Dimer_Tnp_hAT domain-containing protein

Overview
NameDimer_Tnp_hAT domain-containing protein
Smed IDSMED30022631
Length (bp)393
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 Dimer_Tnp_hAT domain-containing protein (SMED30022631) t-SNE clustered cells

Violin plots show distribution of expression levels for Dimer_Tnp_hAT domain-containing protein (SMED30022631) in cells (dots) of each of the 12 neoblast clusters.

 

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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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Homology
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BLAST of Dimer_Tnp_hAT domain-containing protein vs. TrEMBL
Match: H9XVZ5 (Raptor OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 48.1358 bits (113), Expect = 3.954e-9
Identity = 21/25 (84.00%), Postives = 22/25 (88.00%), Query Frame = 1 
Query:   43 KFCIVKNNFDEIEDEHPELVELPDA 117
            K   +KNNFDEIEDEHPELVELPDA
Sbjct: 1287 KVLYIKNNFDEIEDEHPELVELPDA 1311

HSP 2 Score: 40.4318 bits (93), Expect = 3.954e-9
Identity = 19/22 (86.36%), Postives = 19/22 (86.36%), Query Frame = 3 
Query:    3 QLCLAHIIQLAIIKVLYSKK*F 68
            QLCLAHIIQLAIIKVLY K  F
Sbjct: 1274 QLCLAHIIQLAIIKVLYIKNNF 1295
[Close]
BLAST of Dimer_Tnp_hAT domain-containing protein vs. TrEMBL
Match: A0A4Y2DDQ8 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_167293_1 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 6.042e-8
Identity = 28/48 (58.33%), Postives = 35/48 (72.92%), Query Frame = 1 
Query:  250 ITKVCKIFHRTPIKIDEILQKQVKK-LDKRLSLILDCKTRWNSILAML 390
            + K  K+F R+P K D  LQK VK+   K LSLILDC+TRWNS+LAM+
Sbjct:   86 VRKAVKLFKRSPTKYDMYLQKYVKEDTGKELSLILDCRTRWNSLLAMI 133
[Close]
BLAST of Dimer_Tnp_hAT domain-containing protein vs. TrEMBL
Match: A0A0J7KNG8 (Dimer_Tnp_hAT domain-containing protein OS=Lasius niger OX=67767 GN=RF55_8155 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 1.023e-7
Identity = 30/48 (62.50%), Postives = 37/48 (77.08%), Query Frame = 1 
Query:  250 ITKVCKIFHRTPIKIDEILQKQVKKL-DKRLSLILDCKTRWNSILAML 390
            + KV KIF R+P K D ILQK +++  DKRL LILDCKTRWNS++ ML
Sbjct:  235 VRKVVKIFRRSPTKNDLILQKYIQEEHDKRLELILDCKTRWNSLVNML 282
[Close]
BLAST of Dimer_Tnp_hAT domain-containing protein vs. TrEMBL
Match: A0A4Y2K3K4 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_7992_1 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 1.391e-7
Identity = 29/48 (60.42%), Postives = 36/48 (75.00%), Query Frame = 1 
Query:  250 ITKVCKIFHRTPIKIDEILQKQVKK-LDKRLSLILDCKTRWNSILAML 390
            + KV K+F R+P K D  LQK VK+   K LSLILDC+TRWNS+LAM+
Sbjct:   81 VRKVVKLFKRSPTKYDMYLQKYVKEDTGKELSLILDCRTRWNSLLAMI 128
[Close]
BLAST of Dimer_Tnp_hAT domain-containing protein vs. TrEMBL
Match: A0A4Y2PSC5 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_212_1 PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 1.803e-7
Identity = 28/48 (58.33%), Postives = 35/48 (72.92%), Query Frame = 1 
Query:  250 ITKVCKIFHRTPIKIDEILQKQVKK-LDKRLSLILDCKTRWNSILAML 390
            + KV  +F R+P K D  LQK VK+   K LSLILDC+TRWNS+LAM+
Sbjct:   30 VLKVMNLFKRSPTKYDMYLQKYVKEDTGKELSLILDCRTRWNSLLAMI 77
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BLAST of Dimer_Tnp_hAT domain-containing protein vs. Planmine SMEST
Match: SMESG000077975.1 (SMESG000077975.1)

HSP 1 Score: 48.521 bits (114), Expect = 2.655e-7
Identity = 23/46 (50.00%), Postives = 34/46 (73.91%), Query Frame = 1 
Query:  256 KVCKIFHRTPIKIDEILQKQVK-KLDKRLSLILDCKTRWNSILAML 390
            K  + F ++P++ D ILQ+ V+ K  K+L LILDC+TRWNSI+ M+
Sbjct:  310 KTVRFFRKSPVRND-ILQRYVEDKEGKKLKLILDCRTRWNSIIPMM 354
[Close]
BLAST of Dimer_Tnp_hAT domain-containing protein vs. Planmine SMEST
Match: SMESG000061313.1 (SMESG000061313.1)

HSP 1 Score: 47.7506 bits (112), Expect = 4.451e-7
Identity = 22/46 (47.83%), Postives = 34/46 (73.91%), Query Frame = 1 
Query:  256 KVCKIFHRTPIKIDEILQKQVK-KLDKRLSLILDCKTRWNSILAML 390
            K  + F ++P++ D ILQ+ V+ K  K+L LILDC+TRWNS++ M+
Sbjct:  283 KTVRFFRKSPVRND-ILQRYVEDKEGKKLKLILDCRTRWNSLIPMM 327
[Close]
BLAST of Dimer_Tnp_hAT domain-containing protein vs. Planmine SMEST
Match: SMESG000081415.1 (SMESG000081415.1)

