Protein chibby 1

Overview
NameProtein chibby 1
Smed IDSMED30018518
Length (bp)678
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 1 (SMED30018518) t-SNE clustered cells

Violin plots show distribution of expression levels for Protein chibby 1 (SMED30018518) 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 1 (SMED30018518) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Protein chibby 1 (SMED30018518) 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



SMED30018518

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30018518h1SMcG0019588 SmedASXL_008956SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
X1 cellSMED30018518h1SMcG0019588 SmedASXL_008956SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
pharynxSMED30018518h1SMcG0019588 dd_Smed_v4_11618_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30018518h1SMcG0019588 dd_Smed_v4_11618_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018518h1SMcG0019588 Contig50954uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018518h1SMcG0019588 Contig50954newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30018518h1SMcG0019588 dd_Smed_v6_11618_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 1 vs. Planmine SMEST
Match: SMESG000024740.1 (SMESG000024740.1)

HSP 1 Score: 71.2478 bits (173), Expect = 1.026e-15
Identity = 51/103 (49.51%), Postives = 69/103 (66.99%), Query Frame = 2 
Query:   59 HWSVSGTNFPSRICNSTGSLNQNDISIELTEIRGSLGKNEIKFINGSWIR-ENGHQTYNSSFTKNSKESNIXXXXXXXXXXXXXXXXXIDILYNWLTEATADV 364
            H + +   FPSRI  STGSLNQ D+S++L EIRG LGK EIKFING WI+ ++  +  N+    +S E+ +  +   ++EENNLLKLKI ILY+ L E  + V
Sbjct:    3 HSNKTKKEFPSRISYSTGSLNQRDLSMDLIEIRGILGKKEIKFINGIWIKGDSKEKVLNAP---DSVETELTNEVSKIREENNLLKLKISILYDLLGEKISSV 102
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BLAST of Protein chibby 1 vs. Planmine SMEST
Match: SMESG000071266.1 (SMESG000071266.1)

HSP 1 Score: 51.9878 bits (123), Expect = 6.114e-8
Identity = 40/87 (45.98%), Postives = 55/87 (63.22%), Query Frame = 2 
Query:   77 TNFPSRICNSTGSLNQNDISIELTEIRGSLGKNEIKFINGSWIRENGHQTYNSSFTKNSKESNIXXXXXXXXXXXXXXXXXIDILYN 337
            +  P R   S  SLNQ D S+EL EI+G LGK E+ F+NG WI+++           N +E+ +   N+ +KEEN+LLKLKI+ILYN
Sbjct:   10 SKIPPRKSQSMNSLNQVDSSVELIEIKGFLGKEEMIFVNGIWIKKDSSVVMKKD--SNLEETKLANANKLVKEENSLLKLKIEILYN 94
The following BLAST results are available for this feature:
BLAST of Protein chibby 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 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 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 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 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 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 Protein chibby 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 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 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 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 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 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 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 1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000024740.11.026e-1549.51SMESG000024740.1[more]
SMESG000071266.16.114e-845.98SMESG000071266.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018518 ID=SMED30018518|Name=Protein chibby 1|organism=Schmidtea mediterranea sexual|type=transcript|length=678bp
ATTTTTAAATAAATTTAGTCTACATTAACAGAAATATATTGAATAAATAT
CTGAAATGCATTGGTCAGTCAGTGGAACGAATTTTCCTTCTAGGATATGC
AACAGCACTGGCTCATTGAATCAAAATGATATTTCAATTGAATTGACCGA
GATTAGAGGCTCGTTAGGAAAAAATGAAATAAAATTTATCAACGGCTCAT
GGATTAGAGAAAATGGTCACCAAACTTACAACTCAAGTTTTACCAAAAAT
TCAAAAGAATCAAATATTCAACAGCAAAATCAAAACTTGAAGGAAGAAAA
TAATTTATTGAAATTGAAAATTGATATTCTTTATAATTGGTTAACGGAGG
CCACAGCAGATGTCATGCTGAATAACAATGAGCTTGAGCAGTTGCAGAGA
CTTGCCCAAAGAGCTAGATTTCATTGAAATTAATAATGAATGCTTTCAAA
ATGCTTTGTTTTAATACATAGTCTTTGTGTTTTCACTATTTACACCGGTC
TCTATGACTACATTTACCTTGCATAATTTAATCGAATGCTGATGTGACAT
TAATAGTTTTATTTGTCTAAATGGATCACAAAGCACTCGATTAATTAATT
TATATGCACAGTAAAATATAGTTTTATCACTAACTTTCAAAATTAATATT
GCTAATATTTGACAAATTTTCATCAAAC
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protein sequence of SMED30018518-orf-1

>SMED30018518-orf-1 ID=SMED30018518-orf-1|Name=SMED30018518-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=124bp
MHWSVSGTNFPSRICNSTGSLNQNDISIELTEIRGSLGKNEIKFINGSWI
RENGHQTYNSSFTKNSKESNIQQQNQNLKEENNLLKLKIDILYNWLTEAT
ADVMLNNNELEQLQRLAQRARFH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR028118Chibby_fam
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 64..88
NoneNo IPR availablePANTHERPTHR21533:SF20PROTEIN CHIBBY HOMOLOG 1coord: 36..119
NoneNo IPR availablePANTHERPTHR21533LEUCINE-RICH PROTEINcoord: 36..119
IPR028118Chibby familyPFAMPF14645Chibbycoord: 22..110
e-value: 6.1E-22
score: 78.2