SMED30031132

Overview
NameSMED30031132
Smed IDSMED30031132
Length (bp)386
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 SMED30031132 (SMED30031132) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031132 (SMED30031132) 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 SMED30031132 (SMED30031132) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031132 (SMED30031132) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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




SMED30031132

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 systemSMED30031132SMESG000076421.1 dd_Smed_v4_1746_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30031132SMESG000076421.1 dd_Smed_v4_1746_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30031132SMESG000076421.1 dd_Smed_v4_1746_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
Homology
BLAST of SMED30031132 vs. UniProt/SwissProt
Match: sp|P41334|NPF_ARTTR (Neuropeptide F OS=Arthurdendyus triangulatus OX=132421 PE=1 SV=1)

HSP 1 Score: 50.8322 bits (120), Expect = 1.079e-8
Identity = 23/36 (63.89%), Postives = 29/36 (80.56%), Query Frame = -2
Query:  134 KVVYLKTRDHFRSDEDYESYLRKVQKYIQLYGRPRF 241
            KVV+L+ R  F S+++Y+ YLR V KYIQLYGRPRF
Sbjct:    1 KVVHLRPRSSFSSEDEYQIYLRNVSKYIQLYGRPRF 36          
BLAST of SMED30031132 vs. TrEMBL
Match: E3CTL4 (Neuropeptide Y prohormone-4 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 170.244 bits (430), Expect = 1.039e-52
Identity = 80/90 (88.89%), Postives = 85/90 (94.44%), Query Frame = -2
Query:   62 MKFCCAPRLSVIFLAVFIFGISLTAMEVKRKVVYLKTRDHFRSDEDYESYLRKVQKYIQLYGRPRFGKRQIDWYDMKNFEGNENYDS*AF 331
            MKFCCAPRLSV+FLAVFIFGISLTA EVKRKVVYLK+R+HFRSDEDY SYLRKVQKYIQLYGRPRFGKRQ +WYDMKN+EGNENYDS  F
Sbjct:    1 MKFCCAPRLSVLFLAVFIFGISLTAKEVKRKVVYLKSRNHFRSDEDYVSYLRKVQKYIQLYGRPRFGKRQTNWYDMKNYEGNENYDSYTF 90          
BLAST of SMED30031132 vs. Planmine SMEST
Match: SMESG000076421.1 (SMESG000076421.1)

HSP 1 Score: 210.305 bits (534), Expect = 7.027e-72
Identity = 100/100 (100.00%), Postives = 100/100 (100.00%), Query Frame = -2
Query:   74 MVKFWHCQRKIIYQMKFCCAPRLSVIFLAVFIFGISLTAMEVKRKVVYLKTRDHFRSDEDYESYLRKVQKYIQLYGRPRFGKRQIDWYDMKNFEGNENYD 373
            MVKFWHCQRKIIYQMKFCCAPRLSVIFLAVFIFGISLTAMEVKRKVVYLKTRDHFRSDEDYESYLRKVQKYIQLYGRPRFGKRQIDWYDMKNFEGNENYD
Sbjct:    1 MVKFWHCQRKIIYQMKFCCAPRLSVIFLAVFIFGISLTAMEVKRKVVYLKTRDHFRSDEDYESYLRKVQKYIQLYGRPRFGKRQIDWYDMKNFEGNENYD 100          
BLAST of SMED30031132 vs. Planmine SMEST
Match: SMESG000030037.1 (SMESG000030037.1)

HSP 1 Score: 192.586 bits (488), Expect = 5.882e-65
Identity = 92/104 (88.46%), Postives = 97/104 (93.27%), Query Frame = -2
Query:   62 MVKFWHCQRKIIYQMKFCCAPRLSVIFLAVFIFGISLTAMEVKRKVVYLKTRDHFRSDEDYESYLRKVQKYIQLYGRPRFGKRQIDWYDMKNFEGNENYDS*AF 373
            MVKF H QRK IYQMKFCCAPRLSV+FLAVFIFGISLTA EVKRKVVYLK+R+HFRSDEDYESYLRKVQKYIQLYGRPRFGKRQ +WYDMKN+EGNENYDS  F
Sbjct:    1 MVKFRHWQRKTIYQMKFCCAPRLSVLFLAVFIFGISLTAKEVKRKVVYLKSRNHFRSDEDYESYLRKVQKYIQLYGRPRFGKRQTNWYDMKNYEGNENYDSYTF 104          
BLAST of SMED30031132 vs. Planmine SMEST
Match: SMESG000011618.1 (SMESG000011618.1)

