Protein quiver

Overview
NameProtein quiver
Smed IDSMED30030116
Length (bp)531
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 Protein quiver (SMED30030116) t-SNE clustered cells

Violin plots show distribution of expression levels for Protein quiver (SMED30030116) 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 Protein quiver (SMED30030116) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Protein quiver (SMED30030116) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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



SMED30030116

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymaSMED30030116SMESG000040366.1 dd_Smed_v4_11379_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Protein quiver vs. TrEMBL
Match: A0A1I8G1W3 (Protein quiver OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 53.1434 bits (126), Expect = 4.702e-8
Identity = 27/61 (44.26%), Postives = 38/61 (62.30%), Query Frame = 1 
Query:  148 ESDFSKMITCYNCDSNENNSTCSKEFMWNKEVNDSLSTVSCWKGGCVKWV-YKNIDKQVTK 327
            E+DFS  ITCY C+    NSTCS   +   +++  L+ VSC +GGC+KW  YKN   Q+ +
Sbjct:   27 EADFSDHITCYECEGQLGNSTCSTPGV---DIDKVLNQVSCVRGGCLKWAYYKNSQLQLVR 84

HSP 2 Score: 31.5722 bits (70), Expect = 4.702e-8
Identity = 14/41 (34.15%), Postives = 21/41 (51.22%), Query Frame = 2 
Query:  329 KTCSLLLDVKMSLVDACFSNRHEESLFCICSGSYCNSHSVV 451
            +TCSL +++ + L  AC   R      CIC    CNS  ++
Sbjct:   84 RTCSLRVNMSIYLHSACRQERRGNGFICICPNDLCNSAGMI 124
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BLAST of Protein quiver vs. TrEMBL
Match: A0A1I8HE29 (Protein quiver OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 53.1434 bits (126), Expect = 8.186e-8
Identity = 27/61 (44.26%), Postives = 38/61 (62.30%), Query Frame = 1 
Query:  148 ESDFSKMITCYNCDSNENNSTCSKEFMWNKEVNDSLSTVSCWKGGCVKWV-YKNIDKQVTK 327
            E+DFS  ITCY C+    NSTCS   +   +++  L+ VSC +GGC+KW  YKN   Q+ +
Sbjct:   27 EADFSDHITCYECEGQLGNSTCSTPGV---DIDKVLNQVSCVRGGCLKWAYYKNSQLQLVR 84

HSP 2 Score: 31.187 bits (69), Expect = 8.186e-8
Identity = 14/41 (34.15%), Postives = 21/41 (51.22%), Query Frame = 2 
Query:  329 KTCSLLLDVKMSLVDACFSNRHEESLFCICSGSYCNSHSVV 451
            +TCSL +++ + L  AC   R      CIC    CNS ++ 
Sbjct:   84 RTCSLRVNMSIYLHSACRQERRGNGFICICPNDLCNSAAMT 124
[Close]
BLAST of Protein quiver vs. TrEMBL
Match: A0A267DLL8 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig021953g1 PE=4 SV=1)

HSP 1 Score: 53.1434 bits (126), Expect = 1.008e-7
Identity = 27/61 (44.26%), Postives = 38/61 (62.30%), Query Frame = 1 
Query:  148 ESDFSKMITCYNCDSNENNSTCSKEFMWNKEVNDSLSTVSCWKGGCVKWV-YKNIDKQVTK 327
            E+DFS  ITCY C+    NSTCS   +   +++  L+ VSC +GGC+KW  YKN   Q+ +
Sbjct:   43 EADFSDHITCYECEGQLGNSTCSTPGV---DIDKVLNQVSCVRGGCLKWAYYKNSQLQLVR 100

