PiggyBac transposable element-derived protein 4

Overview
NamePiggyBac transposable element-derived protein 4
Smed IDSMED30020382
Length (bp)1462
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 (SMED30020382) t-SNE clustered cells

Violin plots show distribution of expression levels for PiggyBac transposable element-derived protein 4 (SMED30020382) 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 (SMED30020382) 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 (SMED30020382) 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



SMED30020382

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymaSMED30020382h1SMcG0021131 dd_Smed_v4_2069_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30020382h1SMcG0021131 dd_Smed_v4_2069_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30020382h1SMcG0021131 dd_Smed_v4_2069_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30020382h1SMcG0021131 dd_Smed_v4_3842_3_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30020382h1SMcG0021131 dd_Smed_v4_3842_3_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020382h1SMcG0021131 dd_Smed_v4_3842_3_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
anterior sideSMED30020382h1SMcG0021131 dd_Smed_v4_3842_3_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30020382h1SMcG0012966 OX_Smed_1.0.11088ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
head regionSMED30020382h1SMcG0021131 OX_Smed_1.0.11088ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30020382h1SMcG0021131 Contig37979newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30020382h1SMcG0021131 Contig37979uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30020382h1SMcG0022045 Contig37979newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30020382h1SMcG0022045 Contig37979uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of PiggyBac transposable element-derived protein 4 vs. Ensembl Human
Match: PGBD4 (piggyBac transposable element derived 4 [Source:HGNC Symbol;Acc:HGNC:19401])

HSP 1 Score: 58.151 bits (139), Expect = 2.453e-8
Identity = 28/61 (45.90%), Postives = 37/61 (60.66%), Query Frame = 3 
Query: 1281 DDVY-KRLTERHVPSFVPPTPKKEAPTRYCAVCCSKMDSKGKRKRRESRYMCNLCNAGLCA 1460
            DDV   RL+ RH P  +P T  K+ PT  C +CCS+ D  GK+ R+E+RY C  C+  LC 
Sbjct:  512 DDVTPLRLSGRHFPKSIPATSGKQNPTGRCKICCSQYDKDGKKIRKETRYFCAECDVPLCV 572
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BLAST of PiggyBac transposable element-derived protein 4 vs. UniProt/SwissProt
Match: sp|Q96DM1|PGBD4_HUMAN (PiggyBac transposable element-derived protein 4 OS=Homo sapiens OX=9606 GN=PGBD4 PE=2 SV=3)

HSP 1 Score: 58.151 bits (139), Expect = 1.178e-7
Identity = 28/61 (45.90%), Postives = 37/61 (60.66%), Query Frame = 3 
Query: 1281 DDVY-KRLTERHVPSFVPPTPKKEAPTRYCAVCCSKMDSKGKRKRRESRYMCNLCNAGLCA 1460
            DDV   RL+ RH P  +P T  K+ PT  C +CCS+ D  GK+ R+E+RY C  C+  LC 
Sbjct:  512 DDVTPLRLSGRHFPKSIPATSGKQNPTGRCKICCSQYDKDGKKIRKETRYFCAECDVPLCV 572
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BLAST of PiggyBac transposable element-derived protein 4 vs. TrEMBL
Match: A0A499QYJ6 (PiggyBac transposable element-derived protein 4-like OS=Pyxicephalus adspersus OX=30357 GN=LOC108792504 PE=4 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 4.419e-11
Identity = 31/56 (55.36%), Postives = 42/56 (75.00%), Query Frame = 3 
Query: 1293 KRLTERHVPSFVPPTPKKEAPTRYCAVCCSKMDSKGKRKRRESRYMCNLCNAGLCA 1460
            +RLT RH   ++PPT +K APTR C VCCSK D +G++KR+E+R+ C  C+ GLCA
Sbjct:  170 ERLTGRHFIDYIPPTQRKAAPTRMCVVCCSKTDDRGRKKRKETRFYCPDCDVGLCA 225
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BLAST of PiggyBac transposable element-derived protein 4 vs. TrEMBL
Match: B7P8H6 (Tnp_zf-ribbon_2 domain-containing protein OS=Ixodes scapularis OX=6945 GN=8026150 PE=4 SV=1)

