Plant Circular RNA Database

Detail information of Zm00001d013318_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d013318_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008379
					
						Alias
						Zm05circ00013, zma_circ_0001687, GRMZM2G312738_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 8524741-8526566  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d013318						
					
						Parent gene annotation
						
							E3 ubiquitin-protein ligase HOS1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d013318_circ_g.1 Zm00001d013318_circ_g.2 Zm00001d013318_circ_g.4 Zm00001d013318_circ_g.5 						
					
						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
						Zm00001d013318_T023:3
Zm00001d013318_T038:1
Zm00001d013318_T037:3
Zm00001d013318_T035:3
Zm00001d013318_T025:3
Zm00001d013318_T016:3
Zm00001d013318_T030:2
Zm00001d013318_T019:4
Zm00001d013318_T021:3
Zm00001d013318_T007:3
Zm00001d013318_T001:2
Zm00001d013318_T011:3
Zm00001d013318_T036:2
Zm00001d013318_T017:2
Zm00001d013318_T032:3
Zm00001d013318_T024:2
Zm00001d013318_T003:3
Zm00001d013318_T010:3
Zm00001d013318_T015:3
Zm00001d013318_T002:2
Zm00001d013318_T033:4
Zm00001d013318_T028:3
Zm00001d013318_T029:3
Zm00001d013318_T026:1

General Information
CircRNA Name	Zm00001d013318_circ_g.3
ID in PlantcircBase	zma_circ_008379
Alias	Zm05circ00013, zma_circ_0001687, GRMZM2G312738_C1
Organism	Zea mays
Position	chr5: 8524741-8526566 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d013318
Parent gene annotation	E3 ubiquitin-protein ligase HOS1
Parent gene strand	+
Alternative splicing	Zm00001d013318_circ_g.1 Zm00001d013318_circ_g.2 Zm00001d013318_circ_g.4 Zm00001d013318_circ_g.5
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	Zm00001d013318_T023:3 Zm00001d013318_T038:1 Zm00001d013318_T037:3 Zm00001d013318_T035:3 Zm00001d013318_T025:3 Zm00001d013318_T016:3 Zm00001d013318_T030:2 Zm00001d013318_T019:4 Zm00001d013318_T021:3 Zm00001d013318_T007:3 Zm00001d013318_T001:2 Zm00001d013318_T011:3 Zm00001d013318_T036:2 Zm00001d013318_T017:2 Zm00001d013318_T032:3 Zm00001d013318_T024:2 Zm00001d013318_T003:3 Zm00001d013318_T010:3 Zm00001d013318_T015:3 Zm00001d013318_T002:2 Zm00001d013318_T033:4 Zm00001d013318_T028:3 Zm00001d013318_T029:3 Zm00001d013318_T026:1

			
						 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  
						
							TTGTAGTATTGACAGATACCCTTTTAAGAATTTGCGTGAGGCAGTTGATGTACTCTTTCTACAC
GGAGCATCAGACATGGTGATTGCAAAGCAAGCTATTatatcacagatgtttgtttggatgagaa
tgctgtgtcaagtgatccacttctggcttttcttttggatgaggtggtcatcaaggactggtgc
aagagggc

									
								

					

						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: 864
Transcript exons: 8524741-8525190,8526153-8526566
ATATCACAGATGTTTGTTTGGATGAGAATGCTGTGTCAAGTGATCCACTTCTGGCTTTTCTTTT
GGATGAGGTGGTCATCAAGGACTGGTGCAAGAGGGCTGTTAATGTGCTCATTACTGAGATTGGT
GTGATCTGTATCCAAAAATGTTCAATCGACCCTAGATTCAGTTACATGCTTTTTTTTATGTTTC
GTTTTTCATGTGTTCAGGGCCACACATGTTGAGGGAGTGGTACTGCTAATCTGTTAAGTCACTA
ACCTTAACGATATCTTAGATAGGTCTGGATTAGAAACGATGAGATCTAGGTTATCCCAACTGCA
AAAGTTTGCCACACAGTTGGCAGGAATTTACAGTATACTTGAAGTTATGGTTTCATCTTTCAAT
GAAGCAGTTTCAGCGCATGTTAATGACCTGCACCAACTCATTGAGAACACATTGAAGGCAAAGC
AGCATTTGGAGGCCATGATCTGGTGTATCAGGCATAGATTTATTCAGGACATCTGTTCAAGGTA
CACTGATCATACATCATGGAGCTCTGATGTGATTCAAAGGAAGGCATATGCAGAAGAAAGAAAA
TGGCCTGGATTTTCTGATAAAGGGTCAGATATAAATGAAGCCAATCAGACTACACTATTCATCG
AGCAGGCCCTACAAAACCTTGGCATTGAACAAAATTATAGGGATAAGGAGGAAGACATAACAAT
AACATGTTTACAGAATGAACAATCATCATCTATGTTCTGTTCCACAATTACAACCGATCATTGT
AGTATTGACAGATACCCTTTTAAGAATTTGCGTGAGGCAGTTGATGTACTCTTTCTACACGGAG
CATCAGACATGGTGATTGCAAAGCAAGCTATT
						
