Plant Circular RNA Database

Detail information of GLYMA_01G203100_circ_g.3

			
						 General Information
					
						CircRNA Name
						GLYMA_01G203100_circ_g.3
					
						ID in PlantcircBase
						gma_circ_000221
					
						Alias
						Gm01circRNA174
					
						Organism
						
							Glycine max						
					
						Position
						
							chr1: 53591944-53601538  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI
					
						Parent gene
						
							GLYMA_01G203100						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_01G203100_circ_g.4 						
					
						Support reads
						NA
					
						Tissues
						leaf, root, stem
					
						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
						KRH77267:10
KRH77268:3
KRH77269:10
KRH77266:10

General Information
CircRNA Name	GLYMA_01G203100_circ_g.3
ID in PlantcircBase	gma_circ_000221
Alias	Gm01circRNA174
Organism	Glycine max
Position	chr1: 53591944-53601538 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI
Parent gene	GLYMA_01G203100
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_01G203100_circ_g.4
Support reads	NA
Tissues	leaf, root, stem
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	KRH77267:10 KRH77268:3 KRH77269:10 KRH77266:10

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: TGGACTGAAGAGAGTAGCTGTTTGC
 R: TTTGAGAATCTGATGAACCACCTTG
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	Yes 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	F: TGGACTGAAGAGAGTAGCTGTTTGC R: TTTGAGAATCTGATGAACCACCTTG 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  
						
							ACCCGCGGGCTGAATTTCAGCAGCAGCATCACGTACTGGTAAGATGCCAATCAACCCCTTCTCT
TCTCGCTGCCAAAGTTCTTGTTCCACCAACTTTACAtgatcattgaatgctttgttttgttccg
gatcaagaacctctagcaatgcagaagctggatctccacgaacatcggaccctgtcttgtcaat
ttcatcaa

									
								

					

						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: 1419
Transcript exons: 53591944-53592074,53592720-53592926,53593015-53593216,53
593381-53593508,53599471-53599554,53599638-53599817,5360
0126-53600217,53600733-53600902,53601224-53601332,536014
23-53601538
TGATCATTGAATGCTTTGTTTTGTTCCGGATCAAGAACCTCTAGCAATGCAGAAGCTGGATCTC
CACGAACATCGGACCCTGTCTTGTCAATTTCATCAATCAACATGACAGGATTGCAAACAGCTAC
TCTCTTCAGTCCATCTATAAGCCTCCCAGGCATGCTTCCAATGTATGTTCTCCTATGCCCTCTA
ATATCAGCCTCATCCTTGACTCCACCAAGGGATATGCGCACAAATTTTCTGCCCAAAGCAGCAG
CAATAGAGGATGCCAGTGATGTCTTTCCAACACCTGGTGGTCCAACAAAGCACAATACTGGACC
CCTTGCATCTGGCTTAAGCTTGCGAACAGCCAGGTATTCAATTATCCGTTGCTTGACCTTCACT
AAACCATAGTGATCAGTGTCCAGGCGCTCCTGTGCAGCCCTTAAGTCCAGTTCAAGCTCTTTGC
TAGCCTTCTGCCATGGCAAATCAGCAAGAAGATCCAGGTAAGCCCGTGAACTGTTATACCCTGG
TTGCTGAGGCTGCATTTTTTTGAGTCTCCTTAATTCTTTGTGAGCATGCTTCCAGATATTCTGT
GGCATTCCTGCCTTTTGCATCTTTCTTTCCAGGGCAGCCAGGTCATCCTCGTCATCATCATTAT
CACCAAGTTCCTCTTTTATAGCTCTCATCTGCTGTCGAAGAAGAAATTCTTTTTGAGATTTTGA
CAATTGTCCTTCAACCTTTTGTGTAATTTTCTCAGCTACAAGTATTGACTGTAAGTGCCTATCA
ACCAATTCTGTTGCTTTTGAAAGCCTCACTTTAGGGTCAACTGAATCCAACATTGATAGCTGCT
CTTCAAAACTTATCTCAAAGCTAGCAACAAATATATCAGCCAACTTGTGAACTGGAACAGTCTC
CAAAAGAACTTTCGTCCTTCCACCAGTTTTTTGTTTCTGCTCCAGAACAGAAATAAGCTCCATG
GCAGTTGCTTTAAATTGGCGAGATAATGTTATGAAATCTGGGTCTTGTTCCACCTGTTCCATCT
CAGTCTTAGTCATCTCCAGGGATGATATCCTTGCAGTATGGTATGTTCCTCTCGTGCTTAGTTC
CTGGACACTAAATCTGCACAGACCTTCAAGAACAACAATATATGTGACTCTCCCACTAGGTTTC
TCCACTCCCCTTGATAAGTGTAGTGCTCGAGCAGCTACCCCCCTGTTATGCCAATGAACAACAT
CATGCTGATTTTTCACATCAAGCTTTTGAGAATCTGATGAACCACCTTGAACTTTTGAGTTTTG
GTCTAGAGAATCGGTACCTTTGCCGTGAGATATAACTGGACCCGCGGGCTGAATTTCAGCAGCA
GCATCACGTACTGGTAAGATGCCAATCAACCCCTTCTCTTCTCGCTGCCAAAGTTCTTGTTCCA
CCAACTTTACA
						
