Plant Circular RNA Database

Detail information of Zm00001d021972_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d021972_circ_g.4
					
						ID in PlantcircBase
						zma_circ_009456
					
						Alias
						Zm07circ00086, zma_circ_0002553, GRMZM2G411916_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr7: 167319246-167321304  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d021972						
					
						Parent gene annotation
						
							Phospholipid-transporting ATPase 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d021972_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
						Zm00001d021972_T005:6
Zm00001d021972_T001:6
Zm00001d021972_T010:6
Zm00001d021972_T009:6
Zm00001d021972_T011:6
Zm00001d021972_T004:6
Zm00001d021972_T003:6
Zm00001d021972_T002:6
Zm00001d021972_T008:6
Zm00001d021972_T006:6
Zm00001d021972_T007:6

General Information
CircRNA Name	Zm00001d021972_circ_g.4
ID in PlantcircBase	zma_circ_009456
Alias	Zm07circ00086, zma_circ_0002553, GRMZM2G411916_C2
Organism	Zea mays
Position	chr7: 167319246-167321304 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d021972
Parent gene annotation	Phospholipid-transporting ATPase 2
Parent gene strand	-
Alternative splicing	Zm00001d021972_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	Zm00001d021972_T005:6 Zm00001d021972_T001:6 Zm00001d021972_T010:6 Zm00001d021972_T009:6 Zm00001d021972_T011:6 Zm00001d021972_T004:6 Zm00001d021972_T003:6 Zm00001d021972_T002:6 Zm00001d021972_T008:6 Zm00001d021972_T006:6 Zm00001d021972_T007:6

			
						 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  
						
							AACCTTTTTATAGGAATTACTGTATTGCAGAGTGTCATGACTGTCAAAAACTTGATGACATTAG
GAGAATTATTGGCGACAGCGTTCAGTAATTCAACGTctgaagaaatcaagttgcacaaaagagc
aatttgaatggcagtactttgtttatcaccagttaacatccagaagttgattcctgactgcctc
agtatttc

									
								

					

						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: 729
Transcript exons: 167319246-167319366,167319469-167319549,167319626-167319
780,167320763-167320927,167321009-167321118,167321208-16
7321304
CTGAAGAAATCAAGTTGCACAAAAGAGCAATTTGAATGGCAGTACTTTGTTTATCACCAGTTAA
CATCCAGAAGTTGATTCCTGACTGCCTCAGTATTTCGATAGTTTCTGGTACCCCATCCTGGAGG
CGATCTTCTATTGCACTGACACCTAGAATCTCCAAGCTATGTTCTAGCTTTTGGCAAACCTCAG
CAACTTTCCACTCCCTGTCATTCAATGAGCTATTGGCCTCCTTAAATGATTGAGACCATTTAGT
GTATTCCTCTGGTTCCAGCTCACGCCATCCCAAGCAGAGTGTGCGCAACCCCAGCTGAGCATAT
TTGTCAACTGCATCAACAAATGTCTTTGTCTTTTGTCCAGAATAAGCACAAGGAAGCATTGCCT
CATCAGCTCCTTTGGACAAGAGAAAAAACTTGCCACTCTGACAATCCAAAATAACAATAGACAT
TCTTTTCCGGTCAGATGTGAACTCAAGAATGTCAAGTATCTCATATTGCATCACTCGCCGGTTG
AAGTGAATTTCTGCATTGCTTCCATTCTTGCTGACAAGAACCATATGCAAATTTGCAGCTGCAT
TAACCAGGGCATCCTCATCCTGGGACTGGGCTTTATACAAAATTGGTCCAGTAGGACTTTTTAT
AGGAATTACTGTATTGCAGAGTGTCATGACTGTCAAAAACTTGATGACATTAGGAGAATTATTG
GCGACAGCGTTCAGTAATTCAACGT
						
					

