GCR132

Overview
NameGCR132
Smed IDSMED30012624
Length (bp)1322
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 GCR132 (SMED30012624) t-SNE clustered cells

Violin plots show distribution of expression levels for GCR132 (SMED30012624) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30012624

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testisSMED30012624SMESG000025334.1 GCR132smed_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
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BLAST of GCR132 vs. TrEMBL
Match: A0A193KUT8 (GCR132 OS=Schmidtea mediterranea OX=79327 GN=gcr132 PE=2 SV=1)

HSP 1 Score: 687.952 bits (1774), Expect = 0.000e+0
Identity = 388/388 (100.00%), Postives = 388/388 (100.00%), Query Frame = 3 
Query:   63 MVANSKVDIFGISVIILLTVMSVTGLFLNALVFITIIETRXXXXXXXXXXXXXXXXXXXXXGVIIPIYIYVSKANLAKVCQSLVIADNAVNTCGIYFIVFLMVNNCLQKFYPNFSNKQHLKLQLILSILNQVLSSGYNIGLSVYFDKVLNKRNELCLPVNDVVFIWILLSAMYICPLLLCGLLIFIYQSSVKTEEDVFPYKXXXXXXXXXXXXXXXXXKKQLEQTKTSSSIKEIEYIPSHIFVLKPSFYSTNVTLTSVEGQNSNVSTPIPNNIPSNFKHNSPVLTSLNRTGRYLMHKISLSVKIKTSIHPTIIFFIISTPYYVIYICRPYWLGLGIDETLFVWLKLFNWLTIVINPLTFCLSNEVISQRARKNLCKICCVFKRKSIVH 1226
            MVANSKVDIFGISVIILLTVMSVTGLFLNALVFITIIETRLFYLSKFTLLSLLALSDLTKSGVIIPIYIYVSKANLAKVCQSLVIADNAVNTCGIYFIVFLMVNNCLQKFYPNFSNKQHLKLQLILSILNQVLSSGYNIGLSVYFDKVLNKRNELCLPVNDVVFIWILLSAMYICPLLLCGLLIFIYQSSVKTEEDVFPYKSTTILSSFTTSFFERFSKKQLEQTKTSSSIKEIEYIPSHIFVLKPSFYSTNVTLTSVEGQNSNVSTPIPNNIPSNFKHNSPVLTSLNRTGRYLMHKISLSVKIKTSIHPTIIFFIISTPYYVIYICRPYWLGLGIDETLFVWLKLFNWLTIVINPLTFCLSNEVISQRARKNLCKICCVFKRKSIVH
Sbjct:    1 MVANSKVDIFGISVIILLTVMSVTGLFLNALVFITIIETRLFYLSKFTLLSLLALSDLTKSGVIIPIYIYVSKANLAKVCQSLVIADNAVNTCGIYFIVFLMVNNCLQKFYPNFSNKQHLKLQLILSILNQVLSSGYNIGLSVYFDKVLNKRNELCLPVNDVVFIWILLSAMYICPLLLCGLLIFIYQSSVKTEEDVFPYKSTTILSSFTTSFFERFSKKQLEQTKTSSSIKEIEYIPSHIFVLKPSFYSTNVTLTSVEGQNSNVSTPIPNNIPSNFKHNSPVLTSLNRTGRYLMHKISLSVKIKTSIHPTIIFFIISTPYYVIYICRPYWLGLGIDETLFVWLKLFNWLTIVINPLTFCLSNEVISQRARKNLCKICCVFKRKSIVH 388
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BLAST of GCR132 vs. Planmine SMEST
Match: SMESG000025334.1 (SMESG000025334.1)