HSP 1 Score: 45.4394 bits (106), Expect = 2.492e-7
Identity = 20/60 (33.33%), Postives = 36/60 (60.00%), Query Frame = -2
Query:  122 VIFLAVFIFGISLTAMEVKRKVVYLKTRDHFRSDEDYESYLRKVQKYIQLYGRPRFGKRQ 301
            V+  A+F   + ++A + +  +++ K  ++   D D + YL+ +  + Q YGRPRFGKRQ
Sbjct:   11 VMICALFCQIVQISANKDELDILFKKRNNNQLDDPDIQQYLQDLNNFYQFYGRPRFGKRQ 70          
The following BLAST results are available for this feature:
BLAST of SMED30031132 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 SMED30031132 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 SMED30031132 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 SMED30031132 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 SMED30031132 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 SMED30031132 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 SMED30031132 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|P41334|NPF_ARTTR1.079e-863.89Neuropeptide F OS=Arthurdendyus triangulatus OX=13... [more]
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BLAST of SMED30031132 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
E3CTL41.039e-5288.89Neuropeptide Y prohormone-4 OS=Schmidtea mediterra... [more]
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BLAST of SMED30031132 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 SMED30031132 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 SMED30031132 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 SMED30031132 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 SMED30031132 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 SMED30031132 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000076421.17.027e-72100.00SMESG000076421.1[more]
SMESG000030037.15.882e-6588.46SMESG000030037.1[more]
SMESG000011618.12.492e-733.33SMESG000011618.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031132 ID=SMED30031132|Name=SMED30031132|organism=Schmidtea mediterranea sexual|type=transcript|length=386bp
TTTTTTTAAGACAAACTAAATTGTATTCAGCAAAAGGTCCATTCATTCTC
AACCACCACTAAAATGCTTAAGAATCGTAGTTTTCATTTCCTTCGAAATT
CTTCATATCGTACCAGTCAATTTGTCTCTTACCAAACCTTGGTCGGCCAT
ATAATTGGATGTATTTCTGGACCTTTCTCAAATACGATTCATAATCTTCA
TCTGACCGGAAGTGATCTCTTGTTTTCAAGTAAACTACTTTTCGCTTGAC
CTCCATCGCAGTGAGACTGATGCCAAATATGAAAACAGCCAGAAAAATAA
CAGATAAACGGGGGGCACAACAAAACTTCATTTGATAAATTATTTTCCTC
TGACAATGCCAAAATTTGACCATTTATATAACACGG
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protein sequence of SMED30031132-orf-1

>SMED30031132-orf-1 ID=SMED30031132-orf-1|Name=SMED30031132-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
MVKFWHCQRKIIYQMKFCCAPRLSVIFLAVFIFGISLTAMEVKRKVVYLK
TRDHFRSDEDYESYLRKVQKYIQLYGRPRFGKRQIDWYDMKNFEGNENYD
S*
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Aliases
The feature 'SMED30031132' has the following synonyms
Synonym
npy-4
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR001955Pancreatic_hormone-like
IPR020392Pancreatic_hormone-like_CS
Vocabulary: molecular function
TermDefinition
GO:0005179hormone activity
Vocabulary: cellular component
TermDefinition
GO:0005576extracellular region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001955Pancreatic hormone-likeSMARTSM00309PAH_1coord: 44..80
e-value: 4.5E-5
score: 32.9
IPR001955Pancreatic hormone-likePROSITEPS50276PANCREATIC_HORMONE_2coord: 57..80
score: 9.975
IPR020392Pancreatic hormone-like, conserved sitePROSITEPS00265PANCREATIC_HORMONE_1coord: 64..80
NoneNo IPR availableTMHMMTMhelixcoord: 20..42