U14-Liphistoxin-Lth1a_1

Overview
NameU14-Liphistoxin-Lth1a_1
Smed IDSMED30001117
Length (bp)1194
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 U14-Liphistoxin-Lth1a_1 (SMED30001117) t-SNE clustered cells

Violin plots show distribution of expression levels for U14-Liphistoxin-Lth1a_1 (SMED30001117) 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 U14-Liphistoxin-Lth1a_1 (SMED30001117) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for U14-Liphistoxin-Lth1a_1 (SMED30001117) 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



SMED30001117

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
posterior sideSMED30001117h1SMcG0003382 dd_Smed_v4_9141_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30001117h1SMcG0003382 dd_Smed_v4_9141_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 U14-Liphistoxin-Lth1a_1 vs. TrEMBL
Match: A0A267EFH9 (DUF4773 domain-containing protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig015368g1 PE=4 SV=1)

HSP 1 Score: 80.4925 bits (197), Expect = 2.896e-13
Identity = 53/207 (25.60%), Postives = 88/207 (42.51%), Query Frame = 1 
Query:  358 GRKSIKFNSSLVVLNDNLIKFVSNDILIKDMNENXXXXXX--XXXXXPFDYDKNGRFCICSKISQPCVCCVKLAEEVIGLTDSLCSNITYIPKSKAAKISMKYGKLNKPDKYVLVDINNPPPVCLSQSLKFDLKSPELLKQKSNDDVNVGQTLNHCVDLEICFQARNLTYNVNVDASHKTEFKGCSNFYVMLNNMTIRIYPLGCFKA 972
            G  S  + ++L      + + + N + + ++  N +K     S  +KP ++D N   C+C +I++PC CC +L  + + L  + C    Y+   +A +  +        DK +L   + P  +C  +                           H   LE+C + RN +Y V + + HKT   GC    V L N TI  YPLGCF A
Sbjct:   74 GPGSRHYPATLNASKSGVAELLQNPMKLDELRSNVRKTLSYLSHLAKPSEFDANAGSCMCGRIAEPCNCCARLTADRLRLGQTACVQFAYLVHRQAMRTRLLLAGSILVDK-LLSAASMPSALCAGE---------------------------HQPRLELCARFRNASYTVQIHSRHKTRLSGCIELLVNLANTTIYAYPLGCFNA 252
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BLAST of U14-Liphistoxin-Lth1a_1 vs. TrEMBL
Match: A0A1I8HF36 (DUF4773 domain-containing protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig008626g1 PE=4 SV=1)

HSP 1 Score: 80.4925 bits (197), Expect = 2.924e-13
Identity = 53/207 (25.60%), Postives = 88/207 (42.51%), Query Frame = 1 
Query:  358 GRKSIKFNSSLVVLNDNLIKFVSNDILIKDMNENXXXXXX--XXXXXPFDYDKNGRFCICSKISQPCVCCVKLAEEVIGLTDSLCSNITYIPKSKAAKISMKYGKLNKPDKYVLVDINNPPPVCLSQSLKFDLKSPELLKQKSNDDVNVGQTLNHCVDLEICFQARNLTYNVNVDASHKTEFKGCSNFYVMLNNMTIRIYPLGCFKA 972
            G  S  + ++L      + + + N + + ++  N +K     S  +KP ++D N   C+C +I++PC CC +L  + + L  + C    Y+   +A +  +        DK +L   + P  +C  +                           H   LE+C + RN +Y V + + HKT   GC    V L N TI  YPLGCF A
Sbjct:   74 GPGSRHYPATLNASKSGVAELLQNPMKLDELRSNVRKTLSYLSHLAKPSEFDANAGSCMCGRIAEPCNCCARLTADRLRLGQTACVQFAYLVHRQAMRTRLLLAGSILVDK-LLSAASMPSALCAGE---------------------------HQPRLELCARFRNASYTVQIHSRHKTRLSGCIELLVNLANTTIYAYPLGCFNA 252
[Close]
BLAST of U14-Liphistoxin-Lth1a_1 vs. TrEMBL
Match: A0A1I8H541 (DUF4773 domain-containing protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig020279g1 PE=4 SV=1)

