Plant Circular RNA Database

Detail information of Zm00001d028177_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d028177_circ_g.3
					
						ID in PlantcircBase
						zma_circ_006433
					
						Alias
						Zm01circ00039, zma_circ_0000074, GRMZM2G376074_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 25551692-25553584  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d028177						
					
						Parent gene annotation
						
							Ubiquitin carboxyl-terminal hydrolase 26
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d028177_circ_g.1 Zm00001d028177_circ_g.2 						
					
						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
						Zm00001d028177_T013:5
Zm00001d028177_T006:5
Zm00001d028177_T010:5
Zm00001d028177_T012:5
Zm00001d028177_T023:5
Zm00001d028177_T020:5
Zm00001d028177_T024:5
Zm00001d028177_T007:5
Zm00001d028177_T016:5
Zm00001d028177_T026:4
Zm00001d028177_T021:5
Zm00001d028177_T004:5
Zm00001d028177_T018:5
Zm00001d028177_T005:5
Zm00001d028177_T014:5

General Information
CircRNA Name	Zm00001d028177_circ_g.3
ID in PlantcircBase	zma_circ_006433
Alias	Zm01circ00039, zma_circ_0000074, GRMZM2G376074_C1
Organism	Zea mays
Position	chr1: 25551692-25553584 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d028177
Parent gene annotation	Ubiquitin carboxyl-terminal hydrolase 26
Parent gene strand	-
Alternative splicing	Zm00001d028177_circ_g.1 Zm00001d028177_circ_g.2
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	Zm00001d028177_T013:5 Zm00001d028177_T006:5 Zm00001d028177_T010:5 Zm00001d028177_T012:5 Zm00001d028177_T023:5 Zm00001d028177_T020:5 Zm00001d028177_T024:5 Zm00001d028177_T007:5 Zm00001d028177_T016:5 Zm00001d028177_T026:4 Zm00001d028177_T021:5 Zm00001d028177_T004:5 Zm00001d028177_T018:5 Zm00001d028177_T005:5 Zm00001d028177_T014:5

			
						 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  
						
							TAATTTCTGCCAAGCTGCAGCTGATAGACGCTTCATTGATGTGAGTTTAGACACTGGAACTTTT
CCATGCTCACATTGAATTGGTCCATTGTCAATGGATatttgatgttttctgagtgatgcttccg
cgcttacaaacaagatccaaaggcttttgcagcaatctcgaatgctgaaaatataagaaaaaac
cttataca

									
								

					

						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: 844
Transcript exons: 25551692-25551763,25552194-25552401,25552513-25552785,25
553082-25553263,25553476-25553584
ATTTGATGTTTTCTGAGTGATGCTTCCGCGCTTACAAACAAGATCCAAAGGCTTTTGCAGCAAT
CTCGAATGCTTTTCACATATAAGTGAACTGACAACAGCTTCAAGACTTTGAGGTTCTGGTAGTG
AAGAAATATTTTTTCCCGTCGTTGTAATATAAGCTCTCCACTCTGACAACCAAGATGAAGGAAC
CAAATAATATTTTTCACCAGGACGAAGTGCAAAGCTCTTCCCAGATATTAACTTTTCATGTTTG
TATCGTTGCTCAAGTTTCACTGCTCTAAGATTACCCTCAACAGAAGCAACATCAGACAATTCCT
GACTACAGATTTTGCATGGTTGACAGTCTGATGGAAAAGTAACAACATCATCAACCTTCTCGCT
GATGGTTTGATAGAGAAATAACCACAGGCTCTCTGGTACGGATACCCGCTTTGCTCCTGGAGCA
TGCTCCGGCAGGAGATACCCATGGCGACATCTTAAAGCACTCGTTGGTCCATTATCAGCATCAG
AAAGGATACCAGCATTTTTTCTGCGGAGCCAATGAGTCAACCATGCCTTTGAGATGAAGTAAGA
AGGACTATCTGAACAACTACCAGCAAGAGCTGCTTCTGCAAGGTTTTTAAATGATTCTTTGCGG
TCACGGTAGACATCAGCAGATACTGCATTTTTCGCCCCATCTTTAAGACACACCATGCAAAAAT
CATCACCACTCAATGTTGGCCCCCCTCCATATTTTGAAAATAATTTCTGCCAAGCTGCAGCTGA
TAGACGCTTCATTGATGTGAGTTTAGACACTGGAACTTTTCCATGCTCACATTGAATTGGTCCA
TTGTCAATGGAT
						
