SMED30005304

Overview
NameSMED30005304
Smed IDSMED30005304
Length (bp)377
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 SMED30005304 (SMED30005304) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005304 (SMED30005304) 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



SMED30005304

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30005304 dd_Smed_v6_86975_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30005304 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009982:8487..8863 -1867
v31.004338:63887..64241 -1730
Homology
[Close]
BLAST of SMED30005304 vs. TrEMBL
Match: A0A193KUN3 (GCR142 OS=Schmidtea mediterranea OX=79327 GN=gcr142 PE=2 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 6.794e-13
Identity = 40/115 (34.78%), Postives = 74/115 (64.35%), Query Frame = 2 
Query:   35 EATLKYLTTDSSILCQIREAIINFISIFHMTLIVIFVLINYICTFSLFALFYKRIYKGVFQSTSNRKVIKVARITVLSSFLYNVCMIPVFIN-LKDNNLSQLVVYFMYLHIIINP 376
            E +L+Y  +D +I+C IR  +   ++++++ +  +F+++NY C  +LF  F  R+ KG  Q++S R ++K+A+I  +S+FL+N+ ++P  I     +  S  VVY +Y+HII NP
Sbjct:  155 EVSLRYCFSDFTIVCDIRRIVGRILNVYYILIFSLFIIVNYACYATLFLYFIIRL-KGA-QTSSMRNILKMAKILFISAFLFNISLLPTIITAFIGSFFSYTVVYLIYIHIITNP 267
[Close]
BLAST of SMED30005304 vs. TrEMBL
Match: A0A193KUG0 (GCR152 OS=Schmidtea mediterranea OX=79327 GN=gcr152 PE=2 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 1.774e-7
Identity = 34/118 (28.81%), Postives = 68/118 (57.63%), Query Frame = 2 
Query:   26 VALEATLKYLTTDSSILCQIREAIINFISIFHMTLIVIFVLINYICTFSLFALFYKRIYKGVFQSTSNRKVIKVARITVLSSFLYNVCMIP-VFINLKDNNLSQLVVYFMYLHIIINP 376
            V ++  ++Y+ T+  I C IR  ++     +++ L++ F+++NY C  SL   F   + K    ST+ + ++K+  I  +S+ LYN+ +IP ++  LK   +SQ ++  M+L+I +N 
Sbjct:  160 VTIDIVMRYIYTNPDISCSIRYLVVGINGKYYIILLITFIIVNYSCYLSLLTYFINHLCKRKVTSTATKNILKMTAIIFISTVLYNLSLIPAIYAVLKQVLVSQTLLNMMFLNIAMNS 277
The following BLAST results are available for this feature:
BLAST of SMED30005304 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 SMED30005304 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 SMED30005304 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 SMED30005304 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 SMED30005304 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 SMED30005304 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 SMED30005304 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 SMED30005304 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A193KUN36.794e-1334.78GCR142 OS=Schmidtea mediterranea OX=79327 GN=gcr14... [more]
A0A193KUG01.774e-728.81GCR152 OS=Schmidtea mediterranea OX=79327 GN=gcr15... [more]
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BLAST of SMED30005304 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 SMED30005304 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 SMED30005304 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 SMED30005304 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 SMED30005304 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 SMED30005304 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005304 ID=SMED30005304|Name=SMED30005304|organism=Schmidtea mediterranea sexual|type=transcript|length=377bp
CTTAAGTGTATATCTTCCCATTATAGTCGCACTTGAAGCAACGCTGAAAT
ATCTGACAACGGATTCCTCGATTCTATGTCAGATTCGAGAAGCAATAATT
AATTTTATCTCTATTTTTCACATGACTTTAATTGTAATTTTTGTTTTAAT
TAATTATATTTGTACTTTTAGTCTATTTGCACTGTTTTATAAGCGGATAT
ATAAAGGAGTATTTCAATCAACTTCGAACAGAAAGGTAATAAAGGTTGCA
AGAATAACAGTTTTGTCCAGTTTCCTATACAATGTTTGCATGATCCCTGT
ATTCATTAATCTCAAAGACAATAATTTATCCCAACTGGTTGTCTATTTCA
TGTATTTACATATCATTATTAATCCTG
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protein sequence of SMED30005304-orf-1

>SMED30005304-orf-1 ID=SMED30005304-orf-1|Name=SMED30005304-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
LSVYLPIIVALEATLKYLTTDSSILCQIREAIINFISIFHMTLIVIFVLI
NYICTFSLFALFYKRIYKGVFQSTSNRKVIKVARITVLSSFLYNVCMIPV
FINLKDNNLSQLVVYFMYLHIIINP
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000419prepharyngeal region
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
NoneNo IPR availableTMHMMTMhelixcoord: 80..102
NoneNo IPR availableTMHMMTMhelixcoord: 37..59