SMED30031754

Overview
NameSMED30031754
Smed IDSMED30031754
Length (bp)506
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 SMED30031754 (SMED30031754) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031754 (SMED30031754) 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




SMED30031754

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30031754 dd_Smed_v4_14636_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30031754 dd_Smed_v4_14636_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30031754 dd_Smed_v4_14636_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30031754 dd_Smed_v6_14636_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
SMED30031754 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000807:54987..55491 +2486
Homology
BLAST of SMED30031754 vs. TrEMBL
Match: A0A1S3IS64 (transmembrane protein 216 isoform X2 OS=Lingula unguis OX=7574 GN=LOC106166380 PE=4 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 1.522e-13
Identity = 50/131 (38.17%), Postives = 80/131 (61.07%), Query Frame = -3
Query:   46 RGRFS--KSFMSYHMLLNLNKLILGFYYVTEIFCFIYKAEYLIYKFGIVCGELVLLFVIMIFDIIRIYLGQCGNLAELPVYXXXXXXXXXXXXXXXXXXXLWQTYVLYVEFIIGLIAVFFQFLSVIFGIVA 432
            RG+    +S + Y +LL  N    GF+++ EI  +I+K E L Y  G++  E+VLLF +   + +RI+ GQ GNL E  + ++   ++S+  + G LY +LWQTYVL VE I+  I + F  L ++FGI++
Sbjct:    8 RGKVQVIRSSLPYQILLYCNAWYFGFFWIAEILIYIFKGETLPYPNGVLAAEVVLLFFLGGLESLRIFFGQKGNLTERMLTVVLCIVLSLPTLAGILYILLWQTYVLRVEVILSAIELVFIALELLFGIIS 138          
BLAST of SMED30031754 vs. TrEMBL
Match: A0A1S3IQM8 (transmembrane protein 216 isoform X1 OS=Lingula unguis OX=7574 GN=LOC106166380 PE=4 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 1.533e-13
Identity = 50/131 (38.17%), Postives = 80/131 (61.07%), Query Frame = -3
Query:   46 RGRFS--KSFMSYHMLLNLNKLILGFYYVTEIFCFIYKAEYLIYKFGIVCGELVLLFVIMIFDIIRIYLGQCGNLAELPVYXXXXXXXXXXXXXXXXXXXLWQTYVLYVEFIIGLIAVFFQFLSVIFGIVA 432
            RG+    +S + Y +LL  N    GF+++ EI  +I+K E L Y  G++  E+VLLF +   + +RI+ GQ GNL E  + ++   ++S+  + G LY +LWQTYVL VE I+  I + F  L ++FGI++
Sbjct:    8 RGKVQVIRSSLPYQILLYCNAWYFGFFWIAEILIYIFKGETLPYPNGVLAAEVVLLFFLGGLESLRIFFGQKGNLTERMLTVVLCIVLSLPTLAGILYILLWQTYVLRVEVILSAIELVFIALELLFGIIS 138          
BLAST of SMED30031754 vs. TrEMBL
Match: A0A210Q8E8 (Transmembrane protein 216 OS=Mizuhopecten yessoensis OX=6573 GN=KP79_PYT07816 PE=4 SV=1)

