SMED30012303

Overview
NameSMED30012303
Smed IDSMED30012303
Length (bp)261
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



SMED30012303

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30012303SMESG000010464.1 dd_Smed_v4_7906_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30012303SMESG000010599.1 Contig31350newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30012303SMESG000010599.1 Contig31350uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30012303SMESG000010546.1 SMESG000010469.1 SMESG000010468.1 SMESG000010467.1 SMESG000010464.1 SMESG000010218.1 SMESG000010465.1 Contig16092newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30012303SMESG000010546.1 SMESG000010469.1 SMESG000010468.1 SMESG000010467.1 SMESG000010464.1 SMESG000010218.1 SMESG000010465.1 Contig16092uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30012303SMESG000010464.1 dd_Smed_v4_7906_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30012303 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002674:22438..22694 -1231
v31.001170:78985..79241 +1204
v31.003425:17032..17288 +1024
v31.002674:43854..44110 +1024
v31.000505:126036..126292 +1024
v31.000505:112228..112484 -1024
v31.004644:26259..26515 +1015
v31.001682:34627..34883 -1006
Homology
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BLAST of SMED30012303 vs. Planmine SMEST
Match: SMESG000010599.1 (SMESG000010599.1)

HSP 1 Score: 73.9442 bits (180), Expect = 2.965e-29
Identity = 33/37 (89.19%), Postives = 37/37 (100.00%), Query Frame = -1 
Query:    1 KVNFTILHTAISDNDADMVQYILSHPNIVDLNTNNEV 111
            KVNFTILHTAI+DNDADMVQY+L+HPNIVDLNTNNE+
Sbjct:  466 KVNFTILHTAIADNDADMVQYVLNHPNIVDLNTNNEI 502

HSP 2 Score: 70.4774 bits (171), Expect = 2.965e-29
Identity = 34/36 (94.44%), Postives = 36/36 (100.00%), Query Frame = -3 
Query:  152 SLWSKAIDKAKEKGFVEIQEEIQERMILMESRQKVH 259
            SLWSKAIDKAKEKGF+EIQEEIQERMILMESRQKV+
Sbjct:  433 SLWSKAIDKAKEKGFLEIQEEIQERMILMESRQKVN 468
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BLAST of SMED30012303 vs. Planmine SMEST
Match: SMESG000010464.1 (SMESG000010464.1)

HSP 1 Score: 71.2478 bits (173), Expect = 1.006e-28
Identity = 34/36 (94.44%), Postives = 36/36 (100.00%), Query Frame = -3 
Query:  152 SLWSKAIDKAKEKGFVEIQEEIQERMILMESRQKVH 259
            SLWSKAIDKAKEKGF+EIQEEIQERMILMESRQKV+
Sbjct:  365 SLWSKAIDKAKEKGFLEIQEEIQERMILMESRQKVN 400

HSP 2 Score: 71.2478 bits (173), Expect = 1.006e-28
Identity = 33/37 (89.19%), Postives = 37/37 (100.00%), Query Frame = -1 
Query:    1 KVNFTILHTAISDNDADMVQYILSHPNIVDLNTNNEV 111
            KVNFTILHTAI+DNDADMVQY+L+HPNIVDLNTNNE+
Sbjct:  398 KVNFTILHTAIADNDADMVQYVLNHPNIVDLNTNNEI 434
[Close]
BLAST of SMED30012303 vs. Planmine SMEST
Match: SMESG000010464.1 (SMESG000010464.1)

HSP 1 Score: 71.2478 bits (173), Expect = 1.196e-28
Identity = 34/36 (94.44%), Postives = 36/36 (100.00%), Query Frame = -3 
Query:  152 SLWSKAIDKAKEKGFVEIQEEIQERMILMESRQKVH 259
            SLWSKAIDKAKEKGF+EIQEEIQERMILMESRQKV+
Sbjct:  365 SLWSKAIDKAKEKGFLEIQEEIQERMILMESRQKVN 400

