Dolichol-phosphate mannosyltransferase subunit 3

Overview
NameDolichol-phosphate mannosyltransferase subunit 3
Smed IDSMED30009425
Length (bp)358
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 Dolichol-phosphate mannosyltransferase subunit 3 (SMED30009425) t-SNE clustered cells

Violin plots show distribution of expression levels for Dolichol-phosphate mannosyltransferase subunit 3 (SMED30009425) 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 Dolichol-phosphate mannosyltransferase subunit 3 (SMED30009425) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Dolichol-phosphate mannosyltransferase subunit 3 (SMED30009425) 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




SMED30009425

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
epidermisSMED30009425SMESG000032034.1 dd_Smed_v4_2396_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30009425SMESG000032034.1 dd_Smed_v4_2396_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 Dolichol-phosphate mannosyltransferase subunit 3 vs. Ensembl Celegans
Match: dpm-3 (Probable dolichol-phosphate mannosyltransferase subunit 3 [Source:UniProtKB/Swiss-Prot;Acc:Q9XVV5])

HSP 1 Score: 41.9726 bits (97), Expect = 6.926e-6
Identity = 21/49 (42.86%), Postives = 30/49 (61.22%), Query Frame = 2
Query:  149 LH-LCDYLPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAK 292
            LH L +Y P +  LF GI +   ++Y   TFNDC +A+ EL  EI+ A+
Sbjct:   37 LHCLVNYAPFFAVLFLGIYAVFNVVYGVATFNDCAEAKVELLGEIKEAR 85          
BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. Ensembl Fly
Match: CG33977 (gene:FBgn0053977 transcript:FBtr0100020)

HSP 1 Score: 50.447 bits (119), Expect = 3.744e-9
Identity = 20/36 (55.56%), Postives = 28/36 (77.78%), Query Frame = 2
Query:  191 FGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD 298
            FGI S   +LY+T TFNDCP+A +EL++EI+ A+ D
Sbjct:   49 FGIYSVWTVLYRTLTFNDCPEAAKELQDEIQEARKD 84          
BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. Ensembl Zebrafish
Match: dpm3 (dolichyl-phosphate mannosyltransferase subunit 3, regulatory [Source:ZFIN;Acc:ZDB-GENE-040426-1782])

HSP 1 Score: 43.1282 bits (100), Expect = 3.332e-6
Identity = 18/44 (40.91%), Postives = 28/44 (63.64%), Query Frame = 2
Query:  167 LPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD 298
            +P+Y+ + FG  S   + Y+  TFNDC  A +EL+ +I+ AK D
Sbjct:   41 MPVYLLVVFGCYSLATVGYRVATFNDCEDAAKELQAQIKEAKED 84          
BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. Ensembl Zebrafish
Match: dpm3 (dolichyl-phosphate mannosyltransferase subunit 3, regulatory [Source:ZFIN;Acc:ZDB-GENE-040426-1782])

HSP 1 Score: 43.1282 bits (100), Expect = 3.332e-6
Identity = 18/44 (40.91%), Postives = 28/44 (63.64%), Query Frame = 2
Query:  167 LPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD 298
            +P+Y+ + FG  S   + Y+  TFNDC  A +EL+ +I+ AK D
Sbjct:   41 MPVYLLVVFGCYSLATVGYRVATFNDCEDAAKELQAQIKEAKED 84          
BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. TrEMBL
Match: A0A1D1VD17 (Dolichol-phosphate mannosyltransferase subunit 3 OS=Ramazzottius varieornatus OX=947166 GN=RvY_09887 PE=3 SV=1)

HSP 1 Score: 62.3882 bits (150), Expect = 3.277e-10
Identity = 29/53 (54.72%), Postives = 38/53 (71.70%), Query Frame = 2
Query:  140 AFLLHLCDYLPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD 298
            AF  HL  Y+P+Y  + FG+IS  II Y+  TF DCP+A EEL++EIE+AK D
Sbjct:   32 AFEKHLVLYVPLYAVISFGLISLGIICYRVATFRDCPEAAEELQHEIEAAKED 84          
BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. TrEMBL
Match: A0A132A251 (Dolichol-phosphate mannosyltransferase subunit 3 OS=Sarcoptes scabiei OX=52283 GN=QR98_0035750 PE=3 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 1.285e-9
Identity = 29/58 (50.00%), Postives = 42/58 (72.41%), Query Frame = 2
Query:  125 EVSNYAFLLHLCDYLPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD 298
            E+S++  +LHL   LPIY  + FG++S  I+LY+TFTFN+CP+A  EL+ EI  A+ D
Sbjct:   26 ELSSFIPVLHL-KLLPIYCLIGFGLVSVFIVLYRTFTFNNCPEAHAELKAEIIDARQD 82          
BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. TrEMBL
Match: A0A087TJD9 (Dolichol-phosphate mannosyltransferase subunit 3 (Fragment) OS=Stegodyphus mimosarum OX=407821 GN=X975_02033 PE=3 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 5.569e-9
Identity = 25/44 (56.82%), Postives = 34/44 (77.27%), Query Frame = 2
Query:  167 LPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD 298
            +PIY  + FGI S ++ILY+ +TFNDCP+A EEL+ EI+ AK D
Sbjct:   38 VPIYAVIAFGIYSLIVILYRVYTFNDCPEAAEELKMEIKMAKED 81          
BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. TrEMBL
Match: A0A267EC10 (Dolichol-phosphate mannosyltransferase subunit 3 (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig022563g2 PE=3 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 7.559e-9
Identity = 23/49 (46.94%), Postives = 33/49 (67.35%), Query Frame = 2
Query:  152 HLCDYLPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD 298
            H+ ++LP+Y    FG+ SA+ I+Y+   FNDCP+A  EL  EI+ AK D
Sbjct:   40 HVTNWLPLYAGGLFGLASALTIVYRVLMFNDCPEAHSELVREIDEAKAD 88          
BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. TrEMBL
Match: A0A267DAA0 (Dolichol-phosphate mannosyltransferase subunit 3 (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig022563g5 PE=3 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 8.137e-9
Identity = 23/49 (46.94%), Postives = 33/49 (67.35%), Query Frame = 2
Query:  152 HLCDYLPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD 298
            H+ ++LP+Y    FG+ SA+ I+Y+   FNDCP+A  EL  EI+ AK D
Sbjct:   39 HVTNWLPLYAGGLFGLASALTIVYRVLMFNDCPEAHSELVREIDEAKAD 87          
BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. Ensembl Cavefish
Match: dpm3 (dolichyl-phosphate mannosyltransferase subunit 3, regulatory [Source:NCBI gene;Acc:103044152])

HSP 1 Score: 44.669 bits (104), Expect = 7.581e-7
Identity = 18/44 (40.91%), Postives = 29/44 (65.91%), Query Frame = 2
Query:  167 LPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD 298
            +P+Y+ + FG  S   + Y+  TFNDC +A +EL+ +I+ AK D
Sbjct:   41 MPVYLLVVFGCYSLATVGYRVATFNDCEEAAKELQAQIKEAKAD 84          
BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. Ensembl Medaka
Match: dpm3 (dolichyl-phosphate mannosyltransferase subunit 3, regulatory [Source:NCBI gene;Acc:101155283])

HSP 1 Score: 42.3578 bits (98), Expect = 5.643e-6
Identity = 17/44 (38.64%), Postives = 27/44 (61.36%), Query Frame = 2
Query:  167 LPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD 298
            +P+Y+ + FG  S   + Y+  TFNDC  A +EL+ +I  A+ D
Sbjct:   41 MPLYLLVSFGCFSLATVGYRVATFNDCDAAAKELQEQIREARED 84          
BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. Planmine SMEST
Match: SMESG000032034.1 (SMESG000032034.1)

HSP 1 Score: 137.887 bits (346), Expect = 1.404e-43
Identity = 84/84 (100.00%), Postives = 84/84 (100.00%), Query Frame = 2
Query:   47 MIKAXXXXXXXXXXXXXXYAHLTKLVEVSNYAFLLHLCDYLPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD 298
            MIKAFEWIGGIFFILIFWYAHLTKLVEVSNYAFLLHLCDYLPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD
Sbjct:    1 MIKAFEWIGGIFFILIFWYAHLTKLVEVSNYAFLLHLCDYLPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVD 84          
The following BLAST results are available for this feature:
BLAST of Dolichol-phosphate mannosyltransferase subunit 3 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 Dolichol-phosphate mannosyltransferase subunit 3 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 1
Match NameE-valueIdentityDescription
dpm-36.926e-642.86Probable dolichol-phosphate mannosyltransferase su... [more]
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BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CG339773.744e-955.56gene:FBgn0053977 transcript:FBtr0100020[more]
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BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
dpm33.332e-640.91dolichyl-phosphate mannosyltransferase subunit 3, ... [more]
dpm33.332e-640.91dolichyl-phosphate mannosyltransferase subunit 3, ... [more]
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BLAST of Dolichol-phosphate mannosyltransferase subunit 3 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 Dolichol-phosphate mannosyltransferase subunit 3 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 Dolichol-phosphate mannosyltransferase subunit 3 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 Dolichol-phosphate mannosyltransferase subunit 3 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1D1VD173.277e-1054.72Dolichol-phosphate mannosyltransferase subunit 3 O... [more]
A0A132A2511.285e-950.00Dolichol-phosphate mannosyltransferase subunit 3 O... [more]
A0A087TJD95.569e-956.82Dolichol-phosphate mannosyltransferase subunit 3 (... [more]
A0A267EC107.559e-946.94Dolichol-phosphate mannosyltransferase subunit 3 (... [more]
A0A267DAA08.137e-946.94Dolichol-phosphate mannosyltransferase subunit 3 (... [more]
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BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
dpm37.581e-740.91dolichyl-phosphate mannosyltransferase subunit 3, ... [more]
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BLAST of Dolichol-phosphate mannosyltransferase subunit 3 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 Dolichol-phosphate mannosyltransferase subunit 3 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 Dolichol-phosphate mannosyltransferase subunit 3 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 Dolichol-phosphate mannosyltransferase subunit 3 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
dpm35.643e-638.64dolichyl-phosphate mannosyltransferase subunit 3, ... [more]
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BLAST of Dolichol-phosphate mannosyltransferase subunit 3 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000032034.11.404e-43100.00SMESG000032034.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009425 ID=SMED30009425|Name=Dolichol-phosphate mannosyltransferase subunit 3|organism=Schmidtea mediterranea sexual|type=transcript|length=358bp
ATTATACAATAGTTATTTAATTTTTTCTTTCAAGAAACGTAATAGAATGA
TTAAAGCATTTGAGTGGATTGGAGGAATTTTCTTTATATTAATATTTTGG
TATGCCCATTTGACAAAACTTGTGGAAGTGTCAAATTATGCATTTCTTCT
GCATTTGTGTGATTATTTACCCATCTACGTGGCGTTATTTTTTGGAATAA
TATCTGCAGTCATAATACTTTATAAAACTTTTACATTTAATGACTGCCCA
AAAGCTGAAGAAGAACTCAGGAATGAAATTGAAAGTGCTAAAGTCGATCT
AAAGAAAAAAGGATATAAATTTTAATATTTTTTAAATTTGTTTAGAATAA
ATATTTTC
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protein sequence of SMED30009425-orf-1

>SMED30009425-orf-1 ID=SMED30009425-orf-1|Name=SMED30009425-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=108bp
LYNSYLIFSFKKRNRMIKAFEWIGGIFFILIFWYAHLTKLVEVSNYAFLL
HLCDYLPIYVALFFGIISAVIILYKTFTFNDCPKAEEELRNEIESAKVDL
KKKGYKF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0005783endoplasmic reticulum
GO:0005789endoplasmic reticulum membrane
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: biological process
TermDefinition
GO:0006486protein glycosylation
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR013174DPM3
Vocabulary: molecular function
TermDefinition
GO:0016740transferase activity
GO:0016757transferase activity, transferring glycosyl groups
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013174Dolichol-phosphate mannosyltransferase subunit 3PFAMPF08285DPM3coord: 16..106
e-value: 1.7E-21
score: 76.2
IPR013174Dolichol-phosphate mannosyltransferase subunit 3PANTHERPTHR16433FAMILY NOT NAMEDcoord: 16..106
NoneNo IPR availableTMHMMTMhelixcoord: 52..74
NoneNo IPR availableTMHMMTMhelixcoord: 20..37