Post-GPI attachment to proteins factor 2-like

Overview
NamePost-GPI attachment to proteins factor 2-like
Smed IDSMED30034590
Length (bp)890
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 Post-GPI attachment to proteins factor 2-like (SMED30034590) t-SNE clustered cells

Violin plots show distribution of expression levels for Post-GPI attachment to proteins factor 2-like (SMED30034590) 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 Post-GPI attachment to proteins factor 2-like (SMED30034590) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Post-GPI attachment to proteins factor 2-like (SMED30034590) 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




SMED30034590

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
nervous systemSMED30034590h1SMcG0007086 dd_Smed_v4_10182_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30034590h1SMcG0007086 dd_Smed_v4_10182_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30034590h1SMcG0007086 Contig4671GPL15192PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30034590h1SMcG0007086 dd_Smed_v6_10182_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30034590h1SMcG0007086 OX_Smed_1.0.20349ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Post-GPI attachment to proteins factor 2-like vs. Ensembl Fly
Match: CG7990 (gene:FBgn0030997 transcript:FBtr0074695)

HSP 1 Score: 53.5286 bits (127), Expect = 6.790e-8
Identity = 25/49 (51.02%), Postives = 32/49 (65.31%), Query Frame = 1
Query:   64 VITVSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQ 210
            V+T   PL  L  CF+T+   Q+D ++E  C V N IPS+SAITG SPQ
Sbjct:   80 VVTALLPLVTLFTCFVTAYVFQYDDVHETHCRVYNIIPSISAITGVSPQ 128          

HSP 2 Score: 51.6026 bits (122), Expect = 2.692e-7
Identity = 30/71 (42.25%), Postives = 43/71 (60.56%), Query Frame = 2
Query:  212 AMHEKIFITFMVTSCVYMAMTLYLYRLSHGDSANWTKLEMLSYKFKVNFFILILLCTTGLVYFIAIHRIYC 424
             +HE+IFITFMV S  YM  T+ L  + +   A  ++ ++LS K+K   F + +L T GL+ F A HR YC
Sbjct:  200 PVHERIFITFMVCSLCYMLATIKLNGILNAGQA-LSEKQLLSIKWKKILFAVSILSTVGLLVFFAKHRFYC 269          
BLAST of Post-GPI attachment to proteins factor 2-like vs. UniProt/SwissProt
Match: sp|Q9VWK6|PGP2L_DROME (Post-GPI attachment to proteins factor 2-like OS=Drosophila melanogaster OX=7227 GN=CG7990 PE=2 SV=4)

HSP 1 Score: 53.5286 bits (127), Expect = 6.806e-7
Identity = 25/49 (51.02%), Postives = 32/49 (65.31%), Query Frame = 1
Query:   64 VITVSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQ 210
            V+T   PL  L  CF+T+   Q+D ++E  C V N IPS+SAITG SPQ
Sbjct:   80 VVTALLPLVTLFTCFVTAYVFQYDDVHETHCRVYNIIPSISAITGVSPQ 128          

HSP 2 Score: 51.6026 bits (122), Expect = 2.699e-6
Identity = 30/71 (42.25%), Postives = 43/71 (60.56%), Query Frame = 2
Query:  212 AMHEKIFITFMVTSCVYMAMTLYLYRLSHGDSANWTKLEMLSYKFKVNFFILILLCTTGLVYFIAIHRIYC 424
             +HE+IFITFMV S  YM  T+ L  + +   A  ++ ++LS K+K   F + +L T GL+ F A HR YC
Sbjct:  200 PVHERIFITFMVCSLCYMLATIKLNGILNAGQA-LSEKQLLSIKWKKILFAVSILSTVGLLVFFAKHRFYC 269          
BLAST of Post-GPI attachment to proteins factor 2-like vs. TrEMBL
Match: A0A183LBM7 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS1202 PE=4 SV=1)

HSP 1 Score: 70.8626 bits (172), Expect = 1.202e-10
Identity = 31/58 (53.45%), Postives = 39/58 (67.24%), Query Frame = 1
Query:   73 VSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQSNARKDIYNIHG 246
            VS PLFGLIICF  S+Y  FD++ E VCGV NF+PS+SA+TG  PQ    +    +H 
Sbjct:   24 VSLPLFGLIICFFVSTYNTFDEVTESVCGVSNFVPSISAVTGIKPQIYLWRYTVGLHS 81          
BLAST of Post-GPI attachment to proteins factor 2-like vs. TrEMBL
Match: A0A183Q635 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS22071 PE=4 SV=1)

HSP 1 Score: 70.8626 bits (172), Expect = 1.214e-10
Identity = 31/57 (54.39%), Postives = 39/57 (68.42%), Query Frame = 1
Query:   73 VSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQSNARKDIYNIH 243
            VS PLFGLIICF  S+Y  FD++ E VCGV NF+PS+SA+TG  PQ    +    +H
Sbjct:   24 VSLPLFGLIICFFVSTYNTFDEVTESVCGVSNFVPSISAVTGIKPQIYLWRYTVGLH 80          
BLAST of Post-GPI attachment to proteins factor 2-like vs. TrEMBL
Match: A0A183KNT8 (Uncharacterized protein OS=Schistosoma curassoni OX=6186 GN=SCUD_LOCUS16718 PE=4 SV=1)

HSP 1 Score: 70.8626 bits (172), Expect = 1.301e-10
Identity = 31/58 (53.45%), Postives = 39/58 (67.24%), Query Frame = 1
Query:   73 VSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQSNARKDIYNIHG 246
            VS PLFGLIICF  S+Y  FD++ E VCGV NF+PS+SA+TG  PQ    +    +H 
Sbjct:   24 VSLPLFGLIICFFVSTYNTFDEVTESVCGVTNFVPSISAVTGIKPQIYLWRYTVGLHS 81          
BLAST of Post-GPI attachment to proteins factor 2-like vs. TrEMBL
Match: A0A430Q0X2 (Uncharacterized protein OS=Schistosoma bovis OX=6184 GN=DC041_0002180 PE=4 SV=1)

HSP 1 Score: 70.8626 bits (172), Expect = 1.560e-10
Identity = 31/58 (53.45%), Postives = 39/58 (67.24%), Query Frame = 1
Query:   73 VSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQSNARKDIYNIHG 246
            VS PLFGLIICF  S+Y  FD++ E VCGV NF+PS+SA+TG  PQ    +    +H 
Sbjct:   24 VSLPLFGLIICFFVSTYNTFDEVTESVCGVTNFVPSISAVTGIKPQIYLWRYTVGLHS 81          
BLAST of Post-GPI attachment to proteins factor 2-like vs. TrEMBL
Match: A0A183QKU4 (Uncharacterized protein OS=Schistosoma rodhaini OX=6188 PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 3.209e-10
Identity = 31/57 (54.39%), Postives = 39/57 (68.42%), Query Frame = 1
Query:   73 VSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQSNARKDIYNIH 243
            VS  LFGLIICFL S+Y  FD++ E VCGV NF+PS+SA+TG  PQ    +    +H
Sbjct:   24 VSLSLFGLIICFLISTYNSFDEVTESVCGVSNFVPSISAVTGIKPQIYLWRFTVGLH 80          
BLAST of Post-GPI attachment to proteins factor 2-like vs. Planmine SMEST
Match: SMESG000044614.1 (SMESG000044614.1)

HSP 1 Score: 196.438 bits (498), Expect = 9.933e-64
Identity = 110/111 (99.10%), Postives = 111/111 (100.00%), Query Frame = 1
Query:    7 MTLCKKXXXXXXXXXXXXGVITVSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQSNARKDIYNIHGDVLRIYGNDPLFVQIISRGFRQLDETGNAFL 339
            MTLCKKNVNLFNLPFNVLGVITVSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQSNARKDIYNIHGDVLRIYGNDPLFV+IISRGFRQLDETGNAFL
Sbjct:    1 MTLCKKNVNLFNLPFNVLGVITVSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQSNARKDIYNIHGDVLRIYGNDPLFVEIISRGFRQLDETGNAFL 111          
BLAST of Post-GPI attachment to proteins factor 2-like vs. Planmine SMEST
Match: SMESG000044614.1 (SMESG000044614.1)

HSP 1 Score: 118.242 bits (295), Expect = 1.796e-31
Identity = 60/81 (74.07%), Postives = 61/81 (75.31%), Query Frame = 2
Query:  194 PELLLRAMHEKIFITFMVTSCVYMAMTLYLYRLSHGDSANWTKLEMLSYKFKVNFFILILLCTTGLVYFIAIHRIYCTPNG 436
            P +    MHEKIFITFM              RLSHGDSANWTKLEMLSYKFKVNFFILILLCTTGLVYFIAIHRIYCTPN 
Sbjct:  134 PSIDNYPMHEKIFITFM--------------RLSHGDSANWTKLEMLSYKFKVNFFILILLCTTGLVYFIAIHRIYCTPNA 200          

HSP 2 Score: 110.153 bits (274), Expect = 1.571e-28
Identity = 69/80 (86.25%), Postives = 71/80 (88.75%), Query Frame = 1
Query:    7 MTLCKKXXXXXXXXXXXXGVITVSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQSNARKDIYNIHG 246
            MTLCKKNVNLFNLPFNVLGVITVSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQ    +    +H 
Sbjct:    1 MTLCKKNVNLFNLPFNVLGVITVSFPLFGLIICFLTSSYTQFDKINEIVCGVKNFIPSVSAITGTSPQRYIWRVFIALHS 80          
The following BLAST results are available for this feature:
BLAST of Post-GPI attachment to proteins factor 2-like 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 Post-GPI attachment to proteins factor 2-like 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 Post-GPI attachment to proteins factor 2-like vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CG79906.790e-851.02gene:FBgn0030997 transcript:FBtr0074695[more]
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BLAST of Post-GPI attachment to proteins factor 2-like 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 Post-GPI attachment to proteins factor 2-like 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 Post-GPI attachment to proteins factor 2-like 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 Post-GPI attachment to proteins factor 2-like vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q9VWK6|PGP2L_DROME6.806e-751.02Post-GPI attachment to proteins factor 2-like OS=D... [more]
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BLAST of Post-GPI attachment to proteins factor 2-like vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183LBM71.202e-1053.45Uncharacterized protein OS=Schistosoma margrebowie... [more]
A0A183Q6351.214e-1054.39Uncharacterized protein OS=Schistosoma mattheei OX... [more]
A0A183KNT81.301e-1053.45Uncharacterized protein OS=Schistosoma curassoni O... [more]
A0A430Q0X21.560e-1053.45Uncharacterized protein OS=Schistosoma bovis OX=61... [more]
A0A183QKU43.209e-1054.39Uncharacterized protein OS=Schistosoma rodhaini OX... [more]
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BLAST of Post-GPI attachment to proteins factor 2-like 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 Post-GPI attachment to proteins factor 2-like 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 Post-GPI attachment to proteins factor 2-like 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 Post-GPI attachment to proteins factor 2-like 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 Post-GPI attachment to proteins factor 2-like 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 Post-GPI attachment to proteins factor 2-like vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000044614.19.933e-6499.10SMESG000044614.1[more]
SMESG000044614.11.796e-3174.07SMESG000044614.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034590 ID=SMED30034590|Name=Post-GPI attachment to proteins factor 2-like|organism=Schmidtea mediterranea sexual|type=transcript|length=890bp
TGATAAATGACTTTATGCAAAAAAAATGTAAACTTATTTAATTTACCATT
TAATGTATTGGGAGTCATTACAGTTTCATTTCCATTATTTGGTTTAATAA
TTTGTTTCCTGACAAGTTCCTATACTCAGTTTGATAAAATAAATGAAATT
GTCTGTGGCGTTAAAAATTTTATTCCATCTGTTAGTGCAATAACCGGAAC
TTCTCCTCAGAGCAATGCACGAAAAGATATTTATAACATTCATGGTGACG
TCTTGCGTATATATGGCAATGACCCTTTATTTGTACAGATTATCTCACGG
GGATTCCGCCAACTGGACGAAACTGGAAATGCTTTCTTATAAATTTAAAG
TTAATTTCTTTATTTTAATTCTGCTGTGTACAACCGGCCTCGTTTACTTT
ATTGCAATTCACCGAATATATTGCACGCCAAATGGTTAGATCAAATTATA
TTTTATGGACAATGAAATGGAATTTCTAGCAAAATTTTATTTCAATTTAA
AACGAGTAGGTATATGTGTCACACCTAGCATCCCCTCGCATTTCTAAGAA
TAATATTTTGTCGACCAATTAATTTTAGAATGTTGACTAAAATCCGGTGG
AATTTCAAATAATTTTTTTAAAATTTGCCAGGAAAAAAATCTTTTGATAA
ATTCATTTGCGAGACTTGAAAAGATTGGCCTGCCAGGAATGCGAAATGTA
TTTAAATATGGCGTGGCGCATTATTTAATAATTATCAGTATATTTAAAAA
TTTAATGTTTAAATGGCAGTAGCTATCGATGCGCGATTACGCAATTGTTG
AATAAATTTATTATTTTTGACTGTACTAAATTTTTTAATATAAATTAATT
AAATATACATACTTCGCAATTGTCTATTATTGGTCTATTA
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protein sequence of SMED30034590-orf-1

>SMED30034590-orf-1 ID=SMED30034590-orf-1|Name=SMED30034590-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=112bp
MTLCKKNVNLFNLPFNVLGVITVSFPLFGLIICFLTSSYTQFDKINEIVC
GVKNFIPSVSAITGTSPQSNARKDIYNIHGDVLRIYGNDPLFVQIISRGF
RQLDETGNAFL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0000139Golgi membrane
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR039545PGAP2
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePANTHERPTHR12892:SF17POST-GPI ATTACHMENT TO PROTEINS FACTOR 2-LIKEcoord: 8..68
NoneNo IPR availableTMHMMTMhelixcoord: 15..37
IPR039545Post-GPI attachment to proteins factor 2PANTHERPTHR12892FGF RECEPTOR ACTIVATING PROTEIN 1coord: 8..68