HSP 1 Score: 47.7506 bits (112), Expect = 4.841e-7
Identity = 24/59 (40.68%), Postives = 39/59 (66.10%), Query Frame = 1 
Query:  217 NSVQNVQMTSLITKVCKIFHRTPIKIDEILQKQVK-KLDKRLSLILDCKTRWNSILAML 390
            N + N + T +     + F ++P++ D ILQ+ V+ K  K+L LILDC+TRWNS++ M+
Sbjct:  219 NDIDNTEYTYI-----RFFRKSPVRND-ILQRYVEDKEGKKLKLILDCRTRWNSLIHMM 271
[Close]
BLAST of Dimer_Tnp_hAT domain-containing protein vs. Planmine SMEST
Match: SMESG000065760.1 (SMESG000065760.1)

HSP 1 Score: 44.669 bits (104), Expect = 4.600e-6
Identity = 22/46 (47.83%), Postives = 33/46 (71.74%), Query Frame = 1 
Query:  256 KVCKIFHRTPIKIDEILQKQVK-KLDKRLSLILDCKTRWNSILAML 390
            K  +   ++P++ D ILQ+ V+ K  K+L LILDC+TRWNSI+ M+
Sbjct:  310 KTDRFLRKSPVRND-ILQRYVEDKEGKKLKLILDCRTRWNSIIPMM 354
[Close]
BLAST of Dimer_Tnp_hAT domain-containing protein vs. Planmine SMEST
Match: SMESG000022344.1 (SMESG000022344.1)

HSP 1 Score: 44.669 bits (104), Expect = 5.097e-6
Identity = 17/45 (37.78%), Postives = 29/45 (64.44%), Query Frame = 1 
Query:  256 KVCKIFHRTPIKIDEILQKQVKKLDKRLSLILDCKTRWNSILAML 390
            K  + F ++P++ D + +    K  K+  LILDC+TRWNS++ M+
Sbjct:  287 KTVRFFRKSPVRNDILQRYDEDKEGKKFKLILDCRTRWNSLIPMM 331
The following BLAST results are available for this feature:
BLAST of Dimer_Tnp_hAT domain-containing protein 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 Dimer_Tnp_hAT domain-containing protein 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 Dimer_Tnp_hAT domain-containing protein 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 Dimer_Tnp_hAT domain-containing protein 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 Dimer_Tnp_hAT domain-containing protein 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 Dimer_Tnp_hAT domain-containing protein 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 Dimer_Tnp_hAT domain-containing protein 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 Dimer_Tnp_hAT domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
H9XVZ53.954e-984.00Raptor OS=Schmidtea mediterranea OX=79327 PE=2 SV=... [more]
A0A4Y2DDQ86.042e-858.33Uncharacterized protein OS=Araneus ventricosus OX=... [more]
A0A0J7KNG81.023e-762.50Dimer_Tnp_hAT domain-containing protein OS=Lasius ... [more]
A0A4Y2K3K41.391e-760.42Uncharacterized protein OS=Araneus ventricosus OX=... [more]
A0A4Y2PSC51.803e-758.33Uncharacterized protein OS=Araneus ventricosus OX=... [more]
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BLAST of Dimer_Tnp_hAT domain-containing protein 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 Dimer_Tnp_hAT domain-containing protein 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 Dimer_Tnp_hAT domain-containing protein 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 Dimer_Tnp_hAT domain-containing protein 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 Dimer_Tnp_hAT domain-containing protein 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 Dimer_Tnp_hAT domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000077975.12.655e-750.00SMESG000077975.1[more]
SMESG000061313.14.451e-747.83SMESG000061313.1[more]
SMESG000081415.14.841e-740.68SMESG000081415.1[more]
SMESG000065760.14.600e-647.83SMESG000065760.1[more]
SMESG000022344.15.097e-637.78SMESG000022344.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022631 ID=SMED30022631|Name=Dimer_Tnp_hAT domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=393bp
ATCAGTTATGTCTTGCACATATAATACAGTTGGCTATAATCAAAGTTCTG
TATAGTAAAAAATAATTTCGACGAAATTGAGGATGAACATCCAGAACTTG
TTGAATTACCTGATGCAAATGATAATGGCAATCCTGACAAAGGCAACGAC
GAAGATAATGAAGATAATGATGAAGAATTAGAAATAGTACAAAAGATGAT
TACTAATTCTCACTTAAATTCTGTACAAAACGTACAGATGACTTCTCTCA
TAACAAAAGTATGCAAAATATTCCACAGAACCCCGATAAAAATTGATGAA
ATATTACAAAAACAGGTAAAAAAATTAGATAAAAGACTTTCGTTAATACT
TGACTGTAAAACTCGCTGGAATAGTATTTTGGCTATGCTATAG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0046983protein dimerization activity
GO:0003676nucleic acid binding
GO:0004519endonuclease activity
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000136whole organism
PLANA:0000429neoblast
Vocabulary: biological process
TermDefinition
GO:0090305nucleic acid phosphodiester bond hydrolysis