HSP 1 Score: 687.952 bits (1774), Expect = 0.000e+0
Identity = 388/388 (100.00%), Postives = 388/388 (100.00%), Query Frame = 3 
Query:   63 MVANSKVDIFGISVIILLTVMSVTGLFLNALVFITIIETRXXXXXXXXXXXXXXXXXXXXXGVIIPIYIYVSKANLAKVCQSLVIADNAVNTCGIYFIVFLMVNNCLQKFYPNFSNKQHLKLQLILSILNQVLSSGYNIGLSVYFDKVLNKRNELCLPVNDVVFIWILLSAMYICPLLLCGLLIFIYQSSVKTEEDVFPYKXXXXXXXXXXXXXXXXXKKQLEQTKTSSSIKEIEYIPSHIFVLKPSFYSTNVTLTSVEGQNSNVSTPIPNNIPSNFKHNSPVLTSLNRTGRYLMHKISLSVKIKTSIHPTIIFFIISTPYYVIYICRPYWLGLGIDETLFVWLKLFNWLTIVINPLTFCLSNEVISQRARKNLCKICCVFKRKSIVH 1226
            MVANSKVDIFGISVIILLTVMSVTGLFLNALVFITIIETRLFYLSKFTLLSLLALSDLTKSGVIIPIYIYVSKANLAKVCQSLVIADNAVNTCGIYFIVFLMVNNCLQKFYPNFSNKQHLKLQLILSILNQVLSSGYNIGLSVYFDKVLNKRNELCLPVNDVVFIWILLSAMYICPLLLCGLLIFIYQSSVKTEEDVFPYKSTTILSSFTTSFFERFSKKQLEQTKTSSSIKEIEYIPSHIFVLKPSFYSTNVTLTSVEGQNSNVSTPIPNNIPSNFKHNSPVLTSLNRTGRYLMHKISLSVKIKTSIHPTIIFFIISTPYYVIYICRPYWLGLGIDETLFVWLKLFNWLTIVINPLTFCLSNEVISQRARKNLCKICCVFKRKSIVH
Sbjct:    1 MVANSKVDIFGISVIILLTVMSVTGLFLNALVFITIIETRLFYLSKFTLLSLLALSDLTKSGVIIPIYIYVSKANLAKVCQSLVIADNAVNTCGIYFIVFLMVNNCLQKFYPNFSNKQHLKLQLILSILNQVLSSGYNIGLSVYFDKVLNKRNELCLPVNDVVFIWILLSAMYICPLLLCGLLIFIYQSSVKTEEDVFPYKSTTILSSFTTSFFERFSKKQLEQTKTSSSIKEIEYIPSHIFVLKPSFYSTNVTLTSVEGQNSNVSTPIPNNIPSNFKHNSPVLTSLNRTGRYLMHKISLSVKIKTSIHPTIIFFIISTPYYVIYICRPYWLGLGIDETLFVWLKLFNWLTIVINPLTFCLSNEVISQRARKNLCKICCVFKRKSIVH 388
The following BLAST results are available for this feature:
BLAST of GCR132 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 GCR132 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 GCR132 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 GCR132 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 GCR132 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 GCR132 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 GCR132 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 GCR132 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A193KUT80.000e+0100.00GCR132 OS=Schmidtea mediterranea OX=79327 GN=gcr13... [more]
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BLAST of GCR132 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 GCR132 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 GCR132 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 GCR132 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 GCR132 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 GCR132 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000025334.10.000e+0100.00SMESG000025334.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012624 ID=SMED30012624|Name=GCR132|organism=Schmidtea mediterranea sexual|type=transcript|length=1322bp
TGAATATTGATTATATTTTATAATATTCTTTTTAATAAACGTATTTCTTT
AAGAAACGTATCATGGTGGCAAATTCAAAGGTTGACATATTTGGAATCTC
CGTAATTATATTATTAACTGTAATGTCTGTTACAGGGTTATTTTTGAACG
CATTGGTTTTTATAACAATTATTGAAACTCGTCTGTTTTATCTTTCCAAA
TTTACGTTATTAAGTCTTTTAGCATTGTCGGATCTAACGAAGTCTGGGGT
CATCATTCCTATCTATATCTATGTATCCAAGGCTAATTTGGCGAAGGTTT
GCCAATCTTTAGTGATTGCAGATAACGCTGTAAACACGTGCGGGATATAT
TTCATTGTTTTCCTAATGGTAAACAACTGCCTCCAGAAGTTTTATCCGAA
TTTCAGTAATAAACAGCATTTGAAGCTACAGTTGATCTTATCTATTCTTA
ATCAAGTTCTATCAAGTGGGTATAATATCGGATTGTCTGTTTACTTTGAT
AAGGTCCTAAATAAACGAAATGAGTTGTGTTTGCCGGTGAATGACGTTGT
CTTTATCTGGATACTTCTTAGTGCAATGTACATATGTCCTTTGTTATTAT
GTGGGCTGTTAATATTTATTTATCAATCCTCAGTAAAAACTGAAGAAGAC
GTATTCCCTTACAAATCAACAACGATTTTAAGTTCCTTTACAACATCTTT
CTTTGAAAGATTTTCGAAAAAACAACTTGAGCAAACAAAAACGAGTTCAA
GCATTAAAGAAATTGAATACATACCTTCGCATATATTCGTTTTAAAACCT
TCCTTCTATAGTACGAATGTTACACTAACATCAGTCGAAGGTCAAAACTC
GAATGTCTCAACCCCTATTCCAAATAATATTCCAAGTAATTTCAAGCATA
ACAGTCCCGTATTAACTAGTCTAAATAGAACTGGAAGATATCTAATGCAT
AAAATCTCATTGTCTGTGAAAATAAAAACATCCATTCATCCTACAATCAT
CTTCTTCATTATATCAACTCCGTATTATGTTATCTATATTTGTCGCCCTT
ATTGGTTAGGGTTAGGGATCGACGAGACTTTATTCGTGTGGCTGAAACTA
TTCAACTGGTTAACCATTGTCATAAATCCATTGACATTCTGTCTGTCGAA
TGAAGTTATTTCACAGAGAGCCAGAAAGAATTTGTGCAAGATTTGTTGTG
TTTTTAAAAGAAAATCTATTGTCCACTGATACGCTTTATAATTAATTTTT
AATGGATTTAGCATGAGGTTGTTAAACAAGAGTTGGAGAGGCAAAATTCA
TCTTAATGGCTCTATACAAAAT
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protein sequence of SMED30012624-orf-1

>SMED30012624-orf-1 ID=SMED30012624-orf-1|Name=SMED30012624-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=389bp
MVANSKVDIFGISVIILLTVMSVTGLFLNALVFITIIETRLFYLSKFTLL
SLLALSDLTKSGVIIPIYIYVSKANLAKVCQSLVIADNAVNTCGIYFIVF
LMVNNCLQKFYPNFSNKQHLKLQLILSILNQVLSSGYNIGLSVYFDKVLN
KRNELCLPVNDVVFIWILLSAMYICPLLLCGLLIFIYQSSVKTEEDVFPY
KSTTILSSFTTSFFERFSKKQLEQTKTSSSIKEIEYIPSHIFVLKPSFYS
TNVTLTSVEGQNSNVSTPIPNNIPSNFKHNSPVLTSLNRTGRYLMHKISL
SVKIKTSIHPTIIFFIISTPYYVIYICRPYWLGLGIDETLFVWLKLFNWL
TIVINPLTFCLSNEVISQRARKNLCKICCVFKRKSIVH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
Vocabulary: INTERPRO
TermDefinition
IPR006665OmpA-like
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 availableGENE3DG3DSA:1.20.1070.10coord: 17..364
e-value: 1.6E-8
score: 36.1
NoneNo IPR availableGENE3DG3DSA:1.20.120.10coord: 195..299
e-value: 1.6E-8
score: 36.1
NoneNo IPR availableSUPERFAMILYSSF81321Family A G protein-coupled receptor-likecoord: 13..383
NoneNo IPR availableTMHMMTMhelixcoord: 81..103
NoneNo IPR availableTMHMMTMhelixcoord: 49..71
NoneNo IPR availableTMHMMTMhelixcoord: 15..37
NoneNo IPR availableTMHMMTMhelixcoord: 339..361
NoneNo IPR availableTMHMMTMhelixcoord: 165..187
NoneNo IPR availableTMHMMTMhelixcoord: 312..334
NoneNo IPR availableTMHMMTMhelixcoord: 123..145