SMED30035477

Overview
NameSMED30035477
Smed IDSMED30035477
Length (bp)799
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30035477

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30035477h1SMcG0004880 dd_Smed_v4_4179_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30035477h1SMcG0004880 dd_Smed_v4_4179_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30035477h1SMcG0004880 dd_Smed_v4_4179_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30035477h1SMcG0004880 dd_Smed_v4_4179_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30035477h1SMcG0004880 dd_Smed_v4_4179_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30035477h1SMcG0004880 dd_Smed_v4_4179_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
Alignments
SMED30035477 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006617:10779..11621 +3971
Homology
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BLAST of SMED30035477 vs. TrEMBL
Match: A0A5J4N9V2 (Uncharacterized protein OS=Paragonimus westermani OX=34504 GN=DEA37_0013503 PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 5.367e-10
Identity = 46/137 (33.58%), Postives = 70/137 (51.09%), Query Frame = 2 
Query:  155 ERPFQWNTYVSTPCENCGNCVMGSCCIWFSMYDISRFSFNMNNLMSACFCTGLCCCWPIILIKARSLVRKNHNIEGSCVSDILCGSLLCLFPCLTCQLRDEIIFLKQTDLWVMGSDND-ELIYFKALNCLNPIPHAS 562
             R  QWNTY  + CEN GNC     C    M D+  +   +   ++  F   L    P +LI  R  +R+ HN+EG+ +SD++C  L C +PC+ CQ+RD++  L     W +G  N+ E +     +CL  I H +
Sbjct:   18 RRRSQWNTYTVSCCENWGNCCCCLLCFPCFMGDLLHYVCYLPWGLALIFGLVLLPFHPFLLIPLRMRIRRKHNLEGNILSDLIC-LLFCCWPCVFCQMRDQVHHLLSRRQWTLGYANEVEHLPLWMSSCLKFICHPA 153
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BLAST of SMED30035477 vs. TrEMBL
Match: A0A4S2LQI4 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_006867 PE=4 SV=1)

HSP 1 Score: 62.7734 bits (151), Expect = 3.841e-8
Identity = 44/125 (35.20%), Postives = 66/125 (52.80%), Query Frame = 2 
Query:  134 LDEEEVKERPFQWNTYVSTPCENCGNCVMGSCCIWFSMYDISRFSFNMNNLMSACFCTGLCCCWPIILIKARSLVRKNHNIEGSCVSDILCGSLLCLFPCLTCQLRDEIIFLKQTDLWVMGSDND 508
            +D   V+++  QWNTY  + CEN GNC     C    M D+  ++ +M   M+  F   L      + I  R+ +R  H +EGSC SD LC  L C +P + CQ+RDEI +L+    W +G  ++
Sbjct:   20 IDYGFVRKKQ-QWNTYTFSCCENWGNCCYCIFCCPCFMADLFHYANSMPWAMAILFGILLLPLNFFLWIPMRARIRYKHKLEGSCCSD-LCCLLFCCWPFVLCQIRDEIQYLRSRKKWQLGYQDE 142
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BLAST of SMED30035477 vs. TrEMBL
Match: A0A4Z2DC75 (Placenta specific 8 OS=Schistosoma japonicum OX=6182 GN=EWB00_002359 PE=4 SV=1)

HSP 1 Score: 63.929 bits (154), Expect = 4.130e-8
Identity = 43/119 (36.13%), Postives = 70/119 (58.82%), Query Frame = 2 
Query:  143 EEVKERPF-QWNTYVSTPCENCGNCVMGSCCIWFSMYDISRFSFNMNNLMSACFCTGLCCCWPIILIKARSLVRKNHNIEGSCVSDILCGSLLCLFPCLTCQLRDEIIFLKQTDLWVMG 496
            +E  ER + QWNTY  + CENC NC    CC  F+  +I  +++++   ++  F   L     +I++  R  +R+ H +EG+C+SD LC  + C +P + CQLRDEI++L+    W +G
Sbjct:   10 QENHERNYKQWNTYAISCCENCSNCWCCLCCCPFATAEIYHYTWSLPWSIALIFSILLLPLNMLIILLQRMQIRRAHKLEGNCLSD-LCCLICCCWPTIICQLRDEILYLRSQSEWKLG 127
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BLAST of SMED30035477 vs. Planmine SMEST
Match: SMESG000060552.1 (SMESG000060552.1)

