GCR133

Overview
NameGCR133
Smed IDSMED30005151
Length (bp)1041
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30005151

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
testisSMED30005151 GCR133smed_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 GCR133 vs. TrEMBL
Match: A0A193KUP5 (GCR133 OS=Schmidtea mediterranea OX=79327 GN=gcr133 PE=2 SV=1)

HSP 1 Score: 634.795 bits (1636), Expect = 0.000e+0
Identity = 346/346 (100.00%), Postives = 346/346 (100.00%), Query Frame = 2 
Query:    2 KFLINKKMVNKTTNEVMEMIDYYACMALYVIGLGSSIFASFLLTGERIHNAIIVFWLRAICGTDVTCLIYFFLDELLFNFPCKVDYYFSHILLTLSGYTRCAFSLARVIMLITGKCVTFRFHXXXXXXXXXXXXXXXXPTFYFFDYLCVIDRFHETILLLIESVTLLIGIVVMXXXXXXXXXXXXTTITPLFYKVEETEVVNRIINVNFHCKTWSEFYKCVKRGIFWSSIINIIWVVACSPYLIMCFWYLANRSILVQYIKEKTSTLILIPLSLNWLFAVVIDHMLFQEMKTFVLIKWLEFLNILSRIGFSCFHSKFISFHIEPHETNTAESIKHFNENSVNVIKS 1039
            KFLINKKMVNKTTNEVMEMIDYYACMALYVIGLGSSIFASFLLTGERIHNAIIVFWLRAICGTDVTCLIYFFLDELLFNFPCKVDYYFSHILLTLSGYTRCAFSLARVIMLITGKCVTFRFHLYISLFIASIILIIYIPTFYFFDYLCVIDRFHETILLLIESVTLLIGIVVMLFSSSFFLYFLSTTITPLFYKVEETEVVNRIINVNFHCKTWSEFYKCVKRGIFWSSIINIIWVVACSPYLIMCFWYLANRSILVQYIKEKTSTLILIPLSLNWLFAVVIDHMLFQEMKTFVLIKWLEFLNILSRIGFSCFHSKFISFHIEPHETNTAESIKHFNENSVNVIKS
Sbjct:    2 KFLINKKMVNKTTNEVMEMIDYYACMALYVIGLGSSIFASFLLTGERIHNAIIVFWLRAICGTDVTCLIYFFLDELLFNFPCKVDYYFSHILLTLSGYTRCAFSLARVIMLITGKCVTFRFHLYISLFIASIILIIYIPTFYFFDYLCVIDRFHETILLLIESVTLLIGIVVMLFSSSFFLYFLSTTITPLFYKVEETEVVNRIINVNFHCKTWSEFYKCVKRGIFWSSIINIIWVVACSPYLIMCFWYLANRSILVQYIKEKTSTLILIPLSLNWLFAVVIDHMLFQEMKTFVLIKWLEFLNILSRIGFSCFHSKFISFHIEPHETNTAESIKHFNENSVNVIKS 347
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BLAST of GCR133 vs. Planmine SMEST
Match: SMESG000037700.1 (SMESG000037700.1)