					

						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	ACCCGCGGGCTGAATTTCAGCAGCAGCATCACGTACTGGTAAGATGCCAATCAACCCCTTCTCT TCTCGCTGCCAAAGTTCTTGTTCCACCAACTTTACAtgatcattgaatgctttgttttgttccg gatcaagaacctctagcaatgcagaagctggatctccacgaacatcggaccctgtcttgtcaat ttcatcaa
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: 1419 Transcript exons: 53591944-53592074,53592720-53592926,53593015-53593216,53 593381-53593508,53599471-53599554,53599638-53599817,5360 0126-53600217,53600733-53600902,53601224-53601332,536014 23-53601538 TGATCATTGAATGCTTTGTTTTGTTCCGGATCAAGAACCTCTAGCAATGCAGAAGCTGGATCTC CACGAACATCGGACCCTGTCTTGTCAATTTCATCAATCAACATGACAGGATTGCAAACAGCTAC TCTCTTCAGTCCATCTATAAGCCTCCCAGGCATGCTTCCAATGTATGTTCTCCTATGCCCTCTA ATATCAGCCTCATCCTTGACTCCACCAAGGGATATGCGCACAAATTTTCTGCCCAAAGCAGCAG CAATAGAGGATGCCAGTGATGTCTTTCCAACACCTGGTGGTCCAACAAAGCACAATACTGGACC CCTTGCATCTGGCTTAAGCTTGCGAACAGCCAGGTATTCAATTATCCGTTGCTTGACCTTCACT AAACCATAGTGATCAGTGTCCAGGCGCTCCTGTGCAGCCCTTAAGTCCAGTTCAAGCTCTTTGC TAGCCTTCTGCCATGGCAAATCAGCAAGAAGATCCAGGTAAGCCCGTGAACTGTTATACCCTGG TTGCTGAGGCTGCATTTTTTTGAGTCTCCTTAATTCTTTGTGAGCATGCTTCCAGATATTCTGT GGCATTCCTGCCTTTTGCATCTTTCTTTCCAGGGCAGCCAGGTCATCCTCGTCATCATCATTAT CACCAAGTTCCTCTTTTATAGCTCTCATCTGCTGTCGAAGAAGAAATTCTTTTTGAGATTTTGA CAATTGTCCTTCAACCTTTTGTGTAATTTTCTCAGCTACAAGTATTGACTGTAAGTGCCTATCA ACCAATTCTGTTGCTTTTGAAAGCCTCACTTTAGGGTCAACTGAATCCAACATTGATAGCTGCT CTTCAAAACTTATCTCAAAGCTAGCAACAAATATATCAGCCAACTTGTGAACTGGAACAGTCTC CAAAAGAACTTTCGTCCTTCCACCAGTTTTTTGTTTCTGCTCCAGAACAGAAATAAGCTCCATG GCAGTTGCTTTAAATTGGCGAGATAATGTTATGAAATCTGGGTCTTGTTCCACCTGTTCCATCT CAGTCTTAGTCATCTCCAGGGATGATATCCTTGCAGTATGGTATGTTCCTCTCGTGCTTAGTTC CTGGACACTAAATCTGCACAGACCTTCAAGAACAACAATATATGTGACTCTCCCACTAGGTTTC TCCACTCCCCTTGATAAGTGTAGTGCTCGAGCAGCTACCCCCCTGTTATGCCAATGAACAACAT CATGCTGATTTTTCACATCAAGCTTTTGAGAATCTGATGAACCACCTTGAACTTTTGAGTTTTG GTCTAGAGAATCGGTACCTTTGCCGTGAGATATAACTGGACCCGCGGGCTGAATTTCAGCAGCA GCATCACGTACTGGTAAGATGCCAATCAACCCCTTCTCTTCTCGCTGCCAAAGTTCTTGTTCCA CCAACTTTACA
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
						0.291292861