HSP 1 Score: 414.846 bits (1065), Expect = 1.805e-141
Identity = 219/219 (100.00%), Postives = 219/219 (100.00%), Query Frame = 2 
Query:  128 IYLDEEEVKERPFQWNTYVSTPCENCGNCVMGSCCIWFSMYDISRFSFNMNNLMSACFCTGLCCCWPIILIKARSLVRKNHNIEGSCVSDILCGSLLCLFPCLTCQLRDEIIFLKQTDLWVMGSDNDELIYFKALNCLNPIPHASEGGNELMDFAKKHNLLEDLNPEQAMINLGHIQKQYDHYIIFXXXXXXXXXXXXXXXXXXXXXFTTIKQQYVIRN 784
            IYLDEEEVKERPFQWNTYVSTPCENCGNCVMGSCCIWFSMYDISRFSFNMNNLMSACFCTGLCCCWPIILIKARSLVRKNHNIEGSCVSDILCGSLLCLFPCLTCQLRDEIIFLKQTDLWVMGSDNDELIYFKALNCLNPIPHASEGGNELMDFAKKHNLLEDLNPEQAMINLGHIQKQYDHYIIFKNSDNSIIKSDKSKNENSSNKFTTIKQQYVIRN
Sbjct:  521 IYLDEEEVKERPFQWNTYVSTPCENCGNCVMGSCCIWFSMYDISRFSFNMNNLMSACFCTGLCCCWPIILIKARSLVRKNHNIEGSCVSDILCGSLLCLFPCLTCQLRDEIIFLKQTDLWVMGSDNDELIYFKALNCLNPIPHASEGGNELMDFAKKHNLLEDLNPEQAMINLGHIQKQYDHYIIFKNSDNSIIKSDKSKNENSSNKFTTIKQQYVIRN 739
The following BLAST results are available for this feature:
BLAST of SMED30035477 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 SMED30035477 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 SMED30035477 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 SMED30035477 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 SMED30035477 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 SMED30035477 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 SMED30035477 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 SMED30035477 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A5J4N9V25.367e-1033.58Uncharacterized protein OS=Paragonimus westermani ... [more]
A0A4S2LQI43.841e-835.20Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A4Z2DC754.130e-836.13Placenta specific 8 OS=Schistosoma japonicum OX=61... [more]
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BLAST of SMED30035477 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 SMED30035477 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 SMED30035477 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 SMED30035477 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 SMED30035477 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 SMED30035477 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000060552.11.805e-141100.00SMESG000060552.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035477 ID=SMED30035477|Name=SMED30035477|organism=Schmidtea mediterranea sexual|type=transcript|length=799bp
ATTTTGTTCATTTTGTAAATTATTTATTTGATTTTGATTGAATAATTTAT
AAATAATCGCTTAAAATTTCAATTCAATGCTAAATAAGAAAAAAAGAGAT
TTAAAAAAGACTAAAGCTGGAAAACTAATTTATTTAGACGAAGAAGAAGT
CAAAGAAAGACCATTTCAGTGGAATACTTATGTTTCCACACCTTGCGAAA
ATTGCGGCAATTGCGTTATGGGATCTTGTTGCATTTGGTTCAGTATGTAT
GATATATCTAGATTTTCTTTCAACATGAACAATTTAATGTCAGCATGTTT
TTGTACGGGACTTTGTTGTTGTTGGCCAATTATATTGATAAAAGCTCGCA
GTTTAGTTCGAAAAAACCACAATATCGAAGGAAGTTGTGTCAGTGATATT
TTATGTGGTTCATTGCTGTGTTTATTTCCTTGTTTAACTTGCCAACTAAG
AGACGAAATAATTTTTCTTAAACAAACTGACCTATGGGTAATGGGATCAG
ATAATGATGAGCTGATATATTTCAAAGCCCTAAATTGCCTCAATCCAATT
CCCCACGCTAGTGAAGGTGGAAATGAATTGATGGATTTTGCAAAAAAACA
CAATTTATTGGAAGATTTAAATCCCGAACAAGCAATGATTAATTTGGGAC
ACATCCAAAAACAATACGATCATTACATAATTTTTAAAAATTCTGACAAT
TCTATTATTAAAAGTGACAAAAGCAAAAATGAAAACTCAAGCAATAAGTT
TACCACTATTAAACAGCAATATGTGATTAGAAATTAATCTCTGAAATTA
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protein sequence of SMED30035477-orf-1

>SMED30035477-orf-1 ID=SMED30035477-orf-1|Name=SMED30035477-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=237bp
MLNKKKRDLKKTKAGKLIYLDEEEVKERPFQWNTYVSTPCENCGNCVMGS
CCIWFSMYDISRFSFNMNNLMSACFCTGLCCCWPIILIKARSLVRKNHNI
EGSCVSDILCGSLLCLFPCLTCQLRDEIIFLKQTDLWVMGSDNDELIYFK
ALNCLNPIPHASEGGNELMDFAKKHNLLEDLNPEQAMINLGHIQKQYDHY
IIFKNSDNSIIKSDKSKNENSSNKFTTIKQQYVIRN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000106ciliated epithelial cell
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 65..87