Plant Circular RNA Database

Detail information of Zm00001d005108_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d005108_circ_g.1
					
						ID in PlantcircBase
						zma_circ_001129
					
						Alias
						circ2411
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 158565179-158568556  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d005108						
					
						Parent gene annotation
						
							SNF1-related protein kinase catalytic alpha subunit KIN10  
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2
					
						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
						Zm00001d005108_T004:8
Zm00001d005108_T007:9
Zm00001d005108_T003:9
Zm00001d005108_T008:9
Zm00001d005108_T005:9
Zm00001d005108_T006:8
Zm00001d005108_T009:8
Zm00001d005108_T001:9
Zm00001d005108_T002:9

General Information
CircRNA Name	Zm00001d005108_circ_g.1
ID in PlantcircBase	zma_circ_001129
Alias	circ2411
Organism	Zea mays
Position	chr2: 158565179-158568556 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d005108
Parent gene annotation	SNF1-related protein kinase catalytic alpha subunit KIN10
Parent gene strand	+
Alternative splicing	NA
Support reads	2
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	Zm00001d005108_T004:8 Zm00001d005108_T007:9 Zm00001d005108_T003:9 Zm00001d005108_T008:9 Zm00001d005108_T005:9 Zm00001d005108_T006:8 Zm00001d005108_T009:8 Zm00001d005108_T001:9 Zm00001d005108_T002:9

			
						 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  
						
							CTTTCCTGCTCAAATTCATAACAATCATAACTTCAGTGCAGGGTCCATTGAAACTGATAGCCTG
AGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGggcagaggatggagggggcaggcaagga
tggcaacccgttgaggaattatcggattggcaagactctcggaattggctcattcgggaaggtg
aaaattgc

									
								

					

