Transposable element Tc3 transposase

Overview
NameTransposable element Tc3 transposase
Smed IDSMED30001535
Length (bp)2415
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 Transposable element Tc3 transposase (SMED30001535) t-SNE clustered cells

Violin plots show distribution of expression levels for Transposable element Tc3 transposase (SMED30001535) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 Transposable element Tc3 transposase (SMED30001535) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Transposable element Tc3 transposase (SMED30001535) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30001535

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30001535 dd_Smed_v4_32398_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
[Close]
BLAST of Transposable element Tc3 transposase vs. TrEMBL
Match: A0A0J7K067 (Transposase-like protein OS=Lasius niger OX=67767 GN=RF55_19721 PE=4 SV=1)

HSP 1 Score: 56.6102 bits (135), Expect = 7.761e-8
Identity = 29/60 (48.33%), Postives = 35/60 (58.33%), Query Frame = 3 
Query:  585 LIGP*ILPNMSTEAIYLHLFTNN*PGLIEDTPLTHLQLTWFMFYGAPVHFLKMVKEYLNK 764
            LIGP +LPN  T   Y +   N  P L+ED PL     +WFM  GAP HF   V+EYLN+
Sbjct:  207 LIGPVVLPNRLTGPAYQNFLMNTLPPLLEDVPLNLRAASWFMHDGAPPHFSLAVREYLNQ 266

HSP 2 Score: 31.187 bits (69), Expect = 7.761e-8
Identity = 13/28 (46.43%), Postives = 20/28 (71.43%), Query Frame = 2 
Query:  479 GINNYHKIYY*SNENPHAVLVSRLKYRF 562
            GI N+H  +  ++ENPHA++ SR + RF
Sbjct:  167 GIFNFHNTHQWADENPHAIVESRHQQRF 194
[Close]
BLAST of Transposable element Tc3 transposase vs. TrEMBL
Match: A0A026W470 (Uncharacterized protein OS=Ooceraea biroi OX=2015173 GN=X777_11057 PE=4 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 3.075e-7
Identity = 27/63 (42.86%), Postives = 34/63 (53.97%), Query Frame = 3 
Query:  585 LIGP*ILPNMSTEAIYLHLFTNN*PGLIEDTPLTHLQLTWFMFYGAPVHFLKMVKEYLNKQLN 773
            LIGP   PN  T A+Y     N  P L+ED PL      W+M  GAP HF  +V+ +LN+  N
Sbjct:  145 LIGPVFFPNRLTGAVYFDFLNNTLPPLLEDVPLNDRVNLWYMHDGAPPHFAVIVRNFLNETYN 207

HSP 2 Score: 31.9574 bits (71), Expect = 3.075e-7
Identity = 15/28 (53.57%), Postives = 21/28 (75.00%), Query Frame = 2 
Query:  479 GINNYHKIYY*SNENPHAVLVSRLKYRF 562
            GI N+H  +  +NENPHAV+ SR ++RF
Sbjct:  105 GIINFHNNHVWANENPHAVVESRYQHRF 132
[Close]
BLAST of Transposable element Tc3 transposase vs. TrEMBL
Match: A0A3L8DET6 (Uncharacterized protein OS=Ooceraea biroi OX=2015173 GN=DMN91_009163 PE=4 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 6.803e-7
Identity = 27/64 (42.19%), Postives = 34/64 (53.12%), Query Frame = 3 
Query:  585 LIGP*ILPNMSTEAIYLHLFTNN*PGLIEDTPLTHLQLTWFMFYGAPVHFLKMVKEYLNKQLNK 776
            LIGP   PN  T A+Y     N  P L+ED PL      W+M  GAP HF  +V+ +LN+  N 
Sbjct:  106 LIGPVFFPNRLTGAVYFDFLNNTLPPLLEDVPLNDRVNLWYMHDGAPPHFAVIVRNFLNETYNN 169

HSP 2 Score: 30.8018 bits (68), Expect = 6.803e-7
Identity = 14/28 (50.00%), Postives = 21/28 (75.00%), Query Frame = 2 
Query:  479 GINNYHKIYY*SNENPHAVLVSRLKYRF 562
            GI N+H  +  ++ENPHAV+ SR ++RF
Sbjct:   66 GIINFHNNHVWADENPHAVVESRYQHRF 93
[Close]
BLAST of Transposable element Tc3 transposase vs. TrEMBL
Match: A0A026VVT5 (Uncharacterized protein (Fragment) OS=Ooceraea biroi OX=2015173 GN=X777_15252 PE=4 SV=1)

HSP 1 Score: 52.373 bits (124), Expect = 6.116e-6
Identity = 26/60 (43.33%), Postives = 35/60 (58.33%), Query Frame = 3 
Query:  585 LIGP*ILPNMSTEAIYLHLFTNN*PGLIEDTPLTHLQLTWFMFYGAPVHFLKMVKEYLNK 764
            L+GP IL +  T   YL    +N PGL++D PL   Q  W +  GAP HF + V+E+LN 
Sbjct:   66 LVGPYILSDRLTGECYLQFLQDNLPGLLKDVPLHIWQNMWLLQDGAPAHFSQEVQEFLNN 125

HSP 2 Score: 29.261 bits (64), Expect = 6.116e-6
Identity = 13/30 (43.33%), Postives = 18/30 (60.00%), Query Frame = 2 
Query:  479 GINNYHKIYY*SNENPHAVLVSRLKYRFFI 568
            GINN H  +  S ENPHA   +  ++RF +
Sbjct:   26 GINNSHNTHVWSYENPHAAESTNFQHRFSV 55
[Close]
BLAST of Transposable element Tc3 transposase vs. Planmine SMEST
Match: SMESG000047667.1 (SMESG000047667.1)

HSP 1 Score: 75.485 bits (184), Expect = 1.438e-13
Identity = 57/195 (29.23%), Postives = 96/195 (49.23%), Query Frame = 1 
Query:  922 DSNRRKKTIFTKPNLKMHLGR*ISNELFTTIRRLLLTVVKYNFRNTEIRIDAYKIINQYFH*V---LKEPQY----LSKHMLVHQDWLRNLKGNPTNQKIRQNDIDHINALNEIMNEDGR--FKWQQHQTAVADFFQSYCNRNIIVYPRFKKFQKAITLIAERPKAPKKKDYKPTESTPAKITTPNPAQNIEIPF 1479
            D  R +KTIF K   + +L + +SNE F  ++  L+   KY F++   R+ AY+IIN+Y        KE ++     +K   + ++WL++LK  P +     +  D I  + ++++   R  FK Q+ QT+VA+F   +  R+II   R  KFQK I  +A +            + T + I T  P +   +P 
Sbjct:  197 DKTRPRKTIFKKSAFQTYLKKELSNETFVEVKTFLMATHKYRFKDENSRLLAYRIINRYVMETANEFKETEFDMARFAKFFTIPENWLKHLK--PYSTATETSPADRI-KVQKLVDLTCRYPFKTQEEQTSVANFLHFFTQRSIIGISRDYKFQKCIPFMARKTNG---------QETTSTINTTPPTEENRLPM 379
[Close]
BLAST of Transposable element Tc3 transposase vs. Planmine SMEST
Match: SMESG000069571.1 (SMESG000069571.1)

HSP 1 Score: 55.8398 bits (133), Expect = 1.287e-7
Identity = 47/150 (31.33%), Postives = 69/150 (46.00%), Query Frame = 1 
Query: 1039 KYNFRNTEIRIDAYKIINQYFH*VLKE-------PQYLSKHMLVHQDWLRNLKGNPTNQKIRQNDIDHINALNEIMNEDGRFKWQQHQTAVADFFQSYCNRNIIVYPRFKKFQKAITLIAERPKAPKKKDYKPTE------STPAKITTP 1449
            KY F++   R+ AY+IIN+Y     KE           +K  +V + WL++LK   T  +    D   +  L ++      FK Q+ QT+VA+F   +  R+II   R  KFQK I  +A R   P+    + T       S P  I TP
Sbjct:    5 KYRFKDKNSRLLAYRIINRYVMETAKEFKEAEFDMARFAKFFMVPEKWLKHLKSFSTATETSPADRIKVQKLVDLTC-IYPFKTQEEQTSVANFLHFFTQRSIIGISRDYKFQKFIPFMARRNTRPETTSTEVTASLTEQNSLPIVIVTP 153
[Close]
BLAST of Transposable element Tc3 transposase vs. Planmine SMEST
Match: SMESG000031457.1 (SMESG000031457.1)