HSP 1 Score: 68.9366 bits (167), Expect = 1.187e-10
Identity = 34/56 (60.71%), Postives = 37/56 (66.07%), Query Frame = 3 
Query: 1293 KRLTERHVPSFVPPTPKKEAPTRYCAVCCSKMDSKGKRKRRESRYMCNLCNAGLCA 1460
            KRLTERH PS +PPT KK  PTR C VC  K DSKGK  R+E+R  C  C   LCA
Sbjct:   34 KRLTERHFPSHIPPTEKKREPTRRCIVCYMKRDSKGKNVRKETRIWCRWCEKALCA 89
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BLAST of PiggyBac transposable element-derived protein 4 vs. TrEMBL
Match: B7PTF6 (Tnp_zf-ribbon_2 domain-containing protein OS=Ixodes scapularis OX=6945 GN=8031099 PE=4 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 2.489e-10
Identity = 33/56 (58.93%), Postives = 37/56 (66.07%), Query Frame = 3 
Query: 1293 KRLTERHVPSFVPPTPKKEAPTRYCAVCCSKMDSKGKRKRRESRYMCNLCNAGLCA 1460
            KRLTERH PS +PPT KK  PTR C VC  + DSKGK  R+E+R  C  C   LCA
Sbjct:   34 KRLTERHFPSHIPPTEKKREPTRRCIVCYMERDSKGKNIRKETRIWCRWCEKALCA 89
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BLAST of PiggyBac transposable element-derived protein 4 vs. TrEMBL
Match: A0A4Y1ZLH1 (PiggyBac transposable element-derived protein 4 OS=Araneus ventricosus OX=182803 GN=PGBD4_156 PE=4 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 2.877e-10
Identity = 31/55 (56.36%), Postives = 37/55 (67.27%), Query Frame = 3 
Query: 1296 RLTERHVPSFVPPTPKKEAPTRYCAVCCSKMDSKGKRKRRESRYMCNLCNAGLCA 1460
            RLT RH PS + PT KK+APT+ C VC  K + KG+R R+ESRY C  CN  LC 
Sbjct:   33 RLTGRHFPSRIQPTQKKKAPTKICIVCSQKFNEKGQRVRKESRYQCAQCNVTLCV 87
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BLAST of PiggyBac transposable element-derived protein 4 vs. TrEMBL
Match: A0A4Y2LF14 (PiggyBac transposable element-derived protein 4 OS=Araneus ventricosus OX=182803 GN=PGBD4_619 PE=4 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 3.187e-10
Identity = 31/55 (56.36%), Postives = 37/55 (67.27%), Query Frame = 3 
Query: 1296 RLTERHVPSFVPPTPKKEAPTRYCAVCCSKMDSKGKRKRRESRYMCNLCNAGLCA 1460
            RLT RH PS + PT KK+APT+ C VC  K + KG+R R+ESRY C  CN  LC 
Sbjct:  134 RLTGRHFPSLIQPTQKKKAPTKICIVCSQKFNEKGQRVRKESRYQCAQCNVTLCV 188
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BLAST of PiggyBac transposable element-derived protein 4 vs. Planmine SMEST
Match: SMESG000024267.1 (SMESG000024267.1)

HSP 1 Score: 164.081 bits (414), Expect = 7.574e-45
Identity = 81/81 (100.00%), Postives = 81/81 (100.00%), Query Frame = 2 
Query:   38 FSAVSNISKTMETPMQSNPNAPSVFTGNTGPPTIPGLSTQQRNFYPNAMQPPRSSNFQGTCNPNMPGGVQNRPSSANQYFY 280
            FSAVSNISKTMETPMQSNPNAPSVFTGNTGPPTIPGLSTQQRNFYPNAMQPPRSSNFQGTCNPNMPGGVQNRPSSANQYFY
Sbjct:  385 FSAVSNISKTMETPMQSNPNAPSVFTGNTGPPTIPGLSTQQRNFYPNAMQPPRSSNFQGTCNPNMPGGVQNRPSSANQYFY 465
[Close]
BLAST of PiggyBac transposable element-derived protein 4 vs. Planmine SMEST
Match: SMESG000024267.1 (SMESG000024267.1)