						Genomic sequence
						
							CTGAAGAAATCAAGTTGCACAAAAGAGCAATTTGAATGGCAGTACTTTGTTTATCACCAGTTAA
CATCCAGAAGTTGATTCCTGACTGCCTCAGTATTTCGATAGTTTCTGGTACCCCATCCTATGAA
CAGATCCAAGTATAAGGGTCAGGTGGCCCACAAAGGCCAAAAAGAATAATGTACTGTTACATTT
ACATGATATGAAAACAAAGCCAAAGTAGAACCTGGAGGCGATCTTCTATTGCACTGACACCTAG
AATCTCCAAGCTATGTTCTAGCTTTTGGCAAACCTCAGCAACTTTCCACTGAGCAAAGCAAATA
TAGAGGAATTATTTTTTTAATCAAATTTATCTGAATTGAATTAATAAATATGATAATTACCTCC
CTGTCATTCAATGAGCTATTGGCCTCCTTAAATGATTGAGACCATTTAGTGTATTCCTCTGGTT
CCAGCTCACGCCATCCCAAGCAGAGTGTGCGCAACCCCAGCTGAGCATATTTGTCAACTGCATC
AACAAATGTCTTTGTCTTTTGTCCTGAAAATTAACTATCATGAGAACCTCAGCTCAAACACAAA
TCACTAATAGAGTTGCATCAACAAAAAAATATATGTTATGCAAAGACCTGTCAGCCAGAATCCT
GTGTGTGCTGCATGTATCTAGGTTCATTTTGTGTAGGCGCAGTCTTAAGTACTAGCAGATTTTC
AGTAGCAGTTTAGAAGAATAATAGGAAACCATAGTACATTTTTTTCTCGAAAAGCGCAGGAGAA
CTGCACTCCAGTATATTATAGCAGAGAGAAAGGGGAAAAGAACCCCAGATACAAGACACTCCTT
ACGGAGGCCAGACACAAGCATACATAAAACGGTCCATAGGAAAGGCTAAGCCACACAACCCTTA
CGTAGTGGAGAGTAAGGCAGCCAAGAAGGATAATCCCTTGGCACCAGCCACTTGCCACTTCTCC
CTCTCCTCATGAGCAGTCTGCAGGAGAAGAGAGAGGCTAGGAGCCACTCCATAAAAAACCACTC
TATTTCTATGGTTCCAGATCAACCACGCTCCAAGAGAGGAGGGAATCCAGCCCTTTCTTCCTCA
GACCTGTGACCTGACCTAGCTCTCTCTCACACCAGCCCAAAAAGCTGATATCTTCTTGTTGAGA
GACTAAACTGTGCAGGCCAAAAAACCTTAAGATGCTAGTACATTAGTTGGGAGGATATCACGGA
CAGCTCCATCCCTCTCATGAAAAAATGGTGAGGGCTTGTGTGGCCGCGTCGACAAAAAACTAGT
GTTGCTATGTACAGTGTCCACCAGAGAGAAGCTAGCGTGCGTGTTTGTGATAAACTCTCAAGAG
AGAGGAATTGATTTGCAAGAAGACACACAATCAAGAGAACGCAGCCATTTATTACTTCTGAAGT
AAAATGTAGATTAAATTTATGCCACAAAATAAGAAGTATGTAAATGCTAGGTTCTAAAATATTT
AAAGGATATTTAGAAAATGTTATGCTTAATAATTGAGGTAATTACCAGAATAAGCACAAGGAAG
CATTGCCTCATCAGCTCCTTTGGACAAGAGAAAAAACTTGCCACTCTGACAATCCAAAATAACA
ATAGACATTCTTTTCCGGTCAGATGTGAACTCAAGAATGTCAAGTATCTCATATTGCATCACTC
GCCGGTTGAAGTGAATTTCTGCTTTTAGGAGATGTCTAATTATTTATCCAATAAACCATACAAA
ACAAAACAAACAAATTTAGGAACCAGAAAACCTACCTGCATTGCTTCCATTCTTGCTGACAAGA
ACCATATGCAAATTTGCAGCTGCATTAACCAGGGCATCCTCATCCTGGGACTGGGCTTTATACA
AAATTGGTCCAGTAGGACTGGAAGCCATATCATTTGGTCAAGAATAAATATTAAGAAGAATGAA
CAGAATATGTGGGCTAAACTGTCAGGAGGATGAATGTCAAACCTTTTTATAGGAATTACTGTAT
TGCAGAGTGTCATGACTGTCAAAAACTTGATGACATTAGGAGAATTATTGGCGACAGCGTTCAG
TAATTCAACGT
						