HSP 1 Score: 56.9954 bits (136), Expect = 5.863e-9
Identity = 76/276 (27.54%), Postives = 125/276 (45.29%), Query Frame = 2 
Query:   89 VIGLGSSIFASFLLTGERIHNAIIVFWLRAICGTD---VTCLI--YFFLDELLFNFPCKVDYYFSHILLTLSGYTRCAFSLARVIMLITGKCVTFR---FHXXXXXXXXXXXXXXXXPTFYFFDYLCVIDRFHETILLLIESVTLLIGIVVMXXXXXXXXXXXXTTITPLFYKVE---ETEVVNRIINVNFHCKTWSEFYKCVKRGIFWSSIINIIWVVACSPYLIMCFWYL----ANRSILVQYIKEKTSTLILIPLSLNWLFAVVIDHMLFQEM 871
            +IG  SS+ + ++L  ++I++ +I FW+R+ICG D   +TC I  +FF       F   V+Y     L    G+ R  F L R  MLI  + + F      + +       +   +IP       L  +     TI  LI    L +  V +LFSS + +YFL   + P+  ++E   E  +    I  N         Y   KR I W+S + I+WV+   P++ +    L    +N  +      +    ++L PLS++WLF +++   L QEM
Sbjct:   15 LIGFISSLVSLYILKSQKIYDNVISFWMRSICGFDCITLTCFIVNFFFEKSQTTKFDFVVNYLQICSLSITIGF-RTVFFLFRSFMLIYQRILIFYNIYVSIIVMAVFIVFLCSYHIPVLVNHKPLKEVPSELVTIFRLI---FLFLSDVCILFSSIYLIYFLMIQVKPVLLRIEALFEYHLTQEEIQENHQ----RNLYGSTKRTILWTSAMGIVWVLCNLPFIAINILMLNTTDSNLDVYYYSFNDDMMLVMLFPLSISWLFTIILSQPLRQEM 282
The following BLAST results are available for this feature:
BLAST of GCR133 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 GCR133 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 GCR133 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 GCR133 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 GCR133 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 GCR133 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 GCR133 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 GCR133 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A193KUP50.000e+0100.00GCR133 OS=Schmidtea mediterranea OX=79327 GN=gcr13... [more]
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BLAST of GCR133 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 GCR133 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 GCR133 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 GCR133 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 GCR133 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 GCR133 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000037700.15.863e-927.54SMESG000037700.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005151 ID=SMED30005151|Name=GCR133|organism=Schmidtea mediterranea sexual|type=transcript|length=1041bp
GAAGTTTTTAATTAATAAAAAAATGGTTAATAAAACTACAAATGAAGTTA
TGGAAATGATCGACTATTATGCTTGTATGGCTCTTTACGTTATTGGACTA
GGAAGTTCGATCTTTGCGTCGTTTTTATTGACAGGCGAAAGAATTCACAA
TGCGATAATTGTGTTCTGGTTACGGGCAATATGCGGAACGGATGTAACAT
GTTTGATTTATTTTTTTCTCGATGAATTATTATTTAATTTTCCATGCAAA
GTTGACTACTATTTTTCACATATCCTACTTACTCTCTCTGGCTATACTCG
ATGTGCCTTTAGTCTGGCTAGAGTTATCATGTTAATAACGGGGAAATGTG
TGACATTCCGTTTCCATTTGTACATATCACTTTTTATAGCTTCCATAATC
CTGATAATATATATTCCGACATTTTATTTTTTTGACTATTTATGTGTCAT
TGACAGATTTCATGAAACAATTTTACTCCTGATTGAATCGGTGACATTGC
TAATAGGAATTGTGGTTATGTTGTTTTCCTCTTCTTTCTTTTTGTACTTT
CTTTCAACAACGATTACTCCGTTGTTTTATAAGGTCGAGGAGACGGAAGT
GGTTAATAGAATTATTAATGTCAATTTTCATTGTAAAACATGGAGTGAAT
TTTATAAATGTGTCAAAAGAGGAATATTTTGGAGTTCTATTATTAATATC
ATTTGGGTGGTTGCGTGCTCACCATATCTCATAATGTGTTTTTGGTACTT
AGCTAACAGGTCAATCCTCGTGCAATACATTAAGGAAAAAACGTCTACGT
TGATTTTGATACCACTTTCATTAAATTGGTTATTTGCCGTGGTGATTGAC
CATATGTTATTCCAAGAAATGAAGACATTTGTTTTAATTAAATGGTTAGA
ATTTCTCAATATTTTGAGCAGAATTGGATTTTCATGCTTTCATTCCAAAT
TCATATCGTTCCACATAGAACCGCATGAGACAAATACGGCAGAATCTATC
AAACATTTTAATGAAAACTCAGTTAATGTTATAAAAAGCTG
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protein sequence of SMED30005151-orf-1

>SMED30005151-orf-1 ID=SMED30005151-orf-1|Name=SMED30005151-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=346bp
KFLINKKMVNKTTNEVMEMIDYYACMALYVIGLGSSIFASFLLTGERIHN
AIIVFWLRAICGTDVTCLIYFFLDELLFNFPCKVDYYFSHILLTLSGYTR
CAFSLARVIMLITGKCVTFRFHLYISLFIASIILIIYIPTFYFFDYLCVI
DRFHETILLLIESVTLLIGIVVMLFSSSFFLYFLSTTITPLFYKVEETEV
VNRIINVNFHCKTWSEFYKCVKRGIFWSSIINIIWVVACSPYLIMCFWYL
ANRSILVQYIKEKTSTLILIPLSLNWLFAVVIDHMLFQEMKTFVLIKWLE
FLNILSRIGFSCFHSKFISFHIEPHETNTAESIKHFNENSVNVIKS
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
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: 54..73
NoneNo IPR availableTMHMMTMhelixcoord: 266..288
NoneNo IPR availableTMHMMTMhelixcoord: 86..108
NoneNo IPR availableTMHMMTMhelixcoord: 229..251
NoneNo IPR availableTMHMMTMhelixcoord: 20..42
NoneNo IPR availableTMHMMTMhelixcoord: 163..185
NoneNo IPR availableTMHMMTMhelixcoord: 121..143