Expressed conserved protein

Overview
NameExpressed conserved protein
Smed IDSMED30035987
Length (bp)668
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 



 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)




Explore this single cell expression dataset with our NB Cluster Shiny App




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of Expressed conserved protein (SMED30035987) t-SNE clustered cells

Violin plots show distribution of expression levels for Expressed conserved protein (SMED30035987) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of Expressed conserved protein (SMED30035987) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Expressed conserved protein (SMED30035987) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020




SMED30035987

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30035987h1SMcG0007070 dd_Smed_v4_5021_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30035987h1SMcG0007070 dd_Smed_v4_5021_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30035987h1SMcG0007070 dd_Smed_v4_5021_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30035987h1SMcG0007070 dd_Smed_v4_5021_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30035987h1SMcG0007070 dd_Smed_v4_5021_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30035987h1SMcG0007070 dd_Smed_v4_5021_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30035987h1SMcG0007070 dd_Smed_v4_5021_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Expressed conserved protein vs. TrEMBL
Match: G7YVR2 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CLF_112050 PE=4 SV=1)

HSP 1 Score: 64.3142 bits (155), Expect = 9.931e-10
Identity = 38/65 (58.46%), Postives = 50/65 (76.92%), Query Frame = 3
Query:   90 MCELEIFRKLKLYMPFMVXXXXXXXXXXXXXXXXXARQRPDVWIAGILLSIFALPLFVFGLVIFC 284
            MC+L++ ++ KLYMP +  G IL++ S   ISLGIAR R DVWIAGIL++I A+PLF+F L IFC
Sbjct:    1 MCDLDLHKRTKLYMPMLAFGMILVVLSCFMISLGIARAREDVWIAGILVAIIAMPLFIFSLTIFC 65          
BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A4S2LWV6 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_005461 PE=4 SV=1)

HSP 1 Score: 63.929 bits (154), Expect = 1.235e-9
Identity = 37/65 (56.92%), Postives = 51/65 (78.46%), Query Frame = 3
Query:   90 MCELEIFRKLKLYMPFMVXXXXXXXXXXXXXXXXXARQRPDVWIAGILLSIFALPLFVFGLVIFC 284
            MC+L++ ++ KLYMP +  G IL++ S   ISLGIAR+R DVWIAGIL++I ++PLF+F L IFC
Sbjct:    1 MCDLDLHKRTKLYMPMLAFGMILVVLSCFMISLGIAREREDVWIAGILVAIISMPLFIFSLTIFC 65          
BLAST of Expressed conserved protein vs. TrEMBL
Match: G4VIA8 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 GN=Smp_050760 PE=4 SV=1)

HSP 1 Score: 62.7734 bits (151), Expect = 2.998e-9
Identity = 46/104 (44.23%), Postives = 61/104 (58.65%), Query Frame = 3
Query:   90 MCELEIFRKLKLYMPFMVXXXXXXXXXXXXXXXXXARQRPDVWIAGILLSIFALPLFVFGLVIFCCL------------YLKESKNPKAFNPYPKAFMGLQYTA 365
            MCE+E++RK K+ +P +  G IL I S L IS+GIAR R DVWIAGIL++I  LPLF+F L++FC +            Y+     P  F   P A +G  Y A
Sbjct:    1 MCEIELYRKTKIDIPLLAAGMILCILSCLMISVGIARVREDVWIAGILVAIVGLPLFLFSLIVFCVIRTNNYTEVLPKQYVLGKIPPPTFTSIPSA-LGSIYHA 103          
BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A183PP87 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS16173 PE=4 SV=1)

HSP 1 Score: 61.6178 bits (148), Expect = 7.168e-9
Identity = 47/104 (45.19%), Postives = 61/104 (58.65%), Query Frame = 3
Query:   90 MCELEIFRKLKLYMPFMVXXXXXXXXXXXXXXXXXARQRPDVWIAGILLSIFALPLFVFGLVIFCCL------------YLKESKNPKAFNPYPKAFMGLQYTA 365
            MCE+E++RK K+ +P +  G IL I S L IS+GIAR R DVWIAGIL++I  LPLF+F LV+FC +            Y+     P  F   P A +G  Y A
Sbjct:    1 MCEIELYRKTKIDIPLLAAGMILCILSCLMISVGIARVREDVWIAGILVAIVGLPLFLFFLVVFCVIRTNNYTEVLPKQYVLGKIPPPTFTSIPSA-LGSIYHA 103          
BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A183LM08 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS4833 PE=4 SV=1)

