Deuterosome assembly protein 1

Overview
NameDeuterosome assembly protein 1
Smed IDSMED30001860
Length (bp)2194
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 Deuterosome assembly protein 1 (SMED30001860) t-SNE clustered cells

Violin plots show distribution of expression levels for Deuterosome assembly protein 1 (SMED30001860) 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 Deuterosome assembly protein 1 (SMED30001860) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Deuterosome assembly protein 1 (SMED30001860) 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



SMED30001860

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30001860SMESG000061463.1 dd_Smed_v4_13335_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30001860SMESG000061463.1 dd_Smed_v4_13335_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
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BLAST of Deuterosome assembly protein 1 vs. Planmine SMEST
Match: SMESG000061463.1 (SMESG000061463.1)

HSP 1 Score: 1073.92 bits (2776), Expect = 0.000e+0
Identity = 645/648 (99.54%), Postives = 647/648 (99.85%), Query Frame = 3 
Query:  102 MSCDAELQELMIQVDRMVEEKRMEWQEKIKNTENKLNSTLQDNYNLXXXXXXXXXXXXXXXXRMKYTDNISNIFDYDQQVLELRLELSQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXNELRSSQKKYQEEISTYQEHIKEFELKRNTFLIEREALNEQIKLMKTEFNDQLSNYADDERKYSQNLKDLENKLSESKFALQNEIDESKSKLCESLQQVKKTMDEKQQLVIDNDSAKRMIMRLENELSRISTENKIKEKTICKMQQIINVSEKTINEKNEVLRALQVNSASKDYAGTVSKLESDLLDAXXXXXXXXXXXXXLQIEIQILQKRFKDAQEVIENEKIERGNLEASLKRLSVAENEKLNLLDQMKNMELIIENKKTEITNLKSKLERVEMTNEELISNQLRKETEKQVXXXXXXXXXXXXXXXSEEECFMQSAESLLKERNYLLKFCEDKDSIIHRLQLENRILQDFISKLNSGLSNEVPYVNSDLNEDNGLSMLDNYHVLKETFTDYEAPEMNIDKQTENHNHNNPVAXXXXXXXXHAAEYLTNSTDSFSNLNFYHSHESFSETINKSSEDFLTRLMLSNPADHLITDEQESYLKVYPTLAAAKYFTDEREKTRQIERQIDLHMNQLKKKTETK 2045
            MSCDAELQELMIQVDRMVEEKRMEWQEKIKNTENKLNSTLQDNYNLKTIIEEKNNEIANIKNRMKYTDNISNIFDYDQQVLELRLELSQIKKSYEKYYHKYTKKTKEIEKEKEELCKEKINLLKEINELRSSQKKYQEEISTYQEHIKEFELKRNTFLIEREALNEQIKLMKTEFNDQLSNYADDERKYSQNLKDLENKLSESKFALQNEIDESKSKLCESLQQVKKTMDEKQQLVIDNDSAKRMIMRLENELSR+STENKIKEKTICKMQQIINVSEKTINEKNEVLRALQVNSASKDYAGTVSKLESDLLDAKSNVKSSKKNEKSLQIEIQILQKRFKDAQEVIENEKIERGNLEASLKRLSVAENEKLNLLDQMKNMELIIENKKTEITNLKSKLERVEMTNEELISNQLRKETEKQVNNNDNTKNRPDNRRKSEEECFMQSAESLLKERNYLLKFCEDKD IIHRLQLENRILQDFISKLNSGLSNEVPY+NSDLNEDNGLSMLDNYHVLKETFTDYEAPEMNIDKQTENHNHNNPVASSKSSSSKHAAEYLTNSTDSFSNLNFYHSHESFSETINKSSEDFLTRLMLSNPADHLITDEQESYLKVYPTLAAAKYFTDEREKTRQIERQIDLHMNQLKKKTETK
Sbjct:    1 MSCDAELQELMIQVDRMVEEKRMEWQEKIKNTENKLNSTLQDNYNLKTIIEEKNNEIANIKNRMKYTDNISNIFDYDQQVLELRLELSQIKKSYEKYYHKYTKKTKEIEKEKEELCKEKINLLKEINELRSSQKKYQEEISTYQEHIKEFELKRNTFLIEREALNEQIKLMKTEFNDQLSNYADDERKYSQNLKDLENKLSESKFALQNEIDESKSKLCESLQQVKKTMDEKQQLVIDNDSAKRMIMRLENELSRMSTENKIKEKTICKMQQIINVSEKTINEKNEVLRALQVNSASKDYAGTVSKLESDLLDAKSNVKSSKKNEKSLQIEIQILQKRFKDAQEVIENEKIERGNLEASLKRLSVAENEKLNLLDQMKNMELIIENKKTEITNLKSKLERVEMTNEELISNQLRKETEKQVNNNDNTKNRPDNRRKSEEECFMQSAESLLKERNYLLKFCEDKDLIIHRLQLENRILQDFISKLNSGLSNEVPYMNSDLNEDNGLSMLDNYHVLKETFTDYEAPEMNIDKQTENHNHNNPVASSKSSSSKHAAEYLTNSTDSFSNLNFYHSHESFSETINKSSEDFLTRLMLSNPADHLITDEQESYLKVYPTLAAAKYFTDEREKTRQIERQIDLHMNQLKKKTETK 648
[Close]
BLAST of Deuterosome assembly protein 1 vs. Planmine SMEST
Match: SMESG000061463.1 (SMESG000061463.1)

