SMED30014578
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., 2020SMED30014578 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30014578 aligns in the following genomic locations:
Homology
BLAST of SMED30014578 vs. Planmine SMEST
Match: SMESG000033974.1 (SMESG000033974.1) HSP 1 Score: 161.77 bits (408), Expect = 3.325e-66 Identity = 106/160 (66.25%), Postives = 117/160 (73.12%), Query Frame = 1 Query: 457 VVLSN*VQRDVTNAVTIMPALPISNQKHKPXXXXXXXXXXXXXXXLLKENLSAVENANPIGISEATSYESTSMPANSDLEIIYGPPLVDFSQLAPTPSQFNIAIENLITDNPASVQITIFTRSSPIREEGHEISSRRSTLQIISVIESPQVRTSINSTAG 936 V LSN V+ D TN T+ P I N+KHKPNKNRR++EKRR ENALL+ NL +EN N I I E TSYES MPANSDLEII P L+DF Q AP P QFNI++ENL TDN + QI I RSSPIREE HE SS RST QIISV E PQVR SINSTAG Sbjct: 78 VNLSNCVEWDATNVFTLAPVPSIPNRKHKPNKNRRRKEKRRTENALLQVNLITIENPNVIKIPEVTSYESNEMPANSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAG 237 HSP 2 Score: 109.768 bits (273), Expect = 3.325e-66 Identity = 52/73 (71.23%), Postives = 61/73 (83.56%), Query Frame = 3 Query: 237 WCSPEATRELYKKIT*ISQTRDDLIVENKIQRITIADQSAALR*IFTEKKLQALLPDRSIAQLLDIIPAHHQP 455 WCSPEAT++LYKKIT +S+ RDDLIV+N+ QRITIADQ A LR IFTEK+LQA LPDRSI Q L++IP H P Sbjct: 5 WCSPEATKKLYKKITRVSRARDDLIVKNRSQRITIADQCATLRQIFTEKELQARLPDRSITQQLNMIPVQHLP 77
BLAST of SMED30014578 vs. Planmine SMEST
Match: SMESG000056168.1 (SMESG000056168.1) HSP 1 Score: 200.29 bits (508), Expect = 1.634e-58 Identity = 103/115 (89.57%), Postives = 106/115 (92.17%), Query Frame = 1 Query: 592 LLKENLSAVENANPIGISEATSYESTSMPANSDLEIIYGPPLVDFSQLAPTPSQFNIAIENLITDNPASVQITIFTRSSPIREEGHEISSRRSTLQIISVIESPQVRTSINSTAG 936 LLKENLSA+ENANPIGIS+ATSYESTSMPANSDLEIIYGP LVDFSQLAPT SQFNIAIENLITDNPASVQITIFTRSSPIREE HEISSRRSTLQIISVIESPQ R I+ G Sbjct: 41 LLKENLSAIENANPIGISKATSYESTSMPANSDLEIIYGPLLVDFSQLAPTSSQFNIAIENLITDNPASVQITIFTRSSPIREERHEISSRRSTLQIISVIESPQKREVISFYIG 155
BLAST of SMED30014578 vs. Planmine SMEST
Match: SMESG000056168.1 (SMESG000056168.1) HSP 1 Score: 200.675 bits (509), Expect = 2.708e-57 Identity = 103/115 (89.57%), Postives = 106/115 (92.17%), Query Frame = 1 Query: 592 LLKENLSAVENANPIGISEATSYESTSMPANSDLEIIYGPPLVDFSQLAPTPSQFNIAIENLITDNPASVQITIFTRSSPIREEGHEISSRRSTLQIISVIESPQVRTSINSTAG 936 LLKENLSA+ENANPIGIS+ATSYESTSMPANSDLEIIYGP LVDFSQLAPT SQFNIAIENLITDNPASVQITIFTRSSPIREE HEISSRRSTLQIISVIESPQ R I+ G Sbjct: 41 LLKENLSAIENANPIGISKATSYESTSMPANSDLEIIYGPLLVDFSQLAPTSSQFNIAIENLITDNPASVQITIFTRSSPIREERHEISSRRSTLQIISVIESPQKREVISFYIG 155
BLAST of SMED30014578 vs. Planmine SMEST