HSP 1 Score: 80.1073 bits (196), Expect = 4.120e-13
Identity = 53/207 (25.60%), Postives = 88/207 (42.51%), Query Frame = 1 
Query:  358 GRKSIKFNSSLVVLNDNLIKFVSNDILIKDMNENXXXXXX--XXXXXPFDYDKNGRFCICSKISQPCVCCVKLAEEVIGLTDSLCSNITYIPKSKAAKISMKYGKLNKPDKYVLVDINNPPPVCLSQSLKFDLKSPELLKQKSNDDVNVGQTLNHCVDLEICFQARNLTYNVNVDASHKTEFKGCSNFYVMLNNMTIRIYPLGCFKA 972
            G  S  + ++L      + + + N + + ++  N +K     S  +KP ++D N   C+C +I++PC CC +L    + L  + C    Y+   +A +  +        DK +L   + P  +C  +                           H   LE+C + RN +Y V + + HKT   GC    V L N+TI  YPLGCF A
Sbjct:   74 GPGSRHYPATLNASKSGVAELLQNPMKLDELRSNVRKTLSYLSHLAKPSEFDANAGSCMCGRIAEPCNCCARLTAGRLRLGQTACVQFAYLVHRQAMRTRLLLAGSILVDK-LLSAASMPSALCAGE---------------------------HQPRLELCARFRNASYTVQIHSRHKTRLSGCIELLVNLANITIYAYPLGCFNA 252
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BLAST of U14-Liphistoxin-Lth1a_1 vs. TrEMBL
Match: A0A0L8H884 (DUF4773 domain-containing protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22021018mg PE=4 SV=1)

HSP 1 Score: 74.7146 bits (182), Expect = 5.830e-12
Identity = 47/167 (28.14%), Postives = 76/167 (45.51%), Query Frame = 1 
Query:  520 FCICSKISQPCVCCVKLAEEVIGLTDSLCSNITYIPKSKAAKISMKYGKLNKPDKYVLVDINNPPPVCLSQSLKFDLKSPELLKQKSNDDVNVGQTLNHCVDLEICFQARNLTYNVNVDASHKTEFKGCSNFYVMLNNMTIRIYPLGCFKAGYESKDLQIQKMANGI 1020
            FC C  +   CVCC  +    + L++  C+N T +PK +  + + ++   NK      +   NPP +CL    K                             EIC +  N+T+ VNV   HKT+  GC++F + L N TI +YP+GCF+    +K L+  ++ N +
Sbjct:   51 FCRCFHVQ--CVCCAWINMTKLHLSEKACANFTLLPKFQ--EFAFRFVFNNKLVYNQTITAENPPLICLGSKSK---------------------------AAEICVKFSNVTFQVNVHEEHKTQLNGCASFNLNLFNRTIGVYPVGCFQIPDNNKHLERNQLGNWM 186
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BLAST of U14-Liphistoxin-Lth1a_1 vs. TrEMBL
Match: A0A267FXQ9 (DUF4773 domain-containing protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig021171g1 PE=4 SV=1)

HSP 1 Score: 72.7886 bits (177), Expect = 1.363e-10
Identity = 52/222 (23.42%), Postives = 89/222 (40.09%), Query Frame = 1 
Query:  349 IYFGRKSIKFNSSLVVLNDNLIKFVSNDILIKDMNENXXXXXXXXXXXPFDYDKNGRFCICSKISQPCVCCVKLAEEVIGLTDSLCSNITYIPKSKAAKISMKYGKLNKPDKYVLVDINNPPPVCLSQSLKFDLKSPELLKQKSNDDVNVGQTLNHCVDLEICFQARNLTYNVNVDASHKTEFKGCSNFYVMLNNMTIRIYPLGCFKAGYESKDLQIQKMAN 1014
            +  G  S  F  +  V    L++ +++ + + ++ + ++K    + S   D+D N   C C  IS+ C CC ++A   I L  ++C +  Y    K+ +  +            L+    PP +C   +L                              E+C   RN +Y V + + HKT  +GC +  V L N T+  YP+GCF+A   S     Q   N
Sbjct:  115 VLIGPASRHFAFNYNVSQARLVELLADTMQMMELQKTAQKTLAYMVSIQPDFDANAGSCRCGSISELCHCCARVALRPIRLEQTVCIDFRYEVHRKSLRTRIVLANSGTVVVEQLLGAARPPVLCAGSAL------------------------------ELCASFRNTSYTVMLHSEHKTRLRGCLDLLVNLVNSTVAAYPMGCFEAHGRSGGGPQQIAGN 306
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BLAST of U14-Liphistoxin-Lth1a_1 vs. Planmine SMEST
Match: SMESG000018618.1 (SMESG000018618.1)