HSP 1 Score: 61.6178 bits (148), Expect = 7.168e-9
Identity = 47/104 (45.19%), Postives = 61/104 (58.65%), Query Frame = 3
Query:   90 MCELEIFRKLKLYMPFMVXXXXXXXXXXXXXXXXXARQRPDVWIAGILLSIFALPLFVFGLVIFCCL------------YLKESKNPKAFNPYPKAFMGLQYTA 365
            MCE+E++RK K+ +P +  G IL I S L IS+GIAR R DVWIAGIL++I  LPLF+F LV+FC +            Y+     P  F   P A +G  Y A
Sbjct:    1 MCEIELYRKTKIDIPLLAAGMILCILSCLMISVGIARVREDVWIAGILVAIVGLPLFLFFLVVFCVIRTNNYTEVLPKQYVLGKIPPPTFTSIPSA-LGSIYHA 103          
BLAST of Expressed conserved protein vs. Planmine SMEST
Match: SMESG000044572.1 (SMESG000044572.1)

HSP 1 Score: 272.707 bits (696), Expect = 2.262e-94
Identity = 150/150 (100.00%), Postives = 150/150 (100.00%), Query Frame = 3
Query:   90 MCELEIFRKLKLYMPFMVXXXXXXXXXXXXXXXXXARQRPDVWIAGILLSIFALPLFVFGLVIFCCLYLKESKNPKAFNPYPKAFMGLQYTAPSQQESGRRLIDHGSIFSEETNSNLTKKDNLYTNITMEPLLEDDHPPENVDYRYLDPL 539
            MCELEIFRKLKLYMPFMVIGFILIIGSSLTISLGIARQRPDVWIAGILLSIFALPLFVFGLVIFCCLYLKESKNPKAFNPYPKAFMGLQYTAPSQQESGRRLIDHGSIFSEETNSNLTKKDNLYTNITMEPLLEDDHPPENVDYRYLDPL
Sbjct:    1 MCELEIFRKLKLYMPFMVIGFILIIGSSLTISLGIARQRPDVWIAGILLSIFALPLFVFGLVIFCCLYLKESKNPKAFNPYPKAFMGLQYTAPSQQESGRRLIDHGSIFSEETNSNLTKKDNLYTNITMEPLLEDDHPPENVDYRYLDPL 150          
The following BLAST results are available for this feature:
BLAST of Expressed conserved protein vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Expressed conserved protein vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Expressed conserved protein vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Expressed conserved protein vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Expressed conserved protein vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Expressed conserved protein vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Expressed conserved protein vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Expressed conserved protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
G7YVR29.931e-1058.46Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
A0A4S2LWV61.235e-956.92Uncharacterized protein OS=Opisthorchis felineus O... [more]
G4VIA82.998e-944.23Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A183PP877.168e-945.19Uncharacterized protein OS=Schistosoma mattheei OX... [more]
A0A183LM087.168e-945.19Uncharacterized protein OS=Schistosoma margrebowie... [more]
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BLAST of Expressed conserved protein vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Expressed conserved protein vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Expressed conserved protein vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Expressed conserved protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Expressed conserved protein vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Expressed conserved protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000044572.12.262e-94100.00SMESG000044572.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035987 ID=SMED30035987|Name=Expressed conserved protein|organism=Schmidtea mediterranea sexual|type=transcript|length=668bp
TAGATAAATACACACATCAATAATAACCAATAATAGTGCTTTAAATTTTA
AAATTATTTCCGTGATTATTTTAAATTCGCTAATTTTACATGTGTGAATT
AGAAATATTTCGAAAACTGAAATTGTATATGCCATTTATGGTTATTGGAT
TTATCCTCATAATTGGTTCATCTCTAACCATATCCCTAGGCATTGCAAGA
CAAAGACCTGATGTTTGGATAGCTGGAATTTTATTGTCTATATTTGCTTT
GCCATTATTTGTATTTGGTCTTGTTATATTTTGCTGTTTATATTTAAAGG
AATCTAAAAATCCGAAAGCATTCAATCCATATCCAAAAGCATTCATGGGT
CTCCAGTATACTGCTCCGTCTCAACAAGAGAGTGGACGTCGATTAATTGA
TCATGGATCCATATTTTCAGAAGAGACCAATAGTAATTTAACCAAAAAGG
ACAATTTATATACTAATATTACGATGGAACCATTATTAGAAGATGATCAT
CCTCCAGAAAATGTAGACTATAGATATTTAGATCCATTATAAATAATTTA
TGTGAATTATAAAATGGCTGTGAAATTAATTTCATATCAATTCGAACGAT
ATTAAAATCATTTTTTTATCTACATTTGTAATTAGAACCTCTGAAATATA
TATTCCACATTTTAAAAA
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protein sequence of SMED30035987-orf-1

>SMED30035987-orf-1 ID=SMED30035987-orf-1|Name=SMED30035987-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=151bp
MCELEIFRKLKLYMPFMVIGFILIIGSSLTISLGIARQRPDVWIAGILLS
IFALPLFVFGLVIFCCLYLKESKNPKAFNPYPKAFMGLQYTAPSQQESGR
RLIDHGSIFSEETNSNLTKKDNLYTNITMEPLLEDDHPPENVDYRYLDPL
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000099neuron
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 44..66
NoneNo IPR availableTMHMMTMhelixcoord: 12..34