TPA_inf: secreted peptide prohormone-16

Overview
NameTPA_inf: secreted peptide prohormone-16 (DAA33931.1)
Smed IDSMED30001301
Length (bp)584
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 TPA_inf: secreted peptide prohormone-16 (SMED30001301) t-SNE clustered cells

Violin plots show distribution of expression levels for TPA_inf: secreted peptide prohormone-16 (SMED30001301) 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 TPA_inf: secreted peptide prohormone-16 (SMED30001301) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for TPA_inf: secreted peptide prohormone-16 (SMED30001301) 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



SMED30001301

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30001301SMESG000079890.1 dd_Smed_v4_1545_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30001301SMESG000079890.1 dd_Smed_v4_1545_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30001301SMESG000079890.1 dd_Smed_v4_1545_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30001301SMESG000079890.1 dd_Smed_v4_1545_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30001301SMESG000079890.1 dd_Smed_v4_1545_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30001301SMESG000079890.1 dd_Smed_v6_1545_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30001301SMESG000079890.1 BK007042smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
cephalic gangliaSMED30001301SMESG000079890.1 BK007042smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30001301SMESG000079890.1 BK007042smed_ncbi_20200123PMID: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 TPA_inf: secreted peptide prohormone-16 vs. TrEMBL
Match: E3CTL7 (Secreted peptide prohormone-16 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 179.874 bits (455), Expect = 2.753e-55
Identity = 100/100 (100.00%), Postives = 100/100 (100.00%), Query Frame = 3 
Query:  147 MKIYILCXXXXXXXXXXVTRSFPSSNEIYKRQFDPIMYGKLRQFYRRSSKIGKGQFDPTMYEKSIFAKRQFDPIMYKRQSNPYFLSDIRSIKRQFDPIMY 446
            MKIYILCLSLFFLQQLSVTRSFPSSNEIYKRQFDPIMYGKLRQFYRRSSKIGKGQFDPTMYEKSIFAKRQFDPIMYKRQSNPYFLSDIRSIKRQFDPIMY
Sbjct:    1 MKIYILCLSLFFLQQLSVTRSFPSSNEIYKRQFDPIMYGKLRQFYRRSSKIGKGQFDPTMYEKSIFAKRQFDPIMYKRQSNPYFLSDIRSIKRQFDPIMY 100
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BLAST of TPA_inf: secreted peptide prohormone-16 vs. Planmine SMEST
Match: SMESG000079890.1 (SMESG000079890.1)

HSP 1 Score: 179.874 bits (455), Expect = 7.655e-59
Identity = 100/100 (100.00%), Postives = 100/100 (100.00%), Query Frame = 3 
Query:  147 MKIYILCXXXXXXXXXXVTRSFPSSNEIYKRQFDPIMYGKLRQFYRRSSKIGKGQFDPTMYEKSIFAKRQFDPIMYKRQSNPYFLSDIRSIKRQFDPIMY 446
            MKIYILCLSLFFLQQLSVTRSFPSSNEIYKRQFDPIMYGKLRQFYRRSSKIGKGQFDPTMYEKSIFAKRQFDPIMYKRQSNPYFLSDIRSIKRQFDPIMY
Sbjct:    1 MKIYILCLSLFFLQQLSVTRSFPSSNEIYKRQFDPIMYGKLRQFYRRSSKIGKGQFDPTMYEKSIFAKRQFDPIMYKRQSNPYFLSDIRSIKRQFDPIMY 100
The following BLAST results are available for this feature:
BLAST of TPA_inf: secreted peptide prohormone-16 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 TPA_inf: secreted peptide prohormone-16 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 TPA_inf: secreted peptide prohormone-16 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 TPA_inf: secreted peptide prohormone-16 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 TPA_inf: secreted peptide prohormone-16 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 TPA_inf: secreted peptide prohormone-16 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 TPA_inf: secreted peptide prohormone-16 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 TPA_inf: secreted peptide prohormone-16 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
E3CTL72.753e-55100.00Secreted peptide prohormone-16 OS=Schmidtea medite... [more]
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BLAST of TPA_inf: secreted peptide prohormone-16 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 TPA_inf: secreted peptide prohormone-16 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 TPA_inf: secreted peptide prohormone-16 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 TPA_inf: secreted peptide prohormone-16 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 TPA_inf: secreted peptide prohormone-16 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 TPA_inf: secreted peptide prohormone-16 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000079890.17.655e-59100.00SMESG000079890.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30001301
GenBankDAA33931.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001301 ID=SMED30001301|Name=TPA_inf: secreted peptide prohormone-16|organism=Schmidtea mediterranea sexual|type=transcript|length=584bp
CTTTCTTTAATCGCAAATTTTACAGAAGTATAACGAGATATATTATGAGC
TCCATTTGATTGGATAATAATTGTCTACGCCAACCAATCAAATTTTACTG
TTCATGTATATATAAAAGTCAAACAATTGTTATTGTTACTAAAAAAATGA
AAATATATATTTTATGCCTGAGTTTGTTTTTCCTTCAACAATTGTCAGTT
ACGAGGAGCTTTCCAAGTTCTAATGAAATTTATAAAAGACAATTCGATCC
GATTATGTATGGAAAATTGAGACAGTTCTACCGCCGAAGCTCTAAGATTG
GCAAGGGTCAGTTCGATCCAACTATGTATGAAAAATCTATTTTCGCCAAA
AGACAATTCGATCCGATCATGTATAAAAGGCAGTCCAATCCATATTTTCT
CAGTGATATCCGGTCAATAAAAAGACAATTTGATCCAATAATGTATTGAA
ATGATTTTTTCCCATTATGAGTTAGAATAAGTTTTATTTATTGATAAAAA
TGTGAAATCTGACAAATTGTTCACCAGTTTAAAAAGTAAAGTTCAAATTT
AACTTTGTAAAAATTTGAATTAAAATAAATGTGA
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protein sequence of SMED30001301-orf-1

>SMED30001301-orf-1 ID=SMED30001301-orf-1|Name=SMED30001301-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=101bp
MKIYILCLSLFFLQQLSVTRSFPSSNEIYKRQFDPIMYGKLRQFYRRSSK
IGKGQFDPTMYEKSIFAKRQFDPIMYKRQSNPYFLSDIRSIKRQFDPIMY
*
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Aliases
The feature 'TPA_inf: secreted peptide prohormone-16' has the following synonyms
Synonym
spp-16
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
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 availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..21
score: 0.761