Plant Circular RNA Database

Detail information of Zm00001d049449_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d049449_circ_g.2
					
						ID in PlantcircBase
						zma_circ_008005
					
						Alias
						Zm04circ00018, zma_circ_0001389, GRMZM2G064868_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 30659130-30660655  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d049449						
					
						Parent gene annotation
						
							 cold regulated protein homolog1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d049449_circ_g.1 						
					
						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  
						
							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
						Zm00001d049449_T001:6
Zm00001d049449_T003:6
Zm00001d049449_T005:6
Zm00001d049449_T004:6
Zm00001d049449_T002:6

General Information
CircRNA Name	Zm00001d049449_circ_g.2
ID in PlantcircBase	zma_circ_008005
Alias	Zm04circ00018, zma_circ_0001389, GRMZM2G064868_C1
Organism	Zea mays
Position	chr4: 30659130-30660655 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d049449
Parent gene annotation	cold regulated protein homolog1
Parent gene strand	+
Alternative splicing	Zm00001d049449_circ_g.1
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	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	Zm00001d049449_T001:6 Zm00001d049449_T003:6 Zm00001d049449_T005:6 Zm00001d049449_T004:6 Zm00001d049449_T002:6

			
						 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  
						
							GGTGGGGCATCTAGCCGCTAATTGTGAAGGAAAGGCAAAGAGAAAAGCTGGGGAATACGATGAG
AAAGGTGAAGCTATTGTTCCAAAGAAACCATACCAGccctctccaacaacatttgctgaggttt
tccagtgcatgttcgattacatcgatagactcttcatcatggttcgccctaggaagcttatgta
catggcca

									
								

					

						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: 702
Transcript exons: 30659130-30659232,30659420-30659496,30659623-30659814,30
659913-30660032,30660121-30660183,30660509-30660655
CCCTCTCCAACAACATTTGCTGAGGTTTTCCAGTGCATGTTCGATTACATCGATAGACTCTTCA
TCATGGTTCGCCCTAGGAAGCTTATGTACATGGCCATTGATGGTGTGGCTCCACGTGCTAAAAT
GAACCAACAGCGTTCTAGACGATTCAGAGCTGCAAAAGATGCAGCTGATGCGGCTGCAGAGGAA
GAACGGTTGCGTGAAGAGTTTGAGAGGGAAGGAAGAAGGCTTCCTGCAAAACAACAATCACAAA
CTTGTGATTCTAATGTTATTACTCCAGGAACCGAGTTTATGGCTGTTCTTTCAGTTGCGTTACA
GTACTACATTCATCAAAGACTGAATTATGATCCTGGATGGAAAAAAATCAAAGTTATTCTATCT
GATGCCAATGTTCCTGGCGAAGGGGAGCATAAAATAATGTCGTATATTCGTGGTCAACGGAATC
TCCCTGGATTTAATCCAAACACACGCCATTGCTTATATGGCCTGGATGCAGACCTCATAATGTT
AGCTTTAGCAACTCATGAAGTACACTTCTCTATATTGAGAGAGGTAGTTTTTACACCTGGGCAG
CAGGACAAATGCTTCTTATGTGGTCAGGTGGGGCATCTAGCCGCTAATTGTGAAGGAAAGGCAA
AGAGAAAAGCTGGGGAATACGATGAGAAAGGTGAAGCTATTGTTCCAAAGAAACCATACCAG
						
					