					

						Genomic sequence
						
							ATTTGATGTTTTCTGAGTGATGCTTCCGCGCTTACAAACAAGATCCAAAGGCTTTTGCAGCAAT
CTCGAATGCTGAAAATATAAGAAAAAACCTTATACAACTAGAACTAACGAAGGTAAGTAGTGCA
GCTCATATAACACTCAACAGAACACATAGATCCTCCTATCAAGACAAAAATTAATTGAAAAAAC
ATGTACCATGATTTCTTCTCTTCAGATGTAGATTACAAACGTCACTAATAAAAATCTCACAGAT
TGGGTATAGAAGTTCTAACAAGAGCCTTCTTTGAAATTATATAGGTTCTCATTTGTTCTTGGCA
GAAATCTTTTCACTCAAACTCTCAAATTCAAATATCGGAGTTATGTTCTTTTGTTGCCTTTAAG
GCTAAGAACCAGACACACATCAGCAAGTGAAACATATTCAAATATCAGAATTATGTTCTTTTAT
TGCCTTTTAGACTAAGAACCAGACCACATCAGCAAGTGAAACATATTGGTTTACCTTTTCACAT
ATAAGTGAACTGACAACAGCTTCAAGACTTTGAGGTTCTGGTAGTGAAGAAATATTTTTTCCCG
TCGTTGTAATATAAGCTCTCCACTCTGACAACCAAGATGAAGGAACCAAATAATATTTTTCACC
AGGACGAAGTGCAAAGCTCTTCCCAGATATTAACTTTTCATGTTTGTATCGTTGCTCAAGTTTC
ACTGCTCTGTAAACCATAAACCATGTGTCAGAAAATGCATGTAACAGGTATTGTGCAATAAACT
TGAGTGAAGAACCTAATATATGACATTGATTTTCTGACTATATATTATATTACCTAAGATTACC
CTCAACAGAAGCAACATCAGACAATTCCTGACTACAGATTTTGCATGGTTGACAGTCTGATGGA
AAAGTAACAACATCATCAACCTTCTCGCTGATGGTTTGATAGAGAAATAACCACAGGCTCTCTG
GTACGGATACCCGCTTTGCTCCTGGAGCATGCTCCGGCAGGAGATACCCATGGCGACATCTTAA
AGCACTCGTTGGTCCATTATCAGCATCAGAAAGGATACCAGCATTTTTTCTGCGGAGCCAATGA
GTCAACCTAGGAGTAAGCAGCAAAAAATATCAGCGTGAACCAGAGGGTTATGGTTGGTAACGTA
ATGCAACAAGTGGGACAGCAAAGAGTAAAAAGAGGAGTGAAGTTGCTTAGGGGCCATTTGGATC
CCTTTGTTTTGAAGGTATTAAGTTTAATGCAACCAGAGGGTTCTACAGAATGTGTCACCAAAAA
GAGAATCAAGGGCTAGATAGTTTAATCCTAGGTACCCAAAAATATTAGCCTGCACAAATAACTA
AACAGAACCAAGTTCTGAAAACAAGAGAAGGATGTGATTTGCATACCATGCCTTTGAGATGAAG
TAAGAAGGACTATCTGAACAACTACCAGCAAGAGCTGCTTCTGCAAGGTTTTTAAATGATTCTT
TGCGGTCACGGTAGACATCAGCAGATACTGCATTTTTCGCCCCATCTTTAAGACACACCATGCA
AAAATCATCACCACTCAATGTTGGCCCCCCTCCATACTTGAATTATTGCAATAACAAGCAAAGA
ATAATATCCATCAATGCTATTGCATAAGCATTAGAAATGAGTACAAAAGATTATATATTGCGAC
TTATGACTACAGTACTATAACATGGTCCTGAATCCACAGGATTACCAAAAAAAAAACTAATTTA
AGCAATGTGAGGCAAAAATCTATATAGTGCAAATCAGGAACTGCAGACTTTCTTACTTTTGAAA
ATAATTTCTGCCAAGCTGCAGCTGATAGACGCTTCATTGATGTGAGTTTAGACACTGGAACTTT
TCCATGCTCACATTGAATTGGTCCATTGTCAATGGAT
						
