SMED30008391
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Overview
Neoblast Clusters
Zeng et. al., 2018▻ Overview▻ Neoblast Population
Overview
Single cell RNA-seq of pluripotent neoblasts and its early progeniesWe 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
Embryonic Expression
Davies et. al., 2017
Hover the mouse over a column in the graph to view average RPKM values per sample. Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult. back to top Anatomical Expression
PAGE et. al., 2020SMED30008391 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30008391 aligns in the following genomic locations: Homology
BLAST of SMED30008391 vs. Planmine SMEST
Match: SMESG000034853.1 (SMESG000034853.1) HSP 1 Score: 190.66 bits (483), Expect = 9.162e-62 Identity = 92/130 (70.77%), Postives = 107/130 (82.31%), Query Frame = -2
Query: 59 THVNLRFYSVQSGSHVYITTHVADQWRQAWRRTNQERYPDMPQPGENRREDTLLVELTMRQFKKEGRSSDPSPAQDIHIRARALLNHLLDHRRPVDSAVDWARDYLANVEDDLAAGLLADTYPPSPRPAR 448
HVNL F S QSGSHVYI THVADQWRQAWRR N+ERYPDMP+ GE RR+D +V+ TM+QF+ +GRSSDPSPAQDIH+RARA L HL +H+R V+S VD A +YLA+VED+LAAG LAD YPP RPAR
Sbjct: 10 IHVNLLFCSEQSGSHVYIPTHVADQWRQAWRRINRERYPDMPRSGERRRDDIRMVQNTMKQFRPQGRSSDPSPAQDIHVRARAFLAHLKEHQRRVNSLVDRASEYLASVEDELAAGRLADAYPPPQRPAR 139
BLAST of SMED30008391 vs. Planmine SMEST
Match: SMESG000044373.1 (SMESG000044373.1) HSP 1 Score: 180.644 bits (457), Expect = 7.334e-58 Identity = 90/141 (63.83%), Postives = 110/141 (78.01%), Query Frame = -2
Query: 8 SVQSGSHVYITTHVADQWRQAWRRTNQERYPDMPQPGENRREDTLLVELTMRQFKKEGRSSDPSPAQDIHIRARALLNHLLDHRRPVDSAVDWARDYLANVEDDLAAGLLADTYPPSPRPARVSD--FKLLPGGGDKEIFR 424
S +SG +Y+ TH+ADQWRQAWRR +ERYPD+P+PGENRR+D LLVE TMRQFK+ + SDPSPAQ+IH RARALL +L DH+R V+S VDWA +YLANVEDDLAAG +AD YPPSPR AR + ++PG +E R
Sbjct: 18 SRKSGPFIYVHTHLADQWRQAWRRFGRERYPDVPEPGENRRDDMLLVEDTMRQFKQSSQPSDPSPAQEIHDRARALLAYLKDHQRRVNSLVDWASNYLANVEDDLAAGRIADVYPPSPRSARNTKRPLFMIPGYSAEERVR 158
BLAST of SMED30008391 vs. Planmine SMEST
Match: SMESG000049884.1 (SMESG000049884.1) HSP 1 Score: 165.622 bits (418), Expect = 5.719e-52 Identity = 80/120 (66.67%), Postives = 94/120 (78.33%), Query Frame = -2
Query: 59 QSGSHVYITTHVADQWRQAWRRTNQERYPDMPQPGENRREDTLLVELTMRQFKKEGRSSDPSPAQDIHIRARALLNHLLDHRRPVDSAVDWARDYLANVEDDLAAGLLADTYPPSPRPAR 418
QSG +++ T VADQWRQ WRRT +ERYPD+ QPGENR EDTL + TM QF+K+ + SDPSPA DIH+RA+ALL HL +H+R V+S VD A YLANVEDDLA G LAD YPPSPR AR
Sbjct: 23 QSGPFIFVPTSVADQWRQVWRRTCKERYPDVNQPGENRLEDTLFIANTMEQFRKKRQPSDPSPANDIHVRAQALLAHLKEHQRRVNSLVDRASSYLANVEDDLACGRLADVYPPSPRLAR 142
BLAST of SMED30008391 vs. Planmine SMEST
Match: SMESG000025123.1 (SMESG000025123.1) HSP 1 Score: 163.31 bits (412), Expect = 4.722e-51 Identity = 78/120 (65.00%), Postives = 94/120 (78.33%), Query Frame = -2
Query: 59 QSGSHVYITTHVADQWRQAWRRTNQERYPDMPQPGENRREDTLLVELTMRQFKKEGRSSDPSPAQDIHIRARALLNHLLDHRRPVDSAVDWARDYLANVEDDLAAGLLADTYPPSPRPAR 418
+SG ++I T VADQWRQ W+RT +ERYPD+ QPGENR EDTL + TM QF+K+ + SDPSPA DIH+RA+AL HL +H+R V+S VD A YLANVEDDLA G L+D YPPSPRPAR
Sbjct: 23 RSGPFIFIPTPVADQWRQVWKRTCKERYPDVTQPGENRWEDTLFIANTMEQFRKKRQPSDPSPAHDIHVRAQALRTHLKEHQRQVNSLVDRASSYLANVEDDLACGRLSDVYPPSPRPAR 142
BLAST of SMED30008391 vs. Planmine SMEST
Match: SMESG000020463.1 (SMESG000020463.1) HSP 1 Score: 162.155 bits (409), Expect = 2.305e-50 Identity = 82/138 (59.42%), Postives = 103/138 (74.64%), Query Frame = -2
Query: 17 SVQSGSHVYITTHVADQWRQAWRRTNQERYPDMPQPGENRREDTLLVELTMRQFKKEGRSSDPSPAQDIHIRARALLNHLLDHRRPVDSAVDWARDYLANVEDDLAAGLLADTYPPSPRPARVSD--FKLLPGGGDKE 424
S +SG I+ AD+WR+AWRR N+ERYPD+PQPGENR ED LL+E TM+QF+K+G+ SDPSPAQDI +RA+ALL HL +H+R V+S VD A YLANVEDDLA G LAD YP +PRP R + ++PG +E
Sbjct: 33 SDRSGPFFRISVSEADKWRRAWRRANEERYPDVPQPGENRWEDMLLIESTMQQFRKDGQPSDPSPAQDILVRAQALLTHLKEHQRRVNSLVDRASSYLANVEDDLACGRLADVYPSNPRPTRNTKRPVFIVPGYSPEE 170 The following BLAST results are available for this feature:
BLAST of SMED30008391 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30008391 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30008391 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30008391 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30008391 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30008391 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30008391 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30008391 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30008391 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30008391 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30008391 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30008391 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30008391 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30008391 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 5
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30008391 ID=SMED30008391|Name=SMED30008391|organism=Schmidtea mediterranea sexual|type=transcript|length=653bpback to top protein sequence of SMED30008391-orf-1 >SMED30008391-orf-1 ID=SMED30008391-orf-1|Name=SMED30008391-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp MPQPGENRREDTLLVELTMRQFKKEGRSSDPSPAQDIHIRARALLNHLLDback to top Annotated Terms
The following terms have been associated with this transcript:
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