SMED30013899
Overview
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 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
Sub-lethal Irradiated Surviving X1 and X2 Cell 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., 2020SMED30013899 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 7
Alignments
SMED30013899 aligns in the following genomic locations:
Homology
BLAST of SMED30013899 vs. TrEMBL
Match: A0A177B6C2 (DNA-directed RNA polymerase subunit OS=Intoshia linei OX=1819745 GN=A3Q56_02397 PE=3 SV=1) HSP 1 Score: 59.6918 bits (143), Expect = 3.461e-7 Identity = 36/98 (36.73%), Postives = 42/98 (42.86%), Query Frame = 3 Query: 87 NLSCYECSADNSYLNNPSALPNTNNCIYGVSLNRRRCFPQHNGCFITWIYTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTLACNNGTFLN 380 +L CYEC+ D + + P NN Y N R+C N C I N I RGC C GC L GY I C CCQ CN G+ N Sbjct: 31 DLWCYECTGDYVKKYDFNQSPCRNNVTY---FNIRQCSTNDNYCKIEKHQLYNYIMYIDRGCVEKCGYGCRLNGYGIPLKRCKYCCQWSGCNFGSGSN 125
BLAST of SMED30013899 vs. TrEMBL
Match: R7UTY5 (Uncharacterized protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_193274 PE=4 SV=1) HSP 1 Score: 55.8398 bits (133), Expect = 1.262e-6 Identity = 38/104 (36.54%), Postives = 49/104 (47.12%), Query Frame = 3 Query: 87 NLSCYECSADNSYLNNPSALPNTNNCIYGVSLNRRRCFPQHNGCFITWI--YTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTLACNNGTFLNGNII 392 +L CYECS S +P+ P NN + GV R+C C + + Y + SIARGC C GC G I C++CC TLACN + N I Sbjct: 36 DLWCYECSESYSRTYDPADSPCRNN-LTGVIT--RQCAKSEIYCRVERLDLYRFDTMLSIARGCTNKCEYGCRFNGLAITYRRCSSCCTTLACNTDSRTNDRSI 136
BLAST of SMED30013899 vs. TrEMBL
Match: A0A1S3K4L9 (uncharacterized protein LOC106178789 OS=Lingula unguis OX=7574 GN=LOC106178789 PE=4 SV=1) HSP 1 Score: 53.9138 bits (128), Expect = 6.030e-6 Identity = 36/116 (31.03%), Postives = 54/116 (46.55%), Query Frame = 3 Query: 45 IFSIVFSQRNNRTTNLSCYECSADNSYLNNPSALPNTNNCIYGVS-LNRRRCFPQHNGCFITWIYTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTLACNNGTFLNGNI 389 + S+V + + NLSCYECS ++ +N + C + ++ R C + C + Q +I RGC C GC TG+ I TCT+CCQ CN G G++ Sbjct: 23 VISMVVTGMGTFSYNLSCYECS--EAFTDNLKSYEPFTPCQTNLEEVDVRPCGSRDLYCKVERKSFKGQTVTIERGCTQRCLHGCKFTGWGITLMTCTSCCQEHVCNTGNRAPGSL 136
BLAST of SMED30013899 vs. Planmine SMEST
Match: SMESG000020109.1 (SMESG000020109.1) HSP 1 Score: 295.819 bits (756), Expect = 1.569e-104 Identity = 147/148 (99.32%), Postives = 147/148 (99.32%), Query Frame = 3 Query: 24 MIWLFWFIFSIVFSQRNNRTTNLSCYECSADNSYLNNPSALPNTNNCIYGVSLNRRRCFPQHNGCFITWIYTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTLACNNGTFLNGNIIIMPFTILNYFFSFSLTSFAMYFLHY 467 MIWLFWFIFSIVFSQRNNRTTNLSCYECSADNSYLNNPSALPNTNNCIYGVSLNRRRCFPQHNGCFITWIYTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTL CNNGTFLNGNIIIMPFTILNYFFSFSLTSFAMYFLHY Sbjct: 1 MIWLFWFIFSIVFSQRNNRTTNLSCYECSADNSYLNNPSALPNTNNCIYGVSLNRRRCFPQHNGCFITWIYTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTLGCNNGTFLNGNIIIMPFTILNYFFSFSLTSFAMYFLHY 148
BLAST of SMED30013899 vs. Planmine SMEST
Match: SMESG000020114.1 (SMESG000020114.1) HSP 1 Score: 73.559 bits (179), Expect = 2.328e-17 Identity = 39/99 (39.39%), Postives = 55/99 (55.56%), Query Frame = 3 Query: 96 CYECSADNSYLNNPSALPNTN-NCIYGVSLNRRRCFPQHNGCFITWIYTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTLACNNGTFLNGNI 389 C+ECSA + N + N N NC+ G++L+ R C +H C+ IY +Q +I RGC+T+C + C G+ IV CT CC CN+ T NG I Sbjct: 2 CFECSAKDLNSENDAMKRNENRNCLTGLNLSPRYCLRRHTHCYEKSIYIGSQIKTIERGCRTSCESSCFRKGFHIVTQMCTKCCVKSKCNHKTIGNGGI 100 The following BLAST results are available for this feature:
BLAST of SMED30013899 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30013899 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30013899 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30013899 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30013899 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30013899 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30013899 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30013899 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 3
BLAST of SMED30013899 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30013899 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30013899 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30013899 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30013899 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30013899 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 2
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30013899 ID=SMED30013899|Name=SMED30013899|organism=Schmidtea mediterranea sexual|type=transcript|length=489bpback to top Annotated Terms
The following terms have been associated with this transcript:
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
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