Plant Circular RNA Database

Detail information of Zm00001d017812_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d017812_circ_g.1
					
						ID in PlantcircBase
						zma_circ_008790
					
						Alias
						zma_circ_0001984
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 207516379-207517715  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d017812						
					
						Parent gene annotation
						
							P-loop containing nucleoside triphosphate hydrolases superfamily
 protein
							
						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  
						
							GT-AG							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
						Zm00001d017812_T003:5
Zm00001d017812_T002:5
Zm00001d017812_T005:3
Zm00001d017812_T004:5
Zm00001d017812_T001:5

General Information
CircRNA Name	Zm00001d017812_circ_g.1
ID in PlantcircBase	zma_circ_008790
Alias	zma_circ_0001984
Organism	Zea mays
Position	chr5: 207516379-207517715 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d017812
Parent gene annotation	P-loop containing nucleoside triphosphate hydrolases superfamily protein
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	GT-AG 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	Zm00001d017812_T003:5 Zm00001d017812_T002:5 Zm00001d017812_T005:3 Zm00001d017812_T004:5 Zm00001d017812_T001:5

			
						 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  
						
							GTCCACCTGGGTGTACCCTTCAGTCAGTTTTGATTCTGTTCAGAAATCTGTAACCCTCTTCATG
CCAGGCTTTGATAAGTCTGAAATCAAGCTATATCAAtattatgcaagtgaaggcttcaagacat
gcctggttgttcagtcccaagatcctactgcggagcacttgatgggcagtaaaattgggaattc
tctgaccg

									
								

					

						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: 979
Transcript exons: 207516379-207516522,207516625-207516699,207516775-207516
962,207517064-207517233,207517314-207517715
TATTATGCAAGTGAAGGCTTCAAGACATGCCTGGTTGTTCAGTCCCAAGATCCTACTGCGGAGC
ACTTGATGGGCAGTAAAATTGGGAATTCTCTGACCGAGTGTGTGGCCAATCTCTCGGCCATAAA
GCTGGAGACTGGTAAGTTGCTGCTTGAACCCCTAGACCGACTGAAGAAGGTAGACGCCCAGGTC
AATTTTACTCAAGGAATCCTTGAAGGGATTGTAGGAGAGGAGCTTGGAGTTTTACCTGGAATGG
ATTCGATCTGTTTAGTCTTAGCTCTTCAGAAGCTCCTTAATTTCTTTTCATCTGGAAGGAGTAA
TTCACAATCAGAATTTGATGTGATCGTGTATGATTGCAACAATACAGAGGAAATTCTACGGCTG
ATAGGTGCTGCTGACCGGGCAAGTCAGATCTTACTTGAGGTATGTGAGGGACCTTGCTGAGAAG
ACTGACATCGGAAGACTTGCTTCTCCTTCATTACTGAAACTAATATATGATTCTGCAAGGCCAA
ATGGCAAAATTAGTGAGGGGAGACTTAGTACAGAGATATGGAATGAAATTGAACAACTACTTGA
GAAAATCTCAGTATGGTTTGCCGATCCTTCAAAACTTGCATGCTTCCTTATCATGGATCCTAGG
ACATCAATCTCTGTATCCTCTGCATTGCGGTATTGGGGTTGTACCACTCAAGCTGGCGGTCAAA
TATGTGGGGCATTTGGATACACTGAAGACCCTTCTGAAATGCACCGAGAAGTTGCTCAAAAGTT
CGTGCCGTTGTCTTTGTCTTTTCTGCCATTTCTCCCGAATGATTCTTCCGTGGATTGGAGCAGA
GCACTAAGCTCATTGAGCCAAAATACAAAGGAACAGCTGAGGAATGCGTCCACCTGGGTGTACC
CTTCAGTCAGTTTTGATTCTGTTCAGAAATCTGTAACCCTCTTCATGCCAGGCTTTGATAAGTC
TGAAATCAAGCTATATCAA
						
					