					

						Genomic sequence
						
							ATATCACAGATGTTTGTTTGGATGAGAATGCTGTGTCAAGTGATCCACTTCTGGCTTTTCTTTT
GGATGAGGTGGTCATCAAGGACTGGTGCAAGAGGGCTGTTAATGTGCTCATTACTGAGATTGGT
GTGATCTGTATCCAAAAATGTTCAATCGACCCTAGATTCAGTTACATGCTTTTTTTTATGTTTC
GTTTTTCATGTGTTCAGGGCCACACATGTTGAGGGAGTGGTACTGCTAATCTGTTAAGTCACTA
ACCTTAACGATATCTTAGATAGGTCTGGATTAGAAACGATGAGATCTAGGTTATCCCAACTGCA
AAAGTTTGCCACACAGTTGGCAGGAATTTACAGTATACTTGAAGTTATGGTTTCATCTTTCAAT
GAAGCAGTTTCAGCGCATGTTAATGACCTGCACCAACTCATTGAGAACACATTGAAGGCAAAGC
AGGTCTTTCTTTCTTAACCCCTCTATTGCTAATGATTTTAGACCACTGCTTAGAACTAACACTG
AGCTAGTCTAGGTACTTCAATTTGTTCATCCACTGCTGAAATTTCTATAAGATGAGTGTCCCAC
GGGGACACTTTCCATTATATAATTTTGTGTATATATTGGAACAAAACCTTTTTATCTCCCTTTT
GCTTAGTGTCATCATGATCCTGGACAAGTATTGACATAACCACTCAAAATAGTCTGGTGGTTCA
TTTTGGTAACAAGTGCTCCCTCCAAATCTGAATATAAGTCAATTGTTACATTGATACAACCCAC
CATGTGGAGCTTTGTCTAGCAATTTTCATGAAAATATCATATTTAAAATAAAAGGGGTTGTATA
TTATCAAACTAGCCTTCATGATAATTCTACAAACATCAACTTTACGTTCTCATTCTACCTAATT
CCTTATGCATCAATACTAAAAATAGTTAGACCAGCAAGAATCCTGAGACGACTATATGTACAAT
CAGATTGAGTATGTCTCTAGCACTTTTCTTGTTTATGAAACCTTGTGCTTTCTTACACTCTGAT
GCTTGCTAATGATGTAGCGTTATTGCATTAGATCATAGAACAAATTCTGTACCATTTGTTTCTT
GGAGTATCTGTTAAAGATGCCTGCACATCAACAATCCTTTTAGTTGATTTTGTAGCATTACTTT
ACTTCATATGTAATCTTTATTTTAAGGAGTCACTCACTCCAATAGGTGATGTCCTATCTTTCCC
ATTCCTCTTCCCCCATTGGCATTATCACTACACTAAATTTGTGCATAATGCCTCAGTAAACCCT
AAATCTTGAAACATTCTGTATCTTAAGGCCATGCATATCCACTTGTACATAACTGAAACGCTTG
AAAGGATACACTTCTTTCAGAATAATCATTATATCTTGGTAAAGTATTAGTTCTGGCTTTTTCT
TCAGCATTTGGAGGCCATGATCTGGTGTATCAGGCATAGATTTATTCAGGACATCTGTTCAAGG
TACACTGATCATACATCATGGAGCTCTGATGTGATTCAAAGGAAGGCATATGCAGAAGAAAGAA
AATGGCCTGGATTTTCTGATAAAGGGTCAGATATAAATGAAGCCAATCAGACTACACTATTCAT
CGAGCAGGCCCTACAAAACCTTGGCATTGAACAAAATTATAGGGATAAGGAGGAAGACATAACA
ATAACATGTTTACAGAATGAACAATCATCATCTATGTTCTGTTCCACAATTACAACCGATCATT
GTAGTATTGACAGATACCCTTTTAAGAATTTGCGTGAGGCAGTTGATGTACTCTTTCTACACGG
AGCATCAGACATGGTGATTGCAAAGCAAGCTATT
						
