SMED30034447

Overview
NameSMED30034447
Smed IDSMED30034447
Length (bp)491
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 SMED30034447 (SMED30034447) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034447 (SMED30034447) 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.
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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



SMED30034447

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30034447 SmedASXL_062239SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30034447 SmedASXL_062239SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30034447 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009069:10370..10873 +2131
v31.014971:3035..3537 -2116
v31.001532:51287..51787 +1786
v31.028764:957..1433 -1540
Homology
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BLAST of SMED30034447 vs. Ensembl Xenopus
Match: slc10a6 (solute carrier family 10 (sodium/bile acid cotransporter), member 6 [Source:Xenbase;Acc:XB-GENE-988401])

HSP 1 Score: 47.7506 bits (112), Expect = 2.358e-6
Identity = 28/75 (37.33%), Postives = 36/75 (48.00%), Query Frame = -1 
Query:   54 PSIEYNFKQDVDNTAKQTFHLEWLTIYPWIGNSADAKGSFCSLCVLFRPVVHCSSLGSFIAKPCSKCNKFNELAK 278
            PS  Y+FK+D      + F   WL  Y WI  S   KG+ C  CV+F   VH    G+FI  P  K   F+  A+
Sbjct:   10 PSEAYDFKKDAK--GPRCFRHVWLKQYRWICYSPHLKGALCKYCVIFPQPVHRGFQGAFITAPFLKYRDFHNSAR 82
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BLAST of SMED30034447 vs. TrEMBL
Match: X1WYT3 (Uncharacterized protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=1)

HSP 1 Score: 114.775 bits (286), Expect = 1.984e-26
Identity = 51/100 (51.00%), Postives = 68/100 (68.00%), Query Frame = -1 
Query:   54 LDIXMYLNXHINXEERLKLLKTH*VPSIEYNFKQDVDNTAKQTFHLEWLTIYPWIGNSADAKGSFCSLCVLFRPVVHCSSLGSFIAKPCSKCNKFNELAK 353
            LDI +YLN +++ E RLKLLK   VPS  Y+FK+D+ N + + F +EW  +YPW+  SA +KG  C +CVLFRP VH    G+FI  PC K  KFNE++K
Sbjct:   94 LDIGLYLNSYVDDELRLKLLKDPWVPSKTYDFKKDLTNGSTRVFRIEWFALYPWLSYSAVSKGPLCRVCVLFRPRVHRGVQGAFIVSPCIKYQKFNEVSK 193
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BLAST of SMED30034447 vs. TrEMBL
Match: A0A0J7NNB2 (52 kDa repressor of the inhibitor of the protein kinase-like protein OS=Lasius niger OX=67767 GN=RF55_5874 PE=4 SV=1)

HSP 1 Score: 105.145 bits (261), Expect = 4.540e-23
Identity = 58/131 (44.27%), Postives = 76/131 (58.02%), Query Frame = -1 
Query:   54 SMSLPKLSSDLSRKXXTXEETVQSD----LDIXMYL--NXHINXEERLKLLKTH*VPSIEYNFKQDVDNTAKQTFHLEWLTIYPWIGNSADAKGSFCSLCVLFRPVVHCSSLGSFIAKPCSKCNKFNELAK 428
            + + P  S+D  ++    EE+  +     LDI +YL  N H + E RLKLL+    PS  YNFK+DV+  AK+ F  EWLT YPW+  SA AKG  C +CVLFRP       G FI  PC K +KF+E A+
Sbjct:   17 TTATPSSSTDHQKEDGRDEESPLNSGANLLDIGLYLDSNSHADDELRLKLLREPWAPSQMYNFKKDVNIGAKRAFRSEWLTTYPWLTYSAIAKGPLCRVCVLFRPPAQRGLQGQFIVSPCLKYHKFHEAAQ 147
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BLAST of SMED30034447 vs. TrEMBL
Match: A0A2S2QKI7 (Uncharacterized protein OS=Sipha flava OX=143950 GN=g.172901 PE=4 SV=1)

HSP 1 Score: 72.0182 bits (175), Expect = 6.535e-13
Identity = 32/72 (44.44%), Postives = 46/72 (63.89%), Query Frame = -1 
Query:  138 LDIXMYLNXHINXEERLKLLKTH*VPSIEYNFKQDVDNTAKQTFHLEWLTIYPWIGNSADAKGSFCSLCVLF 353
            LDI +YLN +++ E RLKLLK   VPS  Y+FK+D  N + + F +EW  +YPW+  SA +KG + +    F
Sbjct:   61 LDIGLYLNSYVDDELRLKLLKDLWVPSKIYDFKKDFTNGSTRVFRIEWFALYPWLSYSAVSKGHYVAFVYYF 132
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BLAST of SMED30034447 vs. TrEMBL
Match: X1XRP7 (Uncharacterized protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=1)

HSP 1 Score: 74.7146 bits (182), Expect = 1.996e-12
Identity = 46/114 (40.35%), Postives = 62/114 (54.39%), Query Frame = -1 
Query:   57 TXEETVQSD---LDIXMYLNXHINXEE--RLKLLKTH*VPSIEYNFKQDVDNTAKQTFHLEWLTIYPWIGNSADAKGSFCSLCVLFRP-VVHCSSLGSFIAKPCSKCNKFNELA 380
            T +  V++D    DI  Y+  ++N  E  + KLLK   VPSI YNFK+D+     + F  +W +IYPW+  S   KG+FC  CVLF+  V H      FI KP  +  KF E A
Sbjct:   41 TNDLAVENDCDQYDIGHYIKNNLNITEDFKYKLLKNPWVPSIHYNFKKDIV-VGNRAFLFKWFSIYPWLAYSKIFKGTFCLYCVLFQTHVSHGGFQEQFINKPFQRYKKFLEKA 153
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BLAST of SMED30034447 vs. TrEMBL
Match: A0A1Y1KPE9 (Uncharacterized protein (Fragment) OS=Photinus pyralis OX=7054 PE=4 SV=1)

HSP 1 Score: 72.4034 bits (176), Expect = 2.293e-12
Identity = 42/107 (39.25%), Postives = 56/107 (52.34%), Query Frame = -1 
Query:   54 SDLDIXMYLNX----HINXEERLKLLKTH*VPSIEYNFKQDVDNTAKQTFHLEWLTIYPWIGNSADAKGSFCSLCVLFRP-VVHCSSLGSFIAKPCSKCNKFNELAK 359
            SD DI  Y++     ++N   +   L+    P   YNFKQD  +  K+ F  EW  +Y W+  S   KG+FC  CV FRP V   S LG+FI +P     KF+E AK
Sbjct:   79 SDTDIGHYVDTKNICNLNDRTKYLFLQNPWKPEKGYNFKQDAPD-GKRPFLYEWFCLYEWVTYSKYYKGAFCKTCVFFRPHVSRGSLLGAFITRPFRNFKKFHECAK 184
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BLAST of SMED30034447 vs. Ensembl Nematostella
Match: EDO26151 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7TCR4])

HSP 1 Score: 43.5134 bits (101), Expect = 8.064e-6
Identity = 19/59 (32.20%), Postives = 30/59 (50.85%), Query Frame = -1 
Query:  138 EERLKLLKTH*VPSIEYNFKQDVDNTAKQTFHLEWLTIYPWIGNSADAKGSFCSLCVLF 314
            +++LK ++    P   ++F   ++N   + F L WL  YPW+  S    G FC  CV F
Sbjct:   30 QDKLKFIENVWKPGELFDFPVSIENGKSRKFVLNWLKKYPWLAYSKYYNGVFCLACVCF 88
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BLAST of SMED30034447 vs. Planmine SMEST
Match: SMESG000052447.1 (SMESG000052447.1)

HSP 1 Score: 64.3142 bits (155), Expect = 1.218e-12
Identity = 46/123 (37.40%), Postives = 61/123 (49.59%), Query Frame = -1 
Query:   51 SSDLSRKXXTXEET--VQSDLDIXMYLN-XHINXEERLKLLKTH*VPSIEYNFKQD-VDNTAKQTFHLEWLTIYPWIGNSADAKGSFCSLCVLFRPVVHCSSLGSFIAKPCSKCNKFNELAKF 407
            S+  +    T E T  +  +LDI  ++N  H   +   K LK    P   Y+FK D +DN+  QTF   WL  YP +  SA  KG  C  CVLF+P V     G+ I K  +K  KF+E AK 
Sbjct:    6 STPFASTAGTPENTTKIYHELDIGNFINHSHTPDDIIFKALKHPWTPETSYDFKNDSLDNS--QTFRHTWLNDYPEMSYSAKLKGVVCRTCVLFKPHVDRGIQGALILKEFTKYKKFHECAKL 126
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BLAST of SMED30034447 vs. Planmine SMEST
Match: SMESG000029489.1 (SMESG000029489.1)

HSP 1 Score: 60.4622 bits (145), Expect = 3.883e-11
Identity = 46/147 (31.29%), Postives = 63/147 (42.86%), Query Frame = -1 
Query:   54 KRKVNEEIQESSHVPSTSMSLPKLSSDLSRKXXTXEETVQSDLDIXMYLNX----HINXEERLKLLKTH*VPSIEYNFKQDVDNTAKQTFHLEWLTIY-PWIGNSADAKGSFCSLCVLFRPVVHCSSLGSFIAKPCSKCNKFNELAK 479
            K K N E   S  V +T +  P L            E  +   DI +Y+       I+ + + +LL     P + Y+F+ DV  + K+ F    LT Y PW+  S   KG FC  CVL    V     G FI   C+K   FNE A+
Sbjct:   18 KLKRNIEAMHSKDVSATLLPEPDLDK-------LESEDTRLTYDIGLYVKSTTKISIDLKLKYRLLTDPYKPHLSYDFQGDVSESGKRCFRESCLTQYTPWLSYSPKLKGVFCIFCVLIPQPVQRRIQGIFITTACTKYKDFNECAR 157
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BLAST of SMED30034447 vs. Planmine SMEST
Match: SMESG000053255.1 (SMESG000053255.1)

HSP 1 Score: 58.9214 bits (141), Expect = 1.435e-10
Identity = 45/133 (33.83%), Postives = 64/133 (48.12%), Query Frame = -1 
Query:   51 SHVPSTSMSLPKLSSDLSRKXXTXEETVQSDLDIXMYLNX-HINXEERLKLLKTH*VPSIEYNFKQDVDNTAKQTFHLEWLTIYPWIGNSADAKGSFCSLCVLFRPVVHCSSLGSFIAKPCSKCNKFNELAKF 446
            +H    S S P  S+  + +  T    + ++LDI  ++N  H   +   K LK    P   Y+FK D  +++  TF   WL  YP +  SA  KG  C  CVLF+P V     G+FI K  +K  K +E AK 
Sbjct:   31 THAMKASTSTPFASTTGTPENTTK---IYNELDIGNFINHLHTPDDIVFKSLKHPWTPETYYDFKNDSLDSS-WTFRHTWLHDYPEMSYSAKLKGVVCRTCVLFKPHVDRGIQGAFILKEFTKYKKCHECAKL 159
[Close]
BLAST of SMED30034447 vs. Planmine SMEST
Match: SMESG000008969.1 (SMESG000008969.1)

HSP 1 Score: 52.7582 bits (125), Expect = 1.927e-8
Identity = 30/71 (42.25%), Postives = 40/71 (56.34%), Query Frame = -1 
Query:   51 NFKQDVDNTAKQTFHLEWLTIYPWIGNSADAKGSFCSLCVLFRPVVHCSSLGSFIAKPCSKCNKFNELAKF 263
            +FK D  ++++ TF   WL  YP +  SA  KG  C  CVLF+P V     G+FI K  +K  KF+E AK 
Sbjct:   41 DFKNDSLDSSR-TFRHTWLHDYPEMSYSAKLKGVVCRTCVLFKPHVDRGIQGAFILKEFTKYKKFHECAKL 110
The following BLAST results are available for this feature:
BLAST of SMED30034447 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 SMED30034447 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 SMED30034447 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 SMED30034447 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 SMED30034447 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
slc10a62.358e-637.33solute carrier family 10 (sodium/bile acid cotrans... [more]
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BLAST of SMED30034447 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 SMED30034447 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 SMED30034447 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
X1WYT31.984e-2651.00Uncharacterized protein OS=Acyrthosiphon pisum OX=... [more]
A0A0J7NNB24.540e-2344.2752 kDa repressor of the inhibitor of the protein k... [more]
A0A2S2QKI76.535e-1344.44Uncharacterized protein OS=Sipha flava OX=143950 G... [more]
X1XRP71.996e-1240.35Uncharacterized protein OS=Acyrthosiphon pisum OX=... [more]
A0A1Y1KPE92.293e-1239.25Uncharacterized protein (Fragment) OS=Photinus pyr... [more]
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BLAST of SMED30034447 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 SMED30034447 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 SMED30034447 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 SMED30034447 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO261518.064e-632.20Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30034447 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 SMED30034447 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000052447.11.218e-1237.40SMESG000052447.1[more]
SMESG000029489.13.883e-1131.29SMESG000029489.1[more]
SMESG000053255.11.435e-1033.83SMESG000053255.1[more]
SMESG000008969.11.927e-842.25SMESG000008969.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034447 ID=SMED30034447|Name=SMED30034447|organism=Schmidtea mediterranea sexual|type=transcript|length=491bp
AAAATTTTCTGATTGTTTCATTGCATCAGGATGCCATTTGGTGGATGCAA
AAACTTTGCCAATTCATTAAATTTATTACATTTCGAGCATGGCTTTGCAA
TAAACGATCCCAATGAACTGCAATGCACTACAGGTCGAAACAATACACAC
AAGCTGCAAAATGAGCCTTTTGCATCAGCAGAGTTACCTATCCAAGGATA
AATTGTTAACCATTCCAAATGAAATGTTTGTTTTGCAGTATTATCTACGT
CCTGTTTGAAATTATATTCTATACTTGGTACTCAGTGGGTTTTTAAAAGT
TTCAATCGTTCCTCNTCATTAATATGNTTGTTTAAATACATNNNAATATC
TAAATCACTTTGTACTGTTTCTTCNTNAGTGTNNNCTTTTCTTGATAAAT
CAGACGATAACTTTGGCAATGACATAGAAGTGGAAGGTACATGAGAGCTC
TCTTGAATTTCTTCATTAACCTTTCGCTTCTTGATAAAAAT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell