SMED30009408

Overview
NameSMED30009408
Smed IDSMED30009408
Length (bp)804
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 SMED30009408 (SMED30009408) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009408 (SMED30009408) 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 SMED30009408 (SMED30009408) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009408 (SMED30009408) 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




SMED30009408

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30009408SMESG000023140.1 dd_Smed_v4_11207_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30009408SMESG000023140.1 dd_Smed_v4_11207_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
Alignments
SMED30009408 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000408:99437..108235 -3985
Homology
BLAST of SMED30009408 vs. TrEMBL
Match: A0A267EY07 (Profilin OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig020979g1 PE=3 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 1.545e-9
Identity = 33/141 (23.40%), Postives = 70/141 (49.65%), Query Frame = 1
Query:  322 GIIQFAEVANSEVFRKIVDNSIIGTNLIKECVICSNE-GSIIVCNPLNYTPSIEQMSIIINGFENPATIEKSGFQIVTEVYEYLDSDENK--IIGRPXXXXXXXXXXXXKQFFLVGHWTKMGDDPLNLLSEIKAYIENQGF 735
            G ++  +  ++E++  I++ S IGT   K   +CS E G+++ CNP ++TP+++Q++ +   F+  + +  +GF +   VY  LD    K  + G   +    + +   K   L        D   ++L +++ +  +QG 
Sbjct:   87 GEVKIEQGPHTEIWSSIINKSFIGTGAFKRAAVCSLESGAVLACNPADFTPTVQQVAALRENFDCRSGLSAAGFGVADTVYSLLDEAGTKDILCGSDESRGQTLLVCKTKTALLAAACQGAPDRAADMLGDMRQHFISQGM 227          
BLAST of SMED30009408 vs. TrEMBL
Match: A0A1I8GM10 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=3 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 1.965e-9
Identity = 27/89 (30.34%), Postives = 50/89 (56.18%), Query Frame = 1
Query:  301 VKNKDVTGIIQFAEVANSEVFRKIVDNSIIGTNLIKECVICS-NEGSIIVCNPLNYTPSIEQMSIIINGFENPATIEKSGFQIVTEVYE 564
            ++N   TG ++  +   SE++  IV+ S++GT L    V+CS   G +  CNP ++ P+ EQ++++   F NP     +GF +   +Y+
Sbjct:  122 MRNVKATGGVKIEQTPQSEMWWNIVNKSLVGTGLFSRAVVCSLTTGGVFACNPTDFAPAAEQVALLRQNFHNPGAFSAAGFAVGGILYK 210          
BLAST of SMED30009408 vs. TrEMBL
Match: A0A267EPN2 (Profilin (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig010505g1 PE=3 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 3.434e-9
Identity = 27/89 (30.34%), Postives = 50/89 (56.18%), Query Frame = 1
Query:  301 VKNKDVTGIIQFAEVANSEVFRKIVDNSIIGTNLIKECVICS-NEGSIIVCNPLNYTPSIEQMSIIINGFENPATIEKSGFQIVTEVYE 564
            ++N   TG ++  +   SE++  IV+ S++GT L    V+CS   G +  CNP ++ P+ EQ++++   F NP     +GF +   +Y+
Sbjct:  268 MRNVKATGGVKIEQTPQSEMWWNIVNKSLVGTGLFSRAVVCSLTTGGVFACNPTDFAPAAEQVALLRQNFHNPGAFSAAGFAVGGILYK 356          
BLAST of SMED30009408 vs. TrEMBL
Match: A0A267ESZ4 (Profilin (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig019530g1 PE=3 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 7.246e-9
Identity = 26/89 (29.21%), Postives = 50/89 (56.18%), Query Frame = 1
Query:  301 VKNKDVTGIIQFAEVANSEVFRKIVDNSIIGTNLIKECVICS-NEGSIIVCNPLNYTPSIEQMSIIINGFENPATIEKSGFQIVTEVYE 564
            ++N   TG ++  +   S+++  IV+ S++GT L    V+CS   G +  CNP ++ P+ EQ++++   F NP     +GF +   +Y+
Sbjct:  268 MRNVKATGGVKIEQTPQSDMWWNIVNKSLVGTGLFSRAVVCSLTTGGVFACNPADFAPAAEQVALLRQNFHNPGAFSAAGFAVGGILYK 356          
BLAST of SMED30009408 vs. TrEMBL
Match: A0A1I8IIT4 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=3 SV=1)

