CGG triplet repeat-binding protein 1

Overview
NameCGG triplet repeat-binding protein 1
Smed IDSMED30022483
Length (bp)534
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 CGG triplet repeat-binding protein 1 (SMED30022483) t-SNE clustered cells

Violin plots show distribution of expression levels for CGG triplet repeat-binding protein 1 (SMED30022483) 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.
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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



SMED30022483

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30022483SMESG000020470.1 Contig1680newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
pharynxSMED30022483SMESG000020470.1 Contig1680uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30022483SMESG000020470.1 Contig1680newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30022483SMESG000020470.1 Contig1680uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30022483SMESG000020470.1 Contig1680newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30022483SMESG000020470.1 Contig1680uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of CGG triplet repeat-binding protein 1 vs. TrEMBL
Match: A0A3L8D750 (Uncharacterized protein OS=Ooceraea biroi OX=2015173 GN=DMN91_011809 PE=4 SV=1)

HSP 1 Score: 84.3445 bits (207), Expect = 5.649e-17
Identity = 40/62 (64.52%), Postives = 50/62 (80.65%), Query Frame = 3 
Query:   75 MPRVKQSVSNRLKRYVSEFPDFKTDGKIIFCKVF-KLVSAEKIFTIKQHLA--KHIKLTERN 251
            MP+ K S+SNRL +YV EFP FKTDG ++FCK+  K+VSAEKIFT+KQHLA  KHI+L  +N
Sbjct:    1 MPKTKTSISNRLSQYVREFPSFKTDGTVLFCKICNKVVSAEKIFTVKQHLASKKHIELANKN 62
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BLAST of CGG triplet repeat-binding protein 1 vs. TrEMBL
Match: A0A0J7NEC4 (DUF659 domain-containing protein OS=Lasius niger OX=67767 GN=RF55_9308 PE=4 SV=1)

HSP 1 Score: 79.7221 bits (195), Expect = 3.703e-14
Identity = 51/107 (47.66%), Postives = 60/107 (56.07%), Query Frame = 3 
Query:  255 AIQIFYPKITHLTYIVHGLK*VCEQIRSLILTLIG*LQM*KKYF*R--------------LRLE*RSTTNNYTMVT*LTDVNYYANHYEKIVRIFDVLDNEEAASIK 533
            AIQ FYPKITHLT + HGL  VCEQIR L   +   +   KK F +              L L  +     +   T L  VNYYA ++EKIVRIFD LD+EEAASIK
Sbjct:  262 AIQTFYPKITHLTCVAHGLHRVCEQIRGLYTNVDRLISNVKKVFLKAPLRVGIFKDLEPDLALPPQPIITRWG--TWLNAVNYYATNFEKIVRIFDALDDEEAASIK 366
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BLAST of CGG triplet repeat-binding protein 1 vs. TrEMBL
Match: A0A2S2R3M2 (DUF659 domain-containing protein OS=Sipha flava OX=143950 GN=g.122712 PE=4 SV=1)

HSP 1 Score: 63.929 bits (154), Expect = 1.020e-8
Identity = 36/66 (54.55%), Postives = 47/66 (71.21%), Query Frame = 3 
Query:   75 MPRVKQSVSNRLKRYVSEFPD--FKTDGKIIFCKVFKL-VSAEKIFTIKQHLA--KHIKLTERNVA 257
            MP+VK S S RL+ Y++EF D  F TDGKI+FCK+  + V++EK FTI QHL+  KH+K  E N A
Sbjct:    1 MPKVKPSSSLRLREYINEFGDDVFSTDGKILFCKICSVKVASEKKFTITQHLSRDKHVKGLEMNKA 66
[Close]
BLAST of CGG triplet repeat-binding protein 1 vs. TrEMBL
Match: J9L1I2 (Uncharacterized protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=2)

