Plant Circular RNA Database

Detail information of Zm00001d046579_circ_g.7

			
						 General Information
					
						CircRNA Name
						Zm00001d046579_circ_g.7
					
						ID in PlantcircBase
						zma_circ_009986
					
						Alias
						Zm09circ00048
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 96781626-96797627  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d046579						
					
						Parent gene annotation
						
							Transcription initiation factor TFIID subunit 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d046579_circ_g.1 Zm00001d046579_circ_g.2 Zm00001d046579_circ_g.3 Zm00001d046579_circ_g.4 Zm00001d046579_circ_g.5 Zm00001d046579_circ_g.6 Zm00001d046579_circ_g.8 Zm00001d046579_circ_g.9 Zm00001d046579_circ_g.10 Zm00001d046579_circ_g.11 Zm00001d046579_circ_g.12 Zm00001d046579_circ_g.13 Zm00001d046579_circ_g.14 						
					
						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
						Zm00001d046579_T024:13
Zm00001d046579_T020:13
Zm00001d046579_T009:13
Zm00001d046579_T011:13
Zm00001d046579_T031:5
Zm00001d046579_T030:5
Zm00001d046579_T029:7
Zm00001d046579_T001:13
Zm00001d046579_T002:12
Zm00001d046579_T005:13
Zm00001d046579_T027:7
Zm00001d046579_T015:13
Zm00001d046579_T008:12
Zm00001d046579_T003:13
Zm00001d046579_T026:3
Zm00001d046579_T006:13
Zm00001d046579_T023:13
Zm00001d046579_T016:13
Zm00001d046579_T025:12
Zm00001d046579_T018:13
Zm00001d046579_T007:13
Zm00001d046579_T004:12
Zm00001d046579_T019:13

General Information
CircRNA Name	Zm00001d046579_circ_g.7
ID in PlantcircBase	zma_circ_009986
Alias	Zm09circ00048
Organism	Zea mays
Position	chr9: 96781626-96797627 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d046579
Parent gene annotation	Transcription initiation factor TFIID subunit 1
Parent gene strand	+
Alternative splicing	Zm00001d046579_circ_g.1 Zm00001d046579_circ_g.2 Zm00001d046579_circ_g.3 Zm00001d046579_circ_g.4 Zm00001d046579_circ_g.5 Zm00001d046579_circ_g.6 Zm00001d046579_circ_g.8 Zm00001d046579_circ_g.9 Zm00001d046579_circ_g.10 Zm00001d046579_circ_g.11 Zm00001d046579_circ_g.12 Zm00001d046579_circ_g.13 Zm00001d046579_circ_g.14
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	Zm00001d046579_T024:13 Zm00001d046579_T020:13 Zm00001d046579_T009:13 Zm00001d046579_T011:13 Zm00001d046579_T031:5 Zm00001d046579_T030:5 Zm00001d046579_T029:7 Zm00001d046579_T001:13 Zm00001d046579_T002:12 Zm00001d046579_T005:13 Zm00001d046579_T027:7 Zm00001d046579_T015:13 Zm00001d046579_T008:12 Zm00001d046579_T003:13 Zm00001d046579_T026:3 Zm00001d046579_T006:13 Zm00001d046579_T023:13 Zm00001d046579_T016:13 Zm00001d046579_T025:12 Zm00001d046579_T018:13 Zm00001d046579_T007:13 Zm00001d046579_T004:12 Zm00001d046579_T019:13

			
						 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  
						
							TGATGAGGCTATTGAGCTTGCTGCTGCATCACATATCGAGAGGGAACTGCAAATCACTAGCTGG
AATCTTACAAGTAATTTCGTCGCTTGTACTAATCAGatgacgatgacgacgaggattatgagga
gcctggtggaggaaatcacttattggggtttatgttcggcaatgtagatgattctggtgattta
gatgctga

									
								

					

