SMED30009435

Overview
NameSMED30009435
Smed IDSMED30009435
Length (bp)751
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 SMED30009435 (SMED30009435) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009435 (SMED30009435) 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




SMED30009435

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30009435h1SMcG0007705 dd_Smed_v4_28272_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30009435h1SMcG0007705 dd_Smed_v4_28272_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30009435h1SMcG0007705 dd_Smed_v4_28272_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009435 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009907:4635..7017 -3683
v31.009907:12103..12824 +1167
Homology
BLAST of SMED30009435 vs. Planmine SMEST
Match: SMESG000071611.1 (SMESG000071611.1)

HSP 1 Score: 381.333 bits (978), Expect = 2.302e-136
Identity = 184/184 (100.00%), Postives = 184/184 (100.00%), Query Frame = -2
Query:   22 MKQVNQIRSKSLIEEHSPEYTSMMNTVELLTGVMKRRLKEDPGLRFSLLPIYASYRFEPRLQCLNNSIVLNVDNYDYSHRDIKYAVENNLSICRPVKGKNYIKMIQFLPYKLQFYWIHDLKNRWIVQLESETFMLSLIDTGLKVKGHYYLVRDYMEIQRIEIQLWREAKRSDLAISKFSYSPII 573
            MKQVNQIRSKSLIEEHSPEYTSMMNTVELLTGVMKRRLKEDPGLRFSLLPIYASYRFEPRLQCLNNSIVLNVDNYDYSHRDIKYAVENNLSICRPVKGKNYIKMIQFLPYKLQFYWIHDLKNRWIVQLESETFMLSLIDTGLKVKGHYYLVRDYMEIQRIEIQLWREAKRSDLAISKFSYSPII
Sbjct:    1 MKQVNQIRSKSLIEEHSPEYTSMMNTVELLTGVMKRRLKEDPGLRFSLLPIYASYRFEPRLQCLNNSIVLNVDNYDYSHRDIKYAVENNLSICRPVKGKNYIKMIQFLPYKLQFYWIHDLKNRWIVQLESETFMLSLIDTGLKVKGHYYLVRDYMEIQRIEIQLWREAKRSDLAISKFSYSPII 184          
BLAST of SMED30009435 vs. Planmine SMEST
Match: SMESG000071612.1 (SMESG000071612.1)

HSP 1 Score: 258.07 bits (658), Expect = 2.892e-87
Identity = 117/180 (65.00%), Postives = 147/180 (81.67%), Query Frame = -2
Query:   22 NQIRSKSLIEEHSPEYTSMMNTVELLTGVMKRRLKEDPGLRFSLLPIYASYRFEPRLQCLNNSIVLNVDNYDYSHRDIKYAVENNLSICRPVKGKNYIKMIQFLPYKLQFYWIHDLKNRWIVQLESETFMLSLIDTGLKVKGHYYLVRDYMEIQRIEIQLWREAKRSDLAISKFSYSPII 561
            + I+ K + E+HS E+T+M   + L+ GV++R++++DP +   LLP+YASYRFEPRL+ L  SIV N+DNYD SH+D+KYA+E NLSICRP+    YIKMIQF+PYKLQF+WIHDLKNRWI+QLESE  +LSLIDTGLK+ G  Y+VRDYMEIQRIEIQLWREAK +D + SKF YSPII
Sbjct:   22 SDIKEKMITEKHSTEFTAMFENIRLIKGVLERKIRQDPLILDMLLPVYASYRFEPRLRALAKSIVFNIDNYDLSHKDVKYAIEKNLSICRPLSNGKYIKMIQFIPYKLQFFWIHDLKNRWIIQLESENCVLSLIDTGLKIHGKDYVVRDYMEIQRIEIQLWREAKANDKSFSKFEYSPII 201          
BLAST of SMED30009435 vs. Planmine SMEST
Match: SMESG000055435.1 (SMESG000055435.1)

HSP 1 Score: 173.711 bits (439), Expect = 1.125e-54
Identity = 81/145 (55.86%), Postives = 107/145 (73.79%), Query Frame = -2
Query:   73 MMNTVELLTGVMKRRLKEDPGLRFSLLPIYASYRFEPRLQCLNNSIVLNVDNYDYSHRDIKYAVENNLSICRPVKGKNYIKMIQFLPYKLQFYWIHDLKNRWIVQLESETFMLSLIDTGLKVKGHYYLVRDYMEIQRIEIQLWRE 507
            M  T+E + GV++ RL +DP L+  LLP Y+ Y+ EP ++ L  S+ +NVD+Y YSHRDIK AV+N+LS   P     Y+KMIQFLPYKL+F+WI +++NRWI+QL  E  M  LI+TGLK+ G  +LVRDYM+IQR EIQLWRE
Sbjct:    1 MSRTIETIKGVLENRLIKDPALKGLLLPTYSGYKVEPEIRPLPLSVFINVDSYKYSHRDIKIAVDNSLSAIMPSNDNKYVKMIQFLPYKLEFHWISEIENRWIIQLNDENHMQMLIETGLKILGQNHLVRDYMDIQRFEIQLWRE 145          
BLAST of SMED30009435 vs. Planmine SMEST
Match: SMESG000022895.1 (SMESG000022895.1)

