Protein chibby homolog 1

Overview
NameProtein chibby homolog 1
Smed IDSMED30029053
Length (bp)732
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 Protein chibby homolog 1 (SMED30029053) t-SNE clustered cells

Violin plots show distribution of expression levels for Protein chibby homolog 1 (SMED30029053) 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 Protein chibby homolog 1 (SMED30029053) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Protein chibby homolog 1 (SMED30029053) 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



SMED30029053

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30029053SMESG000024740.1 dd_Smed_v4_12205_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029053SMESG000024740.1 dd_Smed_v4_12205_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30029053SMESG000024740.1 dd_Smed_v4_12205_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30029053SMESG000024740.1 dd_Smed_v6_12205_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Protein chibby homolog 1 vs. Ensembl Mouse
Match: Cby1 (chibby family member 1, beta catenin antagonist [Source:MGI Symbol;Acc:MGI:1920989])

HSP 1 Score: 46.9802 bits (110), Expect = 1.959e-6
Identity = 44/127 (34.65%), Postives = 64/127 (50.39%), Query Frame = 3 
Query:   81 TKKEFPSRISYSTGSLNQRDLSMDLIEIRGI--------LGKKEIKFINGIWIKGDSKEKVLNAPDSVETE-LANEVSKIREENNLLKLKISILYDLVSEKLGEKISSVYQNYKELAELQKIYRRNK 434
            + K+ P R S S  +L+  D S   +E+ G+        L  + +KF NG W+  DS   +    D  ET+ L     ++ EENNLL+LK+ IL D++SE   E     +   KEL EL+   RR K
Sbjct:    9 SPKKTPPRKSASLSNLHSLDRSTRELEL-GLDYGTPTMNLAGQSLKFENGQWV-ADSV--ISGGVDRRETQRLRKRNQQLEEENNLLRLKVDILLDMLSETTAES----HLKDKELDELKVTNRRRK 127
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BLAST of Protein chibby homolog 1 vs. Planmine SMEST
Match: SMESG000024740.1 (SMESG000024740.1)

HSP 1 Score: 239.195 bits (609), Expect = 4.037e-81
Identity = 123/128 (96.09%), Postives = 123/128 (96.09%), Query Frame = 3 
Query:   63 MSHSNKTKKEFPSRISYSTGSLNQRDLSMDLIEIRGILGKKEIKFINGIWIKGDSKEKVLNAPDSVETELANEVSKIREENNLLKLKISILYDLVSEKLGEKISSVYQNYKELAELQKIYRRNKYSTQ 446
            MSHSNKTKKEFPSRISYSTGSLNQRDLSMDLIEIRGILGKKEIKFINGIWIKGDSKEKVLNAPDSVETEL NEVSKIREENNLLKLKISILYDL    LGEKISSVYQNYKELAELQKIYRRNKYSTQ
Sbjct:    1 MSHSNKTKKEFPSRISYSTGSLNQRDLSMDLIEIRGILGKKEIKFINGIWIKGDSKEKVLNAPDSVETELTNEVSKIREENNLLKLKISILYDL----LGEKISSVYQNYKELAELQKIYRRNKYSTQ 124
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BLAST of Protein chibby homolog 1 vs. Planmine SMEST
Match: SMESG000071266.1 (SMESG000071266.1)

HSP 1 Score: 83.1889 bits (204), Expect = 4.475e-19
Identity = 49/89 (55.06%), Postives = 62/89 (69.66%), Query Frame = 3 
Query:   96 PSRISYSTGSLNQRDLSMDLIEIRGILGKKEIKFINGIWIKGDSKEKVLNAPDSVETELANEVSKIREENNLLKLKISILYDLVSEKLG 362
            P R S S  SLNQ D S++LIEI+G LGK+E+ F+NGIWIK DS   +    +  ET+LAN    ++EEN+LLKLKI ILY+  SE LG
Sbjct:   13 PPRKSQSMNSLNQVDSSVELIEIKGFLGKEEMIFVNGIWIKKDSSVVMKKDSNLEETKLANANKLVKEENSLLKLKIEILYN-ESESLG 100
[Close]
BLAST of Protein chibby homolog 1 vs. Planmine SMEST
Match: SMESG000071266.1 (SMESG000071266.1)

HSP 1 Score: 76.2554 bits (186), Expect = 1.038e-16
Identity = 45/81 (55.56%), Postives = 58/81 (71.60%), Query Frame = 3 
Query:  120 GSLNQRDLSMDLIEIRGILGKKEIKFINGIWIKGDSKEKVLNAPDSVETELANEVSKIREENNLLKLKISILYDLVSEKLG 362
             SLNQ D S++LIEI+G LGK+E+ F+NGIWIK DS   +    +  ET+LAN    ++EEN+LLKLKI ILY+  SE LG
Sbjct:    2 NSLNQVDSSVELIEIKGFLGKEEMIFVNGIWIKKDSSVVMKKDSNLEETKLANANKLVKEENSLLKLKIEILYN-ESESLG 81
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BLAST of Protein chibby homolog 1 vs. Planmine SMEST
Match: SMESG000047469.1 (SMESG000047469.1)

HSP 1 Score: 50.8322 bits (120), Expect = 4.862e-8
Identity = 42/119 (35.29%), Postives = 66/119 (55.46%), Query Frame = 3 
Query:   93 FPSRISYSTGSLNQRDLSMDLIEIRGILGKKEIKFINGIWIKG-----DSKEKVLNAPDSVETELANEVSK-IREENNLLKLKISILYDLVSEKLGEKISSVYQNYKELAELQKIYRRN 431
            F  R + S   L+     ++L +I+ +LGK+E+ F NG WI       + + KV   P S E  + N ++K I+EENNLL+LKI+IL+D++    G+  + V  +  E   L+ I  RN
Sbjct:   12 FEPRKTKSVLDLSTNFSDLNLEDIKCVLGKEELLFRNGKWITNSLLQINDEYKV---PKS-ERHMMNSINKAIKEENNLLELKINILFDMI----GKLAAEVELSRNEYFHLKNILSRN 122
The following BLAST results are available for this feature:
BLAST of Protein chibby homolog 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 Protein chibby homolog 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 Protein chibby homolog 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 Protein chibby homolog 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 Protein chibby homolog 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 Protein chibby homolog 1 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 1
Match NameE-valueIdentityDescription
Cby11.959e-634.65chibby family member 1, beta catenin antagonist [S... [more]
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BLAST of Protein chibby homolog 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 Protein chibby homolog 1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Protein chibby homolog 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 Protein chibby homolog 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 Protein chibby homolog 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 Protein chibby homolog 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 Protein chibby homolog 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 Protein chibby homolog 1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000024740.14.037e-8196.09SMESG000024740.1[more]
SMESG000071266.14.475e-1955.06SMESG000071266.1[more]
SMESG000071266.11.038e-1655.56SMESG000071266.1[more]
SMESG000047469.14.862e-835.29SMESG000047469.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029053 ID=SMED30029053|Name=Protein chibby homolog 1|organism=Schmidtea mediterranea sexual|type=transcript|length=732bp
CATTTTTCGCTCGGCATTCAGTCTCATAAATTAACATTTTCTGTCCACTT
AATAAACATCAAATGTCTCATTCTAATAAAACAAAAAAAGAGTTTCCATC
AAGAATTTCCTATAGCACCGGATCTTTGAATCAGCGTGATCTATCCATGG
ACTTGATCGAGATTCGAGGCATACTAGGAAAAAAAGAAATAAAATTTATC
AATGGAATCTGGATCAAAGGAGATTCCAAAGAGAAAGTTCTGAATGCCCC
AGATTCAGTTGAGACTGAACTGGCAAATGAAGTCAGTAAAATTCGAGAAG
AAAATAATCTACTCAAATTAAAAATTTCCATTTTATACGATTTAGTAAGT
GAAAAACTAGGTGAGAAAATATCAAGTGTTTATCAAAATTACAAAGAACT
GGCGGAATTGCAGAAAATCTATCGAAGAAATAAATATTCAACCCAATGAG
ATGAGAGGGTGGCAGATAAAATGCTGATCATATAATCATGGGAATCTGTG
AATCATTATTTGGGGAAAAGCATTCGATTAATTTATTTTATAATATTAAT
AAAAAATCTCAATTTGATGTTGAAATGGAAAAGTTTATTCTAGAAAATGT
TATTCTAATCTGGGAAATTTAAACAACAAATTGAATGAAATTGCTGCTAG
TGCATTGATACACTTTAACGGAGTCATGAAAGAGCATTTACCAATTCAAT
TTATCAAAAGAAAGAAAAAACTTCCCAACCAC
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protein sequence of SMED30029053-orf-1

>SMED30029053-orf-1 ID=SMED30029053-orf-1|Name=SMED30029053-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=129bp
MSHSNKTKKEFPSRISYSTGSLNQRDLSMDLIEIRGILGKKEIKFINGIW
IKGDSKEKVLNAPDSVETELANEVSKIREENNLLKLKISILYDLVSEKLG
EKISSVYQNYKELAELQKIYRRNKYSTQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR028118Chibby_fam
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0005794Golgi apparatus
GO:0016607nuclear speck
GO:0036064ciliary basal body
Vocabulary: biological process
TermDefinition
GO:0030154cell differentiation
GO:0045444fat cell differentiation
GO:0055007cardiac muscle cell differentiation
GO:0060271cilium morphogenesis
GO:0090090negative regulation of canonical Wnt signaling pathway
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 67..87
IPR028118Chibby familyPFAMPF14645Chibbycoord: 12..99
e-value: 1.3E-13
score: 51.4