Plant Circular RNA Database

Detail information of Zm00001d004159_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d004159_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007225
					
						Alias
						zma_circ_0001110, GRMZM2G012942_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 87733029-87735008  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d004159						
					
						Parent gene annotation
						
							SNARE-interacting protein KEULE
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d004159_circ_g.1 						
					
						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
						Zm00001d004159_T004:7
Zm00001d004159_T003:7
Zm00001d004159_T006:7
Zm00001d004159_T007:7
Zm00001d004159_T001:7
Zm00001d004159_T005:7
Zm00001d004159_T002:7

General Information
CircRNA Name	Zm00001d004159_circ_g.2
ID in PlantcircBase	zma_circ_007225
Alias	zma_circ_0001110, GRMZM2G012942_C1
Organism	Zea mays
Position	chr2: 87733029-87735008 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d004159
Parent gene annotation	SNARE-interacting protein KEULE
Parent gene strand	-
Alternative splicing	Zm00001d004159_circ_g.1
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	Zm00001d004159_T004:7 Zm00001d004159_T003:7 Zm00001d004159_T006:7 Zm00001d004159_T007:7 Zm00001d004159_T001:7 Zm00001d004159_T005:7 Zm00001d004159_T002:7

			
						 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  
						
							ACAGGGAAGCAGCAAGCTTTGTTGGGACCAAATCTCGTAGTGTCGTCAGAGTAGATGCATCGAT
TGTCCTGGCTACACGATAGTGCACACGAGGAAATTCctgcatcagctttgcacctttctcactt
tcgaaaaatttctctgggtttatggaagcataaatcatcagcaaacgcagcttatgttcacgac
ttacatcc

									
								

					

						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: 771
Transcript exons: 87733029-87733127,87733209-87733334,87733812-87733908,87
734292-87734365,87734441-87734539,87734655-87734738,8773
4817-87735008
CTGCATCAGCTTTGCACCTTTCTCACTTTCGAAAAATTTCTCTGGGTTTATGGAAGCATAAATC
ATCAGCAAACGCAGCTTATGTTCACGACTTACATCCATGCGGGTTCGTAAGAAACTGATTAGTT
CTTTTGTCCCAGCATCACCAAACACAAGATCTTGCTCTAGCTGTCCAACATCTTTAAGGTGGTG
TTCTTTGATTATGTTATTGAGTTTTCCTGCAATCTCAACATGAAGGGTGAGCTTGTCAATTTGA
TCACTGTATTGTGGAAGAGCTTGAACCATTTTCTGCAACTGCTTGGTAGATAACTCTCCACCAG
ATCTTGCCTGCTGTAGTTGAGCTGCTTTGTTCTTTGATACAAAACTGGTCATCTTTTCATGTAG
CGTTTCATTAACATGAGCTATATGTGCATGCCGCAGCTCAAGCCATACTGGATCATGATCCTCC
AACAAAACCTCCTTTTTCTCATTTGCTGAACCATTCTTACTTGGAACCTCTTGCACGTACTTGT
TGCCATCCATACACAATAGATCATGGCACATAGCATCATACGTCCACTCATGAATAATTGGTGC
AATCTGATCTATTGACCGGTCAACAATAAGTAGTTCACATGTTTCTGTTTGTGGAAATTCAGGT
ATCGTTGACTTAAATCTGACAAGGGAATTCCACAGGGAAGCAGCAAGCTTTGTTGGGACCAAAT
CTCGTAGTGTCGTCAGAGTAGATGCATCGATTGTCCTGGCTACACGATAGTGCACACGAGGAAA
TTC
						
					

