SMED30023248

Overview
NameSMED30023248
Smed IDSMED30023248
Length (bp)728
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 SMED30023248 (SMED30023248) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023248 (SMED30023248) 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 SMED30023248 (SMED30023248) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023248 (SMED30023248) 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



SMED30023248

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30023248h1SMcG0018912 dd_Smed_v4_7615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30023248h1SMcG0018912 dd_Smed_v4_7615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023248h1SMcG0020329 Contig215GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023248h1SMcG0018912 Contig215GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30023248 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001019:66854..67712 +3557
Homology
[Close]
BLAST of SMED30023248 vs. Ensembl Xenopus
Match: c20orf27 (chromosome 20 open reading frame 27 [Source:NCBI gene;Acc:493230])

HSP 1 Score: 48.1358 bits (113), Expect = 1.348e-6
Identity = 45/147 (30.61%), Postives = 66/147 (44.90%), Query Frame = 3 
Query:  135 FDEPKSDSV-YATNNEDGKYEVSLGFLAYLHIYNANFKIS--HKLGKVLNYDNTSIKHSSVVSINYLPKESSEENSIFVHEIFLRVTVEIEPWIEEYIIFYDETKANSLI-LILKCKVLTIEMGYPTLKNNVRC----IDKFSESSD 551
            FDE   DSV   +  EDG + V +GFL  LH Y  +F +    +LGK +        +  V+SI      S  E     H I    T   E  ++E +I   ET   + + ++++ +VL    G P L   VRC    ++  SE SD
Sbjct:   15 FDEQLHDSVVMVSQQEDGNFLVKVGFLKILHKYEISFSLPPVQRLGKSICAVPLPTLNLKVLSIT-----SQAEG----HSIKCEYTAHKEGVLKEEMILASETNDKAFVKVVVQARVLDRHHGTPMLLEGVRCTGTELEYDSEQSD 152
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BLAST of SMED30023248 vs. UniProt/SwissProt
Match: sp|Q68FA2|CT027_XENTR (UPF0687 protein C20orf27 homolog OS=Xenopus tropicalis OX=8364 PE=2 SV=1)

HSP 1 Score: 48.521 bits (114), Expect = 8.595e-6
Identity = 45/147 (30.61%), Postives = 66/147 (44.90%), Query Frame = 3 
Query:  135 FDEPKSDSV-YATNNEDGKYEVSLGFLAYLHIYNANFKIS--HKLGKVLNYDNTSIKHSSVVSINYLPKESSEENSIFVHEIFLRVTVEIEPWIEEYIIFYDETKANSLI-LILKCKVLTIEMGYPTLKNNVRC----IDKFSESSD 551
            FDE   DSV   +  EDG + V +GFL  LH Y  +F +    +LGK +        +  V+SI      S  E     H I    T   E  ++E +I   ET   + + ++++ +VL    G P L   VRC    ++  SE SD
Sbjct:   32 FDEQLHDSVVMVSQQEDGNFLVKVGFLKILHKYEISFSLPPVQRLGKSICAVPLPTLNLKVLSIT-----SQAEG----HSIKCEYTAHKEGVLKEEMILASETNDKAFVKVVVQARVLDRHHGTPMLLEGVRCTGTELEYDSEQSD 169
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BLAST of SMED30023248 vs. TrEMBL
Match: T1F8G1 (Uncharacterized protein OS=Helobdella robusta OX=6412 GN=20205110 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 6.371e-7
Identity = 39/121 (32.23%), Postives = 63/121 (52.07%), Query Frame = 3 
Query:  192 EVSLGFLAYLHIYNANFKISHKLGKVLNYDNTSIKHSSVVSINYLPKESSEENSIFVHEIFLRVTVEIEPWIEEYIIFYDETKANSLI-LILKCKVLTIEMGYPTLKNNVRCIDKFSESSD 551
            +V LGFL  LH Y+ NF+I  KLGK L  D   +++ +V  +  +P ++        HE+ L    + E  ++E +I    T +++ I LIL  +VL    G P L++ V CI   ++  D
Sbjct:   47 DVHLGFLQLLHDYHINFRIPDKLGKDLVCD--PLQNLNVQLLEAVPTDNG-------HELLLSFKAQKEKLMKEELIINSATDSDAHIKLILHARVLGKGKGTPALRSGVHCIKVHADDED 158
[Close]
BLAST of SMED30023248 vs. Planmine SMEST
Match: SMESG000044244.1 (SMESG000044244.1)

