Neuropeptide-1

Overview
NameNeuropeptide-1
Smed IDSMED30029097
Length (bp)426
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-1 (SMED30029097) t-SNE clustered cells

Violin plots show distribution of expression levels for Neuropeptide-1 (SMED30029097) 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-1 (SMED30029097) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Neuropeptide-1 (SMED30029097) 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.
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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



SMED30029097

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30029097 SmedASXL_056262SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30029097h1SMcG0019267 Contig50168newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029097h1SMcG0019267 Contig50168uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30029097 dd_Smed_v4_2575_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
nervous systemSMED30029097 dd_Smed_v4_2575_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029097 dd_Smed_v4_2575_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30029097 dd_Smed_v4_2575_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
cilated neuronSMED30029097 dd_Smed_v4_2575_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30029097 BK007036smed_ncbi_20240424PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
pharynxSMED30029097 BK007036.1smed_ncbi_20240424PMID:24737865
Adler et al., 2014		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-1 vs. TrEMBL
Match: E3CTL1 (Neuropeptide-1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 148.288 bits (373), Expect = 9.918e-44
Identity = 94/94 (100.00%), Postives = 94/94 (100.00%), Query Frame = 1 
Query:   25 MKLEIRIXXXXXXXXXXXXDYYNXXXXXXKKRSFVRLGKRASFVRLGRSGYEWQSPFVKKASFVRLGKKSRLDYEPVDDYNKRASFVRLGRTYE 306
            MKLEIRIVVVTVLLSAVLADYYNSDDSDSKKRSFVRLGKRASFVRLGRSGYEWQSPFVKKASFVRLGKKSRLDYEPVDDYNKRASFVRLGRTYE
Sbjct:    1 MKLEIRIVVVTVLLSAVLADYYNSDDSDSKKRSFVRLGKRASFVRLGRSGYEWQSPFVKKASFVRLGKKSRLDYEPVDDYNKRASFVRLGRTYE 94
[Close]
BLAST of Neuropeptide-1 vs. TrEMBL
Match: A0A267EN61 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig028341g1 PE=4 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 3.664e-8
Identity = 41/72 (56.94%), Postives = 50/72 (69.44%), Query Frame = 1 
Query:  112 KKRSFVRLGKRASFVRLGRSGYEWQSPFV---KKASFVRLGKK--------SRLDYEPVDDYNKRASFVRLG 294
            K+ SFVRLGKRASFVRLG+   + ++ FV   K+ASFVRLGK+        S LD E ++D  KRASFVRLG
Sbjct:  130 KRASFVRLGKRASFVRLGK---KKRASFVRLGKRASFVRLGKRPSYEPEDESYLDDEQLNDAKKRASFVRLG 198

HSP 2 Score: 57.7658 bits (138), Expect = 2.298e-7
Identity = 48/100 (48.00%), Postives = 58/100 (58.00%), Query Frame = 1 
Query:  112 KKRSFVRLGKRASFVRLGRSGYEWQSPFVKKASFVRLGKKSRLDYEPVDDYNKRASFVRLGR--TYE*DD---LDHEYQKKALLSDLDD*QKISFFVIFG 396
            K+ SFVRLGKRASFVRLG           K+ASFVRLGKK R  +  +    KRASFVRLG+  +YE +D   LD E         L+D +K + FV  G
Sbjct:  121 KRASFVRLGKRASFVRLG-----------KRASFVRLGKKKRASFVRL---GKRASFVRLGKRPSYEPEDESYLDDE--------QLNDAKKRASFVRLG 198
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BLAST of Neuropeptide-1 vs. TrEMBL
Match: A0A267FJR5 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig028341g2 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 5.281e-8
Identity = 41/72 (56.94%), Postives = 50/72 (69.44%), Query Frame = 1 
Query:  112 KKRSFVRLGKRASFVRLGRSGYEWQSPFV---KKASFVRLGKK--------SRLDYEPVDDYNKRASFVRLG 294
            K+ SFVRLGKRASFVRLG+   + ++ FV   K+ASFVRLGK+        S LD E ++D  KRASFVRLG
Sbjct:  139 KRASFVRLGKRASFVRLGK---KKRASFVRLGKRASFVRLGKRPSYEPEDESYLDDEQLNDAKKRASFVRLG 207