HSP 1 Score: 164.466 bits (415), Expect = 7.726e-45
Identity = 81/81 (100.00%), Postives = 81/81 (100.00%), Query Frame = 2 
Query:   38 FSAVSNISKTMETPMQSNPNAPSVFTGNTGPPTIPGLSTQQRNFYPNAMQPPRSSNFQGTCNPNMPGGVQNRPSSANQYFY 280
            FSAVSNISKTMETPMQSNPNAPSVFTGNTGPPTIPGLSTQQRNFYPNAMQPPRSSNFQGTCNPNMPGGVQNRPSSANQYFY
Sbjct:  404 FSAVSNISKTMETPMQSNPNAPSVFTGNTGPPTIPGLSTQQRNFYPNAMQPPRSSNFQGTCNPNMPGGVQNRPSSANQYFY 484
The following BLAST results are available for this feature:
BLAST of PiggyBac transposable element-derived protein 4 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 1
Match NameE-valueIdentityDescription
PGBD42.453e-845.90piggyBac transposable element derived 4 [Source:HG... [more]
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BLAST of PiggyBac transposable element-derived protein 4 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 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 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 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 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 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q96DM1|PGBD4_HUMAN1.178e-745.90PiggyBac transposable element-derived protein 4 OS... [more]
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BLAST of PiggyBac transposable element-derived protein 4 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A499QYJ64.419e-1155.36PiggyBac transposable element-derived protein 4-li... [more]
B7P8H61.187e-1060.71Tnp_zf-ribbon_2 domain-containing protein OS=Ixode... [more]
B7PTF62.489e-1058.93Tnp_zf-ribbon_2 domain-containing protein OS=Ixode... [more]
A0A4Y1ZLH12.877e-1056.36PiggyBac transposable element-derived protein 4 OS... [more]
A0A4Y2LF143.187e-1056.36PiggyBac transposable element-derived protein 4 OS... [more]
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BLAST of PiggyBac transposable element-derived protein 4 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 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 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 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 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 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000024267.17.574e-45100.00SMESG000024267.1[more]
SMESG000024267.17.726e-45100.00SMESG000024267.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020382 ID=SMED30020382|Name=PiggyBac transposable element-derived protein 4|organism=Schmidtea mediterranea sexual|type=transcript|length=1462bp
TATGCCTCCGAATATGGGCAATACAAATATGCCTCCATTTTCTGCAGTGT
CGAATATTTCTAAAACAATGGAAACCCCAATGCAATCAAATCCAAATGCA
CCTTCGGTTTTTACTGGAAACACCGGCCCTCCCACGATTCCAGGTCTATC
GACACAACAGAGAAATTTTTATCCTAATGCAATGCAACCTCCCAGGTCTT
CAAACTTTCAAGGTACATGTAACCCCAATATGCCAGGGGGCGTACAAAAT
CGGCCTTCAAGTGCAAATCAATACTTCTATCCACCTGGCAATAATAGTCC
TCAATTCAATCCACAATTTAATCAGCAATTACAGAAATAAATGGAATATT
TGTCAAAAACATTTGCAATCATCATATTGTCTATTTGAGATAAATAATAA
TATATCATATTTATCTAATTTTATCTATTCATTGCTCGAGTACGTGAATG
GAAAATGTAAAAGTGACTTTTATTTTACTGGTCATTTAAATGCGTATTTG
TCTTTATTTGGTGATATGATGTAATCATGTAAGATTTATTGTGGAAATGT
TCGATTTCAAGTTTATATTAAATAAACATTCTAAACAATTACATTGTAAT
CTGTCAATATTTTCAACAGTCAAATTTGTTTTGTTTATTCGGTTTATAAA
TTATTATTATTATTATATGCAGTTGGATCATTTTTAGTTGAACTGGCACT
GATCTCAATTTTATGTGATTTCACTGCGGTAACCTTTCAAGTTTTTAGAA
TATCACGTTTGATATATTTTTTAAATCGATTGTTATGCTATTGGAGCTTG
CTGTGTGTGCTTTTCAGATTCCCATTGTATCGATTGGAATTTCTTTCGAA
TCTCCTCATAGGTTTTGCTTTTGGAACCTCTGAAACTAGAATCACCATGG
TTACTACAGCATCGGATATTATGATAAATTTCTACTATAAATATTGCTTC
TGTCTTAAATTTCTTTGATATTTCTCTTTGTCTCAATCGAATTTATTTTT
TCTGAATTGTGAAATGCGTTTCTTCTGTCACCTTGGTTTTGTTGATTTCC
ATTGGTGCTCCATGGCCATTTTTGACAAAGACAGATAAGAATTATTTCCG
GCCCCTTCAACTTCTACCTTTGATTTAGTTTCATGTATTTCCTGAAATAT
TTTATGCCGCAAAAATATTTACACTCGTAAATAATCGAGCATTGAAAATA
ACTCGTTAAAATATTCGTTGATATCCATCATTTTAACTCTATATTGCAAG
CTAAAAAGTTAATAAAATATGGCCTTTTAGGACGATGTTTATAAACGACT
AACTGAACGTCATGTTCCCAGTTTTGTTCCGCCGACCCCAAAAAAAGAAG
CACCCACAAGATATTGTGCTGTGTGTTGTTCAAAAATGGACAGTAAAGGA
AAAAGAAAAAGGAGAGAAAGTCGTTATATGTGCAATCTCTGCAATGCTGG
GCTATGTGCTGC
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protein sequence of SMED30020382-orf-1

>SMED30020382-orf-1 ID=SMED30020382-orf-1|Name=SMED30020382-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=113bp
MPPNMGNTNMPPFSAVSNISKTMETPMQSNPNAPSVFTGNTGPPTIPGLS
TQQRNFYPNAMQPPRSSNFQGTCNPNMPGGVQNRPSSANQYFYPPGNNSP
QFNPQFNQQLQK*
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protein sequence of SMED30020382-orf-2

>SMED30020382-orf-2 ID=SMED30020382-orf-2|Name=SMED30020382-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=174bp
CLRIWAIQICLHFLQCRIFLKQWKPQCNQIQMHLRFLLETPALPRFQVYR
HNREIFILMQCNLPGLQTFKVHVTPICQGAYKIGLQVQINTSIHLAIIVL
NSIHNLISNYRNKWNICQKHLQSSYCLFEINNNISYLSNFIYSLLEYVNG
KCKSDFYFTGHLNAYLSLFGDMM*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR032718PGBD4_C_Znf-ribbon
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..16
score: 0.543