Plant Circular RNA Database

Detail information of Zm00001d046039_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d046039_circ_g.1
					
						ID in PlantcircBase
						zma_circ_009940
					
						Alias
						zma_circ_0003221
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 58114319-58139075  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d046039						
					
						Parent gene annotation
						
							HEAT repeat-containing protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d046039_circ_g.2 Zm00001d046039_circ_g.3 Zm00001d046039_circ_g.4 						
					
						Support reads
						NA
					
						Tissues
						leaf, 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
						Zm00001d046039_T010:18
Zm00001d046039_T015:17
Zm00001d046039_T066:14
Zm00001d046039_T037:17
Zm00001d046039_T031:18
Zm00001d046039_T027:17
Zm00001d046039_T006:17
Zm00001d046039_T036:7
Zm00001d046039_T018:17
Zm00001d046039_T032:17
Zm00001d046039_T039:15
Zm00001d046039_T016:9
Zm00001d046039_T040:17
Zm00001d046039_T023:17
Zm00001d046039_T005:14
Zm00001d046039_T022:17
Zm00001d046039_T014:16
Zm00001d046039_T035:16
Zm00001d046039_T003:15
Zm00001d046039_T008:17
Zm00001d046039_T017:18
Zm00001d046039_T004:16
Zm00001d046039_T012:13
Zm00001d046039_T001:16
Zm00001d046039_T024:17
Zm00001d046039_T033:17
Zm00001d046039_T029:18
Zm00001d046039_T025:17
Zm00001d046039_T021:17
Zm00001d046039_T007:17
Zm00001d046039_T038:17
Zm00001d046039_T052:17
Zm00001d046039_T030:17
Zm00001d046039_T002:17
Zm00001d046039_T011:18
Zm00001d046039_T013:17

General Information
CircRNA Name	Zm00001d046039_circ_g.1
ID in PlantcircBase	zma_circ_009940
Alias	zma_circ_0003221
Organism	Zea mays
Position	chr9: 58114319-58139075 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d046039
Parent gene annotation	HEAT repeat-containing protein
Parent gene strand	-
Alternative splicing	Zm00001d046039_circ_g.2 Zm00001d046039_circ_g.3 Zm00001d046039_circ_g.4
Support reads	NA
Tissues	leaf, 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	Zm00001d046039_T010:18 Zm00001d046039_T015:17 Zm00001d046039_T066:14 Zm00001d046039_T037:17 Zm00001d046039_T031:18 Zm00001d046039_T027:17 Zm00001d046039_T006:17 Zm00001d046039_T036:7 Zm00001d046039_T018:17 Zm00001d046039_T032:17 Zm00001d046039_T039:15 Zm00001d046039_T016:9 Zm00001d046039_T040:17 Zm00001d046039_T023:17 Zm00001d046039_T005:14 Zm00001d046039_T022:17 Zm00001d046039_T014:16 Zm00001d046039_T035:16 Zm00001d046039_T003:15 Zm00001d046039_T008:17 Zm00001d046039_T017:18 Zm00001d046039_T004:16 Zm00001d046039_T012:13 Zm00001d046039_T001:16 Zm00001d046039_T024:17 Zm00001d046039_T033:17 Zm00001d046039_T029:18 Zm00001d046039_T025:17 Zm00001d046039_T021:17 Zm00001d046039_T007:17 Zm00001d046039_T038:17 Zm00001d046039_T052:17 Zm00001d046039_T030:17 Zm00001d046039_T002:17 Zm00001d046039_T011:18 Zm00001d046039_T013:17

			
						 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  
						
							CCTAACCAGATGCTTGTTAATAACACTACAAGCTGTATATGTCAACTTACTCTAAAAGTGTAGC
CATTTCATTTGATGAACTTATCTCTGCAATAACAGActctaaaaattttcctcatgaaagggaa
gatattttggaggaagcatataatatttgagaagcataaattagttgaaacttgttgaaatgat
tggtgtga

									
								

					