						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: 3054
Transcript exons: 96781626-96781738,96782350-96782412,96782495-96782537,96
782693-96782944,96785388-96785500,96785596-96785764,9678
6544-96787549,96790240-96790442,96793885-96794132,967950
73-96795409,96796179-96796385,96796489-96796581,96797421
-96797627
ATGACGATGACGACGAGGATTATGAGGAGCCTGGTGGAGGAAATCACTTATTGGGGTTTATGTT
CGGCAATGTAGATGATTCTGGTGATTTAGATGCTGACTATCTTGATGAGGATGCAAAGGAACAC
CTTTTTGCACTGGCAGATAAGCTTGGTCCATCTCTCAAAGACATTGACCTAATGAAGTCTTCTC
CAGCACCAACTGATCCTTCCGAACAAGACTATGATGAGAAGGCAGAAGATGCTGTTGATTATGA
AGATATTGATGAAGAATATGATGGACCTGAAGTTGAGGCAACTACAGAGGAAGACAATGTGTTG
TCAAAAAAGGATTACTTCTCTTCATCTACAGTGTATGCATCAGTCAACAGTACAGTTTCAGTGT
TTGACGATGAAAACTACGATGAGGAAGAAGAACCACCCAATGATAATGAGCCTCCTGGTGATAG
TGCTGCCCAAAATTTATCTTCAGTTTCTATCGAGCAGGCAGATACGACAACCTCAAGCGATAAC
CTTGCCATGGAAAAGATTGGCTTGTTATCACATCCAGAGGAAAACATGGACTTTGAATATGAAG
ATTTGGAGAATGAAAAGGGCACTGGGGAAGGCCAGCTTGAGCCTGAAAGTGCAACTTCCCTTCC
TGTTTTATGCATAGAGGATGGGAACGCTATCCTGAGATTCTCTGAAATTTTTGGTATCCAAGAG
CCTGTAAGAAAAGTGAAGACAGATCACCACAAACGACCAGTGGATAAAGAGCTTCAGATCGCAA
ATGTTGCTGACAATGTTGAAGAAGATGAGGAACTAATTCTCCGGAGCACTATGCAAAATTTCTC
AACTTTGAAGCACATTCATGTGAATGAAGATTTTGTTGAGAGTGACAGTGATGAGTCTATTTCT
GATGTCACTTTAAGGCTAAAGGATTCATGTCTTTCAGAACAACCAATGAAAGATGTGCATATGG
ATATTCGTATTGTCCAGCGATCTCCAACTTGTCCTGATTTTTATCCACTTGAGCATTATGATTG
GGAAAGTGATATCATTTGGAACAATTCACCAGCAACTGATCAGCAGGCTTATGCAAAAATCTGT
GAATCTGAAGAGAGTGAGGACACTCATGGTGAAGACCAGGGTAAGGATTATGGCCAGGCCTCCA
GGTGTTGGGATGTACAGAGTAAAACCAATGGTTCTCCAGTAATTAAAGAGACTTTTTGTTGTAC
AGAAATGCCTGCTCCAGCTAACTACTGCCCCCCTGGGAAAAGTTACCCTCCATTGACAAACGAA
GATAACTTAGATCACATAATGCCAAATAACTTAGATGATGCAGTTAAAATTGACACCATGGTGC
GTTTAAATAACCTTAGTGTACTAAACAGGGAATTATTAGAAGGATCATGGTTGGACAACATAAT
TTGGGATCCTAATGAGGTTACCCCAAAGCCTAAACTGATCTTTGACCTCAAAGATGATCATATG
CTTTTTGAGATCCTAGATGAAAAGAATGTGGACCATCTCCAGTCTCATGCTCGTGCTATGATTG
TTAGCCAGTCAACTAAGACTTCAACACCAACAGTTGACAATTTTGGCGATCAACCAAAGCCATT
GAGTGGCAGGTTCAACATCTCCAATGACAAGTTTTATTCAAATAGGAAGACTCCACAACAAGCT
AAATCTCATACTAAAAAACGCGCTTTAATGGGCATAAAGGTGGTGCATTCTGCTCCAGCTCATA
AGCTGCAAACCATGAAGCCAGTGTTGAGCAATAAGGAAATTGCAAACTTTCATAGACCAAGAGC
TAAGTGGTACCCACATGAAAATAAAATTGCCTCTCAGTTACAAGGACCTGCTTGTAGCCATGGG
AGGATGGCTGTTTTACTTATGTCATTGGGAGGAAAAGGAGTCAAGATTCTGGTCAATGCTGAGG
ACACTCCGGTCTCTGTCAAATTAAAAGCATCAAAGAAGTTCGCTTTTTGCAGAATTGAAGCCTT
CTGAGAAGATCAAATTGTTCTGTTCTGGGAAAGAGCTTCAGGATGACATCTCGTTAGCAATGCA
AAATGTGCGACCAAACTCCATTGTGCATGCTGTTCGCACTGAAGTGTACCTATGGCCAAAAGCA
CAGAAATTACCTGGTGAGGACAAGCCTCTACGCCCTCCTGGGGCTTTCAGGAAAAAAACTGACT
TGTCTATCAAGGATGGACATGTTTTTTTAATGGAATATTGTGAAGAGAGACCTTTGCTTCTCTC
GAATGCAGGAATGGGAGCCCGTCTCTGTACATATTACCAGAAAACTACCCCTACTGATCAGACA
GCTGCATCACTGCGAAACAACAGTGATGGACTGGGCACAGTGCTTGCAATTGATCCTGCTGATA
AATCCCCTTTTCTAGGAGAGATACATTCTGGGTCCCACCAATCTTGTCTTGAAACAAACATGTA
TAGATCACCTGTATTTCCCCATAAGGTTGCACCAACTGATTACTTATTAGTTCGTTCAGCCAAA
GGGGCTCTTTCCCTCCGTCGCATTGACAAGCTATATGTTGTTGGCCAACAAGAACCTCATATGG
AAGTCTTTTCACCAGGGACTAAGAACATGCAAAATTATCTTCTGAACCGAGTTCTTGCATATGT
TTATCGTGAGTTTCGTGCTAGAGAGAGGCCTGATGCTATTCCTCAGATTCGAGCTGACGAGTTA
CCCATACAAAGTCCTCTGACAGAAGCCATAGTGAAAAAACGATTGAAGCATTGTGCAGATTTGA
AGAAAGGACCAAAGGGGCATTTTTTCTGGACACAGAGACCTGATTTCCGGGTTCCATCAGAAGA
AGAACTGAGGAGATTATTGACGCCAGAAAGTGTTTGCTGTTATGAAAGTATGCAAGCTGGTTTG
TATCGTCTCAAGCGCTTAGGAATTCTGAAGCTTACTCAGCCTGTTGGATTGGCTTCTGCCATGA
ATCAGCTTCCTGATGAGGCTATTGAGCTTGCTGCTGCATCACATATCGAGAGGGAACTGCAAAT
CACTAGCTGGAATCTTACAAGTAATTTCGTCGCTTGTACTAATCAG
						
