Plant Circular RNA Database

Detail information of Zm00001d012661_circ_g.5

			
						 General Information
					
						CircRNA Name
						Zm00001d012661_circ_g.5
					
						ID in PlantcircBase
						zma_circ_009820
					
						Alias
						Zm08circ00086, GRMZM2G468132_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 178194130-178195735  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d012661						
					
						Parent gene annotation
						
							DExH-box ATP-dependent RNA helicase DExH6
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d012661_circ_g.1 Zm00001d012661_circ_g.2 Zm00001d012661_circ_g.3 Zm00001d012661_circ_g.4 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d012661_T003:3
Zm00001d012661_T010:3
Zm00001d012661_T007:3
Zm00001d012661_T013:1
Zm00001d012661_T012:3
Zm00001d012661_T002:3
Zm00001d012661_T004:3
Zm00001d012661_T015:3
Zm00001d012661_T005:3
Zm00001d012661_T018:3
Zm00001d012661_T001:3
Zm00001d012661_T016:3

General Information
CircRNA Name	Zm00001d012661_circ_g.5
ID in PlantcircBase	zma_circ_009820
Alias	Zm08circ00086, GRMZM2G468132_C1
Organism	Zea mays
Position	chr8: 178194130-178195735 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d012661
Parent gene annotation	DExH-box ATP-dependent RNA helicase DExH6
Parent gene strand	-
Alternative splicing	Zm00001d012661_circ_g.1 Zm00001d012661_circ_g.2 Zm00001d012661_circ_g.3 Zm00001d012661_circ_g.4
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d012661_T003:3 Zm00001d012661_T010:3 Zm00001d012661_T007:3 Zm00001d012661_T013:1 Zm00001d012661_T012:3 Zm00001d012661_T002:3 Zm00001d012661_T004:3 Zm00001d012661_T015:3 Zm00001d012661_T005:3 Zm00001d012661_T018:3 Zm00001d012661_T001:3 Zm00001d012661_T016:3

			
						 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  
						
							TTGAAGCGTTAGTTCCTCTTCCTATCAATAATCTCAAAAGAACACCATTTGTGCAGAACAAGAC
TGATGAATTCTTCCCGCCTTTTGACTCCAAACGTATcatacgaagatgaggatacaaaggcaac
aagtctctgcataaaattgtttcgtgaaagctattagtatgttcctatgtgcattttagtaact
agctagtg

									
								

					

						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: 249
Transcript exons: 178194130-178194163,178194255-178194307,178195574-178195
735
CATACGAAGATGAGGATACAAAGGCAACAAGTCTCTTAGAATAGTCAGCATGAAATCAGAAAAC
CTATCCCTTTCATGGATTTCATCCACAATGATGTGCGTTATTCCCAAAACTGCATCATCTAATG
AGCGCTTCTGGTTTCGTGCTTTTGAAGCGTTAGTTCCTCTTCCTATCAATAATCTCAAAAGAAC
ACCATTTGTGCAGAACAAGACTGATGAATTCTTCCCGCCTTTTGACTCCAAACGTAT
						
					