HSP 1 Score: 72.7886 bits (177), Expect = 3.820e-13
Identity = 53/131 (40.46%), Postives = 80/131 (61.07%), Query Frame = -3
Query:   46 RGRFS--KSFMSYHMLLNLNKLILGFYYVTEIFCFIYKAEYLIYKFGIVCGELVLLFVIMIFDIIRIYLGQCGNLAELPVYXXXXXXXXXXXXXXXXXXXLWQTYVLYVEFIIGLIAVFFQFLSVIFGIVA 432
            +GR    +S + Y +LL LN    GF++V EI  FI+K E L Y   ++  E++LLFV+   + +RI+  Q GNL E  V ++ S ++S+  ILG L+ +LWQTYVL V+ I+  I + F  L +I  IV+
Sbjct:   11 KGRVQVIRSSLPYQVLLYLNGWYFGFFFVCEILIFIFKGETLPYADNVLLAEVILLFVLAAIEAMRIFFAQKGNLTERIVGVVVSIMLSVPAILGALFLLLWQTYVLKVDVILAAIQLAFTGLELIMAIVS 141          
BLAST of SMED30031754 vs. TrEMBL
Match: V3Z4X5 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_204590 PE=4 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 3.584e-12
Identity = 48/131 (36.64%), Postives = 82/131 (62.60%), Query Frame = -3
Query:   46 RGRFS--KSFMSYHMLLNLNKLILGFYYVTEIFCFIYKAEYLIYKFGIVCGELVLLFVIMIFDIIRIYLGQCGNLAELPVYXXXXXXXXXXXXXXXXXXXLWQTYVLYVEFIIGLIAVFFQFLSVIFGIVA 432
            RGR    +S + Y +LL LN    GF+ + E+  FI+KAE L +    +  E++L+F++   + +R++ G+ GNL E  V +I S ++SI  ILG ++ +LWQTYVL ++ I+  I + F  L ++FG+++
Sbjct:    6 RGRLQVVRSSLPYQILLYLNGWYFGFFLLAEVLIFIFKAETLPFASNTLAAEVILVFLLAALEGLRLFFGRKGNLTEQTVGVIISVLLSIPAILGAIFILLWQTYVLRLDVILAAIQLAFIALELVFGVIS 136          
BLAST of SMED30031754 vs. TrEMBL
Match: A0A2C9K5I2 (Uncharacterized protein OS=Biomphalaria glabrata OX=6526 GN=106052147 PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 1.130e-11
Identity = 47/118 (39.83%), Postives = 74/118 (62.71%), Query Frame = -3
Query:   79 RGRFSKSFMSYHMLLNLNKLILGFYYVTEIFCFIYKAEYLIYKFGIVCGELVLLFVIMIFDIIRIYLGQCGNLAELPVYXXXXXXXXXXXXXXXXXXXLWQTYVLYVEFIIGLIAVFF 432
            R +F +S + Y +LL LN     F++V EI  F++K E L Y   ++  E++LLF++ I + +R++ G+ GNL E  + ++    +SI  I G L+F+LWQTYVL VE I+  I +FF
Sbjct:   18 RTQFIRSSLPYQILLYLNGWYFAFFFVCEILLFVFKGETLPYATNVLAAEVILLFLLAIVEALRLFFGKRGNLTEQIMGVLVCVFLSIATIFGVLFFLLWQTYVLRVEIILTAIQLFF 135          
The following BLAST results are available for this feature:
BLAST of SMED30031754 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 SMED30031754 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 SMED30031754 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 SMED30031754 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 SMED30031754 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 SMED30031754 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 SMED30031754 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 SMED30031754 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1S3IS641.522e-1338.17transmembrane protein 216 isoform X2 OS=Lingula un... [more]
A0A1S3IQM81.533e-1338.17transmembrane protein 216 isoform X1 OS=Lingula un... [more]
A0A210Q8E83.820e-1340.46Transmembrane protein 216 OS=Mizuhopecten yessoens... [more]
V3Z4X53.584e-1236.64Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
A0A2C9K5I21.130e-1139.83Uncharacterized protein OS=Biomphalaria glabrata O... [more]
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BLAST of SMED30031754 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 SMED30031754 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 SMED30031754 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 SMED30031754 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 SMED30031754 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 SMED30031754 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031754 ID=SMED30031754|Name=SMED30031754|organism=Schmidtea mediterranea sexual|type=transcript|length=506bp
AAAAATTAAAATTATTTATTTAAAAAATTAGTTAATCATTATAATAGCGA
CAATCCCAAAAATTACAGATAAAAATTGAAAAAATACCGCAATCAAACCG
ATAATAAATTCCACATACAAGACATAAGTTTGCCAAAGTATAAAATATAA
GTACCCCAAAATTAGAATTATACTCATAATAAACGAAGCAATTATGTATA
CTGGTAACTCTGCTAGATTACCACATTGTCCCAAATATATTCTGATAATA
TCGAAAATCATTATTACAAATAGCAGCACTAATTCTCCACACACTATGCC
AAACTTATAAATTAAATATTCTGCTTTGTATATGAAGCAAAATATTTCTG
TCACATAATAAAATCCAAGTATCAGTTTATTCAAATTTAATAACATGTGA
TAAGACATAAAAGATTTTGAAAATCTTCCTCGAAGTACAAATTTCGAAGA
TTCCATTTTCAGTTTTAAAAAATATATCTAATAGAATTTAACTTAGTAAC
TCAATA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR019184Uncharacterised_TM-17
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR019184Uncharacterised protein family, transmembrane-17PFAMPF09799Transmemb_17coord: 21..127
e-value: 4.1E-20
score: 72.4
IPR019184Uncharacterised protein family, transmembrane-17PANTHERPTHR13531FAMILY NOT NAMEDcoord: 13..140
NoneNo IPR availableTMHMMTMhelixcoord: 86..108
NoneNo IPR availableTMHMMTMhelixcoord: 49..71
NoneNo IPR availableTMHMMTMhelixcoord: 20..42
NoneNo IPR availableTMHMMTMhelixcoord: 117..139