HSP 2 Score: 30.8018 bits (68), Expect = 1.008e-7
Identity = 14/41 (34.15%), Postives = 20/41 (48.78%), Query Frame = 2 
Query:  329 KTCSLLLDVKMSLVDACFSNRHEESLFCICSGSYCNSHSVV 451
            +TCSL +++ + L  AC   R      CIC    CNS  + 
Sbjct:  100 RTCSLRVNMSIYLHSACRQERRGNGFICICPNDLCNSAGMT 140
[Close]
BLAST of Protein quiver vs. TrEMBL
Match: A0A1I8GRN5 (Protein quiver OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 4.508e-6
Identity = 27/61 (44.26%), Postives = 38/61 (62.30%), Query Frame = 1 
Query:  148 ESDFSKMITCYNCDSNENNSTCSKEFMWNKEVNDSLSTVSCWKGGCVKWV-YKNIDKQVTK 327
            E+DFS  ITCY C+    NSTCS   +   +++  L+ VSC +GGC+KW  YKN   Q+ +
Sbjct:   32 EADFSDHITCYECEGQLGNSTCSTPGV---DIDKVLNQVSCVRGGCLKWAYYKNSQLQLVR 89
The following BLAST results are available for this feature:
BLAST of Protein quiver 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 Protein quiver 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 Protein quiver 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 Protein quiver 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 Protein quiver 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 Protein quiver 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 Protein quiver 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 Protein quiver vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A1I8G1W34.702e-844.26Protein quiver OS=Macrostomum lignano OX=282301 PE... [more]
A0A1I8HE298.186e-844.26Protein quiver OS=Macrostomum lignano OX=282301 PE... [more]
A0A267DLL81.008e-744.26Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A1I8GRN54.508e-644.26Protein quiver OS=Macrostomum lignano OX=282301 PE... [more]
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BLAST of Protein quiver 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 Protein quiver 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 Protein quiver 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 Protein quiver 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 Protein quiver 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 Protein quiver vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030116 ID=SMED30030116|Name=Protein quiver|organism=Schmidtea mediterranea sexual|type=transcript|length=531bp
TTTTCATCGTAGTACAATAAATCAATTTTATTCATTGCATTTGCTTATAA
CTGAAATATGAAGTTCTTAGTTGGACTGATGACTACAATTTGCTCCTTAG
TTATTATATGTTCAATGGTTTTAAATTTTTTGGAGAAAATAGAAGCTGAA
AGTGATTTTTCAAAAATGATAACGTGTTACAACTGTGATTCAAACGAAAA
CAACAGTACGTGTAGCAAGGAATTTATGTGGAATAAAGAAGTGAATGACT
CCTTGTCAACTGTTAGTTGCTGGAAAGGAGGATGCGTAAAGTGGGTCTAC
AAAAATATTGACAAACAAGTAACAAAAAAAAACGTGTTCCTTACTTTTGG
ATGTCAAAATGTCATTAGTAGATGCATGTTTTTCAAATAGGCATGAAGAA
AGTCTTTTCTGTATATGTTCAGGTAGTTATTGCAATTCTCATTCTGTAGT
TAACACTGATTATTTTTTATATTTAATAATAATTCTTGAATTTTATATCA
CACATGAATACTTGTAACAGGCATTGTTTTG
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protein sequence of SMED30030116-orf-1

>SMED30030116-orf-1 ID=SMED30030116-orf-1|Name=SMED30030116-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=111bp
MKFLVGLMTTICSLVIICSMVLNFLEKIEAESDFSKMITCYNCDSNENNS
TCSKEFMWNKEVNDSLSTVSCWKGGCVKWVYKNIDKQVTKKNVFLTFGCQ
NVISRCMFFK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: biological process
TermDefinition
GO:0030431sleep
GO:0032222regulation of synaptic transmission, cholinergic
GO:1903818positive regulation of voltage-gated potassium channel activity
Vocabulary: INTERPRO
TermDefinition
IPR031424QVR
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR031424Protein quiverPFAMPF17064QVRcoord: 36..107
e-value: 6.0E-12
score: 45.7
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..30
score: 0.728
NoneNo IPR availableTMHMMTMhelixcoord: 4..26