						Genomic sequence
						
							CCCTCTCCAACAACATTTGCTGAGGTTTTCCAGTGCATGTTCGATTACATCGATAGACTCTTCA
TCATGGTTCGCCCTAGGAAGCTTATGTACATGGCCATTGGTATGTTTTCCGTAAACCTTTATGC
AGATTACACTGTTCTTACTACTTTATTATAGTGTACTAGAAATTAGGGTTCATATGGTCATATA
TATTAGCTACAATTAGGAACACACACGATAGTTATTCTTTTAAGGTGTTGTTAGAGTTTGTGCC
ACCACATATATGCTGATTATACAGTGGCTTACAGATGGTGTGGCTCCACGTGCTAAAATGAACC
AACAGCGTTCTAGACGATTCAGAGCTGCAAAAGATGCAGCTGATGCGGTCAGTATTCTAGTGGA
ATTATCATCGTCTGTTCAGTTCATGATCATACGCTGTCATTTCAATATTGGTTTTGAAACAGTA
TAAACCATTTGTAGTTGCACTCATTGCTCAGTATTGTTCTATCAGGCTGCAGAGGAAGAACGGT
TGCGTGAAGAGTTTGAGAGGGAAGGAAGAAGGCTTCCTGCAAAACAACAATCACAAACTTGTGA
TTCTAATGTTATTACTCCAGGAACCGAGTTTATGGCTGTTCTTTCAGTTGCGTTACAGTACTAC
ATTCATCAAAGACTGAATTATGATCCTGGATGGAAAAAAATCAAAGTAAGTGCTATATCTGTTG
CCAATTTGGACTTTGATACTTGTAACTCCCGATAGTTAATAATGAAGAAATGGTATGTTCTGAC
CAAATCATTTTGAAGGTTATTCTATCTGATGCCAATGTTCCTGGCGAAGGGGAGCATAAAATAA
TGTCGTATATTCGTGGTCAACGGAATCTCCCTGGATTTAATCCAAACACACGCCATTGCTTATA
TGGCCTGGTACGTTTTGGAAACGAAGATATGCTTTCAGTTGAACTTCGTTTCTTCAGTGCTGCT
GATGCATAGGCTTGCATGTGTACATATGCAGGATGCAGACCTCATAATGTTAGCTTTAGCAACT
CATGAAGTACACTTCTCTATATTGAGAGAGGTAAGCCTTGCTTAGCGAGTTTGAAATTAATTAC
TTTCTTTGTTAAAATATTTGGTCATCTAATTTCTGCTATCTTTGTCACTTTTTAAATCTGTTAA
GAAAACCATTAGTTTCACCTTGTAGTCTTCTAGTAGAGTTTGTTTTTGTTCAGACAATCTTGTA
CACTCTGTAACATTAGTGTGAGTGGGTGTGGATGTGTATCTGTAAGGATTTATTACATTTTTTT
CCTTAATACGATGATACACAACTCTCCTTCATATTCACTTCATTTTAACATTTTTCTTGTAAAA
TCTTCAGTTTAAGATTATGAGTTTTATGTTTGCAGGTAGTTTTTACACCTGGGCAGCAGGACAA
ATGCTTCTTATGTGGTCAGGTGGGGCATCTAGCCGCTAATTGTGAAGGAAAGGCAAAGAGAAAA
GCTGGGGAATACGATGAGAAAGGTGAAGCTATTGTTCCAAAGAAACCATACCAG
						
					

			
		