					

			
		

Sequences
Splice junction sequence	TTGTAGTATTGACAGATACCCTTTTAAGAATTTGCGTGAGGCAGTTGATGTACTCTTTCTACAC GGAGCATCAGACATGGTGATTGCAAAGCAAGCTATTatatcacagatgtttgtttggatgagaa tgctgtgtcaagtgatccacttctggcttttcttttggatgaggtggtcatcaaggactggtgc aagagggc
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: 864 Transcript exons: 8524741-8525190,8526153-8526566 ATATCACAGATGTTTGTTTGGATGAGAATGCTGTGTCAAGTGATCCACTTCTGGCTTTTCTTTT GGATGAGGTGGTCATCAAGGACTGGTGCAAGAGGGCTGTTAATGTGCTCATTACTGAGATTGGT GTGATCTGTATCCAAAAATGTTCAATCGACCCTAGATTCAGTTACATGCTTTTTTTTATGTTTC GTTTTTCATGTGTTCAGGGCCACACATGTTGAGGGAGTGGTACTGCTAATCTGTTAAGTCACTA ACCTTAACGATATCTTAGATAGGTCTGGATTAGAAACGATGAGATCTAGGTTATCCCAACTGCA AAAGTTTGCCACACAGTTGGCAGGAATTTACAGTATACTTGAAGTTATGGTTTCATCTTTCAAT GAAGCAGTTTCAGCGCATGTTAATGACCTGCACCAACTCATTGAGAACACATTGAAGGCAAAGC AGCATTTGGAGGCCATGATCTGGTGTATCAGGCATAGATTTATTCAGGACATCTGTTCAAGGTA CACTGATCATACATCATGGAGCTCTGATGTGATTCAAAGGAAGGCATATGCAGAAGAAAGAAAA TGGCCTGGATTTTCTGATAAAGGGTCAGATATAAATGAAGCCAATCAGACTACACTATTCATCG AGCAGGCCCTACAAAACCTTGGCATTGAACAAAATTATAGGGATAAGGAGGAAGACATAACAAT AACATGTTTACAGAATGAACAATCATCATCTATGTTCTGTTCCACAATTACAACCGATCATTGT AGTATTGACAGATACCCTTTTAAGAATTTGCGTGAGGCAGTTGATGTACTCTTTCTACACGGAG CATCAGACATGGTGATTGCAAAGCAAGCTATT
Genomic sequence	ATATCACAGATGTTTGTTTGGATGAGAATGCTGTGTCAAGTGATCCACTTCTGGCTTTTCTTTT GGATGAGGTGGTCATCAAGGACTGGTGCAAGAGGGCTGTTAATGTGCTCATTACTGAGATTGGT GTGATCTGTATCCAAAAATGTTCAATCGACCCTAGATTCAGTTACATGCTTTTTTTTATGTTTC GTTTTTCATGTGTTCAGGGCCACACATGTTGAGGGAGTGGTACTGCTAATCTGTTAAGTCACTA ACCTTAACGATATCTTAGATAGGTCTGGATTAGAAACGATGAGATCTAGGTTATCCCAACTGCA AAAGTTTGCCACACAGTTGGCAGGAATTTACAGTATACTTGAAGTTATGGTTTCATCTTTCAAT GAAGCAGTTTCAGCGCATGTTAATGACCTGCACCAACTCATTGAGAACACATTGAAGGCAAAGC AGGTCTTTCTTTCTTAACCCCTCTATTGCTAATGATTTTAGACCACTGCTTAGAACTAACACTG AGCTAGTCTAGGTACTTCAATTTGTTCATCCACTGCTGAAATTTCTATAAGATGAGTGTCCCAC GGGGACACTTTCCATTATATAATTTTGTGTATATATTGGAACAAAACCTTTTTATCTCCCTTTT GCTTAGTGTCATCATGATCCTGGACAAGTATTGACATAACCACTCAAAATAGTCTGGTGGTTCA TTTTGGTAACAAGTGCTCCCTCCAAATCTGAATATAAGTCAATTGTTACATTGATACAACCCAC