Profilin

Overview
NameProfilin
Smed IDSMED30021234
Length (bp)872
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 Profilin (SMED30021234) t-SNE clustered cells

Violin plots show distribution of expression levels for Profilin (SMED30021234) 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 Profilin (SMED30021234) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Profilin (SMED30021234) 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



SMED30021234

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30021234h1SMcG0022044 Contig39517uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30021234h1SMcG0022044 Contig39517newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30021234h1SMcG0022044 dd_Smed_v4_6034_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30021234h1SMcG0022044 dd_Smed_v4_6034_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30021234h1SMcG0022044 dd_Smed_v4_6034_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30021234h1SMcG0022044 dd_Smed_v4_6034_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30021234h1SMcG0022044 dd_Smed_v4_6034_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30021234h1SMcG0022044 dd_Smed_v6_6034_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
dorsal ventral margin of the whole animalSMED30021234h1SMcG0022044 dd_Smed_v4_6034_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
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BLAST of Profilin vs. TrEMBL
Match: A0A267ESZ4 (Profilin (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig019530g1 PE=3 SV=1)

HSP 1 Score: 75.485 bits (184), Expect = 1.326e-11
Identity = 44/148 (29.73%), Postives = 72/148 (48.65%), Query Frame = 3 
Query:  243 TGTIKFETATNVPLFRNILDNSMVGTKIVTKGCFCSKSSGNIIACNPPDYTPSVEQINFIVSGFENIDLLKTQGFMVVSDLF--EPSSFESDEICAKTKGDG---EYYEA-LILRTNTTIIIGISQSPVERMKEPLIEIRDMVKNQGF 668
            TG +K E      ++ NI++ S+VGT + ++   CS ++G + ACNP D+ P+ EQ+  +   F N       GF V   L+  EP      E C K    G   ++ E  LI+++ T +I         + +E L ++RD+   QG 
Sbjct:  274 TGGVKIEQTPQSDMWWNIVNKSLVGTGLFSRAVVCSLTTGGVFACNPADFAPAAEQVALLRQNFHNPGAFSAAGFAVGGILYKVEP------EACTKELLSGVNLQHTEGLLIVKSRTALIAAGYTGGRGQAQETLGDLRDLFVQQGL 415
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BLAST of Profilin vs. TrEMBL
Match: A0A267EPN2 (Profilin (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig010505g1 PE=3 SV=1)

HSP 1 Score: 74.7146 bits (182), Expect = 2.440e-11
Identity = 44/148 (29.73%), Postives = 72/148 (48.65%), Query Frame = 3 
Query:  243 TGTIKFETATNVPLFRNILDNSMVGTKIVTKGCFCSKSSGNIIACNPPDYTPSVEQINFIVSGFENIDLLKTQGFMVVSDLF--EPSSFESDEICAKTKGDG---EYYEA-LILRTNTTIIIGISQSPVERMKEPLIEIRDMVKNQGF 668
            TG +K E      ++ NI++ S+VGT + ++   CS ++G + ACNP D+ P+ EQ+  +   F N       GF V   L+  EP      E C K    G   ++ E  LI+++ T +I         + +E L ++RD+   QG 
Sbjct:  274 TGGVKIEQTPQSEMWWNIVNKSLVGTGLFSRAVVCSLTTGGVFACNPTDFAPAAEQVALLRQNFHNPGAFSAAGFAVGGILYKVEP------EACTKELLSGVNLQHTEGLLIVKSRTALIAAGYTGGRGQAQETLGDLRDLFVQQGL 415
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BLAST of Profilin vs. TrEMBL
Match: A0A4Z2D2R6 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_005070 PE=4 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 1.207e-10
Identity = 51/159 (32.08%), Postives = 81/159 (50.94%), Query Frame = 3 
Query:  246 GTIKFETATNVPLFRNILDNSMVGTKIVTKGCFCSKSSGNIIACNPPDYTPSVEQIN--FIVSGFENID-LLKTQGFMVVSD--LFEPSSFESDEICA-------KTKGDGEY----YEALILRTNTTIIIGISQ--SPVERMKEPLIEIRDMVKNQGF 668
            GT+ F+  T   ++  IL NS++GTK++ K   C++ +G I A  P D+TPSVEQIN   ++   E  D  +  + F +  D  L++    E+  + A       +     EY    YE   L T  +++IGI +  + V   K+ LIE+RD +  QG 
Sbjct:   67 GTVTFDHTTQSDVYDRILKNSILGTKLIRKAVICNRYTGAINAYGPEDFTPSVEQINRLLMLLQAERADHTIVDKHFQIAMDSCLYKDVDDETGILLADILQYYTRPNSTNEYNIGKYELSGLLTKNSLLIGIYEVGNQVHESKQLLIEMRDYLDGQGM 225
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BLAST of Profilin vs. TrEMBL
Match: A0A267EY07 (Profilin OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig020979g1 PE=3 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 1.472e-10
Identity = 46/172 (26.74%), Postives = 78/172 (45.35%), Query Frame = 3 
Query:  162 GLCSRGNREPKNDTEXXXXXXX-XXXXXTGTIKFETATNVPLFRNILDNSMVGTKIVTKGCFCSKSSGNIIACNPPDYTPSVEQINFIVSGFENIDLLKTQGFMVVSDLFE--PSSFESDEICAKTKGDGEYYEALILRTNTTIIIGISQSPVERMKEPLIEIRDMVKNQGF 668
            GL  R  R    D E  KP    K     G +K E   +  ++ +I++ S +GT    +   CS  SG ++ACNP D+TP+V+Q+  +   F+    L   GF V   ++     +   D +C   +  G+    L+ +T T ++    Q   +R  + L ++R    +QG 
Sbjct:   58 GLFRRKKRAEAGDQESQKPAEKPKKSGKGGEVKIEQGPHTEIWSSIINKSFIGTGAFKRAAVCSLESGAVLACNPADFTPTVQQVAALRENFDCRSGLSAAGFGVADTVYSLLDEAGTKDILCGSDESRGQTL--LVCKTKTALLAAACQGAPDRAADMLGDMRQHFISQGM 227
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BLAST of Profilin vs. TrEMBL
Match: A0A267F337 (Profilin (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig026365g1 PE=3 SV=1)