HSP 1 Score: 159.073 bits (401), Expect = 1.508e-48
Identity = 71/152 (46.71%), Postives = 103/152 (67.76%), Query Frame = -2
Query:   76 EHSPEYTSMMNTVELLTGVMKRRLKEDPGLRFSLLPIYASYRFEPRLQCLNNSIVLNVDNYDYSHRDIKYAVENNLSICRPVKGKNYIKMIQFLPYKLQFYWIHDLKNRWIVQLESETFMLSLIDTGLKVKGHYYLVRDYMEIQRIEIQLWR 531
            E S E   + +  E LTGV+K+R+ ED  L+   LPIY+++RFEPR + L  ++V  V +Y  SH +++YA E  L+   P  G++ IKMIQF+PY++Q +WIHDL+NRWI+QL+ E     LID GL +     +VRD+ E+QR+EIQ+WR
Sbjct:   19 EKSEEMKDLHSAFESLTGVLKKRISEDEHLKQMALPIYSTFRFEPRYRPLETTVVFQVKDYSLSHSNVRYATETTLARANPKWGRHTIKMIQFIPYRIQIFWIHDLQNRWIIQLDREAAKQYLIDNGLSIFDRKIVVRDFSELQRLEIQMWR 170          
The following BLAST results are available for this feature:
BLAST of SMED30009435 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 SMED30009435 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 SMED30009435 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 SMED30009435 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 SMED30009435 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 SMED30009435 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 SMED30009435 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 SMED30009435 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 SMED30009435 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 SMED30009435 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 SMED30009435 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 SMED30009435 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 SMED30009435 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 SMED30009435 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000071611.12.302e-136100.00SMESG000071611.1[more]
SMESG000071612.12.892e-8765.00SMESG000071612.1[more]
SMESG000055435.11.125e-5455.86SMESG000055435.1[more]
SMESG000022895.11.508e-4846.71SMESG000022895.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009435 ID=SMED30009435|Name=SMED30009435|organism=Schmidtea mediterranea sexual|type=transcript|length=751bp
ATGCGGACTTAAATTCTGCTAAATAATTGGACTATATGAAAATTTTGAAA
TAGCTAAATCGCTTCTTTTAGCCTCTCTCCATAATTGGATTTCTATTCTT
TGAATTTCCATATAATCTCGAACTAAATAATAATGTCCTTTCACTTTTAA
TCCAGTATCAATCAGGGATAGCATGAATGTCTCTGATTCTAATTGGACAA
TCCATCGATTTTTCAGATCGTGTATCCAATAAAATTGCAGCTTGTATGGT
AAAAATTGAATCATTTTTATGTAATTTTTACCTTTTACGGGTCTGCAAAT
TGAAAGATTATTTTCAACAGCATATTTGATATCACGATGAGAGTAATCGT
AATTGTCAACGTTGAGGACTATAGAATTATTCAAACATTGTAACCTTGGC
TCAAATCTATAACTTGCATAAATTGGTAAAAGTGAGAATCTTAATCCGGG
ATCTTCTTTCAATCGCCGCTTCATGACACCAGTTAATAATTCAACTGTAT
TCATCATTGAGGTATATTCAGGAGAATGTTCTTCGATAAGGCTTTTACTT
CGAATTTGATTAACCTGCTTCATGGGTTTTGTTTGTTTGTTTTCTCCTTG
TTCCTTAATCTCCTTAGAAATTGAATGTTCAATATTGGAGCTCCTTCTTG
AAATTTGCATTTCACCAATTGTGTTTGTTAAGATTAAATTGAATTCTTTT
AATTAGTGAGTCAAATTAATAATATATTAGGATTAATTGTTTGACTTTGT
T
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protein sequence of SMED30009435-orf-1

>SMED30009435-orf-1 ID=SMED30009435-orf-1|Name=SMED30009435-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=214bp
MQISRRSSNIEHSISKEIKEQGENKQTKPMKQVNQIRSKSLIEEHSPEYT
SMMNTVELLTGVMKRRLKEDPGLRFSLLPIYASYRFEPRLQCLNNSIVLN
VDNYDYSHRDIKYAVENNLSICRPVKGKNYIKMIQFLPYKLQFYWIHDLK
NRWIVQLESETFMLSLIDTGLKVKGHYYLVRDYMEIQRIEIQLWREAKRS
DLAISKFSYSPII*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR013809ENTH