SMED30030959

Overview
NameSMED30030959
Smed IDSMED30030959
Length (bp)664
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



SMED30030959

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testisSMED30030959SMESG000034723.1 Contig6731_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
early male germ cellSMED30030959SMESG000034723.1 Contig6731_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030959 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009629:5788..6451 -3320
v31.009768:7995..8658 -3230
v31.009768:8647..18550 +2717
v31.020423:7529..8158 +2677
Homology
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BLAST of SMED30030959 vs. Planmine SMEST
Match: SMESG000034723.1 (SMESG000034723.1)

HSP 1 Score: 245.358 bits (625), Expect = 4.795e-83
Identity = 179/179 (100.00%), Postives = 179/179 (100.00%), Query Frame = 1 
Query:   40 MNIIQKWLSFFNLKHVYRQTREFFLIDDLCALVGXXXXXXXXXXXXXXHINEKSRVTQHGYSYIDSEDFDYVVPSVTVDMLRPKVPIWVKVPXXXXXXXXXXXXXXXXXXXXFSYNKTANMPMXXXXXXXXXXXXXXXXXXXALYGEIEERYILHNVSEVEMYKEVVMWKVAEEVSYED 576
            MNIIQKWLSFFNLKHVYRQTREFFLIDDLCALVGSNNSNRSRLNKNESHINEKSRVTQHGYSYIDSEDFDYVVPSVTVDMLRPKVPIWVKVPLICGIVICGIGVIVGILLLIFSYNKTANMPMLYYSLSIFIISSLFSYGLFALYGEIEERYILHNVSEVEMYKEVVMWKVAEEVSYED
Sbjct:    1 MNIIQKWLSFFNLKHVYRQTREFFLIDDLCALVGSNNSNRSRLNKNESHINEKSRVTQHGYSYIDSEDFDYVVPSVTVDMLRPKVPIWVKVPLICGIVICGIGVIVGILLLIFSYNKTANMPMLYYSLSIFIISSLFSYGLFALYGEIEERYILHNVSEVEMYKEVVMWKVAEEVSYED 179
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BLAST of SMED30030959 vs. Planmine SMEST
Match: SMESG000034740.1 (SMESG000034740.1)

HSP 1 Score: 82.8037 bits (203), Expect = 1.394e-19
Identity = 77/182 (42.31%), Postives = 115/182 (63.19%), Query Frame = 1 
Query:   40 MNIIQKWLSFFNLKHVYRQTREFFLIDDLCALVGXXXXXXXXXXXXXXHINEKSRVTQHGY---SYIDSEDFDYVVPSVTVDMLRPKVPIWVKVPXXXXXXXXXXXXXXXXXXXXFSYNKTANMPMXXXXXXXXXXXXXXXXXXXALYGEIEERYILHNVSEVEMYKEVVMWKVAEEVSYED 576
            M +++K LS    K    Q  + F  D+L     S N N      N++  N  SR+++  +   +++D +DFD  VP +T DML+P++ +W K  ++ G VICG+G+I G++L+IF+YN+T N  MLY SL + I+ S+  YGLF LYGE+EE  I  NV+EVEMYKE VM ++A + SY+D
Sbjct:    1 MKVMRKLLSCLKSKRANSQANDLFEFDELNNSNKSRNLNEDSNEFNKNKSNRMSRMSRMSFVSQNFVDPDDFDNFVPPITDDMLKPELALWQKTLMVIGCVICGLGMIGGVILIIFAYNQTPNKGMLYSSLPLLIVCSMILYGLFVLYGEMEEESIEDNVAEVEMYKETVMTQLAAQQSYDD 182
The following BLAST results are available for this feature:
BLAST of SMED30030959 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 SMED30030959 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 SMED30030959 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 SMED30030959 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 SMED30030959 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 SMED30030959 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 SMED30030959 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 SMED30030959 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 SMED30030959 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 SMED30030959 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 SMED30030959 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 SMED30030959 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 SMED30030959 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 SMED30030959 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000034723.14.795e-83100.00SMESG000034723.1[more]
SMESG000034740.11.394e-1942.31SMESG000034740.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030959 ID=SMED30030959|Name=SMED30030959|organism=Schmidtea mediterranea sexual|type=transcript|length=664bp
AATTGATCAATTAAATTTTAATTTAAAAAACAAAATATAATGAATATAAT
CCAGAAATGGCTTTCATTTTTCAACCTCAAGCATGTTTATAGGCAAACAA
GAGAGTTTTTCCTAATAGATGATCTATGCGCCCTGGTCGGTTCTAACAAC
TCCAACAGGTCTCGGTTGAATAAAAATGAAAGTCATATTAATGAAAAATC
TCGCGTGACCCAGCATGGGTACTCTTATATTGATTCAGAAGATTTTGATT
ATGTCGTCCCATCGGTAACAGTGGATATGTTGAGGCCAAAAGTTCCAATT
TGGGTAAAGGTTCCATTGATTTGTGGCATCGTTATTTGCGGAATCGGCGT
GATTGTAGGAATATTGTTATTAATATTCTCCTACAACAAGACCGCCAACA
TGCCAATGCTATATTATAGTCTTTCAATATTTATCATAAGTTCTTTATTT
TCTTATGGACTTTTTGCCCTGTATGGTGAAATAGAAGAAAGGTATATTTT
GCACAATGTTTCAGAAGTCGAGATGTATAAAGAAGTGGTAATGTGGAAGG
TAGCTGAGGAAGTTTCATATGAAGATTAGATTAAAACTAATTTTTTTATC
TATACTTAATCATATAAAATATATAAATATTTTTAGGCGTGACTTTTATT
TGATTGCAATTTGG
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protein sequence of SMED30030959-orf-1

>SMED30030959-orf-1 ID=SMED30030959-orf-1|Name=SMED30030959-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=180bp
MNIIQKWLSFFNLKHVYRQTREFFLIDDLCALVGSNNSNRSRLNKNESHI
NEKSRVTQHGYSYIDSEDFDYVVPSVTVDMLRPKVPIWVKVPLICGIVIC
GIGVIVGILLLIFSYNKTANMPMLYYSLSIFIISSLFSYGLFALYGEIEE
RYILHNVSEVEMYKEVVMWKVAEEVSYED*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0002030early male germ cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 123..145
NoneNo IPR availableTMHMMTMhelixcoord: 91..113