GCR124

Overview
NameGCR124
Smed IDSMED30032017
Length (bp)1812
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 GCR124 (SMED30032017) t-SNE clustered cells

Violin plots show distribution of expression levels for GCR124 (SMED30032017) 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



SMED30032017

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
testisSMED30032017SMESG000025218.1 SMESG000025212.1 GCR124smed_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 GCR124 vs. TrEMBL
Match: A0A193KUD8 (GCR124 OS=Schmidtea mediterranea OX=79327 GN=gcr124 PE=2 SV=1)

HSP 1 Score: 794.267 bits (2050), Expect = 0.000e+0
Identity = 459/462 (99.35%), Postives = 459/462 (99.35%), Query Frame = 1 
Query:  277 MFNRIRHMESLSSLKFCVSWSWNWILMHSIGIVTNSIEDFHLILNGTSVQNYGIFLCTMLELILNVFFIFSTYAQIGMSIVLLQKSHQNPNWIKMYSVSKRWILLVLIIFFITCALSIFTRKIMKNNKCIWINDNDMIWVFAMELIIWFVAPAVTLLAFLFQFYLNVRMEKKLNLYMERGDNXXXXXXXXXXXXXXXXXXXXXXYWILVNSVYHIYTVVEIINLQNSEKFNQITNKIFRCPIYIEIGIFCFSWPFLYKYYQKEKFIRDNKPLVXXXXXXXXXXXXXXXXXXXXXXXXXRMECLERENHKIILPKKVNDNTLSVMSFKSDSFGHVGNSDQNILMEKFINAENQSNPKNNVKEEKYLKIPIRKIKSVKNKTKKCNNCGQKIMISPKYIKSNLRNDKNPKITKRSNNRQQAKLQKNCCDXXXXXXXXXXXXXQAYNITNVDNPSIPLSEFAVYSE 1662
            MFNRIRHMESLSSLKFCVSWSWNWILMHSIGIVTNSIEDFHLILNGTSVQNYGIFLCTMLELILNVFFIFSTYAQIGMSIVLLQKSHQNPNWIKMYSVSKRWILLVLIIFFITCALSIFTRKIMKNNKCIWINDNDMIWVFAMELIIWFVAPAVTLLAFLFQFYLNVRMEKKLNLYMERGDNEIILKEEIILKFIRKLILILNLYWILVNSVYHIYTVVEIINLQNSEKFNQITNKIFRCPIYIEIGIFCFSWPFLYKYYQKEKFIRDNKPLVNSHEEVTSTSNSSNSLKNSENIILSRMECLERENHKIILPKKVNDNTLSVMS KSDSFGHVGNSDQNILMEKFINAENQSNPKNNVKEEKYLKIPIRKIKSVKNKTKKCNNCGQKIMI PKYIKSNLRNDKNPKITKRSNNRQQAKLQKN CDKAKTKFAKNNTNFQAYNITNVDNPSIPLSEFAVYSE
Sbjct:   23 MFNRIRHMESLSSLKFCVSWSWNWILMHSIGIVTNSIEDFHLILNGTSVQNYGIFLCTMLELILNVFFIFSTYAQIGMSIVLLQKSHQNPNWIKMYSVSKRWILLVLIIFFITCALSIFTRKIMKNNKCIWINDNDMIWVFAMELIIWFVAPAVTLLAFLFQFYLNVRMEKKLNLYMERGDNEIILKEEIILKFIRKLILILNLYWILVNSVYHIYTVVEIINLQNSEKFNQITNKIFRCPIYIEIGIFCFSWPFLYKYYQKEKFIRDNKPLVNSHEEVTSTSNSSNSLKNSENIILSRMECLERENHKIILPKKVNDNTLSVMSLKSDSFGHVGNSDQNILMEKFINAENQSNPKNNVKEEKYLKIPIRKIKSVKNKTKKCNNCGQKIMIGPKYIKSNLRNDKNPKITKRSNNRQQAKLQKNGCDKAKTKFAKNNTNFQAYNITNVDNPSIPLSEFAVYSE 484
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BLAST of GCR124 vs. Planmine SMEST
Match: SMESG000025212.1 (SMESG000025212.1)