HSP 1 Score: 520.005 bits (1338), Expect = 0.000e+0
Identity = 297/297 (100.00%), Postives = 297/297 (100.00%), Query Frame = 1 
Query:  133 MLICITKIQLFKVENKSQKKISDFEQSILKTSNQNENPIILNIKYISIXXXXXXXXXXXXXXXXXXXXXXXXIYFGRKSIKFNSSLVVLNDNLIKFVSNDILIKDMNENXXXXXXXXXXXPFDYDKNGRFCICSKISQPCVCCVKLAEEVIGLTDSLCSNITYIPKSKAAKISMKYGKLNKPDKYVLVDINNPPPVCLSQSLKFDLKSPELLKQKSNDDVNVGQTLNHCVDLEICFQARNLTYNVNVDASHKTEFKGCSNFYVMLNNMTIRIYPLGCFKAGYESKDLQIQKMANGIQ 1023
            MLICITKIQLFKVENKSQKKISDFEQSILKTSNQNENPIILNIKYISIKNSSTVSVTTAKKTTVSVQQKQEQIYFGRKSIKFNSSLVVLNDNLIKFVSNDILIKDMNENSKKLDKSLKSKPFDYDKNGRFCICSKISQPCVCCVKLAEEVIGLTDSLCSNITYIPKSKAAKISMKYGKLNKPDKYVLVDINNPPPVCLSQSLKFDLKSPELLKQKSNDDVNVGQTLNHCVDLEICFQARNLTYNVNVDASHKTEFKGCSNFYVMLNNMTIRIYPLGCFKAGYESKDLQIQKMANGIQ
Sbjct:    1 MLICITKIQLFKVENKSQKKISDFEQSILKTSNQNENPIILNIKYISIKNSSTVSVTTAKKTTVSVQQKQEQIYFGRKSIKFNSSLVVLNDNLIKFVSNDILIKDMNENSKKLDKSLKSKPFDYDKNGRFCICSKISQPCVCCVKLAEEVIGLTDSLCSNITYIPKSKAAKISMKYGKLNKPDKYVLVDINNPPPVCLSQSLKFDLKSPELLKQKSNDDVNVGQTLNHCVDLEICFQARNLTYNVNVDASHKTEFKGCSNFYVMLNNMTIRIYPLGCFKAGYESKDLQIQKMANGIQ 297
The following BLAST results are available for this feature:
BLAST of U14-Liphistoxin-Lth1a_1 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 U14-Liphistoxin-Lth1a_1 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 U14-Liphistoxin-Lth1a_1 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 U14-Liphistoxin-Lth1a_1 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 U14-Liphistoxin-Lth1a_1 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 U14-Liphistoxin-Lth1a_1 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 U14-Liphistoxin-Lth1a_1 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 U14-Liphistoxin-Lth1a_1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267EFH92.896e-1325.60DUF4773 domain-containing protein OS=Macrostomum l... [more]
A0A1I8HF362.924e-1325.60DUF4773 domain-containing protein OS=Macrostomum l... [more]
A0A1I8H5414.120e-1325.60DUF4773 domain-containing protein OS=Macrostomum l... [more]
A0A0L8H8845.830e-1228.14DUF4773 domain-containing protein OS=Octopus bimac... [more]
A0A267FXQ91.363e-1023.42DUF4773 domain-containing protein (Fragment) OS=Ma... [more]
