SMED30000682

Overview
NameSMED30000682
Smed IDSMED30000682
Length (bp)328
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ 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



 

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 SMED30000682 (SMED30000682) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30000682 (SMED30000682) in cells (dots) of each of the 12 neoblast clusters.

 

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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 SMED30000682 (SMED30000682) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30000682 (SMED30000682) 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.
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



SMED30000682

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30000682 Contig1308newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30000682 Contig1308uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30000682 SmedASXL_018867SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30000682 dd_Smed_v4_1303_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30000682 dd_Smed_v4_1303_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30000682 dd_Smed_v4_1303_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30000682 dd_Smed_v4_1303_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30000682 dd_Smed_v4_1303_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30000682 dd_Smed_v4_1303_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
Smed sexual biotypeSMED30000682 Contig1308newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000682 Contig1308uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30000682 dd_Smed_v6_1303_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30000682 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000626:25114..25531 -1585
Homology
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BLAST of SMED30000682 vs. Ensembl Human
Match: C9orf116 (chromosome 9 open reading frame 116 [Source:HGNC Symbol;Acc:HGNC:28435])

HSP 1 Score: 47.3654 bits (111), Expect = 2.325e-7
Identity = 20/60 (33.33%), Postives = 34/60 (56.67%), Query Frame = -3 
Query:   27 FRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLNM*LQHHFHLLSHRCL 206
            +RT++  YG   P +H M  V+Y  S  F+++L   GM+RN++LN+ L+         C+
Sbjct:   56 YRTSNQAYGSRAPTVHEMPKVFYPNSNKFSQQLAAGGMFRNNTLNVYLEKSIVTGPDNCI 115
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BLAST of SMED30000682 vs. Ensembl Fly
Match: CG34107 (gene:FBgn0083943 transcript:FBtr0110787)

HSP 1 Score: 44.669 bits (104), Expect = 8.618e-7
Identity = 22/58 (37.93%), Postives = 34/58 (58.62%), Query Frame = -3 
Query:   48 NVNPCFRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLNM*LQHHFH 221
            + N  +RT +S+YG   PN +T+   +Y   Q+F+ E+   GMYRN SLN  +   F+
Sbjct:   57 DSNTMYRTCNSEYGYYAPNAYTIPKRFYPLPQSFSNEVVRFGMYRNFSLNTHMDRTFY 114
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BLAST of SMED30000682 vs. Ensembl Xenopus
Match: tbc1d7 (TBC1 domain family member 7 [Source:Xenbase;Acc:XB-GENE-489046])

HSP 1 Score: 53.5286 bits (127), Expect = 1.580e-9
Identity = 23/45 (51.11%), Postives = 31/45 (68.89%), Query Frame = -3 
Query:   72 FRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLN 206
            F+T+SS+YG L+P   T    ++  SQ F++ LG CGMYRNHS N
Sbjct:  117 FKTSSSEYGALRPTYETAPCSHHPVSQRFSQHLGQCGMYRNHSFN 161
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BLAST of SMED30000682 vs. Ensembl Xenopus
Match: ENSXETT00000032208.1 (chromosome unknown C9orf116 homolog [Source:NCBI gene;Acc:101733379])

HSP 1 Score: 43.8986 bits (102), Expect = 3.462e-6
Identity = 26/81 (32.10%), Postives = 38/81 (46.91%), Query Frame = -3 
Query:   72 HFKRITFYRIFFTF--KIMSSESVKIEERINV-NPCFRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLN 305
            H +   FYR+  +   K    E+ +   R    NP +RT++  YG   P +H M   +   S  F++    CGMYRNH  N
Sbjct:   15 HPQTCDFYRVSESLPPKFNQPETWRRGYRPKTDNPLYRTSNQIYGSRPPTVHEMPTTFNGISDKFSETAVKCGMYRNHGFN 95
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BLAST of SMED30000682 vs. UniProt/SwissProt
Match: sp|Q5BN46|CI116_HUMAN (UPF0691 protein C9orf116 OS=Homo sapiens OX=9606 GN=C9orf116 PE=1 SV=1)

HSP 1 Score: 47.3654 bits (111), Expect = 1.117e-6
Identity = 20/60 (33.33%), Postives = 34/60 (56.67%), Query Frame = -3 
Query:   27 FRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLNM*LQHHFHLLSHRCL 206
            +RT++  YG   P +H M  V+Y  S  F+++L   GM+RN++LN+ L+         C+
Sbjct:   56 YRTSNQAYGSRAPTVHEMPKVFYPNSNKFSQQLAAGGMFRNNTLNVYLEKSIVTGPDNCI 115
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BLAST of SMED30000682 vs. TrEMBL
Match: A0A1S8WNS5 (Uncharacterized protein OS=Opisthorchis viverrini OX=6198 GN=X801_08080 PE=4 SV=1)

