TPA_inf: neuropeptide precursor-4

Overview
NameTPA_inf: neuropeptide precursor-4 (DAA33926.1)
Smed IDSMED30017934
Length (bp)568
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: neuropeptide precursor-4 (SMED30017934) t-SNE clustered cells

Violin plots show distribution of expression levels for TPA_inf: neuropeptide precursor-4 (SMED30017934) 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: neuropeptide precursor-4 (SMED30017934) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for TPA_inf: neuropeptide precursor-4 (SMED30017934) 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



SMED30017934

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30017934SMESG000036661.1 SmedASXL_007206SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30017934SMESG000036661.1 dd_Smed_v4_4417_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30017934SMESG000036661.1 dd_Smed_v4_4417_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30017934SMESG000036661.1 dd_Smed_v4_4417_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30017934SMESG000036661.1 dd_Smed_v4_4417_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017934SMESG000036661.1 Contig42866newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017934SMESG000036661.1 Contig42866uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30017934SMESG000036661.1 dd_Smed_v6_4417_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30017934SMESG000036661.1 OX_Smed_1.0.18148ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30017934SMESG000036661.1 BK007037smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
cephalic gangliaSMED30017934SMESG000036661.1 BK007037smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
Category 2 cellSMED30017934SMESG000036661.1 dd_Smed_v4_4417_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of TPA_inf: neuropeptide precursor-4 vs. TrEMBL
Match: E3CTL2 (Neuropeptide-4 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 221.476 bits (563), Expect = 1.145e-71
Identity = 110/110 (100.00%), Postives = 110/110 (100.00%), Query Frame = 1 
Query:  154 MNSLSITIFVLSILVSWAQSEQKRSSVFRFGKRDQSIDQLTDDSAFSNVPVESTRRNYEQLLSPYPENDQDENKRSVAFRFGKRRGVAFRFGKRGSVFRYGKRQSVFRYG 483
            MNSLSITIFVLSILVSWAQSEQKRSSVFRFGKRDQSIDQLTDDSAFSNVPVESTRRNYEQLLSPYPENDQDENKRSVAFRFGKRRGVAFRFGKRGSVFRYGKRQSVFRYG
Sbjct:    1 MNSLSITIFVLSILVSWAQSEQKRSSVFRFGKRDQSIDQLTDDSAFSNVPVESTRRNYEQLLSPYPENDQDENKRSVAFRFGKRRGVAFRFGKRGSVFRYGKRQSVFRYG 110
[Close]
BLAST of TPA_inf: neuropeptide precursor-4 vs. TrEMBL
Match: A0A1S6JQ32 (LFRFamide-2 OS=Charonia tritonis OX=1960912 PE=2 SV=1)

HSP 1 Score: 62.3882 bits (150), Expect = 7.142e-9
Identity = 38/118 (32.20%), Postives = 63/118 (53.39%), Query Frame = 1 
Query:  142 IETIMNSLSITIFVLSILVSWAQSEQKRSSVFRFGK---RDQSIDQL-TDDSAFSNVPVESTRRNYEQLLSPYPENDQDENKRSVAFRFGKRRGVAFRFGKRGSVFRYGKRQSVFRYG 483
            +  + +++ + +F L +   W + + + S++        + +SI  L +DDSA+  V V+    +    L  +        KR   FRFGK+R   FRFGKR S+FR+GKR S+FR+G
Sbjct:    3 LSQVTHAMVVVLFCLLVAAVWCEEQDQGSALDDLAPSQPQKRSIADLPSDDSAYPAVYVDDDDLDKRSSLFRF-------GKRGSLFRFGKKRSSLFRFGKRSSLFRFGKRGSLFRFG 113
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BLAST of TPA_inf: neuropeptide precursor-4 vs. TrEMBL
Match: A0A1S6JQ40 (LFRFamide-1 OS=Charonia tritonis OX=1960912 PE=2 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 3.128e-8
Identity = 38/116 (32.76%), Postives = 58/116 (50.00%), Query Frame = 1 
Query:  142 IETIMNSLSITIFVLSILVSWAQSEQ--KRSSVFRFGKRDQSIDQLTDDSAFSNVPVESTRRNYEQLLSPYPENDQDENKRSVAFRFGKRRGVAFRFGKRGSVFRYGKRQSVFRYG 483
            +  ++  L++ +  L +   W + +Q  +   +     + +S+    DD A+  V                   D D +KRS  FRFGKR G  FRFGKRGS+FR+GKR S+FR+G
Sbjct:    3 MSQVIQMLTVVMTCLLVAAVWCEEQQGSQLEDMAASQPQKRSVGLPADDEAYPAVYT----------------GDDDMDKRSSLFRFGKR-GSLFRFGKRGSLFRFGKRGSLFRFG 101
[Close]
BLAST of TPA_inf: neuropeptide precursor-4 vs. TrEMBL
Match: A0A2T7PRR4 (Uncharacterized protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_03081 PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 9.714e-7
Identity = 30/45 (66.67%), Postives = 37/45 (82.22%), Query Frame = 1 
Query:  349 PENDQDENKRSVAFRFGKRRGVAFRFGKRGSVFRYGKRQSVFRYG 483
            PE+D D +KRS  FRFGKR  + FRFGKRGS+FR+GKR S+FR+G
Sbjct:   47 PEDD-DLDKRSSLFRFGKRSSL-FRFGKRGSLFRFGKRGSLFRFG 89
[Close]
BLAST of TPA_inf: neuropeptide precursor-4 vs. TrEMBL
Match: A0A0B6Z5R8 (Uncharacterized protein OS=Arion vulgaris OX=1028688 GN=ORF50116 PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 1.877e-6
Identity = 29/50 (58.00%), Postives = 38/50 (76.00%), Query Frame = 1 
Query:  340 SPYPENDQDENKRSVAFRFGKRRGVAFRFGKRGSVFRYGKRQ--SVFRYG 483
            S  P+++ D  KR   FRFGKR+G  FRFGKRGS+FR+GKRQ  ++FR+G
Sbjct:   71 SSLPDDNAD--KRGSLFRFGKRQGSLFRFGKRGSLFRFGKRQGGTLFRFG 118
[Close]
BLAST of TPA_inf: neuropeptide precursor-4 vs. Planmine SMEST
Match: SMESG000036661.1 (SMESG000036661.1)