					

			
		

Sequences
Splice junction sequence	TAATTTCTGCCAAGCTGCAGCTGATAGACGCTTCATTGATGTGAGTTTAGACACTGGAACTTTT CCATGCTCACATTGAATTGGTCCATTGTCAATGGATatttgatgttttctgagtgatgcttccg cgcttacaaacaagatccaaaggcttttgcagcaatctcgaatgctgaaaatataagaaaaaac cttataca
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: 844 Transcript exons: 25551692-25551763,25552194-25552401,25552513-25552785,25 553082-25553263,25553476-25553584 ATTTGATGTTTTCTGAGTGATGCTTCCGCGCTTACAAACAAGATCCAAAGGCTTTTGCAGCAAT CTCGAATGCTTTTCACATATAAGTGAACTGACAACAGCTTCAAGACTTTGAGGTTCTGGTAGTG AAGAAATATTTTTTCCCGTCGTTGTAATATAAGCTCTCCACTCTGACAACCAAGATGAAGGAAC CAAATAATATTTTTCACCAGGACGAAGTGCAAAGCTCTTCCCAGATATTAACTTTTCATGTTTG TATCGTTGCTCAAGTTTCACTGCTCTAAGATTACCCTCAACAGAAGCAACATCAGACAATTCCT GACTACAGATTTTGCATGGTTGACAGTCTGATGGAAAAGTAACAACATCATCAACCTTCTCGCT GATGGTTTGATAGAGAAATAACCACAGGCTCTCTGGTACGGATACCCGCTTTGCTCCTGGAGCA TGCTCCGGCAGGAGATACCCATGGCGACATCTTAAAGCACTCGTTGGTCCATTATCAGCATCAG AAAGGATACCAGCATTTTTTCTGCGGAGCCAATGAGTCAACCATGCCTTTGAGATGAAGTAAGA AGGACTATCTGAACAACTACCAGCAAGAGCTGCTTCTGCAAGGTTTTTAAATGATTCTTTGCGG TCACGGTAGACATCAGCAGATACTGCATTTTTCGCCCCATCTTTAAGACACACCATGCAAAAAT CATCACCACTCAATGTTGGCCCCCCTCCATATTTTGAAAATAATTTCTGCCAAGCTGCAGCTGA TAGACGCTTCATTGATGTGAGTTTAGACACTGGAACTTTTCCATGCTCACATTGAATTGGTCCA TTGTCAATGGAT
Genomic sequence	ATTTGATGTTTTCTGAGTGATGCTTCCGCGCTTACAAACAAGATCCAAAGGCTTTTGCAGCAAT CTCGAATGCTGAAAATATAAGAAAAAACCTTATACAACTAGAACTAACGAAGGTAAGTAGTGCA GCTCATATAACACTCAACAGAACACATAGATCCTCCTATCAAGACAAAAATTAATTGAAAAAAC ATGTACCATGATTTCTTCTCTTCAGATGTAGATTACAAACGTCACTAATAAAAATCTCACAGAT TGGGTATAGAAGTTCTAACAAGAGCCTTCTTTGAAATTATATAGGTTCTCATTTGTTCTTGGCA GAAATCTTTTCACTCAAACTCTCAAATTCAAATATCGGAGTTATGTTCTTTTGTTGCCTTTAAG GCTAAGAACCAGACACACATCAGCAAGTGAAACATATTCAAATATCAGAATTATGTTCTTTTAT TGCCTTTTAGACTAAGAACCAGACCACATCAGCAAGTGAAACATATTGGTTTACCTTTTCACAT ATAAGTGAACTGACAACAGCTTCAAGACTTTGAGGTTCTGGTAGTGAAGAAATATTTTTTCCCG TCGTTGTAATATAAGCTCTCCACTCTGACAACCAAGATGAAGGAACCAAATAATATTTTTCACC AGGACGAAGTGCAAAGCTCTTCCCAGATATTAACTTTTCATGTTTGTATCGTTGCTCAAGTTTC ACTGCTCTGTAAACCATAAACCATGTGTCAGAAAATGCATGTAACAGGTATTGTGCAATAAACT TGAGTGAAGAACCTAATATATGACATTGATTTTCTGACTATATATTATATTACCTAAGATTACC CTCAACAGAAGCAACATCAGACAATTCCTGACTACAGATTTTGCATGGTTGACAGTCTGATGGA AAAGTAACAACATCATCAACCTTCTCGCTGATGGTTTGATAGAGAAATAACCACAGGCTCTCTG GTACGGATACCCGCTTTGCTCCTGGAGCATGCTCCGGCAGGAGATACCCATGGCGACATCTTAA AGCACTCGTTGGTCCATTATCAGCATCAGAAAGGATACCAGCATTTTTTCTGCGGAGCCAATGA GTCAACCTAGGAGTAAGCAGCAAAAAATATCAGCGTGAACCAGAGGGTTATGGTTGGTAACGTA ATGCAACAAGTGGGACAGCAAAGAGTAAAAAGAGGAGTGAAGTTGCTTAGGGGCCATTTGGATC CCTTTGTTTTGAAGGTATTAAGTTTAATGCAACCAGAGGGTTCTACAGAATGTGTCACCAAAAA GAGAATCAAGGGCTAGATAGTTTAATCCTAGGTACCCAAAAATATTAGCCTGCACAAATAACTA AACAGAACCAAGTTCTGAAAACAAGAGAAGGATGTGATTTGCATACCATGCCTTTGAGATGAAG TAAGAAGGACTATCTGAACAACTACCAGCAAGAGCTGCTTCTGCAAGGTTTTTAAATGATTCTT TGCGGTCACGGTAGACATCAGCAGATACTGCATTTTTCGCCCCATCTTTAAGACACACCATGCA AAAATCATCACCACTCAATGTTGGCCCCCCTCCATACTTGAATTATTGCAATAACAAGCAAAGA ATAATATCCATCAATGCTATTGCATAAGCATTAGAAATGAGTACAAAAGATTATATATTGCGAC TTATGACTACAGTACTATAACATGGTCCTGAATCCACAGGATTACCAAAAAAAAAACTAATTTA AGCAATGTGAGGCAAAAATCTATATAGTGCAAATCAGGAACTGCAGACTTTCTTACTTTTGAAA ATAATTTCTGCCAAGCTGCAGCTGATAGACGCTTCATTGATGTGAGTTTAGACACTGGAACTTT TCCATGCTCACATTGAATTGGTCCATTGTCAATGGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.090149571

