Plant Circular RNA Database

Detail information of Zm00001d040416_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d040416_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007558
					
						Alias
						Zm03circ00023, zma_circ_0001049, GRMZM2G111014_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 42365293-42370359  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d040416						
					
						Parent gene annotation
						
							DNA gyrase subunit B mitochondrial
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d040416_circ_g.1 Zm00001d040416_circ_g.3 						
					
						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
						Zm00001d040416_T001:8
Zm00001d040416_T005:7
Zm00001d040416_T002:7
Zm00001d040416_T004:8

General Information
CircRNA Name	Zm00001d040416_circ_g.2
ID in PlantcircBase	zma_circ_007558
Alias	Zm03circ00023, zma_circ_0001049, GRMZM2G111014_C1
Organism	Zea mays
Position	chr3: 42365293-42370359 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d040416
Parent gene annotation	DNA gyrase subunit B mitochondrial
Parent gene strand	-
Alternative splicing	Zm00001d040416_circ_g.1 Zm00001d040416_circ_g.3
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	Zm00001d040416_T001:8 Zm00001d040416_T005:7 Zm00001d040416_T002:7 Zm00001d040416_T004:8

			
						 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  
						
							CTGATAAAGCATTAACAACTGATAAGCCAACACCATGAAGCCCTCCAGAGACACTGTAACCACT
TTTTGAACCTCCAAATTTGCCACCAGCGTGCATTAActtgagagcattaagggactttgatagg
attgaatccagaacatctggatgaagctctaagtactctgttaagttttcttgaacagactgct
caactatt

						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: 876
Transcript exons: 42365293-42365421,42365530-42365628,42365879-42366020,42
366793-42366863,42367796-42367900,42368800-42368876,4236
8971-42369121,42370258-42370359
CTTGAGAGCATTAAGGGACTTTGATAGGATTGAATCCAGAACATCTGGATGAAGCTCTAAGTAC
TCTGTTAAGTTTTCTTGAACAGACTGCTCAACTATTCTCCGTACTTCTGGATTTCCCAACCTTG
TCTTTGTTTGACCCTCAAACTCTGGACTAGGGACCTTCACTGAAATGATGCATGTCATTCCTTC
TCTTACATGCTCCCCACTCAAGGTAATATCCTTATCCTTAATAGTCTTCGACTTCTTTGCAAGG
TTATTAATGGTTCTCGTCAATGAAGCCTTTAGACCATCAATATGAGTACCACCATCAATAGTGC
GGATACTGTTTGCGTATCCTAGCACTGTATCAGAGTAGGAATCAGAGGACCATTGAAGGGAGAC
ATCCACTGTTATACCATCCAACTCCTTTCTGAACGCAATCGGGTCATGCAGGGGTTTCTTGTCA
GTATTCAACCATTTAACATATTCAACAAGGCCACCAGCATAACAATATTCGTTGCGTTGAACTG
TGTGCCCTTCTTCCTTTGTCAAGATTATTGTTAGCTCAGGATTTAGAAAGGCAAGCTCCCGTAT
GCGACTGGAGATTGTATTGAAGTCAAAATCGATCGTGGTGGTAAATATATCTTTATCAGGCCAA
AATCTGATGCGCGTCCCTTGACGAGAGCTTGTTTCACCAGTCAGTGTGCTACTAGTTAGCCTAG
TGGTTGGTTTCCCCCGCGAATAGCTTTGTCTGTGTTCCTTCCCATCACGCCAAACAGTAACTTC
AAGTGTCTCTGATAAAGCATTAACAACTGATAAGCCAACACCATGAAGCCCTCCAGAGACACTG
TAACCACTTTTTGAACCTCCAAATTTGCCACCAGCGTGCATTAA
						
