SMED30034511

Overview
NameSMED30034511
Smed IDSMED30034511
Length (bp)414
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



SMED30034511

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30034511h1SMcG0007086 dd_Smed_v4_10182_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30034511h1SMcG0007086 dd_Smed_v4_10182_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30034511h1SMcG0007086 Contig4671GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30034511h1SMcG0007086 dd_Smed_v6_10182_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30034511h1SMcG0007086 OX_Smed_1.0.20349ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30034511 vs. Planmine SMEST
Match: SMESG000039356.1 (SMESG000039356.1)

HSP 1 Score: 72.4034 bits (176), Expect = 1.318e-17
Identity = 31/44 (70.45%), Postives = 34/44 (77.27%), Query Frame = 3 
Query:  144 CVNFVYQFTRN*CNATHIGRTPRHFCTRILGHCWLKGLANISEH 275
            C + VYQFT N CNAT+IG T RH CTR+L HC LKGL NISEH
Sbjct:  882 CSDLVYQFTCNGCNATYIGETSRHLCTRVLEHCRLKGLTNISEH 925

HSP 2 Score: 33.4982 bits (75), Expect = 1.318e-17
Identity = 15/20 (75.00%), Postives = 16/20 (80.00%), Query Frame = 2 
Query:   89 NLCKVRNMFINKSKPLIVLC 148
            N CK RNMFINKSKP + LC
Sbjct:  863 NSCKGRNMFINKSKPPVGLC 882
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BLAST of SMED30034511 vs. Planmine SMEST
Match: SMESG000007021.1 (SMESG000007021.1)

HSP 1 Score: 72.0182 bits (175), Expect = 2.969e-17
Identity = 31/44 (70.45%), Postives = 34/44 (77.27%), Query Frame = 3 
Query:  144 CVNFVYQFTRN*CNATHIGRTPRHFCTRILGHCWLKGLANISEH 275
            C + VYQFT N CNAT+IG T RH CTR+L HC LKGL NISEH
Sbjct:  330 CSDLVYQFTCNGCNATYIGETSRHLCTRVLEHCRLKGLTNISEH 373

HSP 2 Score: 32.3426 bits (72), Expect = 2.969e-17
Identity = 15/20 (75.00%), Postives = 16/20 (80.00%), Query Frame = 2 
Query:   89 NLCKVRNMFINKSKPLIVLC 148
            N CKVRNMFINKSK  + LC
Sbjct:  311 NSCKVRNMFINKSKTPVGLC 330
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BLAST of SMED30034511 vs. Planmine SMEST
Match: SMESG000029286.1 (SMESG000029286.1)

HSP 1 Score: 70.8626 bits (172), Expect = 7.916e-17
Identity = 42/75 (56.00%), Postives = 46/75 (61.33%), Query Frame = 3 
Query:  144 CVNFVYQFTRN*CNATHIGRTPRHFCTRILGHCWLKGLANISEHI**N----SHI---*FRQFYSRFNNY*ESVI 347
            C + VYQFT N CNAT+IG T RH CTR+L HC LKGL NISEH   N    S I    FR     FN+Y E VI
Sbjct:  284 CSDLVYQFTCNGCNATYIGETSRHLCTRVLEHCRLKGLTNISEH---NRGCKSDIGMSDFRILLRSFNSYWERVI 355

HSP 2 Score: 32.7278 bits (73), Expect = 7.916e-17
Identity = 15/20 (75.00%), Postives = 16/20 (80.00%), Query Frame = 2 
Query:   89 NLCKVRNMFINKSKPLIVLC 148
            N CKVRNMFINKSK  + LC
Sbjct:  265 NSCKVRNMFINKSKTPVGLC 284
[Close]
BLAST of SMED30034511 vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 74.7146 bits (182), Expect = 1.364e-16
Identity = 42/75 (56.00%), Postives = 45/75 (60.00%), Query Frame = 3 
Query:  144 CVNFVYQFTRN*CNATHIGRTPRHFCTRILGHCWLKGLANISEHI**N----SHI---*FRQFYSRFNNY*ESVI 347
            C + VY FT N CNAT+IG T RH CTR+L HC LKGL NISEH   N    S I    FR     FNNY E VI
Sbjct: 2843 CSDLVYHFTCNGCNATYIGETSRHLCTRVLDHCQLKGLTNISEH---NRGCKSEIGMSDFRILLRSFNNYWERVI 2914

HSP 2 Score: 27.7202 bits (60), Expect = 1.364e-16
Identity = 12/22 (54.55%), Postives = 16/22 (72.73%), Query Frame = 1 
Query:    7 EPKFPLIFP*SKGFKYIKRKVS 72
            EPK+ L+ P S+GF   KRK+S
Sbjct: 2790 EPKYVLVLPYSEGFTNYKRKLS 2811
[Close]
BLAST of SMED30034511 vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 74.7146 bits (182), Expect = 1.375e-16
Identity = 42/75 (56.00%), Postives = 45/75 (60.00%), Query Frame = 3 
Query:  144 CVNFVYQFTRN*CNATHIGRTPRHFCTRILGHCWLKGLANISEHI**N----SHI---*FRQFYSRFNNY*ESVI 347
            C + VY FT N CNAT+IG T RH CTR+L HC LKGL NISEH   N    S I    FR     FNNY E VI
Sbjct: 1886 CSDLVYHFTCNGCNATYIGETSRHLCTRVLDHCQLKGLTNISEH---NRGCKSEIGMSDFRILLRSFNNYWERVI 1957

HSP 2 Score: 27.7202 bits (60), Expect = 1.375e-16
Identity = 12/22 (54.55%), Postives = 16/22 (72.73%), Query Frame = 1 
Query:    7 EPKFPLIFP*SKGFKYIKRKVS 72
            EPK+ L+ P S+GF   KRK+S
Sbjct: 1833 EPKYVLVLPYSEGFTNYKRKLS 1854
The following BLAST results are available for this feature:
BLAST of SMED30034511 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 SMED30034511 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 SMED30034511 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 SMED30034511 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 SMED30034511 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 SMED30034511 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 SMED30034511 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 SMED30034511 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 SMED30034511 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 SMED30034511 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 SMED30034511 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 SMED30034511 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 SMED30034511 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 SMED30034511 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000039356.11.318e-1770.45SMESG000039356.1[more]
SMESG000007021.12.969e-1770.45SMESG000007021.1[more]
SMESG000029286.17.916e-1756.00SMESG000029286.1[more]
SMESG000050479.11.364e-1656.00SMESG000050479.1[more]
SMESG000050479.11.375e-1656.00SMESG000050479.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034511 ID=SMED30034511|Name=SMED30034511|organism=Schmidtea mediterranea sexual|type=transcript|length=414bp
AATAATGAGCCTAAATTTCCGTTGATATTTCCTTAGTCGAAAGGCTTTAA
ATACATTAAGAGAAAGGTAAGTAATATAAACTCGTTTAAATTTGTGTAAG
GTACGCAATATGTTCATTAATAAGTCAAAACCTCTGATTGTATTGTGTGA
ATTTTGTTTATCAATTTACACGTAATTGATGTAATGCCACACATATTGGA
CGGACTCCCCGTCATTTCTGTACTCGAATTCTAGGTCATTGTTGGTTGAA
GGGATTGGCCAATATCAGTGAGCACATTTAGTAAAATAGTCATATCTGAT
TCAGACAATTTTACTCACGATTTAATAATTATTAGGAAAGTGTTATATAT
GTGAGGCATTGTTGATAAGGTCGTCATTGGATCCAAATATAAATGTGTAA
AATGCAATGAGAAC
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