						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: 2107
Transcript exons: 58114319-58114454,58114554-58114644,58114821-58114918,58
116066-58116119,58118238-58118681,58118766-58118966,5811
9057-58119185,58119484-58119570,58119787-58119843,581294
34-58129502,58129602-58129749,58129869-58130092,58136667
-58136760,58137501-58137568,58138606-58138662,58138803-5
8138902,58139026-58139075
CTCTAAAAATTTTCCTCATGAAAGGGAAGATATTTTGGAGGAAGCATATAATATTTGAGAAGCA
TAAATTAGTTGAAACTTGTTGAAATGATTGGTGTGAAGTAGATACCACTAACATCACCAGCTTC
CACAAATACTCTCCTTTGATCCGATAAGCCATCGTCTCGCTTGCAATAGACAACTCAGAAATCA
AAGTGTTACTTGAATTATTCTGAGAACTCCCATCCCATTGAAGTATCAGACCCAGATACTGAGA
CAATAACTCTATTGCAGAGAAGACAAAGGCTTCAACCTCAAAAAAATTGTCAGGGCAGAATCTG
ATAATCTGGGTGAATAGGTGGATGATAGGAGCGCTTGAACAATCTGCATATGTAAGTGCCTGGA
GGAGTTGCTGGCAAATATCCACTGAAATAAAATTATTGCTGAAAAAGACTTCTGTTGTGAGGGA
CGAAAGCACGCGTAAGACCTGATCACACGGTCTTTTGTCATCAAGTCCATGAACAATAAATTCC
CCAAAGTTTTTGTCTTGTTTAAAGTCAAGGTTGATCTTCAAAGAATTATTCTTCATTGATTGGC
AGGAATGGAACAGCACAAGGATAGATAACCCCCAAAGAAATTGGAATTCAGTTCTGTCCAATTT
GACCATACAATGCCCAGATATAAATGTTTGTTCGAGTAAATTTTTAGGATTATTCTCATCAAAA
TCCAAAGGCGCGGCATCAAGAGCTGTTGCTTTAAGAATTAATAACCAAACTTCATCAAGATACC
TCTGCACCTTGGACAAGACTAATAATGACTGAATCCCATCAAGGAATGGCTTGTAATTGATTTT
TGAGTGCAAACCAAAACTTATAGAAACATAATCCTTGAGTGCTCGAATCCAGTATTTTCCTAAT
AGAGTTGAACTGTTTACAAGTGAAGGTGCCAATTGCTGGTATTCATTAGGAGCATTTTCCCTCA
TCCTCAAGAATTGATAGGTGTTACACTTGACTGCTGCATGGGCAGTTAGAAGGCGAACTTTTAT
CTTGCACACTACCCAGTCAGCAAAAGATGGATATAGTAGGCCCTCTATGTCACTTAACGGGCGT
GTTATCAGAGAAAACAAGCGACTAAGAGCTAGTCTATCCCCACCAATTATGCTGCTCGTCATAA
CCCTTGTAGCGAGTTCAAGTCCAGCCTCCAAAAGAAGTGGACCAGAAGCAGTGCTTATAGCCAT
TCTAACAGCAGAAACAAGTTGGGCCTGAAATTGTTCCAGCAAGATATGGCCAGGAAATTCCGGA
TCTACTGCCTTGCCGAACTTGTCCATTATCAAACACAAAAGCTTCACACCTATTGGTTGCATTC
CTTCAAATTGCCCAGTACTAATCTGGTATGAAAGTGAGACCAGTTCCTGTAGTTTAAGCACTAG
CCAATCATTTGACAAATAAGTGCCTTGAGATATTGCGCTCCTTGCCAACAAGAGGTCAAAATGA
GCAGGTTCTGCTCCAACTGCAATTGGTACATGGCTAACGCATTCTGCAGCAAAAACCCTGGTAC
GATATCTGAGGTGTTTATTCCTTGGAGGAAACTGGCTGGATATAGAACCAGCACAGCGGATTTG
CTGCTGCTTTGAGCTGGAAATCATGTTGTCTTCATCTTCTCCATAGTACACATCATTCTCAGAT
GTACTATCAGGAGGATTATGCCCAAAACATGACAGAACTTCACCTGTGTTTCTTCTAATTGACG
TAGCAAGAACAATATTTCGTAAAACTGCCAGCCACCGTGATGGACATACTGGACATGATGTATA
CAATAAGCGAATAATAGTTGCACGAACCAACATCGCTGTTTCTGAATCGGTCTCCTCATCAAGC
ATACTGAACAGATTCTCTTCAATATTCTCGTCAATCATTGCAGCCGGGTCCCTTTCAATCAGAT
GGTGCAGTGTCGACACTGCTAAATATCTAAGACTTGGCTGTCTTGAGTAAAGCATTGGGATAAG
ACCTTGAACGTGCAAGTGCACAGGAACAGCTTGAGGAGCAAAAAGCACAAGCTGCTGGGAGAAT
CTAACCGATTCTAAAAGTGTAGCCATTTCATTTGATGAACTTATCTCTGCAATAACAGA
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	CCTAACCAGATGCTTGTTAATAACACTACAAGCTGTATATGTCAACTTACTCTAAAAGTGTAGC CATTTCATTTGATGAACTTATCTCTGCAATAACAGActctaaaaattttcctcatgaaagggaa gatattttggaggaagcatataatatttgagaagcataaattagttgaaacttgttgaaatgat tggtgtga
