SMED30010030

Overview
NameSMED30010030
Smed IDSMED30010030
Length (bp)378
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



SMED30010030

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30010030 SmedASXL_025817SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30010030 dd_Smed_v6_25762_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30010030 OX_Smed_1.0.19591ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30010030 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.029342:950..8867 -1830
Homology
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BLAST of SMED30010030 vs. Planmine SMEST
Match: SMESG000072177.1 (SMESG000072177.1)

HSP 1 Score: 208.379 bits (529), Expect = 4.772e-71
Identity = 99/100 (99.00%), Postives = 99/100 (99.00%), Query Frame = -1 
Query:   37 FRFWLIYSVTVNFQMEEILAIVPLDFPSFAQCSDENQKLTRFCFICLFYSGLISPFELCCGVDSKDDYFEHLARKRETNKINAGRWFCEMITGRTAPILQ 336
            FRFWLIYSVTVNFQ EEILAIVPLDFPSFAQCSDENQKLTRFCFICLFYSGLISPFELCCGVDSKDDYFEHLARKRETNKINAGRWFCEMITGRTAPILQ
Sbjct:   16 FRFWLIYSVTVNFQKEEILAIVPLDFPSFAQCSDENQKLTRFCFICLFYSGLISPFELCCGVDSKDDYFEHLARKRETNKINAGRWFCEMITGRTAPILQ 115
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BLAST of SMED30010030 vs. Planmine SMEST
Match: SMESG000076069.1 (SMESG000076069.1)

HSP 1 Score: 57.7658 bits (138), Expect = 7.762e-12
Identity = 33/82 (40.24%), Postives = 40/82 (48.78%), Query Frame = -1 
Query:   46 PLDFPSFAQCSDEN---QKLTRFCFICLFYSGLISPFELCCG---VDSKDDYFEHLARKRETNKINA-GRWFCEMITGRTAP 270
            P     F +CS+ N    +  RFC  C+FYSGL S +E CCG   + S D             K N  G WFCE+ITG  AP
Sbjct:   24 PQGIARFGRCSENNDPSNRYLRFCSKCMFYSGLSSAYEECCGNFNLQSDDSSIRDRNIMNSNGKSNGEGVWFCEIITGENAP 105
The following BLAST results are available for this feature:
BLAST of SMED30010030 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 SMED30010030 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 SMED30010030 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 SMED30010030 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 SMED30010030 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 SMED30010030 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 SMED30010030 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 SMED30010030 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 SMED30010030 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 SMED30010030 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 SMED30010030 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 SMED30010030 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 SMED30010030 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 SMED30010030 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000072177.14.772e-7199.00SMESG000072177.1[more]
SMESG000076069.17.762e-1240.24SMESG000076069.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010030 ID=SMED30010030|Name=SMED30010030|organism=Schmidtea mediterranea sexual|type=transcript|length=378bp
TGTCAAAATATAATTATTCATGATAAATAACATTTATTGTAAAATAGGCG
CTGTACGGCCGGTTATCATTTCACAAAACCATCGGCCGGCATTAATTTTG
TTTGTTTCTCTTTTTCGCGCTAAATGTTCAAAATAATCATCTTTCGAGTC
GACTCCACAACAGAGCTCAAATGGAGAGATTAGACCGCTGTAAAACAAAC
AAATAAAACAAAATCTAGTTAATTTCTGATTTTCATCACTACATTGAGCG
AAGCTAGGAAAGTCTAAAGGTACAATGGCAAGAATTTCCTCCATCTGAAA
ATTGACTGTTACTGAGTAAATAAGCCAAAATCGAAAAAAATTTATGTTCA
TGCTAATAATACAGTACCAGACTCCCAT
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protein sequence of SMED30010030-orf-1

>SMED30010030-orf-1 ID=SMED30010030-orf-1|Name=SMED30010030-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=115bp
MGVWYCIISMNINFFRFWLIYSVTVNFQMEEILAIVPLDFPSFAQCSDEN
QKLTRFCFICLFYSGLISPFELCCGVDSKDDYFEHLARKRETNKINAGRW
FCEMITGRTAPILQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000419prepharyngeal region