SMED30007284
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., 2020SMED30007284 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 15Note: Hover over icons to view figure legend
Alignments
SMED30007284 aligns in the following genomic locations:
Homology
BLAST of SMED30007284 vs. Planmine SMEST
Match: SMESG000065567.1 (SMESG000065567.1) HSP 1 Score: 169.088 bits (427), Expect = 6.862e-53 Identity = 92/110 (83.64%), Postives = 93/110 (84.55%), Query Frame = 3 Query: 3 MCLAVFINIIWGDFG--EIWVGFHLMRGDCDAGLEWPFKYAVKVDAINPADGNVYSSQSVKCPDSPXXXXXNWGRPARDRNNRICFTNYFTILSAIKNDKLLLKCRIEKL 326 MCLAV I WGD G I+V FHLMRGDCDAGLEWPFKYAVKVDAINPADGNVY SQSVKCPDSPAAA A W RPA DRNN I FTNYFT LSAIKNDKLLLKCRIEKL Sbjct: 67 MCLAVNI---WGDIGLCAIYVCFHLMRGDCDAGLEWPFKYAVKVDAINPADGNVYHSQSVKCPDSPAAADAEWRRPASDRNNPISFTNYFTNLSAIKNDKLLLKCRIEKL 173
BLAST of SMED30007284 vs. Planmine SMEST
Match: SMESG000065606.1 (SMESG000065606.1) HSP 1 Score: 174.481 bits (441), Expect = 4.830e-52 Identity = 91/108 (84.26%), Postives = 95/108 (87.96%), Query Frame = 3 Query: 3 MCLAVFINIIWGDFGEIWVGFHLMRGDCDAGLEWPFKYAVKVDAINPADGNVYSSQSVKCPDSPXXXXXNWGRPARDRNNRICFTNYFTILSAIKNDKLLLKCRIEKL 326 MC+AV I IW G I V F+LMRGDCDAGLEWPFKYAVKVDAINPADGNVYSSQSVKCPDSPAAAAA WGRPA DRN+RI FT+YFT LSAIKNDKLLLKCRIEKL Sbjct: 323 MCVAVNITSIWS--GAIRVRFYLMRGDCDAGLEWPFKYAVKVDAINPADGNVYSSQSVKCPDSPAAAAAKWGRPASDRNDRISFTDYFTNLSAIKNDKLLLKCRIEKL 428
BLAST of SMED30007284 vs. Planmine SMEST
Match: SMESG000000563.1 (SMESG000000563.1) HSP 1 Score: 176.792 bits (447), Expect = 4.987e-52 Identity = 91/112 (81.25%), Postives = 96/112 (85.71%), Query Frame = 3 Query: 3 MCLAVFINIIWGD----FGEIWVGFHLMRGDCDAGLEWPFKYAVKVDAINPADGNVYSSQSVKCPDSPXXXXXNWGRPARDRNNRICFTNYFTILSAIKNDKLLLKCRIEKL 326 MCLAV IN ++G G+I VGFHLMRGDCDAG+EWPFKYAVKVDAINPADGNVYSSQSVKCPDSPAAA WGRPA DRN+ I FTNYFT LSAIKNDKLLLKCRIEKL Sbjct: 409 MCLAVDINSLFGGPTRYDGDIRVGFHLMRGDCDAGMEWPFKYAVKVDAINPADGNVYSSQSVKCPDSPAAAK--WGRPASDRNDAISFTNYFTFLSAIKNDKLLLKCRIEKL 518
BLAST of SMED30007284 vs. Planmine SMEST
Match: SMESG000029699.1 (SMESG000029699.1) HSP 1 Score: 167.548 bits (423), Expect = 1.767e-51 Identity = 91/109 (83.49%), Postives = 95/109 (87.16%), Query Frame = 3 Query: 3 MCLAVFINIIWGDFGEIWVGFHLMRGDCDAGLEWPFKYAVKVDAINPADGNVYSSQSVKCPDSP-XXXXXNWGRPARDRNNRICFTNYFTILSAIKNDKLLLKCRIEKL 326 MCLAVFI ++G G I VGFHLMRGDCDAGLEWPFKY+VKVDAINPADGNVY SQSVKCPDSP AAA A WGRPARDRNN I F N+FT LSAIKNDKLLLKCRIEKL Sbjct: 121 MCLAVFIRGLFG--GVISVGFHLMRGDCDAGLEWPFKYSVKVDAINPADGNVYLSQSVKCPDSPAAAADARWGRPARDRNNPI-FNNHFTYLSAIKNDKLLLKCRIEKL 226
BLAST of SMED30007284 vs. Planmine SMEST
Match: SMESG000029699.1 (SMESG000029699.1) HSP 1 Score: 167.162 bits (422), Expect = 2.151e-51 Identity = 91/109 (83.49%), Postives = 95/109 (87.16%), Query Frame = 3 Query: 3 MCLAVFINIIWGDFGEIWVGFHLMRGDCDAGLEWPFKYAVKVDAINPADGNVYSSQSVKCPDSP-XXXXXNWGRPARDRNNRICFTNYFTILSAIKNDKLLLKCRIEKL 326 MCLAVFI ++G G I VGFHLMRGDCDAGLEWPFKY+VKVDAINPADGNVY SQSVKCPDSP AAA A WGRPARDRNN I F N+FT LSAIKNDKLLLKCRIEKL Sbjct: 124 MCLAVFIRGLFG--GVISVGFHLMRGDCDAGLEWPFKYSVKVDAINPADGNVYLSQSVKCPDSPAAAADARWGRPARDRNNPI-FNNHFTYLSAIKNDKLLLKCRIEKL 229 The following BLAST results are available for this feature:
BLAST of SMED30007284 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30007284 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30007284 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30007284 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30007284 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30007284 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30007284 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30007284 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30007284 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30007284 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30007284 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30007284 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30007284 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30007284 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 >SMED30007284 ID=SMED30007284|Name=SMED30007284|organism=Schmidtea mediterranea sexual|type=transcript|length=731bpback to top protein sequence of SMED30007284-orf-1 >SMED30007284-orf-1 ID=SMED30007284-orf-1|Name=SMED30007284-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp MCLAVFINIIWGDFGEIWVGFHLMRGDCDAGLEWPFKYAVKVDAINPADGback to top Annotated Terms
The following terms have been associated with this transcript:
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