Plant Circular RNA Database

Detail information of Zm00001d007422_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d007422_circ_g.2
					
						ID in PlantcircBase
						zma_circ_001244
					
						Alias
						circ544
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 231386889-231388710  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Zm00001d007422						
					
						Parent gene annotation
						
							aminopeptidase P1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						5
					
						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
						Zm00001d007422_T004:5
Zm00001d007422_T010:6
Zm00001d007422_T008:6
Zm00001d007422_T001:6
Zm00001d007422_T009:6
Zm00001d007422_T003:5
Zm00001d007422_T002:5
Zm00001d007422_T006:5
Zm00001d007422_T005:5
Zm00001d007422_T007:6

General Information
CircRNA Name	Zm00001d007422_circ_g.2
ID in PlantcircBase	zma_circ_001244
Alias	circ544
Organism	Zea mays
Position	chr2: 231386889-231388710 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI
Parent gene	Zm00001d007422
Parent gene annotation	aminopeptidase P1
Parent gene strand	+
Alternative splicing	NA
Support reads	5
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	Zm00001d007422_T004:5 Zm00001d007422_T010:6 Zm00001d007422_T008:6 Zm00001d007422_T001:6 Zm00001d007422_T009:6 Zm00001d007422_T003:5 Zm00001d007422_T002:5 Zm00001d007422_T006:5 Zm00001d007422_T005:5 Zm00001d007422_T007:6

			
						 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  
						
							CCGTGTGATTGATGCTAATACTGAATTGCTTAATGTTGGAAATAGGTTTTGAAAGGCCACATTG
CACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgaaccccacagaactggatggattgagg
aaggcgcatattcgagatggtgccgctgttgtacagtaccttgcttggctggataatcaggtct
gcatagat

									
								

					

						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
						
							GAACCCCACAGAACTGGATGGATTGAGGAAGGCGCATATTCGAGATGGTGCCGCTGTTGTACAG
TACCTTGCTTGGCTGGATAATCAGGTCTGCATAGATTAATGTCTCGTCATACTGAAATATTGCT
GAACTAGTGAACTTATATTTGAATTTCATATACACCTGAAAAATGTTTCGCATCTGTATTCTTC
GAGCATTACCAGCTTTATTTGCATCTTCAGAGCACATCTCATTTTGAAAAAAGGTTATTAAATA
TCCTCTGTAACGTAGTAGTTTTGCTCCATACTTGTTCTGATGTCTCCCCTCCACTTCCAATTCA
GATGCAGGAGAACTATGGAGCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAA
CATTTGTGAGTTTATCTTATTGTTGCACTGGTTTGTTTGGGTATCATATTATCTATCATGTGGA
GCTCGTCTACAAATGCATACATGCCATTAGATTTGCTTGTTTATGCACCATTTCTTTAATTTTT
TTATAAGACTCCAATGTACATTTTCTAAATTGTGTGCCAGAAGAATTGAAATTTAGTTGTTTTA
ATGTTTGAATTTGTTTTCTGTTCTGTAGAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAA
ACTTGAAGGCTTCCGTGCAACAAAAGAGGTATGCTACATCAACATCACTTCTTAAAGCTTAGTT
AAAATAATTGCTTAGATGTTACTGTCCGCAACTATGGAACCTGGAAGTAAGCGGTCAGCCAACA
AGTATTACTTCAGTAGTATTTGTAGAATTTGCTAACAATGGGTTCCAGTACTTTAGATGTCTCT
GTTCAGAATCAACGATAAAACACACAACTTTTTCTTGGTTTCATTTGTCTTTGTTTATTTATTT
ATGGATATTTTCTATCCAGTAAAATAAAAGCAAAGCATTAGTGTTGTACTTTATTTTTAATTTT
TTATCCCCATAACTTTTGATGTTGTATGGCTATCTAAAAAGCTAGTGATTTTTCCCCTCCAGTC
ACTTGATGCACTGCAATGTTTGACAAAATTACAATATTCCTGCAGAACTTTAAAGGTTTGAGTT
TTCCTACAATTTCATCTGTGGGACCAAATGCAGCAGTTATTCACTATAAACCTGAAGCAAGCAC
ATGTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAGGTTAAGTATATT
TAGTCCTTAACTGTCGCTTTATGTTTTGAATCTCTTTGAATCTGCTGACTTCTGGTGTACATGC
AGTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCCTCAGCACATGA
GAAGTCATGCTACACAGCAGTAAGTGCTACCTTTTGAGAAGTATTTCTCTCCCATCCTTACTTC
AGCCCATATATAGTTTCATTTACCAGTTACCACAGTAATTGTAATCATTCTTTCACTCGACCAC
CAGTTCAATAAAGCATCAGTTCTGACAGACTGGGGGATGATAAATGATTGGCTTACAGTATCAC
ACCACCTTTTCTTACTCCGAAAGCCTCTGTCCCTCGTTTTTCTTATGTTTTACAAAAAGTAGCA
ATAGGGCTGAATCAATCAGCGGTCTTTTTTTATTTGTCTTCACAGTGAACTTCATCATGATGCA
TGAATTTATTGAAGTTCATGTTAGATTTATTTGTACTTTAGTTTTTATTTACTTTGTTCCGTGT
GATTGATGCTAATACTGAATTGCTTAATGTTGGAAATAGGTTTTGAAAGGCCACATTGCACTAG
ACATTGCTGTGTTTCCTAATGGGACGACAG
						
					

			
		