						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
						
							GGCAGAGGATGGAGGGGGCAGGCAAGGATGGCAACCCGTTGAGGAATTATCGGATTGGCAAGAC
TCTCGGAATTGGCTCATTCGGGAAGGTGAAAATTGCGGAGCATATCAGCACTGGACACAAGGTG
GCAATCAAGATTCTCAACCGCCGTAAAATCAGAGGCATGGAGATGGAAGAGAAAGGTTGGTGTC
TCATCTAATGGATACTCGTGTTGCCCTGCTAAGCTTACTGATTGAATATAGAGTTTTGTATTGA
ATATACACAAACATTTTCCATGGTGATTTCACTTTTATCCATAGAGTAATTAATTTTTGAGGAA
TATGCTATTATCTGCTATAGTGGTATGTGTTAAGCTTCTATACCGCTGTTATAGTGATTGAATT
TCTCTCGTGGCATACTTAGGGTTAGGGGTGGTAATGGACCACGATCCAAATGTTTCTTCACAAT
TCATTTGAGCCCTTAATTAATTTTAGATTAGATAAAAAATGAATAGAGATAAGAGTCCAATCCT
AATCCGATCTTATCCTTAAATTTTATAGTGTAAAATTTAGAGCCCATGACCACCCTAGCCATAT
TATATGGCATGACACTTTATGTGCACAATTGCAACAGATACAAGCAAGTGGGCCACTGTTTTCT
TGCTGTTCATCTGGAAGGACAAGATTGCACATTTCTTTGTAATGTTAGTTGGGACCAGTAATTA
GAAACCTTTAGCTACTCACCCATTGCAATGATTTTCACTTGTCTTCTATATTTGCTATTACCAT
CTAGTTGCTTGGTGATTGTTTGAACATGTTGTCTGATCTTCTGCTTTTTTAAATCATTTTGCAG
TTAAAAGAGAGATTAAGATATTGAGGTTATTTATGCATCCACATATTATCCGCCTCTATGAGGT
TATAGACACACCGGCTGATATTTATGTTGTTATGGAGTATGTTAAGTGTGGGGAATTATTTGAT
TACATTGTTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGGTGATAC
CATTTCTTTCTGTTTGTTTGTGCTACAATTATGATAAACTTAGGTTTACAAGAAGACAGCAAAT
CAAAACATCTGTGATATTCTTCTCAAGTGTGCTTGTATGTGATAGTATTCTCTTTCTTGCCCCC
TCTTGATACAGATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCT
AAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTGCAGATTTTGGCTTAAGT
AATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTG
AGGTAAGCTTTCTATAATAGGTCAAAGATATAAAGAGGACCCATTAGATCAGTATGGCCGTATT
TCCTACCCCTTTGTTGGCAGGCAGTACAGTATCCTTTTATTTTCTGCAGGTGATATCTGGTAAA
CTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTG
GTACTCTGCCATTTGATGACGAGAACATACCAAACCTTTTTAAGAAAATAAAGGTCAGCAAGTA
TCTACGGTTTTACATTAGAAATGTTCATTGTTACATGTTCCTGCTGATTTAGAGCCTATCTGTA
TCTCCCTCCTTTTCTCTTGCACTTTAGGGTGGAATATATACCCTTCCCAGCCATTTGTCTGGTG
CAGCAAGGGATTTGATTCCAAGAATGCTAGTTGTCGATCCTATGAAGCGGATCACCATTCGTGA
AATTCGCGAACATGATTGGTTCAAAATTCTTCTCCCGCGCTATTTGACTGTGCCTCCTCCAGAT
AGTGCGCAACAAGTCAAAAAGGTATAACATGTTCTGCATTCGACGTACTATATGGACAAAGCTA
ATATAATCTACTAACTGCATTTCTCTGGATTGTGCCTATACTAAACATTTCTCCTCGTGATATC
TGAATTCTGAACCTAACCCTCAATGGACAAATATGACAACATTGTTGATTTGGGATCACTAAAT
AGTATCTATCTTTTAGTTCTAGCACCTTTCCATTTGACGCCATGAATATGATCGACATTTTAGC
TAGCAAGAATGTTGAACTAGAAATACACCCCTATGTTTACACTCTACATGTTTGTCTAAAAAAG
ACCCCCTCACCTGATAACATCTAGGGCTCCCCTGTGTGATGCTTACCTTACCTCATTATGGTAA
AAAAACATAACTACACCTTGCCCCTTATACCATTATTTTGCTCCTGCATTGTTAGTAACTTCTA
TTGCATCAAAGAAATCTCATCTTCCTCACTATGTTTTCTATAATCCTTTTCTAGACATTAACTT
CACTGCAGTATTCACAATATTTTTGTACTCCTTTTTAGAATAATTTTTGTATTGTGTCTGTTGA
TAGTTTGAGAATACGATCAGTTTTGCAGTCATGGATCTACAGTTTGGGAGTGTGGGGCCTTTTC
TTCTGGTCATGTGGTTTAATTAAGAAATATGGTTCAATTTGCTCCCATTTTGTAGGTTGATGAG
GAAACTCTCCGTGAGGTTTTAGGTATGGGATATGACAAGAACCTGTTGGTGGAATCAATCCAAA
AAAGGCTGCAAAATGAGGTATTATTTCTTCTGCATTTTGTTGTCTTCATCCATCTTTTTGTACT
GTAATGGTTGTGACTGGATCACTGGACTTTTATGTACAGGCAACTGTTGCATATTACTTACTCT
TGGACAATAGGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGGTGAG
CAACTGAGTCATATTATATTTGTATCCCTTGATACTTAGGCCTCCTTTTGAGAAAGCATGTTCT
GTATCATATCCTCTGATGTGGTAATTTGAATCGGGACTAATTTTCTGTTTTGGTTTCTTGGCAC
ATAGGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGTGGGAATAGA
CAGCAAATATTTATGGAGTCTCCAGTTGGCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGG
CTCTTGGTCTTCAGGTAATCTAATTTCTAGTAACCTCCACCATTTTATTATTTTATTGCTTTTC
TCATTCAATATTTCTTTGTTTTGTGTTAGTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGT
GCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGC
AGATGGAGTCCTGGCTTTCCTGCTCAAATTCATAACAATCATAACTTCAGTGCAGGGTCCATTG
AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG
						
					

			
		

