hypothetical protein

Overview
Namehypothetical protein (AFJ24807.1)
Smed IDSMED30011516
Length (bp)1523
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 hypothetical protein (SMED30011516) t-SNE clustered cells

Violin plots show distribution of expression levels for hypothetical protein (SMED30011516) 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 hypothetical protein (SMED30011516) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for hypothetical protein (SMED30011516) 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.
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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



SMED30011516

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30011516h1SMcG0010731 SmedASXL_014397SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30011516h1SMcG0010731 SmedASXL_014397SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
protonephridiaSMED30011516h1SMcG0010731 dd_Smed_v4_5959_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30011516h1SMcG0010731 dd_Smed_v4_5959_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30011516h1SMcG0010731 dd_Smed_v4_5959_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30011516h1SMcG0010731 dd_Smed_v4_5959_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
whole organismSMED30011516h1SMcG0010731 Contig40151newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30011516h1SMcG0010731 Contig40151uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30011516h1SMcG0010731 SMED_05169_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011516h1SMcG0010731 SMED_05169_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011516h1SMcG0010731 SMED_02069_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011516h1SMcG0010731 SMED_02069_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of hypothetical protein vs. TrEMBL
Match: I1ZIF3 (Uncharacterized protein (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 747.658 bits (1929), Expect = 0.000e+0
Identity = 359/359 (100.00%), Postives = 359/359 (100.00%), Query Frame = 2 
Query:   41 LFEYFLIMSKTKVTAISLYLKDLKANSAGKFIDKTIATEKFKKLSIQDKDHYEVSAKRINAQTTSEPVFTKQKDTLGYNLKEVGEISDRKTEWENKTRCLIKDIVDSQNVFNKIFYTVKISGVDYCRSEDNQRVYATSEMCFIKFSFSKGIIDKLILFPDIINVAAGYRQHLYEDLEENVGWKPETFRNNHSIKDTIIAIRQFFNGDYEPIYVPTKDHQEEVGLALQTLYDEVLMSCPWIESHEDWGRKCQIYQLEFLVSFMLKKYCDDINYDDTGVSVVLDFWRKLKVDMAPETCERHMQYGLANQCCTNMLLKYLYGSFFMLQFDGMPELQSLVSEEFYKEMDFVVPMDNTDEVLVS 1117
            LFEYFLIMSKTKVTAISLYLKDLKANSAGKFIDKTIATEKFKKLSIQDKDHYEVSAKRINAQTTSEPVFTKQKDTLGYNLKEVGEISDRKTEWENKTRCLIKDIVDSQNVFNKIFYTVKISGVDYCRSEDNQRVYATSEMCFIKFSFSKGIIDKLILFPDIINVAAGYRQHLYEDLEENVGWKPETFRNNHSIKDTIIAIRQFFNGDYEPIYVPTKDHQEEVGLALQTLYDEVLMSCPWIESHEDWGRKCQIYQLEFLVSFMLKKYCDDINYDDTGVSVVLDFWRKLKVDMAPETCERHMQYGLANQCCTNMLLKYLYGSFFMLQFDGMPELQSLVSEEFYKEMDFVVPMDNTDEVLVS
Sbjct:    1 LFEYFLIMSKTKVTAISLYLKDLKANSAGKFIDKTIATEKFKKLSIQDKDHYEVSAKRINAQTTSEPVFTKQKDTLGYNLKEVGEISDRKTEWENKTRCLIKDIVDSQNVFNKIFYTVKISGVDYCRSEDNQRVYATSEMCFIKFSFSKGIIDKLILFPDIINVAAGYRQHLYEDLEENVGWKPETFRNNHSIKDTIIAIRQFFNGDYEPIYVPTKDHQEEVGLALQTLYDEVLMSCPWIESHEDWGRKCQIYQLEFLVSFMLKKYCDDINYDDTGVSVVLDFWRKLKVDMAPETCERHMQYGLANQCCTNMLLKYLYGSFFMLQFDGMPELQSLVSEEFYKEMDFVVPMDNTDEVLVS 359
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BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000039929.1 (SMESG000039929.1)

