phytanoyl-CoA dioxygenase domain-containing protein 1 homolog

Overview
Namephytanoyl-CoA dioxygenase domain-containing protein 1 homolog
Smed IDSMED30002374
Length (bp)163
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 phytanoyl-CoA dioxygenase domain-containing protein 1 homolog (SMED30002374) t-SNE clustered cells

Violin plots show distribution of expression levels for phytanoyl-CoA dioxygenase domain-containing protein 1 homolog (SMED30002374) in cells (dots) of each of the 12 neoblast clusters.

 

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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




SMED30002374

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
muscle cellSMED30002374SMESG000077696.1 SMESG000077694.1 dd_Smed_v4_1292_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
lateral region of the whole animalSMED30002374SMESG000077696.1 SMESG000077694.1 dd_Smed_v4_1292_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30002374SMESG000077696.1 SMESG000077694.1 dd_Smed_v4_1292_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermal cellSMED30002374SMESG000077696.1 SMESG000077694.1 dd_Smed_v4_1292_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
medial muscle cellSMED30002374SMESG000077696.1 SMESG000077694.1 dd_Smed_v4_1292_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30002374SMESG000077696.1 SMESG000077694.1 dd_Smed_v4_1292_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
BLAST of phytanoyl-CoA dioxygenase domain-containing protein 1 homolog vs. TrEMBL
Match: A0A1S3JNQ5 (phytanoyl-CoA dioxygenase domain-containing protein 1 homolog OS=Lingula unguis OX=7574 GN=LOC106174551 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 1.586e-8
Identity = 26/48 (54.17%), Postives = 36/48 (75.00%), Query Frame = 1
Query:   13 LKDFWDKNGFIHVSNVLTMDEVKIYSDIYDQFLSGEIDASNHRHDLGN 156
            L+  +  NG++ V N+L  D ++IY +IYD+ LSGEIDAS HRHDLG+
Sbjct:   23 LRKQFSDNGYVVVHNLLDNDSLEIYQEIYDKLLSGEIDASKHRHDLGS 70          
BLAST of phytanoyl-CoA dioxygenase domain-containing protein 1 homolog vs. TrEMBL
Match: A0A1I8IXG9 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 4.293e-8
Identity = 26/48 (54.17%), Postives = 34/48 (70.83%), Query Frame = 1
Query:   13 LKDFWDKNGFIHVSNVLTMDEVKIYSDIYDQFLSGEIDASNHRHDLGN 156
            LK  +D +G+  V  VLT  EV +  ++YD+ LSG IDAS+HRHDLGN
Sbjct:   24 LKAQFDNDGYAVVRGVLTPSEVALLGELYDRLLSGSIDASSHRHDLGN 71          
BLAST of phytanoyl-CoA dioxygenase domain-containing protein 1 homolog vs. TrEMBL
Match: A0A085EHL8 (Phytanoyl-CoA dioxygenase OS=Flavobacterium gilvum OX=1492737 GN=FEM08_25130 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 4.651e-8
Identity = 24/45 (53.33%), Postives = 35/45 (77.78%), Query Frame = 1
Query:   19 DFWDKNGFIHVSNVLTMDEVKIYSDIYDQFLSGEIDASNHRHDLG 153
            DF++KNG++ V N+LT +EVK Y ++Y+ FLS +IDAS +R DL 
Sbjct:   12 DFFNKNGYLLVENLLTAEEVKTYQNLYEDFLSNKIDASRYRGDLA 56          
BLAST of phytanoyl-CoA dioxygenase domain-containing protein 1 homolog vs. TrEMBL
Match: A0A1I8J227 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 1.362e-7
Identity = 25/48 (52.08%), Postives = 34/48 (70.83%), Query Frame = 1
Query:   13 LKDFWDKNGFIHVSNVLTMDEVKIYSDIYDQFLSGEIDASNHRHDLGN 156
            LK  +D +G+  V  VLT  EV +  ++YD+ L+G IDAS+HRHDLGN
Sbjct:   24 LKAQFDNDGYAVVRGVLTPSEVALLGELYDRLLNGSIDASSHRHDLGN 71          
BLAST of phytanoyl-CoA dioxygenase domain-containing protein 1 homolog vs. TrEMBL
Match: A0A3B9AI63 (Phytanoyl-CoA dioxygenase family protein OS=Saprospirales bacterium OX=2026790 GN=DCF33_03535 PE=4 SV=1)

HSP 1 Score: 52.7582 bits (125), Expect = 1.245e-6
Identity = 21/44 (47.73%), Postives = 29/44 (65.91%), Query Frame = 1
Query:   22 FWDKNGFIHVSNVLTMDEVKIYSDIYDQFLSGEIDASNHRHDLG 153
            FW+ NG++ V N++T +E + Y  IYDQFL   ID   +R DLG
Sbjct:   10 FWETNGYLIVPNIITTEEAETYRRIYDQFLDNTIDTGANRSDLG 53          
BLAST of phytanoyl-CoA dioxygenase domain-containing protein 1 homolog vs. Ensembl Nematostella
Match: EDO48247 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RJD8])

