SMED30027331

Overview
NameSMED30027331
Smed IDSMED30027331
Length (bp)376
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 SMED30027331 (SMED30027331) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027331 (SMED30027331) 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 SMED30027331 (SMED30027331) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30027331 (SMED30027331) 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



SMED30027331

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
ciliated epithelial cellSMED30027331 dd_Smed_v4_15054_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30027331 vs. TrEMBL
Match: A0A026WH11 (General transcription factor II-I repeat domain-containing protein OS=Ooceraea biroi OX=2015173 GN=X777_04805 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 8.927e-8
Identity = 27/44 (61.36%), Postives = 34/44 (77.27%), Query Frame = -1 
Query:  248 IINF*NSLPNEHFPELKNYAKN-TYRFGTTYRREQVFSSMKLIK 376
            +INF  SLP EHFPEL+ +++    RFGTTYR EQ FS+MK+IK
Sbjct:  110 VINFWRSLPCEHFPELRKFSQRYICRFGTTYRCEQAFSAMKMIK 153
[Close]
BLAST of SMED30027331 vs. TrEMBL
Match: H2YR08 (Uncharacterized protein OS=Ciona savignyi OX=51511 PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 1.141e-6
Identity = 29/59 (49.15%), Postives = 40/59 (67.80%), Query Frame = -1 
Query:  203 IINF*NSLPNEHFPELKNYA-KNTYRFGTTYRREQVFSSMKLIKIKTRSRITDINLKNS 376
            ++ F   LP E FP++K+ A K    FG+TY  EQ+F+ MK  K KTRSR+TD +L+NS
Sbjct:  214 LLEFYKRLPEESFPKIKDLARKKMSLFGSTYICEQLFTKMKHTKSKTRSRLTDCHLENS 272
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BLAST of SMED30027331 vs. TrEMBL
Match: A0A4C1UJF2 (General transcription factor II-I repeat domain-containing protein 2 OS=Eumeta variegata OX=151549 GN=GTF2IRD2 PE=4 SV=1)

HSP 1 Score: 55.4546 bits (132), Expect = 1.480e-6
Identity = 27/54 (50.00%), Postives = 36/54 (66.67%), Query Frame = -1 
Query:  194 LPNEHFPELKNYAKNTYRFGTTYRREQVFSSMKLIKIKTRSRITDINLKNSATF 355
            L  +HFP+L+ +A+    FG TY+ EQ FS MK+ K K R+R+TD NLKN   F
Sbjct:  163 LDEDHFPQLRKFARLICAFGGTYKCEQFFSMMKVNKSKHRTRLTDGNLKNFYVF 216
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BLAST of SMED30027331 vs. TrEMBL
Match: A0A423TNC6 (Putative general transcription factor II-I repeat domain-containing protein 2-like OS=Penaeus vannamei OX=6689 GN=C7M84_003335 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 4.468e-6
Identity = 29/65 (44.62%), Postives = 42/65 (64.62%), Query Frame = -1 
Query:  185 IINF*NSLPNEHFPELKNYA-KNTYRFGTTYRREQVFSSMKLIKIKTRSRITDINLKNSATFSDK 376
            +I+F  +LPN+ +P ++ +A K +  FG+TY  EQ FS MKL+K   RSR+TD +L    T S K
Sbjct:  294 LIDFYAALPNDTYPNIRKHAMKMSTLFGSTYICEQTFSRMKLLKTPMRSRLTDEHLHQCLTGSAK 358
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BLAST of SMED30027331 vs. TrEMBL
Match: A0A087YQJ4 (Uncharacterized protein OS=Poecilia formosa OX=48698 PE=4 SV=2)

