hypothetical protein

Overview
Namehypothetical protein (AFJ24740.1)
Smed IDSMED30005357
Length (bp)687
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 (SMED30005357) t-SNE clustered cells

Violin plots show distribution of expression levels for hypothetical protein (SMED30005357) 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 (SMED30005357) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for hypothetical protein (SMED30005357) 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



SMED30005357

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30005357h1SMcG0017245 Contig35471uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005357h1SMcG0017245 Contig35471newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30005357h1SMcG0017245 dd_Smed_v4_775_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30005357h1SMcG0017245 dd_Smed_v4_775_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30005357h1SMcG0017245 SMED30005357smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30005357h1SMcG0017245 SMED30005357smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
Category 3 cellSMED30005357h1SMcG0017245 dd_Smed_v6_775_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30005357h1SMcG0017245 dd_Smed_v4_775_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30005357h1SMcG0017245 SMED_00523_V2_1rGPL14150PMID: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: I1ZI86 (Uncharacterized protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 363.229 bits (931), Expect = 5.120e-126
Identity = 176/177 (99.44%), Postives = 176/177 (99.44%), Query Frame = 3 
Query:   81 MINFNQFSIISLSVVVIFLQSTSAKVPILVRYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKCGNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETCELSLDPYNWRRVEKKYYEAKTSDY 611
            MINFNQ SIISLSVVVIFLQSTSAKVPILVRYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKCGNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETCELSLDPYNWRRVEKKYYEAKTSDY
Sbjct:    1 MINFNQLSIISLSVVVIFLQSTSAKVPILVRYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKCGNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETCELSLDPYNWRRVEKKYYEAKTSDY 177
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BLAST of hypothetical protein vs. TrEMBL
Match: V9XTF1 (X1.A.D4.1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 310.842 bits (795), Expect = 9.302e-106
Identity = 152/153 (99.35%), Postives = 152/153 (99.35%), Query Frame = 3 
Query:   81 MINFNQFSIISLSVVVIFLQSTSAKVPILVRYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKCGNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETC 539
            MINFNQ SIISLSVVVIFLQSTSAKVPILVRYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKCGNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETC
Sbjct:    1 MINFNQLSIISLSVVVIFLQSTSAKVPILVRYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKCGNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETC 153
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BLAST of hypothetical protein vs. TrEMBL
Match: A0A0A1CQX9 (Pmp-10 (Fragment) OS=Schmidtea mediterranea OX=79327 GN=pmp-10 PE=2 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 8.654e-6
Identity = 39/149 (26.17%), Postives = 64/149 (42.95%), Query Frame = 3 
Query:  150 AKVPILVRYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLL----NKCGNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETCELSLDPYNWRRVEKK 584
            AK  I+ R    +C++LIP  + CD   +     C   +  +   C+  F  LT+ CN  E+ +      K G     C  R   LD +C  +   +   C ++Y K++ KC   + +I+ +C  I   Y + CE  +    W    KK
Sbjct:   13 AKALIINRNQRLQCNDLIPEVISCDSAYETIDNYCERKATEIDSFCNRKFSKLTESCNKAENKIKLDCNTKVGYITASCGRRFDRLDKVCRISSTTLSRKCTKKYRKMDNKCNKKYGKINVKCKRIYYRYKDFCETGVANNYWNEKYKK 161
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BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000027979.1 (SMESG000027979.1)

HSP 1 Score: 363.229 bits (931), Expect = 1.424e-129
Identity = 176/177 (99.44%), Postives = 176/177 (99.44%), Query Frame = 3 
Query:   81 MINFNQFSIISLSVVVIFLQSTSAKVPILVRYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKCGNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETCELSLDPYNWRRVEKKYYEAKTSDY 611
            MINFNQ SIISLSVVVIFLQSTSAKVPILVRYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKCGNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETCELSLDPYNWRRVEKKYYEAKTSDY
Sbjct:    1 MINFNQLSIISLSVVVIFLQSTSAKVPILVRYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKCGNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETCELSLDPYNWRRVEKKYYEAKTSDY 177
[Close]
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000053861.1 (SMESG000053861.1)

HSP 1 Score: 137.887 bits (346), Expect = 6.607e-41
Identity = 72/168 (42.86%), Postives = 97/168 (57.74%), Query Frame = 3 
Query:  114 LSVVVIFLQSTSAKVPILV--RYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKCGNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETCELSLDPYNWRRVEKKYYEAKTSDY 611
            L+++ IFL + S    I +  R+GE EC++LIP    CD     A   C   +  L K+CD AF  LT+GCN  E  +L  CG   P C+  ++FLDI CN+AC AI D+C   Y  +  KCEFI  R+++RC GI + Y ETCE +LDPYNW+  E  +      DY
Sbjct:    4 LAILPIFLLTISQYYAIEIQRRFGESECEDLIPFAEHCDRAYLTADNYCDRYASHLDKQCDIAFRKLTNGCNKHEGYILQTCGKKGPRCKVMINFLDITCNQACVAISDYCSDEYDYMTDKCEFINNRLEKRCNGIYQQYEETCEKNLDPYNWQIQENNFESIYHYDY 171
[Close]
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000068743.1 (SMESG000068743.1)

