SMED30023067

Overview
NameSMED30023067
Smed IDSMED30023067
Length (bp)694
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 SMED30023067 (SMED30023067) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023067 (SMED30023067) 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



SMED30023067

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30023067h1SMcG0015474 SmedASXL_056014SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
protonephridiaSMED30023067h1SMcG0015473 dd_Smed_v4_10051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30023067h1SMcG0015474 dd_Smed_v4_10051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30023067h1SMcG0015474 dd_Smed_v6_62605_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
tail regionSMED30023067h1SMcG0015473 dd_Smed_v6_10051_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
tail regionSMED30023067h1SMcG0015474 dd_Smed_v6_10051_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
SMED30023067 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001460:4214..6777 +3301
v31.001460:15781..16375 -1213
Homology
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BLAST of SMED30023067 vs. TrEMBL
Match: A0A2C9L9N4 (Uncharacterized protein OS=Biomphalaria glabrata OX=6526 GN=106072341 PE=4 SV=1)

HSP 1 Score: 55.0694 bits (131), Expect = 3.986e-6
Identity = 33/120 (27.50%), Postives = 63/120 (52.50%), Query Frame = 3 
Query:  276 SVNDLRISFVSYLPLTFSAILIIIFAFVTKRVSFKVNSCYGRPGLAVPMEMINSNENRYAYVMAFLSFSEDIYRAIFVNGTDNMQEPIL-KSLIKLGYVIVFSVTYYPIFAGICAKHLIG 632
            ++ D  I +V+   L  +A +I+  +F+ KR +++ + C GRP L +P+  ++  ENR AY +AFL+        +    T N+  P+  ++LI      V  +T +P FA +  ++ + 
Sbjct:    2 TLEDFNIYYVNNWILIPAAFIILFLSFLEKR-TYRPDVCNGRPALVIPLPFLDGYENRLAYSVAFLTIMNTFVSLLTSQNTINIDIPLWGRALIVYMQAFVGCLTCFPFFACLSTRYRVA 120
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BLAST of SMED30023067 vs. Ensembl Nematostella
Match: EDO30950 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SZB2])

HSP 1 Score: 47.3654 bits (111), Expect = 2.622e-6
Identity = 46/166 (27.71%), Postives = 80/166 (48.19%), Query Frame = 3 
Query:  228 ALQGARDPNETNRPDCSVNDLRISFVSYLPLTFSAILIIIFAFVTKRVSFKVNSC---YGRPGLAVPMEMINSNENRYAYVMAF----------LSFSEDIYRAIFVNGTDNMQ-EPILKSLIKLGYVI----VFSVTYYPIFAGICAKH-LIGYCMGLIFAAVLL 668
            A +G    + +N   C  +  +  F +YL +  +  +I++ +F+  RV+  + SC     RPGL +P+ +++S ENR  Y  AF          L FS+  Y  IF      +Q +P   + + + + I    V  V YYP FA +   + ++G  +G  ++AV L
Sbjct:   72 AYRGIDRASASNSTPCVSSPTKGEF-TYLCVGPAIAIILLLSFLKPRVN-TIKSCGMKIVRPGLCIPLNLLDSYENRLGYACAFGATVSRCLRVLFFSD--YSEIFDERVMKIQSDPATPAWMGMFWRILAMFVIGVAYYPFFACLSTDYKILGGLLGSAYSAVWL 233
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BLAST of SMED30023067 vs. Planmine SMEST
Match: SMESG000041908.1 (SMESG000041908.1)

HSP 1 Score: 233.032 bits (593), Expect = 4.288e-70
Identity = 112/118 (94.92%), Postives = 115/118 (97.46%), Query Frame = 3 
Query:  339 IIIFAFVTKRVSFKVNSCYGRPGLAVPMEMINSNENRYAYVMAFLSFSEDIYRAIFVNGTDNMQEPILKSLIKLGYVIVFSVTYYPIFAGICAKHLIGYCMGLIFAAVLLCCNLELVD 692
            +IIFAFVTKRVSFKVNSCYGRPGLAVPM+MINSNENRYAYVMAFLSFSEDIYRAIFV  TDNMQEPILK LIKLGYVIVFSVTYYPIFAGICAKHLIGYCMGLIFAAVLLCCNLELV+
Sbjct:  835 VIIFAFVTKRVSFKVNSCYGRPGLAVPMDMINSNENRYAYVMAFLSFSEDIYRAIFVYETDNMQEPILKFLIKLGYVIVFSVTYYPIFAGICAKHLIGYCMGLIFAAVLLCCNLELVN 952
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BLAST of SMED30023067 vs. Planmine SMEST
Match: SMESG000031048.1 (SMESG000031048.1)

HSP 1 Score: 206.453 bits (524), Expect = 7.068e-63
Identity = 112/172 (65.12%), Postives = 119/172 (69.19%), Query Frame = 3 
Query:  177 MEYAMYVGAPIMEIITMALQGARDPNETNRPDCSVNDLRISFVSYLPLTFSAILIIIFAFVTKRVSFKVNSCYGRPGLAVPMEMINSNENRYAYVMAFLSFSEDIYRAIFVNGTDNMQEPILKSLIKLGYVIVFSVTYYPIFAGICAKHLIGYCMGLIFAAVLLCCNLELVD 692
            MEYAMYVGAPIMEIITMALQGARDPNETNRPDCSVNDLRISFVSYLPLTFSAILIIIFAFVTKRVSFKVNSCYGRPGLAVPM+MINSNENR           + I+R +  N   N++                             K      MGLIFAAVLLCCNLELV+
Sbjct:    1 MEYAMYVGAPIMEIITMALQGARDPNETNRPDCSVNDLRISFVSYLPLTFSAILIIIFAFVTKRVSFKVNSCYGRPGLAVPMDMINSNENR---------ICDCIFRNVLSNICGNLR-----------------------------KAFDWLLMGLIFAAVLLCCNLELVN 134
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BLAST of SMED30023067 vs. Planmine SMEST
Match: SMESG000031041.1 (SMESG000031041.1)

HSP 1 Score: 115.931 bits (289), Expect = 1.752e-29
Identity = 57/108 (52.78%), Postives = 81/108 (75.00%), Query Frame = 3 
Query:  351 AFVTKRVSFKVNSCYGRPGLAVPMEMINSNENRYAYVMAFLSFSEDIYRAIFVNGTDNMQE--PILKSLIKLGYVIVFSVTYYPIFAGICAKHLIGYCMGLIFAAVLL 668
            AFVTKRVSF V++C GRPGLA+PM+MI+SN+N Y Y++AFLS SE+IY+  F+NG+D  ++   I + L K+ +VI+ S+  YP+FA +C KHL+GY +GL  +   L
Sbjct:   61 AFVTKRVSFNVHACGGRPGLAIPMDMISSNDNIYEYIVAFLSLSENIYQ--FINGSDKFEQFSLIERLLWKIFFVILSSLFSYPLFASLCCKHLVGYTVGLCHSVAFL 166
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BLAST of SMED30023067 vs. Planmine SMEST
Match: SMESG000031046.1 (SMESG000031046.1)

HSP 1 Score: 111.309 bits (277), Expect = 6.000e-28
Identity = 59/112 (52.68%), Postives = 79/112 (70.54%), Query Frame = 3 
Query:  339 IIIFAFVTKRVSFKVNSCYGRPGLAVPMEMINSNENRYAYVMAFLSFSEDIYRAIFVN--GTDNMQEPILKSLIKLGYVIVFSVTYYPIFAGICAKHLIGYCMGLIFAAVLL 668
            I+I  F TKR+SFK+N+C GRPGLA+PM+M+ +NE+   YV+ FLS SEDIY+AIF +   T  M  PI K L+KL  +I +S+  YPIF GI AK L  Y +G I+A +L+
Sbjct:   57 ILILMFNTKRLSFKINTCKGRPGLAIPMDMLKNNEHIIEYVVGFLSLSEDIYQAIFESKYWTPTML-PIEKFLLKLTIIIYYSILSYPIFTGIYAKRLTEYAIGFIYAVLLM 167
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BLAST of SMED30023067 vs. Planmine SMEST
Match: SMESG000041900.1 (SMESG000041900.1)

