCGACACTAGATTTCAGCTTTTAGGCCTTTGGCTTCT
AACAAAGGGATTTTTATGTTCAGTACTCCCTCGGTCCAAAAATATAAGTTCTGGTGCTTAAATA
CTATTCCAGAATATAAGGACTTCTGGGGAGTCAACAATACCAGCCACAAAAAGTAAGGTAATTA
AGAGCGATCACCATTTGTGGTAAGGATTAGCCCAACAGTCTGCCGCAAACTAAGCCAATCAGGA
CTCAGCAATGGTCCCAGCTGTATGATGCACATTTTTCTTCTTAATTGTCCTAAAACTCCCATAA
ATCCTTATATTTTGGGACAAACGGATTATCGTTTTTTTGTCTTGATTAAATTATCCATTTCTAA
TGTTTTCTAGCAAATCGAAAATCAACCATACAAGGATATTTTATAAGAAATTTCACATTGACTT
CAGAATTTTTTTATACAAATCTTCCTAAATATTATATGGGTACTTTGACAAAATAAAAGGCAAA
AATCAATGTAGTACAAAAAGTGGGTAACTTATATTTCTAATGTATTCTATTGGATTGGATTTGT
TCGATAATTCGAAGAATTACAACAAAATCTTTAGAAATCACATTTTTAGTTAGGAACTTCTATG
GATTTTATTCTTCTTTTCTTTGGATCCAAAATAGAAGAATAAAAGAATAGGTATAAGAATTAAG
TCGATCCAAAAAGGAAAGGAGGTTCATGGCCAAGGGCAAAGATGTTAGAATCCGAGTTATTTTG
GAATGTATTAGTTGTGTACGAACAGTAAGTTAATGTGAGACAAGGAAAGCAGAATTTAAAACAA
AATCCAAGCGAAGAACACAAAATAGCAAGTAGATGATTCATTAGTAGCATCAAGCATTTAAAGT
AGTCAAGAGAAAACATTGATTTATACCTCCAAAATAGGGTAAAATCGAGAGAGTGCCCATGTTG
ATTCTTCCCCTGTTCGCTCTTTTCGATTTGTGTGTTTCTTCTGTTATCAACAGGAAGAAAAGAA
TACATCTTCAGATCCAGATTAAATATAGAAATAGAAGCCAAGAAATAACCTACAATGTTTACCT
TGTGAACATCAAATTTCAGTGTAAAACCCCCTACTGAAGACTTTTTGGTATCAGGCCCACATAA
GCAACGCATATTATTTACAGCAATCATGTCATCAGCAGATAATCCTGCCAACTGTAAAACAGCA
TTCCTCAGGTTCAATGTGGCTGTTGACAAGAGTTTGAATGAGATCCATTGAAGGAAATTGTTGA
AGTTAGGAGTTCCACATTATTAATATTTTGATGTAAAACTTAAGACTTCTTTCAGCCAGTCTGC
GTGTCCTTTTTGTGATCAACACATAAGAAACTAAGACTTCTGATCGCTTGGCTAAAAGGGGATT
AACACATCTTGTTGCTTGTCCTTTTTGTGATCAACACTCTGAAACTATCAGCCACATCTTAGTT
TCTTGTGTGTTTGCTAGGCAGGTCTGGCATATTGTGCTTCACACACTCATTGCCGTTGTCAGTC
CTAGTGCTGATAGTCTCTTCAATTCTTGGTAGAGCCGAGCAGCTCGAGTATTACACAAAGAAGA
AAGCAAAGGCTTCAATTCTCTAGTGATCCTAGTGGCTTGGGAACTATGGAAACATAGAAATGCC
AGTGATTTCCAGGGAGTGAGTCCAGATGTTTAAAATGTTGTGATGGCTGCAGTAGATGAAGGTC
AAATGTGGTGCCTGGAGGGTTACAGCTCTACAAGAAGTCACCCTAAAGGTCAGGCCACTTAGGG
TCGTTTTTTGGTTTGTTTTATGTAATTAAGTTGTAAGTCACCCCCTCAGTGTGTGTGTGGGGGG
GGGGGGGGGCTATCCCATCCTTTTTTTTTGTTAATGAAATGACACGCAGCTCTCTTGTGTGTTC
GAAGAAAAAAAAGTTAGTTTTAGAAGTCTTGATGTGGGTTAAAGAATTACCTGCATTAATTTTG
CACCCTTGTCGCTTTCAAACTTCTCTGGGTTAAGTGCTGCATAAATCATCAGCAAGCGTAATTT
ATTTTCACGACTTACAACCTGCATTGAGTCAGAAAATCTGAATACAAAATGTGGTGAAAGCCAA
TGTGTCAACCAATGTAGGTCAAACTAAAATTACCAATTGTGTTCTCAAAAAGTTGATTAGTTCT
TTGGTTCCAGCATCGCCAAACACAAGATCTTGCTCTAGCTGTCCAACATCCCGAAGACATTGTT
CCCTTATTATGTTATTGAGTTTTCCTGCAAT
						