HSP 1 Score: 71.633 bits (174), Expect = 2.328e-14
Identity = 29/49 (59.18%), Postives = 38/49 (77.55%), Query Frame = -3 
Query:   72 VNPCFRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLN 218
            +NP +RT++S+YGRLKPN+HTM+ VY+ +   F K   PCG YRNHSLN
Sbjct:    9 INPMYRTSNSEYGRLKPNVHTMSVVYHQRKAEFQKRFAPCGNYRNHSLN 57
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BLAST of SMED30000682 vs. TrEMBL
Match: A0A3Q0KUW2 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 72.7886 bits (177), Expect = 3.481e-14
Identity = 36/81 (44.44%), Postives = 50/81 (61.73%), Query Frame = -3 
Query:   51 FYRI--FFTFKIMSSESVKIEERINVNPCFRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLNM*LQHHF 287
            +YRI     ++  + +     +R  +NP +RTT+S+YGRLKPN+HTM  VYY K+Q F+K     G YRNHSLN    H +
Sbjct:   34 YYRIDKRLPYRFNNPDKFGGYDRPKLNPLYRTTNSEYGRLKPNVHTMNVVYYNKNQEFSKRYMKAGNYRNHSLNTATDHKY 114
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BLAST of SMED30000682 vs. TrEMBL
Match: A0A5K4F8I0 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 70.8626 bits (172), Expect = 5.629e-14
Identity = 29/46 (63.04%), Postives = 36/46 (78.26%), Query Frame = -3 
Query:   72 CFRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLN 209
             F+TTSSDYG+  PN+HTM NVY+    +F++ LG CGMYRNHSLN
Sbjct:   18 LFKTTSSDYGKFAPNVHTMPNVYFPLKGDFSQHLGKCGMYRNHSLN 63
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BLAST of SMED30000682 vs. TrEMBL
Match: A0A1I8IJ88 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 9.632e-14
Identity = 28/49 (57.14%), Postives = 39/49 (79.59%), Query Frame = -3 
Query:   72 VNPCFRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLN 218
            V+P +RTT+SDYG++ P +HTM   ++  SQ F++ELG CGMYRNHS+N
Sbjct:   49 VHPMYRTTASDYGKMSPTVHTMPTTFHPVSQTFSEELGQCGMYRNHSMN 97
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BLAST of SMED30000682 vs. TrEMBL
Match: A0A267EIF5 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig001436g3 PE=4 SV=1)

HSP 1 Score: 70.8626 bits (172), Expect = 1.529e-13
Identity = 28/49 (57.14%), Postives = 39/49 (79.59%), Query Frame = -3 
Query:   72 VNPCFRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLN 218
            V+P +RTT+SDYG++ P +HTM   ++  SQ F++ELG CGMYRNHS+N
Sbjct:   54 VHPMYRTTASDYGKMSPTVHTMPTTFHPVSQTFSEELGQCGMYRNHSMN 102
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BLAST of SMED30000682 vs. Ensembl Nematostella
Match: EDO42553 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S180])

HSP 1 Score: 61.6178 bits (148), Expect = 8.129e-14
Identity = 26/48 (54.17%), Postives = 33/48 (68.75%), Query Frame = -3 
Query:   72 NPCFRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLN 215
            NP + T+S +YG  +P +HTM   ++ K Q FT  LG CGMYRNHSLN
Sbjct:   59 NPMYMTSSQEYGNRRPTVHTMPTSFHAKCQKFTDHLGKCGMYRNHSLN 106
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BLAST of SMED30000682 vs. Ensembl Medaka
Match: ENSORLT00000019378.2 (pep primary_assembly:ASM223467v1:6:27927387:27931296:1 gene:ENSORLG00000015479.2 transcript:ENSORLT00000019378.2 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 46.2098 bits (108), Expect = 2.312e-7
Identity = 22/45 (48.89%), Postives = 28/45 (62.22%), Query Frame = -3 
Query:   72 FRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLN 206
            +RTTS DYG L P   +    Y+ KSQ F++ L   GMYRN+S N
Sbjct:   58 YRTTSRDYGLLPPTSESAPCTYHPKSQTFSEHLSKAGMYRNNSFN 102
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BLAST of SMED30000682 vs. Planmine SMEST
Match: SMESG000032075.1 (SMESG000032075.1)

HSP 1 Score: 56.225 bits (134), Expect = 2.943e-11
Identity = 23/50 (46.00%), Postives = 37/50 (74.00%), Query Frame = -3 
Query:   69 VNPCFRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLNM 218
             NP +RTT+ +YGR+ PNIHTM  ++ +++  FTK  GP G Y+++S+N+
Sbjct:   77 TNPMYRTTNHEYGRIPPNIHTMPVIFRSRNNFFTKRYGPSGNYKDNSMNI 126
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BLAST of SMED30000682 vs. Planmine SMEST
Match: SMESG000032075.1 (SMESG000032075.1)

HSP 1 Score: 56.225 bits (134), Expect = 3.195e-11
Identity = 23/50 (46.00%), Postives = 37/50 (74.00%), Query Frame = -3 
Query:   69 VNPCFRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLNM 218
             NP +RTT+ +YGR+ PNIHTM  ++ +++  FTK  GP G Y+++S+N+
Sbjct:   80 TNPMYRTTNHEYGRIPPNIHTMPVIFRSRNNFFTKRYGPSGNYKDNSMNI 129
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BLAST of SMED30000682 vs. Planmine SMEST
Match: SMESG000032541.1 (SMESG000032541.1)

HSP 1 Score: 46.2098 bits (108), Expect = 4.894e-7
Identity = 19/46 (41.30%), Postives = 31/46 (67.39%), Query Frame = -3 
Query:   69 FRTTSSDYGRLKPNIHTMANVYYTKSQNFTKELGPCGMYRNHSLNM 206
            ++TT+S+YG+ +PN+HTM  VY  +   F+K  G  G  ++HS N+
Sbjct:  176 YQTTNSEYGKHRPNVHTMPTVYKRQDHGFSKRYGRYGPPKDHSFNI 221
The following BLAST results are available for this feature:
BLAST of SMED30000682 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 1
Match NameE-valueIdentityDescription
C9orf1162.325e-733.33chromosome 9 open reading frame 116 [Source:HGNC S... [more]
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BLAST of SMED30000682 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 SMED30000682 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CG341078.618e-737.93gene:FBgn0083943 transcript:FBtr0110787[more]
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BLAST of SMED30000682 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 SMED30000682 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 2
Match NameE-valueIdentityDescription
tbc1d71.580e-951.11TBC1 domain family member 7 [Source:Xenbase;Acc:XB... [more]
ENSXETT00000032208.13.462e-632.10chromosome unknown C9orf116 homolog [Source:NCBI g... [more]
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BLAST of SMED30000682 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 SMED30000682 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q5BN46|CI116_HUMAN1.117e-633.33UPF0691 protein C9orf116 OS=Homo sapiens OX=9606 G... [more]
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BLAST of SMED30000682 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1S8WNS52.328e-1459.18Uncharacterized protein OS=Opisthorchis viverrini ... [more]
A0A3Q0KUW23.481e-1444.44Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A5K4F8I05.629e-1463.04Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A1I8IJ889.632e-1457.14Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267EIF51.529e-1357.14Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
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BLAST of SMED30000682 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 SMED30000682 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 SMED30000682 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 SMED30000682 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO425538.129e-1454.17Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30000682 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSORLT00000019378.22.312e-748.89pep primary_assembly:ASM223467v1:6:27927387:279312... [more]
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BLAST of SMED30000682 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000032075.12.943e-1146.00SMESG000032075.1[more]
SMESG000032075.13.195e-1146.00SMESG000032075.1[more]
SMESG000032541.14.894e-741.30SMESG000032541.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000682 ID=SMED30000682|Name=SMED30000682|organism=Schmidtea mediterranea sexual|type=transcript|length=328bp
TGACAAGCTTAAGATTTATTTAATAAAAGACATCTGTGAGACAGTAAATG
AAAATGATGTTGCAATCACATATTCAGTGAATGATTGCGATACATTCCAC
AAGGCCCCAATTCTTTTGTGAAATTTTGAGATTTGGTGTAGTAAACATTG
GCCATTGTGTGAATATTTGGTTTCAGTCGTCCATAATCAGATGATGTTGT
ACGGAAACATGGGTTTACATTGATTCTTTCTTCAATTTTCACACTTTCGG
ATGACATGATTTTAAAAGTGAAAAATATTCTATAAAAAGTAATTCTTTTA
AAGTGAATTATTTAGACTAACCGAAATT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR026507UPF0691
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR026507Uncharacterised protein family UPF0691PFAMPF14892DUF4490coord: 11..62
e-value: 3.6E-17
score: 62.3
IPR026507Uncharacterised protein family UPF0691PANTHERPTHR20899UNCHARACTERIZEDcoord: 15..62
NoneNo IPR availablePANTHERPTHR20899:SF1GEO10781P1coord: 15..62