					

			
		

Sequences
Splice junction sequence	AACCTTTTTATAGGAATTACTGTATTGCAGAGTGTCATGACTGTCAAAAACTTGATGACATTAG GAGAATTATTGGCGACAGCGTTCAGTAATTCAACGTctgaagaaatcaagttgcacaaaagagc aatttgaatggcagtactttgtttatcaccagttaacatccagaagttgattcctgactgcctc agtatttc
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: 729 Transcript exons: 167319246-167319366,167319469-167319549,167319626-167319 780,167320763-167320927,167321009-167321118,167321208-16 7321304 CTGAAGAAATCAAGTTGCACAAAAGAGCAATTTGAATGGCAGTACTTTGTTTATCACCAGTTAA CATCCAGAAGTTGATTCCTGACTGCCTCAGTATTTCGATAGTTTCTGGTACCCCATCCTGGAGG CGATCTTCTATTGCACTGACACCTAGAATCTCCAAGCTATGTTCTAGCTTTTGGCAAACCTCAG CAACTTTCCACTCCCTGTCATTCAATGAGCTATTGGCCTCCTTAAATGATTGAGACCATTTAGT GTATTCCTCTGGTTCCAGCTCACGCCATCCCAAGCAGAGTGTGCGCAACCCCAGCTGAGCATAT TTGTCAACTGCATCAACAAATGTCTTTGTCTTTTGTCCAGAATAAGCACAAGGAAGCATTGCCT CATCAGCTCCTTTGGACAAGAGAAAAAACTTGCCACTCTGACAATCCAAAATAACAATAGACAT TCTTTTCCGGTCAGATGTGAACTCAAGAATGTCAAGTATCTCATATTGCATCACTCGCCGGTTG AAGTGAATTTCTGCATTGCTTCCATTCTTGCTGACAAGAACCATATGCAAATTTGCAGCTGCAT TAACCAGGGCATCCTCATCCTGGGACTGGGCTTTATACAAAATTGGTCCAGTAGGACTTTTTAT AGGAATTACTGTATTGCAGAGTGTCATGACTGTCAAAAACTTGATGACATTAGGAGAATTATTG GCGACAGCGTTCAGTAATTCAACGT
Genomic sequence	CTGAAGAAATCAAGTTGCACAAAAGAGCAATTTGAATGGCAGTACTTTGTTTATCACCAGTTAA CATCCAGAAGTTGATTCCTGACTGCCTCAGTATTTCGATAGTTTCTGGTACCCCATCCTATGAA CAGATCCAAGTATAAGGGTCAGGTGGCCCACAAAGGCCAAAAAGAATAATGTACTGTTACATTT ACATGATATGAAAACAAAGCCAAAGTAGAACCTGGAGGCGATCTTCTATTGCACTGACACCTAG AATCTCCAAGCTATGTTCTAGCTTTTGGCAAACCTCAGCAACTTTCCACTGAGCAAAGCAAATA TAGAGGAATTATTTTTTTAATCAAATTTATCTGAATTGAATTAATAAATATGATAATTACCTCC CTGTCATTCAATGAGCTATTGGCCTCCTTAAATGATTGAGACCATTTAGTGTATTCCTCTGGTT CCAGCTCACGCCATCCCAAGCAGAGTGTGCGCAACCCCAGCTGAGCATATTTGTCAACTGCATC AACAAATGTCTTTGTCTTTTGTCCTGAAAATTAACTATCATGAGAACCTCAGCTCAAACACAAA TCACTAATAGAGTTGCATCAACAAAAAAATATATGTTATGCAAAGACCTGTCAGCCAGAATCCT GTGTGTGCTGCATGTATCTAGGTTCATTTTGTGTAGGCGCAGTCTTAAGTACTAGCAGATTTTC AGTAGCAGTTTAGAAGAATAATAGGAAACCATAGTACATTTTTTTCTCGAAAAGCGCAGGAGAA CTGCACTCCAGTATATTATAGCAGAGAGAAAGGGGAAAAGAACCCCAGATACAAGACACTCCTT ACGGAGGCCAGACACAAGCATACATAAAACGGTCCATAGGAAAGGCTAAGCCACACAACCCTTA CGTAGTGGAGAGTAAGGCAGCCAAGAAGGATAATCCCTTGGCACCAGCCACTTGCCACTTCTCC CTCTCCTCATGAGCAGTCTGCAGGAGAAGAGAGAGGCTAGGAGCCACTCCATAAAAAACCACTC TATTTCTATGGTTCCAGATCAACCACGCTCCAAGAGAGGAGGGAATCCAGCCCTTTCTTCCTCA GACCTGTGACCTGACCTAGCTCTCTCTCACACCAGCCCAAAAAGCTGATATCTTCTTGTTGAGA GACTAAACTGTGCAGGCCAAAAAACCTTAAGATGCTAGTACATTAGTTGGGAGGATATCACGGA CAGCTCCATCCCTCTCATGAAAAAATGGTGAGGGCTTGTGTGGCCGCGTCGACAAAAAACTAGT GTTGCTATGTACAGTGTCCACCAGAGAGAAGCTAGCGTGCGTGTTTGTGATAAACTCTCAAGAG AGAGGAATTGATTTGCAAGAAGACACACAATCAAGAGAACGCAGCCATTTATTACTTCTGAAGT AAAATGTAGATTAAATTTATGCCACAAAATAAGAAGTATGTAAATGCTAGGTTCTAAAATATTT AAAGGATATTTAGAAAATGTTATGCTTAATAATTGAGGTAATTACCAGAATAAGCACAAGGAAG CATTGCCTCATCAGCTCCTTTGGACAAGAGAAAAAACTTGCCACTCTGACAATCCAAAATAACA ATAGACATTCTTTTCCGGTCAGATGTGAACTCAAGAATGTCAAGTATCTCATATTGCATCACTC GCCGGTTGAAGTGAATTTCTGCTTTTAGGAGATGTCTAATTATTTATCCAATAAACCATACAAA ACAAAACAAACAAATTTAGGAACCAGAAAACCTACCTGCATTGCTTCCATTCTTGCTGACAAGA ACCATATGCAAATTTGCAGCTGCATTAACCAGGGCATCCTCATCCTGGGACTGGGCTTTATACA AAATTGGTCCAGTAGGACTGGAAGCCATATCATTTGGTCAAGAATAAATATTAAGAAGAATGAA CAGAATATGTGGGCTAAACTGTCAGGAGGATGAATGTCAAACCTTTTTATAGGAATTACTGTAT TGCAGAGTGTCATGACTGTCAAAAACTTGATGACATTAGGAGAATTATTGGCGACAGCGTTCAG TAATTCAACGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.16914295