					

			
		

Sequences
Splice junction sequence	GTTCTTTGGTTCCAGCATCGCCAAACACAAGATCTTGCTCTAGCTGTCCAACATCCCGAAGACA TTGTTCCCTTATTATGTTATTGAGTTTTCCTGCAATcttgaatatccatcatcagagccacgag gtcttgcccatgtgccacctgttcgtctggatcgcattgagtgagcggggcttgttcgggcaga gctactgg
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: 623 Transcript exons: 129471368-129471558,129472738-129472815,129472902-129473 050,129473803-129473881,129473961-129474086 CTTGAATATCCATCATCAGAGCCACGAGGTCTTGCCCATGTGCCACCTGTTCGTCTGGATCGCA TTGAGTGAGCGGGGCTTGTTCGGGCAGAGCTACTGGTTGGCAGTCCATGAACAGTAGGACTAGG GTCATTCATACAGTTATATTCATCTTTTGGCAGCTCACCTTTGCTAAGATTTTCAATCAATTGC TCCAAAATAGGGTAAAATCGAGAGAGTGCCCATGTTGATTCTTCCCCTGTTCGCTCTTTTCGAT TTGTGTGTTTCTTCTTGTGAACATCAAATTTCAGTGTAAAACCCCCTACTGAAGACTTTTTGGT ATCAGGCCCACATAAGCAACGCATATTATTTACAGCAATCATGTCATCAGCAGATAATCCTGCC AACTGTAAAACAGCATTCCTCAGGTTCAATGTGGCCTTGTCGCTTTCAAACTTCTCTGGGTTAA GTGCTGCATAAATCATCAGCAAGCGTAATTTATTTTCACGACTTACAACCAATTGTGTTCTCAA AAAGTTGATTAGTTCTTTGGTTCCAGCATCGCCAAACACAAGATCTTGCTCTAGCTGTCCAACA TCCCGAAGACATTGTTCCCTTATTATGTTATTGAGTTTTCCTGCAAT
Genomic sequence	CTTGAATATCCATCATCAGAGCCACGAGGTCTTGCCCATGTGCCACCTGTTCGTCTGGATCGCA TTGAGTGAGCGGGGCTTGTTCGGGCAGAGCTACTGGTTGGCAGTCCATGAACAGTAGGACTAGG GTCATTCATACAGTTATATTCATCTTTTGGCAGCTCACCTTTGCTAAGATTTTCAATCAATTGC TGCAGGACAGGTGAGAACCTCATTCACATCATTATACCAATACAAACAAAAACTGGTAAAACCA AGGAATAAAGGAATTCTATGGTGGCATTCACATAATTCTAGAGAAAAATAAAATTCTTTCATTG CTTTCTGACAGGGAAGATGGTTTGACTGTAGAAAGGGCAGCCCTGCAGACTAGAATAGTGCTCA AATCCAATTAGTACCCCCATAGGCCTTGTACTCTCCATAGCTTAATGGGATGAGGTATGATCAT TCTGATATCCCAGATAGTAAAGTTTCTTCGACACTAGATTTCAGCTTTTAGGCCTTTGGCTTCT AACAAAGGGATTTTTATGTTCAGTACTCCCTCGGTCCAAAAATATAAGTTCTGGTGCTTAAATA CTATTCCAGAATATAAGGACTTCTGGGGAGTCAACAATACCAGCCACAAAAAGTAAGGTAATTA AGAGCGATCACCATTTGTGGTAAGGATTAGCCCAACAGTCTGCCGCAAACTAAGCCAATCAGGA CTCAGCAATGGTCCCAGCTGTATGATGCACATTTTTCTTCTTAATTGTCCTAAAACTCCCATAA ATCCTTATATTTTGGGACAAACGGATTATCGTTTTTTTGTCTTGATTAAATTATCCATTTCTAA TGTTTTCTAGCAAATCGAAAATCAACCATACAAGGATATTTTATAAGAAATTTCACATTGACTT CAGAATTTTTTTATACAAATCTTCCTAAATATTATATGGGTACTTTGACAAAATAAAAGGCAAA AATCAATGTAGTACAAAAAGTGGGTAACTTATATTTCTAATGTATTCTATTGGATTGGATTTGT TCGATAATTCGAAGAATTACAACAAAATCTTTAGAAATCACATTTTTAGTTAGGAACTTCTATG GATTTTATTCTTCTTTTCTTTGGATCCAAAATAGAAGAATAAAAGAATAGGTATAAGAATTAAG TCGATCCAAAAAGGAAAGGAGGTTCATGGCCAAGGGCAAAGATGTTAGAATCCGAGTTATTTTG GAATGTATTAGTTGTGTACGAACAGTAAGTTAATGTGAGACAAGGAAAGCAGAATTTAAAACAA AATCCAAGCGAAGAACACAAAATAGCAAGTAGATGATTCATTAGTAGCATCAAGCATTTAAAGT AGTCAAGAGAAAACATTGATTTATACCTCCAAAATAGGGTAAAATCGAGAGAGTGCCCATGTTG ATTCTTCCCCTGTTCGCTCTTTTCGATTTGTGTGTTTCTTCTGTTATCAACAGGAAGAAAAGAA TACATCTTCAGATCCAGATTAAATATAGAAATAGAAGCCAAGAAATAACCTACAATGTTTACCT TGTGAACATCAAATTTCAGTGTAAAACCCCCTACTGAAGACTTTTTGGTATCAGGCCCACATAA GCAACGCATATTATTTACAGCAATCATGTCATCAGCAGATAATCCTGCCAACTGTAAAACAGCA TTCCTCAGGTTCAATGTGGCTGTTGACAAGAGTTTGAATGAGATCCATTGAAGGAAATTGTTGA AGTTAGGAGTTCCACATTATTAATATTTTGATGTAAAACTTAAGACTTCTTTCAGCCAGTCTGC GTGTCCTTTTTGTGATCAACACATAAGAAACTAAGACTTCTGATCGCTTGGCTAAAAGGGGATT AACACATCTTGTTGCTTGTCCTTTTTGTGATCAACACTCTGAAACTATCAGCCACATCTTAGTT TCTTGTGTGTTTGCTAGGCAGGTCTGGCATATTGTGCTTCACACACTCATTGCCGTTGTCAGTC CTAGTGCTGATAGTCTCTTCAATTCTTGGTAGAGCCGAGCAGCTCGAGTATTACACAAAGAAGA AAGCAAAGGCTTCAATTCTCTAGTGATCCTAGTGGCTTGGGAACTATGGAAACATAGAAATGCC AGTGATTTCCAGGGAGTGAGTCCAGATGTTTAAAATGTTGTGATGGCTGCAGTAGATGAAGGTC AAATGTGGTGCCTGGAGGGTTACAGCTCTACAAGAAGTCACCCTAAAGGTCAGGCCACTTAGGG TCGTTTTTTGGTTTGTTTTATGTAATTAAGTTGTAAGTCACCCCCTCAGTGTGTGTGTGGGGGG GGGGGGGGGCTATCCCATCCTTTTTTTTTGTTAATGAAATGACACGCAGCTCTCTTGTGTGTTC GAAGAAAAAAAAGTTAGTTTTAGAAGTCTTGATGTGGGTTAAAGAATTACCTGCATTAATTTTG CACCCTTGTCGCTTTCAAACTTCTCTGGGTTAAGTGCTGCATAAATCATCAGCAAGCGTAATTT ATTTTCACGACTTACAACCTGCATTGAGTCAGAAAATCTGAATACAAAATGTGGTGAAAGCCAA TGTGTCAACCAATGTAGGTCAAACTAAAATTACCAATTGTGTTCTCAAAAAGTTGATTAGTTCT TTGGTTCCAGCATCGCCAAACACAAGATCTTGCTCTAGCTGTCCAACATCCCGAAGACATTGTT CCCTTATTATGTTATTGAGTTTTCCTGCAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_014572* osi_circ_003888* osi_circ_011654 osa_circ_014571* 
						
