Unconventional myosin-XVI

Overview
NameUnconventional myosin-XVI
Smed IDSMED30011770
Length (bp)851
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 Unconventional myosin-XVI (SMED30011770) t-SNE clustered cells

Violin plots show distribution of expression levels for Unconventional myosin-XVI (SMED30011770) 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 Unconventional myosin-XVI (SMED30011770) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Unconventional myosin-XVI (SMED30011770) 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




SMED30011770

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30011770h1SMcG0015866 Contig46307newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011770h1SMcG0015866 Contig46307uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
protonephridiaSMED30011770h1SMcG0015866 dd_Smed_v4_4268_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30011770h1SMcG0015866 dd_Smed_v4_4268_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011770h1SMcG0015866 dd_Smed_v4_4268_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30011770h1SMcG0015866 dd_Smed_v4_4268_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30011770h1SMcG0015866 dd_Smed_v4_4268_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30011770h1SMcG0015866 dd_Smed_v4_4268_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30011770h1SMcG0015866 dd_Smed_v4_4268_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30011770h1SMcG0015866 dd_Smed_v6_4268_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30011770h1SMcG0015866 dd_Smed_v6_4268_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Unconventional myosin-XVI vs. Planmine SMEST
Match: SMESG000041981.1 (SMESG000041981.1)

HSP 1 Score: 355.14 bits (910), Expect = 4.098e-125
Identity = 203/205 (99.02%), Postives = 204/205 (99.51%), Query Frame = 1
Query:   91 MENDYCDKDERVNEISTFTSSALVSDYINVFEEKFNQPIENNWGRRSSMQSPTSTREDFSKINNSINRNQNKSLKKTIAINNLNNSTSLEIAEVATMNEMELCTIEDIDFSQIPGYIKIPDNIPDWKKYHLERKNKDAINIYLSXXXXXXXXXXXYGDIPQWXXXXXXXXXXXXXXXXSLESDKFGNIPQWKKDLLVKKQIPNHH 705
            MENDYCDKDERVNEISTFTSSALVSDYINVFEEKFNQPIENNWGRRSSMQSPTSTREDFSKINNSINRNQNKSLKKTIAINNLNNSTSLE+AEVATMNEMELCTIEDIDFSQIPGYIKIPDNIPDWKKYHLERKNKDAINIYLSEKQKEENEKNKYGDIPQWKKNLLMKKEKEKINLESLESDKFGNIPQWKKDLLVKKQIPNH 
Sbjct:    1 MENDYCDKDERVNEISTFTSSALVSDYINVFEEKFNQPIENNWGRRSSMQSPTSTREDFSKINNSINRNQNKSLKKTIAINNLNNSTSLEVAEVATMNEMELCTIEDIDFSQIPGYIKIPDNIPDWKKYHLERKNKDAINIYLSEKQKEENEKNKYGDIPQWKKNLLMKKEKEKINLESLESDKFGNIPQWKKDLLVKKQIPNHQ 205          
The following BLAST results are available for this feature:
BLAST of Unconventional myosin-XVI 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 Unconventional myosin-XVI 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 Unconventional myosin-XVI 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 Unconventional myosin-XVI 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 Unconventional myosin-XVI 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 Unconventional myosin-XVI 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 Unconventional myosin-XVI 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 Unconventional myosin-XVI vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Unconventional myosin-XVI 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 Unconventional myosin-XVI 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 Unconventional myosin-XVI 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 Unconventional myosin-XVI 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 Unconventional myosin-XVI 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 Unconventional myosin-XVI vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000041981.14.098e-12599.02SMESG000041981.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011770 ID=SMED30011770|Name=Unconventional myosin-XVI|organism=Schmidtea mediterranea sexual|type=transcript|length=851bp
TCTATATAAATCTTATATGTGCGGATATCCTTCAATGAAACTGACGTAAT
CATTCAATCGATATTATTTTAATCAATTAAATACCATCTGATGGAGAATG
ATTATTGTGATAAGGACGAAAGAGTGAATGAAATTTCAACTTTTACTAGT
TCTGCTCTAGTCTCAGATTATATCAATGTTTTCGAGGAAAAATTCAATCA
ACCTATAGAAAATAATTGGGGTAGGCGGTCATCAATGCAATCTCCCACAT
CAACAAGAGAGGACTTTAGCAAAATCAATAATTCTATCAATCGGAATCAG
AATAAATCTTTAAAGAAAACTATCGCAATCAATAATTTGAACAATTCTAC
TTCTCTAGAGATTGCAGAGGTCGCCACGATGAACGAAATGGAGCTGTGCA
CAATTGAGGATATTGATTTCAGTCAAATTCCTGGATACATAAAAATACCT
GATAATATTCCAGATTGGAAAAAATATCATCTGGAAAGAAAAAACAAGGA
CGCCATAAATATTTATCTGTCGGAAAAACAGAAAGAAGAAAATGAAAAGA
ATAAATATGGTGACATACCTCAATGGAAAAAGAATTTATTAATGAAAAAA
GAAAAAGAAAAAATAAATTTAGAGAGTTTGGAAAGCGATAAATTCGGAAA
CATTCCTCAATGGAAAAAAGATTTATTAGTAAAAAAGCAAATACCAAATC
ATCATTAACTTTTATAATTATAATTTAAATATTATTGATTAGCACACACA
CATACACAAAATATTATGTGAATAATTTATTATTTATACGTGCTGCAAAT
GTTTTTATTGTGCATTATTGATTCCCACTACTTTCTATAACTATTTTCTA
T
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protein sequence of SMED30011770-orf-1

>SMED30011770-orf-1 ID=SMED30011770-orf-1|Name=SMED30011770-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=206bp
MENDYCDKDERVNEISTFTSSALVSDYINVFEEKFNQPIENNWGRRSSMQ
SPTSTREDFSKINNSINRNQNKSLKKTIAINNLNNSTSLEIAEVATMNEM
ELCTIEDIDFSQIPGYIKIPDNIPDWKKYHLERKNKDAINIYLSEKQKEE
NEKNKYGDIPQWKKNLLMKKEKEKINLESLESDKFGNIPQWKKDLLVKKQ
IPNHH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0000166nucleotide binding
GO:0003774motor activity
GO:0003779actin binding
GO:0005524ATP binding
Vocabulary: cellular component
TermDefinition
GO:0016459myosin complex
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 163..183