Plant Circular RNA Database

Detail information of Zm00001d044498_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d044498_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007915
					
						Alias
						zma_circ_0001393, GRMZM2G392649_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 229736505-229738955  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d044498						
					
						Parent gene annotation
						
							Zinc protease PQQL-like
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						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
						Zm00001d044498_T001:6
Zm00001d044498_T009:6
Zm00001d044498_T005:6
Zm00001d044498_T002:6
Zm00001d044498_T007:6
Zm00001d044498_T012:6
Zm00001d044498_T011:6
Zm00001d044498_T004:6
Zm00001d044498_T003:6

General Information
CircRNA Name	Zm00001d044498_circ_g.1
ID in PlantcircBase	zma_circ_007915
Alias	zma_circ_0001393, GRMZM2G392649_C1
Organism	Zea mays
Position	chr3: 229736505-229738955 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d044498
Parent gene annotation	Zinc protease PQQL-like
Parent gene strand	-
Alternative splicing	NA
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	Zm00001d044498_T001:6 Zm00001d044498_T009:6 Zm00001d044498_T005:6 Zm00001d044498_T002:6 Zm00001d044498_T007:6 Zm00001d044498_T012:6 Zm00001d044498_T011:6 Zm00001d044498_T004:6 Zm00001d044498_T003:6

			
						 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  
						
							TATTGCTTAGATGGTACCACTTCTGATAAAACCGCTTCACGGTCTCATGTGTAACAGTTCGTAT
CACCTTCTCAGTACCAATTGGCAGGCGCTCTGCATAcctggctctggagcttgggcaacaattt
cttctggaatttgttcttcatcccatggaaaaatagatttatcttcttccatactgttgacttt
cagcacaa

									
								

					

						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: 956
Transcript exons: 229736505-229736718,229736887-229736956,229737218-229737
355,229738213-229738470,229738568-229738705,229738818-22
9738955
CCTGGCTCTGGAGCTTGGGCAACAATTTCTTCTGGAATTTGTTCTTCATCCCATGGAAAAATAG
ATTTATCTTCTTCCATACTGTTGACTTTCAGCACAACTGCTTTCAGATCCTCCAAAGAAGCATG
AGCTCGAGGTTCAACTATCTTGATAACACAGCTGCTGGCCGTTGAAAAGTTTTCTGCAAATTTT
GCCACTTCCGCAGAAGAAATATGGGGAAGAAGAGTCTTTTGTAACTGTGCTTCATATTCAATCC
CAACAACAGGTTCCTCACGAAGAAAATGCTGCAAAAACTCATCCCGTAAGCTGGTAGATTGCAT
TTGATCACGCTCCAAATATGCAGATTCCATCTCTGACATCATTAGGGCGCGTACAATGGATATC
TCACGGTCAGAAAATCCATGAAGCCGTACCCTAGCAACCTCAAGAAGCATGGACTCGAGAGCTT
CAACTGTTCCCCTTTCCCGACAACTAGATGTCATAATGTAAGCCTTAACTGGACAGACGAGAGC
ATCTGCAGCTGAGGAGCAAGAAAAATAAGGAGGATCCTTTCTACGAGATATTTTGAAGAGCCTC
TGGTTTAGCGCACAATGAAACATGGACTCTGCCAGTGAATCTTTGTAGTCCTTTACTGTTTTAA
TTCCACCAGCAGGCATCTTGCAGCTGATAACAACAGCCGACCCTGCAGCTTCAGATTCCACAAA
ACATGAAAAGCGTGGTTCCTCATGCGATGGAACTGAAAATTCTGGTATAACTGGAGGAGGGTGG
GGAGCTGGAGCTTTGTGCCCAAAATGCTCATTTATCAACTCCACGACAGCCTGTGTATCTGGGA
AATCACCCACTGCAAATACCGCCATATTGCTTAGATGGTACCACTTCTGATAAAACCGCTTCAC
GGTCTCATGTGTAACAGTTCGTATCACCTTCTCAGTACCAATTGGCAGGCGCTCTGCATA
						
					

						Genomic sequence
						
							CCTGGCTCTGGAGCTTGGGCAACAATTTCTTCTGGAATTTGTTCTTCATCCCATGGAAAAATAG
ATTTATCTTCTTCCATACTGTTGACTTTCAGCACAACTGCTTTCAGATCCTCCAAAGAAGCATG
AGCTCGAGGTTCAACTATCTTGATAACACAGCTGCTGGCCGTTGAAAAGTTTTCTGCAAATTTT
GCCACTTCCGCAGAAGAAATATCTGGTCGAAAGTAAACATATATGAATATAGATGATCGAATAA
CTGTGGTGACGGTATGTAGGTTCATAAGAAATTAATTGGTTGTAAAGGTTTACAAGGGAGAGGG
CAAATAACATCAAGAATTTAACACCTAAGTTTTTACACTAGGCAACACAGAGGTATGCTTACGG
GGAAGAAGAGTCTTTTGTAACTGTGCTTCATATTCAATCCCAACAACAGGTTCCTCACGAAGAA
AATGCTGCAAGAAAATACAAATTGCATCATTGTGCTTAGAAGCTGTATAGATGGGGATCCTGAA
ATTTCACTTAAGTAGTCGACGAACATGTGGAGTTGTGGACTTAGTAGAATTCAATATTATTGGT
GTAAAGTCGTTTGAAAACAGAAATTTCAGGTGGTAAATATTTTGATCTGCAAGATGAGATAAGA
ACTGAAGAGCAACCAGCATGCATATGATATTAATTTAATTTTAGTTGTATTAAACAGCTACAAA
ATTTCAAACCTGCAAAAACTCATCCCGTAAGCTGGTAGATTGCATTTGATCACGCTCCAAATAT
GCAGATTCCATCTCTGACATCATTAGGGCGCGTACAATGGATATCTCACGGTCAGAAAATCCAT
GAAGCCGTACCCTAGCAACCTAAAGAAGCATCTTGTCAGAAGGATATTTTGTGACAAAATGTCA
TTTTGAAAGTGGTGGTGGTTAGACTGCAGACTTAAATTCAGATATCTACATTACATATGTCTGC
TAATGTGCTAATTATCAATCGTCTGTCACTAAAAACTCAACCTGCGGGGTAAGACAGCCCCCCG
AGTATTGTATTAAGACGAAGACCTTCTCACACAGGTCGAGAAAACCCCCAAACCCCTGCCTCAC
CCATACACGGCGGCACCGTAGCCCGTGTGAGAATAACCGCGACCAGAGCAGGGCCTTAGGCCTG
TGCTTCGGCGTGGGACATACAAGGGGAGATTTATTAACCCCAGCCTAAAATTCGCTCCGACGGG
GAGTCGAACTCAGGATTTGAAAAGTGCTAGTCAGACCACCTAACCAACTCAGCTAGAGGCCCTT
TTGCGATCATCTGTCACTAAACGGATGCAAACTAAGAGTCTTAAGACTGAACTAATTGTACAAG
ATATAATAAGTTGATGGCATGGCACACTAGATTATTTGGTCTTATACTACTATACATGAAGGTT
TTACTGGTAACGAAAAATATCCTTAAGGAATATGACATGTTTTCATTTGGTCTGTAACTCTGTA
TCAAAGGCATGATTAATATCTGATGTTGACAATCTGGATGGCTATGAAACTTACCATGCCCTAT
AGTTGGTCATTCCTAAAGAACTTCTAAAGATGTTAGAGCAAATTTTCTCACTTTAGTCTTTTCA
ACTTTTGTGGCACTTACACTGAATATTCACCCATAAACTTGAATAATGCACTATGAAAGAATAC
TAGATTTTATCTTTATTCTTTCAGAGATCAAGGTTCAAAAATACCTCAAGAAGCATGGACTCGA
GAGCTTCAACTGTTCCCCTTTCCCGACAACTAGATGTCATAATGTAAGCCTTAACTGGACAGAC
GAGAGCATCTGCAGCTGAGGAGCAAGAAAAATAAGGAGGATCCTTTCTACGAGATATTTTGAAG
AGCCTCTGGTTTAGCGCACAATGAAACATGGACTCTGCCAGTGAATCTTTGTAGTCCTTTACTG
TTTTAATTCCACCAGCAGGCATCTTGCAGCTGATAACAACAGCCGACTGTTTTTGTTACAAAAG
GAAAACAAAAAAGTACATTATTATCCAAAGTTGATATTAAAAGATATCAAATCTGTTCAAAAGA
ATAAGAAATAACAACCCCTGCAGCTTCAGATTCCACAAAACATGAAAAGCGTGGTTCCTCATGC
GATGGAACTGAAAATTCTGGTATAACTGGAGGAGGGTGGGGAGCTGGAGCTTTGTGCCCAAAAT
GCTCATTTATCAACTCCACGACAGCCTGCAATTTTAAGTCATGAAACACGAAGGATGGTAAATA
TCATTGCAGATACATACCCATAGTTTCTTATTTTTCGAGTAGATACAAGTGAAAAAAAGATGTG
CATAATGACCTGTGTATCTGGGAAATCACCCACTGCAAATACCGCCATATTGCTTAGATGGTAC
CACTTCTGATAAAACCGCTTCACGGTCTCATGTGTAACAGTTCGTATCACCTTCTCAGTACCAA
TTGGCAGGCGCTCTGCATA
						
