SMED30023065

Overview
NameSMED30023065
Smed IDSMED30023065
Length (bp)927
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

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



Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30023065 (SMED30023065) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023065 (SMED30023065) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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



SMED30023065

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



PAGE Curations: 20

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30023065h1SMcG0006393 SmedASXL_004313SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30023065h1SMcG0005166 Contig40297uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023065h1SMcG0005166 Contig40297newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023065h1SMcG0006897 Contig4364GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30023065h1SMcG0006393 dd_Smed_v4_15919_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023065h1SMcG0006393 dd_Smed_v4_15919_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30023065h1SMcG0006393 dd_Smed_v4_15919_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023065h1SMcG0006393 Contig40297uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023065h1SMcG0006393 Contig40297newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30023065h1SMcG0006393 dd_Smed_v4_3239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023065h1SMcG0006393 dd_Smed_v4_3239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023065h1SMcG0006393 dd_Smed_v4_3239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30023065h1SMcG0006393 dd_Smed_v4_3239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30023065h1SMcG0006393 dd_Smed_v4_3239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30023065h1SMcG0006393 dd_Smed_v4_3239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30023065h1SMcG0006393 dd_Smed_v4_7343_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023065h1SMcG0006393 dd_Smed_v4_7343_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30023065h1SMcG0006393 dd_Smed_v4_7343_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30023065h1SMcG0006393 dd_Smed_v4_7343_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023065h1SMcG0006393 Contig4364GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30023065 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.032479:551..4507 -3582
v31.012452:16533..19716 -2937
Homology
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BLAST of SMED30023065 vs. Planmine SMEST
Match: SMESG000056130.1 (SMESG000056130.1)

HSP 1 Score: 430.254 bits (1105), Expect = 1.322e-137
Identity = 266/270 (98.52%), Postives = 268/270 (99.26%), Query Frame = 1 
Query:  118 MNICSLIPNFISKSVDEIEPNLEELNHLCDNDEVCYRIFTCNYHLEVLDFLKNDDPKIKIKTFSILLKIIRFTSGNNESFLLSVTLSVCEILNNVTDVLTHESCLNFLIDICNDSFNGMLSIENKIKLIDTITKAINWRSQNIIFDSLQLLYNLNDSQNAITXXXXXXXXXXXXXXRNLSGARYEXXXXXXXXXXXXXXENIDKEEFESISESNIADVLIKLLFHSHTMISENYYXXXXXXXXXXXXXSVEKETSILTISKENYTYIIIH 927
            MNICSLIPNFISKSVDEIEPNLEELNHLCDNDEVCYRIF CNYHLEVLDFLKNDDPKIKIKTFSILLKIIRFTSGNNE+FLLSVTLSVCEILNNVTDVLTHESCLNFLIDICNDSFNGMLSIENKIKLIDTITKAINWRSQNIIFDSLQLLYNLNDSQNAITKFLLDKLDDLIKELRNLSGARYEKLGI+ICKLLLKVIENIDKEEFESISESNIADVLIKLLFHSHTMISENYYFFIIKLFCKILFFSV KETSILTISKENYTYIIIH
Sbjct:    1 MNICSLIPNFISKSVDEIEPNLEELNHLCDNDEVCYRIFNCNYHLEVLDFLKNDDPKIKIKTFSILLKIIRFTSGNNETFLLSVTLSVCEILNNVTDVLTHESCLNFLIDICNDSFNGMLSIENKIKLIDTITKAINWRSQNIIFDSLQLLYNLNDSQNAITKFLLDKLDDLIKELRNLSGARYEKLGILICKLLLKVIENIDKEEFESISESNIADVLIKLLFHSHTMISENYYFFIIKLFCKILFFSVVKETSILTISKENYTYIIIH 270
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BLAST of SMED30023065 vs. Planmine SMEST
Match: SMESG000056130.1 (SMESG000056130.1)

HSP 1 Score: 430.254 bits (1105), Expect = 1.336e-137
Identity = 266/270 (98.52%), Postives = 268/270 (99.26%), Query Frame = 1 
Query:  118 MNICSLIPNFISKSVDEIEPNLEELNHLCDNDEVCYRIFTCNYHLEVLDFLKNDDPKIKIKTFSILLKIIRFTSGNNESFLLSVTLSVCEILNNVTDVLTHESCLNFLIDICNDSFNGMLSIENKIKLIDTITKAINWRSQNIIFDSLQLLYNLNDSQNAITXXXXXXXXXXXXXXRNLSGARYEXXXXXXXXXXXXXXENIDKEEFESISESNIADVLIKLLFHSHTMISENYYXXXXXXXXXXXXXSVEKETSILTISKENYTYIIIH 927
            MNICSLIPNFISKSVDEIEPNLEELNHLCDNDEVCYRIF CNYHLEVLDFLKNDDPKIKIKTFSILLKIIRFTSGNNE+FLLSVTLSVCEILNNVTDVLTHESCLNFLIDICNDSFNGMLSIENKIKLIDTITKAINWRSQNIIFDSLQLLYNLNDSQNAITKFLLDKLDDLIKELRNLSGARYEKLGI+ICKLLLKVIENIDKEEFESISESNIADVLIKLLFHSHTMISENYYFFIIKLFCKILFFSV KETSILTISKENYTYIIIH
Sbjct:    1 MNICSLIPNFISKSVDEIEPNLEELNHLCDNDEVCYRIFNCNYHLEVLDFLKNDDPKIKIKTFSILLKIIRFTSGNNETFLLSVTLSVCEILNNVTDVLTHESCLNFLIDICNDSFNGMLSIENKIKLIDTITKAINWRSQNIIFDSLQLLYNLNDSQNAITKFLLDKLDDLIKELRNLSGARYEKLGILICKLLLKVIENIDKEEFESISESNIADVLIKLLFHSHTMISENYYFFIIKLFCKILFFSVVKETSILTISKENYTYIIIH 270
The following BLAST results are available for this feature:
BLAST of SMED30023065 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 SMED30023065 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 SMED30023065 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 SMED30023065 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 SMED30023065 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 SMED30023065 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 SMED30023065 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 SMED30023065 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 SMED30023065 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 SMED30023065 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 SMED30023065 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 SMED30023065 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 SMED30023065 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 SMED30023065 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000056130.11.322e-13798.52SMESG000056130.1[more]
SMESG000056130.11.336e-13798.52SMESG000056130.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023065 ID=SMED30023065|Name=SMED30023065|organism=Schmidtea mediterranea sexual|type=transcript|length=927bp
TGCAATATTAAACGCAATATTTTATGCGACCATTAAACCAAATTTTGAAC
TGAGGTGCATAAAATGAATAGCGACACGAAAAAAAAAATTTTTTTAACAA
AACCAATTCAAAATGCAATGAATATTTGTAGTCTAATTCCAAATTTTATT
TCCAAGTCTGTTGATGAAATTGAACCAAATTTGGAGGAACTTAATCATTT
ATGTGATAATGATGAGGTTTGCTATAGAATTTTCACCTGCAATTATCATT
TGGAAGTTCTTGATTTTCTCAAAAACGACGATCCAAAGATCAAAATCAAA
ACTTTTAGTATTTTACTGAAAATTATCAGATTTACCTCGGGAAATAATGA
ATCTTTTCTATTGTCAGTCACACTGTCAGTATGTGAAATTCTCAATAATG
TCACTGACGTCTTGACCCATGAATCTTGTCTTAATTTTCTTATTGACATC
TGTAACGACAGTTTTAATGGAATGCTGTCAATTGAAAATAAAATAAAATT
AATTGATACAATAACTAAAGCAATAAATTGGAGAAGTCAAAATATTATTT
TTGATTCTCTACAATTATTATATAATCTCAACGATTCTCAGAATGCCATT
ACCAAATTTTTATTGGATAAACTTGATGACCTAATCAAGGAGCTGCGAAA
TCTTTCCGGAGCTCGATATGAGAAATTGGGAATTATCATATGCAAATTAC
TATTGAAAGTTATTGAAAACATTGATAAAGAAGAATTTGAATCAATCTCA
GAGAGTAATATCGCTGATGTTTTGATCAAACTTCTTTTTCATAGTCATAC
GATGATTTCAGAAAACTATTATTTTTTCATCATAAAACTTTTCTGCAAGA
TTTTATTTTTTTCAGTTGAAAAAGAAACTTCTATTTTGACAATTTCTAAA
GAAAACTATACATATATTATTATTCAC
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protein sequence of SMED30023065-orf-1

>SMED30023065-orf-1 ID=SMED30023065-orf-1|Name=SMED30023065-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=288bp
MNSDTKKKIFLTKPIQNAMNICSLIPNFISKSVDEIEPNLEELNHLCDND
EVCYRIFTCNYHLEVLDFLKNDDPKIKIKTFSILLKIIRFTSGNNESFLL
SVTLSVCEILNNVTDVLTHESCLNFLIDICNDSFNGMLSIENKIKLIDTI
TKAINWRSQNIIFDSLQLLYNLNDSQNAITKFLLDKLDDLIKELRNLSGA
RYEKLGIIICKLLLKVIENIDKEEFESISESNIADVLIKLLFHSHTMISE
NYYFFIIKLFCKILFFSVEKETSILTISKENYTYIIIH
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR011989ARM-like
IPR016024ARM-type_fold
Vocabulary: molecular function
TermDefinition
GO:0005488binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR011989Armadillo-like helicalGENE3DG3DSA:1.25.10.10coord: 22..246
e-value: 5.8E-6
score: 27.2
IPR016024Armadillo-type foldSUPERFAMILYSSF48371ARM repeatcoord: 25..234