SMED30025924

Overview
NameSMED30025924
Smed IDSMED30025924
Length (bp)1006
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 SMED30025924 (SMED30025924) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30025924 (SMED30025924) 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




SMED30025924

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
parenchymal cellSMED30025924SMESG000035449.1 dd_Smed_v4_14944_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30025924 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.010112:13902..14907 -4922
Homology
BLAST of SMED30025924 vs. Planmine SMEST
Match: SMESG000035449.1 (SMESG000035449.1)

HSP 1 Score: 546.584 bits (1407), Expect = 0.000e+0
Identity = 283/287 (98.61%), Postives = 286/287 (99.65%), Query Frame = 1
Query:   85 MRLQILLQSMNYFRRFVLXXXXXXXXXXXXXXFRPCSNTRCYIDETNATRYVNCTHENVQNGTSLICEYDDEVLKLKNLNFTIGLAEEFANNLFGNLQKNLGRITKLKMENLNVKYFKRSDFLGLPDLKLLQIITPMAIKEDSFKPFNGSQLKMYMNCKLYSSNLHFKLQVQVWAIYLTNCNYSLICSYFVSGAKYEYNIQLYEKNQIPKGKDPITNDNCTQKVSTKNTFQTTSEYKIKTSSFENLHKNAERKLHNLIKMLFFFLNISVILLILVFGFVFYIKLKNL 945
            MRLQILLQSMNYFRRFVLTSVIIISVII ISSFRPCSNTRCYIDETNATRYVNCTHENVQNGTSLICEYDDEVLKLKNLNFTIGLAEEFANNLFGNLQKNLGRITKLKMENLNVKYFKRSDFLGLPDLKLLQIITPMAIKEDSFKPFNGSQLKMYMNCKLYSSNLHFKLQVQ+WAIYLTNCNYSLICSYFVSGAKYEYNIQLYEKNQIPKGKDPITNDNCTQKVSTKNTFQTTS+YKIKT+SFENLHKNAERKLHNLIKMLFFFLNISVILLILVFGFVFYIKLKNL
Sbjct:    1 MRLQILLQSMNYFRRFVLTSVIIISVIIPISSFRPCSNTRCYIDETNATRYVNCTHENVQNGTSLICEYDDEVLKLKNLNFTIGLAEEFANNLFGNLQKNLGRITKLKMENLNVKYFKRSDFLGLPDLKLLQIITPMAIKEDSFKPFNGSQLKMYMNCKLYSSNLHFKLQVQIWAIYLTNCNYSLICSYFVSGAKYEYNIQLYEKNQIPKGKDPITNDNCTQKVSTKNTFQTTSQYKIKTNSFENLHKNAERKLHNLIKMLFFFLNISVILLILVFGFVFYIKLKNL 287          
BLAST of SMED30025924 vs. Planmine SMEST
Match: SMESG000035432.1 (SMESG000035432.1)

HSP 1 Score: 198.364 bits (503), Expect = 1.237e-61
Identity = 108/254 (42.52%), Postives = 154/254 (60.63%), Query Frame = 1
Query:  190 CSNTRCYIDETNATRYVNCTHENVQNGTSLICEY--DDEVLKLKNLNFTIGLAEEFANNLFGNLQKNLGRITKLKMENLNVKYFKRSDFLGLPDLKLLQIITPMAIKEDSFKPFNGSQLKMYMNCKLYSSNLHFKLQVQVWAIYLTNCNYSLICSYFVSGAKYEYNIQLYEKNQIPKGKDPITNDNCTQKVSTKNTFQTTSEYKIKTSSFENLHKNAERKLHNLIKMLFFFLNISVILLILVFGFVFYIKLKNL 945
            C +  CY+D  + T+YVNC+ E+  +  +  C+Y  D++ LKLKN +  +   ++FA+ LF N+QK+LG+I  L +  + VKY K+SDFL L + + L++  PM I EDSF PFN S  ++ M C   SSNL FKLQ++ W IYL  CNY   CS   SG KYEYNIQL    +       ITN+NC++ + TK  F TT   +I T    N    +    +NLI   F ++NISV+LL+++ GF  YI ++NL
Sbjct:   24 CGDLECYVDRISNTQYVNCSREHDPHSKTFECQYNEDEKSLKLKNKDHEVKSVDKFASGLFENIQKDLGKIKDLSINYIQVKYIKKSDFLTLFNARYLEMSIPMEIDEDSFIPFNSSFFEISMKCNNDSSNLQFKLQIEKWRIYLHYCNYRAACSLVRSGEKYEYNIQLNHDGKYTPTTVTITNENCSRLLPTKIYFTTTRPSEIST----NYSTQSSEYFNNLINFSFLYINISVVLLMMIIGFAIYI-IRNL 272          
BLAST of SMED30025924 vs. Planmine SMEST
Match: SMESG000035443.1 (SMESG000035443.1)

HSP 1 Score: 150.984 bits (380), Expect = 2.150e-43
Identity = 98/253 (38.74%), Postives = 136/253 (53.75%), Query Frame = 1
Query:  181 FRPCSNTRCYIDETNATRYVNCTHENVQNGTSLICEYD--DEVLKLKNLNFTIGLAEEFANNLFGNLQKNLGRITKLKMENLNVKYFKRSDFLGLPDLKLLQIITPMAIKEDSFKPFNGSQLKMYMNCKLYSSNLHFKLQVQVWAIYLTNCNYSLICSYFVSGAKYEYNIQLYEKNQIPKGKDPITNDNCTQKVSTKNTFQTTSEYKIKTSSFENLHKNAERKLHNLIKMLFFFLNISVILLILVFGFVFYIK 933
            +RPC NTRCYID TN  RYV C+H NVQ  + L CEYD  D+ L L++    +  A+ FA++LF  L+ + G I KL +EN+ V Y K+SDF  L +L  L I TPM I EDSF     S  ++ M C   SS+  F L+ + W I L  CNY   CS   SG +YEYNI L    +       I+N  C +       F  T +++  TSS    + +  +K ++    LF     S++L +L+ GF  + K
Sbjct:   23 YRPCRNTRCYIDGTNTARYVTCSHGNVQRRSLLKCEYDNMDKSLTLRSPENNMKTADRFADHLFEILETSFGPIEKLTIENIQVNYIKKSDFSSLFNLTYLNIATPMIIDEDSFTSTFRSFFEISMKCNSISSSFRFNLK-KKWKIILHECNYRFECSSAGSGEQYEYNIHLSNDVKYYLDLAVISNAGCEKP------FFITLQHRTITSSSWTSNTSNNKKHYSSFYFLFLISTFSILLFMLI-GFALFTK 267          
BLAST of SMED30025924 vs. Planmine SMEST
Match: SMESG000035450.1 (SMESG000035450.1)

HSP 1 Score: 70.4774 bits (171), Expect = 2.529e-13
Identity = 54/200 (27.00%), Postives = 95/200 (47.50%), Query Frame = 1
Query:  190 CSNTRCYIDETNATRYVNCTHE----NVQNGTSLICEYD--DEVLKLKNLNFTIGLAEEFANNLFGNLQKNLGRITKLKMENLNVKYFKRSDFLGLPDLKLLQIITPMAIKEDSF-KPFNGSQLKMYMNC---KLYSSNLH-FKLQVQVWAIYLTNCNYSLIC--SYFVSGAKY--EYNIQLYEKNQIPKGKDPITNDNC 744
            C +  C+I+   + R + C ++    N  N   L CEYD   + L +K L       +      F    ++L  IT+L + ++ +    RSDF+GL  L+ L ++ P  ++EDSF    N    ++Y+ C   K +SS +   ++  + W I L +C YS  C     V+G +   EY ++   +N+ P+ +  I +  C
Sbjct:   30 CEDIDCFIETDLSARVLGCDYKVLLANKTNLKFLKCEYDLKRKALFIKPLTAGDNSVDGLLTGGFKVFSESLKEITELHIPHVKINNISRSDFVGLEKLRGLTLMNPGNLEEDSFLDIINSEYFQLYIYCNNEKNHSSGISKLRISSKSWRIVLRDCRYSFGCNLGTCVNGVRIGNEYQVKFQLRNKSPESESVIRSSTC 229          
BLAST of SMED30025924 vs. Planmine SMEST
Match: SMESG000035431.1 (SMESG000035431.1)

HSP 1 Score: 56.225 bits (134), Expect = 1.499e-8
Identity = 43/162 (26.54%), Postives = 75/162 (46.30%), Query Frame = 1
Query:  205 CYIDETNATRYVNCTHENVQNGTSLI----CEYDDEVLKLKNLNFTIGLAEEFANNLFGNLQKNLGRITKLKMENLNVKYFKRSDFLGLPDLKLLQIITPMAIKEDSFKPFNGSQL-KMYMNC-----KLYSSN-----LHFKLQVQVWAIYLTNCNYSLIC 645
            C++D +N +  +NC +E V    S +    C  D E L   +    + + + F++ +F  ++ NL +I  +++ ++ V + +RSD   L ++K L I  P     DSF     S L ++Y+ C     K YSS+     L F      W +   NC +   C
Sbjct:   27 CFVDISNQS--LNCGNETVNRNQSKMRRINCALDREELTFSHNYPGMVIVDRFSDQMFQTIKLNLSKIKAVRLSHIKVNHIRRSDLKYLSNIKSLTIANPKTFDIDSFLDIRHSDLFQLYIYCGTEIPKNYSSDYNSTSLSFLFHFTNWRVIQINCLHRYQC 186          
The following BLAST results are available for this feature:
BLAST of SMED30025924 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 SMED30025924 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 SMED30025924 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 SMED30025924 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 SMED30025924 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 SMED30025924 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 SMED30025924 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 SMED30025924 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 SMED30025924 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 SMED30025924 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 SMED30025924 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 SMED30025924 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 SMED30025924 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 SMED30025924 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000035449.10.000e+098.61SMESG000035449.1[more]
SMESG000035432.11.237e-6142.52SMESG000035432.1[more]
SMESG000035443.12.150e-4338.74SMESG000035443.1[more]
SMESG000035450.12.529e-1327.00SMESG000035450.1[more]
SMESG000035431.11.499e-826.54SMESG000035431.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025924 ID=SMED30025924|Name=SMED30025924|organism=Schmidtea mediterranea sexual|type=transcript|length=1006bp
TATAATGCATGTTTCACTGTAAATATGATGTTTACAATATTATTTCAGCA
ATTCACAGTCATGTTCATGGCGGATGTTCAGTGAATGCGATTGCAAATTC
TATTACAGTCAATGAATTACTTCAGGAGGTTCGTTCTGACTTCTGTAATA
ATAATATCAGTGATTATCACAATATCGTCATTCCGACCCTGTAGCAATAC
TCGGTGCTATATTGATGAGACCAATGCTACCCGATATGTGAATTGCACCC
ATGAAAATGTGCAAAATGGAACATCATTAATATGTGAATACGACGACGAA
GTCCTAAAATTAAAGAATCTTAATTTCACAATAGGATTAGCAGAGGAATT
TGCAAATAATCTGTTTGGAAACCTTCAAAAAAATCTCGGACGAATAACTA
AGTTGAAAATGGAGAATCTTAACGTGAAATACTTTAAAAGATCTGATTTT
CTTGGTTTACCTGACTTGAAATTGTTGCAAATAATAACCCCAATGGCAAT
TAAAGAAGACAGCTTCAAACCCTTCAATGGATCTCAGTTGAAAATGTATA
TGAATTGCAAATTATATTCCAGCAATCTCCATTTCAAATTGCAAGTGCAA
GTATGGGCAATATATCTAACAAACTGCAACTACAGCTTAATATGCTCATA
TTTTGTGTCTGGCGCAAAATACGAATACAATATCCAACTGTATGAGAAAA
ACCAAATCCCTAAGGGAAAAGATCCTATAACAAATGATAACTGCACACAG
AAAGTCTCAACAAAAAACACTTTCCAAACAACGAGTGAATATAAAATCAA
AACAAGCTCTTTTGAAAACCTTCACAAAAATGCGGAGAGAAAGTTGCACA
ATTTAATCAAAATGTTATTTTTCTTTTTAAATATTTCTGTTATTTTACTC
ATATTGGTATTCGGGTTTGTATTTTATATAAAACTAAAAAATCTGTAAGT
GTGATGTTCCAAATAAATTACAATTTGAAGCATCCTAGAATCCATTTTAC
TATAGC
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protein sequence of SMED30025924-orf-1

>SMED30025924-orf-1 ID=SMED30025924-orf-1|Name=SMED30025924-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=288bp
MRLQILLQSMNYFRRFVLTSVIIISVIITISSFRPCSNTRCYIDETNATR
YVNCTHENVQNGTSLICEYDDEVLKLKNLNFTIGLAEEFANNLFGNLQKN
LGRITKLKMENLNVKYFKRSDFLGLPDLKLLQIITPMAIKEDSFKPFNGS
QLKMYMNCKLYSSNLHFKLQVQVWAIYLTNCNYSLICSYFVSGAKYEYNI
QLYEKNQIPKGKDPITNDNCTQKVSTKNTFQTTSEYKIKTSSFENLHKNA
ERKLHNLIKMLFFFLNISVILLILVFGFVFYIKLKNL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 260..282
NoneNo IPR availableTMHMMTMhelixcoord: 171..193
NoneNo IPR availableTMHMMTMhelixcoord: 12..34