SMED30011163

Overview
NameSMED30011163
Smed IDSMED30011163
Length (bp)465
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30011163

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30011163h1SMcG0005925 dd_Smed_v4_79849_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011163h1SMcG0005925 dd_Smed_v4_79849_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30011163h1SMcG0005925 dd_Smed_v4_79849_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30011163h1SMcG0005925 Contig9987newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30011163h1SMcG0005925 Contig9987uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30011163h1SMcG0005925 Contig17639uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30011163h1SMcG0005925 Contig17639newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011163 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006146:5167..7333 +2319
v31.024153:2940..5124 +2301
Homology
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BLAST of SMED30011163 vs. Planmine SMEST
Match: SMESG000031073.1 (SMESG000031073.1)

HSP 1 Score: 305.449 bits (781), Expect = 9.470e-97
Identity = 149/150 (99.33%), Postives = 150/150 (100.00%), Query Frame = 2 
Query:   14 MSTFLELSKLFDQNLDIKNVDNLFREIAECSKAMERDIDKINYALGPIKMELSIIKQFSEDQIRSQSAAIEKKIRNFMKEIKSLKKFIRNKNQLISEILDKLEIHCKLAQEGYENVKYNNVGTEGTSAPTSDENLFYTNLTNAKRLIANL 463
            MSTFLELSKLFDQNLDIKNV+NLFREIAECSKAMERDIDKINYALGPIKMELSIIKQFSEDQIRSQSAAIEKKIRNFMKEIKSLKKFIRNKNQLISEILDKLEIHCKLAQEGYENVKYNNVGTEGTSAPTSDENLFYTNLTNAKRLIANL
Sbjct:    1 MSTFLELSKLFDQNLDIKNVNNLFREIAECSKAMERDIDKINYALGPIKMELSIIKQFSEDQIRSQSAAIEKKIRNFMKEIKSLKKFIRNKNQLISEILDKLEIHCKLAQEGYENVKYNNVGTEGTSAPTSDENLFYTNLTNAKRLIANL 150
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BLAST of SMED30011163 vs. Planmine SMEST
Match: SMESG000031073.1 (SMESG000031073.1)

HSP 1 Score: 298.901 bits (764), Expect = 2.123e-94
Identity = 148/150 (98.67%), Postives = 149/150 (99.33%), Query Frame = 2 
Query:   14 MSTFLELSKLFDQNLDIKNVDNLFREIAECSKAMERDIDKINYALGPIKMELSIIKQFSEDQIRSQSAAIEKKIRNFMKEIKSLKKFIRNKNQLISEILDKLEIHCKLAQEGYENVKYNNVGTEGTSAPTSDENLFYTNLTNAKRLIANL 463
            MSTFLELSKLFDQNLDIKNV+NLFREIAECSKAMERDIDKINYALGPIKMELSIIKQFSEDQIRSQSAAIEKKIRNFMKEIKSLKKFIRNKNQLISEILDKLEIHCKLAQEGYENVKYNN GTEGTSAPTSDENLFYTNLTNAKRLIANL
Sbjct:    1 MSTFLELSKLFDQNLDIKNVNNLFREIAECSKAMERDIDKINYALGPIKMELSIIKQFSEDQIRSQSAAIEKKIRNFMKEIKSLKKFIRNKNQLISEILDKLEIHCKLAQEGYENVKYNN-GTEGTSAPTSDENLFYTNLTNAKRLIANL 149
[Close]
BLAST of SMED30011163 vs. Planmine SMEST
Match: SMESG000031073.1 (SMESG000031073.1)

HSP 1 Score: 241.121 bits (614), Expect = 2.978e-74
Identity = 117/117 (100.00%), Postives = 117/117 (100.00%), Query Frame = 2 
Query:  113 MERDIDKINYALGPIKMELSIIKQFSEDQIRSQSAAIEKKIRNFMKEIKSLKKFIRNKNQLISEILDKLEIHCKLAQEGYENVKYNNVGTEGTSAPTSDENLFYTNLTNAKRLIANL 463
            MERDIDKINYALGPIKMELSIIKQFSEDQIRSQSAAIEKKIRNFMKEIKSLKKFIRNKNQLISEILDKLEIHCKLAQEGYENVKYNNVGTEGTSAPTSDENLFYTNLTNAKRLIANL
Sbjct:    1 MERDIDKINYALGPIKMELSIIKQFSEDQIRSQSAAIEKKIRNFMKEIKSLKKFIRNKNQLISEILDKLEIHCKLAQEGYENVKYNNVGTEGTSAPTSDENLFYTNLTNAKRLIANL 117
The following BLAST results are available for this feature:
BLAST of SMED30011163 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 SMED30011163 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 SMED30011163 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 SMED30011163 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 SMED30011163 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 SMED30011163 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 SMED30011163 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 SMED30011163 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 SMED30011163 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 SMED30011163 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 SMED30011163 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 SMED30011163 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 SMED30011163 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 SMED30011163 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000031073.19.470e-9799.33SMESG000031073.1[more]
SMESG000031073.12.123e-9498.67SMESG000031073.1[more]
SMESG000031073.12.978e-74100.00SMESG000031073.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011163 ID=SMED30011163|Name=SMED30011163|organism=Schmidtea mediterranea sexual|type=transcript|length=465bp
CAAATCTTTCTCAATGTCAACATTTTTAGAGCTTTCTAAATTATTTGACC
AAAATTTAGATATTAAAAATGTGGATAATTTATTTCGAGAAATTGCTGAA
TGTAGCAAGGCAATGGAGCGTGACATAGATAAAATAAATTATGCCTTGGG
TCCAATAAAAATGGAATTATCAATCATTAAACAGTTTTCGGAGGATCAGA
TTCGTAGTCAATCAGCCGCTATTGAAAAAAAAATTCGAAATTTCATGAAA
GAAATAAAAAGCCTAAAAAAATTCATTCGAAACAAAAACCAACTGATTTC
AGAAATTTTAGACAAGCTCGAAATCCATTGCAAACTGGCACAGGAGGGTT
ATGAAAATGTAAAATATAATAATGTAGGTACTGAAGGAACCTCAGCACCG
ACCTCTGATGAAAATCTATTCTATACTAATCTAACAAATGCCAAAAGATT
AATTGCAAACTTGAC
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protein sequence of SMED30011163-orf-1

>SMED30011163-orf-1 ID=SMED30011163-orf-1|Name=SMED30011163-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=154bp
KSFSMSTFLELSKLFDQNLDIKNVDNLFREIAECSKAMERDIDKINYALG
PIKMELSIIKQFSEDQIRSQSAAIEKKIRNFMKEIKSLKKFIRNKNQLIS
EILDKLEIHCKLAQEGYENVKYNNVGTEGTSAPTSDENLFYTNLTNAKRL
IANL
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