HSP 1 Score: 854.358 bits (2206), Expect = 0.000e+0
Identity = 426/427 (99.77%), Postives = 427/427 (100.00%), Query Frame = 2 
Query:   62 MSKTKVTAISLYLKDLKANSAGKFIDKTIATEKFKKLSIQDKDHYEVSAKRINAQTTSEPVFTKQKDTLGYNLKEVGEISDRKTEWENKTRCLIKDIVDSQNVFNKIFYTVKISGVDYCRSEDNQRVYATSEMCFIKFSFSKGIIDKLILFPDIINVAAGYRQHLYEDLEENVGWKPETFRNNHSIKDTIIAIRQFFNGDYEPIYVPTKDHQEEVGLALQTLYDEVLMSCPWIESHEDWGRKCQIYQLEFLVSFMLKKYCDDINYDDTGVSVVLDFWRKLKVDMAPETCERHMQYGLANQCCTNMLLKYLYGSFFMLQFDGMPELQSLVSEEFYKEMDFVVPMDNTDEVLVSPQPPKITISWNNYFFDHSNIEDVISNLAGIDILSTDSASXXXXXXXXXXXXXMARRQDYNGIPGLAAAIKIKLPK 1342
            MSKTKVTAISLYLKDLKANSAGKFIDKTIATEKFKKLSIQDKDHYEVSAKRINAQTTSEPVFTKQKDTLGYNLKEVGEISDRKTEWENKTRCLIKDIVDSQNVFNKIFYTVKISGVDYCRSEDNQRVYATSEMCFIKFSFSKGIIDKLILFPDIINVAAGYRQHLYEDLEENVGWKPETFRNNHSIKDTIIAIRQFFNGDYEPIYVPTKDHQEEVGLALQTLYDEVLMSCPWIESHEDWGRKCQIYQLEFLVSFMLKKYCDDINYDDTGVSVVLDFWRKLKVDMAPETCERHMQYGLANQCCTNMLLKYLYGSFFMLQFDGMPELQSLVSEEFYKEMDFVVPMDNTDEVLVSPQPPKITISWNNYFFDHSNIEDVISNLAGIDILSTDSASGDRRQGDWGRGRGMARRQD+NGIPGLAAAIKIKLPK
Sbjct:    1 MSKTKVTAISLYLKDLKANSAGKFIDKTIATEKFKKLSIQDKDHYEVSAKRINAQTTSEPVFTKQKDTLGYNLKEVGEISDRKTEWENKTRCLIKDIVDSQNVFNKIFYTVKISGVDYCRSEDNQRVYATSEMCFIKFSFSKGIIDKLILFPDIINVAAGYRQHLYEDLEENVGWKPETFRNNHSIKDTIIAIRQFFNGDYEPIYVPTKDHQEEVGLALQTLYDEVLMSCPWIESHEDWGRKCQIYQLEFLVSFMLKKYCDDINYDDTGVSVVLDFWRKLKVDMAPETCERHMQYGLANQCCTNMLLKYLYGSFFMLQFDGMPELQSLVSEEFYKEMDFVVPMDNTDEVLVSPQPPKITISWNNYFFDHSNIEDVISNLAGIDILSTDSASGDRRQGDWGRGRGMARRQDHNGIPGLAAAIKIKLPK 427
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BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000046449.1 (SMESG000046449.1)