Match: SMESG000068983.1 (SMESG000068983.1) HSP 1 Score: 174.096 bits (440), Expect = 1.411e-52 Identity = 103/143 (72.03%), Postives = 118/143 (82.52%), Query Frame = 1 Query: 592 LLKENLSAVENANPIGISEATSYESTSMPANSDLEIIYGPPLVDFSQLAPTPSQFNIAIENLITDNPASVQITIFTRSSPIREEGHEISSRRSTLQIISVIESPQVRTSINSTAGXXXXXXXXXXXXXXXKRYLPIDMDTEDE 1020 LL+ NLSA+ENAN IGISE T Y+ SMP +SDLEIIY P LV FSQL P SQFNI++ENL T NPA+V ITI TRSSP+REEGHEI+S RST QIISVIE PQVRTS+NST NISR+ PNPS R PRKRYLP+D+D+ED+ Sbjct: 66 LLQANLSAIENANSIGISETTPYKPISMPTDSDLEIIYAPRLVAFSQLDPVRSQFNISMENLTTGNPANVPITISTRSSPVREEGHEITSGRSTPQIISVIEPPQVRTSVNSTVENISRQYPNPSPRRPRKRYLPVDIDSEDD 208
BLAST of SMED30014578 vs. Planmine SMEST
Match: SMESG000032225.1 (SMESG000032225.1) HSP 1 Score: 115.931 bits (289), Expect = 2.939e-45 Identity = 72/118 (61.02%), Postives = 82/118 (69.49%), Query Frame = 3 Query: 111 MPLPKIPKISSAPAVIAAAQHLAXXXXXXXXXXXXXXXXXXXWCSPEATRELYKKIT*ISQTRDDLIVENKIQRITIADQSAALR*IFTEKKLQALLPDRSIAQLLDIIPAHHQPSSS 464 MPLPKIP IS A +V LA L + K EK+KG WCSPEAT+ELYK IT IS+ RDDLIVEN+ QRITI D+S ALR +FTEK+LQA LP RS AQ L+II HH P S Sbjct: 1 MPLPKIPNISPALSV------LAPLNTWQIWRIVKYEKMKGTWCSPEATKELYKNITRISRARDDLIVENRTQRITIVDKSPALRQLFTEKELQARLPGRSTAQQLNIISVHHLPVYS 112 HSP 2 Score: 85.5001 bits (210), Expect = 2.939e-45 Identity = 57/85 (67.06%), Postives = 66/85 (77.65%), Query Frame = 1 Query: 457 VVLSN*VQRDVTNAVTIMPALPISNQKHKPXXXXXXXXXXXXXXXLLKENLSAVENANPIGISEATSYESTSMPANSDLEIIYGP 711 V SN ++RDVTNAV P LPI N+KHKPNKN+R+REKRR ENALL+ NL+A+EN IGISE T YE SMPA+SDL IIY P Sbjct: 110 VYSSNRIERDVTNAVMTRPVLPICNRKHKPNKNQRRREKRRTENALLQANLNAIENVISIGISETTPYEPISMPADSDLAIIYAP 194 The following BLAST results are available for this feature:
BLAST of SMED30014578 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30014578 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30014578 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30014578 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30014578 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30014578 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30014578 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30014578 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30014578 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30014578 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30014578 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30014578 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30014578 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30014578 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 >SMED30014578 ID=SMED30014578|Name=SMED30014578|organism=Schmidtea mediterranea sexual|type=transcript|length=1129bpback to top protein sequence of SMED30014578-orf-1 >SMED30014578-orf-1 ID=SMED30014578-orf-1|Name=SMED30014578-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=172bp MPALPISNQKHKPNKNRRKREKRRAENALLKENLSAVENANPIGISEATSback 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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