						Genomic sequence
						
							CATACGAAGATGAGGATACAAAGGCAACAAGTCTCTGCATAAAATTGTTTCGTGAAAGCTATTA
GTATGTTCCTATGTGCATTTTAGTAACTAGCTAGTGTACAAAACAAGTTTTGGTGTGATACCTT
AGAATAGTCAGCATGAAATCAGAAAACCTATCCCTTTCATGGATTTCATCCTGAACAGTAACAA
AATATAATTAGCTCATGTCAATTATATTATAGAATAATACACAGCCTACATTACAAAAGTGGAA
TAATTGCATATCCTGTGCAAAATCGGCTGAATAAAATTAATAAATCAAATATGGAAACTATAAC
ATATTAACATATTTTGCACATAATTTCCCAGGGGCGCGTGCAAATAAACAATCCACACACCAAA
CTATGCCTTGGTGCTGTTTCATTACCACTCACTCCAATTCCAACAGTAGTTTGGTTTAGCCTTT
TCAACTTTTCTAAATCATCCTAGAACTTCTATACATAGTTTACCCTTTTCTTCTTTGCTTGCCC
CTGCTTCGTAAGTGCTACTACTAAAAGATGAGTGGGTCTTCTTTTCCACAAAGAATAAATGGAG
GGCACTAAGGTGAGGAGGGAGTATTATTAATACTATTTCATGTTTCCTACCTCTACTTGGGACA
ACAAATTTTGTTTTGATTTGAAGGGAAAACAGTAGGGGAGGCACCTATTGTGGTAGTGCTATTT
TTACAAAAGGCTCTATTGTTATTTTGCCCCTGAATTCTGCACAGAATATCAGGTTCTACCCCCA
AAGGTCAAGAAGATTCACAAGGATGAAATAGTACAAAGTAATATTTCAGAAAAGGCTATCATGG
CCAAAATTCGTCACATTGCAAGCTCAGTTGAGAAGCATAAACTTTAAATCCCATCATAAAATGA
CTTGAGGGTAACTTAAGAAGAAATTGCCCCCGAATTAACAAAATGGCCACACATTCATAATCAT
ATGTTTGAAGAAAATCCGATCAGAAGTCAAAAGCATTGATGTTAGAAAAAAATCCCTTATGGGA
CCATGAAGATGGACACGCCTATCAAATTACTTGATACTTGTTGGTAAATGTTCTAAGAAATACA
TTTGATTCCAAAACAGCCACTCCATCTCTACAAAACTTATTGTCCATACAGGACATTAACAGTC
TTGAATGGATAGCTCACCATTGCTTTTCCAATTATATACACTTGAAAGTATCTAAGCAACAATC
ATACGCAAACGCAAGTAATGTTATTATCATTTTGATGTAAAAATAAATATACTTCTGTCTATAT
CAGTACAGCTTAGAAGTTGATAACACACTTTGCAAAACGATATGTAGTTAGAAGGGAGTACAAA
CTACTGAAAATTGAATTGTTTTTTTTCTCGAAAACATACTGAAAATTGAATTGTTACATGATAA
CATGTACACAGTGAAATATTAGCTATATAGCATTACCACAATGATGTGCGTTATTCCCAAAACT
GCATCATCTAATGAGCGCTTCTGGTTTCGTGCTTTTGAAGCGTTAGTTCCTCTTCCTATCAATA
ATCTCAAAAGAACACCATTTGTGCAGAACAAGACTGATGAATTCTTCCCGCCTTTTGACTCCAA
ACGTAT
						
					

			
		