Conservation Information
Conserved circRNAs	NA
PMCS	0.291292861

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							53600747-53591946(-)
						
					

						Potential amino acid sequence
						
							MTKTEMEQVEQDPDFITLSRQFKATAMELISVLEQKQKTGGRTKVLLETVPVHKLADIFVASFE
ISFEEQLSMLDSVDPKVRLSKATELVDRHLQSILVAEKITQKVEGQLSKSQKEFLLRQQMRAIK
EELGDNDDDEDDLAALERKMQKAGMPQNIWKHAHKELRRLKKMQPQQPGYNSSRAYLDLLADLP
WQKASKELELDLRAAQERLDTDHYGLVKVKQRIIEYLAVRKLKPDARGPVLCFVGPPGVGKTSL
ASSIAAALGRKFVRISLGGVKDEADIRGHRRTYIGSMPGRLIDGLKRVAVCNPVMLIDEIDKTG
SDVRGDPASALLEVLDPEQNKAFNDHVKLVEQELWQREEKGLIGILPVRDAAAEIQPAGPVISH
GKGTDSLDQNSKVQGGSSDSQKLDVKNQHDVVHWHNRGVAARALHLSRGVEKPSGRVTYIVVLE
GLCRFSVQELSTRGTYHTARISSLEMTKTEMEQVEQDPDFITLSRQFKATAMELISVLEQKQKT
GGRTKVLLETVPVHKLADIFVASFEISFEEQLSMLDSVDPKVRLSKATELVDRHLQSILVAEKI
TQKVEGQLSKSQKEFLLRQQMRAIKEELGDNDDDEDDLAALERKMQKAGMPQNIWKHAHKELRR
LKKMQPQQPGYNSSRAYLDLLADLPWQKASKELELDLRAAQERLDTDHYGLVKVKQRIIEYLAV
RKLKPDARGPVLCFVGPPGVGKTSLASSIAAALGRKFVRISLGGVKDEADIRGHRRTYIGSMPG
RLIDGLKRVAVCNPVMLIDEIDKTGSDVRGDPASALLEVLDPEQNKAFNDHVKLVEQELWQREE
KGLIGILPVRDAAAEIQPAGPVISHGKGTDSLDQNSKVQGGSSDSQKLDVKNQHDVVHWHNRGV
AARALHLSRGVEKPSGRVTYIVVLEGLCRFSVQELSTRGTYHTARISSLEMTKTEMEQVEQDPD
FITLSRQFKATAMELISVLEQKQKTGGRTKVLLETVPVHKLADIFVASFEISFEEQLSMLDSVD
PKVRLSKATELVDRHLQSILVAEKITQKVEGQLSKSQKEFLLRQQMRAIKEELGDNDDDEDDLA
ALERKMQKAGMPQNIWKHAHKELRRLKKMQPQQPGYNSSRAYLDLLADLPWQKASKELELDLRA
AQERLDTDHYGLVKVKQRIIEYLAVRKLKPDARGPVLCFVGPPGVGKTSLASSIAAALGRKFVR
ISLGGVKDEADIRGHRRTYIGSMPGRLIDGLKRVAVCNPVMLIDEIDKTGSDVRGDPASALLEV
LDPEQNKAFNDHVKLVEQELWQREEKGLIGILPVRDAAAEIQPAGPVISHGKGTDSLDQNSKVQ
GGSSDSQKLDVKNQHDVVHWHNRGVAARALHLSRGVEKPSGRVTYIVVLEGLCRFSVQELSTRG
TYHTARISSLEMTKTEMEQVEQDPDFITLSRQFKATAMELISVLEQKQKTGGRTKVLLETVPVH
KLADIFVASFEISFEEQLSMLDSVDPKVRLSKATELVDRHLQSILVAEKITQKVEGQLSKSQKE
FLLRQQMRAIKEELGDNDDDEDDLAALERKMQKAGMPQNIWKHAHKELRRLKKMQPQQPGYNSS
RAYLDLLADLPWQKASKELELDLRAAQERLDTDHYGLVKVKQRIIEYLAVRKLKPDARGPVLCF
VGPPGVGKTSLASSIAAALGRKFVRISLGGVKDEADIRGHRRTYIGSMPGRLIDGLKRVAVCNP
VMLIDEIDKTGSDVRGDPASALLEVLDPEQNKAFND(-)
						