CATGTGGAGCTTTGTCTAGCAATTTTCATGAAAATATCATATTTAAAATAAAAGGGGTTGTATA TTATCAAACTAGCCTTCATGATAATTCTACAAACATCAACTTTACGTTCTCATTCTACCTAATT CCTTATGCATCAATACTAAAAATAGTTAGACCAGCAAGAATCCTGAGACGACTATATGTACAAT CAGATTGAGTATGTCTCTAGCACTTTTCTTGTTTATGAAACCTTGTGCTTTCTTACACTCTGAT GCTTGCTAATGATGTAGCGTTATTGCATTAGATCATAGAACAAATTCTGTACCATTTGTTTCTT GGAGTATCTGTTAAAGATGCCTGCACATCAACAATCCTTTTAGTTGATTTTGTAGCATTACTTT ACTTCATATGTAATCTTTATTTTAAGGAGTCACTCACTCCAATAGGTGATGTCCTATCTTTCCC ATTCCTCTTCCCCCATTGGCATTATCACTACACTAAATTTGTGCATAATGCCTCAGTAAACCCT AAATCTTGAAACATTCTGTATCTTAAGGCCATGCATATCCACTTGTACATAACTGAAACGCTTG AAAGGATACACTTCTTTCAGAATAATCATTATATCTTGGTAAAGTATTAGTTCTGGCTTTTTCT TCAGCATTTGGAGGCCATGATCTGGTGTATCAGGCATAGATTTATTCAGGACATCTGTTCAAGG TACACTGATCATACATCATGGAGCTCTGATGTGATTCAAAGGAAGGCATATGCAGAAGAAAGAA AATGGCCTGGATTTTCTGATAAAGGGTCAGATATAAATGAAGCCAATCAGACTACACTATTCAT CGAGCAGGCCCTACAAAACCTTGGCATTGAACAAAATTATAGGGATAAGGAGGAAGACATAACA ATAACATGTTTACAGAATGAACAATCATCATCTATGTTCTGTTCCACAATTACAACCGATCATT GTAGTATTGACAGATACCCTTTTAAGAATTTGCGTGAGGCAGTTGATGTACTCTTTCTACACGG AGCATCAGACATGGTGATTGCAAAGCAAGCTATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							tae_circ_000060* osa_circ_021746 osi_circ_005087 osi_circ_013609 
						
						PMCS
						0.162102701

Conservation Information
Conserved circRNAs	tae_circ_000060* osa_circ_021746 osi_circ_005087 osi_circ_013609
PMCS	0.162102701

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8526166-8524869(+)
						
						Potential amino acid sequence
						
							MIWCIRHRFIQDICSRYTDHTSWSSDVIQRKAYAEERKWPGFSDKGSDINEANQTTLFIEQALQ
NLGIEQNYRDKEEDITITCLQNEQSSSMFCSTITTDHCSIDRYPFKNLREAVDVLFLHGASDMV
IAKQAIISQMFVWMRMLCQVIHFWLFFWMRWSSRTGARGLLMCSLLRLV*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	8526166-8524869(+)
Potential amino acid sequence	MIWCIRHRFIQDICSRYTDHTSWSSDVIQRKAYAEERKWPGFSDKGSDINEANQTTLFIEQALQ NLGIEQNYRDKEEDITITCLQNEQSSSMFCSTITTDHCSIDRYPFKNLREAVDVLFLHGASDMV IAKQAIISQMFVWMRMLCQVIHFWLFFWMRWSSRTGARGLLMCSLLRLV*(+)
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 Zm00001d013318_circ_g.3

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