Conservation Information
Conserved circRNAs	NA
PMCS	0.090149571

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25553522-25553578(-)
						
						Potential amino acid sequence
						
							MKRLSAAAWQKLFSKYGGGPTLSGDDFCMVCLKDGAKNAVSADVYRDRKESFKNLAEAALAGSC
SDSPSYFISKAWLTHWLRRKNAGILSDADNGPTSALRCRHGYLLPEHAPGAKRVSVPESLWLFL
YQTISEKVDDVVTFPSDCQPCKICSQELSDVASVEGNLRAVKLEQRYKHEKLISGKSFALRPGE
KYYLVPSSWLSEWRAYITTTGKNISSLPEPQSLEAVVSSLICEKHSRLLQKPLDLVCKRGSITQ
KTSNIH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25553522-25553578(-)
Potential amino acid sequence	MKRLSAAAWQKLFSKYGGGPTLSGDDFCMVCLKDGAKNAVSADVYRDRKESFKNLAEAALAGSC SDSPSYFISKAWLTHWLRRKNAGILSDADNGPTSALRCRHGYLLPEHAPGAKRVSVPESLWLFL YQTISEKVDDVVTFPSDCQPCKICSQELSDVASVEGNLRAVKLEQRYKHEKLISGKSFALRPGE KYYLVPSSWLSEWRAYITTTGKNISSLPEPQSLEAVVSSLICEKHSRLLQKPLDLVCKRGSITQ KTSNIH*(-)
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 Zm00001d028177_circ_g.3

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