Plant Circular RNA Database

Detail information of Zm00001d028546_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d028546_circ_g.2
					
						ID in PlantcircBase
						zma_circ_006469
					
						Alias
						Zm01circ00050
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 38906523-38907986  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d028546						
					
						Parent gene annotation
						
							SH3 domain-containing protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d028546_circ_g.1 						
					
						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  
						
							GT-AG							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
						Zm00001d028546_T006:3
Zm00001d028546_T016:3
Zm00001d028546_T040:2
Zm00001d028546_T034:3
Zm00001d028546_T008:3
Zm00001d028546_T013:2
Zm00001d028546_T001:3
Zm00001d028546_T021:3
Zm00001d028546_T011:3
Zm00001d028546_T035:3
Zm00001d028546_T025:3
Zm00001d028546_T032:3
Zm00001d028546_T022:3
Zm00001d028546_T038:2
Zm00001d028546_T003:3
Zm00001d028546_T031:3
Zm00001d028546_T027:3
Zm00001d028546_T018:3
Zm00001d028546_T009:3
Zm00001d028546_T028:4
Zm00001d028546_T037:3
Zm00001d028546_T015:3

General Information
CircRNA Name	Zm00001d028546_circ_g.2
ID in PlantcircBase	zma_circ_006469
Alias	Zm01circ00050
Organism	Zea mays
Position	chr1: 38906523-38907986 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d028546
Parent gene annotation	SH3 domain-containing protein
Parent gene strand	+
Alternative splicing	Zm00001d028546_circ_g.1
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	GT-AG 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	Zm00001d028546_T006:3 Zm00001d028546_T016:3 Zm00001d028546_T040:2 Zm00001d028546_T034:3 Zm00001d028546_T008:3 Zm00001d028546_T013:2 Zm00001d028546_T001:3 Zm00001d028546_T021:3 Zm00001d028546_T011:3 Zm00001d028546_T035:3 Zm00001d028546_T025:3 Zm00001d028546_T032:3 Zm00001d028546_T022:3 Zm00001d028546_T038:2 Zm00001d028546_T003:3 Zm00001d028546_T031:3 Zm00001d028546_T027:3 Zm00001d028546_T018:3 Zm00001d028546_T009:3 Zm00001d028546_T028:4 Zm00001d028546_T037:3 Zm00001d028546_T015:3

			
						 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  
						
							AGTACAGTTCCCTCCTTTATCAACTTCTTCTGGATCCCAGTGACAGGGTCTGCTTTGAGGCCAT
AAATTGTGTGTTGGGAAAAGTCGACAACACAGAAAGgcaaaagtgcacaacccggtggtatgct
tcctttttcttcagcatcttttgttagtcttctttaatcatttgaatacaaacatgttccaaag
tgatttca

						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
						
							GCAAAAGTGCACAACCCGGTGGTATGCTTCCTTTTTCTTCAGCATCTTTTGTTAGTCTTCTTTA
ATCATTTGAATACAAACATGTTCCAAAGTGATTTCAGCTAATAGTTTATAACTTTCTATTGCCC
ATGATAAATGTTTCAAACAATACAGTTATCAGTAAAAAGCAAGTAAAGCGAGGTTATTAAATAG
CTAGCTTTAGATTGGCTATTTTTAGCTATATTTTGACGCCTCGACACTATGCCACTTGTTTGCT
ACAAACTCTATTTAAAATGCTGGGCAAAACAATTCTAGTTTTCATTTGATTTGAGTTACAAGAA
TCAAGATTTTTGTGCAAAATACAGATATACCAATGAATTTGGTATTGTGGAGAAGTGAATATCT
TAATTGCTCTTTGTAAAGAAAAAGCTAGACCAACCTAGGAGGAACTAGGCGGCTGTATATTGTA
AGGCCAGTCTCAGTGGGGGTTTCATGTCCCTGTTTTTAAGACTCACAAGTCACAAGTGTTGGAA
ACAGTGCAAACAATGAAACTTTTATCATCTTTCTCTCTTCATTTATGCTATGCCACCATTGCCA
TGTCATCTTATTCAATGCCCATGAAATTCTCACGAAAGTCCCATTGAGCCTGGCCTAAGAAGAA
AACAAACAGCCAGATGAGGACTCGGACTTATGTGGTTTAGGCATATATCTACATCCTCAATCAA
TGGAGCTAGGCTCAGTTCATACTGCCCTTCATAACTATCCCTTTAAATATGTTTACTCATTGTC
ATTGGCCTACCCGATTATAAGTAACATGCAGGGGACAATATATCTTCTTGTCAGTGTCTCAAGT
ATTACATCATCATTAACAACAACAACAAAACCTTTTAGTCCCAAGCAAGTCAGGGTAGTCTAGT
GTTTCAAGTATTACATGCTCTAAATAATATCAGGAAAATATCGTATAACTTTGTGTAATATCTG
GTTACAGTGGCCAATTCTACTACCAATTTCTCCCAGCTCTATCTAAAAGCCATTACTTCTTAGA
TTGTATATAATTGATTCCTTCCTCTTTTGTCAAATCCAGTTATGTTAAAATTTCTTATTTTCAC
TTCGATGTACTTATTTGTGTACAATATCATATATCATTGTTCCAAACTGAAACAGGAGCTCTTC
AGGACATTCTTCATTTGCATGATGTCCTTGCCAGGGTTTACCTTGCAAAGTTGTGTCATTCGAT
ATCTAGAGCACGTGTATTGGACCGTAAGTGAATTGTTTTGTGCATAACCTGAATTTATGTGTGA
TTTGTGATGCAAATCAGGGTGCATGCATCAAATCGCGGTTCTAATCATATACAATTTATGCAGA
GAGGCCTGACATAAAGTCACAGTACAGTTCCCTCCTTTATCAACTTCTTCTGGATCCCAGTGAC
AGGGTCTGCTTTGAGGCCATAAATTGTGTGTTGGGAAAAGTCGACAACACAGAAAG