Sequences
Splice junction sequence	CTTTCCTGCTCAAATTCATAACAATCATAACTTCAGTGCAGGGTCCATTGAAACTGATAGCCTG AGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGggcagaggatggagggggcaggcaagga tggcaacccgttgaggaattatcggattggcaagactctcggaattggctcattcgggaaggtg aaaattgc
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	GGCAGAGGATGGAGGGGGCAGGCAAGGATGGCAACCCGTTGAGGAATTATCGGATTGGCAAGAC TCTCGGAATTGGCTCATTCGGGAAGGTGAAAATTGCGGAGCATATCAGCACTGGACACAAGGTG GCAATCAAGATTCTCAACCGCCGTAAAATCAGAGGCATGGAGATGGAAGAGAAAGGTTGGTGTC TCATCTAATGGATACTCGTGTTGCCCTGCTAAGCTTACTGATTGAATATAGAGTTTTGTATTGA ATATACACAAACATTTTCCATGGTGATTTCACTTTTATCCATAGAGTAATTAATTTTTGAGGAA TATGCTATTATCTGCTATAGTGGTATGTGTTAAGCTTCTATACCGCTGTTATAGTGATTGAATT TCTCTCGTGGCATACTTAGGGTTAGGGGTGGTAATGGACCACGATCCAAATGTTTCTTCACAAT TCATTTGAGCCCTTAATTAATTTTAGATTAGATAAAAAATGAATAGAGATAAGAGTCCAATCCT AATCCGATCTTATCCTTAAATTTTATAGTGTAAAATTTAGAGCCCATGACCACCCTAGCCATAT TATATGGCATGACACTTTATGTGCACAATTGCAACAGATACAAGCAAGTGGGCCACTGTTTTCT TGCTGTTCATCTGGAAGGACAAGATTGCACATTTCTTTGTAATGTTAGTTGGGACCAGTAATTA GAAACCTTTAGCTACTCACCCATTGCAATGATTTTCACTTGTCTTCTATATTTGCTATTACCAT CTAGTTGCTTGGTGATTGTTTGAACATGTTGTCTGATCTTCTGCTTTTTTAAATCATTTTGCAG TTAAAAGAGAGATTAAGATATTGAGGTTATTTATGCATCCACATATTATCCGCCTCTATGAGGT TATAGACACACCGGCTGATATTTATGTTGTTATGGAGTATGTTAAGTGTGGGGAATTATTTGAT TACATTGTTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGGTGATAC CATTTCTTTCTGTTTGTTTGTGCTACAATTATGATAAACTTAGGTTTACAAGAAGACAGCAAAT CAAAACATCTGTGATATTCTTCTCAAGTGTGCTTGTATGTGATAGTATTCTCTTTCTTGCCCCC TCTTGATACAGATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCT AAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTGCAGATTTTGGCTTAAGT AATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTG AGGTAAGCTTTCTATAATAGGTCAAAGATATAAAGAGGACCCATTAGATCAGTATGGCCGTATT TCCTACCCCTTTGTTGGCAGGCAGTACAGTATCCTTTTATTTTCTGCAGGTGATATCTGGTAAA CTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTG GTACTCTGCCATTTGATGACGAGAACATACCAAACCTTTTTAAGAAAATAAAGGTCAGCAAGTA TCTACGGTTTTACATTAGAAATGTTCATTGTTACATGTTCCTGCTGATTTAGAGCCTATCTGTA TCTCCCTCCTTTTCTCTTGCACTTTAGGGTGGAATATATACCCTTCCCAGCCATTTGTCTGGTG CAGCAAGGGATTTGATTCCAAGAATGCTAGTTGTCGATCCTATGAAGCGGATCACCATTCGTGA AATTCGCGAACATGATTGGTTCAAAATTCTTCTCCCGCGCTATTTGACTGTGCCTCCTCCAGAT AGTGCGCAACAAGTCAAAAAGGTATAACATGTTCTGCATTCGACGTACTATATGGACAAAGCTA ATATAATCTACTAACTGCATTTCTCTGGATTGTGCCTATACTAAACATTTCTCCTCGTGATATC TGAATTCTGAACCTAACCCTCAATGGACAAATATGACAACATTGTTGATTTGGGATCACTAAAT AGTATCTATCTTTTAGTTCTAGCACCTTTCCATTTGACGCCATGAATATGATCGACATTTTAGC TAGCAAGAATGTTGAACTAGAAATACACCCCTATGTTTACACTCTACATGTTTGTCTAAAAAAG ACCCCCTCACCTGATAACATCTAGGGCTCCCCTGTGTGATGCTTACCTTACCTCATTATGGTAA AAAAACATAACTACACCTTGCCCCTTATACCATTATTTTGCTCCTGCATTGTTAGTAACTTCTA TTGCATCAAAGAAATCTCATCTTCCTCACTATGTTTTCTATAATCCTTTTCTAGACATTAACTT CACTGCAGTATTCACAATATTTTTGTACTCCTTTTTAGAATAATTTTTGTATTGTGTCTGTTGA TAGTTTGAGAATACGATCAGTTTTGCAGTCATGGATCTACAGTTTGGGAGTGTGGGGCCTTTTC TTCTGGTCATGTGGTTTAATTAAGAAATATGGTTCAATTTGCTCCCATTTTGTAGGTTGATGAG GAAACTCTCCGTGAGGTTTTAGGTATGGGATATGACAAGAACCTGTTGGTGGAATCAATCCAAA AAAGGCTGCAAAATGAGGTATTATTTCTTCTGCATTTTGTTGTCTTCATCCATCTTTTTGTACT GTAATGGTTGTGACTGGATCACTGGACTTTTATGTACAGGCAACTGTTGCATATTACTTACTCT TGGACAATAGGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGGTGAG CAACTGAGTCATATTATATTTGTATCCCTTGATACTTAGGCCTCCTTTTGAGAAAGCATGTTCT GTATCATATCCTCTGATGTGGTAATTTGAATCGGGACTAATTTTCTGTTTTGGTTTCTTGGCAC ATAGGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGTGGGAATAGA CAGCAAATATTTATGGAGTCTCCAGTTGGCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGG CTCTTGGTCTTCAGGTAATCTAATTTCTAGTAACCTCCACCATTTTATTATTTTATTGCTTTTC TCATTCAATATTTCTTTGTTTTGTGTTAGTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGT GCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGC AGATGGAGTCCTGGCTTTCCTGCTCAAATTCATAACAATCATAACTTCAGTGCAGGGTCCATTG AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.12976139