						Genomic sequence
						
							TATTATGCAAGTGAAGGCTTCAAGACATGCCTGGTTGTTCAGTCCCAAGATCCTACTGCGGAGC
ACTTGATGGGCAGTAAAATTGGGAATTCTCTGACCGAGTGTGTGGCCAATCTCTCGGCCATAAA
GCTGGAGACTGGTAAGGTAAAATACTTTGTTGAAAAAAAATCACATGTTTAGAATTTAAACTTG
TGCTATTCTGGAATATGTATCGATATTGAAGAATGTTTTCTTGTTGAATCATAGTTGCTGCTTG
AACCCCTAGACCGACTGAAGAAGGTAGACGCCCAGGTCAATTTTACTCAAGGAATCCTTGAAGG
GGTAGGTTATTACTTTGCTATAACATGTCTGGTGAGGATAAAACATTCATTTTGGTTGATGTTT
TCCTTGTGACAGATTGTAGGAGAGGAGCTTGGAGTTTTACCTGGAATGGATTCGATCTGTTTAG
TCTTAGCTCTTCAGAAGCTCCTTAATTTCTTTTCATCTGGAAGGAGTAATTCACAATCAGAATT
TGATGTGATCGTGTATGATTGCAACAATACAGAGGAAATTCTACGGCTGATAGGTGCTGCTGAC
CGGGCAAGGTATATGTTCTCCTAGTTTGGCCATAATCTTGACTTCAATCAGGATTCTGAATTCC
CTTAAAAAGGCTGGATTCTAAATTTAGTTTTATGCTCCACAAAAGTCAGATCTTACTTGAGGTA
TGTGAGGGACCTTGCTGAGAAGACTGACATCGGAAGACTTGCTTCTCCTTCATTACTGAAACTA
ATATATGATTCTGCAAGGCCAAATGGCAAAATTAGTGAGGGGAGACTTAGTACAGAGATATGGA
ATGAAATTGAACAACTACTTGAGGTAAATTTTCCTGGTTTCATTTAACTAAATACAATGCATTT
AATTTGTGATATTACTTAAAAAGTTGCTAAATTTTGTAGAAAATCTCAGTATGGTTTGCCGATC
CTTCAAAACTTGCATGCTTCCTTATCATGGATCCTAGGACATCAATCTCTGTATCCTCTGCATT
GCGGTATTGGGGTTGTACCACTCAAGCTGGCGGTCAAATATGTGGGGCATTTGGATACACTGAA
GACCCTTCTGAAATGCACCGAGAAGTTGCTCAAAAGTTCGTGCCGTTGTCTTTGTCTTTTCTGC
CATTTCTCCCGAATGATTCTTCCGTGGATTGGAGCAGAGCACTAAGCTCATTGAGCCAAAATAC
AAAGGAACAGCTGAGGAATGCGTCCACCTGGGTGTACCCTTCAGTCAGTTTTGATTCTGTTCAG
AAATCTGTAACCCTCTTCATGCCAGGCTTTGATAAGTCTGAAATCAAGCTATATCAA
						
					

			
		