Sequences
Splice junction sequence	AGTACAGTTCCCTCCTTTATCAACTTCTTCTGGATCCCAGTGACAGGGTCTGCTTTGAGGCCAT AAATTGTGTGTTGGGAAAAGTCGACAACACAGAAAGgcaaaagtgcacaacccggtggtatgct tcctttttcttcagcatcttttgttagtcttctttaatcatttgaatacaaacatgttccaaag tgatttca
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	GCAAAAGTGCACAACCCGGTGGTATGCTTCCTTTTTCTTCAGCATCTTTTGTTAGTCTTCTTTA ATCATTTGAATACAAACATGTTCCAAAGTGATTTCAGCTAATAGTTTATAACTTTCTATTGCCC ATGATAAATGTTTCAAACAATACAGTTATCAGTAAAAAGCAAGTAAAGCGAGGTTATTAAATAG CTAGCTTTAGATTGGCTATTTTTAGCTATATTTTGACGCCTCGACACTATGCCACTTGTTTGCT ACAAACTCTATTTAAAATGCTGGGCAAAACAATTCTAGTTTTCATTTGATTTGAGTTACAAGAA TCAAGATTTTTGTGCAAAATACAGATATACCAATGAATTTGGTATTGTGGAGAAGTGAATATCT TAATTGCTCTTTGTAAAGAAAAAGCTAGACCAACCTAGGAGGAACTAGGCGGCTGTATATTGTA AGGCCAGTCTCAGTGGGGGTTTCATGTCCCTGTTTTTAAGACTCACAAGTCACAAGTGTTGGAA ACAGTGCAAACAATGAAACTTTTATCATCTTTCTCTCTTCATTTATGCTATGCCACCATTGCCA TGTCATCTTATTCAATGCCCATGAAATTCTCACGAAAGTCCCATTGAGCCTGGCCTAAGAAGAA AACAAACAGCCAGATGAGGACTCGGACTTATGTGGTTTAGGCATATATCTACATCCTCAATCAA TGGAGCTAGGCTCAGTTCATACTGCCCTTCATAACTATCCCTTTAAATATGTTTACTCATTGTC ATTGGCCTACCCGATTATAAGTAACATGCAGGGGACAATATATCTTCTTGTCAGTGTCTCAAGT ATTACATCATCATTAACAACAACAACAAAACCTTTTAGTCCCAAGCAAGTCAGGGTAGTCTAGT GTTTCAAGTATTACATGCTCTAAATAATATCAGGAAAATATCGTATAACTTTGTGTAATATCTG GTTACAGTGGCCAATTCTACTACCAATTTCTCCCAGCTCTATCTAAAAGCCATTACTTCTTAGA TTGTATATAATTGATTCCTTCCTCTTTTGTCAAATCCAGTTATGTTAAAATTTCTTATTTTCAC TTCGATGTACTTATTTGTGTACAATATCATATATCATTGTTCCAAACTGAAACAGGAGCTCTTC AGGACATTCTTCATTTGCATGATGTCCTTGCCAGGGTTTACCTTGCAAAGTTGTGTCATTCGAT ATCTAGAGCACGTGTATTGGACCGTAAGTGAATTGTTTTGTGCATAACCTGAATTTATGTGTGA TTTGTGATGCAAATCAGGGTGCATGCATCAAATCGCGGTTCTAATCATATACAATTTATGCAGA GAGGCCTGACATAAAGTCACAGTACAGTTCCCTCCTTTATCAACTTCTTCTGGATCCCAGTGAC AGGGTCTGCTTTGAGGCCATAAATTGTGTGTTGGGAAAAGTCGACAACACAGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.045378751

Conservation Information
Conserved circRNAs	NA
PMCS	0.045378751

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							38907735-38907743(-)
						
						Potential amino acid sequence
						
							MTQLCKVNPGKDIMQMKNVLKSSTGLCTFAFLCCRLFPTHNLWPQSRPCHWDPEEVDKGGNCTV
TLCQASGPIHVL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	38907735-38907743(-)
Potential amino acid sequence	MTQLCKVNPGKDIMQMKNVLKSSTGLCTFAFLCCRLFPTHNLWPQSRPCHWDPEEVDKGGNCTV TLCQASGPIHVL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d028546_circ_g.2

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