Plant Circular RNA Database

Detail information of Zm00001d041445_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d041445_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007628
					
						Alias
						Zm03circ00039, zma_circ_0001116, GRMZM2G701689_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 120196697-120197204  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d041445						
					
						Parent gene annotation
						
							Protein tesmin/TSO1-like CXC 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d041445_circ_g.1 Zm00001d041445_circ_g.3 						
					
						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
						Zm00001d041445_T019:3
Zm00001d041445_T016:3
Zm00001d041445_T017:3
Zm00001d041445_T004:3
Zm00001d041445_T015:3
Zm00001d041445_T005:3
Zm00001d041445_T010:3
Zm00001d041445_T008:3
Zm00001d041445_T011:1
Zm00001d041445_T013:3
Zm00001d041445_T006:3
Zm00001d041445_T020:3
Zm00001d041445_T022:3
Zm00001d041445_T018:3
Zm00001d041445_T012:3
Zm00001d041445_T014:3
Zm00001d041445_T002:3
Zm00001d041445_T007:3

General Information
CircRNA Name	Zm00001d041445_circ_g.2
ID in PlantcircBase	zma_circ_007628
Alias	Zm03circ00039, zma_circ_0001116, GRMZM2G701689_C1
Organism	Zea mays
Position	chr3: 120196697-120197204 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d041445
Parent gene annotation	Protein tesmin/TSO1-like CXC 2
Parent gene strand	-
Alternative splicing	Zm00001d041445_circ_g.1 Zm00001d041445_circ_g.3
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	Zm00001d041445_T019:3 Zm00001d041445_T016:3 Zm00001d041445_T017:3 Zm00001d041445_T004:3 Zm00001d041445_T015:3 Zm00001d041445_T005:3 Zm00001d041445_T010:3 Zm00001d041445_T008:3 Zm00001d041445_T011:1 Zm00001d041445_T013:3 Zm00001d041445_T006:3 Zm00001d041445_T020:3 Zm00001d041445_T022:3 Zm00001d041445_T018:3 Zm00001d041445_T012:3 Zm00001d041445_T014:3 Zm00001d041445_T002:3 Zm00001d041445_T007:3

			
						 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  
						
							CGTAGATAGAACAGTTTCCGTATGACTCTGGTTGTTCATACAGCCGATACACGAACAAGGCTCA
GAACAATAGACTCCAGCAGCAAAACACTCACAGTAAcctcccgttttccaaaagcattcttaca
gccctcgcatctgcaacttatggagcatcccacaccacccttgatgaagagtaaagataagatg
catacaga

						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: 344
Transcript exons: 120196697-120196763,120196848-120196943,120197024-120197
204
CCTCCCGTTTTCCAAAAGCATTCTTACAGCCCTCGCATCTGCAACTTATGGAGCATCCCACACC
ACCCTGAAAACATTCACAGTATTTTTTTAGACATGACGACTTCTTGCAATTGCATCCCCTTTTG
TGACGAGCTGAAGCAGGAGTTTTATTGGAGAAGTCCCTTAGTTCCAGACCAGGCTCAGATGTAT
GAATTACTTTAGGAGCAAATGCTAATGGATTGCGAGATTCAATCTGTTGCCGCGTAGATAGAAC
AGTTTCCGTATGACTCTGGTTGTTCATACAGCCGATACACGAACAAGGCTCAGAACAATAGACT
CCAGCAGCAAAACACTCACAGTAA
						
						Genomic sequence
						
							CCTCCCGTTTTCCAAAAGCATTCTTACAGCCCTCGCATCTGCAACTTATGGAGCATCCCACACC
ACCCTTGATGAAGAGTAAAGATAAGATGCATACAGAGGGATTAAGAAGAAAAAAGAGAGAGCAT
TAAATCAATGTAGGAGTTGAAACCTGAAAACATTCACAGTATTTTTTTAGACATGACGACTTCT
TGCAATTGCATCCCCTTTTGTGACGAGCTGAAGCAGGAGTTTTATTGGAGAAGTCCTACAATAT
TGAAGATGATGATATTAGCAACAGACAAGATTAAGGGAAGTACTCAGATACAATAAGTTAGTGT
CTCTTACCCTTAGTTCCAGACCAGGCTCAGATGTATGAATTACTTTAGGAGCAAATGCTAATGG
ATTGCGAGATTCAATCTGTTGCCGCGTAGATAGAACAGTTTCCGTATGACTCTGGTTGTTCATA
CAGCCGATACACGAACAAGGCTCAGAACAATAGACTCCAGCAGCAAAACACTCACAGTAA