					

						Sponge-miRNAs
						
							gma-miR164d gma-miR164k 						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	53600747-53591946(-)
Potential amino acid sequence	MTKTEMEQVEQDPDFITLSRQFKATAMELISVLEQKQKTGGRTKVLLETVPVHKLADIFVASFE ISFEEQLSMLDSVDPKVRLSKATELVDRHLQSILVAEKITQKVEGQLSKSQKEFLLRQQMRAIK EELGDNDDDEDDLAALERKMQKAGMPQNIWKHAHKELRRLKKMQPQQPGYNSSRAYLDLLADLP WQKASKELELDLRAAQERLDTDHYGLVKVKQRIIEYLAVRKLKPDARGPVLCFVGPPGVGKTSL ASSIAAALGRKFVRISLGGVKDEADIRGHRRTYIGSMPGRLIDGLKRVAVCNPVMLIDEIDKTG SDVRGDPASALLEVLDPEQNKAFNDHVKLVEQELWQREEKGLIGILPVRDAAAEIQPAGPVISH GKGTDSLDQNSKVQGGSSDSQKLDVKNQHDVVHWHNRGVAARALHLSRGVEKPSGRVTYIVVLE GLCRFSVQELSTRGTYHTARISSLEMTKTEMEQVEQDPDFITLSRQFKATAMELISVLEQKQKT GGRTKVLLETVPVHKLADIFVASFEISFEEQLSMLDSVDPKVRLSKATELVDRHLQSILVAEKI TQKVEGQLSKSQKEFLLRQQMRAIKEELGDNDDDEDDLAALERKMQKAGMPQNIWKHAHKELRR LKKMQPQQPGYNSSRAYLDLLADLPWQKASKELELDLRAAQERLDTDHYGLVKVKQRIIEYLAV RKLKPDARGPVLCFVGPPGVGKTSLASSIAAALGRKFVRISLGGVKDEADIRGHRRTYIGSMPG RLIDGLKRVAVCNPVMLIDEIDKTGSDVRGDPASALLEVLDPEQNKAFNDHVKLVEQELWQREE KGLIGILPVRDAAAEIQPAGPVISHGKGTDSLDQNSKVQGGSSDSQKLDVKNQHDVVHWHNRGV AARALHLSRGVEKPSGRVTYIVVLEGLCRFSVQELSTRGTYHTARISSLEMTKTEMEQVEQDPD FITLSRQFKATAMELISVLEQKQKTGGRTKVLLETVPVHKLADIFVASFEISFEEQLSMLDSVD PKVRLSKATELVDRHLQSILVAEKITQKVEGQLSKSQKEFLLRQQMRAIKEELGDNDDDEDDLA ALERKMQKAGMPQNIWKHAHKELRRLKKMQPQQPGYNSSRAYLDLLADLPWQKASKELELDLRA AQERLDTDHYGLVKVKQRIIEYLAVRKLKPDARGPVLCFVGPPGVGKTSLASSIAAALGRKFVR ISLGGVKDEADIRGHRRTYIGSMPGRLIDGLKRVAVCNPVMLIDEIDKTGSDVRGDPASALLEV LDPEQNKAFNDHVKLVEQELWQREEKGLIGILPVRDAAAEIQPAGPVISHGKGTDSLDQNSKVQ GGSSDSQKLDVKNQHDVVHWHNRGVAARALHLSRGVEKPSGRVTYIVVLEGLCRFSVQELSTRG TYHTARISSLEMTKTEMEQVEQDPDFITLSRQFKATAMELISVLEQKQKTGGRTKVLLETVPVH KLADIFVASFEISFEEQLSMLDSVDPKVRLSKATELVDRHLQSILVAEKITQKVEGQLSKSQKE FLLRQQMRAIKEELGDNDDDEDDLAALERKMQKAGMPQNIWKHAHKELRRLKKMQPQQPGYNSS RAYLDLLADLPWQKASKELELDLRAAQERLDTDHYGLVKVKQRIIEYLAVRKLKPDARGPVLCF VGPPGVGKTSLASSIAAALGRKFVRISLGGVKDEADIRGHRRTYIGSMPGRLIDGLKRVAVCNP VMLIDEIDKTGSDVRGDPASALLEVLDPEQNKAFND(-)
Sponge-miRNAs	gma-miR164d gma-miR164k
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_01G203100_circ_g.3

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