SMED30022713
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., 2020SMED30022713 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 7
Alignments
SMED30022713 aligns in the following genomic locations:
Homology
BLAST of SMED30022713 vs. Planmine SMEST
Match: SMESG000017126.1 (SMESG000017126.1) HSP 1 Score: 164.081 bits (414), Expect = 8.705e-52 Identity = 79/87 (90.80%), Postives = 80/87 (91.95%), Query Frame = 3 Query: 162 VASYPSSSCANCSFKTDWSFDEALQSLSRNFVKCMVEQRKYLNELIANASVPVADIQCLDSNCYRYGYRQDRNLVISNYLGTCPNYL 422 VAS PSSSCANCSFKTDWSFD ALQS SR FV C VEQRKYLNELIANASVPVADIQCLDS CYRYGYRQDRNLVISNYLGTCPNY+ Sbjct: 19 VASCPSSSCANCSFKTDWSFDAALQSSSRTFVNCKVEQRKYLNELIANASVPVADIQCLDSKCYRYGYRQDRNLVISNYLGTCPNYM 105
BLAST of SMED30022713 vs. Planmine SMEST
Match: SMESG000017127.1 (SMESG000017127.1) HSP 1 Score: 155.221 bits (391), Expect = 4.926e-47 Identity = 88/197 (44.67%), Postives = 121/197 (61.42%), Query Frame = 3 Query: 60 NQRNDVSCFFGRCTVVNYQWERLANDTFKLNKNIVASYPSSSCANCSFKTDWSFDEALQSLSRNFVKCMVEQRKYLNELIANASVPVADIQCLDSNCYRYGYRQDRNLVISNYLGTCPNYLCTNCMRSDIWKYNVLYSYVERESNSCPLMSKINVEDFFILSKYEFFDGGRITAITISCASFIFLVICLTVCFTCRN 650 N+R D SC +G C +V+YQ E + ++ + V S S SCANC+ K+DW+ + LSR V C+ EQRK+++E+ A+ +ADIQC ++ C +Y Y +NYLG+C ++ C++C+RS IW YN Y+ER+ SCP SKI EDFFI FFD GRI AI ISC SFI + I L VCF C+ Sbjct: 22 NKRYDFSCNYGTCRLVSYQLESIYGR-LTVSSSQVGSCSSLSCANCTVKSDWNIFSGI--LSRTVVNCLTEQRKFVSEIFTYAAYTMADIQCFNNKCSKYSYSSYFPYE-TNYLGSCQDWQCSDCLRSMIWTYNA-NGYLERDVYSCPAASKITAEDFFIYPTISFFDDGRIIAIIISCLSFISITIILIVCFACKK 213
BLAST of SMED30022713 vs. Planmine SMEST
Match: SMESG000048698.1 (SMESG000048698.1) HSP 1 Score: 115.931 bits (289), Expect = 1.080e-31 Identity = 66/197 (33.50%), Postives = 111/197 (56.35%), Query Frame = 3 Query: 60 NQRNDVSCFFGRCTVVNYQWERLANDTFKLNKNIVASYPSSSCANCSFKTDWSFD--EALQSLSRNFVKCMVEQRKYLNELIANASVPVADIQCLDSNCYRYGYRQDRNLVISNYLGTCPNYLCTNCMRSDIWKYNVLYSYVERESNSCPLMSKINVEDFFILSKY--EFFDGGRITAITISCASFIFLVICLTVCF 638 N+R D++C G C+V++Y + + + +K+ K ++ + C NC+ K DWS + + + R KC+ + +L N PV+D C C +Y Y + N++ +Y+G C + C +C SD W ++L Y++R + SC ++ KI +ED+F++ ++ F+ R AITISCASF+ LVI L VCF Sbjct: 28 NERADITCETGSCSVLSYTLQ-IDDQIYKVKKGFKSACSTRLCENCAHKGDWSMRLIDGNKYMVRQVNKCLTNNILAVEQLFTNLYTPVSDFTCSLHKCSKYNYSYNGNMISFSYIGVCDHSYCDSCRYSDNW--SLLTGYLQRTTISCYVVDKIRLEDYFLIPEFTETFYTLIRKLAITISCASFLCLVIILLVCF 221
BLAST of SMED30022713 vs. Planmine SMEST