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: 2107 Transcript exons: 58114319-58114454,58114554-58114644,58114821-58114918,58 116066-58116119,58118238-58118681,58118766-58118966,5811 9057-58119185,58119484-58119570,58119787-58119843,581294 34-58129502,58129602-58129749,58129869-58130092,58136667 -58136760,58137501-58137568,58138606-58138662,58138803-5 8138902,58139026-58139075 CTCTAAAAATTTTCCTCATGAAAGGGAAGATATTTTGGAGGAAGCATATAATATTTGAGAAGCA TAAATTAGTTGAAACTTGTTGAAATGATTGGTGTGAAGTAGATACCACTAACATCACCAGCTTC CACAAATACTCTCCTTTGATCCGATAAGCCATCGTCTCGCTTGCAATAGACAACTCAGAAATCA AAGTGTTACTTGAATTATTCTGAGAACTCCCATCCCATTGAAGTATCAGACCCAGATACTGAGA CAATAACTCTATTGCAGAGAAGACAAAGGCTTCAACCTCAAAAAAATTGTCAGGGCAGAATCTG ATAATCTGGGTGAATAGGTGGATGATAGGAGCGCTTGAACAATCTGCATATGTAAGTGCCTGGA GGAGTTGCTGGCAAATATCCACTGAAATAAAATTATTGCTGAAAAAGACTTCTGTTGTGAGGGA CGAAAGCACGCGTAAGACCTGATCACACGGTCTTTTGTCATCAAGTCCATGAACAATAAATTCC CCAAAGTTTTTGTCTTGTTTAAAGTCAAGGTTGATCTTCAAAGAATTATTCTTCATTGATTGGC AGGAATGGAACAGCACAAGGATAGATAACCCCCAAAGAAATTGGAATTCAGTTCTGTCCAATTT GACCATACAATGCCCAGATATAAATGTTTGTTCGAGTAAATTTTTAGGATTATTCTCATCAAAA TCCAAAGGCGCGGCATCAAGAGCTGTTGCTTTAAGAATTAATAACCAAACTTCATCAAGATACC TCTGCACCTTGGACAAGACTAATAATGACTGAATCCCATCAAGGAATGGCTTGTAATTGATTTT TGAGTGCAAACCAAAACTTATAGAAACATAATCCTTGAGTGCTCGAATCCAGTATTTTCCTAAT AGAGTTGAACTGTTTACAAGTGAAGGTGCCAATTGCTGGTATTCATTAGGAGCATTTTCCCTCA TCCTCAAGAATTGATAGGTGTTACACTTGACTGCTGCATGGGCAGTTAGAAGGCGAACTTTTAT CTTGCACACTACCCAGTCAGCAAAAGATGGATATAGTAGGCCCTCTATGTCACTTAACGGGCGT GTTATCAGAGAAAACAAGCGACTAAGAGCTAGTCTATCCCCACCAATTATGCTGCTCGTCATAA CCCTTGTAGCGAGTTCAAGTCCAGCCTCCAAAAGAAGTGGACCAGAAGCAGTGCTTATAGCCAT TCTAACAGCAGAAACAAGTTGGGCCTGAAATTGTTCCAGCAAGATATGGCCAGGAAATTCCGGA TCTACTGCCTTGCCGAACTTGTCCATTATCAAACACAAAAGCTTCACACCTATTGGTTGCATTC CTTCAAATTGCCCAGTACTAATCTGGTATGAAAGTGAGACCAGTTCCTGTAGTTTAAGCACTAG CCAATCATTTGACAAATAAGTGCCTTGAGATATTGCGCTCCTTGCCAACAAGAGGTCAAAATGA GCAGGTTCTGCTCCAACTGCAATTGGTACATGGCTAACGCATTCTGCAGCAAAAACCCTGGTAC GATATCTGAGGTGTTTATTCCTTGGAGGAAACTGGCTGGATATAGAACCAGCACAGCGGATTTG CTGCTGCTTTGAGCTGGAAATCATGTTGTCTTCATCTTCTCCATAGTACACATCATTCTCAGAT GTACTATCAGGAGGATTATGCCCAAAACATGACAGAACTTCACCTGTGTTTCTTCTAATTGACG TAGCAAGAACAATATTTCGTAAAACTGCCAGCCACCGTGATGGACATACTGGACATGATGTATA CAATAAGCGAATAATAGTTGCACGAACCAACATCGCTGTTTCTGAATCGGTCTCCTCATCAAGC ATACTGAACAGATTCTCTTCAATATTCTCGTCAATCATTGCAGCCGGGTCCCTTTCAATCAGAT GGTGCAGTGTCGACACTGCTAAATATCTAAGACTTGGCTGTCTTGAGTAAAGCATTGGGATAAG ACCTTGAACGTGCAAGTGCACAGGAACAGCTTGAGGAGCAAAAAGCACAAGCTGCTGGGAGAAT CTAACCGATTCTAAAAGTGTAGCCATTTCATTTGATGAACTTATCTCTGCAATAACAGA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.12203454

