G_PROTEIN_RECEP_F1_2 domain-containing protein

Overview
NameG_PROTEIN_RECEP_F1_2 domain-containing protein
Smed IDSMED30025062
Length (bp)344
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 G_PROTEIN_RECEP_F1_2 domain-containing protein (SMED30025062) t-SNE clustered cells

Violin plots show distribution of expression levels for G_PROTEIN_RECEP_F1_2 domain-containing protein (SMED30025062) 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 G_PROTEIN_RECEP_F1_2 domain-containing protein (SMED30025062) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for G_PROTEIN_RECEP_F1_2 domain-containing protein (SMED30025062) 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



SMED30025062

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30025062 dd_Smed_v4_1699_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30025062 dd_Smed_v4_1699_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30025062 dd_Smed_v4_1699_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30025062 dd_Smed_v4_1699_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30025062 dd_Smed_v4_1699_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30025062 dd_Smed_v4_1699_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30025062 Contig1366newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30025062 Contig1366uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30025062 dd_Smed_v4_1699_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
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BLAST of G_PROTEIN_RECEP_F1_2 domain-containing protein vs. TrEMBL
Match: A0A1I8GZL1 (G_PROTEIN_RECEP_F1_2 domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 119.398 bits (298), Expect = 9.208e-29
Identity = 47/68 (69.12%), Postives = 53/68 (77.94%), Query Frame = 1 
Query:   34 NRVLYYSMCRWGCGSTDTTYMCKWCGTRFCNLCFRGDFHGLMKEEGWCRVCNQKRCVGKRVEYVVRPQ 237
            +R L  +MCRWGC   DTTYMCKWCGTRFC  C  GDF+G MKE G CRVCNQKRC GKRVE+V +P+
Sbjct:  946 SRGLLVAMCRWGCSLVDTTYMCKWCGTRFCKECLLGDFYGRMKEPGQCRVCNQKRCQGKRVEFVTKPR 1013
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BLAST of G_PROTEIN_RECEP_F1_2 domain-containing protein vs. TrEMBL
Match: A0A267FJ62 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig010229g1 PE=4 SV=1)

HSP 1 Score: 98.5969 bits (244), Expect = 3.437e-24
Identity = 45/66 (68.18%), Postives = 50/66 (75.76%), Query Frame = 1 
Query:   55 MCRWGCGSTDTTYMCKWCGTRFCNLCFRGDFHGLMKEEGWCRVCNQKRCVGKRVEYVVRPQTKETD 252
            MCRWGC   DTTYMCKWCGTRFC  C  GDF+G MKE G CRVCNQKRC GKRVE+V +P+    +
Sbjct:    1 MCRWGCSLVDTTYMCKWCGTRFCKECLLGDFYGRMKEPGQCRVCNQKRCQGKRVEFVTKPRDPADE 66
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BLAST of G_PROTEIN_RECEP_F1_2 domain-containing protein vs. TrEMBL
Match: A0A267H9C0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig010606g2 PE=4 SV=1)

HSP 1 Score: 98.2117 bits (243), Expect = 4.213e-24
Identity = 44/66 (66.67%), Postives = 50/66 (75.76%), Query Frame = 1 
Query:   55 MCRWGCGSTDTTYMCKWCGTRFCNLCFRGDFHGLMKEEGWCRVCNQKRCVGKRVEYVVRPQTKETD 252
            MCRWGC   D+TYMCKWCGTRFC  C  GDF+G MKE G CRVCNQKRC GKRVE+V +P+    +
Sbjct:    1 MCRWGCSLVDSTYMCKWCGTRFCKECLLGDFYGRMKEPGQCRVCNQKRCQGKRVEFVTKPRDPADE 66
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BLAST of G_PROTEIN_RECEP_F1_2 domain-containing protein vs. TrEMBL
Match: A0A267H7I4 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig010606g1 PE=4 SV=1)

HSP 1 Score: 98.2117 bits (243), Expect = 4.699e-24
Identity = 44/66 (66.67%), Postives = 50/66 (75.76%), Query Frame = 1 
Query:   55 MCRWGCGSTDTTYMCKWCGTRFCNLCFRGDFHGLMKEEGWCRVCNQKRCVGKRVEYVVRPQTKETD 252
            MCRWGC   D+TYMCKWCGTRFC  C  GDF+G MKE G CRVCNQKRC GKRVE+V +P+    +
Sbjct:    1 MCRWGCSLVDSTYMCKWCGTRFCKECLLGDFYGRMKEPGQCRVCNQKRCQGKRVEFVTKPRDPADE 66
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BLAST of G_PROTEIN_RECEP_F1_2 domain-containing protein vs. TrEMBL
Match: K1QGJ9 (Uncharacterized protein OS=Crassostrea gigas OX=29159 GN=CGI_10013634 PE=4 SV=1)

HSP 1 Score: 97.4413 bits (241), Expect = 6.686e-24
Identity = 44/77 (57.14%), Postives = 54/77 (70.13%), Query Frame = 1 
Query:   55 MCRWGCGSTDTTYMCKWCGTRFCNLCFRGDFHGLMKEEGWCRVCNQKRCVGKRVEYVVRPQTKETDPRKKNNLSSYK 285
            MCRWGC   +TTYMCKWCGTR+C  C +G+F G MKE   CRVCNQ RC G RVEYV RP+T+E D ++  +    +
Sbjct:    1 MCRWGCALPNTTYMCKWCGTRYCKECLKGEFTGEMKEPNKCRVCNQVRCQGLRVEYVPRPKTEEDDKKRSKSAPPSR 77
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BLAST of G_PROTEIN_RECEP_F1_2 domain-containing protein vs. Planmine SMEST
Match: SMESG000018450.1 (SMESG000018450.1)

HSP 1 Score: 166.007 bits (419), Expect = 1.005e-54
Identity = 77/78 (98.72%), Postives = 77/78 (98.72%), Query Frame = 1 
Query:   55 MCRWGCGSTDTTYMCKWCGTRFCNLCFRGDFHGLMKEEGWCRVCNQKRCVGKRVEYVVRPQTKETDPRKKNNLSSYKT 288
            MCRWGCGSTDTTYMCKWCGTRFCNLCFRGDFHGLMKEEGWCRVCNQKRCVGKRVEYVVRPQTKETDPRKKNNLSS KT
Sbjct:    1 MCRWGCGSTDTTYMCKWCGTRFCNLCFRGDFHGLMKEEGWCRVCNQKRCVGKRVEYVVRPQTKETDPRKKNNLSSSKT 78
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BLAST of G_PROTEIN_RECEP_F1_2 domain-containing protein vs. Planmine SMEST
Match: SMESG000065254.1 (SMESG000065254.1)

HSP 1 Score: 61.2326 bits (147), Expect = 9.743e-13
Identity = 32/67 (47.76%), Postives = 40/67 (59.70%), Query Frame = 1 
Query:   34 NRVLYYS----MCRWG-CGSTDTTYMCKWCGTRFCNLCFRGDFHGLMKEEGWCRVCNQKRCVGKRVE 219
            NR  Y S    MCRW  C +  TT+ CK+CGTRFC  C RG+F GLM +   C VC Q  C G+ ++
Sbjct:   86 NRKFYISIHVLMCRWEYCLALGTTFKCKYCGTRFCTECLRGEFIGLMADPDKCFVCRQNNCHGEMID 152
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BLAST of G_PROTEIN_RECEP_F1_2 domain-containing protein vs. Planmine SMEST
Match: SMESG000054504.1 (SMESG000054504.1)

HSP 1 Score: 60.077 bits (144), Expect = 2.847e-12
Identity = 30/65 (46.15%), Postives = 38/65 (58.46%), Query Frame = 1 
Query:   55 MCRW-GCGSTDTTYMCKWCGTRFCNLCFRGDFHGLMKEEGWCRVCNQKRCVGKRVEYVVRPQTKE 246
            MCRW  C    TT MCK+CG RFC LC RGDF+GL++ +  C +C       + VE   +P  KE
Sbjct:    1 MCRWKSCIGVGTTKMCKFCGVRFCTLCLRGDFNGLIQNDK-CAICKNYIFSAETVELANKPARKE 64
The following BLAST results are available for this feature:
BLAST of G_PROTEIN_RECEP_F1_2 domain-containing protein 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 G_PROTEIN_RECEP_F1_2 domain-containing protein 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 G_PROTEIN_RECEP_F1_2 domain-containing protein 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 G_PROTEIN_RECEP_F1_2 domain-containing protein 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 G_PROTEIN_RECEP_F1_2 domain-containing protein 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 G_PROTEIN_RECEP_F1_2 domain-containing protein 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 G_PROTEIN_RECEP_F1_2 domain-containing protein 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 G_PROTEIN_RECEP_F1_2 domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8GZL19.208e-2969.12G_PROTEIN_RECEP_F1_2 domain-containing protein OS=... [more]
A0A267FJ623.437e-2468.18Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267H9C04.213e-2466.67Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267H7I44.699e-2466.67Uncharacterized protein OS=Macrostomum lignano OX=... [more]
K1QGJ96.686e-2457.14Uncharacterized protein OS=Crassostrea gigas OX=29... [more]
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BLAST of G_PROTEIN_RECEP_F1_2 domain-containing protein 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 G_PROTEIN_RECEP_F1_2 domain-containing 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
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BLAST of G_PROTEIN_RECEP_F1_2 domain-containing protein 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 G_PROTEIN_RECEP_F1_2 domain-containing protein 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 G_PROTEIN_RECEP_F1_2 domain-containing protein 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 G_PROTEIN_RECEP_F1_2 domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000018450.11.005e-5498.72SMESG000018450.1[more]
SMESG000065254.19.743e-1347.76SMESG000065254.1[more]
SMESG000054504.12.847e-1246.15SMESG000054504.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025062 ID=SMED30025062|Name=G_PROTEIN_RECEP_F1_2 domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=344bp
CTCATTTATTTAGAAATTAGCATCGCCATCTGTAACAGAGTTCTCTATTA
TTCAATGTGCCGATGGGGATGCGGATCTACTGACACGACATACATGTGCA
AATGGTGTGGCACGAGATTTTGTAATCTTTGTTTTCGAGGTGATTTCCAT
GGACTGATGAAGGAAGAAGGTTGGTGTCGTGTTTGTAATCAGAAAAGATG
TGTCGGTAAGCGAGTCGAGTACGTTGTTCGTCCACAAACTAAAGAAACTG
ATCCAAGAAAGAAAAACAATCTTTCCTCATATAAAACACGATCAAAGTCA
GCAAGGTCACAAAACAAATCAGCAAAGAAAAAGTCGAAAAAAAG
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protein sequence of SMED30025062-orf-1

>SMED30025062-orf-1 ID=SMED30025062-orf-1|Name=SMED30025062-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp
LIYLEISIAICNRVLYYSMCRWGCGSTDTTYMCKWCGTRFCNLCFRGDFH
GLMKEEGWCRVCNQKRCVGKRVEYVVRPQTKETDPRKKNNLSSYKTRSKS
ARSQNKSAKKKSKK
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 78..114