					

			
		

Sequences
Splice junction sequence	TATTGCTTAGATGGTACCACTTCTGATAAAACCGCTTCACGGTCTCATGTGTAACAGTTCGTAT CACCTTCTCAGTACCAATTGGCAGGCGCTCTGCATAcctggctctggagcttgggcaacaattt cttctggaatttgttcttcatcccatggaaaaatagatttatcttcttccatactgttgacttt cagcacaa
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: 956 Transcript exons: 229736505-229736718,229736887-229736956,229737218-229737 355,229738213-229738470,229738568-229738705,229738818-22 9738955 CCTGGCTCTGGAGCTTGGGCAACAATTTCTTCTGGAATTTGTTCTTCATCCCATGGAAAAATAG ATTTATCTTCTTCCATACTGTTGACTTTCAGCACAACTGCTTTCAGATCCTCCAAAGAAGCATG AGCTCGAGGTTCAACTATCTTGATAACACAGCTGCTGGCCGTTGAAAAGTTTTCTGCAAATTTT GCCACTTCCGCAGAAGAAATATGGGGAAGAAGAGTCTTTTGTAACTGTGCTTCATATTCAATCC CAACAACAGGTTCCTCACGAAGAAAATGCTGCAAAAACTCATCCCGTAAGCTGGTAGATTGCAT TTGATCACGCTCCAAATATGCAGATTCCATCTCTGACATCATTAGGGCGCGTACAATGGATATC TCACGGTCAGAAAATCCATGAAGCCGTACCCTAGCAACCTCAAGAAGCATGGACTCGAGAGCTT CAACTGTTCCCCTTTCCCGACAACTAGATGTCATAATGTAAGCCTTAACTGGACAGACGAGAGC ATCTGCAGCTGAGGAGCAAGAAAAATAAGGAGGATCCTTTCTACGAGATATTTTGAAGAGCCTC TGGTTTAGCGCACAATGAAACATGGACTCTGCCAGTGAATCTTTGTAGTCCTTTACTGTTTTAA TTCCACCAGCAGGCATCTTGCAGCTGATAACAACAGCCGACCCTGCAGCTTCAGATTCCACAAA ACATGAAAAGCGTGGTTCCTCATGCGATGGAACTGAAAATTCTGGTATAACTGGAGGAGGGTGG GGAGCTGGAGCTTTGTGCCCAAAATGCTCATTTATCAACTCCACGACAGCCTGTGTATCTGGGA AATCACCCACTGCAAATACCGCCATATTGCTTAGATGGTACCACTTCTGATAAAACCGCTTCAC GGTCTCATGTGTAACAGTTCGTATCACCTTCTCAGTACCAATTGGCAGGCGCTCTGCATA
Genomic sequence	CCTGGCTCTGGAGCTTGGGCAACAATTTCTTCTGGAATTTGTTCTTCATCCCATGGAAAAATAG ATTTATCTTCTTCCATACTGTTGACTTTCAGCACAACTGCTTTCAGATCCTCCAAAGAAGCATG AGCTCGAGGTTCAACTATCTTGATAACACAGCTGCTGGCCGTTGAAAAGTTTTCTGCAAATTTT GCCACTTCCGCAGAAGAAATATCTGGTCGAAAGTAAACATATATGAATATAGATGATCGAATAA CTGTGGTGACGGTATGTAGGTTCATAAGAAATTAATTGGTTGTAAAGGTTTACAAGGGAGAGGG CAAATAACATCAAGAATTTAACACCTAAGTTTTTACACTAGGCAACACAGAGGTATGCTTACGG GGAAGAAGAGTCTTTTGTAACTGTGCTTCATATTCAATCCCAACAACAGGTTCCTCACGAAGAA AATGCTGCAAGAAAATACAAATTGCATCATTGTGCTTAGAAGCTGTATAGATGGGGATCCTGAA ATTTCACTTAAGTAGTCGACGAACATGTGGAGTTGTGGACTTAGTAGAATTCAATATTATTGGT GTAAAGTCGTTTGAAAACAGAAATTTCAGGTGGTAAATATTTTGATCTGCAAGATGAGATAAGA ACTGAAGAGCAACCAGCATGCATATGATATTAATTTAATTTTAGTTGTATTAAACAGCTACAAA ATTTCAAACCTGCAAAAACTCATCCCGTAAGCTGGTAGATTGCATTTGATCACGCTCCAAATAT GCAGATTCCATCTCTGACATCATTAGGGCGCGTACAATGGATATCTCACGGTCAGAAAATCCAT GAAGCCGTACCCTAGCAACCTAAAGAAGCATCTTGTCAGAAGGATATTTTGTGACAAAATGTCA TTTTGAAAGTGGTGGTGGTTAGACTGCAGACTTAAATTCAGATATCTACATTACATATGTCTGC TAATGTGCTAATTATCAATCGTCTGTCACTAAAAACTCAACCTGCGGGGTAAGACAGCCCCCCG AGTATTGTATTAAGACGAAGACCTTCTCACACAGGTCGAGAAAACCCCCAAACCCCTGCCTCAC CCATACACGGCGGCACCGTAGCCCGTGTGAGAATAACCGCGACCAGAGCAGGGCCTTAGGCCTG TGCTTCGGCGTGGGACATACAAGGGGAGATTTATTAACCCCAGCCTAAAATTCGCTCCGACGGG GAGTCGAACTCAGGATTTGAAAAGTGCTAGTCAGACCACCTAACCAACTCAGCTAGAGGCCCTT TTGCGATCATCTGTCACTAAACGGATGCAAACTAAGAGTCTTAAGACTGAACTAATTGTACAAG ATATAATAAGTTGATGGCATGGCACACTAGATTATTTGGTCTTATACTACTATACATGAAGGTT TTACTGGTAACGAAAAATATCCTTAAGGAATATGACATGTTTTCATTTGGTCTGTAACTCTGTA TCAAAGGCATGATTAATATCTGATGTTGACAATCTGGATGGCTATGAAACTTACCATGCCCTAT AGTTGGTCATTCCTAAAGAACTTCTAAAGATGTTAGAGCAAATTTTCTCACTTTAGTCTTTTCA ACTTTTGTGGCACTTACACTGAATATTCACCCATAAACTTGAATAATGCACTATGAAAGAATAC TAGATTTTATCTTTATTCTTTCAGAGATCAAGGTTCAAAAATACCTCAAGAAGCATGGACTCGA GAGCTTCAACTGTTCCCCTTTCCCGACAACTAGATGTCATAATGTAAGCCTTAACTGGACAGAC GAGAGCATCTGCAGCTGAGGAGCAAGAAAAATAAGGAGGATCCTTTCTACGAGATATTTTGAAG AGCCTCTGGTTTAGCGCACAATGAAACATGGACTCTGCCAGTGAATCTTTGTAGTCCTTTACTG TTTTAATTCCACCAGCAGGCATCTTGCAGCTGATAACAACAGCCGACTGTTTTTGTTACAAAAG GAAAACAAAAAAGTACATTATTATCCAAAGTTGATATTAAAAGATATCAAATCTGTTCAAAAGA ATAAGAAATAACAACCCCTGCAGCTTCAGATTCCACAAAACATGAAAAGCGTGGTTCCTCATGC GATGGAACTGAAAATTCTGGTATAACTGGAGGAGGGTGGGGAGCTGGAGCTTTGTGCCCAAAAT GCTCATTTATCAACTCCACGACAGCCTGCAATTTTAAGTCATGAAACACGAAGGATGGTAAATA TCATTGCAGATACATACCCATAGTTTCTTATTTTTCGAGTAGATACAAGTGAAAAAAAGATGTG CATAATGACCTGTGTATCTGGGAAATCACCCACTGCAAATACCGCCATATTGCTTAGATGGTAC CACTTCTGATAAAACCGCTTCACGGTCTCATGTGTAACAGTTCGTATCACCTTCTCAGTACCAA TTGGCAGGCGCTCTGCATA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.083933666

