hypothetical protein

Overview
Namehypothetical protein (AFJ24770.1)
Smed IDSMED30007420
Length (bp)1620
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 (SMED30007420) t-SNE clustered cells

Violin plots show distribution of expression levels for hypothetical protein (SMED30007420) 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 (SMED30007420) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for hypothetical protein (SMED30007420) 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



SMED30007420

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30007420SMESG000037088.1 SMESG000032688.1 SmedASXL_018051SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30007420SMESG000037088.1 SMESG000032688.1 SmedASXL_018051SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
cephalic gangliaSMED30007420SMESG000037088.1 SMESG000032688.1 dd_Smed_v4_10376_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007420SMESG000037088.1 SMESG000032688.1 dd_Smed_v4_10376_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30007420SMESG000037088.1 SMESG000032688.1 dd_Smed_v4_10376_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of hypothetical protein vs. TrEMBL
Match: I1ZIB6 (Uncharacterized protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 539.65 bits (1389), Expect = 0.000e+0
Identity = 286/291 (98.28%), Postives = 288/291 (98.97%), Query Frame = 2 
Query:   59 MNKIRHDELEKIKRRRKQKSKGIIAATVTSKAQKAFMKHIDASRYEIEKSRFRYLIKDGNKSRSKLTLGIFDNAVGSRNINHIFNPVLKKENFVDLQAACLYQPPIMQQNLVIDAKHEISLEASLVDLADSCCKMLNIHKTDGDLPGTGDVXXXXXXXXXXXXXXXXXXXXXVNVKNGVSFVGKKSETGLKSFKFNNRKETLFDKTNYPVLSASTSISNSLILFRPLITNIPMKRKSIELDNHYKTSHPIWDTPEDLRTSHLRSFSDRSIIDKTITNLGTSKFGTSLWLDD 931
            MNKIRHDELEKIKRRRKQKSKGIIAATVTSKAQKAFMKHIDASRYEIEKSRFRY  KDGNKSRSKLTLGIFDNAVGSRNINHIFNPVLKKENFVDLQAACLYQPPIMQQNLVIDAKHEISLEASLVDLADSCCKMLNIHKTDGDLPGTGD RLRLREAKADAKRDDKLKLIDVNVKNGVSFVGKKSETGLKSFKFNNRKETLFDKTNYPVLSASTSISNSLILFRPLITNIP+KRKSIELDNHYKTSHPIWDTPEDLRTSHLRSFSDRSIIDK+ITNLGTSKFGTSLWLDD
Sbjct:    1 MNKIRHDELEKIKRRRKQKSKGIIAATVTSKAQKAFMKHIDASRYEIEKSRFRYYFKDGNKSRSKLTLGIFDNAVGSRNINHIFNPVLKKENFVDLQAACLYQPPIMQQNLVIDAKHEISLEASLVDLADSCCKMLNIHKTDGDLPGTGDARLRLREAKADAKRDDKLKLIDVNVKNGVSFVGKKSETGLKSFKFNNRKETLFDKTNYPVLSASTSISNSLILFRPLITNIPIKRKSIELDNHYKTSHPIWDTPEDLRTSHLRSFSDRSIIDKSITNLGTSKFGTSLWLDD 291
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BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000032688.1 (SMESG000032688.1)