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BLAST of U14-Liphistoxin-Lth1a_1 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 U14-Liphistoxin-Lth1a_1 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 U14-Liphistoxin-Lth1a_1 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 U14-Liphistoxin-Lth1a_1 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 U14-Liphistoxin-Lth1a_1 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 U14-Liphistoxin-Lth1a_1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000018618.10.000e+0100.00SMESG000018618.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001117 ID=SMED30001117|Name=U14-Liphistoxin-Lth1a_1|organism=Schmidtea mediterranea sexual|type=transcript|length=1194bp
CCTTACATAATGTTGTCTTTAATATTGAACTAAATGAACCAATTTTTAAT
TACTTTTCAGACTTATTTACTGCGTTTTATATATGGGAAATCTATTTTCC
GTTTGGTTACACTTATTACTTTGGTTGCTTTAATGTTGATTTGTATCACT
AAAATACAATTATTTAAAGTGGAGAATAAATCTCAAAAAAAGATATCAGA
TTTTGAACAGTCTATATTAAAAACCTCTAATCAAAATGAAAATCCTATTA
TATTAAATATTAAATATATTTCAATTAAAAATTCTAGTACTGTTAGTGTA
ACAACTGCTAAAAAAACGACAGTTTCAGTGCAGCAAAAACAGGAACAAAT
TTATTTTGGAAGGAAATCCATTAAATTTAATTCATCGCTTGTTGTATTAA
ATGATAATTTAATAAAATTTGTTTCAAATGACATTCTGATTAAAGATATG
AATGAAAATTCAAAAAAATTAGACAAATCTCTCAAAAGTAAGCCATTTGA
TTATGATAAAAATGGACGATTTTGTATTTGTTCTAAAATAAGTCAACCGT
GTGTATGTTGTGTGAAGTTAGCAGAAGAAGTTATTGGACTGACCGACTCA
TTGTGTTCGAATATAACGTATATTCCAAAAAGCAAAGCGGCGAAAATATC
TATGAAATATGGAAAATTAAACAAACCAGATAAATATGTGTTAGTAGACA
TCAACAATCCTCCACCAGTTTGTCTTTCTCAATCCTTAAAATTTGACCTA
AAAAGTCCAGAATTATTGAAACAAAAATCAAATGACGATGTTAATGTCGG
ACAAACATTGAATCATTGTGTTGATTTAGAAATATGTTTTCAAGCAAGAA
ATCTTACTTATAATGTCAACGTAGATGCTTCTCATAAAACTGAATTTAAA
GGCTGTTCGAATTTTTATGTCATGTTAAATAATATGACAATTCGTATTTA
TCCATTAGGATGTTTTAAAGCCGGTTATGAATCTAAAGACTTGCAAATTC
AAAAAATGGCTAATGGAATACAATAGATTTATTAATAAATTGATTTTATA
TTAAAATTTGGTAAAATTTAAGATTTCAATGGTTTAATTGTTTAAGTTTT
ATTTTTTATTACTTATTTGTTTCGCGTGTAAATTTGCATGGAATTATCTA
ATAATAGTTACATGAGGATTGAAAGTGATTTGCATTTTACTTTT
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protein sequence of SMED30001117-orf-1

>SMED30001117-orf-1 ID=SMED30001117-orf-1|Name=SMED30001117-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=331bp
MNQFLITFQTYLLRFIYGKSIFRLVTLITLVALMLICITKIQLFKVENKS
QKKISDFEQSILKTSNQNENPIILNIKYISIKNSSTVSVTTAKKTTVSVQ
QKQEQIYFGRKSIKFNSSLVVLNDNLIKFVSNDILIKDMNENSKKLDKSL
KSKPFDYDKNGRFCICSKISQPCVCCVKLAEEVIGLTDSLCSNITYIPKS
KAAKISMKYGKLNKPDKYVLVDINNPPPVCLSQSLKFDLKSPELLKQKSN
DDVNVGQTLNHCVDLEICFQARNLTYNVNVDASHKTEFKGCSNFYVMLNN
MTIRIYPLGCFKAGYESKDLQIQKMANGIQ*
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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
Vocabulary: INTERPRO
TermDefinition
IPR031941DUF4773
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR031941Domain of unknown function DUF4773PFAMPF15998DUF4773coord: 164..274
e-value: 3.6E-8
score: 33.9
NoneNo IPR availableTMHMMTMhelixcoord: 21..43