Sequences
Splice junction sequence	GGTGGGGCATCTAGCCGCTAATTGTGAAGGAAAGGCAAAGAGAAAAGCTGGGGAATACGATGAG AAAGGTGAAGCTATTGTTCCAAAGAAACCATACCAGccctctccaacaacatttgctgaggttt tccagtgcatgttcgattacatcgatagactcttcatcatggttcgccctaggaagcttatgta catggcca
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: 702 Transcript exons: 30659130-30659232,30659420-30659496,30659623-30659814,30 659913-30660032,30660121-30660183,30660509-30660655 CCCTCTCCAACAACATTTGCTGAGGTTTTCCAGTGCATGTTCGATTACATCGATAGACTCTTCA TCATGGTTCGCCCTAGGAAGCTTATGTACATGGCCATTGATGGTGTGGCTCCACGTGCTAAAAT GAACCAACAGCGTTCTAGACGATTCAGAGCTGCAAAAGATGCAGCTGATGCGGCTGCAGAGGAA GAACGGTTGCGTGAAGAGTTTGAGAGGGAAGGAAGAAGGCTTCCTGCAAAACAACAATCACAAA CTTGTGATTCTAATGTTATTACTCCAGGAACCGAGTTTATGGCTGTTCTTTCAGTTGCGTTACA GTACTACATTCATCAAAGACTGAATTATGATCCTGGATGGAAAAAAATCAAAGTTATTCTATCT GATGCCAATGTTCCTGGCGAAGGGGAGCATAAAATAATGTCGTATATTCGTGGTCAACGGAATC TCCCTGGATTTAATCCAAACACACGCCATTGCTTATATGGCCTGGATGCAGACCTCATAATGTT AGCTTTAGCAACTCATGAAGTACACTTCTCTATATTGAGAGAGGTAGTTTTTACACCTGGGCAG CAGGACAAATGCTTCTTATGTGGTCAGGTGGGGCATCTAGCCGCTAATTGTGAAGGAAAGGCAA AGAGAAAAGCTGGGGAATACGATGAGAAAGGTGAAGCTATTGTTCCAAAGAAACCATACCAG
Genomic sequence	CCCTCTCCAACAACATTTGCTGAGGTTTTCCAGTGCATGTTCGATTACATCGATAGACTCTTCA TCATGGTTCGCCCTAGGAAGCTTATGTACATGGCCATTGGTATGTTTTCCGTAAACCTTTATGC AGATTACACTGTTCTTACTACTTTATTATAGTGTACTAGAAATTAGGGTTCATATGGTCATATA TATTAGCTACAATTAGGAACACACACGATAGTTATTCTTTTAAGGTGTTGTTAGAGTTTGTGCC ACCACATATATGCTGATTATACAGTGGCTTACAGATGGTGTGGCTCCACGTGCTAAAATGAACC AACAGCGTTCTAGACGATTCAGAGCTGCAAAAGATGCAGCTGATGCGGTCAGTATTCTAGTGGA ATTATCATCGTCTGTTCAGTTCATGATCATACGCTGTCATTTCAATATTGGTTTTGAAACAGTA TAAACCATTTGTAGTTGCACTCATTGCTCAGTATTGTTCTATCAGGCTGCAGAGGAAGAACGGT TGCGTGAAGAGTTTGAGAGGGAAGGAAGAAGGCTTCCTGCAAAACAACAATCACAAACTTGTGA TTCTAATGTTATTACTCCAGGAACCGAGTTTATGGCTGTTCTTTCAGTTGCGTTACAGTACTAC ATTCATCAAAGACTGAATTATGATCCTGGATGGAAAAAAATCAAAGTAAGTGCTATATCTGTTG CCAATTTGGACTTTGATACTTGTAACTCCCGATAGTTAATAATGAAGAAATGGTATGTTCTGAC CAAATCATTTTGAAGGTTATTCTATCTGATGCCAATGTTCCTGGCGAAGGGGAGCATAAAATAA TGTCGTATATTCGTGGTCAACGGAATCTCCCTGGATTTAATCCAAACACACGCCATTGCTTATA TGGCCTGGTACGTTTTGGAAACGAAGATATGCTTTCAGTTGAACTTCGTTTCTTCAGTGCTGCT GATGCATAGGCTTGCATGTGTACATATGCAGGATGCAGACCTCATAATGTTAGCTTTAGCAACT CATGAAGTACACTTCTCTATATTGAGAGAGGTAAGCCTTGCTTAGCGAGTTTGAAATTAATTAC TTTCTTTGTTAAAATATTTGGTCATCTAATTTCTGCTATCTTTGTCACTTTTTAAATCTGTTAA GAAAACCATTAGTTTCACCTTGTAGTCTTCTAGTAGAGTTTGTTTTTGTTCAGACAATCTTGTA CACTCTGTAACATTAGTGTGAGTGGGTGTGGATGTGTATCTGTAAGGATTTATTACATTTTTTT CCTTAATACGATGATACACAACTCTCCTTCATATTCACTTCATTTTAACATTTTTCTTGTAAAA TCTTCAGTTTAAGATTATGAGTTTTATGTTTGCAGGTAGTTTTTACACCTGGGCAGCAGGACAA ATGCTTCTTATGTGGTCAGGTGGGGCATCTAGCCGCTAATTGTGAAGGAAAGGCAAAGAGAAAA GCTGGGGAATACGATGAGAAAGGTGAAGCTATTGTTCCAAAGAAACCATACCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.143463163

Conservation Information
Conserved circRNAs	NA
PMCS	0.143463163

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30659167-30660652(+)
30660616-30659443(+)
30659169-30660555(-)
						