HSP 1 Score: 60.4622 bits (145), Expect = 2.073e-8
Identity = 30/61 (49.18%), Postives = 45/61 (73.77%), Query Frame = 3 
Query:   75 MPRVKQSVSNRLKRYVSEFPD--FKTDGKIIFCKVFKL-VSAEKIFTIKQHL--AKHIKLT 242
            MP+VK S SNRL+ +V EF +    TDG I++CK+ ++ V +E+ FT++QH+  AKHI+LT
Sbjct:    1 MPKVKSSCSNRLRGFVKEFGEHVLTTDGSILYCKLCEVNVGSERRFTVEQHMNIAKHIRLT 61
[Close]
BLAST of CGG triplet repeat-binding protein 1 vs. TrEMBL
Match: X1WQV4 (Uncharacterized protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 5.026e-8
Identity = 29/62 (46.77%), Postives = 46/62 (74.19%), Query Frame = 3 
Query:   72 IMPRVKQSVSNRLKRYVSEFPD--FKTDGKIIFCKVFKL-VSAEKIFTIKQHL--AKHIKLT 242
            +MP+VK S SNRL+ +V EF +    TDG I++CK+ ++ V +E+ FT++QH+  AKHI+L+
Sbjct:   53 VMPKVKSSCSNRLRGFVKEFGEHVLTTDGSILYCKLCEVKVGSERRFTVEQHMNTAKHIRLS 114
The following BLAST results are available for this feature:
BLAST of CGG triplet repeat-binding protein 1 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 CGG triplet repeat-binding protein 1 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 CGG triplet repeat-binding protein 1 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 CGG triplet repeat-binding protein 1 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 CGG triplet repeat-binding protein 1 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 CGG triplet repeat-binding protein 1 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 CGG triplet repeat-binding protein 1 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 CGG triplet repeat-binding protein 1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A3L8D7505.649e-1764.52Uncharacterized protein OS=Ooceraea biroi OX=20151... [more]
A0A0J7NEC43.703e-1447.66DUF659 domain-containing protein OS=Lasius niger O... [more]
A0A2S2R3M21.020e-854.55DUF659 domain-containing protein OS=Sipha flava OX... [more]
J9L1I22.073e-849.18Uncharacterized protein OS=Acyrthosiphon pisum OX=... [more]
X1WQV45.026e-846.77Uncharacterized protein OS=Acyrthosiphon pisum OX=... [more]
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BLAST of CGG triplet repeat-binding protein 1 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 CGG triplet repeat-binding protein 1 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 CGG triplet repeat-binding protein 1 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 CGG triplet repeat-binding protein 1 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 CGG triplet repeat-binding protein 1 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 CGG triplet repeat-binding protein 1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022483 ID=SMED30022483|Name=CGG triplet repeat-binding protein 1|organism=Schmidtea mediterranea sexual|type=transcript|length=534bp
TTATTGCAATAGTTATTTAATATACAACATTAAATTATAAGTTGCAATTT
AAATAAATTTAATTTTTGTAAATTATGCCGAGGGTAAAGCAATCCGTATC
TAACAGATTGAAGCGGTATGTAAGCGAATTTCCAGATTTCAAAACTGATG
GAAAGATTATTTTTTGTAAAGTGTTTAAGTTGGTGTCAGCAGAAAAAATA
TTTACGATAAAACAGCACCTCGCTAAACATATCAAGCTTACTGAAAGAAA
TGTAGCAATACAAATATTTTACCCAAAAATAACTCATTTGACTTACATTG
TTCATGGACTAAAATGAGTGTGTGAGCAAATACGAAGCCTTATACTAACG
TTGATAGGTTAATTGCAAATGTAAAAAAAGTATTTTTAAAGGCTCCGCCT
AGAGTAGAGGTCCACAACCAATAACTACACGATGGTGACTTGACTTACAG
ACGTAAATTACTATGCAAATCACTATGAGAAGATTGTGAGAATATTTGAT
GTGTTAGACAATGAAGAAGCAGCCTCAATCAAAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: biological process
TermDefinition
GO:0000122negative regulation of transcription from RNA polymerase II promoter
GO:0006357regulation of transcription from RNA polymerase II promoter
Vocabulary: molecular function
TermDefinition
GO:0001227transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003690double-stranded DNA binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0000070intestinal phagocyte