Sequences
Splice junction sequence	GTCCACCTGGGTGTACCCTTCAGTCAGTTTTGATTCTGTTCAGAAATCTGTAACCCTCTTCATG CCAGGCTTTGATAAGTCTGAAATCAAGCTATATCAAtattatgcaagtgaaggcttcaagacat gcctggttgttcagtcccaagatcctactgcggagcacttgatgggcagtaaaattgggaattc tctgaccg
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: 979 Transcript exons: 207516379-207516522,207516625-207516699,207516775-207516 962,207517064-207517233,207517314-207517715 TATTATGCAAGTGAAGGCTTCAAGACATGCCTGGTTGTTCAGTCCCAAGATCCTACTGCGGAGC ACTTGATGGGCAGTAAAATTGGGAATTCTCTGACCGAGTGTGTGGCCAATCTCTCGGCCATAAA GCTGGAGACTGGTAAGTTGCTGCTTGAACCCCTAGACCGACTGAAGAAGGTAGACGCCCAGGTC AATTTTACTCAAGGAATCCTTGAAGGGATTGTAGGAGAGGAGCTTGGAGTTTTACCTGGAATGG ATTCGATCTGTTTAGTCTTAGCTCTTCAGAAGCTCCTTAATTTCTTTTCATCTGGAAGGAGTAA TTCACAATCAGAATTTGATGTGATCGTGTATGATTGCAACAATACAGAGGAAATTCTACGGCTG ATAGGTGCTGCTGACCGGGCAAGTCAGATCTTACTTGAGGTATGTGAGGGACCTTGCTGAGAAG ACTGACATCGGAAGACTTGCTTCTCCTTCATTACTGAAACTAATATATGATTCTGCAAGGCCAA ATGGCAAAATTAGTGAGGGGAGACTTAGTACAGAGATATGGAATGAAATTGAACAACTACTTGA GAAAATCTCAGTATGGTTTGCCGATCCTTCAAAACTTGCATGCTTCCTTATCATGGATCCTAGG ACATCAATCTCTGTATCCTCTGCATTGCGGTATTGGGGTTGTACCACTCAAGCTGGCGGTCAAA TATGTGGGGCATTTGGATACACTGAAGACCCTTCTGAAATGCACCGAGAAGTTGCTCAAAAGTT CGTGCCGTTGTCTTTGTCTTTTCTGCCATTTCTCCCGAATGATTCTTCCGTGGATTGGAGCAGA GCACTAAGCTCATTGAGCCAAAATACAAAGGAACAGCTGAGGAATGCGTCCACCTGGGTGTACC CTTCAGTCAGTTTTGATTCTGTTCAGAAATCTGTAACCCTCTTCATGCCAGGCTTTGATAAGTC TGAAATCAAGCTATATCAA
Genomic sequence	TATTATGCAAGTGAAGGCTTCAAGACATGCCTGGTTGTTCAGTCCCAAGATCCTACTGCGGAGC ACTTGATGGGCAGTAAAATTGGGAATTCTCTGACCGAGTGTGTGGCCAATCTCTCGGCCATAAA GCTGGAGACTGGTAAGGTAAAATACTTTGTTGAAAAAAAATCACATGTTTAGAATTTAAACTTG TGCTATTCTGGAATATGTATCGATATTGAAGAATGTTTTCTTGTTGAATCATAGTTGCTGCTTG AACCCCTAGACCGACTGAAGAAGGTAGACGCCCAGGTCAATTTTACTCAAGGAATCCTTGAAGG GGTAGGTTATTACTTTGCTATAACATGTCTGGTGAGGATAAAACATTCATTTTGGTTGATGTTT TCCTTGTGACAGATTGTAGGAGAGGAGCTTGGAGTTTTACCTGGAATGGATTCGATCTGTTTAG TCTTAGCTCTTCAGAAGCTCCTTAATTTCTTTTCATCTGGAAGGAGTAATTCACAATCAGAATT TGATGTGATCGTGTATGATTGCAACAATACAGAGGAAATTCTACGGCTGATAGGTGCTGCTGAC CGGGCAAGGTATATGTTCTCCTAGTTTGGCCATAATCTTGACTTCAATCAGGATTCTGAATTCC CTTAAAAAGGCTGGATTCTAAATTTAGTTTTATGCTCCACAAAAGTCAGATCTTACTTGAGGTA TGTGAGGGACCTTGCTGAGAAGACTGACATCGGAAGACTTGCTTCTCCTTCATTACTGAAACTA ATATATGATTCTGCAAGGCCAAATGGCAAAATTAGTGAGGGGAGACTTAGTACAGAGATATGGA ATGAAATTGAACAACTACTTGAGGTAAATTTTCCTGGTTTCATTTAACTAAATACAATGCATTT AATTTGTGATATTACTTAAAAAGTTGCTAAATTTTGTAGAAAATCTCAGTATGGTTTGCCGATC CTTCAAAACTTGCATGCTTCCTTATCATGGATCCTAGGACATCAATCTCTGTATCCTCTGCATT GCGGTATTGGGGTTGTACCACTCAAGCTGGCGGTCAAATATGTGGGGCATTTGGATACACTGAA GACCCTTCTGAAATGCACCGAGAAGTTGCTCAAAAGTTCGTGCCGTTGTCTTTGTCTTTTCTGC CATTTCTCCCGAATGATTCTTCCGTGGATTGGAGCAGAGCACTAAGCTCATTGAGCCAAAATAC AAAGGAACAGCTGAGGAATGCGTCCACCTGGGTGTACCCTTCAGTCAGTTTTGATTCTGTTCAG AAATCTGTAACCCTCTTCATGCCAGGCTTTGATAAGTCTGAAATCAAGCTATATCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.224987274

Conservation Information
Conserved circRNAs	NA
PMCS	0.224987274

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							207516449-207517712(+)
						
