PIGA protein

Overview
NamePIGA protein
Smed IDSMED30032377
Length (bp)719
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 PIGA protein (SMED30032377) t-SNE clustered cells

Violin plots show distribution of expression levels for PIGA protein (SMED30032377) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

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 PIGA protein (SMED30032377) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for PIGA protein (SMED30032377) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top


 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30032377

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
parapharyngeal regionSMED30032377 SmedASXL_007516SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30032377 dd_Smed_v4_14814_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30032377 dd_Smed_v4_14814_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30032377 dd_Smed_v4_14814_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30032377 dd_Smed_v4_14814_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30032377 dd_Smed_v4_14814_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 PIGA protein vs. TrEMBL
Match: A0A1I8HA02 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 93.2041 bits (230), Expect = 4.166e-20
Identity = 38/76 (50.00%), Postives = 61/76 (80.26%), Query Frame = 3
Query:  291 KQHRFSSVALDLLRVNDNEDIHPFGRGGKFTGVLYGNQKIKNRIDHSKIFVWILFIGFALTGSALIIILAEIDRKQ 518
            +++RFS+VA+++LR  ++ D+HP+GRGG+F GVLY ++++K ++DH+K   WI+F GF L  S  IIILAE++R+Q
Sbjct:   43 QENRFSAVAIEMLREQEDRDLHPYGRGGRFEGVLY-SRRVKVQVDHAKFLAWIVFAGFILLTSGAIIILAEMERRQ 117          
BLAST of PIGA protein vs. TrEMBL
Match: A0A1I8IHX0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 93.5893 bits (231), Expect = 3.756e-18
Identity = 38/76 (50.00%), Postives = 61/76 (80.26%), Query Frame = 3
Query:  291 KQHRFSSVALDLLRVNDNEDIHPFGRGGKFTGVLYGNQKIKNRIDHSKIFVWILFIGFALTGSALIIILAEIDRKQ 518
            +++RFS+VA+++LR  ++ D+HP+GRGG+F GVLY ++++K ++DH+K   WI+F GF L  S  IIILAE++R+Q
Sbjct:   43 QENRFSAVAIEMLREQEDRDLHPYGRGGRFEGVLY-SRRVKVQVDHAKFLAWIVFAGFILLTSGAIIILAEMERRQ 117          
BLAST of PIGA protein vs. TrEMBL
Match: A0A1I8HJ73 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 1.829e-11
Identity = 28/57 (49.12%), Postives = 44/57 (77.19%), Query Frame = 3
Query:  282 NKSKQHRFSSVALDLLRVNDNEDIHPFGRGGKFTGVLYGNQKIKNRIDHSKIFVWIL 452
            NK    RFS+VA+++LR  ++ D+HPFGRGG+F GVLY ++++K ++DH+K   WI+
Sbjct:   68 NKELDKRFSAVAMEMLREQEDRDLHPFGRGGRFEGVLY-SRRVKVQVDHTKFLAWIV 123          
BLAST of PIGA protein vs. TrEMBL
Match: A0A1I8HLH4 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 3.911e-8
Identity = 27/52 (51.92%), Postives = 38/52 (73.08%), Query Frame = 3
Query:  282 NKSKQHRFSSVALDLLRVNDNEDIHPFGRGGKFTGVLYGNQK---IKNRIDH 428
            NK    RFS+VA+++LR  ++ D+HPFGRGG+F GVLY  +K   +KNR +H
Sbjct:  130 NKELDKRFSAVAMEMLREQEDRDLHPFGRGGRFEGVLYSRRKWNAVKNRNNH 181          
BLAST of PIGA protein vs. TrEMBL
Match: A0A183WGT4 (Uncharacterized protein OS=Trichobilharzia regenti OX=157069 GN=TRE_LOCUS11334 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 6.011e-8
Identity = 27/79 (34.18%), Postives = 48/79 (60.76%), Query Frame = 3
Query:  270 STNP--NKSKQHRFSSVALDLLRVNDNEDIHPFGRGGKFTGVLYGNQKIKNRIDHSKIFVWILFIGFALTGSALIIILA 500
            +T P   + +Q R SSV L++L   +  DIHP+GRGG + G+LY + + + ++D +  FVW +F+   +  S  I+ ++
Sbjct:   65 TTRPVLTEEQQMRLSSVTLEMLMEREEIDIHPYGRGGIYEGILYKS-RAEEQMDFTAAFVWFIFVSSVIMMSGSIVFVS 142          
BLAST of PIGA protein vs. Planmine SMEST
Match: SMESG000081746.1 (SMESG000081746.1)

HSP 1 Score: 251.906 bits (642), Expect = 3.526e-86
Identity = 122/122 (100.00%), Postives = 122/122 (100.00%), Query Frame = 3
Query:  177 MSSKNENCVNGNCETLVEMIENDTLNFMLSMSTNPNKSKQHRFSSVALDLLRVNDNEDIHPFGRGGKFTGVLYGNQKIKNRIDHSKIFVWILFIGFALTGSALIIILAEIDRKQTKSFGSIT 542
            MSSKNENCVNGNCETLVEMIENDTLNFMLSMSTNPNKSKQHRFSSVALDLLRVNDNEDIHPFGRGGKFTGVLYGNQKIKNRIDHSKIFVWILFIGFALTGSALIIILAEIDRKQTKSFGSIT
Sbjct:    1 MSSKNENCVNGNCETLVEMIENDTLNFMLSMSTNPNKSKQHRFSSVALDLLRVNDNEDIHPFGRGGKFTGVLYGNQKIKNRIDHSKIFVWILFIGFALTGSALIIILAEIDRKQTKSFGSIT 122          
BLAST of PIGA protein vs. Planmine SMEST
Match: SMESG000079358.1 (SMESG000079358.1)

HSP 1 Score: 74.3294 bits (181), Expect = 1.301e-16
Identity = 43/103 (41.75%), Postives = 64/103 (62.14%), Query Frame = 3
Query:  213 CETLVEMIENDTLNFMLSMSTN---PNKSKQHRFSSVALDLLRVNDNEDIHPFGRGGKFTGVLYGNQKIKNRIDHSKIFVWILFIGFALTGSALIIILAEIDR 512
             + L++ +E +T  F+ S + +    N  K  RFS+VA+D+LR  ++ DIHP+GRGG+F GVLY  +KI+ R++ +K   W+  IG  L  S  II LAE  R
Sbjct:   31 SDKLIQSVEENTNAFISSYNKDKLYSNVPKVPRFSTVAMDILRSTEDHDIHPYGRGGRFEGVLYTGRKIRIRLESNKWLAWLTLIGLLLMLSLTIIFLAEQHR 133          
BLAST of PIGA protein vs. Planmine SMEST
Match: SMESG000048041.1 (SMESG000048041.1)

HSP 1 Score: 62.3882 bits (150), Expect = 2.792e-12
Identity = 31/75 (41.33%), Postives = 42/75 (56.00%), Query Frame = 3
Query:  297 HRFSSVALDLLRVNDNEDIHPFGRGGKFTGVLYGNQKIKNRIDHSKIFVWILFIGFALTGSALIIILAEIDRKQT 521
             RFS +A+ +L+  D  D HP+GRG    G    +   K+  D S I VW +F+GF L    +IIILAE+ R Q 
Sbjct:   53 RRFSDIAITMLKDKDETDEHPYGRGKTVDGCFNRSSSGKDS-DQSMIIVWFIFVGFLLGSCVMIIILAELYRSQA 126          
BLAST of PIGA protein vs. Planmine SMEST
Match: SMESG000047330.1 (SMESG000047330.1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.021e-11
Identity = 23/59 (38.98%), Postives = 40/59 (67.80%), Query Frame = 3
Query:  342 NEDIHPFGRGGKFTGVLYGNQKIKNRIDHSKIFVWILFIGFALTGSALIIILAEIDRKQ 518
            + DIHP+G    ++ +++G +++K ++DH+K   WI F+ F L  SA II+LAE +R +
Sbjct:   47 DRDIHPYGETRCYSDIIFGQREVKVKLDHTKFLAWISFVVFLLIISATIIVLAEFERTE 105          
The following BLAST results are available for this feature:
BLAST of PIGA protein vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of PIGA protein vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of PIGA protein vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of PIGA protein vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of PIGA protein vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of PIGA protein vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of PIGA protein vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of PIGA protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8HA024.166e-2050.00Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8IHX03.756e-1850.00Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8HJ731.829e-1149.12Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8HLH43.911e-851.92Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A183WGT46.011e-834.18Uncharacterized protein OS=Trichobilharzia regenti... [more]
back to top
BLAST of PIGA protein vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of PIGA protein vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of PIGA protein vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of PIGA protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of PIGA protein vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of PIGA protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000081746.13.526e-86100.00SMESG000081746.1[more]
SMESG000079358.11.301e-1641.75SMESG000079358.1[more]
SMESG000048041.12.792e-1241.33SMESG000048041.1[more]
SMESG000047330.11.021e-1138.98SMESG000047330.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032377 ID=SMED30032377|Name=PIGA protein|organism=Schmidtea mediterranea sexual|type=transcript|length=719bp
AACTGTTGATATTTTAATAAGAATCACTATTCGTTACTGATATTTTTTTA
GATATATTGGATTACAAATCAATATCCAGCTGTTGTGATTCTGAAATAAT
CTATGGAAACTTTGAAAAATATTTTCTTAACTACTCAATAACATATTTTT
AGGTCATTTTGGAATATTATTTTTTTATGTCATCGAAAAATGAAAACTGT
GTAAATGGAAATTGTGAAACTCTGGTAGAAATGATTGAAAATGACACTTT
GAATTTTATGCTATCTATGAGTACCAATCCAAATAAATCAAAACAGCACA
GGTTTTCGAGTGTGGCATTAGACCTACTTCGAGTTAATGATAATGAAGAT
ATTCATCCATTCGGCAGAGGAGGGAAGTTTACAGGTGTGCTGTATGGAAA
CCAAAAAATAAAAAATAGGATAGATCATTCAAAAATATTTGTGTGGATTC
TTTTCATTGGATTTGCTTTAACAGGATCTGCGTTAATTATAATACTAGCA
GAAATTGATCGTAAACAAACAAAATCATTTGGATCAATCACCAATCGGTC
AGTGTGATCATAAAATAGTCATTTCAATTCTAGCTAGATAGTTATAAACA
CAGACTTTGCTCAAATCCGCATCAAAATTGTCCGGGATTTTCATTGTTTT
AATAAATTGACTTTCACTTATTACTACTTCATTATTATGTAATCAGTAAA
AATACATTTTCATTTTTAA
back to top

protein sequence of SMED30032377-orf-1

>SMED30032377-orf-1 ID=SMED30032377-orf-1|Name=SMED30032377-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=127bp
MSSKNENCVNGNCETLVEMIENDTLNFMLSMSTNPNKSKQHRFSSVALDL
LRVNDNEDIHPFGRGGKFTGVLYGNQKIKNRIDHSKIFVWILFIGFALTG
SALIIILAEIDRKQTKSFGSITNRSV*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: biological process
TermDefinition
GO:0006506GPI anchor biosynthetic process
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000101muscle cell
PLANA:0000420parapharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 87..109