HSP 1 Score: 52.7582 bits (125), Expect = 1.326e-6
Identity = 40/124 (32.26%), Postives = 66/124 (53.23%), Query Frame = 1 
Query: 1039 KYNFRNTEIRIDAYKIINQYFH*V---LKEPQY----LSKHMLVHQDWLRNLKGNPTNQKIRQNDIDHINALNEIMNEDGR--FKWQQHQTAVADFFQSYCNRNIIVYPRFKKFQKAITLIAER 1383
            KY F++   R+ AY+IIN+Y        KE ++     +K   + ++WL++LK  P +     +  D I  + ++++   R  FK QQ QT+VA+F   +  R+II   R  KFQK I  +A +
Sbjct:    5 KYRFKDENSRLLAYRIINRYVMETANEFKETEFDMARFAKFFTIPENWLKHLK--PYSTATETSPADRIK-VQKLVDLTCRYPFKTQQEQTSVANFLHFFTQRSIIGISRDYKFQKCIPFMARK 125
The following BLAST results are available for this feature:
BLAST of Transposable element Tc3 transposase vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Transposable element Tc3 transposase vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Transposable element Tc3 transposase vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Transposable element Tc3 transposase vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Transposable element Tc3 transposase vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Transposable element Tc3 transposase vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Transposable element Tc3 transposase vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Transposable element Tc3 transposase vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A0J7K0677.761e-848.33Transposase-like protein OS=Lasius niger OX=67767 ... [more]
A0A026W4703.075e-742.86Uncharacterized protein OS=Ooceraea biroi OX=20151... [more]
A0A3L8DET66.803e-742.19Uncharacterized protein OS=Ooceraea biroi OX=20151... [more]
A0A026VVT56.116e-643.33Uncharacterized protein (Fragment) OS=Ooceraea bir... [more]
back to top
BLAST of Transposable element Tc3 transposase vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Transposable element Tc3 transposase vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Transposable element Tc3 transposase vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Transposable element Tc3 transposase vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Transposable element Tc3 transposase vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Transposable element Tc3 transposase vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000047667.11.438e-1329.23SMESG000047667.1[more]
SMESG000069571.11.287e-731.33SMESG000069571.1[more]
SMESG000031457.11.326e-632.26SMESG000031457.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001535 ID=SMED30001535|Name=Transposable element Tc3 transposase|organism=Schmidtea mediterranea sexual|type=transcript|length=2415bp
CATGGAACAAAGTTAGCCTTGTAGAGACATGATTTTGAATACTTCTTATT
TTATTATATATATTAGGGCGGTCGTATTCATACCATACCGCAAAACAAAG
GAGAATGCTACTGAAGCAATACAATTATATGAAGAAGCTTTCCCAAATTA
CAGATGCCCAAGCAGGAAATGTTTAGCAAAATCCATCAATATTTATGCAA
