piggyBac transposable element-derived protein 4-like

Overview
NamepiggyBac transposable element-derived protein 4-like
Smed IDSMED30006326
Length (bp)1604
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 piggyBac transposable element-derived protein 4-like (SMED30006326) t-SNE clustered cells

Violin plots show distribution of expression levels for piggyBac transposable element-derived protein 4-like (SMED30006326) 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 piggyBac transposable element-derived protein 4-like (SMED30006326) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for piggyBac transposable element-derived protein 4-like (SMED30006326) 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



SMED30006326

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
pharynxSMED30006326 dd_Smed_v4_14301_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30006326 dd_Smed_v4_14301_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 piggyBac transposable element-derived protein 4-like vs. TrEMBL
Match: A0A1B6HS81 (DDE_Tnp_1_7 domain-containing protein (Fragment) OS=Homalodisca liturata OX=320908 GN=g.822 PE=4 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 4.013e-11
Identity = 38/82 (46.34%), Postives = 51/82 (62.20%), Query Frame = 1 
Query:  622 KIGEEETVVNGNLLALKW*DKRDVFMLSTIHPYIIADTAKR-TRINKIIRKPQCIIDYNMKIDAIDHMHMQISFTECVRKAV 864
            ++GE E   +G +LA KW DKRDV MLST H + + +T KR  R  + I KP C++DYN+ + AID   M I   ECVR+  
Sbjct:  143 QVGEVECFNDGTILATKWTDKRDVHMLSTEHSHEMKNTGKRDPRTKENIIKPSCVLDYNVNMGAIDRSDMMIVHLECVRRTT 224
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BLAST of piggyBac transposable element-derived protein 4-like vs. TrEMBL
Match: A0A2S2PHE4 (PiggyBac transposable element-derived protein 4 (Fragment) OS=Schizaphis graminum OX=13262 GN=PGBD4_8 PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 2.233e-10
Identity = 32/80 (40.00%), Postives = 52/80 (65.00%), Query Frame = 1 
Query:  625 IGEEETVVNGNLLALKW*DKRDVFMLSTIHPYIIADTAKRTRINKIIRKPQCIIDYNMKIDAIDHMHMQISFTECVRKAV 864
            +G  ++    N++ LKW D+R+VFMLST++   +AD+ K  R   +I+KP C+++YN  + +ID   M +S  ECVRK +
Sbjct:   44 VGGVQSSHTKNMMVLKWLDRREVFMLSTLYDNKLADSGKVDRKGVMIKKPNCVVNYNACMGSIDKTDMLLSSVECVRKTL 123
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BLAST of piggyBac transposable element-derived protein 4-like vs. TrEMBL
Match: A0A4Y2IXP7 (DDE_Tnp_1_7 domain-containing protein OS=Araneus ventricosus OX=182803 GN=AVEN_84807_1 PE=4 SV=1)

HSP 1 Score: 68.5514 bits (166), Expect = 2.414e-10
Identity = 35/84 (41.67%), Postives = 53/84 (63.10%), Query Frame = 1 
Query:  619 NKIGEEETVVNG--NLLALKW*DKRDVFMLSTIHPYIIADTAKRTRINKIIRKPQCIIDYNMKIDAIDHMHMQISFTECVRKAV 864
            +K+ E E V     NLLA+KW D+++ +MLSTI+    A+  K++R N+ I KP+C+IDYN  +  ID   M IS  +  RK++
Sbjct:    6 DKLKEGEVVFRSSENLLAMKWSDRKEFYMLSTINTAEFAEVPKKSRENEFILKPKCVIDYNSSMGIIDKSDMVISTIDATRKSL 89
[Close]
BLAST of piggyBac transposable element-derived protein 4-like vs. TrEMBL
Match: A0A1S3QE43 (piggyBac transposable element-derived protein 4-like OS=Salmo salar OX=8030 GN=LOC106591513 PE=4 SV=1)

HSP 1 Score: 69.707 bits (169), Expect = 2.881e-10
Identity = 36/79 (45.57%), Postives = 48/79 (60.76%), Query Frame = 1 
Query:  628 GEEETVVNGNLLALKW*DKRDVFMLSTIHPYIIADTAKRTRINKIIR-KPQCIIDYNMKIDAIDHMHMQISFTECVRKA 861
            GE E   NG  LA+KW DKRDV +LST+H   ++ T K   +    + KP C++DYN+K+ A+D   M  SF EC RK 
Sbjct:   12 GEVEFQENGQQLAVKWHDKRDVHVLSTVHTATMSATGKVDHLTGERKIKPDCVLDYNVKMGAVDKADMINSFVECTRKT 90
[Close]
BLAST of piggyBac transposable element-derived protein 4-like vs. TrEMBL
Match: A0A1S3QPH0 (piggyBac transposable element-derived protein 4-like OS=Salmo salar OX=8030 GN=LOC106594435 PE=4 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 7.358e-10
Identity = 36/80 (45.00%), Postives = 48/80 (60.00%), Query Frame = 1 
Query:  628 GEEETVVNGNLLALKW*DKRDVFMLSTIHPYIIADTAKRTRINKIIR-KPQCIIDYNMKIDAIDHMHMQISFTECVRKAV 864
            GE E   NG  LA+KW DKRDV +LST+H   ++ T K   +    + KP C++DYN+K+ A+D   M  SF EC RK  
Sbjct:   93 GEVEFQENGQQLAVKWHDKRDVHVLSTVHTATMSATGKVDHLTGERKIKPDCVLDYNVKMGAVDKADMINSFVECTRKTT 172
The following BLAST results are available for this feature:
BLAST of piggyBac transposable element-derived protein 4-like 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 piggyBac transposable element-derived protein 4-like 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 piggyBac transposable element-derived protein 4-like 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 piggyBac transposable element-derived protein 4-like 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 piggyBac transposable element-derived protein 4-like 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 piggyBac transposable element-derived protein 4-like 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 piggyBac transposable element-derived protein 4-like 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 piggyBac transposable element-derived protein 4-like vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1B6HS814.013e-1146.34DDE_Tnp_1_7 domain-containing protein (Fragment) O... [more]
A0A2S2PHE42.233e-1040.00PiggyBac transposable element-derived protein 4 (F... [more]
A0A4Y2IXP72.414e-1041.67DDE_Tnp_1_7 domain-containing protein OS=Araneus v... [more]
A0A1S3QE432.881e-1045.57piggyBac transposable element-derived protein 4-li... [more]
A0A1S3QPH07.358e-1045.00piggyBac transposable element-derived protein 4-li... [more]
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BLAST of piggyBac transposable element-derived protein 4-like 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 piggyBac transposable element-derived protein 4-like 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 piggyBac transposable element-derived protein 4-like 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 piggyBac transposable element-derived protein 4-like 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 piggyBac transposable element-derived protein 4-like 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 piggyBac transposable element-derived protein 4-like 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

>SMED30006326 ID=SMED30006326|Name=piggyBac transposable element-derived protein 4-like|organism=Schmidtea mediterranea sexual|type=transcript|length=1604bp
TTTTAAAATTTTATTAATTTTAAAAATATAATTAATTAATTTTACATCTA
TCTTTTTTTAACGTCGAAGATGTTAAATAAGAATTTTTAAGTGTGTCAAA
AGAGATAAAGTCTTGAGAACTCCTGTTCTAAACCATAAATGCCAAATTTT
ACCCCTCAAAATTTGATTTTTTTAAAGTACGAGAACCGCATTTAACTTAT
GTACGTTTTTATACATGATTTTCTTATTTGCAAATATTATTAAATTATAG
GACATGCCCATTTTTAGCTATTATCATTCGATTTATTTCACATAGTGATT
AATTTTTATAAAGTATGACCTAATCCGCGTATAAAATTATACAATACTTT
CTTGTTTAATTAAAATGATTACATAGTTCTTTATTGAGTTTTTCATTTGC
TTCAGTTTTATTTAAAATTCAAATTTTTTGTTTAATATATTTGATCTTAT
AAATTTTATATTTTTAAGATATTTCTTTTCTGTAAATCTTTTCAATTGTT
TTTGTTCAATTTAATGCCTGACAAATCAAATGATTTATGACATATATTGT
ATGTCATTTATGAGTCAATATTTTATTTTGGGATTTGCATAGTTAAAATA
TTGAAATGTTAGCATAGAAATAAAATAGGTGAAGAGGAAACAGTTGTGAA
TGGAAATTTACTCGCATTGAAATGGTAGGACAAAAGGGATGTATTTATGC
TGTCTACAATCCATCCATATATAATTGCTGATACTGCTAAGCGAACTCGA
ATCAATAAAATCATAAGGAAACCACAATGCATTATAGACTATAACATGAA
AATTGACGCAATCGATCACATGCACATGCAAATATCTTTTACAGAATGTG
TACGAAAAGCTGTAATAGTATAAAAATAATATACAAGAAAAAACAAAATC
AAGCATGTCGCTATATGATTTCAAAAAAGAACTGGTTCGACAAATGCTCG
AAAATGTAAAACTGAGGAGTAAATGGTTATGTCACCGCTGGACCAGTACT
CCCGGGGTAAAATTTGGGATGAGCCATGCTCTTTGCTTAAATGACCTTGA
AAACCTATGATGACTCGTCCAATGACCTTGAATGAGTATGTCTCAGAAAA
AATTTGTACTTTTAGACTTAGAAAAATTTTTTTAACTCCCGGTGATGAGT
ACTGTTCCAGCGATGACATAACCATTTACTTTGATGCTTCAGTTGTTGGT
AGACTGTCATCTCAATCTGATCCAGCAAGAGTAGTAGATAGACACTTTCC
TGACTATACTGGTGTTTTAAGAAGACGAAGAAAAGATGTATTTGTTGGAA
ATCAGGAAATGAGGTCAAAACTCTTTAAATGTGAACAATGTGATGTTGGC
TTGTGCATTCACACTTGTTTTAAATCTTATCACACAAATCTTACTTAATA
ATATTATATCAATCATATTCAATTTTTTTAGAATTTTTATAACATTTTTT
GAAAATAATTTTCTTCTAACTCAAAGGATTTTTCAAATTTTTAAATGTGT
AAAATGTAGAGGTCGACCGATTAATCGGTAATATTCACAATCGGGCCGAT
TATAGGAGTAAAATGTCGCAATCGTAAATCGGTTGCCCATCCAGAGATAA
ATAA
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protein sequence of SMED30006326-orf-1

>SMED30006326-orf-1 ID=SMED30006326-orf-1|Name=SMED30006326-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp
MMTRPMTLNEYVSEKICTFRLRKIFLTPGDEYCSSDDITIYFDASVVGRL
SSQSDPARVVDRHFPDYTGVLRRRRKDVFVGNQEMRSKLFKCEQCDVGLC
IHTCFKSYHTNLT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 7..29