HSP 2 Score: 71.2478 bits (173), Expect = 1.196e-28
Identity = 33/37 (89.19%), Postives = 37/37 (100.00%), Query Frame = -1 
Query:    1 KVNFTILHTAISDNDADMVQYILSHPNIVDLNTNNEV 111
            KVNFTILHTAI+DNDADMVQY+L+HPNIVDLNTNNE+
Sbjct:  398 KVNFTILHTAIADNDADMVQYVLNHPNIVDLNTNNEI 434
[Close]
BLAST of SMED30012303 vs. Planmine SMEST
Match: SMESG000010218.1 (SMESG000010218.1)

HSP 1 Score: 73.559 bits (179), Expect = 2.830e-27
Identity = 34/36 (94.44%), Postives = 36/36 (100.00%), Query Frame = -1 
Query:    4 KVNFTILHTAISDNDADMVQYILSHPNIVDLNTNNE 111
            KVNFT+LHTAISDNDADMVQYIL+HPNIVDLNTNNE
Sbjct:  331 KVNFTVLHTAISDNDADMVQYILNHPNIVDLNTNNE 366

HSP 2 Score: 64.3142 bits (155), Expect = 2.830e-27
Identity = 30/36 (83.33%), Postives = 34/36 (94.44%), Query Frame = -3 
Query:  152 SLWSKAIDKAKEKGFVEIQEEIQERMILMESRQKVH 259
            SLW KAID AKEKGFVEIQEE+QERM+LMESR+KV+
Sbjct:  298 SLWIKAIDAAKEKGFVEIQEEMQERMLLMESRKKVN 333
[Close]
BLAST of SMED30012303 vs. Planmine SMEST
Match: SMESG000010218.1 (SMESG000010218.1)

HSP 1 Score: 74.3294 bits (181), Expect = 2.928e-27
Identity = 34/36 (94.44%), Postives = 36/36 (100.00%), Query Frame = -1 
Query:    4 KVNFTILHTAISDNDADMVQYILSHPNIVDLNTNNE 111
            KVNFT+LHTAISDNDADMVQYIL+HPNIVDLNTNNE
Sbjct:  331 KVNFTVLHTAISDNDADMVQYILNHPNIVDLNTNNE 366

HSP 2 Score: 63.5438 bits (153), Expect = 2.928e-27
Identity = 30/36 (83.33%), Postives = 34/36 (94.44%), Query Frame = -3 
Query:  152 SLWSKAIDKAKEKGFVEIQEEIQERMILMESRQKVH 259
            SLW KAID AKEKGFVEIQEE+QERM+LMESR+KV+
Sbjct:  298 SLWIKAIDAAKEKGFVEIQEEMQERMLLMESRKKVN 333
The following BLAST results are available for this feature:
BLAST of SMED30012303 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 SMED30012303 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 SMED30012303 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 SMED30012303 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 SMED30012303 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 SMED30012303 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 SMED30012303 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 SMED30012303 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 SMED30012303 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 SMED30012303 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 SMED30012303 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 SMED30012303 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 SMED30012303 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 SMED30012303 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000010599.12.965e-2989.19SMESG000010599.1[more]
SMESG000010464.11.006e-2894.44SMESG000010464.1[more]
SMESG000010464.11.196e-2894.44SMESG000010464.1[more]
SMESG000010218.12.830e-2794.44SMESG000010218.1[more]
SMESG000010218.12.928e-2794.44SMESG000010218.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012303 ID=SMED30012303|Name=SMED30012303|organism=Schmidtea mediterranea sexual|type=transcript|length=261bp
TACTTCATTATTTGTATTGAGATCAACAATATTCGGATGACTCAGGATAT
ATTGCACCATATCAGCATCATTATCGGAAATGGCTGTGTGCAATATTGTG
AAATTTACCTTCAGAATTAATAATATTAGTTATTGATTTTATGTGATTTT
GATGCACCTTTTGTCGAGATTCCATCAGAATCATTCTTTCTTGAATTTCT
TCTTGTATTTCCACGAACCCCTTTTCCTTTGCTTTGTCAATGGCCTTGCT
CCATAACGATC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000106ciliated epithelial cell
Vocabulary: INTERPRO
TermDefinition
IPR020683Ankyrin_rpt-contain_dom