Sequences
Splice junction sequence	CGTAGATAGAACAGTTTCCGTATGACTCTGGTTGTTCATACAGCCGATACACGAACAAGGCTCA GAACAATAGACTCCAGCAGCAAAACACTCACAGTAAcctcccgttttccaaaagcattcttaca gccctcgcatctgcaacttatggagcatcccacaccacccttgatgaagagtaaagataagatg catacaga
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: 344 Transcript exons: 120196697-120196763,120196848-120196943,120197024-120197 204 CCTCCCGTTTTCCAAAAGCATTCTTACAGCCCTCGCATCTGCAACTTATGGAGCATCCCACACC ACCCTGAAAACATTCACAGTATTTTTTTAGACATGACGACTTCTTGCAATTGCATCCCCTTTTG TGACGAGCTGAAGCAGGAGTTTTATTGGAGAAGTCCCTTAGTTCCAGACCAGGCTCAGATGTAT GAATTACTTTAGGAGCAAATGCTAATGGATTGCGAGATTCAATCTGTTGCCGCGTAGATAGAAC AGTTTCCGTATGACTCTGGTTGTTCATACAGCCGATACACGAACAAGGCTCAGAACAATAGACT CCAGCAGCAAAACACTCACAGTAA
Genomic sequence	CCTCCCGTTTTCCAAAAGCATTCTTACAGCCCTCGCATCTGCAACTTATGGAGCATCCCACACC ACCCTTGATGAAGAGTAAAGATAAGATGCATACAGAGGGATTAAGAAGAAAAAAGAGAGAGCAT TAAATCAATGTAGGAGTTGAAACCTGAAAACATTCACAGTATTTTTTTAGACATGACGACTTCT TGCAATTGCATCCCCTTTTGTGACGAGCTGAAGCAGGAGTTTTATTGGAGAAGTCCTACAATAT TGAAGATGATGATATTAGCAACAGACAAGATTAAGGGAAGTACTCAGATACAATAAGTTAGTGT CTCTTACCCTTAGTTCCAGACCAGGCTCAGATGTATGAATTACTTTAGGAGCAAATGCTAATGG ATTGCGAGATTCAATCTGTTGCCGCGTAGATAGAACAGTTTCCGTATGACTCTGGTTGTTCATA CAGCCGATACACGAACAAGGCTCAGAACAATAGACTCCAGCAGCAAAACACTCACAGTAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.165803841

Conservation Information
Conserved circRNAs	NA
PMCS	0.165803841

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							120197127-120196848(+)
120197145-120197142(-)
						
						Potential amino acid sequence
						
							MTLVVHTADTRTRLRTIDSSSKTLTVTSRFPKAFLQPSHLQLMEHPTPP*(+)
MNNQSHTETVLSTRQQIESRNPLAFAPKVIHTSEPGLELRDFSNKTPASARHKRGCNCKKSSCL
KKYCECFQGGVGCSISCRCEGCKNAFGKREVTVSVLLLESIVLSLVRVSAV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	120197127-120196848(+) 120197145-120197142(-)
Potential amino acid sequence	MTLVVHTADTRTRLRTIDSSSKTLTVTSRFPKAFLQPSHLQLMEHPTPP(+) MNNQSHTETVLSTRQQIESRNPLAFAPKVIHTSEPGLELRDFSNKTPASARHKRGCNCKKSSCL KKYCECFQGGVGCSISCRCEGCKNAFGKREVTVSVLLLESIVLSLVRVSAV(-)
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 Zm00001d041445_circ_g.2

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