HSP 1 Score: 796.964 bits (2057), Expect = 0.000e+0
Identity = 459/462 (99.35%), Postives = 460/462 (99.57%), Query Frame = 1 
Query:  277 MFNRIRHMESLSSLKFCVSWSWNWILMHSIGIVTNSIEDFHLILNGTSVQNYGIFLCTMLELILNVFFIFSTYAQIGMSIVLLQKSHQNPNWIKMYSVSKRWILLVLIIFFITCALSIFTRKIMKNNKCIWINDNDMIWVFAMELIIWFVAPAVTLLAFLFQFYLNVRMEKKLNLYMERGDNXXXXXXXXXXXXXXXXXXXXXXYWILVNSVYHIYTVVEIINLQNSEKFNQITNKIFRCPIYIEIGIFCFSWPFLYKYYQKEKFIRDNKPLVXXXXXXXXXXXXXXXXXXXXXXXXXRMECLERENHKIILPKKVNDNTLSVMSFKSDSFGHVGNSDQNILMEKFINAENQSNPKNNVKEEKYLKIPIRKIKSVKNKTKKCNNCGQKIMISPKYIKSNLRNDKNPKITKRSNNRQQAKLQKNCCDXXXXXXXXXXXXXQAYNITNVDNPSIPLSEFAVYSE 1662
            MFNRIRHMESLSSLKFCVSWSWNWILMHSIGIVTNSIEDFHLILNGTSVQNYGIFLCTMLELILNVFFIFSTYAQIGMSIVLLQKSHQNPNWIKMYSVSKRWILLVLIIFFITCALSIFTRKIMKNNKCIWINDNDMIWVFAMELIIWFVAPAVTLLAFLFQFYLNVRMEKKLNLYMERGDNEIILKEEIILKFIRKLILILNLYWILVNS+YHIYTVVEIINLQNSEKFNQITNKIFRCPIYIEIGIFCFSWPFLYKYYQKEKFIRDNKPLVNSHEEVTSTSNSSNSLKNSENIILSRMECLERENHKIILPKKVNDNTLSVMS KSDSFGHVGNSDQNILMEKFINAENQSNPKNNVKEEKYLKIPIRKIKSVKNKTKKCNNCGQKIMI PKYIKSNLRNDKNPKITKRSNNRQQAKLQKNCCDKAKTKFAKNNTNFQAYNITNVDNPSIPLSEFAVYSE
Sbjct:   23 MFNRIRHMESLSSLKFCVSWSWNWILMHSIGIVTNSIEDFHLILNGTSVQNYGIFLCTMLELILNVFFIFSTYAQIGMSIVLLQKSHQNPNWIKMYSVSKRWILLVLIIFFITCALSIFTRKIMKNNKCIWINDNDMIWVFAMELIIWFVAPAVTLLAFLFQFYLNVRMEKKLNLYMERGDNEIILKEEIILKFIRKLILILNLYWILVNSIYHIYTVVEIINLQNSEKFNQITNKIFRCPIYIEIGIFCFSWPFLYKYYQKEKFIRDNKPLVNSHEEVTSTSNSSNSLKNSENIILSRMECLERENHKIILPKKVNDNTLSVMSLKSDSFGHVGNSDQNILMEKFINAENQSNPKNNVKEEKYLKIPIRKIKSVKNKTKKCNNCGQKIMIGPKYIKSNLRNDKNPKITKRSNNRQQAKLQKNCCDKAKTKFAKNNTNFQAYNITNVDNPSIPLSEFAVYSE 484
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BLAST of GCR124 vs. Planmine SMEST
Match: SMESG000025218.1 (SMESG000025218.1)