Conservation Information
Conserved circRNAs	NA
PMCS	0.12976139

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							158565188-158565217(+)
158565261-158568538(-)
						
						Potential amino acid sequence
						
							MEGAGKDGNPLRNYRIGKTLGIGSFGKVKIAEHISTGHKVAIKILNRRKIRGMEMEEKVKREIK
ILRLFMHPHIIRLYEVIDTPADIYVVMEYVKCGELFDYIVEKGRLQEEEARRFFQQIISGVEYC
HRNMVVHRDLKPENLLLDSKCNVKIADFGLSNVMRDGHFLKTSCGSPNYAAPEVISGKLYAGPE
VDVWSCGVILYALLCGTLPFDDENIPNLFKKIKGGIYTLPSHLSGAARDLIPRMLVVDPMKRIT
IREIREHDWFKILLPRYLTVPPPDSAQQVKKVDEETLREVLGMGYDKNLLVESIQKRLQNEATV
AYYLLLDNRLRTTSGYLGAECQEAMDSSFSNIASYETPSSARGNRQQIFMESPVGLRPHLPAER
KWALGLQSRAHPKEIMSEVLKALQELNVYWKKIGHYNMKCRWSPGFPAQIHNNHNFSAGSIETD
SLSERLSLIKFEIQGRGWRGQARMATR*(+)
MSQFRESCQSDNSSTGCHPCLPPPSSALNFKLN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	158565188-158565217(+) 158565261-158568538(-)
Potential amino acid sequence	MEGAGKDGNPLRNYRIGKTLGIGSFGKVKIAEHISTGHKVAIKILNRRKIRGMEMEEKVKREIK ILRLFMHPHIIRLYEVIDTPADIYVVMEYVKCGELFDYIVEKGRLQEEEARRFFQQIISGVEYC HRNMVVHRDLKPENLLLDSKCNVKIADFGLSNVMRDGHFLKTSCGSPNYAAPEVISGKLYAGPE VDVWSCGVILYALLCGTLPFDDENIPNLFKKIKGGIYTLPSHLSGAARDLIPRMLVVDPMKRIT IREIREHDWFKILLPRYLTVPPPDSAQQVKKVDEETLREVLGMGYDKNLLVESIQKRLQNEATV AYYLLLDNRLRTTSGYLGAECQEAMDSSFSNIASYETPSSARGNRQQIFMESPVGLRPHLPAER KWALGLQSRAHPKEIMSEVLKALQELNVYWKKIGHYNMKCRWSPGFPAQIHNNHNFSAGSIETD SLSERLSLIKFEIQGRGWRGQARMATR(+) MSQFRESCQSDNSSTGCHPCLPPPSSALNFKLN(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d005108_circ_g.1

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