Thionin

Overview
NameThionin
Smed IDSMED30020051
Length (bp)714
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 Thionin (SMED30020051) t-SNE clustered cells

Violin plots show distribution of expression levels for Thionin (SMED30020051) 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 Thionin (SMED30020051) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Thionin (SMED30020051) 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



SMED30020051

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30020051h1SMcG0012690 SmedASXL_061543SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30020051h1SMcG0012690 dd_Smed_v4_3063_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30020051h1SMcG0012690 dd_Smed_v4_3063_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30020051h1SMcG0012690 dd_Smed_v4_3063_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30020051h1SMcG0012690 dd_Smed_v4_3063_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020051h1SMcG0012690 Contig47053newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020051h1SMcG0012690 Contig47053uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
neuronSMED30020051h1SMcG0012690 dd_3063dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
head regionSMED30020051h1SMcG0012690 dd_Smed_v6_3063_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
photoreceptor neuronSMED30020051h1SMcG0012690 SMED30020051smed_20140614PMID:22884275
Lapan et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Thionin vs. TrEMBL
Match: A0A504Y678 (Uncharacterized protein OS=Fasciola gigantica OX=46835 GN=FGIG_02038 PE=4 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 3.366e-8
Identity = 37/134 (27.61%), Postives = 64/134 (47.76%), Query Frame = 2 
Query:  200 VISGIFSLTILTVNSINYKRNFDRNGYEKLLGQQSVYKYCGEKDDSCMFTNQCCEEFVCDPYENICKMPISTQTDKN-VNYKCLNDNDCSPNECCRLIRGIESTRICSTDCSPERDVVEHVENPSYMSRTWWKK 598
            +I G+   + +T+ +           YE LLG +S+ + CG + D C+ +  CC EF C   E +C++ ++  T    +  +C+ D DC  + CC   +G    R C+T C P     E +   +Y  R +W +
Sbjct:    5 LIFGVLLYSAITIEAAT-------RAYENLLGARSIMRKCGSEGDVCISSVNCCPEFTCSE-ELVCELLVTNPTGAGALGTRCITDVDCQVSLCC---QGSLYERTCTTYC-PRISEAETIPAGTYYGRQFWNQ 126
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BLAST of Thionin vs. TrEMBL
Match: A0A2H1CIT5 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_003402 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 3.803e-8
Identity = 37/136 (27.21%), Postives = 64/136 (47.06%), Query Frame = 2 
Query:  194 LVVISGIFSLTILTVNSINYKRNFDRNGYEKLLGQQSVYKYCGEKDDSCMFTNQCCEEFVCDPYENICKMPISTQTDKN-VNYKCLNDNDCSPNECCRLIRGIESTRICSTDCSPERDVVEHVENPSYMSRTWWKK 598
             ++I G+   + +TV + +         YE LLG +S+ + CG + D C+ +  CC EF C   E +C++ ++  T    +  +C+ D DC    CC   +G    R C+  C P     E +   +Y  R +W +
Sbjct:    3 FLLIFGVLFYSAITVEAAS-------RAYENLLGARSIMRKCGSEGDVCISSVNCCPEFACSE-ELVCELLVTNPTGAGALGTRCITDVDCQVGLCC---QGSLYERTCTRYC-PRISEAETIPAGTYYGRQFWNQ 126
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BLAST of Thionin vs. TrEMBL
Match: A0A5K3ER81 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 2.257e-6
Identity = 31/87 (35.63%), Postives = 43/87 (49.43%), Query Frame = 2 
Query:  275 GYEKLLGQQSVYKYCGEKDDSCMFTNQCCEEFVCDPYENI--CKMPISTQTDKNVNYKCLNDNDCSPNECCRLIRGIESTRICSTDC 529
            GY++LLG+ ++ KYC E  + CMF+  CC    C    N+  C   +S  T      KCL+D DC   +CC   R      IC+  C
Sbjct:   24 GYQRLLGENALRKYCSEDGEECMFSTHCCRGLYCAVQGNVGTCLTHLSALT------KCLSDADCPETKCCHRQRHHGGFGICAYVC 104
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BLAST of Thionin vs. Planmine SMEST
Match: SMESG000031412.1 (SMESG000031412.1)