HSP 1 Score: 299.286 bits (765), Expect = 6.793e-98
Identity = 153/155 (98.71%), Postives = 154/155 (99.35%), Query Frame = 3 
Query: 1584 VNSDLNEDNGLSMLDNYHVLKETFTDYEAPEMNIDKQTENHNHNNPVAXXXXXXXXHAAEYLTNSTDSFSNLNFYHSHESFSETINKSSEDFLTRLMLSNPADHLITDEQESYLKVYPTLAAAKYFTDEREKTRQIERQIDLHMNQLKKKTETKR 2048
            +NSDLNEDNGLSMLDNYHVLKETFTDYEAPEMNIDKQTENHNHNNPVASSKSSSSKHAAEYLTNSTDSFSNLNFYHSHESFSETINKSSEDFLTRLMLSNPADHLITDEQESYLKVYPTLAAAKYFTDEREKTRQIERQIDLHMNQLKKKTETK 
Sbjct:    1 MNSDLNEDNGLSMLDNYHVLKETFTDYEAPEMNIDKQTENHNHNNPVASSKSSSSKHAAEYLTNSTDSFSNLNFYHSHESFSETINKSSEDFLTRLMLSNPADHLITDEQESYLKVYPTLAAAKYFTDEREKTRQIERQIDLHMNQLKKKTETKH 155
The following BLAST results are available for this feature:
BLAST of Deuterosome assembly 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 Deuterosome assembly 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 Deuterosome assembly 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 Deuterosome assembly 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 Deuterosome assembly 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 Deuterosome assembly 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 Deuterosome assembly 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 Deuterosome assembly protein 1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Deuterosome assembly 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 Deuterosome assembly 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 Deuterosome assembly 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 Deuterosome assembly 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 Deuterosome assembly 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 Deuterosome assembly protein 1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000061463.10.000e+099.54SMESG000061463.1[more]
SMESG000061463.16.793e-9898.71SMESG000061463.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001860 ID=SMED30001860|Name=Deuterosome assembly protein 1|organism=Schmidtea mediterranea sexual|type=transcript|length=2194bp
GAACAATTTATTTTAACTTCAATTTATAAGTTTCTTAAATTCATGCTGAA
AATTGCACCATTTGTCACAAATTTAAGTTGAATTATATTTCAAATTCTTA
AATGTCTTGTGATGCAGAATTACAGGAATTAATGATTCAAGTTGACCGAA
TGGTCGAAGAGAAAAGAATGGAATGGCAAGAAAAAATTAAGAATACTGAA
AACAAATTGAACAGTACATTACAGGATAATTATAATTTGAAAACGATTAT
TGAAGAAAAAAATAATGAGATAGCTAATATCAAAAATAGAATGAAATATA
CAGATAACATATCAAATATTTTTGATTATGATCAGCAAGTGCTAGAATTG
CGATTGGAATTGTCACAAATCAAGAAATCCTATGAAAAATACTATCATAA
ATACACGAAAAAAACCAAAGAAATTGAAAAAGAGAAAGAGGAATTATGCA
AAGAAAAGATTAATCTTCTCAAAGAAATTAACGAACTTCGTAGTTCCCAA
AAGAAATATCAAGAGGAAATCAGTACTTATCAAGAGCACATTAAAGAATT
TGAGTTGAAAAGAAATACTTTCCTGATTGAACGTGAAGCTTTGAATGAAC
AAATCAAATTAATGAAAACGGAATTCAATGATCAACTAAGCAATTATGCT
GATGATGAAAGAAAATATTCACAGAACCTTAAAGATTTAGAAAATAAATT
GTCTGAATCTAAGTTTGCACTTCAGAATGAAATCGATGAAAGTAAATCGA
AACTTTGTGAGTCCCTGCAGCAAGTCAAAAAAACAATGGATGAAAAGCAA
CAATTGGTTATTGACAATGATTCTGCGAAGCGCATGATTATGCGACTAGA
AAACGAGCTAAGCCGAATAAGTACTGAAAATAAAATCAAGGAAAAAACCA
TTTGTAAAATGCAACAAATTATAAATGTTTCAGAAAAAACAATCAATGAA
AAAAATGAAGTTTTAAGGGCCCTGCAAGTCAATTCAGCGTCTAAAGATTA
TGCTGGAACGGTTTCCAAGCTGGAGAGTGATTTACTCGATGCAAAATCAA
ATGTTAAATCAAGCAAGAAAAATGAAAAATCTTTACAAATTGAAATTCAA
ATCCTACAGAAAAGATTCAAAGATGCTCAGGAAGTGATTGAAAATGAAAA
GATTGAACGAGGGAATTTGGAGGCTTCTTTGAAACGATTATCAGTAGCAG
AGAATGAGAAATTGAACCTGCTCGACCAAATGAAAAATATGGAATTAATT
ATTGAAAATAAAAAGACAGAAATTACTAATCTGAAATCGAAATTGGAAAG
GGTGGAAATGACAAACGAAGAACTGATTAGTAATCAGTTACGAAAGGAAA
CTGAGAAACAAGTGAATAATAATGACAACACTAAGAATAGGCCTGATAAT
CGAAGGAAAAGTGAAGAGGAATGCTTTATGCAATCTGCTGAAAGTTTACT
CAAAGAACGAAACTATTTATTGAAATTCTGTGAAGATAAGGATTCGATCA
TTCATCGCTTGCAATTAGAAAATCGAATTTTACAAGATTTCATTTCAAAA
TTAAACAGTGGCTTGTCAAATGAAGTTCCGTATGTGAATTCTGACTTGAA
CGAAGATAATGGCTTATCAATGCTTGACAATTACCATGTGTTAAAGGAAA
CATTTACAGATTACGAAGCACCTGAGATGAATATTGACAAACAAACAGAA
AATCACAATCACAATAATCCTGTCGCTTCTTCGAAATCTTCATCTAGTAA
ACACGCGGCGGAATATCTGACAAACTCCACAGATTCATTTTCGAATTTAA
ATTTCTATCATTCTCATGAATCTTTCTCCGAAACTATTAACAAATCATCA
GAAGATTTTCTAACCCGTCTAATGCTGTCGAATCCAGCTGATCATTTGAT
AACTGATGAACAGGAATCATATTTGAAAGTCTACCCGACTCTGGCTGCTG
CCAAATATTTCACAGATGAGCGGGAAAAAACACGGCAGATCGAAAGACAA
ATCGATTTACACATGAATCAATTGAAGAAAAAAACAGAAACAAAACGCTC
TATCAGTAATCAATAATTCCATTGTTAATTTCAATTCCAGATGATTTTTT
ATTTTTTGATTGATTTGTAATCAATAATCATGATTGGTAATATATGATCA
TCAGCTGTCAATCAAACTTGACAAATATTGTCAGTGTAATTTCT
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protein sequence of SMED30001860-orf-1

>SMED30001860-orf-1 ID=SMED30001860-orf-1|Name=SMED30001860-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=655bp
MSCDAELQELMIQVDRMVEEKRMEWQEKIKNTENKLNSTLQDNYNLKTII
EEKNNEIANIKNRMKYTDNISNIFDYDQQVLELRLELSQIKKSYEKYYHK
YTKKTKEIEKEKEELCKEKINLLKEINELRSSQKKYQEEISTYQEHIKEF
ELKRNTFLIEREALNEQIKLMKTEFNDQLSNYADDERKYSQNLKDLENKL
SESKFALQNEIDESKSKLCESLQQVKKTMDEKQQLVIDNDSAKRMIMRLE
NELSRISTENKIKEKTICKMQQIINVSEKTINEKNEVLRALQVNSASKDY
AGTVSKLESDLLDAKSNVKSSKKNEKSLQIEIQILQKRFKDAQEVIENEK
IERGNLEASLKRLSVAENEKLNLLDQMKNMELIIENKKTEITNLKSKLER
VEMTNEELISNQLRKETEKQVNNNDNTKNRPDNRRKSEEECFMQSAESLL
KERNYLLKFCEDKDSIIHRLQLENRILQDFISKLNSGLSNEVPYVNSDLN
EDNGLSMLDNYHVLKETFTDYEAPEMNIDKQTENHNHNNPVASSKSSSSK
HAAEYLTNSTDSFSNLNFYHSHESFSETINKSSEDFLTRLMLSNPADHLI
TDEQESYLKVYPTLAAAKYFTDEREKTRQIERQIDLHMNQLKKKTETKRS
ISNQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: biological process
TermDefinition
GO:0030030cell projection organization
GO:0098535de novo centriole assembly involved in multi-ciliated epithelial cell differentiation
GO:1903251multi-ciliated epithelial cell differentiation
GO:0000910cytokinesis
GO:0001525angiogenesis
GO:0006509membrane protein ectodomain proteolysis
GO:0006911phagocytosis, engulfment
GO:0007155cell adhesion
GO:0008360regulation of cell shape
GO:0015031protein transport
GO:0030048actin filament-based movement
GO:0030220platelet formation
GO:0030224monocyte differentiation
GO:0031532actin cytoskeleton reorganization
GO:0043534blood vessel endothelial cell migration
GO:1903919negative regulation of actin filament severing
GO:1903923positive regulation of protein processing in phagocytic vesicle
Vocabulary: cellular component
TermDefinition
GO:0098536deuterosome
GO:0001725stress fiber
GO:0001726ruffle
GO:0005634nucleus
GO:0005737cytoplasm
GO:0005826actomyosin contractile ring
GO:0005829cytosol
GO:0005856cytoskeleton
GO:0005886plasma membrane
GO:0005938cell cortex
GO:0015629actin cytoskeleton
GO:0016459myosin complex
GO:0031252cell leading edge
GO:0032154cleavage furrow
GO:0043234protein complex
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
Vocabulary: INTERPRO
TermDefinition
IPR031470Cep63/Deup1_N
Vocabulary: molecular function
TermDefinition
GO:0000146microfilament motor activity
GO:0000166nucleotide binding
GO:0003774motor activity
GO:0003779actin binding
GO:0005516calmodulin binding
GO:0005524ATP binding
GO:0016887ATPase activity
GO:0042803protein homodimerization activity
GO:0043495protein anchor
GO:0051015actin filament binding