HSP 1 Score: 53.1434 bits (126), Expect = 8.510e-6
Identity = 27/56 (48.21%), Postives = 40/56 (71.43%), Query Frame = -1 
Query:  212 IINF*NSLPNEHFPELKNYA-KNTYRFGTTYRREQVFSSMKLIKIKTRSRITDINL 376
            +I+F  +LPN+ +P ++ +A K +  FG+TY  EQ FS MKL+K  TRSR+TD +L
Sbjct:  125 LIDFYAALPNDTYPNIRKHAMKMSTLFGSTYICEQTFSRMKLLKSPTRSRLTDEHL 180
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BLAST of SMED30027331 vs. Ensembl Cavefish
Match: ENSAMXT00000037411.1 (pep primary_assembly:Astyanax_mexicanus-2.0:13:18144228:18145385:-1 gene:ENSAMXG00000033115.1 transcript:ENSAMXT00000037411.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 53.9138 bits (128), Expect = 3.358e-9
Identity = 27/56 (48.21%), Postives = 39/56 (69.64%), Query Frame = -1 
Query:  212 IINF*NSLPNEHFPELKNYA-KNTYRFGTTYRREQVFSSMKLIKIKTRSRITDINL 376
            +I+F  +LPN+ +P +K +A K +  FG+TY  EQ FS MKL+K   RSR+TD +L
Sbjct:  302 LIDFYAALPNDTYPNIKKHAMKMSTLFGSTYICEQTFSHMKLLKTPMRSRLTDEHL 357
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BLAST of SMED30027331 vs. Ensembl Cavefish
Match: ENSAMXT00000044284.1 (pep primary_assembly:Astyanax_mexicanus-2.0:14:30442742:30446828:1 gene:ENSAMXG00000031237.1 transcript:ENSAMXT00000044284.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 47.3654 bits (111), Expect = 4.575e-7
Identity = 25/49 (51.02%), Postives = 33/49 (67.35%), Query Frame = -1 
Query:  233 IINF*NSLPNEHFPELKNYA-KNTYRFGTTYRREQVFSSMKLIKIKTRS 376
            +++F  SLP E +P LK +A K T  FG+TY  EQ FS MK +K +TRS
Sbjct:  134 LVDFYASLPGETYPNLKKHALKMTTIFGSTYICEQTFSRMKQLKCRTRS 182
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BLAST of SMED30027331 vs. Ensembl Cavefish
Match: ENSAMXT00000050833.1 (pep primary_assembly:Astyanax_mexicanus-2.0:APWO02000549.1:45261:46892:1 gene:ENSAMXG00000036460.1 transcript:ENSAMXT00000050833.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 45.4394 bits (106), Expect = 2.187e-6
Identity = 27/57 (47.37%), Postives = 34/57 (59.65%), Query Frame = -1 
Query:  209 IINF*NSLPNEHFPEL-KNYAKNTYRFGTTYRREQVFSSMKLIKIKTRSRITDINLK 376
            ++ F  SL  E FP L  N  K    FG+TY  EQ+FS MKL K   R+R+TD NL+
Sbjct:  127 LLEFYQSLDREQFPNLFANAQKWISMFGSTYICEQMFSLMKLNKSPLRTRLTDENLQ 183
[Close]
BLAST of SMED30027331 vs. Ensembl Cavefish
Match: ENSAMXT00000048309.1 (pep primary_assembly:Astyanax_mexicanus-2.0:APWO02000491.1:94927:99076:1 gene:ENSAMXG00000033081.1 transcript:ENSAMXT00000048309.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 45.8246 bits (107), Expect = 2.618e-6
Identity = 32/83 (38.55%), Postives = 46/83 (55.42%), Query Frame = -1 
Query:  131 INF*NSLPNEHFPELKNYAKN-TYRFGTTYRREQVFSSMKLIKIKTRSRITDINLKNSATF-SDKFNNKHQNTS*IQANPKVS 373
            I+F   LP   FP L+++A +    FG+TY  E  FS+MK IK K R+R+TD  L +     + K N   Q+    QA P++S
Sbjct:  471 ISFWRLLPEARFPRLRDFALSMASMFGSTYIYESSFSTMKHIKSKERNRLTDDTLFHLMRIGTTKINIDIQSMVSQQAKPQLS 553
[Close]
BLAST of SMED30027331 vs. Ensembl Cavefish
Match: ENSAMXT00000036928.1 (pep primary_assembly:Astyanax_mexicanus-2.0:7:19677316:19680173:1 gene:ENSAMXG00000037520.1 transcript:ENSAMXT00000036928.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 45.4394 bits (106), Expect = 3.147e-6
Identity = 27/57 (47.37%), Postives = 34/57 (59.65%), Query Frame = -1 
Query:  209 IINF*NSLPNEHFPEL-KNYAKNTYRFGTTYRREQVFSSMKLIKIKTRSRITDINLK 376
            ++ F  SL  E FP L  N  K    FG+TY  EQ+FS MKL K   R+R+TD NL+
Sbjct:  430 LLEFYQSLDREQFPNLFANAQKWISMFGSTYICEQMFSLMKLNKSPLRTRLTDENLQ 486
[Close]
BLAST of SMED30027331 vs. Ensembl Medaka
Match: ENSORLT00000027093.1 (general transcription factor II-I repeat domain-containing protein 2B-like [Source:NCBI gene;Acc:111947639])

HSP 1 Score: 46.2098 bits (108), Expect = 1.616e-6
Identity = 25/56 (44.64%), Postives = 36/56 (64.29%), Query Frame = -1 
Query:  212 IINF*NSLPNEHFPELKNYAKNTY-RFGTTYRREQVFSSMKLIKIKTRSRITDINL 376
            +++F +SL  E+FP L+ +A+     FG+TY  EQ FS MK  K K RS +TD +L
Sbjct:  499 LLDFYSSLKKENFPHLRRHAQKILVLFGSTYHCEQAFSVMKFNKSKHRSSVTDDHL 554
The following BLAST results are available for this feature:
BLAST of SMED30027331 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 SMED30027331 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 SMED30027331 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 SMED30027331 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 SMED30027331 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 SMED30027331 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 SMED30027331 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 SMED30027331 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A026WH118.927e-861.36General transcription factor II-I repeat domain-co... [more]
H2YR081.141e-649.15Uncharacterized protein OS=Ciona savignyi OX=51511... [more]
A0A4C1UJF21.480e-650.00General transcription factor II-I repeat domain-co... [more]
A0A423TNC64.468e-644.62Putative general transcription factor II-I repeat ... [more]
A0A087YQJ48.510e-648.21Uncharacterized protein OS=Poecilia formosa OX=486... [more]
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BLAST of SMED30027331 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 5
Match NameE-valueIdentityDescription
ENSAMXT00000037411.13.358e-948.21pep primary_assembly:Astyanax_mexicanus-2.0:13:181... [more]
ENSAMXT00000044284.14.575e-751.02pep primary_assembly:Astyanax_mexicanus-2.0:14:304... [more]
ENSAMXT00000050833.12.187e-647.37pep primary_assembly:Astyanax_mexicanus-2.0:APWO02... [more]
ENSAMXT00000048309.12.618e-638.55pep primary_assembly:Astyanax_mexicanus-2.0:APWO02... [more]
ENSAMXT00000036928.13.147e-647.37pep primary_assembly:Astyanax_mexicanus-2.0:7:1967... [more]
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BLAST of SMED30027331 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 SMED30027331 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 SMED30027331 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 SMED30027331 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSORLT00000027093.11.616e-644.64general transcription factor II-I repeat domain-co... [more]
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BLAST of SMED30027331 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

>SMED30027331 ID=SMED30027331|Name=SMED30027331|organism=Schmidtea mediterranea sexual|type=transcript|length=376bp
GTTATTTATAACTTTTAGATAATTTAAGGTCAGTAAAATTATTTTGATTA
AAAATTTAGATAAAAATGATGACGAAGCTGAAAAATATGAAAACAATTTG
ATAACAGCACGAAAACATTACTATGTTTATTGAAACTTTTGGGTTGGCTT
GGATTTAGCTAGTATTTTGATGTTTATTGTTGAATTTGTCACTGAAAGTA
GCAGAATTTTTCAAATTTATATCAGTTATTCGTGATCTTGTTTTGATTTT
AATCAATTTCATAGACGAAAATACTTGTTCACGTCTGTATGTCGTTCCAA
AGCGATATGTATTTTTTGCATAATTTTTTAGCTCGGGGAAATGTTCATTT
GGTAATGAATTCTAGAAATTAATTAT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000106ciliated epithelial cell