Neuropeptide-3

Overview
NameNeuropeptide-3
Smed IDSMED30031540
Length (bp)295
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 Neuropeptide-3 (SMED30031540) t-SNE clustered cells

Violin plots show distribution of expression levels for Neuropeptide-3 (SMED30031540) 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 Neuropeptide-3 (SMED30031540) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Neuropeptide-3 (SMED30031540) 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



SMED30031540

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30031540SMESG000014460.1 SmedASXL_079293SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30031540SMESG000014460.1 dd_Smed_v4_798_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30031540SMESG000014460.1 dd_Smed_v4_798_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30031540SMESG000014460.1 dd_Smed_v4_798_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30031540SMESG000014460.1 dd_Smed_v4_798_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30031540SMESG000014460.1 dd_Smed_v4_798_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30031540SMESG000014460.1 dd_Smed_v4_798_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031540SMESG000014460.1 Contig52797newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031540SMESG000014460.1 Contig52797uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30031540SMESG000014460.1 dd_Smed_v6_798_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
cephalic gangliaSMED30031540SMESG000014460.1 BK007025smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30031540SMESG000014460.1 BK007025smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30031540SMESG000014460.1 BK007025smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
eyeSMED30031540SMESG000014460.1 BK007025.1smed_ncbi_20200123PMID:26884331
Ong et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Neuropeptide-3 vs. TrEMBL
Match: E3CTK0 (1020HH-2 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 155.606 bits (392), Expect = 1.276e-47
Identity = 77/77 (100.00%), Postives = 77/77 (100.00%), Query Frame = 1 
Query:   16 MIMKTVIVFFISVLLYGLLSISEAVPRSAENLRTYDSLLEELNDYDPIYKRQSYLTGGIRYKKQVPGKRYLTGGIRY 246
            MIMKTVIVFFISVLLYGLLSISEAVPRSAENLRTYDSLLEELNDYDPIYKRQSYLTGGIRYKKQVPGKRYLTGGIRY
Sbjct:    1 MIMKTVIVFFISVLLYGLLSISEAVPRSAENLRTYDSLLEELNDYDPIYKRQSYLTGGIRYKKQVPGKRYLTGGIRY 77
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BLAST of Neuropeptide-3 vs. TrEMBL
Match: A0A193PE63 (Neuropeptide-3 (Fragment) OS=Dugesia japonica OX=6161 GN=DjNp3 PE=2 SV=1)

HSP 1 Score: 105.531 bits (262), Expect = 7.298e-28
Identity = 48/64 (75.00%), Postives = 57/64 (89.06%), Query Frame = 1 
Query:   40 FFISVLLYGLLSISEAVPRSAENLRTYDSLLEELNDYDPIYKRQSYLTGGIRYKKQVPGKRYLT 231
            FFIS + YGL S++EA+PR  +NLRTYDS+LEELN+Y+PIYKRQSYLTGGIRYKK+  GKRYLT
Sbjct:    1 FFISTIFYGLFSLTEALPRHGDNLRTYDSVLEELNNYEPIYKRQSYLTGGIRYKKRELGKRYLT 64
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BLAST of Neuropeptide-3 vs. Planmine SMEST
Match: SMESG000014460.1 (SMESG000014460.1)

HSP 1 Score: 155.606 bits (392), Expect = 3.548e-51
Identity = 77/77 (100.00%), Postives = 77/77 (100.00%), Query Frame = 1 
Query:   16 MIMKTVIVFFISVLLYGLLSISEAVPRSAENLRTYDSLLEELNDYDPIYKRQSYLTGGIRYKKQVPGKRYLTGGIRY 246
            MIMKTVIVFFISVLLYGLLSISEAVPRSAENLRTYDSLLEELNDYDPIYKRQSYLTGGIRYKKQVPGKRYLTGGIRY
Sbjct:    1 MIMKTVIVFFISVLLYGLLSISEAVPRSAENLRTYDSLLEELNDYDPIYKRQSYLTGGIRYKKQVPGKRYLTGGIRY 77
[Close]
BLAST of Neuropeptide-3 vs. Planmine SMEST
Match: SMESG000014460.1 (SMESG000014460.1)

HSP 1 Score: 151.754 bits (382), Expect = 1.200e-49
Identity = 75/75 (100.00%), Postives = 75/75 (100.00%), Query Frame = 1 
Query:   22 MKTVIVFFISVLLYGLLSISEAVPRSAENLRTYDSLLEELNDYDPIYKRQSYLTGGIRYKKQVPGKRYLTGGIRY 246
            MKTVIVFFISVLLYGLLSISEAVPRSAENLRTYDSLLEELNDYDPIYKRQSYLTGGIRYKKQVPGKRYLTGGIRY
Sbjct:    1 MKTVIVFFISVLLYGLLSISEAVPRSAENLRTYDSLLEELNDYDPIYKRQSYLTGGIRYKKQVPGKRYLTGGIRY 75
The following BLAST results are available for this feature:
BLAST of Neuropeptide-3 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 Neuropeptide-3 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 Neuropeptide-3 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 Neuropeptide-3 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 Neuropeptide-3 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 Neuropeptide-3 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 Neuropeptide-3 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 Neuropeptide-3 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
E3CTK01.276e-47100.001020HH-2 OS=Schmidtea mediterranea OX=79327 PE=2 S... [more]
A0A193PE637.298e-2875.00Neuropeptide-3 (Fragment) OS=Dugesia japonica OX=6... [more]
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BLAST of Neuropeptide-3 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 Neuropeptide-3 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 Neuropeptide-3 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 Neuropeptide-3 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 Neuropeptide-3 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 Neuropeptide-3 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000014460.13.548e-51100.00SMESG000014460.1[more]
SMESG000014460.11.200e-49100.00SMESG000014460.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031540 ID=SMED30031540|Name=Neuropeptide-3|organism=Schmidtea mediterranea sexual|type=transcript|length=295bp
GCCGTTGCAAAGAAAATGATAATGAAAACTGTAATAGTATTTTTCATAAG
CGTTCTCTTATACGGATTACTTTCTATATCAGAAGCTGTGCCTAGATCTG
CGGAAAACTTAAGAACATATGATTCTTTGTTGGAAGAATTGAATGACTAT
GATCCAATATACAAAAGACAAAGCTATTTGACTGGCGGTATTCGATATAA
AAAGCAAGTTCCAGGCAAAAGATATCTTACTGGAGGAATAAGATACTAAA
TTTCATCTCATAATTTTGTATTGATATTAATAAAAGATTTTGGTT
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Aliases
The feature 'Neuropeptide-3' has the following synonyms
Synonym
1020HH-2
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000036eye
PLANA:0000044cephalic ganglia
PLANA:0000097ventral nerve cord
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000420parapharyngeal region
Vocabulary: biological process
TermDefinition
GO:0007218neuropeptide signaling pathway
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 12..31