TACTTTGAAATTTAAGTCCAATTTAATTTACTATGATTGACCACAATCCG
TTAGAACACATGTATTCGACGAAACCATTTTGCGGATGTTTGAAAAAAAT
CCTAAAACATCAGGATGAAGGATTACTGTGAAAGAACATCTATCAATTCA
TCGTACCGTTTTTATAACAACGTATATGCATAAGAACGTATCAGCTTTTA
TAATAATGCAATGGTTACATTTTGTCAATGGCTCATTAATTGTTTCACTC
CGTTCCACTGATCTTTTAAGGGGATATCGGAATCAATAATTACCACAAAA
TTTATTATTAATCAAATGAGAATCCTCATGCAGTTTTAGTATCAAGGCTC
AAGTATCGCTTTTTTATTATGTCTGTACTGGAATCTTATTGGGCCCTAAA
TTTTGCCTAATATGTCGACAGAAGCTATTTATCTTCATTTATTCACAAAT
AACTAGCCTGGACTTATTGAAGATACTCCACTAACCCATTTACAACTTAC
ATGGTTCATGTTTTATGGTGCCCCTGTCCATTTTCTAAAAATGGTTAAAG
AATATTTAAACAAACAGTTAAATAAAATGAGTAAGACATGGTGCGTGACC
ACCTTGTTCACCGGATTACAAGAGCGATGTGCACCCTAAATACGTAAATT
CCGATACTGCTGACAAACTCAAATGGTACTTGCACACGGTCTATTATCTC
CTATCATACGATGATAAAAAAGATTCAAACCGGCGAAAAAAGACAATCTT
CACCAAACCAAATTTGAAAATGCACTTGGGAAGATAAATATCAAATGAAC
TTTTCACAACTATCAGAAGATTACTTCTCACTGTTGTAAAGTACAACTTC
AGGAATACCGAAATCAGAATTGATGCCTATAAAATAATCAACCAATACTT
CCACTAAGTGTTGAAGGAACCACAATACCTATCAAAGCACATGTTAGTGC
ATCAAGACTGGCTCAGAAATCTCAAAGGAAATCCTACTAACCAAAAAATC
AGACAGAATGATATCGATCACATCAATGCATTAAATGAAATAATGAACGA
AGATGGACGATTCAAATGGCAACAACATCAAACAGCTGTAGCCGATTTCT
TTCAATCCTACTGCAATAGAAATATAATTGTCTACCCTAGATTCAAAAAA
TTCCAAAAGGCAATAACTCTAATCGCAGAAAGACCCAAAGCTCCAAAGAA
AAAAGATTACAAACCAACTGAAAGCACACCTGCTAAAATCACAACTCCAA
ATCCAGCCCAAAATATCGAGATCCCATTTAAAAGAAGTTAATCCATAGAA
TCCGAATCTTAGTCGGATCCACCAGAGCCCGACTATTATCAAGCACTCAT
TAAGGAATATACTAGCTCGTCCGAATACGAAGGCGACTACCTGGTGTCCT
TAATTCTGGTTAATCCGAATCAGAAATTCTCGCAAAAAGAGCTAAAGTGA
AACTCGATAAGATGGCATAGGAAAACAGATTTTGTGAGTTCAATCGTCGA
TTGGCTAAACTCGAAAAGTAATTTGATTCGAATCCCTCGTCGAAAATAAC
ATCAATAAAACCTTATAGCCCTAAGGATGTTGAAAGACCAAAACAAACAT
ACAAAATAATTAATCAAGCCAAAATCCAAAAGGAACTGGAAATTGAAAAG
GTAAAAACAGAACTTCCTAACAAAGAGCACGCTAATTACAATGCCAGCAA
ATAAAACCAAACATCAAAAAATCAAAAAGAAACATATAAACAAAGATATT
CACCCAAAACTAAAAAGATACCATTATACATAATGAGACATTTTTAAGAA
TATCATAAAAGATCCGACAAGGCTACCAAATAGCTGTAGATAATTGTGCC
CGCATCTTTAAAATGACATTAGTAAATATTTTGCCTTTCAAGAGTATTGT
GTCAATATTATGGAAAAAGCGAGGTATATAACTGAAAACTGTTATCAGGA
AATACGAAAGAATTTCGGGAATCTTTTAACGTGTTCGATCGTCAATGAGG
TGTAATACATGAATAAAAGGATTTATCGAAAATCTTCTGTAGATAAAATT
CATTTTGATATTTTAATATTATTTAATATTTTAATAATTATTGTGAGTTG
TTTGATGTGTGTGTAAGTTATTGTATATTTGAAGCATATTATTTCACATT
CATTATTATACAATAGTCTTCGATTCCAAAAGGATAAACACTAGAACTGT
TATGTCATAAAATAG
back to top

protein sequence of SMED30001535-orf-1

>SMED30001535-orf-1 ID=SMED30001535-orf-1|Name=SMED30001535-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=117bp
MLVHQDWLRNLKGNPTNQKIRQNDIDHINALNEIMNEDGRFKWQQHQTAV
ADFFQSYCNRNIIVYPRFKKFQKAITLIAERPKAPKKKDYKPTESTPAKI
TTPNPAQNIEIPFKRS*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR032135DUF4817
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding
Vocabulary: biological process
TermDefinition
GO:0006313transposition, DNA-mediated
GO:0015074DNA integration