						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	CTGATAAAGCATTAACAACTGATAAGCCAACACCATGAAGCCCTCCAGAGACACTGTAACCACT TTTTGAACCTCCAAATTTGCCACCAGCGTGCATTAActtgagagcattaagggactttgatagg attgaatccagaacatctggatgaagctctaagtactctgttaagttttcttgaacagactgct caactatt
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: 876 Transcript exons: 42365293-42365421,42365530-42365628,42365879-42366020,42 366793-42366863,42367796-42367900,42368800-42368876,4236 8971-42369121,42370258-42370359 CTTGAGAGCATTAAGGGACTTTGATAGGATTGAATCCAGAACATCTGGATGAAGCTCTAAGTAC TCTGTTAAGTTTTCTTGAACAGACTGCTCAACTATTCTCCGTACTTCTGGATTTCCCAACCTTG TCTTTGTTTGACCCTCAAACTCTGGACTAGGGACCTTCACTGAAATGATGCATGTCATTCCTTC TCTTACATGCTCCCCACTCAAGGTAATATCCTTATCCTTAATAGTCTTCGACTTCTTTGCAAGG TTATTAATGGTTCTCGTCAATGAAGCCTTTAGACCATCAATATGAGTACCACCATCAATAGTGC GGATACTGTTTGCGTATCCTAGCACTGTATCAGAGTAGGAATCAGAGGACCATTGAAGGGAGAC ATCCACTGTTATACCATCCAACTCCTTTCTGAACGCAATCGGGTCATGCAGGGGTTTCTTGTCA GTATTCAACCATTTAACATATTCAACAAGGCCACCAGCATAACAATATTCGTTGCGTTGAACTG TGTGCCCTTCTTCCTTTGTCAAGATTATTGTTAGCTCAGGATTTAGAAAGGCAAGCTCCCGTAT GCGACTGGAGATTGTATTGAAGTCAAAATCGATCGTGGTGGTAAATATATCTTTATCAGGCCAA AATCTGATGCGCGTCCCTTGACGAGAGCTTGTTTCACCAGTCAGTGTGCTACTAGTTAGCCTAG TGGTTGGTTTCCCCCGCGAATAGCTTTGTCTGTGTTCCTTCCCATCACGCCAAACAGTAACTTC AAGTGTCTCTGATAAAGCATTAACAACTGATAAGCCAACACCATGAAGCCCTCCAGAGACACTG TAACCACTTTTTGAACCTCCAAATTTGCCACCAGCGTGCATTAA
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
						0.051000371

Conservation Information
Conserved circRNAs	NA
PMCS	0.051000371

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							42370358-42365295(-)
						