HSP 1 Score: 94.3597 bits (233), Expect = 4.565e-22
Identity = 55/134 (41.04%), Postives = 82/134 (61.19%), Query Frame = 3 
Query:  264 RPDCSVNDLRISFVSYLPLTFSAILIIIFAFVTKRVSFKVNSCYGRPGLAVPMEMINSNENRYAYVMAFLSFSEDIYRAIFVNGTDNMQE-PILKSLIKLGYVIVFSVTYYPIFAGICAKHLIGYCMGLIFAAV 662
            + +CS +     +  Y    +  I IIIF+ + KRVS+K + C G+PGL +PM M+NS+     Y + FLS SE+IY  IF +  +  +  P++K  IKL  VI+FS+  YPIFA I ++HL GY + ++ AAV
Sbjct:   51 KLNCSRSSPATEYAEYAIGIYYVICIIIFSTMVKRVSYKRDHCNGKPGLVLPMNMLNSHNYILEYTLVFLSLSEEIYAYIFGSKVEVSKLIPVVKFFIKLFIVIMFSILSYPIFAAITSRHLFGY-VTVMLAAV 183
The following BLAST results are available for this feature:
BLAST of SMED30023067 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 SMED30023067 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 SMED30023067 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 SMED30023067 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 SMED30023067 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 SMED30023067 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 SMED30023067 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 SMED30023067 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A2C9L9N43.986e-627.50Uncharacterized protein OS=Biomphalaria glabrata O... [more]
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BLAST of SMED30023067 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 SMED30023067 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 SMED30023067 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 SMED30023067 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO309502.622e-627.71Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30023067 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 SMED30023067 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000041908.14.288e-7094.92SMESG000041908.1[more]
SMESG000031048.17.068e-6365.12SMESG000031048.1[more]
SMESG000031041.11.752e-2952.78SMESG000031041.1[more]
SMESG000031046.16.000e-2852.68SMESG000031046.1[more]
SMESG000041900.14.565e-2241.04SMESG000041900.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023067 ID=SMED30023067|Name=SMED30023067|organism=Schmidtea mediterranea sexual|type=transcript|length=694bp
GTTTTCCAAATATTGAACGGAAAGGTTTGGCCATATCTCCCATAGACTCA
TTTCACATTTATTAACAATATATAACAGAACTTTGAAACAAATACATTTC
TTTTATGAAAATTGGGGAGAGATTTCTATTTTCCATTACGCTCTCGACTC
TTGCCATTCTATAATTAAGACTCTTGATGGAGTATGCAATGTATGTCGGT
GCACCAATTATGGAAATAATTACGATGGCACTACAAGGAGCAAGAGATCC
AAACGAGACTAATCGACCCGACTGTTCTGTCAACGATTTACGGATTTCAT
TTGTATCCTATTTGCCGTTGACATTTTCTGCGATACTTATAATCATTTTT
GCTTTTGTTACAAAACGGGTATCATTCAAGGTCAACTCATGCTATGGTCG
ACCGGGATTGGCGGTACCGATGGAAATGATAAACAGCAATGAAAACCGGT
ACGCATATGTTATGGCTTTTCTGTCGTTTTCCGAAGATATATACAGAGCA
ATATTTGTAAATGGAACTGACAATATGCAAGAACCGATTTTGAAATCTTT
AATTAAATTAGGATATGTGATTGTATTTTCCGTAACGTATTATCCAATAT
TTGCGGGAATTTGCGCAAAGCATTTGATTGGCTACTGCATGGGACTGATA
TTTGCCGCTGTGCTGTTGTGCTGTAATTTGGAATTGGTAGATCG
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protein sequence of SMED30023067-orf-1

>SMED30023067-orf-1 ID=SMED30023067-orf-1|Name=SMED30023067-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=172bp
MEYAMYVGAPIMEIITMALQGARDPNETNRPDCSVNDLRISFVSYLPLTF
SAILIIIFAFVTKRVSFKVNSCYGRPGLAVPMEMINSNENRYAYVMAFLS
FSEDIYRAIFVNGTDNMQEPILKSLIKLGYVIVFSVTYYPIFAGICAKHL
IGYCMGLIFAAVLLCCNLELVD
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000419prepharyngeal region