Conservation Information
Conserved circRNAs	NA
PMCS	0.16914295

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							167321242-167319277(+)
167321244-167319248(-)
						
						Potential amino acid sequence
						
							MTVKNLMTLGELLATAFSNSTSEEIKLHKRAI*(+)
MTLCNTVIPIKSPTGPILYKAQSQDEDALVNAAANLHMVLVSKNGSNAEIHFNRRVMQYEILDI
LEFTSDRKRMSIVILDCQSGKFFLLSKGADEAMLPCAYSGQKTKTFVDAVDKYAQLGLRTLCLG
WRELEPEEYTKWSQSFKEANSSLNDREWKVAEVCQKLEHSLEILGVSAIEDRLQDGVPETIEIL
RQSGINFWMLTGDKQSTAIQIALLCNLISSDVELLNAVANNSPNVIKFLTVMTLCNTVIPIKSP
TGPILYKAQSQDEDALVNAAANLHMVLVSKNGSNAEIHFNRRVMQYEILDILEFTSDRKRMSIV
ILDCQSGKFFLLSKGADEAMLPCAYSGQKTKTFVDAVDKYAQLGLRTLCLGWRELEPEEYTKWS
QSFKEANSSLNDREWKVAEVCQKLEHSLEILGVSAIEDRLQDGVPETIEILRQSGINFWMLTGD
KQSTAIQIALLCNLISSDVELLNAVANNSPNVIKFLTVMTLCNTVIPIKSPTGPILYKAQSQDE
DALVNAAANLHMVLVSKNGSNAEIHFNRRVMQYEILDILEFTSDRKRMSIVILDCQSGKFFLLS
KGADEAMLPCAYSGQKTKTFVDAVDKYAQLGLRTLCLGWRELEPEEYTKWSQSFKEANSSLNDR
EWKVAEVCQKLEHSLEILGVSAIEDRLQDGVPETIEILRQSGINFWMLTGDKQSTAIQIALLCN
LISSDVELLNAVANNSPNVIKFLTVMTLCNTVIPIKSPTGPILYKAQSQDEDALVNAAANLHMV
LVSKNGSNAEIHFNRRVMQYEILDILEFTSDRKRMSIVILDCQSGKFFLLSKGADEAMLPCAYS
GQKTKTFVDAVDKYAQLGLRTLCLGWRELEPEEYTKWSQSFKEANSSLNDREWKVAEVCQKLEH
SLEILGVSAIEDRLQDGVPETIEILRQSGINFWMLTGDKQSTAIQIALLCNLISS(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	167321242-167319277(+) 167321244-167319248(-)
Potential amino acid sequence	MTVKNLMTLGELLATAFSNSTSEEIKLHKRAI*(+) MTLCNTVIPIKSPTGPILYKAQSQDEDALVNAAANLHMVLVSKNGSNAEIHFNRRVMQYEILDI LEFTSDRKRMSIVILDCQSGKFFLLSKGADEAMLPCAYSGQKTKTFVDAVDKYAQLGLRTLCLG WRELEPEEYTKWSQSFKEANSSLNDREWKVAEVCQKLEHSLEILGVSAIEDRLQDGVPETIEIL RQSGINFWMLTGDKQSTAIQIALLCNLISSDVELLNAVANNSPNVIKFLTVMTLCNTVIPIKSP TGPILYKAQSQDEDALVNAAANLHMVLVSKNGSNAEIHFNRRVMQYEILDILEFTSDRKRMSIV ILDCQSGKFFLLSKGADEAMLPCAYSGQKTKTFVDAVDKYAQLGLRTLCLGWRELEPEEYTKWS QSFKEANSSLNDREWKVAEVCQKLEHSLEILGVSAIEDRLQDGVPETIEILRQSGINFWMLTGD KQSTAIQIALLCNLISSDVELLNAVANNSPNVIKFLTVMTLCNTVIPIKSPTGPILYKAQSQDE DALVNAAANLHMVLVSKNGSNAEIHFNRRVMQYEILDILEFTSDRKRMSIVILDCQSGKFFLLS KGADEAMLPCAYSGQKTKTFVDAVDKYAQLGLRTLCLGWRELEPEEYTKWSQSFKEANSSLNDR EWKVAEVCQKLEHSLEILGVSAIEDRLQDGVPETIEILRQSGINFWMLTGDKQSTAIQIALLCN LISSDVELLNAVANNSPNVIKFLTVMTLCNTVIPIKSPTGPILYKAQSQDEDALVNAAANLHMV LVSKNGSNAEIHFNRRVMQYEILDILEFTSDRKRMSIVILDCQSGKFFLLSKGADEAMLPCAYS GQKTKTFVDAVDKYAQLGLRTLCLGWRELEPEEYTKWSQSFKEANSSLNDREWKVAEVCQKLEH SLEILGVSAIEDRLQDGVPETIEILRQSGINFWMLTGDKQSTAIQIALLCNLISS(-)
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 Zm00001d021972_circ_g.4

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