Myomodulin prohormone like-1

Overview
NameMyomodulin prohormone like-1
Smed IDSMED30011959
Length (bp)400
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 Myomodulin prohormone like-1 (SMED30011959) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Myomodulin prohormone like-1 (SMED30011959) 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



SMED30011959

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
head regionSMED30011959SMESG000078202.1 SmedASXL_003975SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30011959SMESG000078202.1 dd_Smed_v4_1902_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011959SMESG000078202.1 dd_Smed_v4_1902_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30011959SMESG000078202.1 dd_Smed_v4_1902_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30011959SMESG000078202.1 dd_Smed_v4_1902_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30011959SMESG000078202.1 dd_Smed_v4_1902_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011959SMESG000078202.1 BK007017smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30011959SMESG000078202.1 BK007017smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30011959SMESG000078202.1 BK007017smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
reproductive organSMED30011959SMESG000078202.1 Contig34280newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30011959SMESG000078202.1 Contig34280uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Myomodulin prohormone like-1 vs. TrEMBL
Match: E3CTJ2 (Myomodulin prohormone like-1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 155.221 bits (391), Expect = 8.662e-47
Identity = 76/76 (100.00%), Postives = 76/76 (100.00%), Query Frame = 3 
Query:  132 MSKLTYFIFMIMLFIFVQTIDINSNQYEEDYDPNDDHELDKRAYRLMRMGKRAVRLMRMGKKAVRLMRLGKRSDMA 359
            MSKLTYFIFMIMLFIFVQTIDINSNQYEEDYDPNDDHELDKRAYRLMRMGKRAVRLMRMGKKAVRLMRLGKRSDMA
Sbjct:    1 MSKLTYFIFMIMLFIFVQTIDINSNQYEEDYDPNDDHELDKRAYRLMRMGKRAVRLMRMGKKAVRLMRLGKRSDMA 76
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BLAST of Myomodulin prohormone like-1 vs. Planmine SMEST
Match: SMESG000078202.1 (SMESG000078202.1)

HSP 1 Score: 155.221 bits (391), Expect = 2.409e-50
Identity = 76/76 (100.00%), Postives = 76/76 (100.00%), Query Frame = 3 
Query:  132 MSKLTYFIFMIMLFIFVQTIDINSNQYEEDYDPNDDHELDKRAYRLMRMGKRAVRLMRMGKKAVRLMRLGKRSDMA 359
            MSKLTYFIFMIMLFIFVQTIDINSNQYEEDYDPNDDHELDKRAYRLMRMGKRAVRLMRMGKKAVRLMRLGKRSDMA
Sbjct:    1 MSKLTYFIFMIMLFIFVQTIDINSNQYEEDYDPNDDHELDKRAYRLMRMGKRAVRLMRMGKKAVRLMRLGKRSDMA 76
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BLAST of Myomodulin prohormone like-1 vs. Planmine SMEST
Match: SMESG000040636.1 (SMESG000040636.1)

HSP 1 Score: 44.669 bits (104), Expect = 9.070e-7
Identity = 29/65 (44.62%), Postives = 35/65 (53.85%), Query Frame = 3 
Query:  159 MIML---FIFVQTIDINSNQYEEDYDPNDDHELDKRAYRLMRMGKRAVRLMRMGKKAVRLMRLGK 344
            MI+L    +F+ T   +      D D  DD  LDK+AY   RMGKRA    RMGKKA    R+GK
Sbjct:   33 MILLTSGCLFMNTFAEDLGSLNADIDL-DDSRLDKKAYWASRMGKRAYWASRMGKKAYWASRMGK 96
The following BLAST results are available for this feature:
BLAST of Myomodulin prohormone like-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 Myomodulin prohormone like-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 Myomodulin prohormone like-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 Myomodulin prohormone like-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 Myomodulin prohormone like-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 Myomodulin prohormone like-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 Myomodulin prohormone like-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 Myomodulin prohormone like-1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
E3CTJ28.662e-47100.00Myomodulin prohormone like-1 (Fragment) OS=Schmidt... [more]
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BLAST of Myomodulin prohormone like-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 Myomodulin prohormone like-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 Myomodulin prohormone like-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 Myomodulin prohormone like-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 Myomodulin prohormone like-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 Myomodulin prohormone like-1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000078202.12.409e-50100.00SMESG000078202.1[more]
SMESG000040636.19.070e-744.62SMESG000040636.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011959 ID=SMED30011959|Name=Myomodulin prohormone like-1|organism=Schmidtea mediterranea sexual|type=transcript|length=400bp
ATTCCTCGTTGATTTTACTTCATTTCGTCCGATTTCAGATTTTCGACCTA
TCAAATCACAAGAAATTGCTTATAAAACTCAGAGATTTTGAAAAATCCGA
ATTAAACGTGATTTAACATCCATAAAAAAAGATGTCAAAACTAACGTATT
TTATTTTCATGATAATGCTCTTCATTTTCGTTCAAACAATTGATATCAAT
TCAAATCAGTACGAAGAGGACTATGATCCAAATGATGATCATGAGCTTGA
CAAACGGGCGTATCGGTTAATGAGAATGGGAAAACGAGCGGTCCGATTGA
TGAGAATGGGAAAGAAAGCAGTGAGACTGATGAGGCTTGGTAAAAGAAGC
GATATGGCATAGATATTTATGTATCAATGATTTCATACAAAAAATAAGAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000044cephalic ganglia
PLANA:0000097ventral nerve cord
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0002089reproductive organ
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.862
NoneNo IPR availableTMHMMTMhelixcoord: 5..22