SMED30029717

Overview
NameSMED30029717
Smed IDSMED30029717
Length (bp)471
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



SMED30029717

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
epidermisSMED30029717SMESG000018042.1 dd_Smed_v4_11486_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029717SMESG000018042.1 dd_Smed_v4_11486_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30029717SMESG000018042.1 SMED30029717smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30029717SMESG000018042.1 SMED30029717smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
Category 3 cellSMED30029717SMESG000018042.1 dd_Smed_v6_11486_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30029717SMESG000018042.1 dd_Smed_v4_11486_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
SMED30029717 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014029:15691..16204 -2233
Homology
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BLAST of SMED30029717 vs. Planmine SMEST
Match: SMESG000018042.1 (SMESG000018042.1)

HSP 1 Score: 93.5893 bits (231), Expect = 6.142e-23
Identity = 48/56 (85.71%), Postives = 51/56 (91.07%), Query Frame = -2 
Query:   96 LMHKLINNFQAISNLLGALVISILLHMIHYWGQFTVATLFALFSLSLTQFFPTSEK 263
            +++ LI    AISNLLGALVISILLHMIHYWGQFTVATLFALFSLSLTQFFPTSEK
Sbjct:  371 ILYGLIYFGYAISNLLGALVISILLHMIHYWGQFTVATLFALFSLSLTQFFPTSEK 426
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BLAST of SMED30029717 vs. Planmine SMEST
Match: SMESG000060691.1 (SMESG000060691.1)

HSP 1 Score: 55.4546 bits (132), Expect = 1.516e-9
Identity = 28/46 (60.87%), Postives = 34/46 (73.91%), Query Frame = -2 
Query:   96 AISNLLGALVISILLHMIHYWGQFTVATLFALFSLSLTQFFPTSEK 233
            A+S++LGALV S LL +I YWGQF +AT  A+ SL LTQFFPT   
Sbjct:  332 AMSSILGALVTSNLLEVIEYWGQFLLATCSAIISLILTQFFPTKSS 377
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BLAST of SMED30029717 vs. Planmine SMEST
Match: SMESG000060691.1 (SMESG000060691.1)

HSP 1 Score: 55.4546 bits (132), Expect = 1.676e-9
Identity = 28/46 (60.87%), Postives = 34/46 (73.91%), Query Frame = -2 
Query:   96 AISNLLGALVISILLHMIHYWGQFTVATLFALFSLSLTQFFPTSEK 233
            A+S++LGALV S LL +I YWGQF +AT  A+ SL LTQFFPT   
Sbjct:  347 AMSSILGALVTSNLLEVIEYWGQFLLATCSAIISLILTQFFPTKSS 392
[Close]
BLAST of SMED30029717 vs. Planmine SMEST
Match: SMESG000060691.1 (SMESG000060691.1)

HSP 1 Score: 55.4546 bits (132), Expect = 1.721e-9
Identity = 28/46 (60.87%), Postives = 34/46 (73.91%), Query Frame = -2 
Query:   96 AISNLLGALVISILLHMIHYWGQFTVATLFALFSLSLTQFFPTSEK 233
            A+S++LGALV S LL +I YWGQF +AT  A+ SL LTQFFPT   
Sbjct:  369 AMSSILGALVTSNLLEVIEYWGQFLLATCSAIISLILTQFFPTKSS 414
[Close]
BLAST of SMED30029717 vs. Planmine SMEST
Match: SMESG000060699.1 (SMESG000060699.1)

HSP 1 Score: 46.9802 bits (110), Expect = 1.298e-6
Identity = 24/42 (57.14%), Postives = 32/42 (76.19%), Query Frame = -2 
Query:  108 AISNLLGALVISILLHMIHYWGQFTVATLFALFSLSLTQFFP 233
            A+S ++GAL+ S LL +I+Y G F VATL ++ SL LTQFFP
Sbjct:  429 AVSGVIGALICSSLLSLINYGGLFIVATLSSIISLVLTQFFP 470
The following BLAST results are available for this feature:
BLAST of SMED30029717 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 SMED30029717 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 SMED30029717 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 SMED30029717 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 SMED30029717 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 SMED30029717 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 SMED30029717 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 SMED30029717 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 SMED30029717 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 SMED30029717 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 SMED30029717 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 SMED30029717 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 SMED30029717 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 SMED30029717 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000018042.16.142e-2385.71SMESG000018042.1[more]
SMESG000060691.11.516e-960.87SMESG000060691.1[more]
SMESG000060691.11.676e-960.87SMESG000060691.1[more]
SMESG000060691.11.721e-960.87SMESG000060691.1[more]
SMESG000060699.11.298e-657.14SMESG000060699.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029717 ID=SMED30029717|Name=SMED30029717|organism=Schmidtea mediterranea sexual|type=transcript|length=471bp
TCCTTCATCAGTTAACCAATTTATTTGTATAATTAGGTTAATTTTTCATA
TGTTTTCCGAATATTGTTAGAACTTTTAGTTTGAAAATATTTCTATTTTT
CTGATGTTGGAAAGAACTGGGTTAATGAAAGGCTGAATAATGCAAATAAT
GTTGCTACAGTAAATTGTCCCCAATAATGTATCATATGTAGCAGAATGCT
TATGACCAACGCGCCAAGTAAATTAGATATTGCCTGGAAATTATTAATTA
ATTTATGCATTAATTATAAAATAATTTTAGTTGGGATGTAAGACTACTTT
GCTTGATTTCGTGAAACTACAGTTTTGCTATATTATACGACATACATGCA
TACATGCTTAATCTGAGCTTATTAACACAATTTTCTGTGGTTCTCATAGT
TCTAATGATTATATACTATTTTCAGCTAAAGCAAGAAATCTTATAACATC
AGGATATTTTCGGAATTTCGA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000035Category 3 cell
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 availableTMHMMTMhelixcoord: 33..50
NoneNo IPR availableTMHMMTMhelixcoord: 7..29