Death-associated protein 1

Overview
NameDeath-associated protein 1
Smed IDSMED30020914
Length (bp)712
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 (SMED30020914) t-SNE clustered cells

Violin plots show distribution of expression levels for Death-associated protein 1 (SMED30020914) 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 (SMED30020914) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Death-associated protein 1 (SMED30020914) 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



SMED30020914

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
X1 cellSMED30020914SMESG000023167.1 SmedASXL_004532SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30020914SMESG000023167.1 SmedASXL_004532SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
pharynxSMED30020914SMESG000023167.1 dd_Smed_v4_955_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30020914SMESG000023167.1 dd_Smed_v4_955_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30020914SMESG000023167.1 dd_Smed_v4_955_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020914SMESG000023167.1 dd_Smed_v4_955_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30020914SMESG000023167.1 dd_Smed_v4_955_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020914SMESG000023167.1 dd_Smed_v4_955_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30020914SMESG000023167.1 dd_Smed_v4_955_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30020914SMESG000023167.1 dd_Smed_v4_955_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
whole organismSMED30020914SMESG000023167.1 Contig42729newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30020914SMESG000023167.1 Contig42729uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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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: 147.902 bits (372), Expect = 4.586e-42
Identity = 71/95 (74.74%), Postives = 82/95 (86.32%), Query Frame = 2 
Query:  104 VRGHLPASKVGGMRVPLRSRGDSSSEKVTTEEIRKQEVEYGTEVQPTIGAEIIPGVEIDEKKAFPTVAIKAYHEKPLPTHNKPTKIVQHHINQPR 388
            V+GH PA+KVGGMRV +RSR DS SEK++ +EI++QE EYGTE+Q TIGAEIIPGVEIDEKKAFP  AIKA+H+KP PTHNKP K V HHINQPR
Sbjct:    6 VKGHPPAAKVGGMRVRMRSRDDSGSEKISADEIKRQEEEYGTEIQATIGAEIIPGVEIDEKKAFPPEAIKAFHDKPRPTHNKPNKPVPHHINQPR 100
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BLAST of Death-associated protein 1 vs. TrEMBL
Match: A0A1I8JBV7 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 91.2781 bits (225), Expect = 5.682e-20
Identity = 47/96 (48.96%), Postives = 61/96 (63.54%), Query Frame = 2 
Query:  110 GHLPASKVGGMRVP---LRSRGDSSSEKVTTEEIRKQEVEYGTEVQPTIGAEIIPGVEIDEKKAFPTVAIKAYHEKPLPTHNKPTKIVQHHINQPR 388
            GH PA+KVG MRV     R+    S EK++ EE+RKQE EYGTEV      +++ G  + E KAF   A+KAYH+KP+P H KP     H+I+QPR
Sbjct:   11 GHAPAAKVGNMRVAGHRTRNTSSGSGEKLSAEELRKQEAEYGTEVDEAKQGQVVAGSLVKEDKAFTPDAVKAYHDKPVPKHEKPHAPPAHNIHQPR 106
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BLAST of Death-associated protein 1 vs. TrEMBL
Match: A0A267DLG0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig023356g3 PE=4 SV=1)

HSP 1 Score: 90.8929 bits (224), Expect = 7.991e-20
Identity = 47/96 (48.96%), Postives = 60/96 (62.50%), Query Frame = 2 
Query:  110 GHLPASKVGGMRVP---LRSRGDSSSEKVTTEEIRKQEVEYGTEVQPTIGAEIIPGVEIDEKKAFPTVAIKAYHEKPLPTHNKPTKIVQHHINQPR 388
            GH PA+KVG MRV     R+    S EK+  EE+RKQE EYGTEV      +++ G  + E KAF   A+KAYH+KP+P H KP     H+I+QPR
Sbjct:   11 GHAPAAKVGNMRVAGHRTRNTSSGSGEKLNAEELRKQEAEYGTEVDEAKQGQVVAGSLVKEDKAFTPDAVKAYHDKPVPKHEKPHAPPAHNIHQPR 106
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BLAST of Death-associated protein 1 vs. TrEMBL
Match: A0A267FK26 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig023356g1 PE=4 SV=1)

HSP 1 Score: 77.411 bits (189), Expect = 7.404e-15
Identity = 40/87 (45.98%), Postives = 54/87 (62.07%), Query Frame = 2 
Query:  128 KVGGMRVPLRSRGDSSSEKVTTEEIRKQEVEYGTEVQPTIGAEIIPGVEIDEKKAFPTVAIKAYHEKPLPTHNKPTKIVQHHINQPR 388
            +V G R   R+    S EK++ EE+RKQE EYGTEV      +++ G  + E KAF   A+KAYH+KP+P H KP     H+I+QPR
Sbjct:    3 RVAGHRT--RNTSSGSGEKLSAEELRKQEAEYGTEVDEAKQGQVVAGSLVKEDKAFTPDAVKAYHDKPVPKHEKPHAPPAHNIHQPR 87
[Close]
BLAST of Death-associated protein 1 vs. TrEMBL
Match: A0A267H2C9 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig023356g5 PE=4 SV=1)

