SMED30008401

Overview
NameSMED30008401
Smed IDSMED30008401
Length (bp)890
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



SMED30008401

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X2 cellSMED30008401 SmedASXL_082686SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30008401 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000276:194669..195558 +4450
Homology
[Close]
BLAST of SMED30008401 vs. Planmine SMEST
Match: SMESG000077490.1 (SMESG000077490.1)

HSP 1 Score: 43.8986 bits (102), Expect = 9.296e-7
Identity = 32/86 (37.21%), Postives = 50/86 (58.14%), Query Frame = -3 
Query:  382 CRDLLIAETRVQKLVISNQSAAFMKIFSXXXXXXXXXXRCVTEQAKVIPSNDISTPDVRTT*TNPSIFIKSNPCRNKRRRMQR*AD 639
            CR+ LIAE R Q++VI++QSA  +  F+E EL +RL  R +  +  +IP+ND+   +       P    K NP +N+  R +R A+
Sbjct:   70 CREDLIAENRAQRIVINDQSAVLIASFTETELTKRLASRDLAVKLNLIPANDLPERNQIGPAQTPKTSKKHNPSKNRSGRERRRAE 155

HSP 2 Score: 27.335 bits (59), Expect = 9.296e-7
Identity = 10/24 (41.67%), Postives = 15/24 (62.50%), Query Frame = -2 
Query:  644 EKIKGAWFQPAVLKELKQMIYQLV 715
            E+  G WF P V+K L + I++L 
Sbjct:   45 ERTLGTWFAPEVVKALHKQIHRLT 68
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BLAST of SMED30008401 vs. Planmine SMEST
Match: SMESG000036854.1 (SMESG000036854.1)

HSP 1 Score: 41.9726 bits (97), Expect = 8.525e-6
Identity = 29/77 (37.66%), Postives = 45/77 (58.44%), Query Frame = -3 
Query:  412 QCRDLLIAETRVQKLVISNQSAAFMKIFSXXXXXXXXXXRCVTEQAKVIPSNDISTPDVRTT*TNPSIFIKSNPCRN 642
            +CR+ LIAE+R Q+++I+NQSA  +  F+E EL +RL  R +  +  +IP+N I+          P    K NP +N
Sbjct:  187 RCREDLIAESRAQRIIINNQSAVLVASFNEDELTKRLASRDLAIKLNLIPANHITGKGTTGPPQTPKTNKKHNPSKN 263

HSP 2 Score: 25.7942 bits (55), Expect = 8.525e-6
Identity = 9/24 (37.50%), Postives = 13/24 (54.17%), Query Frame = -2 
Query:  644 EKIKGAWFQPAVLKELKQMIYQLV 715
            E+  G WF P  +K L   I++L 
Sbjct:  163 ERTLGTWFAPEAVKALHNQIHRLT 186
The following BLAST results are available for this feature:
BLAST of SMED30008401 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 SMED30008401 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 SMED30008401 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 SMED30008401 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 SMED30008401 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 SMED30008401 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 SMED30008401 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 SMED30008401 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 SMED30008401 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 SMED30008401 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 SMED30008401 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 SMED30008401 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 SMED30008401 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 SMED30008401 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000077490.19.296e-737.21SMESG000077490.1[more]
SMESG000036854.18.525e-637.66SMESG000036854.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008401 ID=SMED30008401|Name=SMED30008401|organism=Schmidtea mediterranea sexual|type=transcript|length=890bp
TTCTTATACCATGTTATTACAACCATATTTAAATACGACAAAAATAATAA
AATTGATCAAGATTTTCAGAAGTTTATCCACTTGCGAAAAGAACAGGGTC
TTTAGTTACTGGATCCCATATCCAAGGAGAAATTTCAATTCTGTGGTCTT
CACTACACTGGTTATCGGACGTTTTGAGCCAGCGTGGAAAAGTTATTGAT
TCAGGTTGCTGTATTTCCAAAGCTGCTTCTTGGCATGGGGGAGTTGCATT
GTACTCGTTTGTAGCAACATCGACAATTGAAGAGGTGAGTGTGGATATAC
TTAGCAGATTGATGCTAGAATCAAAGAAGGCTGCTGGTCAGCTCTTATAG
AGGTGGCCATTGCCAAATTTGACGCGGCCTTGTCAGCTCAACGTTGCATT
CTCCGCCGCTTATTTCTGCATGGATTGCTTTTGATAAATATAGAAGGATT
AGTTTAAGTGGTTCGAACATCTGGGGTCGATATATCGTTGGATGGAATAA
CCTTGGCCTGCTCGGTAACGCATCGCTTCTATAACCGCTCTCGCAACTCC
AATTCGCTAAATATTTTCATAAAGGCGGCCGACTGATTAGAAATCACCAG
TTTCTGCACTCGGGTTTCCGCGATGAGCAAATCTCGGCACTGAAACTAAT
TGGTAGATCATTTGTTTCAACTCCTTAAGGACTGCTGGCTGGAACCACGC
ACCCTTGATCTTTTCCAATTTAAATTTTAGATGTACCACCTTTTCTTTGA
TGAGAGAAATTTCCGAGTATCGATGTTAATTTAACATAAATGCTGATTAG
GGTTTTGATTAATTGACAATGACGAGATTTTATCAGTAGGTAATTAGATT
TCCAGAAAAATAATTTCTGAGTATGAATTTGTGATACGAG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell