Secreted peptide prohormone-11

Overview
NameSecreted peptide prohormone-11
Smed IDSMED30034847
Length (bp)397
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 Secreted peptide prohormone-11 (SMED30034847) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Secreted peptide prohormone-11 (SMED30034847) 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




SMED30034847

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30034847SMESG000069589.1 dd_Smed_v4_1724_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30034847SMESG000069589.1 dd_Smed_v4_1724_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30034847SMESG000069589.1 dd_Smed_v4_1724_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30034847SMESG000069589.1 dd_Smed_v4_1724_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30034847SMESG000069589.1 dd_Smed_v6_1724_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30034847SMESG000069589.1 SMESG000047799.1 SMESG000038528.1 SMESG000038497.1 OX_Smed_1.0.12815ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30034847SMESG000069589.1 BK007014smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism asexual adult colorimetric in situ hybridization evidence
cephalic gangliaSMED30034847SMESG000069589.1 BK007014smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30034847SMESG000069589.1 BK007014smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism asexual adult colorimetric in situ hybridization evidence
reproductive organSMED30034847SMESG000069589.1 Contig50788newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30034847SMESG000069589.1 Contig50788uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Secreted peptide prohormone-11 vs. TrEMBL
Match: E3CTI9 (Secreted peptide prohormone-11 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 145.206 bits (365), Expect = 8.016e-43
Identity = 72/72 (100.00%), Postives = 72/72 (100.00%), Query Frame = 3
Query:   57 MKLLFVAALFLVIMDVYAIQEKRYIRFGKRHQQLFPNKRYIRFGKREYIPLDKRNDLLDSEFLNDMNENLEK 272
            MKLLFVAALFLVIMDVYAIQEKRYIRFGKRHQQLFPNKRYIRFGKREYIPLDKRNDLLDSEFLNDMNENLEK
Sbjct:    1 MKLLFVAALFLVIMDVYAIQEKRYIRFGKRHQQLFPNKRYIRFGKREYIPLDKRNDLLDSEFLNDMNENLEK 72          
BLAST of Secreted peptide prohormone-11 vs. Planmine SMEST
Match: SMESG000069589.1 (SMESG000069589.1)

HSP 1 Score: 145.206 bits (365), Expect = 2.229e-46
Identity = 72/72 (100.00%), Postives = 72/72 (100.00%), Query Frame = 3
Query:   57 MKLLFVAALFLVIMDVYAIQEKRYIRFGKRHQQLFPNKRYIRFGKREYIPLDKRNDLLDSEFLNDMNENLEK 272
            MKLLFVAALFLVIMDVYAIQEKRYIRFGKRHQQLFPNKRYIRFGKREYIPLDKRNDLLDSEFLNDMNENLEK
Sbjct:    1 MKLLFVAALFLVIMDVYAIQEKRYIRFGKRHQQLFPNKRYIRFGKREYIPLDKRNDLLDSEFLNDMNENLEK 72          
BLAST of Secreted peptide prohormone-11 vs. Planmine SMEST
Match: SMESG000069589.1 (SMESG000069589.1)

HSP 1 Score: 120.553 bits (301), Expect = 8.844e-37
Identity = 59/59 (100.00%), Postives = 59/59 (100.00%), Query Frame = 3
Query:   96 MDVYAIQEKRYIRFGKRHQQLFPNKRYIRFGKREYIPLDKRNDLLDSEFLNDMNENLEK 272
            MDVYAIQEKRYIRFGKRHQQLFPNKRYIRFGKREYIPLDKRNDLLDSEFLNDMNENLEK
Sbjct:    1 MDVYAIQEKRYIRFGKRHQQLFPNKRYIRFGKREYIPLDKRNDLLDSEFLNDMNENLEK 59          
The following BLAST results are available for this feature:
BLAST of Secreted peptide prohormone-11 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 Secreted peptide prohormone-11 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 Secreted peptide prohormone-11 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 Secreted peptide prohormone-11 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 Secreted peptide prohormone-11 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 Secreted peptide prohormone-11 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 Secreted peptide prohormone-11 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 Secreted peptide prohormone-11 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
E3CTI98.016e-43100.00Secreted peptide prohormone-11 OS=Schmidtea medite... [more]
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BLAST of Secreted peptide prohormone-11 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 Secreted peptide prohormone-11 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 Secreted peptide prohormone-11 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 Secreted peptide prohormone-11 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 Secreted peptide prohormone-11 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 Secreted peptide prohormone-11 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000069589.12.229e-46100.00SMESG000069589.1[more]
SMESG000069589.18.844e-37100.00SMESG000069589.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034847 ID=SMED30034847|Name=Secreted peptide prohormone-11|organism=Schmidtea mediterranea sexual|type=transcript|length=397bp
CATTCACTTGTCCACCTGAAACAGAGCAAAATTACCAAGAAAAATAACTG
TTAGAAATGAAACTTTTATTCGTTGCTGCATTGTTCCTAGTAATTATGGA
TGTTTACGCCATACAAGAAAAAAGATACATTAGGTTTGGGAAACGTCATC
AACAATTATTTCCAAATAAAAGGTACATCAGGTTTGGGAAAAGAGAATAT
ATTCCATTAGACAAAAGAAACGACCTTCTTGATAGTGAATTTCTAAATGA
TATGAATGAAAACTTGGAAAAAAGATATATTCGATTCGGCCGACGATGAT
TTCGAGTGTATTTTTAACTTTCACTTTGAGCGTTTGTAATATTTATTTGT
AAAATCTTAATAAAAGAAAGTAATTAACAATTTACGAATTGAATTTT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000044cephalic ganglia
PLANA:0000097ventral nerve cord
PLANA:0000418head
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR002544FMRFamid-related_peptide-like
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
IPR002544FMRFamide-related peptide-likePFAMPF01581FARPcoord: 71..79
e-value: 0.81
score: 10.5
coord: 20..29
e-value: 0.43
score: 11.3
coord: 36..45
e-value: 0.46
score: 11.2
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..18
score: 0.871