Match: SMESG000004193.1 (SMESG000004193.1) HSP 1 Score: 115.161 bits (287), Expect = 1.708e-30 Identity = 66/197 (33.50%), Postives = 111/197 (56.35%), Query Frame = 3 Query: 60 NQRNDVSCFFGRCTVVNYQWERLANDTFKLNKNIVASYPSSSCANCSFKTDWSFD--EALQSLSRNFVKCMVEQRKYLNELIANASVPVADIQCLDSNCYRYGYRQDRNLVISNYLGTCPNYLCTNCMRSDIWKYNVLYSYVERESNSCPLMSKINVEDFFILSKY--EFFDGGRITAITISCASFIFLVICLTVCF 638 N+R D++C G C+V++Y + + + +K+ K ++ + C NC+ K DWS + + + R KC+ + +L N PV+D C C +Y Y + N++ +Y+G C + C +C SD W ++L Y++R + SC ++ KI +ED+F++ ++ F+ R AITISCASF+ LVI L VCF Sbjct: 127 NERADITCEPGSCSVLSYTLQ-IDDQIYKVKKGFKSACSTRLCENCAHKGDWSMRLIDGNKYMVRQVNKCLTNNILAVEQLFTNLYTPVSDFTCSLHKCSKYNYSYNGNMISFSYIGVCDHSYCDSCRYSDNW--SLLTGYLQRTTISCYVVDKIRLEDYFLIPEFTETFYTLIRKLAITISCASFLCLVIILLVCF 320
BLAST of SMED30022713 vs. Planmine SMEST
Match: SMESG000017181.1 (SMESG000017181.1) HSP 1 Score: 103.605 bits (257), Expect = 6.346e-27 Identity = 71/207 (34.30%), Postives = 110/207 (53.14%), Query Frame = 3 Query: 60 NQRNDVSCFFGRCTVVNYQWERLAND--TFKLNKNIVASY--PSSSCANCSFKTDWSFDEALQS--LSRNFVKCMVEQRKYLNELIANAS-VPVADIQCLDSNCYRYGYRQDRNLVISNYLGTCPNYLCTNCMRSDIWKY--NVLYSYVERESNSCPLMSKINVEDFF-----ILSKYEFFDGGRITAITISCASFIFLVICLTVCF 638 N+RND++C C V Y RL D ++ N+ PS +C NCS+K +W +A + L R+ C + + E+ ++S + V DI C + C +Y Y + + + + YLG C C C W+Y Y+ ++R +SCP +++IN+EDFF I EF+DGGRI ++ ISC SF+ L+I L+VCF Sbjct: 21 NERNDITCANRTCNNVRY---RLYYDDQSYHYYVNVAGESVCPSVNCNNCSYKGNWMLGKASGTYFLYRSTNSCSTDSIRNFTEIFPSSSPLNVTDIACSNYGCSKYNYLFESSKLYTKYLGNCSYPSCEGCKTLTPWQYVNGNSYNLLQRNVSSCPSITRINMEDFFRRLDQISFVKEFWDGGRILSVIISCVSFVALIIILSVCF 224 The following BLAST results are available for this feature:
BLAST of SMED30022713 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30022713 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30022713 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30022713 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30022713 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30022713 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30022713 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30022713 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30022713 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30022713 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30022713 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30022713 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30022713 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30022713 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 >SMED30022713 ID=SMED30022713|Name=SMED30022713|organism=Schmidtea mediterranea sexual|type=transcript|length=689bpback to top protein sequence of SMED30022713-orf-1 >SMED30022713-orf-1 ID=SMED30022713-orf-1|Name=SMED30022713-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=219bp SDLCVILVLLPSLILSQIVNQRNDVSCFFGRCTVVNYQWERLANDTFKLNback to top Annotated Terms
The following terms have been associated with this transcript:
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