						Potential amino acid sequence
						
							MFDYIDRLFIMVRPRKLMYMAIDGVAPRAKMNQQRSRRFRAAKDAADAAAEEERLREEFEREGR
RLPAKQQSQTCDSNVITPGTEFMAVLSVALQYYIHQRLNYDPGWKKIKVILSDANVPGEGEHKI
MSYIRGQRNLPGFNPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQVGH
LAANCEGKAKRKAGEYDEKGEAIVPKKPYQPSPTTFAEVFQCMFDYIDRLFIMVRPRKLMYMAI
DGVAPRAKMNQQRSRRFRAAKDAADAAAEEERLREEFEREGRRLPAKQQSQTCDSNVITPGTEF
MAVLSVALQYYIHQRLNYDPGWKKIKVILSDANVPGEGEHKIMSYIRGQRNLPGFNPNTRHCLY
GLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQVGHLAANCEGKAKRKAGEYDEKGEA
IVPKKPYQPSPTTFAEVFQCMFDYIDRLFIMVRPRKLMYMAIDGVAPRAKMNQQRSRRFRAAKD
AADAAAEEERLREEFEREGRRLPAKQQSQTCDSNVITPGTEFMAVLSVALQYYIHQRLNYDPGW
KKIKVILSDANVPGEGEHKIMSYIRGQRNLPGFNPNTRHCLYGLDADLIMLALATHEVHFSILR
EVVFTPGQQDKCFLCGQVGHLAANCEGKAKRKAGEYDEKGEAIVPKKPYQPSPTTFAEVFQCMF
DYIDRLFIMVRPRKLMYMAIDGVAPRAKMNQQRSRRFRAAKDAADAAAEEERLREEFEREGRRL
PAKQQSQTCDSNVITPGTEFMAVLSVALQYYIHQRLNYDPGWKKIKVILSDANVPGEGEHKIMS
YIRGQRNLPGFNPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQVGHLA
ANCEGKAKRKAGEYDEKGEAIVPKKPYQ(+)
MRKVKLLFQRNHTSPLQQHLLRFSSACSITSIDSSSWFALGSLCTWPLMVWLHVLK*(+)
MHWKTSANVVGEGWYGFFGTIASPFSSYSPAFLFAFPSQLAARCPT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	30659167-30660652(+) 30660616-30659443(+) 30659169-30660555(-)
Potential amino acid sequence	MFDYIDRLFIMVRPRKLMYMAIDGVAPRAKMNQQRSRRFRAAKDAADAAAEEERLREEFEREGR RLPAKQQSQTCDSNVITPGTEFMAVLSVALQYYIHQRLNYDPGWKKIKVILSDANVPGEGEHKI MSYIRGQRNLPGFNPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQVGH LAANCEGKAKRKAGEYDEKGEAIVPKKPYQPSPTTFAEVFQCMFDYIDRLFIMVRPRKLMYMAI DGVAPRAKMNQQRSRRFRAAKDAADAAAEEERLREEFEREGRRLPAKQQSQTCDSNVITPGTEF MAVLSVALQYYIHQRLNYDPGWKKIKVILSDANVPGEGEHKIMSYIRGQRNLPGFNPNTRHCLY GLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQVGHLAANCEGKAKRKAGEYDEKGEA IVPKKPYQPSPTTFAEVFQCMFDYIDRLFIMVRPRKLMYMAIDGVAPRAKMNQQRSRRFRAAKD AADAAAEEERLREEFEREGRRLPAKQQSQTCDSNVITPGTEFMAVLSVALQYYIHQRLNYDPGW KKIKVILSDANVPGEGEHKIMSYIRGQRNLPGFNPNTRHCLYGLDADLIMLALATHEVHFSILR EVVFTPGQQDKCFLCGQVGHLAANCEGKAKRKAGEYDEKGEAIVPKKPYQPSPTTFAEVFQCMF DYIDRLFIMVRPRKLMYMAIDGVAPRAKMNQQRSRRFRAAKDAADAAAEEERLREEFEREGRRL PAKQQSQTCDSNVITPGTEFMAVLSVALQYYIHQRLNYDPGWKKIKVILSDANVPGEGEHKIMS YIRGQRNLPGFNPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQVGHLA ANCEGKAKRKAGEYDEKGEAIVPKKPYQ(+) MRKVKLLFQRNHTSPLQQHLLRFSSACSITSIDSSSWFALGSLCTWPLMVWLHVLK(+) MHWKTSANVVGEGWYGFFGTIASPFSSYSPAFLFAFPSQLAARCPT(-)
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 Zm00001d049449_circ_g.2

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