HSP 1 Score: 46.9802 bits (110), Expect = 2.191e-8
Identity = 20/46 (43.48%), Postives = 32/46 (69.57%), Query Frame = 1
Query:   16 KDFWDKNGFIHVSNVLTMDEVKIYSDIYDQFLSGEIDASNHRHDLG 153
            K+ ++K+G++ V  ++  D V+IY D+Y + L+GEID   HR DLG
Sbjct:   34 KETFEKDGYLVVHGLIDKDFVEIYKDVYMKLLNGEIDTRRHRQDLG 79          
BLAST of phytanoyl-CoA dioxygenase domain-containing protein 1 homolog vs. Planmine SMEST
Match: SMESG000077696.1 (SMESG000077696.1)

HSP 1 Score: 103.219 bits (256), Expect = 5.276e-29
Identity = 48/50 (96.00%), Postives = 49/50 (98.00%), Query Frame = 1
Query:   13 LKDFWDKNGFIHVSNVLTMDEVKIYSDIYDQFLSGEIDASNHRHDLGNIN 162
             +DFWDKNGFIHVSNVLTMDEVKIYSDIYDQFLSGEIDASNHRHDLGNIN
Sbjct:   25 FRDFWDKNGFIHVSNVLTMDEVKIYSDIYDQFLSGEIDASNHRHDLGNIN 74          
BLAST of phytanoyl-CoA dioxygenase domain-containing protein 1 homolog vs. Planmine SMEST
Match: SMESG000077696.1 (SMESG000077696.1)

HSP 1 Score: 103.219 bits (256), Expect = 5.894e-29
Identity = 48/50 (96.00%), Postives = 49/50 (98.00%), Query Frame = 1
Query:   13 LKDFWDKNGFIHVSNVLTMDEVKIYSDIYDQFLSGEIDASNHRHDLGNIN 162
             +DFWDKNGFIHVSNVLTMDEVKIYSDIYDQFLSGEIDASNHRHDLGNIN
Sbjct:   33 FRDFWDKNGFIHVSNVLTMDEVKIYSDIYDQFLSGEIDASNHRHDLGNIN 82          
BLAST of phytanoyl-CoA dioxygenase domain-containing protein 1 homolog vs. Planmine SMEST
Match: SMESG000077696.1 (SMESG000077696.1)

HSP 1 Score: 68.5514 bits (166), Expect = 4.191e-16
Identity = 32/32 (100.00%), Postives = 32/32 (100.00%), Query Frame = 1
Query:   67 MDEVKIYSDIYDQFLSGEIDASNHRHDLGNIN 162
            MDEVKIYSDIYDQFLSGEIDASNHRHDLGNIN
Sbjct:    1 MDEVKIYSDIYDQFLSGEIDASNHRHDLGNIN 32          
The following BLAST results are available for this feature:
BLAST of phytanoyl-CoA dioxygenase domain-containing protein 1 homolog 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 phytanoyl-CoA dioxygenase domain-containing protein 1 homolog 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 phytanoyl-CoA dioxygenase domain-containing protein 1 homolog 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 phytanoyl-CoA dioxygenase domain-containing protein 1 homolog 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 phytanoyl-CoA dioxygenase domain-containing protein 1 homolog 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 phytanoyl-CoA dioxygenase domain-containing protein 1 homolog 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 phytanoyl-CoA dioxygenase domain-containing protein 1 homolog 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 phytanoyl-CoA dioxygenase domain-containing protein 1 homolog vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1S3JNQ51.586e-854.17phytanoyl-CoA dioxygenase domain-containing protei... [more]
A0A1I8IXG94.293e-854.17Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A085EHL84.651e-853.33Phytanoyl-CoA dioxygenase OS=Flavobacterium gilvum... [more]
A0A1I8J2271.362e-752.08Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A3B9AI631.245e-647.73Phytanoyl-CoA dioxygenase family protein OS=Sapros... [more]
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BLAST of phytanoyl-CoA dioxygenase domain-containing protein 1 homolog 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 phytanoyl-CoA dioxygenase domain-containing protein 1 homolog 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 phytanoyl-CoA dioxygenase domain-containing protein 1 homolog 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 phytanoyl-CoA dioxygenase domain-containing protein 1 homolog vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO482472.191e-843.48Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of phytanoyl-CoA dioxygenase domain-containing protein 1 homolog 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 phytanoyl-CoA dioxygenase domain-containing protein 1 homolog vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000077696.15.276e-2996.00SMESG000077696.1[more]
SMESG000077696.15.894e-2996.00SMESG000077696.1[more]
SMESG000077696.14.191e-16100.00SMESG000077696.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002374 ID=SMED30002374|Name=phytanoyl-CoA dioxygenase domain-containing protein 1 homolog|organism=Schmidtea mediterranea sexual|type=transcript|length=163bp
ATGGTCATTATTTTAAAAGATTTTTGGGACAAAAATGGTTTTATACATGT
TTCAAATGTTTTAACTATGGATGAAGTGAAAATTTACTCTGATATTTATG
ATCAATTTTTGAGCGGTGAAATAGATGCGTCAAATCACCGACATGATTTA
GGAAATATAAACG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000101muscle cell
PLANA:0002032epidermal cell
PLANA:0002056medial muscle cell
PLANA:0003001lateral region of the whole animal
PLANA:0003116parenchymal cell
Vocabulary: molecular function
TermDefinition
GO:0051213dioxygenase activity
Vocabulary: biological process
TermDefinition
GO:0055114oxidation-reduction process