HSP 1 Score: 69.707 bits (169), Expect = 9.540e-10
Identity = 42/147 (28.57%), Postives = 70/147 (47.62%), Query Frame = 3 
Query:  246 GTIKFETATNVPLFRNILDNSMVGTKIVTKGCFCSKSSGNIIACNPPDYTPSVEQINFIVSGFENIDLLKTQGFMVVSDLF--EPSSFESDEICAKTKGDG---EYYEA-LILRTNTTIIIGISQSPVERMKEPLIEIRDMVKNQGF 668
            G +K E      ++ NI++ S+VGT + ++   CS ++G + ACNP D+ P+ EQ+  +   F N       GF V   L+  EP      E C K    G   ++ E  LI+++ T +I         + +E L ++ D+   QG 
Sbjct:  273 GGVKIEQTPQSEMWWNIVNKSLVGTGLFSRAVVCSLTTGGVFACNPADFAPAAEQVALLRENFHNPGAFSAAGFAVGGILYKVEP------EACTKELLSGVNLQHTEGLLIVKSRTALIAAGYTGGRGQAQETLGDLLDLFVQQGL 413
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BLAST of Profilin vs. Planmine SMEST
Match: SMESG000005022.1 (SMESG000005022.1)

HSP 1 Score: 397.127 bits (1019), Expect = 1.964e-141
Identity = 209/210 (99.52%), Postives = 210/210 (100.00%), Query Frame = 3 
Query:   39 MSETQNETVQEINQVPNDTCIESKPKSSGKAGKTVLAFFTCGLCSRGNREPKNDTEXXXXXXXXXXXXTGTIKFETATNVPLFRNILDNSMVGTKIVTKGCFCSKSSGNIIACNPPDYTPSVEQINFIVSGFENIDLLKTQGFMVVSDLFEPSSFESDEICAKTKGDGEYYEALILRTNTTIIIGISQSPVERMKEPLIEIRDMVKNQGF 668
            MSETQNETVQEINQVPNDTCIESKPKSSGKAGKTVLAFFTCGLCSRGNREPKN+TEKPKPKMVKNKNVTGTIKFETATNVPLFRNILDNSMVGTKIVTKGCFCSKSSGNIIACNPPDYTPSVEQINFIVSGFENIDLLKTQGFMVVSDLFEPSSFESDEICAKTKGDGEYYEALILRTNTTIIIGISQSPVERMKEPLIEIRDMVKNQGF
Sbjct:    1 MSETQNETVQEINQVPNDTCIESKPKSSGKAGKTVLAFFTCGLCSRGNREPKNETEKPKPKMVKNKNVTGTIKFETATNVPLFRNILDNSMVGTKIVTKGCFCSKSSGNIIACNPPDYTPSVEQINFIVSGFENIDLLKTQGFMVVSDLFEPSSFESDEICAKTKGDGEYYEALILRTNTTIIIGISQSPVERMKEPLIEIRDMVKNQGF 210
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BLAST of Profilin vs. Planmine SMEST
Match: SMESG000023140.1 (SMESG000023140.1)

HSP 1 Score: 86.6557 bits (213), Expect = 2.504e-20
Identity = 59/172 (34.30%), Postives = 97/172 (56.40%), Query Frame = 3 
Query:  165 LCSRGNREPKNDTEXXXXXXXXXXXXTGTIKFETATNVPLFRNILDNSMVGTKIVTKGCFCSKSSGNIIACNPPDYTPSVEQINFIVSGFENIDLLKTQGFMVVSDLFEPSSFESDEICAK----TKGDGEYYEALILRTNTTIIIGISQSPVERMKEPLIEIRDMVKNQGF 668
             C + ++EPK +        VKNK+VTG I+F    N  +FR I+DNS++GT ++ +   CS + G+II CNP +YTPS+EQ++ I++GFEN   ++  GF +V++++E    + ++I  +    T G G      IL      ++G      +     L EI+  ++NQGF
Sbjct:   39 FCRKTHKEPKFNM-------VKNKDVTGIIQFAEVANSEVFRKIVDNSIIGTNLIKECVICS-NEGSIIVCNPLNYTPSIEQMSIIINGFENPATIEKSGFQIVTEVYEYLDSDENKIIGRPLNGTGGIG------ILNGKQFFLVGHWTKMGDDPLNLLSEIKAYIENQGF 196
The following BLAST results are available for this feature:
BLAST of Profilin 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 Profilin 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 Profilin 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 Profilin 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 Profilin 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 Profilin 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 Profilin 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 Profilin vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267ESZ41.326e-1129.73Profilin (Fragment) OS=Macrostomum lignano OX=2823... [more]
A0A267EPN22.440e-1129.73Profilin (Fragment) OS=Macrostomum lignano OX=2823... [more]
A0A4Z2D2R61.207e-1032.08Uncharacterized protein OS=Schistosoma japonicum O... [more]
A0A267EY071.472e-1026.74Profilin OS=Macrostomum lignano OX=282301 GN=BOX15... [more]
A0A267F3379.540e-1028.57Profilin (Fragment) OS=Macrostomum lignano OX=2823... [more]
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BLAST of Profilin 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 Profilin 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 Profilin 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 Profilin 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 Profilin 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 Profilin vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000005022.11.964e-14199.52SMESG000005022.1[more]
SMESG000023140.12.504e-2034.30SMESG000023140.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021234 ID=SMED30021234|Name=Profilin|organism=Schmidtea mediterranea sexual|type=transcript|length=872bp
TTTTATTTCAATTTTTTGGATCAAATTTTGTTTAAACTATGTCTGAAACT
CAGAATGAAACAGTTCAAGAAATAAATCAAGTTCCAAATGACACTTGCAT
TGAATCGAAACCAAAATCTTCGGGAAAGGCTGGCAAAACAGTTTTGGCCT
TTTTTACTTGTGGATTGTGTAGCCGTGGAAATCGAGAACCTAAGAACGAT
ACTGAAAAACCAAAGCCAAAAATGGTAAAGAACAAAAACGTTACGGGAAC
GATTAAATTCGAAACTGCAACAAATGTTCCTTTATTTAGAAATATTCTTG
ATAACAGCATGGTTGGAACGAAGATAGTTACAAAAGGATGTTTTTGTTCT
AAATCATCTGGAAACATCATAGCCTGTAACCCTCCAGATTATACGCCATC
AGTTGAGCAAATAAATTTCATTGTATCCGGATTTGAGAACATCGATTTGC
TAAAGACACAAGGATTCATGGTTGTTTCAGATCTTTTTGAACCAAGCTCA
TTCGAATCCGATGAAATATGCGCTAAGACTAAGGGTGATGGGGAATATTA
TGAAGCATTAATTCTTCGAACGAATACTACCATTATAATCGGAATATCTC
AATCCCCAGTTGAGCGGATGAAGGAGCCATTAATTGAAATCAGAGACATG
GTGAAAAATCAAGGATTTTAATGAGATAAATTTAATAAGAACACATTAGG
TAAAGGGTATTTTTTACTTGAATTAAACCGTTTTTTATTATTTCGACAGA
CATTTTTATCCAAAGTTTAAGTAATTGAGAAAACTTTGTATTTTATTGAT
TTCATGTTTAATTTTAACAAAAATATAATTGCTTTTACAAGAAATATATC
ATTTTGCATTCGCCAAAAAAAA
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protein sequence of SMED30021234-orf-1

>SMED30021234-orf-1 ID=SMED30021234-orf-1|Name=SMED30021234-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=211bp
MSETQNETVQEINQVPNDTCIESKPKSSGKAGKTVLAFFTCGLCSRGNRE
PKNDTEKPKPKMVKNKNVTGTIKFETATNVPLFRNILDNSMVGTKIVTKG
CFCSKSSGNIIACNPPDYTPSVEQINFIVSGFENIDLLKTQGFMVVSDLF
EPSSFESDEICAKTKGDGEYYEALILRTNTTIIIGISQSPVERMKEPLIE
IRDMVKNQGF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003779actin binding
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000043dorsal ventral margin of the whole animal
PLANA:0000418head
PLANA:0002032epidermal cell
PLANA:0003117parapharyngeal cell
Vocabulary: INTERPRO
TermDefinition
IPR036140PFN_sf
IPR005455PFN
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: 83..210
e-value: 3.7E-10
score: 41.9
IPR005455ProfilinPFAMPF00235Profilincoord: 85..191
e-value: 2.4E-9
score: 37.5
IPR036140Profilin superfamilySUPERFAMILYSSF55770Profilin (actin-binding protein)coord: 85..192