hypothetical protein

Overview
Namehypothetical protein (AFJ24831.1)
Smed IDSMED30011050
Length (bp)615
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 hypothetical protein (SMED30011050) t-SNE clustered cells

Violin plots show distribution of expression levels for hypothetical protein (SMED30011050) 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 hypothetical protein (SMED30011050) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for hypothetical protein (SMED30011050) 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




SMED30011050

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
X1 cellSMED30011050h1SMcG0008404 SmedASXL_006501SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30011050h1SMcG0008404 SmedASXL_006501SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
protonephridiaSMED30011050h1SMcG0008404 dd_Smed_v4_8839_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30011050h1SMcG0008404 dd_Smed_v4_8839_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011050h1SMcG0008404 dd_Smed_v4_8839_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30011050h1SMcG0008404 dd_Smed_v4_8839_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30011050h1SMcG0008404 dd_Smed_v4_8839_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30011050h1SMcG0008404 dd_Smed_v4_8839_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
whole organismSMED30011050h1SMcG0008404 Contig50891uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30011050h1SMcG0008404 Contig50891newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
BLAST of hypothetical protein vs. TrEMBL
Match: I1ZIH7 (Uncharacterized protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 256.144 bits (653), Expect = 8.618e-85
Identity = 127/128 (99.22%), Postives = 127/128 (99.22%), Query Frame = 3
Query:   72 MENLKDDGFSTVNLKNIIRSSFRKYQSIKKSKGNQNLLQTLMITKIVHKASMWLSKDEDRNMKDSFKRKNENIFSSNDQISRKSSKVAFINKNYEKSTPINQSFHYFSSQERLLQEPKVGFNFELTVL 455
            MENLKDDGFSTVNLKNIIRSSFRKYQSIKKSKGNQNLLQTLMITKIVHKASMWLSKDEDRNMKDSFKRKNENIFSSNDQISRKSSKV FINKNYEKSTPINQSFHYFSSQERLLQEPKVGFNFELTVL
Sbjct:    1 MENLKDDGFSTVNLKNIIRSSFRKYQSIKKSKGNQNLLQTLMITKIVHKASMWLSKDEDRNMKDSFKRKNENIFSSNDQISRKSSKVTFINKNYEKSTPINQSFHYFSSQERLLQEPKVGFNFELTVL 128          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000044135.1 (SMESG000044135.1)

HSP 1 Score: 253.062 bits (645), Expect = 3.752e-87
Identity = 126/128 (98.44%), Postives = 126/128 (98.44%), Query Frame = 3
Query:   72 MENLKDDGFSTVNLKNIIRSSFRKYQSIKKSKGNQNLLQTLMITKIVHKASMWLSKDEDRNMKDSFKRKNENIFSSNDQISRKSSKVAFINKNYEKSTPINQSFHYFSSQERLLQEPKVGFNFELTVL 455
            MENLKDDGFSTVNLKNIIRSSFRKYQSIKKSKGNQNLLQTLMITKIVHKASMWLSKDEDRNMKDSFKRKNENIFSSNDQISRKSSKV FINKNYEKSTPINQSFHYFSSQ RLLQEPKVGFNFELTVL
Sbjct:    1 MENLKDDGFSTVNLKNIIRSSFRKYQSIKKSKGNQNLLQTLMITKIVHKASMWLSKDEDRNMKDSFKRKNENIFSSNDQISRKSSKVTFINKNYEKSTPINQSFHYFSSQVRLLQEPKVGFNFELTVL 128          
The following BLAST results are available for this feature:
BLAST of hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZIH78.618e-8599.22Uncharacterized protein OS=Schmidtea mediterranea ... [more]
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BLAST of hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000044135.13.752e-8798.44SMESG000044135.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30011050
GenBankAFJ24831.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011050 ID=SMED30011050|Name=hypothetical protein|organism=Schmidtea mediterranea sexual|type=transcript|length=615bp
TCATGAACTTACCAAAATAATCAACCAATCAGATTTCAGAATCATAATAA
TCATATCATAATTTATACTTCATGGAAAATTTAAAGGATGACGGATTCTC
TACGGTAAATCTGAAAAATATTATTCGAAGTTCATTTAGAAAATATCAAT
CTATCAAAAAAAGTAAAGGTAATCAAAATCTTCTGCAAACGTTGATGATA
ACAAAAATCGTGCACAAAGCCTCTATGTGGCTATCTAAAGATGAAGACAG
AAATATGAAGGATTCTTTCAAAAGAAAAAACGAGAATATATTTTCATCAA
ATGATCAAATCTCAAGAAAGTCATCAAAAGTCGCATTTATCAATAAGAAC
TATGAAAAATCAACTCCAATTAATCAGAGTTTTCATTACTTTTCGAGCCA
GGAAAGGTTGCTACAAGAACCGAAAGTTGGTTTCAATTTTGAATTAACAG
TTTTGTAAGTGTCCTCCTATTTGTTTTGTACAAATTTATTGAGATTATTG
ATTTATATTATGTATTATAAGTGAAATGTATTATTGTTTACAAATTGATT
TAATGTTGTTGGAAAATATTTTTCGGCGAAATTATTTGTTATAAATACAT
TTTTATTAATTAAAA
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protein sequence of SMED30011050-orf-1

>SMED30011050-orf-1 ID=SMED30011050-orf-1|Name=SMED30011050-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=129bp
MENLKDDGFSTVNLKNIIRSSFRKYQSIKKSKGNQNLLQTLMITKIVHKA
SMWLSKDEDRNMKDSFKRKNENIFSSNDQISRKSSKVAFINKNYEKSTPI
NQSFHYFSSQERLLQEPKVGFNFELTVL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000136whole organism
PLANA:0002109X1 cell
PLANA:0002111X2 cell
PLANA:0003116parenchymal cell