SMED30028688
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., 2020SMED30028688 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30028688 aligns in the following genomic locations:
Homology
BLAST of SMED30028688 vs. TrEMBL
Match: A0A504Z448 (Uncharacterized protein (Fragment) OS=Fasciola gigantica OX=46835 GN=FGIG_11484 PE=4 SV=1) HSP 1 Score: 70.8626 bits (172), Expect = 5.051e-10 Identity = 30/88 (34.09%), Postives = 56/88 (63.64%), Query Frame = 1 Query: 784 NERRNENMNVPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWN 1047 +ERR + F+ + R +++KL+L+Y LVW + A+ ++ +LWH+FT++C+LQ++Y+ ++ +F+RPVL IH W+ Sbjct: 136 SERR--------DAFLLAHLPHLDARLWITIKLALTYCLVWTIAFIAIFYASVALWHVFTLLCSLQAIYVTVNSVFSRPVLDLIHQWH 215
BLAST of SMED30028688 vs. TrEMBL
Match: A0A2H1BYI7 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_008391 PE=4 SV=1) HSP 1 Score: 70.8626 bits (172), Expect = 1.194e-9 Identity = 30/88 (34.09%), Postives = 56/88 (63.64%), Query Frame = 1 Query: 784 NERRNENMNVPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWN 1047 +ERR + F+ + R +++KL+L+Y LVW + A+ ++ +LWH+FT++C+LQ++Y+ ++ +F+RPVL IH W+ Sbjct: 136 SERR--------DAFLLAHLPHLDARLWITIKLALTYCLVWTIAFIAIFYASVALWHVFTLLCSLQAIYVTVNSVFSRPVLDLIHQWH 215
BLAST of SMED30028688 vs. TrEMBL
Match: A0A183AGH7 (Uncharacterized protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS6061 PE=4 SV=1) HSP 1 Score: 68.1662 bits (165), Expect = 1.148e-8 Identity = 27/76 (35.53%), Postives = 51/76 (67.11%), Query Frame = 1 Query: 820 EQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWN 1047 + F+ + R ++VKL+ +Y L+W + A+ ++ +LWH+FT++C+LQ++Y+ ++ IF+RPVL IH W+ Sbjct: 145 DGFLLAHLPHLNARLWITVKLAATYCLIWTMAFLAIFYASVALWHVFTLLCSLQAIYVTVNSIFSRPVLDLIHQWH 220
BLAST of SMED30028688 vs. TrEMBL
Match: A0A183Q6S8 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS22314 PE=4 SV=1) HSP 1 Score: 58.5362 bits (140), Expect = 6.104e-6 Identity = 26/65 (40.00%), Postives = 45/65 (69.23%), Query Frame = 1 Query: 850 IQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNW 1044 I R +++K ++++ LVW + ALI + S+WH+FT++ +LQ++YI ++ FTRPVL I+ W Sbjct: 92 ISARFWITLKFTMTHSLVWLIAFIALIQASTSIWHVFTLLYSLQAIYITVNCTFTRPVLDLIYQW 156
BLAST of SMED30028688 vs. Planmine SMEST
Match: SMESG000042109.1 (SMESG000042109.1) HSP 1 Score: 707.212 bits (1824), Expect = 0.000e+0 Identity = 349/350 (99.71%), Postives = 349/350 (99.71%), Query Frame = 1 Query: 61 MLNESSHPINATDNFQSSSISHVCFGITIVCHLVHLGIIICIRDLKFLYGLAITLSLLTNTIGFIILIVSCSTRIAISKDQIISSTWPEITTESLFLSAVSWNLIAILQVALLTKFTVFLPTRKFSITNYHPRLFTQLFLKIVYFILEVSFAIGFPLFFGIWRGISRSATKTSFPIYDSKYHEIECSLSQSKTLFEMFLTPLLIIIFLQSIGGIGLLIVLRSKHRMLYSMENGIVDETQQTNERRNENMNVPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWNYRGPSNPFNIRPSLNHIHFDR 1110 MLNESSHPINATDNFQSSSISHVCFGITIVCHLVHLGIIICIRDLKFLYGLAITLSLLTNTIGFIILIVSCSTRIAISKDQIISSTWPEITTESLFLSAVSWNLIAILQVALLTKFTVFLPTRKFSITNYHPRLFTQLFLKIVYFILEVSFAIGFPLFFGIWRGISRSATKTSFPIYDSKYHEIECSLSQSKTLFEMFLTPLLIIIFLQSIGGIGLLIVLRSKHRMLYSMENGIVDETQQTNER NENMNVPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWNYRGPSNPFNIRPSLNHIHFDR Sbjct: 1 MLNESSHPINATDNFQSSSISHVCFGITIVCHLVHLGIIICIRDLKFLYGLAITLSLLTNTIGFIILIVSCSTRIAISKDQIISSTWPEITTESLFLSAVSWNLIAILQVALLTKFTVFLPTRKFSITNYHPRLFTQLFLKIVYFILEVSFAIGFPLFFGIWRGISRSATKTSFPIYDSKYHEIECSLSQSKTLFEMFLTPLLIIIFLQSIGGIGLLIVLRSKHRMLYSMENGIVDETQQTNERHNENMNVPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWNYRGPSNPFNIRPSLNHIHFDR 350
BLAST of SMED30028688 vs. Planmine SMEST
Match: SMESG000011191.1 (SMESG000011191.1) HSP 1 Score: 111.694 bits (278), Expect = 9.785e-27 Identity = 89/320 (27.81%), Postives = 141/320 (44.06%), Query Frame = 1 Query: 88 NATDNFQSSSISHVCFGITIVCHLVHLGIIICIRDLKFLYGLAITLSLLTNTIGFIILIVSCSTRI-----AISKDQIISSTWPEITTESLFLSAVSWNLIAILQVALLTKFTVFLPTRKFSITNYHPRLF--TQLFLKIVYFILEVSFAIGFPLFFGIWRGISRSATKTSFPIYDSKYHEIECSLSQSKTLFEMFLTPLLIIIFLQSIGGIGLLIVLRSKHRMLYSMENGIVDETQQTNERRNENMNVPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVL 1026 N T+ FQ S++S VCF + I+ H + CIR ++ LYG I +L T +I + SCS I A + I + E ++ F+S++ WNL A Q+ L+ + T +LF Q F + + F + W ++ I D+ HEIECS + S F P IF + + +L+++ T + N+ R + + + Q I + M KL +YL++W GA A P LWH+FT+ C+LQ+L+I ++FIF+RPVL Sbjct: 20 NLTNQFQPSAVSKVCFAVAILTMSTHCLFVTCIRHIRMLYGSFILTNLYMMTFSYIFFMTSCSMDIKTIQYAFQYNWINKRSIMESISQFSFVSSIYWNLAASCQICLVI--------YRGCHTESTYKLFDCVQYFWGTIMSFVMPGLCCYFKFYLDNWLDLNPK-------IVDNLKHEIECSFNSSVNTDIFFYLP----IFTGMMITVAILVIIY----------------TMRCNKSREDRIIMFQNQEISARYG-------MCCKLVFTYLVIWVTGAAATHIISPPLWHVFTLCCSLQTLFIAVNFIFSRPVL 297
BLAST of SMED30028688 vs. Planmine SMEST
Match: SMESG000043863.1 (SMESG000043863.1) HSP 1 Score: 68.5514 bits (166), Expect = 3.855e-12 Identity = 30/67 (44.78%), Postives = 49/67 (73.13%), Query Frame = 1 Query: 850 IQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWNY 1050 ++ R M +KL L+ L+W + FA+ F+ S+WH+FT+ C+LQS+++ ISFIF+RPVL +HN ++ Sbjct: 230 MKSRHFMHIKLVLTNTLIWTIAFFAVEFNITSMWHIFTLSCSLQSIFLAISFIFSRPVLDVLHNGDH 296 The following BLAST results are available for this feature:
BLAST of SMED30028688 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30028688 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30028688 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30028688 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30028688 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30028688 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30028688 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30028688 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 4
BLAST of SMED30028688 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30028688 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30028688 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30028688 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30028688 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30028688 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 3
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30028688 ID=SMED30028688|Name=SMED30028688|organism=Schmidtea mediterranea sexual|type=transcript|length=2053bpback to top protein sequence of SMED30028688-orf-1 >SMED30028688-orf-1 ID=SMED30028688-orf-1|Name=SMED30028688-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=351bp MLNESSHPINATDNFQSSSISHVCFGITIVCHLVHLGIIICIRDLKFLYGback 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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