GCR153

Overview
NameGCR153
Smed IDSMED30000064
Length (bp)1315
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 GCR153 (SMED30000064) t-SNE clustered cells

Violin plots show distribution of expression levels for GCR153 (SMED30000064) 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 GCR153 (SMED30000064) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for GCR153 (SMED30000064) 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




SMED30000064

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
intestinal phagocyteSMED30000064SMESG000035163.1 Contig2047GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gutSMED30000064SMESG000035163.1 dd_Smed_v4_3051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30000064SMESG000035163.1 dd_Smed_v4_3051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30000064SMESG000035163.1 dd_Smed_v4_3051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30000064SMESG000035163.1 GCR153smed_ncbi_20200123PMID:27163480
Saberi et al., 2016
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
BLAST of GCR153 vs. TrEMBL
Match: A0A193KUF4 (GCR153 OS=Schmidtea mediterranea OX=79327 GN=gcr153 PE=2 SV=1)

HSP 1 Score: 627.861 bits (1618), Expect = 0.000e+0
Identity = 319/323 (98.76%), Postives = 319/323 (98.76%), Query Frame = 3
Query:  147 MLDGIQAYNSNYYEAYHFIMNAYVPSVCIFSSMVGXXXXXXXXXXXYHEVRNPLSIIQPYLRDVLVAFTFTNTIGQIVAMISSIAFLCYFKCMYAKTSDYNNNGARFLGMMYVWIRLSNSFLIWLMLFKSLTKNPFSYWNQLLISSVFGPFFISIAALYMDVTGFHYSQLPLGSCSIVMVPKSPTFINCIIWIYCIEFFDLWLFVFNCLRIIKLKLDKMNRTSNPEVFEIMGNRRDKLIPDAKHLLAYISCVMMIAKSMEVIRIISVSCMFSEMTSDKAYRLGLFNVLMLLIQAMFEIAQPVLTYACVRTFLNMETSLFRCLK 1115
            MLDGIQ YNSNYYEAY FIMNAYVPSVCIFSSMVGIIICILLWCIIYHEVRNPLSIIQPYLRDVLVAFTFTNTIGQIVAMISSIAFLCYFKCMYAKTSDYNNNGARFLGMMYVWIRLSNSFLIWLMLFKSLTKNPFSYWNQLLISSVFGPFFISIAALYMDVTGFHYSQLPLGSCSIVMVPKSPTFINCIIWIYCIEFFDLWLFVFNCLRIIKLKLDKMNRTSNPEVFEIMGNRRDKLIPDAKHLLAYISCVMMIAKSMEVIRIISVSCMFSEM SD AYRLGLFNVLMLLIQAMFEIAQPVLTYACVRTFLNMETSLFRCLK
Sbjct:    1 MLDGIQTYNSNYYEAYRFIMNAYVPSVCIFSSMVGIIICILLWCIIYHEVRNPLSIIQPYLRDVLVAFTFTNTIGQIVAMISSIAFLCYFKCMYAKTSDYNNNGARFLGMMYVWIRLSNSFLIWLMLFKSLTKNPFSYWNQLLISSVFGPFFISIAALYMDVTGFHYSQLPLGSCSIVMVPKSPTFINCIIWIYCIEFFDLWLFVFNCLRIIKLKLDKMNRTSNPEVFEIMGNRRDKLIPDAKHLLAYISCVMMIAKSMEVIRIISVSCMFSEMNSDAAYRLGLFNVLMLLIQAMFEIAQPVLTYACVRTFLNMETSLFRCLK 323          
BLAST of GCR153 vs. Planmine SMEST
Match: SMESG000035163.1 (SMESG000035163.1)

HSP 1 Score: 627.861 bits (1618), Expect = 0.000e+0
Identity = 319/323 (98.76%), Postives = 319/323 (98.76%), Query Frame = 3
Query:  147 MLDGIQAYNSNYYEAYHFIMNAYVPSVCIFSSMVGXXXXXXXXXXXYHEVRNPLSIIQPYLRDVLVAFTFTNTIGQIVAMISSIAFLCYFKCMYAKTSDYNNNGARFLGMMYVWIRLSNSFLIWLMLFKSLTKNPFSYWNQLLISSVFGPFFISIAALYMDVTGFHYSQLPLGSCSIVMVPKSPTFINCIIWIYCIEFFDLWLFVFNCLRIIKLKLDKMNRTSNPEVFEIMGNRRDKLIPDAKHLLAYISCVMMIAKSMEVIRIISVSCMFSEMTSDKAYRLGLFNVLMLLIQAMFEIAQPVLTYACVRTFLNMETSLFRCLK 1115
            MLDGIQ YNSNYYEAY FIMNAYVPSVCIFSSMVGIIICILLWCIIYHEVRNPLSIIQPYLRDVLVAFTFTNTIGQIVAMISSIAFLCYFKCMYAKTSDYNNNGARFLGMMYVWIRLSNSFLIWLMLFKSLTKNPFSYWNQLLISSVFGPFFISIAALYMDVTGFHYSQLPLGSCSIVMVPKSPTFINCIIWIYCIEFFDLWLFVFNCLRIIKLKLDKMNRTSNPEVFEIMGNRRDKLIPDAKHLLAYISCVMMIAKSMEVIRIISVSCMFSEM SD AYRLGLFNVLMLLIQAMFEIAQPVLTYACVRTFLNMETSLFRCLK
Sbjct:    1 MLDGIQTYNSNYYEAYRFIMNAYVPSVCIFSSMVGIIICILLWCIIYHEVRNPLSIIQPYLRDVLVAFTFTNTIGQIVAMISSIAFLCYFKCMYAKTSDYNNNGARFLGMMYVWIRLSNSFLIWLMLFKSLTKNPFSYWNQLLISSVFGPFFISIAALYMDVTGFHYSQLPLGSCSIVMVPKSPTFINCIIWIYCIEFFDLWLFVFNCLRIIKLKLDKMNRTSNPEVFEIMGNRRDKLIPDAKHLLAYISCVMMIAKSMEVIRIISVSCMFSEMNSDAAYRLGLFNVLMLLIQAMFEIAQPVLTYACVRTFLNMETSLFRCLK 323          
BLAST of GCR153 vs. Planmine SMEST
Match: SMESG000035163.1 (SMESG000035163.1)

HSP 1 Score: 508.064 bits (1307), Expect = 0.000e+0
Identity = 258/261 (98.85%), Postives = 259/261 (99.23%), Query Frame = 3
Query:  147 MLDGIQAYNSNYYEAYHFIMNAYVPSVCIFSSMVGXXXXXXXXXXXYHEVRNPLSIIQPYLRDVLVAFTFTNTIGQIVAMISSIAFLCYFKCMYAKTSDYNNNGARFLGMMYVWIRLSNSFLIWLMLFKSLTKNPFSYWNQLLISSVFGPFFISIAALYMDVTGFHYSQLPLGSCSIVMVPKSPTFINCIIWIYCIEFFDLWLFVFNCLRIIKLKLDKMNRTSNPEVFEIMGNRRDKLIPDAKHLLAYISCVMMIAKSMEV 929
            MLDGIQ YNSNYYEAY FIMNAYVPSVCIFSSMVGIIICILLWCIIYHEVRNPLSIIQPYLRDVLVAFTFTNTIGQIVAMISSIAFLCYFKCMYAKTSDYNNNGARFLGMMYVWIRLSNSFLIWLMLFKSLTKNPFSYWNQLLISSVFGPFFISIAALYMDVTGFHYSQLPLGSCSIVMVPKSPTFINCIIWIYCIEFFDLWLFVFNCLRIIKLKLDKMNRTSNPEVFEIMGNRRDKLIPDAKHLLAYISCVMMIAKSME+
Sbjct:    1 MLDGIQTYNSNYYEAYRFIMNAYVPSVCIFSSMVGIIICILLWCIIYHEVRNPLSIIQPYLRDVLVAFTFTNTIGQIVAMISSIAFLCYFKCMYAKTSDYNNNGARFLGMMYVWIRLSNSFLIWLMLFKSLTKNPFSYWNQLLISSVFGPFFISIAALYMDVTGFHYSQLPLGSCSIVMVPKSPTFINCIIWIYCIEFFDLWLFVFNCLRIIKLKLDKMNRTSNPEVFEIMGNRRDKLIPDAKHLLAYISCVMMIAKSMEM 261          
The following BLAST results are available for this feature:
BLAST of GCR153 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 GCR153 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 GCR153 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 GCR153 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 GCR153 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 GCR153 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 GCR153 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 GCR153 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A193KUF40.000e+098.76GCR153 OS=Schmidtea mediterranea OX=79327 GN=gcr15... [more]
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BLAST of GCR153 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 GCR153 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 GCR153 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 GCR153 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 GCR153 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 GCR153 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000035163.10.000e+098.76SMESG000035163.1[more]
SMESG000035163.10.000e+098.85SMESG000035163.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000064 ID=SMED30000064|Name=GCR153|organism=Schmidtea mediterranea sexual|type=transcript|length=1315bp
AGATTGTGCATGTGATTTTCAATGAACTTTGGTTCTTTCAATTGAATAAT
GATTCATATATAAGTAAAATGTGCGTGTTTATCAGAATCGGATAAATCTA
CTAAATTCAAACCATAAAAAATTGACATTCACGTTTAGATATTAGGATGT
TAGATGGGATACAGGCCTACAACAGCAATTACTATGAAGCGTATCATTTC
ATAATGAACGCTTATGTTCCGTCAGTTTGTATTTTTAGTAGTATGGTCGG
AATAATAATATGCATATTACTTTGGTGCATAATCTATCACGAGGTCCGAA
ATCCTCTCTCAATCATACAACCGTATTTGAGAGATGTTTTGGTGGCTTTT
ACTTTTACCAATACGATCGGTCAGATTGTCGCAATGATTTCGTCTATTGC
ATTTCTATGTTATTTCAAATGTATGTACGCTAAAACTTCGGATTATAACA
ATAACGGCGCCAGATTTCTAGGAATGATGTACGTGTGGATTAGGTTATCT
AATTCTTTTCTTATATGGTTGATGCTCTTTAAAAGTTTGACAAAAAATCC
ATTTTCTTATTGGAATCAACTGTTAATAAGCAGTGTATTCGGACCATTTT
TCATATCAATCGCTGCCTTGTATATGGATGTAACTGGATTTCATTATTCT
CAGTTACCACTTGGATCTTGTTCTATAGTTATGGTTCCGAAAAGTCCTAC
GTTTATAAACTGTATCATTTGGATATATTGTATTGAGTTCTTTGATCTCT
GGCTATTCGTCTTCAATTGTTTGCGAATAATTAAACTTAAATTAGATAAA
ATGAATCGTACCTCGAATCCTGAAGTTTTCGAAATCATGGGTAATAGGAG
AGACAAACTCATTCCAGATGCGAAGCATTTACTGGCATACATATCTTGTG
TAATGATGATTGCGAAATCTATGGAAGTTATACGAATAATATCAGTTTCA
TGTATGTTTAGTGAAATGACTTCAGATAAGGCATACCGACTAGGACTTTT
TAATGTACTCATGTTGCTTATTCAAGCAATGTTTGAAATTGCGCAACCGG
TCTTAACTTATGCCTGTGTGAGGACCTTTCTCAACATGGAGACCAGCTTG
TTTCGCTGCCTCAAACCAATAAATGAAAATGTTGAGCCCAATTAAAACTG
AATTTTAACAATAATTTCAGATTTTTCAATATAAATATTCTAAATTTCAA
AAAAAGATTTTTATAAAATAAATTAGAAGTATTAAATATGATTCAATATG
TTGAAATATCGAGAAATCTTTTGTTTATATATGTCGATTTAATGAAAATA
AAGATTTTAAAATTC
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protein sequence of SMED30000064-orf-1

>SMED30000064-orf-1 ID=SMED30000064-orf-1|Name=SMED30000064-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=333bp
MLDGIQAYNSNYYEAYHFIMNAYVPSVCIFSSMVGIIICILLWCIIYHEV
RNPLSIIQPYLRDVLVAFTFTNTIGQIVAMISSIAFLCYFKCMYAKTSDY
NNNGARFLGMMYVWIRLSNSFLIWLMLFKSLTKNPFSYWNQLLISSVFGP
FFISIAALYMDVTGFHYSQLPLGSCSIVMVPKSPTFINCIIWIYCIEFFD
LWLFVFNCLRIIKLKLDKMNRTSNPEVFEIMGNRRDKLIPDAKHLLAYIS
CVMMIAKSMEVIRIISVSCMFSEMTSDKAYRLGLFNVLMLLIQAMFEIAQ
PVLTYACVRTFLNMETSLFRCLKPINENVEPN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0003116parenchymal cell
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 190..212
NoneNo IPR availableTMHMMTMhelixcoord: 106..128
NoneNo IPR availableTMHMMTMhelixcoord: 245..267
NoneNo IPR availableTMHMMTMhelixcoord: 64..86
NoneNo IPR availableTMHMMTMhelixcoord: 22..44
NoneNo IPR availableTMHMMTMhelixcoord: 141..163
NoneNo IPR availableTMHMMTMhelixcoord: 282..304