						Genomic sequence
						
							CTGCATCAGCTTTGCACCTTTCTCACTTTCGAAAAATTTCTCTGGGTTTATGGAAGCATAAATC
ATCAGCAAACGCAGCTTATGTTCACGACTTACATCCTGAATTAGTTAAGCAAAATATCTTGAGA
GGTGTAGAGACAAGTGCAGAATCTTATATGCTGTAGTTCAAACAACAATTACCATGCGGGTTCG
TAAGAAACTGATTAGTTCTTTTGTCCCAGCATCACCAAACACAAGATCTTGCTCTAGCTGTCCA
ACATCTTTAAGGTGGTGTTCTTTGATTATGTTATTGAGTTTTCCTGCAATCTGTAGTAACATGA
AACGGTAAATATTGTATTTCATGTCACACTGCTATTCTCTTCTTGGAAAACACCAGATTATGAT
TTCTTCCTCTAGTAAGTGTTATTCAAAATGACGATTCATGTGGACAACTGGACATGTTCCCCAG
CCCAAATGAATGCATCCAAATGTAATCTGATGACCCAAATGGTTAGTAAGCAAGTTAGGTGTTA
AATCTATCCAATCAAACTCTTGCTGGTTGTAGAGCTCACCGTGCAACTAAACTATACAATTGTT
TCTTATAGAATTATCAACATTTGTATATTGATACCTGAACTCCAGAATTTTCAAGGAGCAGAAG
GCAAAAAATGAGAAGCTAATGGCAATCACTATAATATATCAACAGACAAATCTACTGAAGTAGA
TAGAACAGTTATAAGAAATATTGTCTTTGTTAGTTTGTTGAGTTTGCAGATGCATGTCATGTAA
AACAAAACTACTAACCTCAACATGAAGGGTGAGCTTGTCAATTTGATCACTGTATTGTGGAAGA
GCTTGAACCATTTTCTGCAACTGCTTGGTAGATAACTCTCCACCAGATCTGACACTCAAAATAG
ATCCTATGAATAAATGTTAACCAGATCCATTGACACAGCTATCAAGCAGCTAATACTTTAGCTA
ACAGCATTGCTTGGCCCTTTAGTTATTTTGTAAACATAACTGGCAACAACAATTCACAGGGACA
TTTAGCAGAAAATGCTGTCAGACAAGAAAATTTAACCATTTTGAGTATCCTTTAAACCATCGAA
TTTAAAGATTGCACACATACACTAAGCACCCAGGTCTTAGTCTGCGCAGCAAACTGCTGATAAG
ACAGAACAACAGAAATGTCCATAGTATGAACAATGGTAAAAATTATTGTAACAGTTGCAAAAAT
ACACACGGGACACTCTAATATGCAGAAGTAGCATTTCTTGAACAAACCTTGCCTGCTGTAGTTG
AGCTGCTTTGTTCTTTGATACAAAACTGGTCATCTTTTCATGTAGCGTTTCATTAACCTGAAAT
GTTGATTTCATCATTATGTCAACAAAGCATATGACTATAGTTAAAGATGGAAGTGGCAACAATC
TTACATGAGCTATATGTGCATGCCGCAGCTCAAGCCATACTGGATCATGATCCTCCAACAAAAC
CTCCTTTTTCTCATTTGCTGAACCATTCTTACTTGGAACCTATTGTTTGAGGGTGGCATAAATT
TTAAGAGTCATGCATCAAAAACATAGTAAGAACTGAATAAGGTAAACTAGTGAGGTACAGTGTA
AGACTGTATGCTGCTGATGTACTCACCTCTTGCACGTACTTGTTGCCATCCATACACAATAGAT
CATGGCACATAGCATCATACGTCCACTCATGAATAATTGGTGCAATCTGTAGTGCTCAAGGAAA
CATGATATCAAAGGATGCATCAGCAATATGGAAATGTGTAAACTGGAATTCACCACCTACCTGA
TCTATTGACCGGTCAACAATAAGTAGTTCACATGTTTCTGTTTGTGGAAATTCAGGTATCGTTG
ACTTAAATCTGACAAGGGAATTCCACAGGGAAGCAGCAAGCTTTGTTGGGACCAAATCTCGTAG
TGTCGTCAGAGTAGATGCATCGATTGTCCTGGCTACACGATAGTGCACACGAGGAAATTC
						
					

			
		

Sequences
Splice junction sequence	ACAGGGAAGCAGCAAGCTTTGTTGGGACCAAATCTCGTAGTGTCGTCAGAGTAGATGCATCGAT TGTCCTGGCTACACGATAGTGCACACGAGGAAATTCctgcatcagctttgcacctttctcactt tcgaaaaatttctctgggtttatggaagcataaatcatcagcaaacgcagcttatgttcacgac ttacatcc
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: 771 Transcript exons: 87733029-87733127,87733209-87733334,87733812-87733908,87 734292-87734365,87734441-87734539,87734655-87734738,8773 4817-87735008 CTGCATCAGCTTTGCACCTTTCTCACTTTCGAAAAATTTCTCTGGGTTTATGGAAGCATAAATC ATCAGCAAACGCAGCTTATGTTCACGACTTACATCCATGCGGGTTCGTAAGAAACTGATTAGTT CTTTTGTCCCAGCATCACCAAACACAAGATCTTGCTCTAGCTGTCCAACATCTTTAAGGTGGTG TTCTTTGATTATGTTATTGAGTTTTCCTGCAATCTCAACATGAAGGGTGAGCTTGTCAATTTGA TCACTGTATTGTGGAAGAGCTTGAACCATTTTCTGCAACTGCTTGGTAGATAACTCTCCACCAG ATCTTGCCTGCTGTAGTTGAGCTGCTTTGTTCTTTGATACAAAACTGGTCATCTTTTCATGTAG CGTTTCATTAACATGAGCTATATGTGCATGCCGCAGCTCAAGCCATACTGGATCATGATCCTCC AACAAAACCTCCTTTTTCTCATTTGCTGAACCATTCTTACTTGGAACCTCTTGCACGTACTTGT TGCCATCCATACACAATAGATCATGGCACATAGCATCATACGTCCACTCATGAATAATTGGTGC AATCTGATCTATTGACCGGTCAACAATAAGTAGTTCACATGTTTCTGTTTGTGGAAATTCAGGT ATCGTTGACTTAAATCTGACAAGGGAATTCCACAGGGAAGCAGCAAGCTTTGTTGGGACCAAAT CTCGTAGTGTCGTCAGAGTAGATGCATCGATTGTCCTGGCTACACGATAGTGCACACGAGGAAA TTC
Genomic sequence	CTGCATCAGCTTTGCACCTTTCTCACTTTCGAAAAATTTCTCTGGGTTTATGGAAGCATAAATC ATCAGCAAACGCAGCTTATGTTCACGACTTACATCCTGAATTAGTTAAGCAAAATATCTTGAGA GGTGTAGAGACAAGTGCAGAATCTTATATGCTGTAGTTCAAACAACAATTACCATGCGGGTTCG TAAGAAACTGATTAGTTCTTTTGTCCCAGCATCACCAAACACAAGATCTTGCTCTAGCTGTCCA ACATCTTTAAGGTGGTGTTCTTTGATTATGTTATTGAGTTTTCCTGCAATCTGTAGTAACATGA AACGGTAAATATTGTATTTCATGTCACACTGCTATTCTCTTCTTGGAAAACACCAGATTATGAT