HSP 1 Score: 77.411 bits (189), Expect = 7.849e-15
Identity = 41/88 (46.59%), Postives = 54/88 (61.36%), Query Frame = 2 
Query:  134 GGMRVP---LRSRGDSSSEKVTTEEIRKQEVEYGTEVQPTIGAEIIPGVEIDEKKAFPTVAIKAYHEKPLPTHNKPTKIVQHHINQPR 388
            G MRV     R+    S EK++ EE+RKQE EYGTEV      +++ G  + E KAF   A+KAYH+KP+P H KP     H+I+QPR
Sbjct:    1 GNMRVAGHRTRNTSSGSGEKLSAEELRKQEAEYGTEVDEAKQGQVVAGSLVKEDKAFTPDAVKAYHDKPVPKHEKPHVPPAHNIHQPR 88
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BLAST of Death-associated protein 1 vs. Ensembl Medaka
Match: dap (death associated protein [Source:NCBI gene;Acc:101164104])

HSP 1 Score: 45.0542 bits (105), Expect = 5.126e-6
Identity = 38/108 (35.19%), Postives = 51/108 (47.22%), Query Frame = 2 
Query:   74 MSSLKTDDVGVRG-HLPASKVGGMRVPLRSRGDSSSEKVTTEEIRKQEVEYGTEVQPTIGAEIIPGVEIDEKKAFPTVAIKAYHEKPLPTHNK--PTKIVQHHINQPR 388
            MSS   + V  +G HLPA K GGMR+  + +     E    +E    E EY     P     I+ GV     K F   A +  H+KP P+  K  PT+ +  HI+QPR
Sbjct:    1 MSSPPKEKVETKGGHLPAVKAGGMRIVQKHQAPPPVEPPQKDE---DEEEY-VSTSPPKAPVIVSGVVTKGDKDFTPAAAQVAHQKPQPSVPKLPPTQHINQHIHQPR 104
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BLAST of Death-associated protein 1 vs. Planmine SMEST
Match: SMESG000023167.1 (SMESG000023167.1)

HSP 1 Score: 213.001 bits (541), Expect = 3.750e-71
Identity = 105/105 (100.00%), Postives = 105/105 (100.00%), Query Frame = 2 
Query:   74 MSSLKTDDVGVRGHLPASKVGGMRVPLRSRGDSSSEKVTTEEIRKQEVEYGTEVQPTIGAEIIPGVEIDEKKAFPTVAIKAYHEKPLPTHNKPTKIVQHHINQPR 388
            MSSLKTDDVGVRGHLPASKVGGMRVPLRSRGDSSSEKVTTEEIRKQEVEYGTEVQPTIGAEIIPGVEIDEKKAFPTVAIKAYHEKPLPTHNKPTKIVQHHINQPR
Sbjct:    1 MSSLKTDDVGVRGHLPASKVGGMRVPLRSRGDSSSEKVTTEEIRKQEVEYGTEVQPTIGAEIIPGVEIDEKKAFPTVAIKAYHEKPLPTHNKPTKIVQHHINQPR 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: 5
Match NameE-valueIdentityDescription
A0SIE24.586e-4274.74Death-associated protein 1 OS=Girardia tigrina OX=... [more]
A0A1I8JBV75.682e-2048.96Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267DLG07.991e-2048.96Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267FK267.404e-1545.98Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267H2C97.849e-1546.59Uncharacterized protein (Fragment) OS=Macrostomum ... [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: 1
Match NameE-valueIdentityDescription
dap5.126e-635.19death associated protein [Source:NCBI gene;Acc:101... [more]
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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
SMESG000023167.13.750e-71100.00SMESG000023167.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020914 ID=SMED30020914|Name=Death-associated protein 1|organism=Schmidtea mediterranea sexual|type=transcript|length=712bp
TTTAATTAAAATTTTATCATACTAATCTTTGTTTCTCTAATTATTTTATT
TCTTTATCTGTTATATTAAATTCATGTCATCTTTAAAAACTGATGATGTT
GGAGTTAGAGGTCATCTTCCGGCTTCAAAGGTAGGGGGGATGCGAGTACC
ATTACGAAGTCGTGGCGATTCTAGCAGTGAGAAAGTGACTACTGAAGAAA
TTCGAAAACAAGAAGTAGAATACGGAACTGAAGTTCAACCTACTATAGGA
GCAGAAATAATTCCGGGTGTTGAAATCGACGAAAAAAAAGCTTTTCCTAC
TGTAGCAATAAAAGCTTATCATGAAAAACCTTTGCCAACACACAATAAGC
CTACTAAAATCGTTCAACATCATATTAATCAGCCTCGATAAATATCTTTA
GTTAAAGAAGTTTATTGTGCAATTATGATATATTTCATTGACTCATTAAG
TTAAGCTGCATTGTTGGTCATGTTTTGTAACAAAGTTATGTACTTTTAGG
GAATTCTATATTATATGCATTACGTTTAGTTTTAACCTTGATGTTTTTAT
ATTTATTATAAACTTTCCTGTGTTTCTATTCAACTACACGTAATAATTGT
CATGAATCTTTTTTAGCAATATCTAAACCGAACTTAAAGTTTGAATGTGG
TTATTTTATACGTGTCTAGTTTGGAATGGTTGAAAGTAAATGTTTTTTTT
GTGAAAAAAAAA
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protein sequence of SMED30020914-orf-1

>SMED30020914-orf-1 ID=SMED30020914-orf-1|Name=SMED30020914-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=106bp
MSSLKTDDVGVRGHLPASKVGGMRVPLRSRGDSSSEKVTTEEIRKQEVEY
GTEVQPTIGAEIIPGVEIDEKKAFPTVAIKAYHEKPLPTHNKPTKIVQHH
INQPR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000136whole organism
PLANA:0000429neoblast
PLANA:0002032epidermal cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR024130DAP1/DAPL1
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR024130DAP1/DAPL1PFAMPF15228DAPcoord: 13..105
e-value: 3.9E-16
score: 60.0
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..43
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 85..105