HSP 1 Score: 221.476 bits (563), Expect = 3.183e-75
Identity = 110/110 (100.00%), Postives = 110/110 (100.00%), Query Frame = 1 
Query:  154 MNSLSITIFVLSILVSWAQSEQKRSSVFRFGKRDQSIDQLTDDSAFSNVPVESTRRNYEQLLSPYPENDQDENKRSVAFRFGKRRGVAFRFGKRGSVFRYGKRQSVFRYG 483
            MNSLSITIFVLSILVSWAQSEQKRSSVFRFGKRDQSIDQLTDDSAFSNVPVESTRRNYEQLLSPYPENDQDENKRSVAFRFGKRRGVAFRFGKRGSVFRYGKRQSVFRYG
Sbjct:    1 MNSLSITIFVLSILVSWAQSEQKRSSVFRFGKRDQSIDQLTDDSAFSNVPVESTRRNYEQLLSPYPENDQDENKRSVAFRFGKRRGVAFRFGKRGSVFRYGKRQSVFRYG 110
The following BLAST results are available for this feature:
BLAST of TPA_inf: neuropeptide precursor-4 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: neuropeptide precursor-4 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: neuropeptide precursor-4 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: neuropeptide precursor-4 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: neuropeptide precursor-4 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: neuropeptide precursor-4 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: neuropeptide precursor-4 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: neuropeptide precursor-4 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
E3CTL21.145e-71100.00Neuropeptide-4 OS=Schmidtea mediterranea OX=79327 ... [more]
A0A1S6JQ327.142e-932.20LFRFamide-2 OS=Charonia tritonis OX=1960912 PE=2 S... [more]
A0A1S6JQ403.128e-832.76LFRFamide-1 OS=Charonia tritonis OX=1960912 PE=2 S... [more]
A0A2T7PRR49.714e-766.67Uncharacterized protein OS=Pomacea canaliculata OX... [more]
A0A0B6Z5R81.877e-658.00Uncharacterized protein OS=Arion vulgaris OX=10286... [more]
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BLAST of TPA_inf: neuropeptide precursor-4 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: neuropeptide precursor-4 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: neuropeptide precursor-4 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: neuropeptide precursor-4 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: neuropeptide precursor-4 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: neuropeptide precursor-4 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000036661.13.183e-75100.00SMESG000036661.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30017934
GenBankDAA33926.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017934 ID=SMED30017934|Name=TPA_inf: neuropeptide precursor-4|organism=Schmidtea mediterranea sexual|type=transcript|length=568bp
GAAAAATTTAAAACTTGTACAGTCAAAAAAGAACAATTGCTCTTTCAATA
AATTTTTAGAAACTGCAATTGTTATTATTGAGTTTTTAAAAGTGAAGTTA
TTTGAAGAGAATTTAGAAAAGAAAAGGATTAGAAATAAAAGATTGAAACT
ATAATGAATTCATTATCAATAACCATATTCGTTTTGAGTATTCTTGTTTC
ATGGGCGCAATCGGAACAGAAAAGGAGTTCGGTATTTCGGTTCGGAAAGC
GAGATCAATCCATTGATCAGCTGACCGATGATTCGGCATTTTCAAATGTT
CCGGTAGAGTCTACGAGAAGAAATTACGAGCAATTATTGTCACCATATCC
AGAAAATGATCAGGATGAAAATAAACGAAGTGTAGCATTTAGGTTCGGTA
AAAGGCGCGGAGTGGCTTTTCGTTTTGGAAAACGTGGATCAGTTTTCAGA
TACGGGAAACGACAATCTGTTTTCAGATATGGATAAATGATATTATTGGA
TTATGTTTAGTATTAAATTTTTTGGCTGATTGTTTGACTGTATCAAATTT
TTTAAATGTAAAAATGGG
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protein sequence of SMED30017934-orf-1

>SMED30017934-orf-1 ID=SMED30017934-orf-1|Name=SMED30017934-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=111bp
MNSLSITIFVLSILVSWAQSEQKRSSVFRFGKRDQSIDQLTDDSAFSNVP
VESTRRNYEQLLSPYPENDQDENKRSVAFRFGKRRGVAFRFGKRGSVFRY
GKRQSVFRYG*
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Aliases
The feature 'TPA_inf: neuropeptide precursor-4' has the following synonyms
Synonym
npp-4
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000028Category 2 cell
PLANA:0000044cephalic ganglia
PLANA:0000099neuron
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..20
score: 0.802