HSP 1 Score: 432.565 bits (1111), Expect = 2.021e-148
Identity = 257/258 (99.61%), Postives = 257/258 (99.61%), Query Frame = 1 
Query:  889 YWILVNSVYHIYTVVEIINLQNSEKFNQITNKIFRCPIYIEIGIFCFSWPFLYKYYQKEKFIRDNKPLVXXXXXXXXXXXXXXXXXXXXXXXXXRMECLERENHKIILPKKVNDNTLSVMSFKSDSFGHVGNSDQNILMEKFINAENQSNPKNNVKEEKYLKIPIRKIKSVKNKTKKCNNCGQKIMISPKYIKSNLRNDKNPKITKRSNNRQQAKLQKNCCDXXXXXXXXXXXXXQAYNITNVDNPSIPLSEFAVYSE 1662
            YWILVNSVYHIYTVVEIINLQNSEKFNQITNKIFRCPIYIEIGIFCFSWPFLYKYYQKEKFIRDNKPLVNSHEEVTSTSNSSNSLKNSENIILSRMECLERENHKIILPKKVNDNTLSVMSFKSDSFGHVGNSDQNILMEKFINAENQSNPKNNVKEEKYLKIPIRKIKSVKNKTKKCNNCGQKIMISPKYIKSNLRNDKNPKITKRSNNRQQAKLQKN CDKAKTKFAKNNTNFQAYNITNVDNPSIPLSEFAVYSE
Sbjct:   67 YWILVNSVYHIYTVVEIINLQNSEKFNQITNKIFRCPIYIEIGIFCFSWPFLYKYYQKEKFIRDNKPLVNSHEEVTSTSNSSNSLKNSENIILSRMECLERENHKIILPKKVNDNTLSVMSFKSDSFGHVGNSDQNILMEKFINAENQSNPKNNVKEEKYLKIPIRKIKSVKNKTKKCNNCGQKIMISPKYIKSNLRNDKNPKITKRSNNRQQAKLQKNGCDKAKTKFAKNNTNFQAYNITNVDNPSIPLSEFAVYSE 324

