SMED30034369

Overview
NameSMED30034369
Smed IDSMED30034369
Length (bp)717
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30034369 (SMED30034369) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034369 (SMED30034369) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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



SMED30034369

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
reproductive organSMED30034369SMESG000057926.1 Contig51664newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30034369SMESG000057926.1 Contig51664uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oviductSMED30034369SMESG000057926.1 PL04015A2A04ncbi_smed_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
copulatory apparatusSMED30034369SMESG000057926.1 PL04015A2A04ncbi_smed_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
copulatory apparatusSMED30034369SMESG000057926.1 Contig2621GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30034369 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003631:39635..40397 -3492
v31.000350:150117..151419 -2663
v31.005844:22574..23269 +1983
v31.000350:137260..141352 -1149
Homology
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BLAST of SMED30034369 vs. Ensembl Nematostella
Match: EDO38480 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SCX4])

HSP 1 Score: 46.9802 bits (110), Expect = 1.569e-6
Identity = 23/64 (35.94%), Postives = 36/64 (56.25%), Query Frame = 1 
Query:  256 GEECCTEEQCNSAMKSNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYER 447
            G    T+ +  +   SN+P+G T   N+P+GTT  SN P+G    SN+P+G    +N+P+   R
Sbjct:    1 GTIFTTDFRHGTTHTSNSPDGTTRTTNSPDGTTRTSNSPDGTTHTSNSPDGTTRTSNSPDGTTR 64
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BLAST of SMED30034369 vs. Planmine SMEST
Match: SMESG000057926.1 (SMESG000057926.1)

HSP 1 Score: 277.715 bits (709), Expect = 1.933e-94
Identity = 141/161 (87.58%), Postives = 142/161 (88.20%), Query Frame = 1 
Query:   43 IAVFNTQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGCKSCLTNIKNNIISKSCSNRTCENKEAGEECCTEEQCNSAMKSNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYERNIISILLEFNRIICSVVWLIHSNILF 525
            I   NTQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGC                +NRTCENKEAGEECCTEEQCNSAMKSNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYERNIISILLEFNRIICSVVWLIHSNILF
Sbjct:  110 ITAKNTQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGC----------------NNRTCENKEAGEECCTEEQCNSAMKSNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYERNIISILLEFNRIICSVVWLIHSNILF 254

HSP 2 Score: 111.309 bits (277), Expect = 1.811e-29
Identity = 60/96 (62.50%), Postives = 67/96 (69.79%), Query Frame = 1 
Query:   13 MRLKAFLFIAIAVFNTQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGCKSCLTNIKNNIISKSCSNRTCENKEAGEECCTEEQCNSAMK 300
            MRLKAFLFIAIAVFN QLGTVHSISC  C  CWNS  D       ++Q      CKSC   IKNNI+SKSCS  TC+NK A EECCTEE CN+ ++
Sbjct:    1 MRLKAFLFIAIAVFNIQLGTVHSISCIKCGLCWNSDRDD------MDQTSRQHNCKSCRKIIKNNILSKSCSENTCDNKGADEECCTEEFCNADIE 90
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BLAST of SMED30034369 vs. Planmine SMEST
Match: SMESG000057926.1 (SMESG000057926.1)

HSP 1 Score: 276.559 bits (706), Expect = 3.105e-94
Identity = 140/157 (89.17%), Postives = 141/157 (89.81%), Query Frame = 1 
Query:   55 NTQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGCKSCLTNIKNNIISKSCSNRTCENKEAGEECCTEEQCNSAMKSNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYERNIISILLEFNRIICSVVWLIHSNILF 525
            NTQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGC                +NRTCENKEAGEECCTEEQCNSAMKSNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYERNIISILLEFNRIICSVVWLIHSNILF
Sbjct:  104 NTQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGC----------------NNRTCENKEAGEECCTEEQCNSAMKSNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYERNIISILLEFNRIICSVVWLIHSNILF 244

HSP 2 Score: 110.923 bits (276), Expect = 2.009e-29
Identity = 60/96 (62.50%), Postives = 67/96 (69.79%), Query Frame = 1 
Query:   13 MRLKAFLFIAIAVFNTQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGCKSCLTNIKNNIISKSCSNRTCENKEAGEECCTEEQCNSAMK 300
            MRLKAFLFIAIAVFN QLGTVHSISC  C  CWNS  D       ++Q      CKSC   IKNNI+SKSCS  TC+NK A EECCTEE CN+ ++
Sbjct:    1 MRLKAFLFIAIAVFNIQLGTVHSISCIKCGLCWNSDRDD------MDQTSRQHNCKSCRKIIKNNILSKSCSENTCDNKGADEECCTEEFCNADIE 90
[Close]
BLAST of SMED30034369 vs. Planmine SMEST
Match: SMESG000057926.1 (SMESG000057926.1)

HSP 1 Score: 274.633 bits (701), Expect = 1.219e-93
Identity = 139/156 (89.10%), Postives = 140/156 (89.74%), Query Frame = 1 
Query:   58 TQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGCKSCLTNIKNNIISKSCSNRTCENKEAGEECCTEEQCNSAMKSNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYERNIISILLEFNRIICSVVWLIHSNILF 525
            TQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGC                +NRTCENKEAGEECCTEEQCNSAMKSNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYERNIISILLEFNRIICSVVWLIHSNILF
Sbjct:   93 TQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGC----------------NNRTCENKEAGEECCTEEQCNSAMKSNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYERNIISILLEFNRIICSVVWLIHSNILF 232
[Close]
BLAST of SMED30034369 vs. Planmine SMEST
Match: SMESG000042052.1 (SMESG000042052.1)

HSP 1 Score: 223.402 bits (568), Expect = 3.151e-74
Identity = 127/216 (58.80%), Postives = 136/216 (62.96%), Query Frame = 1 
Query:   13 MRLKAFLFIAIAVFNTQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGCKSCLTNIKNNIISKSCSNRTCENKEAGEECCTEEQCNSAMKSNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYERNIISILLEFNRIICSVVWLIHSNILF*LFIFTANPFIFEQFIYSF*TIQQH*VVLLYEIIHYSLFIYTYQE 660
            M+LKAFLFIAI V N QL TV SISC ICNPCWNSTSD QY+DGF N N+ +SGCKSC TNIKNNII KSCS  TC+ KEAGEECCTEE CNS                                   A N K AK+NA +KY+RN+ISILLEFN IICS V               ANPFI EQFI SF TIQQH VVL  EIIHY LFIY YQE
Sbjct:    1 MQLKAFLFIAITVVNIQLRTVESISCKICNPCWNSTSDDQYSDGFSNGNMRLSGCKSCRTNIKNNIIMKSCSEETCDKKEAGEECCTEELCNS-----------------------------------AKNRKTAKSNARSKYKRNVISILLEFNGIICSAV--------------CANPFISEQFISSFDTIQQHRVVLFNEIIHYILFIYLYQE 167
[Close]
BLAST of SMED30034369 vs. Planmine SMEST
Match: SMESG000042059.1 (SMESG000042059.1)

HSP 1 Score: 221.09 bits (562), Expect = 2.202e-73
Identity = 125/216 (57.87%), Postives = 138/216 (63.89%), Query Frame = 1 
Query:   13 MRLKAFLFIAIAVFNTQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISGCKSCLTNIKNNIISKSCSNRTCENKEAGEECCTEEQCNSAMKSNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYERNIISILLEFNRIICSVVWLIHSNILF*LFIFTANPFIFEQFIYSF*TIQQH*VVLLYEIIHYSLFIYTYQE 660
            M+LKAFLFIAI V N QL TV SISC+ICNPCW+STSD QY+DGF N+N+ I+GCKSC TNIKNNII KSCS  TC+ KEAGEECCTEE CNS                                   A N K AK+NA +KY+RN+ISILLEFN IICS V               ANPFI EQFI SF TI+QH VVL  EIIHY LFIY YQE
Sbjct:    1 MQLKAFLFIAITVVNIQLRTVESISCNICNPCWSSTSDDQYSDGFSNENMRITGCKSCRTNIKNNIIMKSCSEETCDKKEAGEECCTEELCNS-----------------------------------AKNRKTAKSNARSKYKRNVISILLEFNGIICSAV--------------CANPFISEQFISSFDTIRQHRVVLFNEIIHYILFIYFYQE 167
The following BLAST results are available for this feature:
BLAST of SMED30034369 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 SMED30034369 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 SMED30034369 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 SMED30034369 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 SMED30034369 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 SMED30034369 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 SMED30034369 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 SMED30034369 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 SMED30034369 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 SMED30034369 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 SMED30034369 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 SMED30034369 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO384801.569e-635.94Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30034369 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 SMED30034369 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000057926.11.933e-9487.58SMESG000057926.1[more]
SMESG000057926.13.105e-9489.17SMESG000057926.1[more]
SMESG000057926.11.219e-9389.10SMESG000057926.1[more]
SMESG000042052.13.151e-7458.80SMESG000042052.1[more]
SMESG000042059.12.202e-7357.87SMESG000042059.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034369 ID=SMED30034369|Name=SMED30034369|organism=Schmidtea mediterranea sexual|type=transcript|length=717bp
TGGAATCCAAAAATGCGACTGAAAGCGTTTCTCTTCATTGCTATTGCGGT
ATTCAATACTCAACTAGGCACCGTTCACTCGATTAGTTGCCACATTTGCA
ACCCATGCTGGAACTCTACCTCAGACTACCAGTATACAGATGGATTCCTA
AACCAGAATTTACTAATTAGTGGTTGCAAGTCTTGTCTAACAAATATTAA
AAACAATATTATCAGTAAATCCTGTAGTAATAGAACATGTGAAAATAAGG
AGGCGGGGGAAGAATGTTGCACTGAAGAACAGTGTAATTCTGCGATGAAA
AGTAATGCACCAAATGGGATAACTGCTAAAGGTAATGCACCAAATGGGAC
AACTGCTAAAAGTAATCCACCAAATGGGAAAATTGCTAAAAGTAATGCAC
CAAATGGGAAAATTGCTAAAAATAATGCACCAAATAAATATGAAAGAAAT
ATTATTTCAATTTTGCTGGAGTTTAATAGAATCATCTGCTCAGTAGTCTG
GTTGATCCATTCGAATATTTTGTTTTAATTATTTATTTTTACTGCAAATC
CTTTCATATTTGAACAATTTATTTATAGCTTTTAGACTATTCAGCAACAT
TGAGTCGTTTTATTGTATGAAATTATTCATTATAGCTTGTTTATTTATAC
ATATCAAGAAAGGAAATTTTTTACTAATAAATAAAAATGATTTCAAAAAA
AAAAAAAAAAAATGCGA
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protein sequence of SMED30034369-orf-1

>SMED30034369-orf-1 ID=SMED30034369-orf-1|Name=SMED30034369-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=176bp
WNPKMRLKAFLFIAIAVFNTQLGTVHSISCHICNPCWNSTSDYQYTDGFL
NQNLLISGCKSCLTNIKNNIISKSCSNRTCENKEAGEECCTEEQCNSAMK
SNAPNGITAKGNAPNGTTAKSNPPNGKIAKSNAPNGKIAKNNAPNKYERN
IISILLEFNRIICSVVWLIHSNILF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000232copulatory apparatus
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 115..135
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..27
score: 0.741