Plant Circular RNA Database

Detail information of Zm00001d031863_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d031863_circ_g.1
					
						ID in PlantcircBase
						zma_circ_006732
					
						Alias
						Zm01circ00123, zma_circ_0000363, ZmciR25
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 204521024-204522460  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d031863						
					
						Parent gene annotation
						
							Mediator of RNA polymerase II transcription subunit 15a
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						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  
						
							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
						Zm00001d031863_T021:1
Zm00001d031863_T019:1
Zm00001d031863_T023:1
Zm00001d031863_T033:1
Zm00001d031863_T034:2
Zm00001d031863_T035:1
Zm00001d031863_T027:1
Zm00001d031863_T037:1
Zm00001d031863_T018:1
Zm00001d031863_T012:1
Zm00001d031863_T001:2
Zm00001d031863_T013:1
Zm00001d031863_T005:2
Zm00001d031863_T032:1
Zm00001d031863_T010:2
Zm00001d031863_T022:1
Zm00001d031863_T025:1
Zm00001d031863_T031:1
Zm00001d031863_T036:1
Zm00001d031863_T009:1
Zm00001d031863_T007:2
Zm00001d031863_T006:2
Zm00001d031863_T017:1
Zm00001d031863_T015:2
Zm00001d031863_T028:1
Zm00001d031863_T024:1
Zm00001d031863_T038:1

General Information
CircRNA Name	Zm00001d031863_circ_g.1
ID in PlantcircBase	zma_circ_006732
Alias	Zm01circ00123, zma_circ_0000363, ZmciR25
Organism	Zea mays
Position	chr1: 204521024-204522460 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d031863
Parent gene annotation	Mediator of RNA polymerase II transcription subunit 15a
Parent gene strand	-
Alternative splicing	NA
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	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	Zm00001d031863_T021:1 Zm00001d031863_T019:1 Zm00001d031863_T023:1 Zm00001d031863_T033:1 Zm00001d031863_T034:2 Zm00001d031863_T035:1 Zm00001d031863_T027:1 Zm00001d031863_T037:1 Zm00001d031863_T018:1 Zm00001d031863_T012:1 Zm00001d031863_T001:2 Zm00001d031863_T013:1 Zm00001d031863_T005:2 Zm00001d031863_T032:1 Zm00001d031863_T010:2 Zm00001d031863_T022:1 Zm00001d031863_T025:1 Zm00001d031863_T031:1 Zm00001d031863_T036:1 Zm00001d031863_T009:1 Zm00001d031863_T007:2 Zm00001d031863_T006:2 Zm00001d031863_T017:1 Zm00001d031863_T015:2 Zm00001d031863_T028:1 Zm00001d031863_T024:1 Zm00001d031863_T038:1

			
						 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  
						
							TTTGAGCGGGCATGTGGTTGTCAATATTTTGTATCTTCATGGATATCTTATTGTACACATCATT
CAATTCCGCAAAGTATTGGTCCTTTAAACTCTTAATtgctttaagcaagcgatcgagaggcctt
tctgctgcgcttgattttgttggaacttgagttggtacgctaacctgacctccatcagcacttg
tgaattct

									
								

					

						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: 1415
Transcript exons: 204521024-204521982,204522005-204522460
TGCTTTAAGCAAGCGATCGAGAGGCCTTTCTGCTGCGCTTGATTTTGTTGGAACTTGAGTTGGT
ACGCTAACCTGACCTCCATCAGCACTTGTGAATTCTGCAAGCAAGGGTGACGCTGATATACCTG
GTGTGTTAACAGCTATAGATTGTGTTAGAGGTGCAAGGGATGTTTGCTGATGTCCAGCCTGCCC
AGCACTAGTGAGTGAAGATAGGTTGGAGAGTGGTTTATCTGAATCCAGTGGGACCGGTGATGGG
GCAACAGGAGGAGATGGAGATGGGACAAATGGTGAGTTAGCTGAATGCAACGGTGTCCCGGTTT
TCACTTGAGATTGCAACAGACTGTGCTGATCAACATGAGAATAGTGTGAAATTTGTGGGGACGA
TGCTTGGAGGTTTTGCGGAGAAGAAATTGGAAAGACATCCCCCCGTTTTATCTGCTGATAATAG
TTACGCTGGTTCAGCGGTTGATACATTCCAGATTTGATTGCAGCTCCTTGCCTGACCTTTAGCT
CATTCACATCATTTCCAGAATGAAGTTGTTGAACCTGAATCGGCCCTTGCTGCTGTTGTTTCTG
TAGTTGTTGTATTGGGAGCTGTTGTTGAAGTATTTTCTTTTGCTGCATCTGCTGCAGCATCTGC
TGACGCTGCTTCATTTGCTGATTTTGCATCATCTGATGCTCCTGATGTTGCTTTAGCTGCTGCA
ATGAATTCACGTTTGCTTGCATGGCATTGGTATTAGTCTGCATTGTACTCATTGCATTGTTGGA
TATCATGTTACTATTGGACTGATGCTGTGCATTCAATGCACCCTGCATGGGACCAGTGCTTCCC
TGTTGCAATGCAGTACCCATTGAACCATGCTGCACAGGATTAAAATTATTTCCCTGAGCATTCT
CCGGATTAGAGGCAGCCTGCGGTGCATTTGTGACATTTTGCTGTGTTGTTGGAACACCAAAGTA
TGCTGAATGCCAGGTGCTCCAGAGGTCGGTACTCCTGTGTTCATACTTGGTAAACTTGCTTGAG
GCATCTGATTAGTATGACTATCATGCTGCTGCAAACCTTGGGAAGTCTGATGCTGCTGTGACAT
ATTAGAGCTAGGAGCTTGCCCACCAGATTGCTGAAACGTTTGCTGTCCAGGTGCCTGCACAGGC
TTCCTTCTTTGTGAACTCATGATACTGAGAATTTGCCTCTCGAAAATAGAGATTTTTTCCCTAA
AACCTGGCTGAATGCTGCTCTTGTTAGCTTGCAGGAAATGCAATATGCGCTCCAACATTCCTTT
AAAGCCTTTCAGCCTTTCATACTGCTCCGCTGACTTTTGAGCGGGCATGTGGTTGTCAATATTT
TGTATCTTCATGGATATCTTATTGTACACATCATTCAATTCCGCAAAGTATTGGTCCTTTAAAC
TCTTAAT
						
					

						Genomic sequence
						
							TGCTTTAAGCAAGCGATCGAGAGGCCTTTCTGCTGCGCTTGATTTTGTTGGAACTTGAGTTGGT
ACGCTAACCTGACCTCCATCAGCACTTGTGAATTCTGCAAGCAAGGGTGACGCTGATATACCTG
GTGTGTTAACAGCTATAGATTGTGTTAGAGGTGCAAGGGATGTTTGCTGATGTCCAGCCTGCCC
AGCACTAGTGAGTGAAGATAGGTTGGAGAGTGGTTTATCTGAATCCAGTGGGACCGGTGATGGG
GCAACAGGAGGAGATGGAGATGGGACAAATGGTGAGTTAGCTGAATGCAACGGTGTCCCGGTTT
TCACTTGAGATTGCAACAGACTGTGCTGATCAACATGAGAATAGTGTGAAATTTGTGGGGACGA
TGCTTGGAGGTTTTGCGGAGAAGAAATTGGAAAGACATCCCCCCGTTTTATCTGCTGATAATAG
TTACGCTGGTTCAGCGGTTGATACATTCCAGATTTGATTGCAGCTCCTTGCCTGACCTTTAGCT
CATTCACATCATTTCCAGAATGAAGTTGTTGAACCTGAATCGGCCCTTGCTGCTGTTGTTTCTG
TAGTTGTTGTATTGGGAGCTGTTGTTGAAGTATTTTCTTTTGCTGCATCTGCTGCAGCATCTGC
TGACGCTGCTTCATTTGCTGATTTTGCATCATCTGATGCTCCTGATGTTGCTTTAGCTGCTGCA
ATGAATTCACGTTTGCTTGCATGGCATTGGTATTAGTCTGCATTGTACTCATTGCATTGTTGGA
TATCATGTTACTATTGGACTGATGCTGTGCATTCAATGCACCCTGCATGGGACCAGTGCTTCCC
TGTTGCAATGCAGTACCCATTGAACCATGCTGCACAGGATTAAAATTATTTCCCTGAGCATTCT
CCGGATTAGAGGCAGCCTGCGGTGCATTTGTGACATTTTGCTGTGTTGTTGGAACACCAAAGTT
TGATGCTTGAGGCGCAGGTACATGCTGAATGCCAGGTGCTCCAGAGGTCGGTACTCCTGTGTTC
ATACTTGGTAAACTTGCTTGAGGCATCTGATTAGTATGACTATCATGCTGCTGCAAACCTTGGG
AAGTCTGATGCTGCTGTGACATATTAGAGCTAGGAGCTTGCCCACCAGATTGCTGAAACGTTTG
CTGTCCAGGTGCCTGCACAGGCTTCCTTCTTTGTGAACTCATGATACTGAGAATTTGCCTCTCG
AAAATAGAGATTTTTTCCCTAAAACCTGGCTGAATGCTGCTCTTGTTAGCTTGCAGGAAATGCA
ATATGCGCTCCAACATTCCTTTAAAGCCTTTCAGCCTTTCATACTGCTCCGCTGACTTTTGAGC
GGGCATGTGGTTGTCAATATTTTGTATCTTCATGGATATCTTATTGTACACATCATTCAATTCC
GCAAAGTATTGGTCCTTTAAACTCTTAAT
						
					

			
		