						Potential amino acid sequence
						
							MGSKIGNSLTECVANLSAIKLETGKLLLEPLDRLKKVDAQVNFTQGILEGIVGEELGVLPGMDS
ICLVLALQKLLNFFSSGRSNSQSEFDVIVYDCNNTEEILRLIGAADRARSYLRYVRDLAEKTDI
GRLASPSLLKLIYDSARPNGKISEGRLSTEIWNEIEQLLEKISVWFADPSKLACFLIMDPRTSI
SVSSALRYWGCTTQAGGQICGAFGYTEDPSEMHREVAQKFVPLSLSFLPFLPNDSSVDWSRALS
SLSQNTKEQLRNASTWVYPSVSFDSVQKSVTLFMPGFDKSEIKLYQYYASEGFKTCLVVQSQDP
TAEHLMGSKIGNSLTECVANLSAIKLETGKLLLEPLDRLKKVDAQVNFTQGILEGIVGEELGVL
PGMDSICLVLALQKLLNFFSSGRSNSQSEFDVIVYDCNNTEEILRLIGAADRARSYLRYVRDLA
EKTDIGRLASPSLLKLIYDSARPNGKISEGRLSTEIWNEIEQLLEKISVWFADPSKLACFLIMD
PRTSISVSSALRYWGCTTQAGGQICGAFGYTEDPSEMHREVAQKFVPLSLSFLPFLPNDSSVDW
SRALSSLSQNTKEQLRNASTWVYPSVSFDSVQKSVTLFMPGFDKSEIKLYQYYASEGFKTCLVV
QSQDPTAEHLMGSKIGNSLTECVANLSAIKLETGKLLLEPLDRLKKVDAQVNFTQGILEGIVGE
ELGVLPGMDSICLVLALQKLLNFFSSGRSNSQSEFDVIVYDCNNTEEILRLIGAADRARSYLRY
VRDLAEKTDIGRLASPSLLKLIYDSARPNGKISEGRLSTEIWNEIEQLLEKISVWFADPSKLAC
FLIMDPRTSISVSSALRYWGCTTQAGGQICGAFGYTEDPSEMHREVAQKFVPLSLSFLPFLPND
SSVDWSRALSSLSQNTKEQLRNASTWVYPSVSFDSVQKSVTLFMPGFDKSEIKLYQYYASEGFK
TCLVVQSQDPTAEHLMGSKIGNSLTECVANLSAIKLETGKLLLEPLDRLKKVDAQVNFTQGILE
GIVGEELGVLPGMDSICLVLALQKLLNFFSSGRSNSQSEFDVIVYDCNNTEEILRLIGAADRAR
SYLRYVRDLAEKTDIGRLASPSLLKLIYDSARPNGKISEGRLSTEIWNEIEQLLEKISVWFADP
SKLACFLIMDPRTSISVSSALRYWGCTTQAGGQICGAFGYTEDPSEMHREVAQKFVPLSLSFLP
FLPNDSSVDWSRALSSLSQNTKEQLRNASTWVYPSVSFDSVQKSVTLFMPGFDKSEIKLYQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	207516449-207517712(+)
Potential amino acid sequence	MGSKIGNSLTECVANLSAIKLETGKLLLEPLDRLKKVDAQVNFTQGILEGIVGEELGVLPGMDS ICLVLALQKLLNFFSSGRSNSQSEFDVIVYDCNNTEEILRLIGAADRARSYLRYVRDLAEKTDI GRLASPSLLKLIYDSARPNGKISEGRLSTEIWNEIEQLLEKISVWFADPSKLACFLIMDPRTSI SVSSALRYWGCTTQAGGQICGAFGYTEDPSEMHREVAQKFVPLSLSFLPFLPNDSSVDWSRALS SLSQNTKEQLRNASTWVYPSVSFDSVQKSVTLFMPGFDKSEIKLYQYYASEGFKTCLVVQSQDP TAEHLMGSKIGNSLTECVANLSAIKLETGKLLLEPLDRLKKVDAQVNFTQGILEGIVGEELGVL PGMDSICLVLALQKLLNFFSSGRSNSQSEFDVIVYDCNNTEEILRLIGAADRARSYLRYVRDLA EKTDIGRLASPSLLKLIYDSARPNGKISEGRLSTEIWNEIEQLLEKISVWFADPSKLACFLIMD PRTSISVSSALRYWGCTTQAGGQICGAFGYTEDPSEMHREVAQKFVPLSLSFLPFLPNDSSVDW SRALSSLSQNTKEQLRNASTWVYPSVSFDSVQKSVTLFMPGFDKSEIKLYQYYASEGFKTCLVV QSQDPTAEHLMGSKIGNSLTECVANLSAIKLETGKLLLEPLDRLKKVDAQVNFTQGILEGIVGE ELGVLPGMDSICLVLALQKLLNFFSSGRSNSQSEFDVIVYDCNNTEEILRLIGAADRARSYLRY VRDLAEKTDIGRLASPSLLKLIYDSARPNGKISEGRLSTEIWNEIEQLLEKISVWFADPSKLAC FLIMDPRTSISVSSALRYWGCTTQAGGQICGAFGYTEDPSEMHREVAQKFVPLSLSFLPFLPND SSVDWSRALSSLSQNTKEQLRNASTWVYPSVSFDSVQKSVTLFMPGFDKSEIKLYQYYASEGFK TCLVVQSQDPTAEHLMGSKIGNSLTECVANLSAIKLETGKLLLEPLDRLKKVDAQVNFTQGILE GIVGEELGVLPGMDSICLVLALQKLLNFFSSGRSNSQSEFDVIVYDCNNTEEILRLIGAADRAR SYLRYVRDLAEKTDIGRLASPSLLKLIYDSARPNGKISEGRLSTEIWNEIEQLLEKISVWFADP SKLACFLIMDPRTSISVSSALRYWGCTTQAGGQICGAFGYTEDPSEMHREVAQKFVPLSLSFLP FLPNDSSVDWSRALSSLSQNTKEQLRNASTWVYPSVSFDSVQKSVTLFMPGFDKSEIKLYQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d017812_circ_g.1

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