					

						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	TGATGAGGCTATTGAGCTTGCTGCTGCATCACATATCGAGAGGGAACTGCAAATCACTAGCTGG AATCTTACAAGTAATTTCGTCGCTTGTACTAATCAGatgacgatgacgacgaggattatgagga gcctggtggaggaaatcacttattggggtttatgttcggcaatgtagatgattctggtgattta gatgctga
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: 3054 Transcript exons: 96781626-96781738,96782350-96782412,96782495-96782537,96 782693-96782944,96785388-96785500,96785596-96785764,9678 6544-96787549,96790240-96790442,96793885-96794132,967950 73-96795409,96796179-96796385,96796489-96796581,96797421 -96797627 ATGACGATGACGACGAGGATTATGAGGAGCCTGGTGGAGGAAATCACTTATTGGGGTTTATGTT CGGCAATGTAGATGATTCTGGTGATTTAGATGCTGACTATCTTGATGAGGATGCAAAGGAACAC CTTTTTGCACTGGCAGATAAGCTTGGTCCATCTCTCAAAGACATTGACCTAATGAAGTCTTCTC CAGCACCAACTGATCCTTCCGAACAAGACTATGATGAGAAGGCAGAAGATGCTGTTGATTATGA AGATATTGATGAAGAATATGATGGACCTGAAGTTGAGGCAACTACAGAGGAAGACAATGTGTTG TCAAAAAAGGATTACTTCTCTTCATCTACAGTGTATGCATCAGTCAACAGTACAGTTTCAGTGT TTGACGATGAAAACTACGATGAGGAAGAAGAACCACCCAATGATAATGAGCCTCCTGGTGATAG TGCTGCCCAAAATTTATCTTCAGTTTCTATCGAGCAGGCAGATACGACAACCTCAAGCGATAAC CTTGCCATGGAAAAGATTGGCTTGTTATCACATCCAGAGGAAAACATGGACTTTGAATATGAAG ATTTGGAGAATGAAAAGGGCACTGGGGAAGGCCAGCTTGAGCCTGAAAGTGCAACTTCCCTTCC TGTTTTATGCATAGAGGATGGGAACGCTATCCTGAGATTCTCTGAAATTTTTGGTATCCAAGAG CCTGTAAGAAAAGTGAAGACAGATCACCACAAACGACCAGTGGATAAAGAGCTTCAGATCGCAA ATGTTGCTGACAATGTTGAAGAAGATGAGGAACTAATTCTCCGGAGCACTATGCAAAATTTCTC AACTTTGAAGCACATTCATGTGAATGAAGATTTTGTTGAGAGTGACAGTGATGAGTCTATTTCT GATGTCACTTTAAGGCTAAAGGATTCATGTCTTTCAGAACAACCAATGAAAGATGTGCATATGG ATATTCGTATTGTCCAGCGATCTCCAACTTGTCCTGATTTTTATCCACTTGAGCATTATGATTG GGAAAGTGATATCATTTGGAACAATTCACCAGCAACTGATCAGCAGGCTTATGCAAAAATCTGT GAATCTGAAGAGAGTGAGGACACTCATGGTGAAGACCAGGGTAAGGATTATGGCCAGGCCTCCA GGTGTTGGGATGTACAGAGTAAAACCAATGGTTCTCCAGTAATTAAAGAGACTTTTTGTTGTAC AGAAATGCCTGCTCCAGCTAACTACTGCCCCCCTGGGAAAAGTTACCCTCCATTGACAAACGAA GATAACTTAGATCACATAATGCCAAATAACTTAGATGATGCAGTTAAAATTGACACCATGGTGC GTTTAAATAACCTTAGTGTACTAAACAGGGAATTATTAGAAGGATCATGGTTGGACAACATAAT TTGGGATCCTAATGAGGTTACCCCAAAGCCTAAACTGATCTTTGACCTCAAAGATGATCATATG CTTTTTGAGATCCTAGATGAAAAGAATGTGGACCATCTCCAGTCTCATGCTCGTGCTATGATTG TTAGCCAGTCAACTAAGACTTCAACACCAACAGTTGACAATTTTGGCGATCAACCAAAGCCATT GAGTGGCAGGTTCAACATCTCCAATGACAAGTTTTATTCAAATAGGAAGACTCCACAACAAGCT AAATCTCATACTAAAAAACGCGCTTTAATGGGCATAAAGGTGGTGCATTCTGCTCCAGCTCATA AGCTGCAAACCATGAAGCCAGTGTTGAGCAATAAGGAAATTGCAAACTTTCATAGACCAAGAGC TAAGTGGTACCCACATGAAAATAAAATTGCCTCTCAGTTACAAGGACCTGCTTGTAGCCATGGG AGGATGGCTGTTTTACTTATGTCATTGGGAGGAAAAGGAGTCAAGATTCTGGTCAATGCTGAGG ACACTCCGGTCTCTGTCAAATTAAAAGCATCAAAGAAGTTCGCTTTTTGCAGAATTGAAGCCTT CTGAGAAGATCAAATTGTTCTGTTCTGGGAAAGAGCTTCAGGATGACATCTCGTTAGCAATGCA AAATGTGCGACCAAACTCCATTGTGCATGCTGTTCGCACTGAAGTGTACCTATGGCCAAAAGCA CAGAAATTACCTGGTGAGGACAAGCCTCTACGCCCTCCTGGGGCTTTCAGGAAAAAAACTGACT TGTCTATCAAGGATGGACATGTTTTTTTAATGGAATATTGTGAAGAGAGACCTTTGCTTCTCTC GAATGCAGGAATGGGAGCCCGTCTCTGTACATATTACCAGAAAACTACCCCTACTGATCAGACA GCTGCATCACTGCGAAACAACAGTGATGGACTGGGCACAGTGCTTGCAATTGATCCTGCTGATA AATCCCCTTTTCTAGGAGAGATACATTCTGGGTCCCACCAATCTTGTCTTGAAACAAACATGTA TAGATCACCTGTATTTCCCCATAAGGTTGCACCAACTGATTACTTATTAGTTCGTTCAGCCAAA GGGGCTCTTTCCCTCCGTCGCATTGACAAGCTATATGTTGTTGGCCAACAAGAACCTCATATGG AAGTCTTTTCACCAGGGACTAAGAACATGCAAAATTATCTTCTGAACCGAGTTCTTGCATATGT TTATCGTGAGTTTCGTGCTAGAGAGAGGCCTGATGCTATTCCTCAGATTCGAGCTGACGAGTTA CCCATACAAAGTCCTCTGACAGAAGCCATAGTGAAAAAACGATTGAAGCATTGTGCAGATTTGA AGAAAGGACCAAAGGGGCATTTTTTCTGGACACAGAGACCTGATTTCCGGGTTCCATCAGAAGA AGAACTGAGGAGATTATTGACGCCAGAAAGTGTTTGCTGTTATGAAAGTATGCAAGCTGGTTTG TATCGTCTCAAGCGCTTAGGAATTCTGAAGCTTACTCAGCCTGTTGGATTGGCTTCTGCCATGA ATCAGCTTCCTGATGAGGCTATTGAGCTTGCTGCTGCATCACATATCGAGAGGGAACTGCAAAT CACTAGCTGGAATCTTACAAGTAATTTCGTCGCTTGTACTAATCAG
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
						0.127648243

Conservation Information
Conserved circRNAs	NA
PMCS	0.127648243

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							96797531-96781626(+)
96793967-96781697(+)
						
						Potential amino acid sequence
						
							MRLLSLLLHHISRGNCKSLAGILQVISSLVLIR*(+)
MQNVRPNSIVHAVRTEVYLWPKAQKLPGEDKPLRPPGAFRKKTDLSIKDGHVFLMEYCEERPLL
LSNAGMGARLCTYYQKTTPTDQTAASLRNNSDGLGTVLAIDPADKSPFLGEIHSGSHQSCLETN
MYRSPVFPHKVAPTDYLLVRSAKGALSLRRIDKLYVVGQQEPHMEVFSPGTKNMQNYLLNRVLA
YVYREFRARERPDAIPQIRADELPIQSPLTEAIVKKRLKHCADLKKGPKGHFFWTQRPDFRVPS
EEELRRLLTPESVCCYESMQAGLYRLKRLGILKLTQPVGLASAMNQLPDEAIELAAASHIEREL
QITSWNLTSNFVACTNQMTMTTRIMRSLVEEITYWGLCSAM*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	96797531-96781626(+) 96793967-96781697(+)
Potential amino acid sequence	MRLLSLLLHHISRGNCKSLAGILQVISSLVLIR(+) MQNVRPNSIVHAVRTEVYLWPKAQKLPGEDKPLRPPGAFRKKTDLSIKDGHVFLMEYCEERPLL LSNAGMGARLCTYYQKTTPTDQTAASLRNNSDGLGTVLAIDPADKSPFLGEIHSGSHQSCLETN MYRSPVFPHKVAPTDYLLVRSAKGALSLRRIDKLYVVGQQEPHMEVFSPGTKNMQNYLLNRVLA YVYREFRARERPDAIPQIRADELPIQSPLTEAIVKKRLKHCADLKKGPKGHFFWTQRPDFRVPS EEELRRLLTPESVCCYESMQAGLYRLKRLGILKLTQPVGLASAMNQLPDEAIELAAASHIEREL QITSWNLTSNFVACTNQMTMTTRIMRSLVEEITYWGLCSAM(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d046579_circ_g.7

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