Conservation Information
Conserved circRNAs	NA
PMCS	0.083933666

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							229738867-229736630(+)
229738858-229738921(-)
229736555-229738929(-)
						
						Potential amino acid sequence
						
							MVPLLIKPLHGLMCNSSYHLLSTNWQALCIPGSGAWATISSGICSSSHGKIDLSSSILLTFSTT
AFRSSKEA*(+)
MAVFAVGDFPDTQAVVELINEHFGHKAPAPHPPPVIPEFSVPSHEEPRFSCFVESEAAGVQKQS
AVVISCKMPAGGIKTVKDYKDSLAESMFHCALNQRLFKISRRKDPPYFSCSSAADALVCPVKAY
IMTSSCRERGTVEALESMLLEVARVRLHGFSDREISIVRALMMSEMESAYLERDQMQSTSLRDE
FLQHFLREEPVVGIEYEAQLQKTLLPHISSAEVAKFAENFSTASSCVIKIVEPRAHASLEDLKA
VVLKVNSMEEDKSIFPWDEEQIPEEIVAQAPEPGMQSACQLVLRR*(-)
MKNKFQKKLLPKLQSQVCRAPANWY*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	229738867-229736630(+) 229738858-229738921(-) 229736555-229738929(-)
Potential amino acid sequence	MVPLLIKPLHGLMCNSSYHLLSTNWQALCIPGSGAWATISSGICSSSHGKIDLSSSILLTFSTT AFRSSKEA(+) MAVFAVGDFPDTQAVVELINEHFGHKAPAPHPPPVIPEFSVPSHEEPRFSCFVESEAAGVQKQS AVVISCKMPAGGIKTVKDYKDSLAESMFHCALNQRLFKISRRKDPPYFSCSSAADALVCPVKAY IMTSSCRERGTVEALESMLLEVARVRLHGFSDREISIVRALMMSEMESAYLERDQMQSTSLRDE FLQHFLREEPVVGIEYEAQLQKTLLPHISSAEVAKFAENFSTASSCVIKIVEPRAHASLEDLKA VVLKVNSMEEDKSIFPWDEEQIPEEIVAQAPEPGMQSACQLVLRR(-) MKNKFQKKLLPKLQSQVCRAPANWY*(-)
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 Zm00001d044498_circ_g.1

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