						Potential amino acid sequence
						
							MHAGGKFGGSKSGYSVSGGLHGVGLSVVNALSETLEVTVWRDGKEHRQSYSRGKPTTRLTSSTL
TGETSSRQGTRIRFWPDKDIFTTTIDFDFNTISSRIRELAFLNPELTIILTKEEGHTVQRNEYC
YAGGLVEYVKWLNTDKKPLHDPIAFRKELDGITVDVSLQWSSDSYSDTVLGYANSIRTIDGGTH
IDGLKASLTRTINNLAKKSKTIKDKDITLSGEHVREGMTCIISVKVPSPEFEGQTKTRLGNPEV
RRIVEQSVQENLTEYLELHPDVLDSILSKSLNALKLMHAGGKFGGSKSGYSVSGGLHGVGLSVV
NALSETLEVTVWRDGKEHRQSYSRGKPTTRLTSSTLTGETSSRQGTRIRFWPDKDIFTTTIDFD
FNTISSRIRELAFLNPELTIILTKEEGHTVQRNEYCYAGGLVEYVKWLNTDKKPLHDPIAFRKE
LDGITVDVSLQWSSDSYSDTVLGYANSIRTIDGGTHIDGLKASLTRTINNLAKKSKTIKDKDIT
LSGEHVREGMTCIISVKVPSPEFEGQTKTRLGNPEVRRIVEQSVQENLTEYLELHPDVLDSILS
KSLNALKLMHAGGKFGGSKSGYSVSGGLHGVGLSVVNALSETLEVTVWRDGKEHRQSYSRGKPT
TRLTSSTLTGETSSRQGTRIRFWPDKDIFTTTIDFDFNTISSRIRELAFLNPELTIILTKEEGH
TVQRNEYCYAGGLVEYVKWLNTDKKPLHDPIAFRKELDGITVDVSLQWSSDSYSDTVLGYANSI
RTIDGGTHIDGLKASLTRTINNLAKKSKTIKDKDITLSGEHVREGMTCIISVKVPSPEFEGQTK
TRLGNPEVRRIVEQSVQENLTEYLELHPDVLDSILSKSLNALKLMHAGGKFGGSKSGYSVSGGL
HGVGLSVVNALSETLEVTVWRDGKEHRQSYSRGKPTTRLTSSTLTGETSSRQGTRIRFWPDKDI
FTTTIDFDFNTISSRIRELAFLNPELTIILTKEEGHTVQRNEYCYAGGLVEYVKWLNTDKKPLH
DPIAFRKELDGITVDVSLQWSSDSYSDTVLGYANSIRTIDGGTHIDGLKASLTRTINNLAKKSK
TIKDKDITLSGEHVREGMTCIISVKVPSPEFEGQTKTRLGNPEVRRIVEQSVQENLTEYLELHP
DVLDSILSKSLNALK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	42370358-42365295(-)
Potential amino acid sequence	MHAGGKFGGSKSGYSVSGGLHGVGLSVVNALSETLEVTVWRDGKEHRQSYSRGKPTTRLTSSTL TGETSSRQGTRIRFWPDKDIFTTTIDFDFNTISSRIRELAFLNPELTIILTKEEGHTVQRNEYC YAGGLVEYVKWLNTDKKPLHDPIAFRKELDGITVDVSLQWSSDSYSDTVLGYANSIRTIDGGTH IDGLKASLTRTINNLAKKSKTIKDKDITLSGEHVREGMTCIISVKVPSPEFEGQTKTRLGNPEV RRIVEQSVQENLTEYLELHPDVLDSILSKSLNALKLMHAGGKFGGSKSGYSVSGGLHGVGLSVV NALSETLEVTVWRDGKEHRQSYSRGKPTTRLTSSTLTGETSSRQGTRIRFWPDKDIFTTTIDFD FNTISSRIRELAFLNPELTIILTKEEGHTVQRNEYCYAGGLVEYVKWLNTDKKPLHDPIAFRKE LDGITVDVSLQWSSDSYSDTVLGYANSIRTIDGGTHIDGLKASLTRTINNLAKKSKTIKDKDIT LSGEHVREGMTCIISVKVPSPEFEGQTKTRLGNPEVRRIVEQSVQENLTEYLELHPDVLDSILS KSLNALKLMHAGGKFGGSKSGYSVSGGLHGVGLSVVNALSETLEVTVWRDGKEHRQSYSRGKPT TRLTSSTLTGETSSRQGTRIRFWPDKDIFTTTIDFDFNTISSRIRELAFLNPELTIILTKEEGH TVQRNEYCYAGGLVEYVKWLNTDKKPLHDPIAFRKELDGITVDVSLQWSSDSYSDTVLGYANSI RTIDGGTHIDGLKASLTRTINNLAKKSKTIKDKDITLSGEHVREGMTCIISVKVPSPEFEGQTK TRLGNPEVRRIVEQSVQENLTEYLELHPDVLDSILSKSLNALKLMHAGGKFGGSKSGYSVSGGL HGVGLSVVNALSETLEVTVWRDGKEHRQSYSRGKPTTRLTSSTLTGETSSRQGTRIRFWPDKDI FTTTIDFDFNTISSRIRELAFLNPELTIILTKEEGHTVQRNEYCYAGGLVEYVKWLNTDKKPLH DPIAFRKELDGITVDVSLQWSSDSYSDTVLGYANSIRTIDGGTHIDGLKASLTRTINNLAKKSK TIKDKDITLSGEHVREGMTCIISVKVPSPEFEGQTKTRLGNPEVRRIVEQSVQENLTEYLELHP DVLDSILSKSLNALK(-)
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 Zm00001d040416_circ_g.2

Address

Any questions?

Supported by