HSP 2 Score: 93.5893 bits (231), Expect = 1.692e-20
Identity = 42/42 (100.00%), Postives = 42/42 (100.00%), Query Frame = 3 
Query:  690 MGFCHGANNLVCSPGGYTASIPISILSKCQDGEKTKPLHGKG 815
            MGFCHGANNLVCSPGGYTASIPISILSKCQDGEKTKPLHGKG
Sbjct:    1 MGFCHGANNLVCSPGGYTASIPISILSKCQDGEKTKPLHGKG 42
The following BLAST results are available for this feature:
BLAST of GCR124 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 GCR124 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 GCR124 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 GCR124 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 GCR124 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 GCR124 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 GCR124 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 GCR124 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A193KUD80.000e+099.35GCR124 OS=Schmidtea mediterranea OX=79327 GN=gcr12... [more]
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BLAST of GCR124 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 GCR124 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 GCR124 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 GCR124 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 GCR124 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 GCR124 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000025212.10.000e+099.35SMESG000025212.1[more]
SMESG000025218.12.021e-14899.61SMESG000025218.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032017 ID=SMED30032017|Name=GCR124|organism=Schmidtea mediterranea sexual|type=transcript|length=1812bp
AGATTTTTGAAATTTTGAAATAATTACTTAATTATTATCCATAAAACAGT
TATCGCAGCTCTGCAATTCTTGAGATTCTTGTACGTGGATCAAAGCGACA
TGAGGTTTACTCAACTCTCCTCTATACAGTTAATGAAGAAAGTATTTCAA
TTCATACGATACATCGATAAAGCAATTTTTAATATATAATAAGAATATAT
TTCTATAATAATGGACACTTCTATTATTGTCTTGAGTCATTCCGTATCAT
TGATATCTGTAAGCATTTCTATTTTAATGTTTAATCGGATTAGACACATG
GAAAGTTTGTCAAGTTTAAAGTTTTGCGTCAGCTGGAGCTGGAACTGGAT
ACTGATGCATAGCATTGGCATTGTAACAAATTCCATTGAAGATTTTCATT
TGATCTTAAACGGGACCTCGGTGCAAAATTACGGCATATTTTTATGCACA
ATGTTGGAATTGATTTTGAACGTTTTTTTCATTTTTTCAACATATGCCCA
AATAGGAATGTCTATTGTTCTTCTGCAAAAGTCCCATCAAAATCCAAATT
GGATCAAAATGTATTCCGTGTCCAAAAGATGGATATTGCTGGTGTTGATT
ATATTCTTTATAACATGCGCATTATCCATATTTACTAGGAAAATAATGAA
AAATAACAAATGTATTTGGATTAATGACAATGATATGATATGGGTTTTTG
CCATGGAGCTAATAATTTGGTTTGTAGCCCCGGCGGTTACACTGCTAGCA
TTCCTATTTCAATTCTATCTAAATGTCAGGATGGAGAAAAAACTAAACCT
TTACATGGAAAGGGGAGACAATGAAATCATTTTAAAAGAAGAGATAATTT
TAAAATTTATTCGCAAATTAATTTTAATTCTTAATTTATATTGGATTTTA
GTGAATTCCGTCTATCACATCTACACAGTTGTTGAAATTATTAATCTTCA
AAACAGTGAAAAATTCAACCAAATAACAAATAAAATATTTCGATGCCCTA
TTTATATCGAAATAGGAATATTTTGTTTTTCTTGGCCTTTTTTATACAAA
TATTATCAAAAAGAAAAATTTATTAGAGATAATAAGCCCCTCGTGAATAG
CCATGAAGAGGTCACTTCAACAAGCAACTCATCAAACAGTTTGAAAAATA
GCGAAAATATCATTCTTTCCCGAATGGAATGTTTAGAACGGGAAAACCAT
AAAATCATTTTACCAAAAAAAGTAAATGATAACACTCTTTCAGTTATGTC
ATTTAAGTCCGACTCGTTTGGCCATGTGGGAAACAGTGATCAAAACATTC
TAATGGAGAAATTCATTAACGCAGAAAATCAGTCTAATCCAAAAAATAAT
GTCAAAGAAGAAAAATATTTGAAAATCCCAATCCGAAAAATCAAGTCAGT
AAAAAACAAGACTAAAAAATGTAATAATTGTGGACAAAAAATTATGATTA
GTCCAAAATATATAAAATCAAACCTAAGAAATGACAAAAACCCAAAAATA
ACCAAAAGGTCAAATAATCGACAACAAGCGAAGTTACAAAAGAATTGCTG
TGATAAAGCAAAAACTAAATTCGCGAAAAATAATACAAACTTTCAAGCTT
ACAATATTACAAATGTTGACAATCCGTCTATACCGTTATCTGAATTTGCA
GTATATTCGGAAAGGAAAATTAAAAAGGAAAATGAACCGAAGAAAAATAG
AAAAATAAAAAGGAAATTCAGGCGGCAGAGTAAAGTATAAAAATCCTAAT
AAAATAAATTTGAAAATTTGATAACGATTGCGACTATGAATGAGATCGAT
ATAGTTTATATT
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protein sequence of SMED30032017-orf-1

>SMED30032017-orf-1 ID=SMED30032017-orf-1|Name=SMED30032017-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=510bp
MDTSIIVLSHSVSLISVSISILMFNRIRHMESLSSLKFCVSWSWNWILMH
SIGIVTNSIEDFHLILNGTSVQNYGIFLCTMLELILNVFFIFSTYAQIGM
SIVLLQKSHQNPNWIKMYSVSKRWILLVLIIFFITCALSIFTRKIMKNNK
CIWINDNDMIWVFAMELIIWFVAPAVTLLAFLFQFYLNVRMEKKLNLYME
RGDNEIILKEEIILKFIRKLILILNLYWILVNSVYHIYTVVEIINLQNSE
KFNQITNKIFRCPIYIEIGIFCFSWPFLYKYYQKEKFIRDNKPLVNSHEE
VTSTSNSSNSLKNSENIILSRMECLERENHKIILPKKVNDNTLSVMSFKS
DSFGHVGNSDQNILMEKFINAENQSNPKNNVKEEKYLKIPIRKIKSVKNK
TKKCNNCGQKIMISPKYIKSNLRNDKNPKITKRSNNRQQAKLQKNCCDKA
KTKFAKNNTNFQAYNITNVDNPSIPLSEFAVYSERKIKKENEPKKNRKIK
RKFRRQSKV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
Vocabulary: INTERPRO
TermDefinition
IPR013136WSTF_Acf1_Cbp146
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane