Plant Circular RNA Database

Detail information of Zm00001d042639_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d042639_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007714
					
						Alias
						Zm03circ00064, GRMZM2G129444_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 174877179-174878114  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d042639						
					
						Parent gene annotation
						
							Mitotic spindle checkpoint protein MAD1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d042639_circ_g.1 Zm00001d042639_circ_g.2 Zm00001d042639_circ_g.4 Zm00001d042639_circ_g.5 Zm00001d042639_circ_g.6 Zm00001d042639_circ_g.7 						
					
						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
						Zm00001d042639_T006:4
Zm00001d042639_T003:4
Zm00001d042639_T009:4
Zm00001d042639_T004:4
Zm00001d042639_T002:4
Zm00001d042639_T010:4
Zm00001d042639_T007:4
Zm00001d042639_T008:4
Zm00001d042639_T005:4

General Information
CircRNA Name	Zm00001d042639_circ_g.3
ID in PlantcircBase	zma_circ_007714
Alias	Zm03circ00064, GRMZM2G129444_C1
Organism	Zea mays
Position	chr3: 174877179-174878114 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d042639
Parent gene annotation	Mitotic spindle checkpoint protein MAD1
Parent gene strand	-
Alternative splicing	Zm00001d042639_circ_g.1 Zm00001d042639_circ_g.2 Zm00001d042639_circ_g.4 Zm00001d042639_circ_g.5 Zm00001d042639_circ_g.6 Zm00001d042639_circ_g.7
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	Zm00001d042639_T006:4 Zm00001d042639_T003:4 Zm00001d042639_T009:4 Zm00001d042639_T004:4 Zm00001d042639_T002:4 Zm00001d042639_T010:4 Zm00001d042639_T007:4 Zm00001d042639_T008:4 Zm00001d042639_T005:4

			
						 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  
						
							TTGGTCGCATACCTTTCTTCACGTTTTTCAAGTGTCGCAATTTGATTCTTAAGTTGTGCTAACT
TTTCAGCAATATTAGCGTCTACCACGGTTCCAGGATctgccgagcaatttcttgttgggatgtg
taatcgttgacctgtatatatcactaacatcaaaatatgttccaataaaatatatgaaagacca
tttcaaca

						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
						
							CTGCCGAGCAATTTCTTGTTGGGATGTGTAATCGTTGACCTGTATATATCACTAACATCAAAAT
ATGTTCCAATAAAATATATGAAAGACCATTTCAACAGTGTGAGTCTTACCACGATATTAGTGCT
TCCTGATTCATAGTCAAACTCAAGCTTTTCATCATCGCTTTGGGCATACACTGACTGCAGAATA
AAGCGTGTTACGGGAATCCCATTTGACTGCTGCTGATCATTCATCACTATCTAGAACCATGAAA
CAAGTGTCAGATTATCATTTATGTTGAATAGCTGGATAGAGTTAGAATCATGCAAGGAAAATTC
AACAAAATATAGTAACAGAGGAAAAAATGCAGTACGTGTATAGTTGATGTTTACTGAAATGGAC
ATCACAAATGCAAACCTCAATTTTTCCTCGAGAAGACAAGCTGAGGATTATCATTACAATAAAA
GTACAAAGATGGACTCTATTGACCTCCAGTAACAAGGTGTGTGTTGCTTTTTAATTCTGTTAAA
ATCGACATTGAACAACAAGATCTATAGCTACATTTCAAGATCCTGTTAGTCATCTTTCAATTGA
TTGTGTCTAAGAAAAATGAATGAAGAATTTCTACAGGTGGCTAAAACAGTTAAATGGAGAGAGA
AGGGGTCGGGGTTGTTTAGCAAAAAGCTGCCCTCATATGGTGTGTGTTACATTATCATTACCTT
GTAACCGAAAAGGGAGCAGCAGGCTTTCCGGAAGACCGAGATCCTCTCTGCAAACACCGCCTTG
TATCTGTTTTGAACAAAGTATAATGTTATAACAAACAAAATGTGCAACAGATTCTAGAGGAGAA
ATAATTGGTCGCATACCTTTCTTCACGTTTTTCAAGTGTCGCAATTTGATTCTTAAGTTGTGCT
AACTTTTCAGCAATATTAGCGTCTACCACGGTTCCAGGAT

Sequences
Splice junction sequence	TTGGTCGCATACCTTTCTTCACGTTTTTCAAGTGTCGCAATTTGATTCTTAAGTTGTGCTAACT TTTCAGCAATATTAGCGTCTACCACGGTTCCAGGATctgccgagcaatttcttgttgggatgtg taatcgttgacctgtatatatcactaacatcaaaatatgttccaataaaatatatgaaagacca tttcaaca
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	CTGCCGAGCAATTTCTTGTTGGGATGTGTAATCGTTGACCTGTATATATCACTAACATCAAAAT ATGTTCCAATAAAATATATGAAAGACCATTTCAACAGTGTGAGTCTTACCACGATATTAGTGCT TCCTGATTCATAGTCAAACTCAAGCTTTTCATCATCGCTTTGGGCATACACTGACTGCAGAATA AAGCGTGTTACGGGAATCCCATTTGACTGCTGCTGATCATTCATCACTATCTAGAACCATGAAA CAAGTGTCAGATTATCATTTATGTTGAATAGCTGGATAGAGTTAGAATCATGCAAGGAAAATTC AACAAAATATAGTAACAGAGGAAAAAATGCAGTACGTGTATAGTTGATGTTTACTGAAATGGAC ATCACAAATGCAAACCTCAATTTTTCCTCGAGAAGACAAGCTGAGGATTATCATTACAATAAAA GTACAAAGATGGACTCTATTGACCTCCAGTAACAAGGTGTGTGTTGCTTTTTAATTCTGTTAAA ATCGACATTGAACAACAAGATCTATAGCTACATTTCAAGATCCTGTTAGTCATCTTTCAATTGA TTGTGTCTAAGAAAAATGAATGAAGAATTTCTACAGGTGGCTAAAACAGTTAAATGGAGAGAGA AGGGGTCGGGGTTGTTTAGCAAAAAGCTGCCCTCATATGGTGTGTGTTACATTATCATTACCTT GTAACCGAAAAGGGAGCAGCAGGCTTTCCGGAAGACCGAGATCCTCTCTGCAAACACCGCCTTG TATCTGTTTTGAACAAAGTATAATGTTATAACAAACAAAATGTGCAACAGATTCTAGAGGAGAA ATAATTGGTCGCATACCTTTCTTCACGTTTTTCAAGTGTCGCAATTTGATTCTTAAGTTGTGCT AACTTTTCAGCAATATTAGCGTCTACCACGGTTCCAGGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.070948424

Conservation Information
Conserved circRNAs	NA
PMCS	0.070948424

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							174877355-174878092(-)
174877416-174878099(-)
						
						Potential amino acid sequence
						
							MPKAMMKSLSLTMNQEALISWSTITHPNKKLLGRSWNRGRR*(-)
MNDQQQSNGIPVTRFILQSVYAQSDDEKLEFDYESGSTNIVVNDYTSQQEIARQILEPW*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	174877355-174878092(-) 174877416-174878099(-)
Potential amino acid sequence	MPKAMMKSLSLTMNQEALISWSTITHPNKKLLGRSWNRGRR(-) MNDQQQSNGIPVTRFILQSVYAQSDDEKLEFDYESGSTNIVVNDYTSQQEIARQILEPW(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d042639_circ_g.3

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