Sequences
Splice junction sequence	CCGTGTGATTGATGCTAATACTGAATTGCTTAATGTTGGAAATAGGTTTTGAAAGGCCACATTG CACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgaaccccacagaactggatggattgagg aaggcgcatattcgagatggtgccgctgttgtacagtaccttgcttggctggataatcaggtct gcatagat
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	GAACCCCACAGAACTGGATGGATTGAGGAAGGCGCATATTCGAGATGGTGCCGCTGTTGTACAG TACCTTGCTTGGCTGGATAATCAGGTCTGCATAGATTAATGTCTCGTCATACTGAAATATTGCT GAACTAGTGAACTTATATTTGAATTTCATATACACCTGAAAAATGTTTCGCATCTGTATTCTTC GAGCATTACCAGCTTTATTTGCATCTTCAGAGCACATCTCATTTTGAAAAAAGGTTATTAAATA TCCTCTGTAACGTAGTAGTTTTGCTCCATACTTGTTCTGATGTCTCCCCTCCACTTCCAATTCA GATGCAGGAGAACTATGGAGCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAA CATTTGTGAGTTTATCTTATTGTTGCACTGGTTTGTTTGGGTATCATATTATCTATCATGTGGA GCTCGTCTACAAATGCATACATGCCATTAGATTTGCTTGTTTATGCACCATTTCTTTAATTTTT TTATAAGACTCCAATGTACATTTTCTAAATTGTGTGCCAGAAGAATTGAAATTTAGTTGTTTTA ATGTTTGAATTTGTTTTCTGTTCTGTAGAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAA ACTTGAAGGCTTCCGTGCAACAAAAGAGGTATGCTACATCAACATCACTTCTTAAAGCTTAGTT AAAATAATTGCTTAGATGTTACTGTCCGCAACTATGGAACCTGGAAGTAAGCGGTCAGCCAACA AGTATTACTTCAGTAGTATTTGTAGAATTTGCTAACAATGGGTTCCAGTACTTTAGATGTCTCT GTTCAGAATCAACGATAAAACACACAACTTTTTCTTGGTTTCATTTGTCTTTGTTTATTTATTT ATGGATATTTTCTATCCAGTAAAATAAAAGCAAAGCATTAGTGTTGTACTTTATTTTTAATTTT TTATCCCCATAACTTTTGATGTTGTATGGCTATCTAAAAAGCTAGTGATTTTTCCCCTCCAGTC ACTTGATGCACTGCAATGTTTGACAAAATTACAATATTCCTGCAGAACTTTAAAGGTTTGAGTT TTCCTACAATTTCATCTGTGGGACCAAATGCAGCAGTTATTCACTATAAACCTGAAGCAAGCAC ATGTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAGGTTAAGTATATT TAGTCCTTAACTGTCGCTTTATGTTTTGAATCTCTTTGAATCTGCTGACTTCTGGTGTACATGC AGTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCCTCAGCACATGA GAAGTCATGCTACACAGCAGTAAGTGCTACCTTTTGAGAAGTATTTCTCTCCCATCCTTACTTC AGCCCATATATAGTTTCATTTACCAGTTACCACAGTAATTGTAATCATTCTTTCACTCGACCAC CAGTTCAATAAAGCATCAGTTCTGACAGACTGGGGGATGATAAATGATTGGCTTACAGTATCAC ACCACCTTTTCTTACTCCGAAAGCCTCTGTCCCTCGTTTTTCTTATGTTTTACAAAAAGTAGCA ATAGGGCTGAATCAATCAGCGGTCTTTTTTTATTTGTCTTCACAGTGAACTTCATCATGATGCA TGAATTTATTGAAGTTCATGTTAGATTTATTTGTACTTTAGTTTTTATTTACTTTGTTCCGTGT GATTGATGCTAATACTGAATTGCTTAATGTTGGAAATAGGTTTTGAAAGGCCACATTGCACTAG ACATTGCTGTGTTTCCTAATGGGACGACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.205666461

Conservation Information
Conserved circRNAs	NA
PMCS	0.205666461

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							231387211-231386911(+)
231388700-231386969(+)
231387277-231388244(-)
						
						Potential amino acid sequence
						
							MQENYGASGYFSEIKGSHKNEHLATKLTEVSVSDKLEGFRATKENFKGLSFPTISSVGPNAAVI
HYKPEASTCSEMDADKIYLCDSGAQYLDGTTDITRTVHFGKPSAHEKSCYTAVLKGHIALDIAV
FPNGTTGTPQNWMD*(+)
MGRQEPHRTGWIEEGAYSRWCRCCTVPCLAG*(+)
MFIFMRPFYLTEITRSSIVLLHLIIQPSKVLYNSGTISNMRLPQSIQFCGVPVVPLGNTAMSSA
MWPFKTAV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	231387211-231386911(+) 231388700-231386969(+) 231387277-231388244(-)
Potential amino acid sequence	MQENYGASGYFSEIKGSHKNEHLATKLTEVSVSDKLEGFRATKENFKGLSFPTISSVGPNAAVI HYKPEASTCSEMDADKIYLCDSGAQYLDGTTDITRTVHFGKPSAHEKSCYTAVLKGHIALDIAV FPNGTTGTPQNWMD(+) MGRQEPHRTGWIEEGAYSRWCRCCTVPCLAG(+) MFIFMRPFYLTEITRSSIVLLHLIIQPSKVLYNSGTISNMRLPQSIQFCGVPVVPLGNTAMSSA MWPFKTAV*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d007422_circ_g.2

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