Sequences
Splice junction sequence	TTTGAGCGGGCATGTGGTTGTCAATATTTTGTATCTTCATGGATATCTTATTGTACACATCATT CAATTCCGCAAAGTATTGGTCCTTTAAACTCTTAATtgctttaagcaagcgatcgagaggcctt tctgctgcgcttgattttgttggaacttgagttggtacgctaacctgacctccatcagcacttg tgaattct
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: 1415 Transcript exons: 204521024-204521982,204522005-204522460 TGCTTTAAGCAAGCGATCGAGAGGCCTTTCTGCTGCGCTTGATTTTGTTGGAACTTGAGTTGGT ACGCTAACCTGACCTCCATCAGCACTTGTGAATTCTGCAAGCAAGGGTGACGCTGATATACCTG GTGTGTTAACAGCTATAGATTGTGTTAGAGGTGCAAGGGATGTTTGCTGATGTCCAGCCTGCCC AGCACTAGTGAGTGAAGATAGGTTGGAGAGTGGTTTATCTGAATCCAGTGGGACCGGTGATGGG GCAACAGGAGGAGATGGAGATGGGACAAATGGTGAGTTAGCTGAATGCAACGGTGTCCCGGTTT TCACTTGAGATTGCAACAGACTGTGCTGATCAACATGAGAATAGTGTGAAATTTGTGGGGACGA TGCTTGGAGGTTTTGCGGAGAAGAAATTGGAAAGACATCCCCCCGTTTTATCTGCTGATAATAG TTACGCTGGTTCAGCGGTTGATACATTCCAGATTTGATTGCAGCTCCTTGCCTGACCTTTAGCT CATTCACATCATTTCCAGAATGAAGTTGTTGAACCTGAATCGGCCCTTGCTGCTGTTGTTTCTG TAGTTGTTGTATTGGGAGCTGTTGTTGAAGTATTTTCTTTTGCTGCATCTGCTGCAGCATCTGC TGACGCTGCTTCATTTGCTGATTTTGCATCATCTGATGCTCCTGATGTTGCTTTAGCTGCTGCA ATGAATTCACGTTTGCTTGCATGGCATTGGTATTAGTCTGCATTGTACTCATTGCATTGTTGGA TATCATGTTACTATTGGACTGATGCTGTGCATTCAATGCACCCTGCATGGGACCAGTGCTTCCC TGTTGCAATGCAGTACCCATTGAACCATGCTGCACAGGATTAAAATTATTTCCCTGAGCATTCT CCGGATTAGAGGCAGCCTGCGGTGCATTTGTGACATTTTGCTGTGTTGTTGGAACACCAAAGTA TGCTGAATGCCAGGTGCTCCAGAGGTCGGTACTCCTGTGTTCATACTTGGTAAACTTGCTTGAG GCATCTGATTAGTATGACTATCATGCTGCTGCAAACCTTGGGAAGTCTGATGCTGCTGTGACAT ATTAGAGCTAGGAGCTTGCCCACCAGATTGCTGAAACGTTTGCTGTCCAGGTGCCTGCACAGGC TTCCTTCTTTGTGAACTCATGATACTGAGAATTTGCCTCTCGAAAATAGAGATTTTTTCCCTAA AACCTGGCTGAATGCTGCTCTTGTTAGCTTGCAGGAAATGCAATATGCGCTCCAACATTCCTTT AAAGCCTTTCAGCCTTTCATACTGCTCCGCTGACTTTTGAGCGGGCATGTGGTTGTCAATATTT TGTATCTTCATGGATATCTTATTGTACACATCATTCAATTCCGCAAAGTATTGGTCCTTTAAAC TCTTAAT
Genomic sequence	TGCTTTAAGCAAGCGATCGAGAGGCCTTTCTGCTGCGCTTGATTTTGTTGGAACTTGAGTTGGT ACGCTAACCTGACCTCCATCAGCACTTGTGAATTCTGCAAGCAAGGGTGACGCTGATATACCTG GTGTGTTAACAGCTATAGATTGTGTTAGAGGTGCAAGGGATGTTTGCTGATGTCCAGCCTGCCC AGCACTAGTGAGTGAAGATAGGTTGGAGAGTGGTTTATCTGAATCCAGTGGGACCGGTGATGGG GCAACAGGAGGAGATGGAGATGGGACAAATGGTGAGTTAGCTGAATGCAACGGTGTCCCGGTTT TCACTTGAGATTGCAACAGACTGTGCTGATCAACATGAGAATAGTGTGAAATTTGTGGGGACGA TGCTTGGAGGTTTTGCGGAGAAGAAATTGGAAAGACATCCCCCCGTTTTATCTGCTGATAATAG TTACGCTGGTTCAGCGGTTGATACATTCCAGATTTGATTGCAGCTCCTTGCCTGACCTTTAGCT CATTCACATCATTTCCAGAATGAAGTTGTTGAACCTGAATCGGCCCTTGCTGCTGTTGTTTCTG TAGTTGTTGTATTGGGAGCTGTTGTTGAAGTATTTTCTTTTGCTGCATCTGCTGCAGCATCTGC TGACGCTGCTTCATTTGCTGATTTTGCATCATCTGATGCTCCTGATGTTGCTTTAGCTGCTGCA ATGAATTCACGTTTGCTTGCATGGCATTGGTATTAGTCTGCATTGTACTCATTGCATTGTTGGA TATCATGTTACTATTGGACTGATGCTGTGCATTCAATGCACCCTGCATGGGACCAGTGCTTCCC TGTTGCAATGCAGTACCCATTGAACCATGCTGCACAGGATTAAAATTATTTCCCTGAGCATTCT CCGGATTAGAGGCAGCCTGCGGTGCATTTGTGACATTTTGCTGTGTTGTTGGAACACCAAAGTT TGATGCTTGAGGCGCAGGTACATGCTGAATGCCAGGTGCTCCAGAGGTCGGTACTCCTGTGTTC ATACTTGGTAAACTTGCTTGAGGCATCTGATTAGTATGACTATCATGCTGCTGCAAACCTTGGG AAGTCTGATGCTGCTGTGACATATTAGAGCTAGGAGCTTGCCCACCAGATTGCTGAAACGTTTG CTGTCCAGGTGCCTGCACAGGCTTCCTTCTTTGTGAACTCATGATACTGAGAATTTGCCTCTCG AAAATAGAGATTTTTTCCCTAAAACCTGGCTGAATGCTGCTCTTGTTAGCTTGCAGGAAATGCA ATATGCGCTCCAACATTCCTTTAAAGCCTTTCAGCCTTTCATACTGCTCCGCTGACTTTTGAGC GGGCATGTGGTTGTCAATATTTTGTATCTTCATGGATATCTTATTGTACACATCATTCAATTCC GCAAAGTATTGGTCCTTTAAACTCTTAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.211338889

Conservation Information
Conserved circRNAs	NA
PMCS	0.211338889

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							204522373-204521078(+)
204521108-204522450(-)
204521877-204521826(-)
						
						Potential amino acid sequence
						
							MWLSIFCIFMDILLYTSFNSAKYWSFKLLIALSKRSRGLSAALDFVGT*(+)
MEVRLAYQLKFQQNQAQQKGLSIACLKQLRV*(-)
MGTALQQGSTGPMQGALNAQHQSNSNMISNNAMSTMQTNTNAMQANVNSLQQLKQHQEHQMMQN
QQMKQRQQMLQQMQQKKILQQQLPIQQLQKQQQQGPIQVQQLHSGNDVNELKVRQGAAIKSGMY
QPLNQRNYYQQIKRGDVFPISSPQNLQASSPQISHYSHVDQHSLLQSQVKTGTPLHSANSPFVP
SPSPPVAPSPVPLDSDKPLSNLSSLTSAGQAGHQQTSLAPLTQSIAVNTPGISASPLLAEFTSA
DGGQVSVPTQVPTKSSAAERPLDRLLKAIKSLKDQYFAELNDVYNKISMKIQNIDNHMPAQKSA
EQYERLKGFKGMLERILHFLQANKSSIQPGFREKISIFERQILSIMSSQRRKPVQAPGQQTFQQ
SGGQAPSSNMSQQHQTSQGLQQHDSHTNQMPQASLPSMNTGVPTSGAPGIQHTLVFQQHSKMSQ
MHRRLPLIRRMLREIILILCSMVQWVLHCNREALVPCRVH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	204522373-204521078(+) 204521108-204522450(-) 204521877-204521826(-)
Potential amino acid sequence	MWLSIFCIFMDILLYTSFNSAKYWSFKLLIALSKRSRGLSAALDFVGT(+) MEVRLAYQLKFQQNQAQQKGLSIACLKQLRV(-) MGTALQQGSTGPMQGALNAQHQSNSNMISNNAMSTMQTNTNAMQANVNSLQQLKQHQEHQMMQN QQMKQRQQMLQQMQQKKILQQQLPIQQLQKQQQQGPIQVQQLHSGNDVNELKVRQGAAIKSGMY QPLNQRNYYQQIKRGDVFPISSPQNLQASSPQISHYSHVDQHSLLQSQVKTGTPLHSANSPFVP SPSPPVAPSPVPLDSDKPLSNLSSLTSAGQAGHQQTSLAPLTQSIAVNTPGISASPLLAEFTSA DGGQVSVPTQVPTKSSAAERPLDRLLKAIKSLKDQYFAELNDVYNKISMKIQNIDNHMPAQKSA EQYERLKGFKGMLERILHFLQANKSSIQPGFREKISIFERQILSIMSSQRRKPVQAPGQQTFQQ SGGQAPSSNMSQQHQTSQGLQQHDSHTNQMPQASLPSMNTGVPTSGAPGIQHTLVFQQHSKMSQ MHRRLPLIRRMLREIILILCSMVQWVLHCNREALVPCRVH*(-)
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 Zm00001d031863_circ_g.1

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