HSP 1 Score: 640.958 bits (1652), Expect = 0.000e+0
Identity = 309/429 (72.03%), Postives = 361/429 (84.15%), Query Frame = 2 
Query:   62 MSKTKVTAISLYLKDLKANSAGKFIDKTIATEKFKKLSIQDKDHYEVSAKRINAQTTSEPVFTKQKDTLGYNLKEVGEISDRKTEWENKTRCLIKDIVDSQNVFNKIFYTVKISGVDYCRSEDNQRVYATSEMCFIKFSFSKGIIDKLILFPDIINVAAGYRQHLYEDLEENVGWKPETFRNNHSIKDTIIAIRQFFNGDYEPIYVPTKDHQEEVGLALQTLYDEVLMSCPWIESHEDWGRKCQIYQLEFLVSFMLKKYCDDINYDDTGVSVVLDFWRKLKVDMAPETCERHMQYGLANQCCTNMLLKYLYGSFFMLQFDGMPELQSLVSEEFYKEMDFVVPMDNTDEVLVSPQPPKITISWNNYFFDHSNIEDVISNLAGIDILS--TDSASXXXXXXXXXXXXXMARRQDYNGIPGLAAAIKIKLPK 1342
            M++ KV+AISLY+KDLK ++ GKFID  IA+EKFKKLSIQDKD+Y+VSAKRIN+Q  SEPVFTKQKDTLG NLKE+GEIS RK EWE KTR LI D+ +S+NV +K FYTVKISGVD+CRSEDN+RVYA SE+C IKFSF KGIIDKLILFPD+I VAAGYRQHLYEDLEENVGWKP+TFRNNHSI +T+IAIR FFN +YEPIYVPTKDHQEEVGL LQTLYDEV MSCPWIES EDWGRKCQIYQLE+LV+ +LKKYCD+ N DD GVSVVLDFWRKLKV++APETCERHMQYGLANQCCTNMLLKYLYGSF ML FDG  E+Q+LVSEEF++++DF++P+DN DE  VS Q  K+  +WNNYFFDH+NIED+IS+ +GI I +    + S  R+         + R+++   IPG +A  KIKLPK
Sbjct:    1 MNRKKVSAISLYMKDLKGDT-GKFIDSKIASEKFKKLSIQDKDYYDVSAKRINSQIPSEPVFTKQKDTLGNNLKEIGEISARKAEWETKTRKLILDVANSENVLHKQFYTVKISGVDFCRSEDNERVYAISEICLIKFSFMKGIIDKLILFPDVITVAAGYRQHLYEDLEENVGWKPDTFRNNHSIDETVIAIRNFFNRNYEPIYVPTKDHQEEVGLGLQTLYDEVQMSCPWIESFEDWGRKCQIYQLEYLVTSILKKYCDNTNNDDIGVSVVLDFWRKLKVEIAPETCERHMQYGLANQCCTNMLLKYLYGSFLMLTFDGKLEIQNLVSEEFFRDLDFIIPIDNIDENPVSAQSKKVNSNWNNYFFDHANIEDIISSFSGIAIKNDVVPATSYIRQGDRGRGRGLVRRQENNINIPGSSATAKIKLPK 428
The following BLAST results are available for this feature:
BLAST of hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZIF30.000e+0100.00Uncharacterized protein (Fragment) OS=Schmidtea me... [more]
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BLAST of hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000039929.10.000e+099.77SMESG000039929.1[more]
SMESG000046449.10.000e+072.03SMESG000046449.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30011516
GenBankAFJ24807.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011516 ID=SMED30011516|Name=hypothetical protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1523bp
TTGTTTTGTTTAATAATAGCTCTCCATACTTTTCAACTAGTTGTTTGAAT
ATTTTCTAATTATGAGTAAAACTAAAGTAACTGCGATATCTTTGTACCTG
AAAGATTTAAAAGCTAATAGTGCCGGGAAATTTATCGATAAAACTATTGC
TACTGAGAAATTTAAAAAATTAAGTATTCAAGATAAAGATCACTATGAAG
TTTCAGCAAAACGTATTAACGCACAGACCACTTCTGAACCTGTATTTACT
AAACAAAAGGACACGTTAGGATATAATTTAAAGGAAGTAGGCGAAATTTC
TGATAGGAAAACGGAGTGGGAAAATAAAACCCGATGCTTAATTAAAGATA
TTGTTGATTCTCAAAATGTATTTAATAAAATATTTTACACTGTAAAGATC
TCTGGAGTAGATTATTGCAGAAGTGAAGACAATCAACGAGTCTATGCAAC
AAGTGAAATGTGTTTTATTAAATTTAGTTTTTCGAAAGGAATAATTGACA
AATTAATATTATTTCCCGACATTATTAATGTTGCAGCAGGATATCGACAA
CATTTATACGAAGATTTGGAAGAAAATGTTGGTTGGAAACCGGAAACTTT
TAGAAATAATCACTCTATTAAAGATACTATTATCGCCATTAGACAATTTT
TTAATGGAGATTATGAGCCTATTTATGTACCAACAAAAGATCATCAAGAA
GAAGTTGGATTAGCCTTACAAACACTGTATGATGAAGTTCTAATGTCTTG
TCCTTGGATTGAATCACATGAGGATTGGGGTAGAAAATGCCAGATTTATC
AACTCGAATTTTTGGTGTCATTTATGTTAAAGAAATATTGTGATGATATT
AATTATGATGATACTGGTGTTTCTGTGGTTTTGGATTTCTGGCGGAAATT
AAAGGTTGACATGGCTCCGGAAACGTGTGAAAGACATATGCAATATGGAT
TAGCAAATCAATGCTGTACAAATATGCTTCTTAAATATCTTTATGGAAGT
TTTTTTATGCTTCAATTCGATGGAATGCCTGAGTTACAAAGTTTAGTTTC
TGAAGAATTTTATAAAGAAATGGATTTTGTAGTTCCTATGGATAATACCG
ATGAAGTTTTAGTTTCTCCACAACCACCGAAAATCACTATTAGCTGGAAC
AATTATTTCTTTGACCATTCGAATATTGAAGATGTCATTTCTAATTTAGC
GGGAATCGATATTTTAAGCACTGACTCGGCATCGGGTGATAGAAGACAAG
GAGACTGGGGCCGTGGGCGGGGAATGGCAAGGCGTCAGGACTACAATGGC
ATTCCTGGGTTAGCCGCAGCAATTAAAATTAAATTGCCAAAGGTCGTATG
CTAGGAGGAATTATGTTGTTGATTGTGTAATAGATTTTCAACGTTCTCTT
TTACAGTTTGCTTGTGAACTGATAAGTGATTGTAATTATGAATATATTGA
ATGTCCTTTGTTACCTCTGTTCAATTTTGGATTTTCAACTGTCATTTCTC
TATAATAATATAGTCAAGTTAGC
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protein sequence of SMED30011516-orf-1

>SMED30011516-orf-1 ID=SMED30011516-orf-1|Name=SMED30011516-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=431bp
MSKTKVTAISLYLKDLKANSAGKFIDKTIATEKFKKLSIQDKDHYEVSAK
RINAQTTSEPVFTKQKDTLGYNLKEVGEISDRKTEWENKTRCLIKDIVDS
QNVFNKIFYTVKISGVDYCRSEDNQRVYATSEMCFIKFSFSKGIIDKLIL
FPDIINVAAGYRQHLYEDLEENVGWKPETFRNNHSIKDTIIAIRQFFNGD
YEPIYVPTKDHQEEVGLALQTLYDEVLMSCPWIESHEDWGRKCQIYQLEF
LVSFMLKKYCDDINYDDTGVSVVLDFWRKLKVDMAPETCERHMQYGLANQ
CCTNMLLKYLYGSFFMLQFDGMPELQSLVSEEFYKEMDFVVPMDNTDEVL
VSPQPPKITISWNNYFFDHSNIEDVISNLAGIDILSTDSASGDRRQGDWG
RGRGMARRQDYNGIPGLAAAIKIKLPKVVC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000136whole organism
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell
PLANA:0003116parenchymal cell