HSP 1 Score: 68.1662 bits (165), Expect = 4.842e-13
Identity = 40/153 (26.14%), Postives = 66/153 (43.14%), Query Frame = 3 
Query:  135 LQSTSAKVPILVRYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKC----GNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETCELSLDPYNWRRVEK 581
            L    AK  IL +   ++C+ LIP    CD+  +     C   +  + K+CD +F  L + CNT E+++  +C    G     C      LD +C          C + Y K++ +C   + +I  +C  I + Y + CE  + P  W    K
Sbjct:   26 LAVKKAKSLILNKAQREQCNLLIPEADSCDQAYQTVDKYCDEKASSIDKECDISFKKLVEKCNTAENSIKERCQKKNGYVTAECGRLFERLDNVCRIVSSTQSRHCTKLYRKMDNECYKKYSKITLKCKRIFDRYKDFCESDMSPNYWNEAYK 178
[Close]
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000068428.1 (SMESG000068428.1)

HSP 1 Score: 65.855 bits (159), Expect = 3.232e-12
Identity = 51/186 (27.42%), Postives = 80/186 (43.01%), Query Frame = 3 
Query:   39 LFFV*TFIFYSFKKMINFNQFSIISLSVVVIFLQSTSAKVPILVRYGEQECDELIPLKLKCDEFRKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKC----GNPKPVCENRLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYHETCELSLDPYNWRRVEKK 584
            L F+  FIFY     I+ N+  I  LSV +       AK  I+ R    +C++LIP  + CD   +     C   +  +   C+  F  LT+ CN  E+ +   C    G     C  R   LD +C  +   +   C ++Y K++ KC   + +I+ +C  I   Y + CE  +    W    KK
Sbjct:    7 LLFI--FIFYE----IHQNRCEIGDLSVKI-------AKALIINRNQRLQCNDLIPEVISCDSAYETIDNYCERKATEIDSFCNRKFSKLTESCNKAENKIKLDCNTKVGYITASCGRRFDRLDKVCRISSTTLSRKCTKKYRKMDNKCNKKYGKINVKCKRIYYRYKDFCETGVANNYWNEKYKK 179
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: 3
Match NameE-valueIdentityDescription
I1ZI865.120e-12699.44Uncharacterized protein OS=Schmidtea mediterranea ... [more]
V9XTF19.302e-10699.35X1.A.D4.1 (Fragment) OS=Schmidtea mediterranea OX=... [more]
A0A0A1CQX98.654e-626.17Pmp-10 (Fragment) OS=Schmidtea mediterranea OX=793... [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: 4
Match NameE-valueIdentityDescription
SMESG000027979.11.424e-12999.44SMESG000027979.1[more]
SMESG000053861.16.607e-4142.86SMESG000053861.1[more]
SMESG000068743.14.842e-1326.14SMESG000068743.1[more]
SMESG000068428.13.232e-1227.42SMESG000068428.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30005357
GenBankAFJ24740.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005357 ID=SMED30005357|Name=hypothetical protein|organism=Schmidtea mediterranea sexual|type=transcript|length=687bp
GTTTCACAGTCCTACTAATACACTAAACTACAAAAGCATTATTTTTTGTT
TGAACATTTATTTTCTATTCATTTAAAAAAATGATAAATTTCAATCAGTT
TTCTATTATATCATTGAGTGTTGTGGTGATATTTCTCCAATCAACCTCAG
CCAAAGTACCAATTCTAGTTCGATACGGTGAACAGGAATGTGACGAGCTT
ATACCCCTCAAGTTGAAATGCGACGAGTTTCGTAAACACGCCGGTCTGGT
ATGCAGAGGAGCGAGCGATGTATTGGCCAAAAAATGCGACACAGCTTTCC
ATCATTTGACAGATGGTTGCAATACTAAAGAGTCAAATTTGCTCAATAAA
TGTGGAAATCCGAAGCCGGTCTGTGAAAATCGTTTGCATTTCCTAGACAT
AATTTGCAACAAAGCCTGTGATGCCATCAAAGACTTTTGTAGACGACGAT
ATATCAAAATCAACAGAAAATGCGAATTCATTTTCAAAAGAATAGATGAA
AGATGTCTAGGAATAGATGAACACTATCATGAAACCTGTGAACTGAGTCT
TGATCCATACAATTGGAGACGGGTTGAGAAGAAATACTACGAAGCTAAAA
CAAGTGATTATTGAAAAACGTTAAGCAGTGACATTTGGTGAAATATTTGA
AAGCACAATATAAAATAAAATTCACCTTCGAATGATG
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protein sequence of SMED30005357-orf-1

>SMED30005357-orf-1 ID=SMED30005357-orf-1|Name=SMED30005357-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=178bp
MINFNQFSIISLSVVVIFLQSTSAKVPILVRYGEQECDELIPLKLKCDEF
RKHAGLVCRGASDVLAKKCDTAFHHLTDGCNTKESNLLNKCGNPKPVCEN
RLHFLDIICNKACDAIKDFCRRRYIKINRKCEFIFKRIDERCLGIDEHYH
ETCELSLDPYNWRRVEKKYYEAKTSDY*
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Aliases
The feature 'hypothetical protein' has the following synonyms
Synonym
pmp-10
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000035Category 3 cell
PLANA:0000429neoblast
PLANA:0002032epidermal cell
PLANA:0002142parenchyma
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..24
score: 0.774