SMED30005322
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., 2020SMED30005322 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 10
Alignments
SMED30005322 aligns in the following genomic locations:
Homology
BLAST of SMED30005322 vs. TrEMBL
Match: A0A267F9X9 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig026293g1 PE=4 SV=1) HSP 1 Score: 67.0106 bits (162), Expect = 1.345e-10 Identity = 51/138 (36.96%), Postives = 72/138 (52.17%), Query Frame = 2 Query: 68 ITFHQVTMSLLISTVAFSITSVVTKNWD-DSRSIWELTNHSNDVVTKVFVIIGTVCACLAFLMELLIQLSSTFSLSNAIRILTXXXXXXXXXXXXXXXXXXXXYRCAGECGFSYWFAAISSVLMFQAVIFYMIAWRCT 478 ITFHQ+T+ L +A SI S T+ W S +++L N + K F IIG + LME+L+ S+TF LS A+ +L I LL SLL+ + + + G G+S W +V +A FY I WRCT Sbjct: 6 ITFHQITIITLCFGIACSIASCATRAWQSGSGGLFDLPNEAWANTIKAFAIIGVAMLGFSLLMEILMVASNTFKLSRAMHLLCFICCLLSAASLLISLGLYSRHYSYG--GYSVWLLTAGTVFALEAFFFYTIQWRCT 141
BLAST of SMED30005322 vs. TrEMBL
Match: A0A267EGW5 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig016342g1 PE=4 SV=1) HSP 1 Score: 64.6994 bits (156), Expect = 7.837e-10 Identity = 50/137 (36.50%), Postives = 71/137 (51.82%), Query Frame = 2 Query: 68 ITFHQVTMSLLISTVAFSITSVVTKNWDDSRSIWELTNHSNDVVTKVFVIIGTVCACLAFLMELLIQLSSTFSLSNAIRILTXXXXXXXXXXXXXXXXXXXXYRCAGECGFSYWFAAISSVLMFQAVIFYMIAWRCT 478 ITFHQ+T+ L +A SI S T+ W S +++L N + K F IIG + ME+L+ S+TF LS A+ +L I LL SLL+ + + + G G+S W +V +A FY I WRCT Sbjct: 6 ITFHQITIITLCFGIACSIASCATRAWK-SGGLFDLPNEAWANTIKAFAIIGVAMLGFSLFMEILMVASNTFKLSRAMHLLCFICCLLSAASLLISLGLYSRHYSYG--GYSVWLLTAGTVFALEAFFFYTIQWRCT 139
BLAST of SMED30005322 vs. TrEMBL
Match: A0A1I8IAF0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1) HSP 1 Score: 60.4622 bits (145), Expect = 4.470e-8 Identity = 45/146 (30.82%), Postives = 76/146 (52.05%), Query Frame = 2 Query: 56 TMVVITFHQVTMSLLISTVAFSITSVVTKNWDDS-----RSIWELTNHSNDVVTKVFVIIGTVCACLAFLMELLIQLSSTFSLSNAIRILTXXXXXXXXXXXXXXXXXXXXYRCAGECGFSYWFAAISSVLMFQAVIFYMIAWRCT 478 +M I+FHQ+ +++L +A I + + +W S +++L N+S K IIG L+E+L+ +S+TF LS A+ +L L+ ++ LL+G+ V G G+S W S+V +A+ FY+I WRC Sbjct: 6 SMATISFHQICITVLSLGLACGIIACASSSWQMSWNARGSGLFDLPNNSEGNSVKALTIIGVAFLAFGLLLEILMIVSNTFKLSKAVNLLCLVCCIIAVAGLLIGLIVYAAKFSYG--GYSVWLLTASTVFAIEALFFYIIQWRCA 149
BLAST of SMED30005322 vs. TrEMBL
Match: A0A1I8IRB7 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig011666g1 PE=4 SV=1) HSP 1 Score: 59.6918 bits (143), Expect = 6.515e-8 Identity = 45/145 (31.03%), Postives = 75/145 (51.72%), Query Frame = 2 Query: 59 MVVITFHQVTMSLLISTVAFSITSVVTKNWDDS-----RSIWELTNHSNDVVTKVFVIIGTVCACLAFLMELLIQLSSTFSLSNAIRILTXXXXXXXXXXXXXXXXXXXXYRCAGECGFSYWFAAISSVLMFQAVIFYMIAWRCT 478 M I+FHQ+ +++L +A I + + +W S +++L N+S K IIG L+E+L+ +S+TF LS A+ +L L+ ++ LL+G+ V G G+S W S+V +A+ FY+I WRC Sbjct: 1 MATISFHQICITVLSLGLACGIIACASSSWQMSWNARGSGLFDLPNNSEGNSVKALTIIGVAFLAFGLLLEILMIVSNTFKLSKAVNLLCLVCCIIAVAGLLIGLIVYAAKFSYG--GYSVWLLTASTVFAIEALFFYIIQWRCA 143
BLAST of SMED30005322 vs. Planmine SMEST
Match: SMESG000078208.1 (SMESG000078208.1) HSP 1 Score: 234.187 bits (596), Expect = 1.203e-79 Identity = 140/140 (100.00%), Postives = 140/140 (100.00%), Query Frame = 2 Query: 59 MVVITFHQVTMSLLISTVAFSITSVVTKNWDDSRSIWELTNHSNDVVTKVFVIIGTVCACLAFLMELLIQLSSTFSLSNAIRILTXXXXXXXXXXXXXXXXXXXXYRCAGECGFSYWFAAISSVLMFQAVIFYMIAWRCT 478 MVVITFHQVTMSLLISTVAFSITSVVTKNWDDSRSIWELTNHSNDVVTKVFVIIGTVCACLAFLMELLIQLSSTFSLSNAIRILTLIFVLLGFGSLLVGVSVGGVYRCAGECGFSYWFAAISSVLMFQAVIFYMIAWRCT Sbjct: 1 MVVITFHQVTMSLLISTVAFSITSVVTKNWDDSRSIWELTNHSNDVVTKVFVIIGTVCACLAFLMELLIQLSSTFSLSNAIRILTLIFVLLGFGSLLVGVSVGGVYRCAGECGFSYWFAAISSVLMFQAVIFYMIAWRCT 140 The following BLAST results are available for this feature:
BLAST of SMED30005322 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30005322 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30005322 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30005322 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30005322 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30005322 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30005322 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30005322 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 4
BLAST of SMED30005322 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30005322 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30005322 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30005322 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30005322 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30005322 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 1
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30005322 ID=SMED30005322|Name=SMED30005322|organism=Schmidtea mediterranea sexual|type=transcript|length=603bpback to top protein sequence of SMED30005322-orf-1 >SMED30005322-orf-1 ID=SMED30005322-orf-1|Name=SMED30005322-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=141bp MVVITFHQVTMSLLISTVAFSITSVVTKNWDDSRSIWELTNHSNDVVTKVback 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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