HSP 2 Score: 57.7658 bits (138), Expect = 2.620e-7
Identity = 48/100 (48.00%), Postives = 58/100 (58.00%), Query Frame = 1 
Query:  112 KKRSFVRLGKRASFVRLGRSGYEWQSPFVKKASFVRLGKKSRLDYEPVDDYNKRASFVRLGR--TYE*DD---LDHEYQKKALLSDLDD*QKISFFVIFG 396
            K+ SFVRLGKRASFVRLG           K+ASFVRLGKK R  +  +    KRASFVRLG+  +YE +D   LD E         L+D +K + FV  G
Sbjct:  130 KRASFVRLGKRASFVRLG-----------KRASFVRLGKKKRASFVRL---GKRASFVRLGKRPSYEPEDESYLDDE--------QLNDAKKRASFVRLG 207
[Close]
BLAST of Neuropeptide-1 vs. TrEMBL
Match: A0A1I8HVF7 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 4.151e-6
Identity = 36/62 (58.06%), Postives = 42/62 (67.74%), Query Frame = 1 
Query:  112 KKRSFVRLGKRASFVRLGRSGYEWQSPFVKKASFVRLGKKSRLDYEPVDDYNKRASFVRLGR 297
            K+ SFVRLGKRASFVRLG+          K+ASFVRLGKK R  +  +    KRASFVRLG+
Sbjct:  122 KRASFVRLGKRASFVRLGKK---------KRASFVRLGKKKRASFVRL---GKRASFVRLGK 171
[Close]
BLAST of Neuropeptide-1 vs. Planmine SMEST
Match: SMESG000024498.1 (SMESG000024498.1)

HSP 1 Score: 148.288 bits (373), Expect = 2.758e-47
Identity = 94/94 (100.00%), Postives = 94/94 (100.00%), Query Frame = 1 
Query:   25 MKLEIRIXXXXXXXXXXXXDYYNXXXXXXKKRSFVRLGKRASFVRLGRSGYEWQSPFVKKASFVRLGKKSRLDYEPVDDYNKRASFVRLGRTYE 306
            MKLEIRIVVVTVLLSAVLADYYNSDDSDSKKRSFVRLGKRASFVRLGRSGYEWQSPFVKKASFVRLGKKSRLDYEPVDDYNKRASFVRLGRTYE
Sbjct:    1 MKLEIRIVVVTVLLSAVLADYYNSDDSDSKKRSFVRLGKRASFVRLGRSGYEWQSPFVKKASFVRLGKKSRLDYEPVDDYNKRASFVRLGRTYE 94
The following BLAST results are available for this feature:
BLAST of Neuropeptide-1 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-1 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-1 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-1 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-1 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-1 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-1 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-1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
E3CTL19.918e-44100.00Neuropeptide-1 OS=Schmidtea mediterranea OX=79327 ... [more]
A0A267EN613.664e-856.94Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267FJR55.281e-856.94Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A1I8HVF74.151e-658.06Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of Neuropeptide-1 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-1 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-1 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-1 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-1 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-1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000024498.12.758e-47100.00SMESG000024498.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029097 ID=SMED30029097|Name=Neuropeptide-1|organism=Schmidtea mediterranea sexual|type=transcript|length=426bp
AAATTTGTTTATTTCAGACGAGATATGAAATTGGAAATTCGCATTGTTGT
TGTAACCGTTTTGCTATCTGCAGTTCTCGCCGATTACTATAATTCTGACG
ATTCAGATTCAAAGAAACGCTCATTTGTTAGACTTGGAAAACGAGCATCG
TTCGTGAGATTAGGCCGGTCTGGCTATGAATGGCAATCTCCATTTGTGAA
AAAAGCATCCTTCGTGAGATTGGGCAAGAAAAGTCGACTTGATTATGAAC
CAGTAGATGATTATAATAAAAGAGCTTCATTTGTAAGATTGGGTCGAACT
TACGAATAAGACGACCTTGATCACGAATATCAGAAGAAAGCTCTTTTGTC
AGACTTGGATGATTGACAAAAAATTTCTTTTTTTGTGATTTTTGGATTTA
AAATAAAAAATTACTGTATCTTTTCA
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protein sequence of SMED30029097-orf-1

>SMED30029097-orf-1 ID=SMED30029097-orf-1|Name=SMED30029097-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp
KFVYFRRDMKLEIRIVVVTVLLSAVLADYYNSDDSDSKKRSFVRLGKRAS
FVRLGRSGYEWQSPFVKKASFVRLGKKSRLDYEPVDDYNKRASFVRLGRT
YE*
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Aliases
The feature 'Neuropeptide-1' has the following synonyms
Synonym
npp-1
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000099neuron
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: 13..30