HSP 1 Score: 65.4698 bits (158), Expect = 9.590e-9
Identity = 32/132 (24.24%), Postives = 66/132 (50.00%), Query Frame = 1
Query:  349 NSEVFRKIVDNSIIGTNLIKECVICSNE-GSIIVCNPLNYTPSIEQMSIIINGFENPATIEKSGFQIVTEVYEYLDSDENK--IIGRPXXXXXXXXXXXXKQFFLVGHWTKMGDDPLNLLSEIKAYIENQGF 735
            ++E++  I++ S IGT   K   +CS E G+++ CNP ++TP+++Q++ +   F+  + +  +GF +   VY  LD    K  + G   +    + +   K   L        D   ++L +++ +  +QG 
Sbjct:  142 HAEMWSSIINKSFIGTGAFKRAAVCSLESGAVLACNPADFTPTVQQVAALRENFDCRSGLSAAGFGVADTVYSLLDEAGTKDILCGSDESRGQTLLVCKTKTALLAAACQGAPDRAADMLGDMRQHFISQGI 273          
BLAST of SMED30009408 vs. Ensembl Yeast
Match: PFY1 (Profilin; binds actin, phosphatidylinositol 4,5-bisphosphate, and polyproline regions; involved in cytoskeleton organization; required for normal timing of actin polymerization in response to thermal stress; protein abundance increases in response to DNA replication stress; highly conserved protein; human PFN1 (profilin 1) complements temperature sensitive pfy1 mutants, PFN1 mutations are a rare cause of ALS [Source:SGD;Acc:S000005648])

HSP 1 Score: 43.1282 bits (100), Expect = 4.713e-6
Identity = 22/80 (27.50%), Postives = 40/80 (50.00%), Query Frame = 1
Query:  361 FRKIVDNSIIGTNLIKECVICSNEGSIIVCNPLNYTPSIEQMSIIINGFENPATIEKSGFQIVTEVYEYLDSDENKIIGR 600
            ++   DN +IGT  + + VI S  G  +       +    ++  I+ GF+NPA ++ +G  I  + +  L +D+  I GR
Sbjct:    3 WQAYTDN-LIGTGKVDKAVIYSRAGDAVWATSGGLSLQPNEIGEIVQGFDNPAGLQSNGLHIQGQKFMLLRADDRSIYGR 81          
BLAST of SMED30009408 vs. Planmine SMEST
Match: SMESG000023140.1 (SMESG000023140.1)

HSP 1 Score: 370.933 bits (951), Expect = 1.218e-131
Identity = 196/196 (100.00%), Postives = 196/196 (100.00%), Query Frame = 1
Query:  148 MENSNQSEKQEVRKKKGIFETLFHRQKPINEKSLTTKFFCRKTHKEPKFNMVKNKDVTGIIQFAEVANSEVFRKIVDNSIIGTNLIKECVICSNEGSIIVCNPLNYTPSIEQMSIIINGFENPATIEKSGFQIVTEVYEYLDSDENKIIGRPXXXXXXXXXXXXKQFFLVGHWTKMGDDPLNLLSEIKAYIENQGF 735
            MENSNQSEKQEVRKKKGIFETLFHRQKPINEKSLTTKFFCRKTHKEPKFNMVKNKDVTGIIQFAEVANSEVFRKIVDNSIIGTNLIKECVICSNEGSIIVCNPLNYTPSIEQMSIIINGFENPATIEKSGFQIVTEVYEYLDSDENKIIGRPLNGTGGIGILNGKQFFLVGHWTKMGDDPLNLLSEIKAYIENQGF
Sbjct:    1 MENSNQSEKQEVRKKKGIFETLFHRQKPINEKSLTTKFFCRKTHKEPKFNMVKNKDVTGIIQFAEVANSEVFRKIVDNSIIGTNLIKECVICSNEGSIIVCNPLNYTPSIEQMSIIINGFENPATIEKSGFQIVTEVYEYLDSDENKIIGRPLNGTGGIGILNGKQFFLVGHWTKMGDDPLNLLSEIKAYIENQGF 196          
BLAST of SMED30009408 vs. Planmine SMEST
Match: SMESG000005022.1 (SMESG000005022.1)