						PMCS
						0.080450499

Conservation Information
Conserved circRNAs	osa_circ_014572* osi_circ_003888* osi_circ_011654 osa_circ_014571*
PMCS	0.080450499

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							129474065-129471485(+)
129473850-129474064(-)
129471502-129474069(-)
						
						Potential amino acid sequence
						
							MLLSFPAILNIHHQSHEVLPMCHLFVWIALSERGLFGQSYWLAVHEQ*(+)
MIYAALNPEKFESDKATLNLRNAVLQLAGLSADDMIAVNNMRCLCGPDTKKSSVGGFTLKFDVH
KKKHTNRKERTGEESTWALSRFYPILEQLIENLSKGELPKDEYNCMNDPSPTVHGLPTSSSART
SPAHSMRSRRTGGTWARPRGSDDGYSRLQENSIT*(-)
MTLVLLFMDCQPVALPEQAPLTQCDPDEQVAHGQDLVALMMDIQDCRKTQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	129474065-129471485(+) 129473850-129474064(-) 129471502-129474069(-)
Potential amino acid sequence	MLLSFPAILNIHHQSHEVLPMCHLFVWIALSERGLFGQSYWLAVHEQ(+) MIYAALNPEKFESDKATLNLRNAVLQLAGLSADDMIAVNNMRCLCGPDTKKSSVGGFTLKFDVH KKKHTNRKERTGEESTWALSRFYPILEQLIENLSKGELPKDEYNCMNDPSPTVHGLPTSSSART SPAHSMRSRRTGGTWARPRGSDDGYSRLQENSIT(-) MTLVLLFMDCQPVALPEQAPLTQCDPDEQVAHGQDLVALMMDIQDCRKTQ*(-)
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 Zm00001d015890_circ_g.2

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