HSP 1 Score: 294.278 bits (752), Expect = 9.195e-103
Identity = 142/143 (99.30%), Postives = 143/143 (100.00%), Query Frame = 2 
Query:  176 MFSTTFLVVISGIFSLTILTVNSINYKRNFDRNGYEKLLGQQSVYKYCGEKDDSCMFTNQCCEEFVCDPYENICKMPISTQTDKNVNYKCLNDNDCSPNECCRLIRGIESTRICSTDCSPERDVVEHVENPSYMSRTWWKKSV 604
            MFSTTFLVVISGIFSLTILTVNSINYKRNFDRNGYEKLLGQQSVYKYCGEKDDSCMFTNQCCEEFVCDPYENICKMPIS+QTDKNVNYKCLNDNDCSPNECCRLIRGIESTRICSTDCSPERDVVEHVENPSYMSRTWWKKSV
Sbjct:    1 MFSTTFLVVISGIFSLTILTVNSINYKRNFDRNGYEKLLGQQSVYKYCGEKDDSCMFTNQCCEEFVCDPYENICKMPISSQTDKNVNYKCLNDNDCSPNECCRLIRGIESTRICSTDCSPERDVVEHVENPSYMSRTWWKKSV 143
The following BLAST results are available for this feature:
BLAST of Thionin 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 Thionin 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 Thionin 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 Thionin 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 Thionin 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 Thionin 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 Thionin 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 Thionin vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A504Y6783.366e-827.61Uncharacterized protein OS=Fasciola gigantica OX=4... [more]
A0A2H1CIT53.803e-827.21Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A5K3ER812.257e-635.63Uncharacterized protein OS=Mesocestoides corti OX=... [more]
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BLAST of Thionin 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 Thionin 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 Thionin 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 Thionin 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 Thionin 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 Thionin vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000031412.19.195e-10399.30SMESG000031412.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020051 ID=SMED30020051|Name=Thionin|organism=Schmidtea mediterranea sexual|type=transcript|length=714bp
CAGAAATTAAAGCAGAGTTCAGCAGACAAATTTTTCTTTTCTTTAATCTC
ATCTTATTGGTGACTTTTTAATGTCTAAAATCGAGAAAAATTTGCCACAT
AGCAACGCACTGAGCTGGATTTTTGTTTATAAATTGAGTTCATTCTGACT
TGGGATCCATTGCTTGGTTTTACCAATGTTTTCAACGACTTTTCTCGTGG
TAATTTCTGGAATTTTTTCCTTGACAATTCTTACAGTAAATTCGATTAAC
TATAAACGTAATTTCGACAGAAACGGCTATGAAAAGCTCCTGGGCCAGCA
ATCTGTTTACAAATATTGTGGTGAGAAAGACGATTCGTGTATGTTTACAA
ATCAATGTTGCGAAGAATTCGTCTGCGATCCATACGAGAACATTTGTAAA
ATGCCCATATCGACCCAAACCGACAAGAATGTAAATTACAAATGTCTTAA
TGATAATGACTGCTCCCCAAACGAATGCTGTAGGCTAATACGTGGAATTG
AAAGTACGAGAATTTGCAGTACCGATTGTTCACCAGAAAGAGACGTTGTT
GAACATGTGGAAAATCCTTCGTACATGTCAAGAACATGGTGGAAAAAATC
TGTATAATAATTGAGTAACCATTCGTTAAAAAGGTTGTGCGAAAAATCTT
TGGTTGTGATAAAATGTCATTATTTGTTGAACTTTTCAATTGAAATAAAT
TTTTGCATTGAAAA
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protein sequence of SMED30020051-orf-1

>SMED30020051-orf-1 ID=SMED30020051-orf-1|Name=SMED30020051-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=144bp
MFSTTFLVVISGIFSLTILTVNSINYKRNFDRNGYEKLLGQQSVYKYCGE
KDDSCMFTNQCCEEFVCDPYENICKMPISTQTDKNVNYKCLNDNDCSPNE
CCRLIRGIESTRICSTDCSPERDVVEHVENPSYMSRTWWKKSV*
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Aliases
The feature 'Thionin' has the following synonyms
Synonym
Smed_08951
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000017photoreceptor neuron
PLANA:0000099neuron
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 4..26