HSP 1 Score: 96.2857 bits (238), Expect = 5.356e-24
Identity = 47/104 (45.19%), Postives = 74/104 (71.15%), Query Frame = 1
Query:  280 KEPKFNMVKNKDVTGIIQFAEVANSEVFRKIVDNSIIGTNLIKECVICS-NEGSIIVCNPLNYTPSIEQMSIIINGFENPATIEKSGFQIVTEVYE--YLDSDE 582
            ++PK  MVKNK+VTG I+F    N  +FR I+DNS++GT ++ +   CS + G+II CNP +YTPS+EQ++ I++GFEN   ++  GF +V++++E    +SDE
Sbjct:   56 EKPKPKMVKNKNVTGTIKFETATNVPLFRNILDNSMVGTKIVTKGCFCSKSSGNIIACNPPDYTPSVEQINFIVSGFENIDLLKTQGFMVVSDLFEPSSFESDE 159          
The following BLAST results are available for this feature:
BLAST of SMED30009408 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 SMED30009408 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 SMED30009408 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 SMED30009408 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 SMED30009408 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 SMED30009408 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 SMED30009408 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 SMED30009408 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267EY071.545e-923.40Profilin OS=Macrostomum lignano OX=282301 GN=BOX15... [more]
A0A1I8GM101.965e-930.34Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267EPN23.434e-930.34Profilin (Fragment) OS=Macrostomum lignano OX=2823... [more]
A0A267ESZ47.246e-929.21Profilin (Fragment) OS=Macrostomum lignano OX=2823... [more]
A0A1I8IIT49.590e-924.24Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30009408 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 SMED30009408 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 SMED30009408 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 1
Match NameE-valueIdentityDescription
PFY14.713e-627.50Profilin; binds actin, phosphatidylinositol 4,5-bi... [more]
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BLAST of SMED30009408 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 SMED30009408 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 SMED30009408 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000023140.11.218e-131100.00SMESG000023140.1[more]
SMESG000005022.15.356e-2445.19SMESG000005022.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009408 ID=SMED30009408|Name=SMED30009408|organism=Schmidtea mediterranea sexual|type=transcript|length=804bp
TTAACTTAATAGGCCGCCTATTATAAGCGTAAATGACAGAAAGTATATTT
AGAAAAATATATAAGTCCGAGGCACACACACCCAAAGCATGAGTGCAATA
TTGATTTAAATTCTGACTATTTTCCTTTACAATTTGTTTTGAGTAACATG
GAAAATTCAAACCAAAGTGAAAAACAAGAAGTTCGTAAGAAAAAGGGTAT
TTTTGAAACTTTATTTCACAGACAAAAACCGATCAATGAAAAATCTTTGA
CAACGAAATTTTTTTGTCGAAAAACTCATAAAGAACCCAAATTTAATATG
GTGAAAAATAAGGACGTAACAGGAATAATTCAATTCGCTGAAGTGGCCAA
TAGTGAAGTATTTCGAAAGATTGTTGATAATAGTATAATTGGTACAAATC
TTATTAAAGAATGTGTAATATGCAGCAATGAAGGGTCTATAATTGTTTGT
AATCCACTTAATTATACACCGTCTATTGAACAAATGTCTATTATAATAAA
CGGTTTCGAGAATCCAGCAACTATTGAAAAATCAGGATTTCAAATCGTAA
CAGAAGTTTATGAATATTTAGATTCTGATGAAAATAAAATCATCGGAAGA
CCACTGAATGGTACTGGGGGCATTGGAATCTTGAATGGTAAACAATTTTT
CTTGGTAGGTCACTGGACTAAGATGGGAGACGATCCGTTGAATTTACTCA
GTGAAATCAAGGCGTATATTGAAAATCAAGGATTTTAAATAATATATTGT
TAATAATTTACTATGGTTAATTTTTGTATTTCACTTCCTTTTGATACAAT
GACG
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protein sequence of SMED30009408-orf-1

>SMED30009408-orf-1 ID=SMED30009408-orf-1|Name=SMED30009408-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=197bp
MENSNQSEKQEVRKKKGIFETLFHRQKPINEKSLTTKFFCRKTHKEPKFN
MVKNKDVTGIIQFAEVANSEVFRKIVDNSIIGTNLIKECVICSNEGSIIV
CNPLNYTPSIEQMSIIINGFENPATIEKSGFQIVTEVYEYLDSDENKIIG
RPLNGTGGIGILNGKQFFLVGHWTKMGDDPLNLLSEIKAYIENQGF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003117parapharyngeal cell
Vocabulary: INTERPRO
TermDefinition
IPR036140PFN_sf
IPR005455PFN
Vocabulary: molecular function
TermDefinition
GO:0003779actin binding
GO:0003785actin monomer binding
GO:0005085guanyl-nucleotide exchange factor activity
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0005829cytosol
GO:0005937mating projection
GO:0031097medial cortex
GO:0051285cell cortex of cell tip
Vocabulary: biological process
TermDefinition
GO:0030041actin filament polymerization
GO:0032220plasma membrane fusion involved in cytogamy
GO:0043547positive regulation of GTPase activity
GO:0044396actin cortical patch organization
GO:1903475mitotic actomyosin contractile ring assembly
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:3.30.450.30coord: 72..196
e-value: 1.1E-12
score: 50.2
IPR005455ProfilinPFAMPF00235Profilincoord: 73..175
e-value: 8.7E-13
score: 48.7
IPR036140Profilin superfamilySUPERFAMILYSSF55770Profilin (actin-binding protein)coord: 74..174