Plant Circular RNA Database

Detail information of Zm00001d046579_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d046579_circ_g.4
					
						ID in PlantcircBase
						zma_circ_009983
					
						Alias
						Zm09circ00045, zma_circ_0002987, GRMZM2G394722_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 96781626-96782944  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						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.5 Zm00001d046579_circ_g.6 Zm00001d046579_circ_g.7 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, 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  
						
							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_T015:4
Zm00001d046579_T025:3
Zm00001d046579_T024:4
Zm00001d046579_T005:4
Zm00001d046579_T002:4
Zm00001d046579_T006:4
Zm00001d046579_T011:4
Zm00001d046579_T008:4
Zm00001d046579_T001:4
Zm00001d046579_T003:4
Zm00001d046579_T009:4
Zm00001d046579_T018:4
Zm00001d046579_T019:4
Zm00001d046579_T007:4
Zm00001d046579_T020:4
Zm00001d046579_T026:1
Zm00001d046579_T004:4
Zm00001d046579_T023:4
Zm00001d046579_T016:4

General Information
CircRNA Name	Zm00001d046579_circ_g.4
ID in PlantcircBase	zma_circ_009983
Alias	Zm09circ00045, zma_circ_0002987, GRMZM2G394722_C1
Organism	Zea mays
Position	chr9: 96781626-96782944 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
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.5 Zm00001d046579_circ_g.6 Zm00001d046579_circ_g.7 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, 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	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_T015:4 Zm00001d046579_T025:3 Zm00001d046579_T024:4 Zm00001d046579_T005:4 Zm00001d046579_T002:4 Zm00001d046579_T006:4 Zm00001d046579_T011:4 Zm00001d046579_T008:4 Zm00001d046579_T001:4 Zm00001d046579_T003:4 Zm00001d046579_T009:4 Zm00001d046579_T018:4 Zm00001d046579_T019:4 Zm00001d046579_T007:4 Zm00001d046579_T020:4 Zm00001d046579_T026:1 Zm00001d046579_T004:4 Zm00001d046579_T023:4 Zm00001d046579_T016:4

			
						 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  
						
							ACAGTTTCAGTGTTTGACGATGAAAACTACGATGAGGAAGAAGAACCACCCAATGATAATGAGC
CTCCTGGTGATAGTGCTGCCCAAAATTTATCTTCAGatgacgatgacgacgaggattatgagga
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: 471
Transcript exons: 96781626-96781738,96782350-96782412,96782495-96782537,96
782693-96782944
ATGACGATGACGACGAGGATTATGAGGAGCCTGGTGGAGGAAATCACTTATTGGGGTTTATGTT
CGGCAATGTAGATGATTCTGGTGATTTAGATGCTGACTATCTTGATGAGGATGCAAAGGAACAC
CTTTTTGCACTGGCAGATAAGCTTGGTCCATCTCTCAAAGACATTGACCTAATGAAGTCTTCTC
CAGCACCAACTGATCCTTCCGAACAAGACTATGATGAGAAGGCAGAAGATGCTGTTGATTATGA
AGATATTGATGAAGAATATGATGGACCTGAAGTTGAGGCAACTACAGAGGAAGACAATGTGTTG
TCAAAAAAGGATTACTTCTCTTCATCTACAGTGTATGCATCAGTCAACAGTACAGTTTCAGTGT
TTGACGATGAAAACTACGATGAGGAAGAAGAACCACCCAATGATAATGAGCCTCCTGGTGATAG
TGCTGCCCAAAATTTATCTTCAG
						
					

						Genomic sequence
						
							ATGACGATGACGACGAGGATTATGAGGAGCCTGGTGGAGGAAATCACTTATTGGGGTTTATGTT
CGGCAATGTAGATGATTCTGGTGATTTAGATGCTGACTATCTTGATGAGGTAGACACTTCTTTA
TCTGTTTTTGTTGACATGCAAATGTCCTGTTTTTTGTTGTTTTTATTATTTTATTTCATGTGTC
TGTCTCTAGGAGATGACATTCATTTTATTCGTTTCACCTTTTCAATTGTGTGGATGTCTGATAT
CTGTATCTGTTTTTGATCTTAGTGCATTCTCAATTGGTCATGATTTTATACAGATTTAACTTCT
TTGTTGGTTCTCTTTTTCTTAACATTTTGATCCTTAGACTTGTGTTTTAGGGTGCTCGGTTGCT
TTATAGGAACCATCATCACTATAAGAACCATATTCCTCTGATTAAATTAATTTAATTTGAGTTC
TGGAAATGATGAGATAGGGAAATTCAATGCGACGAAACCAAATTTCTCAGTCCATGCATTGTAA
TTTTCTCGTAATTTGGATGTTTTTTGAATAATAGTTAGTAGAACTCACTAAATTTTAGCCAGAA
TAAAGGTTAGTTGCTAAACCTTAGGGTACTTTGGTTTTATTGTTTTTCCATTGTCTGCAGGAAA
CAAAGTCATTGTTTATTGTTTAGTTATGTTTATAATGCAATTTGGATGTTGCATTTATTTATAC
TTTTATTTTGCTTAACTCAGGATGCAAAGGAACACCTTTTTGCACTGGCAGATAAGCTTGGTCC
ATCTCTCAAAGACATTGACGTAAGTTATCTTATGCGTATAGTTAATCTTACTTATCTATTTCAT
TACCAAACAAGTTAATACTATGTTGTTTGCTAATTAGCTAATGAAGTCTTCTCCAGCACCAACT
GATCCTTCCGAACAAGGTTAGTGACATATTACTGTTTCCATATAAGCTGCACCTACAGTTTTGA
GAGTTATTCATCAAGCCAACTTTGCCATTGCTTAGGAAGACCTTATTCTTCTTTTTCGTGTCAA
ACTATGCACATAATTGATAACACATCTTTTTGTTGTTATGTAGACTATGATGAGAAGGCAGAAG
ATGCTGTTGATTATGAAGATATTGATGAAGAATATGATGGACCTGAAGTTGAGGCAACTACAGA
GGAAGACAATGTGTTGTCAAAAAAGGATTACTTCTCTTCATCTACAGTGTATGCATCAGTCAAC
AGTACAGTTTCAGTGTTTGACGATGAAAACTACGATGAGGAAGAAGAACCACCCAATGATAATG
AGCCTCCTGGTGATAGTGCTGCCCAAAATTTATCTTCAG
						
					

			
		

Sequences
Splice junction sequence	ACAGTTTCAGTGTTTGACGATGAAAACTACGATGAGGAAGAAGAACCACCCAATGATAATGAGC CTCCTGGTGATAGTGCTGCCCAAAATTTATCTTCAGatgacgatgacgacgaggattatgagga 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: 471 Transcript exons: 96781626-96781738,96782350-96782412,96782495-96782537,96 782693-96782944 ATGACGATGACGACGAGGATTATGAGGAGCCTGGTGGAGGAAATCACTTATTGGGGTTTATGTT CGGCAATGTAGATGATTCTGGTGATTTAGATGCTGACTATCTTGATGAGGATGCAAAGGAACAC CTTTTTGCACTGGCAGATAAGCTTGGTCCATCTCTCAAAGACATTGACCTAATGAAGTCTTCTC CAGCACCAACTGATCCTTCCGAACAAGACTATGATGAGAAGGCAGAAGATGCTGTTGATTATGA AGATATTGATGAAGAATATGATGGACCTGAAGTTGAGGCAACTACAGAGGAAGACAATGTGTTG TCAAAAAAGGATTACTTCTCTTCATCTACAGTGTATGCATCAGTCAACAGTACAGTTTCAGTGT TTGACGATGAAAACTACGATGAGGAAGAAGAACCACCCAATGATAATGAGCCTCCTGGTGATAG TGCTGCCCAAAATTTATCTTCAG
Genomic sequence	ATGACGATGACGACGAGGATTATGAGGAGCCTGGTGGAGGAAATCACTTATTGGGGTTTATGTT CGGCAATGTAGATGATTCTGGTGATTTAGATGCTGACTATCTTGATGAGGTAGACACTTCTTTA TCTGTTTTTGTTGACATGCAAATGTCCTGTTTTTTGTTGTTTTTATTATTTTATTTCATGTGTC TGTCTCTAGGAGATGACATTCATTTTATTCGTTTCACCTTTTCAATTGTGTGGATGTCTGATAT CTGTATCTGTTTTTGATCTTAGTGCATTCTCAATTGGTCATGATTTTATACAGATTTAACTTCT TTGTTGGTTCTCTTTTTCTTAACATTTTGATCCTTAGACTTGTGTTTTAGGGTGCTCGGTTGCT TTATAGGAACCATCATCACTATAAGAACCATATTCCTCTGATTAAATTAATTTAATTTGAGTTC TGGAAATGATGAGATAGGGAAATTCAATGCGACGAAACCAAATTTCTCAGTCCATGCATTGTAA TTTTCTCGTAATTTGGATGTTTTTTGAATAATAGTTAGTAGAACTCACTAAATTTTAGCCAGAA TAAAGGTTAGTTGCTAAACCTTAGGGTACTTTGGTTTTATTGTTTTTCCATTGTCTGCAGGAAA CAAAGTCATTGTTTATTGTTTAGTTATGTTTATAATGCAATTTGGATGTTGCATTTATTTATAC TTTTATTTTGCTTAACTCAGGATGCAAAGGAACACCTTTTTGCACTGGCAGATAAGCTTGGTCC ATCTCTCAAAGACATTGACGTAAGTTATCTTATGCGTATAGTTAATCTTACTTATCTATTTCAT TACCAAACAAGTTAATACTATGTTGTTTGCTAATTAGCTAATGAAGTCTTCTCCAGCACCAACT GATCCTTCCGAACAAGGTTAGTGACATATTACTGTTTCCATATAAGCTGCACCTACAGTTTTGA GAGTTATTCATCAAGCCAACTTTGCCATTGCTTAGGAAGACCTTATTCTTCTTTTTCGTGTCAA ACTATGCACATAATTGATAACACATCTTTTTGTTGTTATGTAGACTATGATGAGAAGGCAGAAG ATGCTGTTGATTATGAAGATATTGATGAAGAATATGATGGACCTGAAGTTGAGGCAACTACAGA GGAAGACAATGTGTTGTCAAAAAAGGATTACTTCTCTTCATCTACAGTGTATGCATCAGTCAAC AGTACAGTTTCAGTGTTTGACGATGAAAACTACGATGAGGAAGAAGAACCACCCAATGATAATG AGCCTCCTGGTGATAGTGCTGCCCAAAATTTATCTTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.214296188

Conservation Information
Conserved circRNAs	NA
PMCS	0.214296188

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							96782697-96781697(+)
96781686-96782941(+)
						
						Potential amino acid sequence
						
							MMRRQKMLLIMKILMKNMMDLKLRQLQRKTMCCQKRITSLHLQCMHQSTVQFQCLTMKTTMRKK
NHPMIMSLLVIVLPKIYLQMTMTTRIMRSLVEEITYWGLCSAM*(+)
MFGNVDDSGDLDADYLDEDAKEHLFALADKLGPSLKDIDLMKSSPAPTDPSEQDYDEKAEDAVD
YEDIDEEYDGPEVEATTEEDNVLSKKDYFSSSTVYASVNSTVSVFDDENYDEEEEPPNDNEPPG
DSAAQNLSSDDDDDEDYEEPGGGNHLLGFMFGNVDDSGDLDADYLDEDAKEHLFALADKLGPSL
KDIDLMKSSPAPTDPSEQDYDEKAEDAVDYEDIDEEYDGPEVEATTEEDNVLSKKDYFSSSTVY
ASVNSTVSVFDDENYDEEEEPPNDNEPPGDSAAQNLSSDDDDDEDYEEPGGGNHLLGFMFGNVD
DSGDLDADYLDEDAKEHLFALADKLGPSLKDIDLMKSSPAPTDPSEQDYDEKAEDAVDYEDIDE
EYDGPEVEATTEEDNVLSKKDYFSSSTVYASVNSTVSVFDDENYDEEEEPPNDNEPPGDSAAQN
LSSDDDDDEDYEEPGGGNHLLGFMFGNVDDSGDLDADYLDEDAKEHLFALADKLGPSLKDIDLM
KSSPAPTDPSEQDYDEKAEDAVDYEDIDEEYDGPEVEATTEEDNVLSKKDYFSSSTVYASVNST
VSVFDDENYDEEEEPPNDNEPPGDSAAQNLSS(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	96782697-96781697(+) 96781686-96782941(+)
Potential amino acid sequence	MMRRQKMLLIMKILMKNMMDLKLRQLQRKTMCCQKRITSLHLQCMHQSTVQFQCLTMKTTMRKK NHPMIMSLLVIVLPKIYLQMTMTTRIMRSLVEEITYWGLCSAM*(+) MFGNVDDSGDLDADYLDEDAKEHLFALADKLGPSLKDIDLMKSSPAPTDPSEQDYDEKAEDAVD YEDIDEEYDGPEVEATTEEDNVLSKKDYFSSSTVYASVNSTVSVFDDENYDEEEEPPNDNEPPG DSAAQNLSSDDDDDEDYEEPGGGNHLLGFMFGNVDDSGDLDADYLDEDAKEHLFALADKLGPSL KDIDLMKSSPAPTDPSEQDYDEKAEDAVDYEDIDEEYDGPEVEATTEEDNVLSKKDYFSSSTVY ASVNSTVSVFDDENYDEEEEPPNDNEPPGDSAAQNLSSDDDDDEDYEEPGGGNHLLGFMFGNVD DSGDLDADYLDEDAKEHLFALADKLGPSLKDIDLMKSSPAPTDPSEQDYDEKAEDAVDYEDIDE EYDGPEVEATTEEDNVLSKKDYFSSSTVYASVNSTVSVFDDENYDEEEEPPNDNEPPGDSAAQN LSSDDDDDEDYEEPGGGNHLLGFMFGNVDDSGDLDADYLDEDAKEHLFALADKLGPSLKDIDLM KSSPAPTDPSEQDYDEKAEDAVDYEDIDEEYDGPEVEATTEEDNVLSKKDYFSSSTVYASVNST VSVFDDENYDEEEEPPNDNEPPGDSAAQNLSS(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d046579_circ_g.4

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