SMED30002422
Overview
Neoblast Clusters
Zeng et. al., 2018
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 AppEmbryonic 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., 2020SMED30002422 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 11
Alignments
SMED30002422 aligns in the following genomic locations:
Homology
BLAST of SMED30002422 vs. TrEMBL
Match: A0A1S3JJT4 (microtubule-associated protein futsch OS=Lingula unguis OX=7574 GN=LOC106173549 PE=4 SV=1) HSP 1 Score: 86.6557 bits (213), Expect = 2.192e-13 Identity = 48/161 (29.81%), Postives = 89/161 (55.28%), Query Frame = 3 Query: 1833 MLPSTDCLKQTFHVDHEDEELLQTPIIYD-ANGERIENLSETNNFKSVTEYVTLRISDLKALIKIEISVEMFHNINPIEDNWKRKTVRLTRMIELDLSKIKDSRKL-QNIMKRCRMDKPQISWTDENGSVVNQYNQENVLTGKETFDVFFNLLSITHEEEE 2309 ++P ++Q+ HVD E+EE+ I+ + A+G + S T NF +V E V L I + A + ++++ E +NP++D WK+ V +TR+IE DL ++R++ + I+ + +K ++++ D G + + L KET VF L++ E+ E Sbjct: 1927 LVPIPRNVRQSIHVDREEEEIQGGGILLNHADGSGYKTDSSTVNFDTVNECVDLGIENGVARVAVKVTCERIVPVNPVQDVWKKNAVIVTRLIEFDLEANPETRRMYERIINSRKTNKREVAYIDSRGREHIETQADRTLNAKETMKVFSTLMNAAGEKNE 2087
BLAST of SMED30002422 vs. Planmine SMEST
Match: SMESG000074454.1 (SMESG000074454.1) HSP 1 Score: 977.622 bits (2526), Expect = 0.000e+0 Identity = 476/477 (99.79%), Postives = 476/477 (99.79%), Query Frame = 3 Query: 1017 MHSSTSEIEIKEPEKNLSFTIDKVQEYNYTNNTVKPKERERPRVKESSTVEMKIHSPKPEIDFVNIEIYNGNEPPVRSDSVKMKKEWVEYKQLPVETNHRSEIKRDYNSEILYPIGSTRSKNSNAVYFNNKLSDYKIKPTETSSFEQISKGYSSKDLCDTHNSYVPSMYNTGQTGKSDSVTMKEEWTEFLTVPIFSTSANSITQKENPKSNATYPYASKIYDHYSYRYEDPIKTEKLQNLASTTLENAPRTYHSSERVVQALYDSLSKKHKPMLPSTDCLKQTFHVDHEDEELLQTPIIYDANGERIENLSETNNFKSVTEYVTLRISDLKALIKIEISVEMFHNINPIEDNWKRKTVRLTRMIELDLSKIKDSRKLQNIMKRCRMDKPQISWTDENGSVVNQYNQENVLTGKETFDVFFNLLSITHEEEEQCQPSKVNKDEFYLTRSPSGQITNVPCEPQYLINGYSNVERSYLYY 2447 MHSSTSEIEIKEPEKNLSFTIDKVQEYNYTNNTVKPKERERPRVKESSTVEMKIHSPKPEIDFVNIEIYNGNEPPVRSDSVKMKKEWVEYKQLPVETNHRSEIKRDYNSEILYPI STRSKNSNAVYFNNKLSDYKIKPTETSSFEQISKGYSSKDLCDTHNSYVPSMYNTGQTGKSDSVTMKEEWTEFLTVPIFSTSANSITQKENPKSNATYPYASKIYDHYSYRYEDPIKTEKLQNLASTTLENAPRTYHSSERVVQALYDSLSKKHKPMLPSTDCLKQTFHVDHEDEELLQTPIIYDANGERIENLSETNNFKSVTEYVTLRISDLKALIKIEISVEMFHNINPIEDNWKRKTVRLTRMIELDLSKIKDSRKLQNIMKRCRMDKPQISWTDENGSVVNQYNQENVLTGKETFDVFFNLLSITHEEEEQCQPSKVNKDEFYLTRSPSGQITNVPCEPQYLINGYSNVERSYLYY Sbjct: 1 MHSSTSEIEIKEPEKNLSFTIDKVQEYNYTNNTVKPKERERPRVKESSTVEMKIHSPKPEIDFVNIEIYNGNEPPVRSDSVKMKKEWVEYKQLPVETNHRSEIKRDYNSEILYPIDSTRSKNSNAVYFNNKLSDYKIKPTETSSFEQISKGYSSKDLCDTHNSYVPSMYNTGQTGKSDSVTMKEEWTEFLTVPIFSTSANSITQKENPKSNATYPYASKIYDHYSYRYEDPIKTEKLQNLASTTLENAPRTYHSSERVVQALYDSLSKKHKPMLPSTDCLKQTFHVDHEDEELLQTPIIYDANGERIENLSETNNFKSVTEYVTLRISDLKALIKIEISVEMFHNINPIEDNWKRKTVRLTRMIELDLSKIKDSRKLQNIMKRCRMDKPQISWTDENGSVVNQYNQENVLTGKETFDVFFNLLSITHEEEEQCQPSKVNKDEFYLTRSPSGQITNVPCEPQYLINGYSNVERSYLYY 477
BLAST of SMED30002422 vs. Planmine SMEST
Match: SMESG000077614.1 (SMESG000077614.1) HSP 1 Score: 73.9442 bits (180), Expect = 2.020e-13 Identity = 49/155 (31.61%), Postives = 78/155 (50.32%), Query Frame = 3 Query: 1833 MLPSTDCLKQTFHVDHEDEELLQTPIIYDANGERIENLSETNNFKSVTEYVTLRISDLKAL-IKIEISVEMFHNINPIEDNWKRKTVRLTRMIELDLSKIKDSRKLQNIMKRCRMDKPQISWTDENGSVVNQYNQENVLTGKETFDVFFNLLSIT 2294 MLP KQ FHV ++EELL P+IYD NG +I NL TN F V+E V++ IS L + + + I V + + I+ W +KT+ + R I +++ K++ ++ +K + D S+ ++ LTG VF L+ I Sbjct: 281 MLPVGTFAKQKFHVVQDEEELLGRPVIYDLNGLQIPNLEITNEFDCVSESVSINISKLTNVEVVVTILVSKYISKKQIDKPWTKKTIEIIRTISINVEASGKKEKVEKLINDLMKNKSE--KFDIKASIYRLKGEKIQLTGYSALKVFKILMKIA 433 The following BLAST results are available for this feature:
BLAST of SMED30002422 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30002422 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30002422 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30002422 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30002422 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30002422 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30002422 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30002422 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of SMED30002422 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30002422 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30002422 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30002422 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30002422 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30002422 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 >SMED30002422 ID=SMED30002422|Name=SMED30002422|organism=Schmidtea mediterranea sexual|type=transcript|length=2507bpback to top protein sequence of SMED30002422-orf-1 >SMED30002422-orf-1 ID=SMED30002422-orf-1|Name=SMED30002422-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=793bp MTEVIEQRRVEKVIKTHHKIQEDEPMIHKKIIDITIHPVDDAESFVINKSback 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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