HSP 1 Score: 57.7658 bits (138), Expect = 2.939e-10
Identity = 43/121 (35.54%), Postives = 62/121 (51.24%), Query Frame = 3 
Query:  186 KYEVSLGFLAYLHIYNANFKISHKLGKVLNYDNTSIKHSSVVSINYLPKESSEENSIFV---HEIFLRVTVEIEPWIEEYIIFYDETKANSLILILKCKVLTIEMGYPTLKNNVRCIDKFS 539
            KY  SLGFLA+ + Y A   + H  G  ++  N+S K+  +  I +L    ++   I     H++ + V V  EP IEE   F  E K     L+L CKVLT +MG P L  NVR   +++
Sbjct:   34 KYFSSLGFLAFKNTYEAVIYLDHSYGTTISVVNSSGKYFKIEEILHL--TGTDVPPICTSNYHKLLVSVEVASEPLIEETFNFKGE-KNLHFDLLLHCKVLTKKMGLPNLNKNVRLTGRYA 151
The following BLAST results are available for this feature:
BLAST of SMED30023248 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 SMED30023248 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 SMED30023248 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 SMED30023248 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 SMED30023248 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
c20orf271.348e-630.61chromosome 20 open reading frame 27 [Source:NCBI g... [more]
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BLAST of SMED30023248 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 SMED30023248 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q68FA2|CT027_XENTR8.595e-630.61UPF0687 protein C20orf27 homolog OS=Xenopus tropic... [more]
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BLAST of SMED30023248 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
T1F8G16.371e-732.23Uncharacterized protein OS=Helobdella robusta OX=6... [more]
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BLAST of SMED30023248 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 SMED30023248 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 SMED30023248 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 SMED30023248 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 SMED30023248 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 SMED30023248 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000044244.12.939e-1035.54SMESG000044244.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023248 ID=SMED30023248|Name=SMED30023248|organism=Schmidtea mediterranea sexual|type=transcript|length=728bp
GTTAATTTACAAATTTGATTGAAATATTTTTATAAATTATATATTTTGAT
AGTTTTATTATATTTTAATTTTACTTATTATTCCAATTTCGGTAAACAAT
TGTCAAAATGTCTAAGAAGAAAGTCAGTATTAAGTTTGATGAGCCAAAAT
CTGATAGTGTTTACGCCACAAATAATGAAGATGGAAAATATGAAGTTTCA
CTTGGATTTTTAGCATATCTGCATATATATAATGCAAACTTCAAAATTTC
TCATAAACTTGGAAAGGTTTTAAATTATGATAATACAAGCATCAAACACT
CTTCAGTAGTATCAATAAATTATCTACCTAAAGAATCATCTGAAGAAAAT
TCTATTTTCGTGCATGAAATTTTCCTCAGAGTCACTGTGGAAATTGAGCC
CTGGATTGAAGAATATATTATTTTCTATGATGAAACTAAAGCGAATTCTT
TAATATTGATTTTAAAGTGCAAAGTTTTAACAATCGAAATGGGATATCCA
ACACTGAAAAATAATGTCAGATGCATTGATAAATTTTCCGAAAGCAGTGA
TTAATTATAAAGTTGATAATTGTTTTCCTGTTAAATAGAACTTATTTTTA
TGATTTTAAAATCTTTAACAAATCTTCGGGTGTTCCTCAACAAACTTGAT
GCATTTATATTTGTCATAGTATTTATTAGTCTGTAACTTGCGTTTTTCAG
CCATTAGGAATTGGAAAATAAATCACGC
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protein sequence of SMED30023248-orf-1

>SMED30023248-orf-1 ID=SMED30023248-orf-1|Name=SMED30023248-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=149bp
MSKKKVSIKFDEPKSDSVYATNNEDGKYEVSLGFLAYLHIYNANFKISHK
LGKVLNYDNTSIKHSSVVSINYLPKESSEENSIFVHEIFLRVTVEIEPWI
EEYIIFYDETKANSLILILKCKVLTIEMGYPTLKNNVRCIDKFSESSD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR026794UPF0687
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR026794Uncharacterised protein family UPF0687PFAMPF15006DUF4517coord: 13..143
e-value: 2.2E-14
score: 53.9
IPR026794Uncharacterised protein family UPF0687PANTHERPTHR13287UNCHARACTERIZEDcoord: 5..144