Conservation Information
Conserved circRNAs	NA
PMCS	0.12203454

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							58139044-58139046(-)
						
						Potential amino acid sequence
						
							MATLLESVRFSQQLVLFAPQAVPVHLHVQGLIPMLYSRQPSLRYLAVSTLHHLIERDPAAMIDE
NIEENLFSMLDEETDSETAMLVRATIIRLLYTSCPVCPSRWLAVLRNIVLATSIRRNTGEVLSC
FGHNPPDSTSENDVYYGEDEDNMISSSKQQQIRCAGSISSQFPPRNKHLRYRTRVFAAECVSHV
PIAVGAEPAHFDLLLARSAISQGTYLSNDWLVLKLQELVSLSYQISTGQFEGMQPIGVKLLCLI
MDKFGKAVDPEFPGHILLEQFQAQLVSAVRMAISTASGPLLLEAGLELATRVMTSSIIGGDRLA
LSRLFSLITRPLSDIEGLLYPSFADWVVCKIKVRLLTAHAAVKCNTYQFLRMRENAPNEYQQLA
PSLVNSSTLLGKYWIRALKDYVSISFGLHSKINYKPFLDGIQSLLVLSKVQRYLDEVWLLILKA
TALDAAPLDFDENNPKNLLEQTFISGHCMVKLDRTEFQFLWGLSILVLFHSCQSMKNNSLKINL
DFKQDKNFGEFIVHGLDDKRPCDQVLRVLSSLTTEVFFSNNFISVDICQQLLQALTYADCSSAP
IIHLFTQIIRFCPDNFFEVEAFVFSAIELLSQYLGLILQCRDGSSQNNSSNTLISELSIASETM
AYRIKGEYLWKLVMLVVSTSHQSFQQVSTNLCFSNIICFLQNIFPFMRKIFRVCYCRDKFIK*(
-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	58139044-58139046(-)
Potential amino acid sequence	MATLLESVRFSQQLVLFAPQAVPVHLHVQGLIPMLYSRQPSLRYLAVSTLHHLIERDPAAMIDE NIEENLFSMLDEETDSETAMLVRATIIRLLYTSCPVCPSRWLAVLRNIVLATSIRRNTGEVLSC FGHNPPDSTSENDVYYGEDEDNMISSSKQQQIRCAGSISSQFPPRNKHLRYRTRVFAAECVSHV PIAVGAEPAHFDLLLARSAISQGTYLSNDWLVLKLQELVSLSYQISTGQFEGMQPIGVKLLCLI MDKFGKAVDPEFPGHILLEQFQAQLVSAVRMAISTASGPLLLEAGLELATRVMTSSIIGGDRLA LSRLFSLITRPLSDIEGLLYPSFADWVVCKIKVRLLTAHAAVKCNTYQFLRMRENAPNEYQQLA PSLVNSSTLLGKYWIRALKDYVSISFGLHSKINYKPFLDGIQSLLVLSKVQRYLDEVWLLILKA TALDAAPLDFDENNPKNLLEQTFISGHCMVKLDRTEFQFLWGLSILVLFHSCQSMKNNSLKINL DFKQDKNFGEFIVHGLDDKRPCDQVLRVLSSLTTEVFFSNNFISVDICQQLLQALTYADCSSAP IIHLFTQIIRFCPDNFFEVEAFVFSAIELLSQYLGLILQCRDGSSQNNSSNTLISELSIASETM AYRIKGEYLWKLVMLVVSTSHQSFQQVSTNLCFSNIICFLQNIFPFMRKIFRVCYCRDKFIK*( -)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d046039_circ_g.1

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