Sequences
Splice junction sequence	TTGAAGCGTTAGTTCCTCTTCCTATCAATAATCTCAAAAGAACACCATTTGTGCAGAACAAGAC TGATGAATTCTTCCCGCCTTTTGACTCCAAACGTATcatacgaagatgaggatacaaaggcaac aagtctctgcataaaattgtttcgtgaaagctattagtatgttcctatgtgcattttagtaact agctagtg
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: 249 Transcript exons: 178194130-178194163,178194255-178194307,178195574-178195 735 CATACGAAGATGAGGATACAAAGGCAACAAGTCTCTTAGAATAGTCAGCATGAAATCAGAAAAC CTATCCCTTTCATGGATTTCATCCACAATGATGTGCGTTATTCCCAAAACTGCATCATCTAATG AGCGCTTCTGGTTTCGTGCTTTTGAAGCGTTAGTTCCTCTTCCTATCAATAATCTCAAAAGAAC ACCATTTGTGCAGAACAAGACTGATGAATTCTTCCCGCCTTTTGACTCCAAACGTAT
Genomic sequence	CATACGAAGATGAGGATACAAAGGCAACAAGTCTCTGCATAAAATTGTTTCGTGAAAGCTATTA GTATGTTCCTATGTGCATTTTAGTAACTAGCTAGTGTACAAAACAAGTTTTGGTGTGATACCTT AGAATAGTCAGCATGAAATCAGAAAACCTATCCCTTTCATGGATTTCATCCTGAACAGTAACAA AATATAATTAGCTCATGTCAATTATATTATAGAATAATACACAGCCTACATTACAAAAGTGGAA TAATTGCATATCCTGTGCAAAATCGGCTGAATAAAATTAATAAATCAAATATGGAAACTATAAC ATATTAACATATTTTGCACATAATTTCCCAGGGGCGCGTGCAAATAAACAATCCACACACCAAA CTATGCCTTGGTGCTGTTTCATTACCACTCACTCCAATTCCAACAGTAGTTTGGTTTAGCCTTT TCAACTTTTCTAAATCATCCTAGAACTTCTATACATAGTTTACCCTTTTCTTCTTTGCTTGCCC CTGCTTCGTAAGTGCTACTACTAAAAGATGAGTGGGTCTTCTTTTCCACAAAGAATAAATGGAG GGCACTAAGGTGAGGAGGGAGTATTATTAATACTATTTCATGTTTCCTACCTCTACTTGGGACA ACAAATTTTGTTTTGATTTGAAGGGAAAACAGTAGGGGAGGCACCTATTGTGGTAGTGCTATTT TTACAAAAGGCTCTATTGTTATTTTGCCCCTGAATTCTGCACAGAATATCAGGTTCTACCCCCA AAGGTCAAGAAGATTCACAAGGATGAAATAGTACAAAGTAATATTTCAGAAAAGGCTATCATGG CCAAAATTCGTCACATTGCAAGCTCAGTTGAGAAGCATAAACTTTAAATCCCATCATAAAATGA CTTGAGGGTAACTTAAGAAGAAATTGCCCCCGAATTAACAAAATGGCCACACATTCATAATCAT ATGTTTGAAGAAAATCCGATCAGAAGTCAAAAGCATTGATGTTAGAAAAAAATCCCTTATGGGA CCATGAAGATGGACACGCCTATCAAATTACTTGATACTTGTTGGTAAATGTTCTAAGAAATACA TTTGATTCCAAAACAGCCACTCCATCTCTACAAAACTTATTGTCCATACAGGACATTAACAGTC TTGAATGGATAGCTCACCATTGCTTTTCCAATTATATACACTTGAAAGTATCTAAGCAACAATC ATACGCAAACGCAAGTAATGTTATTATCATTTTGATGTAAAAATAAATATACTTCTGTCTATAT CAGTACAGCTTAGAAGTTGATAACACACTTTGCAAAACGATATGTAGTTAGAAGGGAGTACAAA CTACTGAAAATTGAATTGTTTTTTTTCTCGAAAACATACTGAAAATTGAATTGTTACATGATAA CATGTACACAGTGAAATATTAGCTATATAGCATTACCACAATGATGTGCGTTATTCCCAAAACT GCATCATCTAATGAGCGCTTCTGGTTTCGTGCTTTTGAAGCGTTAGTTCCTCTTCCTATCAATA ATCTCAAAAGAACACCATTTGTGCAGAACAAGACTGATGAATTCTTCCCGCCTTTTGACTCCAA ACGTAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.145826078

Conservation Information
Conserved circRNAs	NA
PMCS	0.145826078

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							178194271-178194139(+)
178195703-178194261(+)
178194273-178194132(-)
						
						Potential amino acid sequence
						
							MKSENLSLSWISSTMMCVIPKTASSNERFWFRAFEALVPLPINNLKRTPFVQNKTDEFFPPFDS
KRIIRR*(+)
MNSSRLLTPNVSYEDEDTKATSLLE*(+)
MLTILRDLLPLYPHLRMIRLESKGGKNSSVLFCTNGVLLRLLIGRGTNASKARNQKRSLDDAVL
GITHIIVDEIHERDRFSDFMLTILRDLLPLYPHLRMIRLESKGGKNSSVLFCTNGVLLRLLIGR
GTNASKARNQKRSLDDAVLGITHIIVDEIHERDRFSDFMLTILRDLLPLYPHLRMIRLESKGGK
NSSVLFCTNGVLLRLLIGRGTNASKARNQKRSLDDAVLGITHIIVDEIHERDRFSDFMLTILRD
LLPLYPHLRM(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	178194271-178194139(+) 178195703-178194261(+) 178194273-178194132(-)
Potential amino acid sequence	MKSENLSLSWISSTMMCVIPKTASSNERFWFRAFEALVPLPINNLKRTPFVQNKTDEFFPPFDS KRIIRR(+) MNSSRLLTPNVSYEDEDTKATSLLE(+) MLTILRDLLPLYPHLRMIRLESKGGKNSSVLFCTNGVLLRLLIGRGTNASKARNQKRSLDDAVL GITHIIVDEIHERDRFSDFMLTILRDLLPLYPHLRMIRLESKGGKNSSVLFCTNGVLLRLLIGR GTNASKARNQKRSLDDAVLGITHIIVDEIHERDRFSDFMLTILRDLLPLYPHLRMIRLESKGGK NSSVLFCTNGVLLRLLIGRGTNASKARNQKRSLDDAVLGITHIIVDEIHERDRFSDFMLTILRD LLPLYPHLRM(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d012661_circ_g.5

Address

Any questions?

Supported by