TTCTTCCTCTAGTAAGTGTTATTCAAAATGACGATTCATGTGGACAACTGGACATGTTCCCCAG CCCAAATGAATGCATCCAAATGTAATCTGATGACCCAAATGGTTAGTAAGCAAGTTAGGTGTTA AATCTATCCAATCAAACTCTTGCTGGTTGTAGAGCTCACCGTGCAACTAAACTATACAATTGTT TCTTATAGAATTATCAACATTTGTATATTGATACCTGAACTCCAGAATTTTCAAGGAGCAGAAG GCAAAAAATGAGAAGCTAATGGCAATCACTATAATATATCAACAGACAAATCTACTGAAGTAGA TAGAACAGTTATAAGAAATATTGTCTTTGTTAGTTTGTTGAGTTTGCAGATGCATGTCATGTAA AACAAAACTACTAACCTCAACATGAAGGGTGAGCTTGTCAATTTGATCACTGTATTGTGGAAGA GCTTGAACCATTTTCTGCAACTGCTTGGTAGATAACTCTCCACCAGATCTGACACTCAAAATAG ATCCTATGAATAAATGTTAACCAGATCCATTGACACAGCTATCAAGCAGCTAATACTTTAGCTA ACAGCATTGCTTGGCCCTTTAGTTATTTTGTAAACATAACTGGCAACAACAATTCACAGGGACA TTTAGCAGAAAATGCTGTCAGACAAGAAAATTTAACCATTTTGAGTATCCTTTAAACCATCGAA TTTAAAGATTGCACACATACACTAAGCACCCAGGTCTTAGTCTGCGCAGCAAACTGCTGATAAG ACAGAACAACAGAAATGTCCATAGTATGAACAATGGTAAAAATTATTGTAACAGTTGCAAAAAT ACACACGGGACACTCTAATATGCAGAAGTAGCATTTCTTGAACAAACCTTGCCTGCTGTAGTTG AGCTGCTTTGTTCTTTGATACAAAACTGGTCATCTTTTCATGTAGCGTTTCATTAACCTGAAAT GTTGATTTCATCATTATGTCAACAAAGCATATGACTATAGTTAAAGATGGAAGTGGCAACAATC TTACATGAGCTATATGTGCATGCCGCAGCTCAAGCCATACTGGATCATGATCCTCCAACAAAAC CTCCTTTTTCTCATTTGCTGAACCATTCTTACTTGGAACCTATTGTTTGAGGGTGGCATAAATT TTAAGAGTCATGCATCAAAAACATAGTAAGAACTGAATAAGGTAAACTAGTGAGGTACAGTGTA AGACTGTATGCTGCTGATGTACTCACCTCTTGCACGTACTTGTTGCCATCCATACACAATAGAT CATGGCACATAGCATCATACGTCCACTCATGAATAATTGGTGCAATCTGTAGTGCTCAAGGAAA CATGATATCAAAGGATGCATCAGCAATATGGAAATGTGTAAACTGGAATTCACCACCTACCTGA TCTATTGACCGGTCAACAATAAGTAGTTCACATGTTTCTGTTTGTGGAAATTCAGGTATCGTTG ACTTAAATCTGACAAGGGAATTCCACAGGGAAGCAGCAAGCTTTGTTGGGACCAAATCTCGTAG TGTCGTCAGAGTAGATGCATCGATTGTCCTGGCTACACGATAGTGCACACGAGGAAATTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.073043712

Conservation Information
Conserved circRNAs	NA
PMCS	0.073043712

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							87734964-87733228(+)
87734704-87733031(-)
						
						Potential amino acid sequence
						
							MHRLSWLHDSAHEEIPASALHLSHFRKISLGLWKHKSSANAAYVHDLHPCGFVRN*(+)
MCHDLLCMDGNKYVQEVPSKNGSANEKKEVLLEDHDPVWLELRHAHIAHVNETLHEKMTSFVSK
NKAAQLQQARSGGELSTKQLQKMVQALPQYSDQIDKLTLHVEIAGKLNNIIKEHHLKDVGQLEQ
DLVFGDAGTKELISFLRTRMDVSREHKLRLLMIYASINPEKFFESEKGAKLMQEFPRVHYRVAR
TIDASTLTTLRDLVPTKLAASLWNSLVRFKSTIPEFPQTETCELLIVDRSIDQIAPIIHEWTYD
AMCHDLLCMDGNKYVQEVPSKNGSANEKKEVLLEDHDPVWLELRHAHIAHVNETLHEKMTSFVS
KNKAAQLQQARSGGELSTKQLQKMVQALPQYSDQIDKLTLHVEIAGKLNNIIKEHHLKDVGQLE
QDLVFGDAGTKELISFLRTRMDVSREHKLRLLMIYASINPEKFFESEKGAKLMQEFPRVHYRVA
RTIDASTLTTLRDLVPTKLAASLWNSLVRFKSTIPEFPQTETCELLIVDRSIDQIAPIIHEWTY
DAMCHDLLCMDGNKYVQEVPSKNGSANEKKEVLLEDHDPVWLELRHAHIAHVNETLHEKMTSFV
SKNKAAQLQQARSGGELSTKQLQKMVQALPQYSDQIDKLTLHVEIAGKLNNIIKEHHLKDVGQL
EQDLVFGDAGTKELISFLRTRMDVSREHKLRLLMIYASINPEKFFESEKGAKLMQEFPRVHYRV
ARTIDASTLTTLRDLVPTKLAASLWNSLVRFKSTIPEFPQTETCELLIVDRSIDQIAPIIHEWT
YDAMCHDLLCMDGNKYVQEVPSKNGSANEKKEVLLEDHDPVWLELRHAHIAHVNETLHEKMTSF
VSKNKAAQLQQARSGGELSTKQLQKMVQALPQYSDQIDKLTLHVEIAGKLNNIIKEHHLKDVGQ
LEQDLVFGDAGTKELISFLRTRMDVSREHKLRLLMIYASINPEKFFESEKGAKLMQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	87734964-87733228(+) 87734704-87733031(-)
Potential amino acid sequence	MHRLSWLHDSAHEEIPASALHLSHFRKISLGLWKHKSSANAAYVHDLHPCGFVRN*(+) MCHDLLCMDGNKYVQEVPSKNGSANEKKEVLLEDHDPVWLELRHAHIAHVNETLHEKMTSFVSK NKAAQLQQARSGGELSTKQLQKMVQALPQYSDQIDKLTLHVEIAGKLNNIIKEHHLKDVGQLEQ DLVFGDAGTKELISFLRTRMDVSREHKLRLLMIYASINPEKFFESEKGAKLMQEFPRVHYRVAR TIDASTLTTLRDLVPTKLAASLWNSLVRFKSTIPEFPQTETCELLIVDRSIDQIAPIIHEWTYD AMCHDLLCMDGNKYVQEVPSKNGSANEKKEVLLEDHDPVWLELRHAHIAHVNETLHEKMTSFVS KNKAAQLQQARSGGELSTKQLQKMVQALPQYSDQIDKLTLHVEIAGKLNNIIKEHHLKDVGQLE QDLVFGDAGTKELISFLRTRMDVSREHKLRLLMIYASINPEKFFESEKGAKLMQEFPRVHYRVA RTIDASTLTTLRDLVPTKLAASLWNSLVRFKSTIPEFPQTETCELLIVDRSIDQIAPIIHEWTY DAMCHDLLCMDGNKYVQEVPSKNGSANEKKEVLLEDHDPVWLELRHAHIAHVNETLHEKMTSFV SKNKAAQLQQARSGGELSTKQLQKMVQALPQYSDQIDKLTLHVEIAGKLNNIIKEHHLKDVGQL EQDLVFGDAGTKELISFLRTRMDVSREHKLRLLMIYASINPEKFFESEKGAKLMQEFPRVHYRV ARTIDASTLTTLRDLVPTKLAASLWNSLVRFKSTIPEFPQTETCELLIVDRSIDQIAPIIHEWT YDAMCHDLLCMDGNKYVQEVPSKNGSANEKKEVLLEDHDPVWLELRHAHIAHVNETLHEKMTSF VSKNKAAQLQQARSGGELSTKQLQKMVQALPQYSDQIDKLTLHVEIAGKLNNIIKEHHLKDVGQ LEQDLVFGDAGTKELISFLRTRMDVSREHKLRLLMIYASINPEKFFESEKGAKLMQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d004159_circ_g.2

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