Neuropeptide-42

Overview
NameNeuropeptide-42
Smed IDSMED30029782
Length (bp)591
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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-42 (SMED30029782) t-SNE clustered cells

Violin plots show distribution of expression levels for Neuropeptide-42 (SMED30029782) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30029782

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30029782 SmedASXL_079573SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30029782 SmedASXL_079573SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
cephalic gangliaSMED30029782 GU295177smed_ncbi_20240424PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30029782 GU295177smed_ncbi_20240424PMID:20967238
Collins JJ et al., 2010		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-42 vs. TrEMBL
Match: E3T7T9 (Secreted peptide prohormone 6 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 126.716 bits (317), Expect = 9.213e-35
Identity = 63/63 (100.00%), Postives = 63/63 (100.00%), Query Frame = 3 
Query:  312 MIKIRILMSVLLFMAICLAAGLAEIDKRIPGIGFNRNFAIYKRMLEKRLIDPMTFGYGFSNLK 500
            MIKIRILMSVLLFMAICLAAGLAEIDKRIPGIGFNRNFAIYKRMLEKRLIDPMTFGYGFSNLK
Sbjct:    1 MIKIRILMSVLLFMAICLAAGLAEIDKRIPGIGFNRNFAIYKRMLEKRLIDPMTFGYGFSNLK 63
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BLAST of Neuropeptide-42 vs. TrEMBL
Match: E3T7U0 (Secreted peptide prohormone 7 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 78.9518 bits (193), Expect = 4.282e-16
Identity = 34/60 (56.67%), Postives = 47/60 (78.33%), Query Frame = 3 
Query:  321 IRILMSVLLFMAICLAAGLAEIDKRIPGIGFNRNFAIYKRMLEKRLIDPMTFGYGFSNLK 500
            ++ ++S+ + + +C+   ++EIDKR  G GFNRN  +YKRMLEKRLIDPMTFG GF+NLK
Sbjct:    1 MKFIISLFVVLFLCVVMAMSEIDKRTVGFGFNRNLHLYKRMLEKRLIDPMTFGSGFANLK 60
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BLAST of Neuropeptide-42 vs. TrEMBL
Match: E3T7U3 (Secreted peptide prohormone 8 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 77.411 bits (189), Expect = 1.781e-15
Identity = 37/62 (59.68%), Postives = 48/62 (77.42%), Query Frame = 3 
Query:  315 IKIRILMSVLLFMAICLAAGLAEIDKRIPGIGFNRNFAIYKRMLEKRLIDPMTFGYGFSNLK 500
            +KI IL+++  F+A+C    L E++KR  G GFNRN  +YKRMLEKRLIDPMTFG GF+NL+
Sbjct:    1 MKIIILLAI--FLAVCAFEALGEVEKRTMGFGFNRNMLLYKRMLEKRLIDPMTFGSGFANLR 60
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BLAST of Neuropeptide-42 vs. TrEMBL
Match: A0A193PE78 (Neuropeptide-42 (Fragment) OS=Dugesia japonica OX=6161 GN=DjNp42 PE=2 SV=1)

HSP 1 Score: 57.3806 bits (137), Expect = 4.558e-8
Identity = 25/42 (59.52%), Postives = 30/42 (71.43%), Query Frame = 3 
Query:  360 CLAAGLAEIDKRIPGIGFNRNFAIYKRMLEKRLIDPMTFGYG 485
            C    L E++KR  G G N N+ +YKR+LEKRLIDPMTFG G
Sbjct:    2 CAMGALCELEKRTMGFGLNSNYRLYKRLLEKRLIDPMTFGSG 43
[Close]
BLAST of Neuropeptide-42 vs. TrEMBL
Match: E3CTK1 (Secreted peptide prohormone-9 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 53.5286 bits (127), Expect = 1.821e-6
Identity = 26/56 (46.43%), Postives = 37/56 (66.07%), Query Frame = 3 
Query:  330 LMSVLLFMAICLAAGLAEIDKRIPGIGFNRNFAIYKRMLEKRLIDPMTFGYGFSNL 497
            L+ +L+   +CLA     + KR   + +N  + +YKR +EKRLIDP+TFG GFSNL
Sbjct:    4 LIILLIVALVCLANVCCGVQKR--SLPYNPEYELYKRFVEKRLIDPLTFGSGFSNL 57
The following BLAST results are available for this feature:
BLAST of Neuropeptide-42 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-42 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-42 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-42 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-42 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-42 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-42 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-42 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
E3T7T99.213e-35100.00Secreted peptide prohormone 6 OS=Schmidtea mediter... [more]
E3T7U04.282e-1656.67Secreted peptide prohormone 7 OS=Schmidtea mediter... [more]
E3T7U31.781e-1559.68Secreted peptide prohormone 8 OS=Schmidtea mediter... [more]
A0A193PE784.558e-859.52Neuropeptide-42 (Fragment) OS=Dugesia japonica OX=... [more]
E3CTK11.821e-646.43Secreted peptide prohormone-9 OS=Schmidtea mediter... [more]
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BLAST of Neuropeptide-42 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-42 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-42 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-42 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-42 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-42 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029782 ID=SMED30029782|Name=Neuropeptide-42|organism=Schmidtea mediterranea sexual|type=transcript|length=591bp
GCAGTTATTATTACTAGGAAAAAAGTAAACATTTATAAAACTCAGTTCAC
GCATTTGCTCCCAGTCACACAATGAAAGAATCCGGCAGTGAGATAAAAAA
AGATATTAGTTAATGCAAATGGCCATTTAAACAGTTGCGAAACTGAAGAA
ACAAGATAATTTCCATGAAATTTTCATTCATTCATTCATTCCCTTGATTG
AGAAATCTTTCAAACTCAGACGAAATCCGCGCCGCCGGCCATTAAATTCA
TTAACTAATTGCCTATTCTTTCTATATAAATTAGGTAATTCCTGAGAAGG
GCATTATCAACATGATCAAGATCAGAATTTTAATGTCGGTCCTCTTATTC
ATGGCAATTTGTCTGGCTGCCGGACTCGCGGAAATTGACAAACGGATTCC
CGGAATCGGATTCAACAGGAACTTCGCAATTTATAAACGGATGCTGGAGA
AACGCCTTATAGATCCAATGACATTCGGATACGGGTTTTCCAATCTGAAA
TGATGAACTTGGGTCCTTTGATATTTGGTTTATTTTCCATTAAATTTGTT
GTCAAAATTCTTTTGTTCAATAAAAATATATAAAATTAAAA
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Aliases
The feature 'Neuropeptide-42' has the following synonyms
Synonym
spp-6
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000044cephalic ganglia
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 availableCDDcd04299GT35_Glycogen_Phosphorylase-likecoord: 19..52
e-value: 0.00142035
score: 32.7062
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..23
score: 0.859
NoneNo IPR availableTMHMMTMhelixcoord: 7..25