Death-associated protein 1

Overview
NameDeath-associated protein 1
Smed IDSMED30010443
Length (bp)915
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 Death-associated protein 1 (SMED30010443) t-SNE clustered cells

Violin plots show distribution of expression levels for Death-associated protein 1 (SMED30010443) 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 Death-associated protein 1 (SMED30010443) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Death-associated protein 1 (SMED30010443) 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




SMED30010443

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30010443 dd_Smed_v4_946_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30010443 dd_Smed_v4_946_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30010443 dd_Smed_v4_946_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30010443 dd_Smed_v4_946_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30010443 dd_Smed_v4_946_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Death-associated protein 1 vs. TrEMBL
Match: A0SIE2 (Death-associated protein 1 OS=Girardia tigrina OX=6162 GN=dap1 PE=2 SV=1)

HSP 1 Score: 86.6557 bits (213), Expect = 1.199e-17
Identity = 76/95 (80.00%), Postives = 87/95 (91.58%), Query Frame = 2
Query:   53 VKGHPPAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXVQPTIGAEIIPGVEIDEKKAFPTEAIKSYHEKPLPAYSKPTKPVQHHINQPR 337
            VKGHPPA+KVGGMRVR+RSR DSGSEKI+ +EI+RQEEEYGTE+Q TIGAEIIPGVEIDEKKAFP EAIK++H+KP P ++KP KPV HHINQPR
Sbjct:    6 VKGHPPAAKVGGMRVRMRSRDDSGSEKISADEIKRQEEEYGTEIQATIGAEIIPGVEIDEKKAFPPEAIKAFHDKPRPTHNKPNKPVPHHINQPR 100          
BLAST of Death-associated protein 1 vs. Planmine SMEST
Match: SMESG000023167.1 (SMESG000023167.1)

HSP 1 Score: 95.5153 bits (236), Expect = 1.643e-24
Identity = 46/52 (88.46%), Postives = 49/52 (94.23%), Query Frame = 2
Query:  182 VQPTIGAEIIPGVEIDEKKAFPTEAIKSYHEKPLPAYSKPTKPVQHHINQPR 337
            VQPTIGAEIIPGVEIDEKKAFPT AIK+YHEKPLP ++KPTK VQHHINQPR
Sbjct:   54 VQPTIGAEIIPGVEIDEKKAFPTVAIKAYHEKPLPTHNKPTKIVQHHINQPR 105          
The following BLAST results are available for this feature:
BLAST of Death-associated protein 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 Death-associated protein 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 Death-associated protein 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 Death-associated protein 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 Death-associated protein 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 Death-associated protein 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 Death-associated protein 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 Death-associated protein 1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0SIE21.199e-1780.00Death-associated protein 1 OS=Girardia tigrina OX=... [more]
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BLAST of Death-associated protein 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 Death-associated protein 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 Death-associated protein 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 Death-associated protein 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 Death-associated protein 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 Death-associated protein 1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000023167.11.643e-2488.46SMESG000023167.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010443 ID=SMED30010443|Name=Death-associated protein 1|organism=Schmidtea mediterranea sexual|type=transcript|length=915bp
TCCGATCTTCATTATTTAATTTGATATGTCATCTCCAAAAAGCGAACCTC
ATGTCAAAGGCCATCCCCCGGCTTCAAAGGTAGGAGGAATGCGAGTCCGA
GTGCGAAGTCGAGGAGATTCTGGTAGTGAAAAAATAACTACTGAAGAAAT
TCGCAGACAAGAAGAAGAATATGGAACTGAAGTTCAACCGACAATCGGTG
CGGAAATAATTCCTGGCGTGGAAATTGATGAAAAGAAGGCTTTTCCTACT
GAAGCAATAAAAAGTTACCACGAAAAGCCTTTACCAGCTTATAGCAAGCC
AACGAAACCTGTTCAACATCATATTAATCAACCACGATAAATGTACTGTA
TCCTAACTTCTTATTGCGAGGTTTCTGGTGCTTTTTTAAATTACAATTAC
GATTATTTAATAAACTAAGGTTGATTGCTTACATTTTGGAAAAAATTATG
TGAAAAAATTTAAATTTACATGTATCAATATTACGTCATATATATTATAT
TATTCGTGATTGATGTGGAATTTTTTTACATTTTAAAGTTGAATGAATTA
TTATCTGGTGTATAATTATATAGTGTTTTTGAAATCTTTAAAAAAGCATT
TTATCGGCTAGTTTATATATATATATACTAATTTATTTAATCATAACAGT
CATTACTTTTATTGTTTGACTGAAGTGATAATTTTGTAAGTAGTATTACT
GTGGTATACGATCTTTATGTTTATCTGGTGTCTACTATGCGGTTATTTGC
TTTATCCCATTAATGTTTATTCGTCAGCATAATTATTCTGTTATGGCTAA
GTTAGAACAATTGATATGATGCAATCCATAATAGTTTGCTGGAAATTAGT
TATCTGTATTTTTATTTTTTTATACTAAATTTATGAAGTTTTAATAATTA
TTAATTCAAAATGAA
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protein sequence of SMED30010443-orf-1

>SMED30010443-orf-1 ID=SMED30010443-orf-1|Name=SMED30010443-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp
MSSPKSEPHVKGHPPASKVGGMRVRVRSRGDSGSEKITTEEIRRQEEEYG
TEVQPTIGAEIIPGVEIDEKKAFPTEAIKSYHEKPLPAYSKPTKPVQHHI
NQPR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR024130DAP1/DAPL1