SMED30012026

Overview
NameSMED30012026
Smed IDSMED30012026
Length (bp)319
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




SMED30012026

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
tail regionSMED30012026 SmedASXL_071929SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30012026 Contig51798newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30012026 Contig51798uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Category 3 cellSMED30012026 dd_Smed_v6_617_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30012026 SMED_35806_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30012026 SMED_35806_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30012026 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008989:16826..17183 +1374
v31.005087:27734..28098 -1356
v31.008989:14757..15114 -1267
Homology
BLAST of SMED30012026 vs. Planmine SMEST
Match: SMESG000043866.1 (SMESG000043866.1)

HSP 1 Score: 83.1889 bits (204), Expect = 2.328e-22
Identity = 42/47 (89.36%), Postives = 43/47 (91.49%), Query Frame = 1
Query:    1 IGNLEEFNEKSLENMKSTKDENEQEENVGKKKCWMNCSGVKCVTRCT 141
            I NLEEFNEKSLENMKS KDENEQEENVGKKKCW +CSG KCVTRCT
Sbjct:   32 IENLEEFNEKSLENMKSAKDENEQEENVGKKKCWKHCSGGKCVTRCT 78          
BLAST of SMED30012026 vs. Planmine SMEST
Match: SMESG000043866.1 (SMESG000043866.1)

HSP 1 Score: 77.411 bits (189), Expect = 3.912e-20
Identity = 38/42 (90.48%), Postives = 39/42 (92.86%), Query Frame = 1
Query:   16 EFNEKSLENMKSTKDENEQEENVGKKKCWMNCSGVKCVTRCT 141
            EFNEKSLENMKS KDENEQEENVGKKKCW +CSG KCVTRCT
Sbjct:   35 EFNEKSLENMKSAKDENEQEENVGKKKCWKHCSGGKCVTRCT 76          
BLAST of SMED30012026 vs. Planmine SMEST
Match: SMESG000043307.1 (SMESG000043307.1)

HSP 1 Score: 76.6406 bits (187), Expect = 8.383e-20
Identity = 38/47 (80.85%), Postives = 41/47 (87.23%), Query Frame = 1
Query:    1 IGNLEEFNEKSLENMKSTKDENEQEENVGKKKCWMNCSGVKCVTRCT 141
            + NLEEFNEKSLENMKS KDENEQEENV KKKCW +CSG +C TRCT
Sbjct:   32 VENLEEFNEKSLENMKSAKDENEQEENVDKKKCWKHCSGRQCSTRCT 78          
BLAST of SMED30012026 vs. Planmine SMEST
Match: SMESG000043307.1 (SMESG000043307.1)

HSP 1 Score: 71.633 bits (174), Expect = 8.575e-18
Identity = 35/42 (83.33%), Postives = 37/42 (88.10%), Query Frame = 1
Query:   16 EFNEKSLENMKSTKDENEQEENVGKKKCWMNCSGVKCVTRCT 141
            EFNEKSLENMKS KDENEQEENV KKKCW +CSG +C TRCT
Sbjct:   35 EFNEKSLENMKSAKDENEQEENVDKKKCWKHCSGRQCSTRCT 76          
BLAST of SMED30012026 vs. Planmine SMEST
Match: SMESG000043867.1 (SMESG000043867.1)

HSP 1 Score: 70.0922 bits (170), Expect = 3.743e-17
Identity = 36/46 (78.26%), Postives = 39/46 (84.78%), Query Frame = 1
Query:    1 IGNLEEFNEKSLENMKSTKDENEQEENVGKKKCWMNCSGVKCVTRC 138
            I NLEEFNEKSLENMKS KDE E EENVGKK+C+ +CS  KCVTRC
Sbjct:   32 IENLEEFNEKSLENMKSAKDEYELEENVGKKRCFKDCSRGKCVTRC 77          
The following BLAST results are available for this feature:
BLAST of SMED30012026 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 SMED30012026 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 SMED30012026 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 SMED30012026 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 SMED30012026 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 SMED30012026 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 SMED30012026 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 SMED30012026 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 SMED30012026 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 SMED30012026 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 SMED30012026 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 SMED30012026 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 SMED30012026 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 SMED30012026 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000043866.12.328e-2289.36SMESG000043866.1[more]
SMESG000043866.13.912e-2090.48SMESG000043866.1[more]
SMESG000043307.18.383e-2080.85SMESG000043307.1[more]
SMESG000043307.18.575e-1883.33SMESG000043307.1[more]
SMESG000043867.13.743e-1778.26SMESG000043867.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012026 ID=SMED30012026|Name=SMED30012026|organism=Schmidtea mediterranea sexual|type=transcript|length=319bp
ATAGGAAATTTAGAAGAATTCAATGAAAAATCTCTGGAAAATATGAAAAG
CACCAAAGACGAAAATGAACAGGAGGAAAATGTCGGTAAAAAGAAATGCT
GGATGAATTGCTCAGGCGTAAAATGTGTAACACGTTGCACAAGATAAATA
AACAAATAAAATTTTGCTTAGCTTTCTTTTTCGTATTTTTTTGTTCATTT
TTAAATGAGAAATAAATTTCCGCATTCAAATGTAAAAATTCATTAAAATG
TAATTTTATGGAAATATAAAATTCACTTTGCACATTTTGATCTCCGTTTA
TTAATGTGACACCAAAATT
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protein sequence of SMED30012026-orf-1

>SMED30012026-orf-1 ID=SMED30012026-orf-1|Name=SMED30012026-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp
NFGVTLINGDQNVQSEFYISIKLHFNEFLHLNAEIYFSFKNEQKNTKKKA
KQNFICLFILCNVLHILRLSNSSSISFYRHFPPVHFRLWCFSYFPEIFH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
PLANA:0000421tail
PLANA:0000429neoblast
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 5..25
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..28