HSP 1 Score: 548.51 bits (1412), Expect = 0.000e+0
Identity = 290/291 (99.66%), Postives = 291/291 (100.00%), Query Frame = 2 
Query:   59 MNKIRHDELEKIKRRRKQKSKGIIAATVTSKAQKAFMKHIDASRYEIEKSRFRYLIKDGNKSRSKLTLGIFDNAVGSRNINHIFNPVLKKENFVDLQAACLYQPPIMQQNLVIDAKHEISLEASLVDLADSCCKMLNIHKTDGDLPGTGDVXXXXXXXXXXXXXXXXXXXXXVNVKNGVSFVGKKSETGLKSFKFNNRKETLFDKTNYPVLSASTSISNSLILFRPLITNIPMKRKSIELDNHYKTSHPIWDTPEDLRTSHLRSFSDRSIIDKTITNLGTSKFGTSLWLDD 931
            MNKIRHDELEKIKRRRKQKSKGIIAATVTSKAQKAFMKHIDASRYEIEKSRFRYLIKDGNKSRSKLTLGIFDNAVGSRNINHIFNPVLKKENFVDLQAACLYQPPIMQQNLVIDAKHEISLEASLVDLADSCCKMLNIHKTDGDLPGTGDVRLRLREAKA+AKRDDKLKLIDVNVKNGVSFVGKKSETGLKSFKFNNRKETLFDKTNYPVLSASTSISNSLILFRPLITNIPMKRKSIELDNHYKTSHPIWDTPEDLRTSHLRSFSDRSIIDKTITNLGTSKFGTSLWLDD
Sbjct:    1 MNKIRHDELEKIKRRRKQKSKGIIAATVTSKAQKAFMKHIDASRYEIEKSRFRYLIKDGNKSRSKLTLGIFDNAVGSRNINHIFNPVLKKENFVDLQAACLYQPPIMQQNLVIDAKHEISLEASLVDLADSCCKMLNIHKTDGDLPGTGDVRLRLREAKAEAKRDDKLKLIDVNVKNGVSFVGKKSETGLKSFKFNNRKETLFDKTNYPVLSASTSISNSLILFRPLITNIPMKRKSIELDNHYKTSHPIWDTPEDLRTSHLRSFSDRSIIDKTITNLGTSKFGTSLWLDD 291
[Close]
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000037088.1 (SMESG000037088.1)

HSP 1 Score: 367.081 bits (941), Expect = 8.200e-126
Identity = 201/212 (94.81%), Postives = 206/212 (97.17%), Query Frame = 2 
Query:  296 INHIFNPVLKKENFVDLQAACLYQPPIMQQNLVIDAKHEISLEASLVDLADSCCKMLNIHKTDGDLPGTGDVXXXXXXXXXXXXXXXXXXXXXVNVKNGVSFVGKKSETGLKSFKFNNRKETLFDKTNYPVLSASTSISNSLILFRPLITNIPMKRKSIELDNHYKTSHPIWDTPEDLRTSHLRSFSDRSIIDKTITNLGTSKFGTSLWLDD 931
            +NHIFNPVLKKE+FVDLQAACLYQPPIMQQNLVIDAKHEISLEASLVDLADSCCKML+IHKTDGDLPGT DVRLRLREAKADAKRDDKLKLIDV VKNG SFVGKK ETGLKSFK NNRKETLFDKTNYPVLSASTSISNSLILFRPLITNIP+KRKSIELDNHYKTSHPIWDTPEDLR SHLRSFSDRSIIDK+ITNLGTSKFGTSLWLDD
Sbjct:    1 MNHIFNPVLKKESFVDLQAACLYQPPIMQQNLVIDAKHEISLEASLVDLADSCCKMLSIHKTDGDLPGTEDVRLRLREAKADAKRDDKLKLIDVKVKNGFSFVGKKLETGLKSFKINNRKETLFDKTNYPVLSASTSISNSLILFRPLITNIPIKRKSIELDNHYKTSHPIWDTPEDLRMSHLRSFSDRSIIDKSITNLGTSKFGTSLWLDD 212
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
I1ZIB60.000e+098.28Uncharacterized protein OS=Schmidtea mediterranea ... [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
SMESG000032688.10.000e+099.66SMESG000032688.1[more]
SMESG000037088.18.200e-12694.81SMESG000037088.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30007420
GenBankAFJ24770.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007420 ID=SMED30007420|Name=hypothetical protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1620bp
TTTATCATTGAAATAATATAAATTTAAAGTTGAACTCATTAATCTTTGTT
ATTGGATAATGAATAAAATACGCCATGATGAATTAGAGAAAATTAAAAGA
CGACGAAAGCAGAAATCAAAAGGAATAATTGCCGCTACAGTTACATCTAA
AGCACAAAAAGCTTTTATGAAACATATTGATGCCTCTAGATATGAAATTG
AGAAGAGTAGATTTAGATATTTAATTAAAGATGGAAATAAAAGCCGTAGT
AAATTGACCCTCGGAATATTCGATAATGCAGTAGGCTCGAGGAATATTAA
TCATATATTCAATCCAGTTCTCAAGAAAGAAAATTTTGTCGATTTACAAG
CTGCTTGTTTGTATCAGCCTCCAATAATGCAACAGAATCTAGTTATAGAT
GCTAAACATGAAATTAGTTTAGAAGCGTCTCTTGTTGATTTGGCCGATAG
TTGTTGTAAAATGCTAAATATTCATAAAACCGATGGTGATTTACCTGGCA
CTGGAGATGTAAGGTTAAGGCTGAGAGAGGCCAAAGCGGATGCCAAACGC
GATGATAAATTAAAGTTGATTGATGTTAACGTGAAAAATGGCGTCAGTTT
CGTTGGTAAGAAATCGGAAACTGGTTTGAAGTCATTTAAGTTCAATAATC
GTAAAGAAACTTTATTTGACAAAACAAATTATCCAGTTCTTTCTGCTTCA
ACTTCGATTTCTAATTCCTTAATATTATTTCGTCCTCTGATTACCAATAT
TCCCATGAAAAGAAAATCAATCGAATTAGACAATCATTATAAAACCAGCC
ATCCAATTTGGGACACTCCTGAAGATTTACGGACGTCCCATCTCAGATCA
TTTTCTGATCGTTCAATTATCGACAAAACCATAACAAATTTGGGAACGTC
GAAATTCGGAACAAGCTTGTGGCTCGACGATTGATATGGTAACTGATTTA
TTTCATTCTGGGGAGCGGTTAAATCGGCAAATCCCCATGAAAACCCATTA
ATTTTATATATATTGATTAATTATGTTTTACTTTATCGTTGTAACTAAAT
TCATAAATCTTTAGAACAGCGTTTGAATAATGACAAATTGTCGACTTCTC
CCTGGTGAGGCGGTGACGGACCTTGCAATCCTGGACTAAATAACATATAA
GCTCATTATTCGCTGAGCTTTGTGAAATCTGGATTTTGAATCTCTATTAT
TTCTAATGTGAAATTACTGAATTATTGATATCACGTTGAGGTTGATTGCT
GCCCTATTTCATACGACATTGCTGGTTTCAAGCTGAAGGTTGAGCTAATT
TAATTTGACTTTATTTCATTCCTATGCATTGTGGTAGTAGGCACCTGTGT
GCCCGTCAATTTTGACTGACAACCACTGTAAGTCCTTGGGAACCTCTGTT
GGTACTTCCAATAGTGGCTTAATGATCTACAAGCACTGCTTCTTGAATAT
GGTCCACAATTGGGTTAACTTCTGGTGTAGCCCATGTCGCGTTATTGTGG
TCACCTTGAAAATTATCTTCATTTAAATTTAATTAAATGCGTTTTTCTAT
TTCCTAAATTTTATTAAAATCTAATTACTACAGAAATAATATAAATTACA
TAAATTAAATGCAAATCTAA
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protein sequence of SMED30007420-orf-1

>SMED30007420-orf-1 ID=SMED30007420-orf-1|Name=SMED30007420-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=292bp
MNKIRHDELEKIKRRRKQKSKGIIAATVTSKAQKAFMKHIDASRYEIEKS
RFRYLIKDGNKSRSKLTLGIFDNAVGSRNINHIFNPVLKKENFVDLQAAC
LYQPPIMQQNLVIDAKHEISLEASLVDLADSCCKMLNIHKTDGDLPGTGD
VRLRLREAKADAKRDDKLKLIDVNVKNGVSFVGKKSETGLKSFKFNNRKE
TLFDKTNYPVLSASTSISNSLILFRPLITNIPMKRKSIELDNHYKTSHPI
WDTPEDLRTSHLRSFSDRSIIDKTITNLGTSKFGTSLWLDD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell