GCR148

Overview
NameGCR148
Smed IDSMED30024905
Length (bp)713
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 GCR148 (SMED30024905) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for GCR148 (SMED30024905) 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




SMED30024905

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
cephalic gangliaSMED30024905h1SMcG0000120 dd_Smed_v4_63832_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30024905h1SMcG0000120 dd_Smed_v4_42827_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30024905h1SMcG0000120 dd_Smed_v4_42827_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30024905h1SMcG0000120 dd_Smed_v4_42827_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30024905h1SMcG0000120 dd_Smed_v6_42827_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of GCR148 vs. TrEMBL
Match: A0A193KUE9 (GCR146 OS=Schmidtea mediterranea OX=79327 GN=gcr146 PE=2 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 1.581e-10
Identity = 54/221 (24.43%), Postives = 108/221 (48.87%), Query Frame = 2
Query:    8 GDSILFVGFRYLFICLFLSLNIVLLAFLFKHQMASKTATLLIKFQTXXXXXXXXXXXXXXXKEELPFRTKSEAYGLFYCYFTFTDTLVYVLINSSIFLMVSLSVDRFICIVFPLFYRRKCNKCVYIYIIPSILCGIVVFVPYCYFTEI---EIRETNSTEMDLNYIFSCTLSKSLIATLIYLIMYAISPVTIILLLNILSIKCLIQSLKNINKSVKSRKRM 661
            GD+ +F GFR   +     +NI      FK ++ S+    LI+ Q+++  I+++       +E   F  +++ Y +FYCY  +     ++    S+++M  +S DRFICIVFPL+Y++   + ++I ++    C  +V    C  + I    I + N+T++     + CT   ++   +I    + + P+  +   N +S + L ++ K     +   KR+
Sbjct:   10 GDNEIFFGFRASLLIFLCIINIYFFIVSFKFKITSRNGLTLIRCQSVVSFILIVIYFFDYFRENEKFSNENKIYSIFYCYIWYFSIFYWIFSTISVYIMALISFDRFICIVFPLYYKKLTVRFIFILLLIMSFCVSIV----CVVSTILYVNIAKNNNTDL-----YFCTSKITISGAIINTCFHGLIPIISLAGFNAMSARNLARNSKTQLLRLDDIKRL 221          
BLAST of GCR148 vs. TrEMBL
Match: A0A193KUN8 (GCR148 OS=Schmidtea mediterranea OX=79327 GN=gcr148 PE=2 SV=1)

HSP 1 Score: 62.3882 bits (150), Expect = 9.198e-8
Identity = 61/243 (25.10%), Postives = 118/243 (48.56%), Query Frame = 2
Query:    8 GDSILFVGFRYLFICLFLSLNIVLLAFLFKHQMASKTATLLIKFQTXXXXXXXXXXXXXXXKEELPFRTKSEAYGLFYCYFTFTDTLVYVLINSSIFLMVSLSVDRFICIVFPLFYRRKCNKCVYIYIIPSIL----CGIVVFVPYCYFTEIEIRETNSTEMDLNYIFSCTLSKSLIATLIYLIMYAISPVTIILLLNILSIKCLIQSLKNI---NKSVK--SRKRMITKFTIANIFSNFFYT 709
            GD+ +F G R   +      N+      FK ++ S     LI+ Q+++  ++LI   +   KE   F ++++ Y +FYCY      + ++    SI+ M+ +S DRF+CIVFPL+Y++   +   I +I         G+V+ +       I++   N+T       + CT   +L   +I L +  + P+  + L N++S + L+++ K     + ++K   RK +  +F+I+      FY+
Sbjct:   10 GDNEIFFGLRSGLVIFLFFTNLFFFIVSFKIKITSTNGLALIRCQSVVSFVLLITYVLDFFKETEIFPSENKFYSIFYCYILHFSFIYWIFCAISIYTMILISFDRFVCIVFPLYYKKLTKRFTIISLISISSFVFSYGLVISM-----NNIKLEIINNTGNQNKQPYICTTKFTLTDIIINLCVQGMIPLISLALFNVMSARSLLRNSKTQLLRSDAIKRLKRKNLFYRFSISTFIMTLFYS 247          
BLAST of GCR148 vs. Planmine SMEST
Match: SMESG000000478.1 (SMESG000000478.1)

HSP 1 Score: 155.606 bits (392), Expect = 5.873e-46
Identity = 101/231 (43.72%), Postives = 151/231 (65.37%), Query Frame = 2
Query:    5 LGDSILFVGFRYLFICLFLSLNIVLLAFLFKHQMASKTATLLIKFQTXXXXXXXXXXXXXXXKEELPFRTKSEAYGLFYCYFTFTDTLVYVLINSSIFLMVSLSVDRFICIVFPLFYRRKCNKCVYIYIIPSILCGIVVFVPYCYFTEIEIRETNSTEMDLNYIFSCTLSKSLIATLIYLIMYAISPVTIILLLNILSIKCLIQSLKN-INKS----VKSRKRMITKFTIA 682
            LGDS+ F+  RY  + +F  +N++LL F+ KH++ASK A+ LIK +T  D+IVL+ +     KE   F++   +Y  FYCYF F + L + ++  SI+LM+SLS+DRF+CIV P +Y+R     VY YII SI+ G++      +F +I++   N T   L   +SC L KS+  T++Y++ YAI PV +I++LNILSIK L+ SLKN +N S    V SRK++I +FT+A
Sbjct:    8 LGDSLAFILIRYAIVLIFFIINLILLIFISKHKIASKNASSLIKTETCFDLIVLLCLVFSMFKEHPVFQSHDVSYVRFYCYFIFGNQLFWSMLTISIYLMISLSIDRFVCIVLPFYYKRVKRITVYFYIISSIVFGLLFGFVNLFFIKIKVIRKNETNRQLKVNYSCPLPKSVTNTIVYILTYAIGPVIVIVILNILSIKSLVHSLKNKVNSSTNPIVFSRKKVIMRFTVA 238          
BLAST of GCR148 vs. Planmine SMEST
Match: SMESG000056470.1 (SMESG000056470.1)

HSP 1 Score: 54.6842 bits (130), Expect = 1.098e-8
Identity = 56/232 (24.14%), Postives = 107/232 (46.12%), Query Frame = 2
Query:    8 GDSILFVGFRYLFICLFLSLNIVLLAFLFKHQMASKTATLLIKFQTXXXXXXXXXXXXXXXKEELPFRTKSEAYGLFYCYFTFTDTLVYVLINSSIFLMVSLSVDRFICIVFPLFYRRKCNKCVYIYIIPSILCGIVVFVPYCYF-----TEIEIRETNSTEMDLNYIFSCTLSKSLIATL------IYLIMYAISPVTIILLLNILSIKCLIQSLKNINKSVKSRKRMITK 670
             D+  F  FR   + +    N+ L+ FL   ++ SK ++ L+KFQ+ +D++  I + +     +         +GL YC F +  T +++ +  S + ++  S+DRFI I+FP  YR    K +Y  +      G++V V +C       T    R    ++ +  Y+   T S     T       ++LI   + P+  ++++NI  I CL +  + I+      KR +++
Sbjct:   10 SDTEAFFSFRVCLVVIGFIFNVFLILFLRHERIGSKKSSFLVKFQSSVDLVGSIGVLMAMFSNDSSITDLDYIFGLIYCKFLYVKTTLWLCLEISTYTLLLTSIDRFIAILFPFKYREI--KLLYYQL------GLLVAVVFCVLFISPVTFETYRREYLSKSNGTYVTKVTCSYQSRDTFWVTYSYLWLIFSFLLPLLCLMIINIKIISCLTKFNETISSQSNEIKRKLSR 233          
The following BLAST results are available for this feature:
BLAST of GCR148 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 GCR148 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 GCR148 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 GCR148 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 GCR148 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 GCR148 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 GCR148 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 GCR148 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A193KUE91.581e-1024.43GCR146 OS=Schmidtea mediterranea OX=79327 GN=gcr14... [more]
A0A193KUN89.198e-825.10GCR148 OS=Schmidtea mediterranea OX=79327 GN=gcr14... [more]
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BLAST of GCR148 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 GCR148 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 GCR148 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 GCR148 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 GCR148 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 GCR148 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000000478.15.873e-4643.72SMESG000000478.1[more]
SMESG000056470.11.098e-824.14SMESG000056470.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024905 ID=SMED30024905|Name=GCR148|organism=Schmidtea mediterranea sexual|type=transcript|length=713bp
GACATTGGGCGATTCTATTTTGTTTGTTGGATTTAGATATTTATTTATTT
GTCTTTTCTTGTCATTAAATATCGTTTTATTAGCGTTTTTGTTTAAACAT
CAAATGGCATCGAAAACCGCAACTTTACTCATTAAATTTCAGACAATAAT
TGACATAATTGTTTTAATTTTCATTCCCGTGATACCTGTCAAAGAAGAGC
TGCCGTTTCGAACAAAGTCAGAAGCCTACGGATTATTTTATTGTTATTTT
ACTTTCACGGACACCTTGGTCTATGTGTTAATAAATTCTAGCATTTTCCT
CATGGTATCTTTGTCAGTAGACAGATTTATTTGCATTGTTTTCCCATTGT
TTTATCGGAGAAAATGCAATAAATGTGTTTATATATATATAATTCCTTCA
ATTCTTTGCGGTATCGTAGTATTTGTCCCTTATTGTTATTTTACAGAAAT
TGAAATCCGAGAGACAAATTCGACAGAAATGGATCTGAATTATATTTTCT
CATGTACATTGTCAAAGTCTTTAATAGCTACCCTCATCTATCTTATAATG
TACGCCATAAGTCCCGTTACAATCATTTTATTGTTGAATATTCTCTCCAT
AAAATGCCTCATTCAAAGCCTAAAAAACATCAACAAATCCGTCAAATCTA
GGAAGAGAATGATAACAAAATTTACAATTGCAAATATTTTTTCGAATTTT
TTTTACACATTTA
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protein sequence of SMED30024905-orf-1

>SMED30024905-orf-1 ID=SMED30024905-orf-1|Name=SMED30024905-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=237bp
TLGDSILFVGFRYLFICLFLSLNIVLLAFLFKHQMASKTATLLIKFQTII
DIIVLIFIPVIPVKEELPFRTKSEAYGLFYCYFTFTDTLVYVLINSSIFL
MVSLSVDRFICIVFPLFYRRKCNKCVYIYIIPSILCGIVVFVPYCYFTEI
EIRETNSTEMDLNYIFSCTLSKSLIATLIYLIMYAISPVTIILLLNILSI
KCLIQSLKNINKSVKSRKRMITKFTIANIFSNFFYTF
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR000276GPCR_Rhodpsn
IPR017452GPCR_Rhodpsn_7TM
Vocabulary: biological process
TermDefinition
GO:0007186G-protein coupled receptor signaling pathway
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
GO:0016020membrane
Vocabulary: molecular function
TermDefinition
GO:0004930G-protein coupled receptor activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.20.1070.10coord: 3..235
e-value: 1.1E-18
score: 69.3
NoneNo IPR availablePANTHERPTHR45698:SF1TRACE AMINE-ASSOCIATED RECEPTOR 19Ncoord: 21..217
NoneNo IPR availablePANTHERPTHR45698FAMILY NOT NAMEDcoord: 21..217
NoneNo IPR availableCDDcd153907tmA_TACRcoord: 75..150
e-value: 1.68273E-6
score: 45.7483
NoneNo IPR availableSUPERFAMILYSSF81321Family A G protein-coupled receptor-likecoord: 7..226
NoneNo IPR availableTMHMMTMhelixcoord: 5..27
NoneNo IPR availableTMHMMTMhelixcoord: 40..62
NoneNo IPR availableTMHMMTMhelixcoord: 175..197
NoneNo IPR availableTMHMMTMhelixcoord: 124..146
NoneNo IPR availableTMHMMTMhelixcoord: 82..104
IPR000276G protein-coupled receptor, rhodopsin-likePFAMPF000017tm_1coord: 23..214
e-value: 1.7E-10
score: 40.7
IPR000276G protein-coupled receptor, rhodopsin-likePROSITEPS00237G_PROTEIN_RECEP_F1_1coord: 95..111
IPR017452GPCR, rhodopsin-like, 7TMPROSITEPS50262G_PROTEIN_RECEP_F1_2coord: 21..236
score: 16.48