SMED30011235
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., 2020SMED30011235 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 13Note: Hover over icons to view figure legend
Alignments
SMED30011235 aligns in the following genomic locations:
Homology
BLAST of SMED30011235 vs. Planmine SMEST
Match: SMESG000014786.1 (SMESG000014786.1) HSP 1 Score: 241.506 bits (615), Expect = 3.594e-82 Identity = 143/161 (88.82%), Postives = 143/161 (88.82%), Query Frame = 3 Query: 105 MKIYSESYRNSNKMTTLTVRQLLIFVYIVSFVTLIIGIATEPQNFNVNSSSRAKAYAAFQXXXXXXXXXXXXXXXXXAFTSAVKDNRTVQLISTVFMVIAC------------------VSTVIACAVYSAYHFPYGWTVAACTLVIEALFIFIVTHMWIH 533 MKIYSESYRNSNKMTTLTVRQLLIFVYIVSFVTLIIGIATEPQNFNVNSSSRAKAYAAFQVIGVVSLGVVIILEILSAFTSAVKDNRTVQLISTVFMVIAC VSTVIACAVYSAYHFPYGWTVAACTLVIEALFIFIVTHMWIH Sbjct: 1 MKIYSESYRNSNKMTTLTVRQLLIFVYIVSFVTLIIGIATEPQNFNVNSSSRAKAYAAFQVIGVVSLGVVIILEILSAFTSAVKDNRTVQLISTVFMVIACKVSYGKLNLSELSFILVGVSTVIACAVYSAYHFPYGWTVAACTLVIEALFIFIVTHMWIH 161
BLAST of SMED30011235 vs. Planmine SMEST
Match: SMESG000014788.1 (SMESG000014788.1) HSP 1 Score: 212.616 bits (540), Expect = 5.845e-71 Identity = 130/148 (87.84%), Postives = 130/148 (87.84%), Query Frame = 3 Query: 144 MTTLTVRQLLIFVYIVSFVTLIIGIATEPQNFNVNSSSRAKAYAAFQXXXXXXXXXXXXXXXXXAFTSAVKDNRTVQLISTVFMVIAC------------------VSTVIACAVYSAYHFPYGWTVAACTLVIEALFIFIVTHMWIH 533 MTTLTVRQLLIFVYIVSFVTLIIGIATEPQNFNVNSSSRAKAYAAFQVIGVVSLGVVIILEILSAFTSAVKDNRTVQLISTVFMVIAC VSTVIACAVYSAYHFPYGWTVAACTLVIEALFIFIVTHMWIH Sbjct: 1 MTTLTVRQLLIFVYIVSFVTLIIGIATEPQNFNVNSSSRAKAYAAFQVIGVVSLGVVIILEILSAFTSAVKDNRTVQLISTVFMVIACKVSYGKLNLSELSFILVGVSTVIACAVYSAYHFPYGWTVAACTLVIEALFIFIVTHMWIH 148
BLAST of SMED30011235 vs. Planmine SMEST
Match: SMESG000045652.1 (SMESG000045652.1) HSP 1 Score: 97.0561 bits (240), Expect = 7.770e-26 Identity = 57/120 (47.50%), Postives = 87/120 (72.50%), Query Frame = 3 Query: 162 RQLLIFVYIVSFVTLIIGIATEPQNFNVNSSSRAKAYAAFQXXXXXXXXXXXXXXXXXAFTSAVKDNRTVQLISTVFMVIACVSTVIACAVYSAYHFPYGWTVAACTLVIEALFIFIVTH 521 +++L+F+++++ II +AT+P F +S K Y AF +IG+V+L VV++LE+L AF S+V+ N ++Q++ V MVIA V +IACAVY+ + PYGWTVA CTLVIEA+ I ++TH Sbjct: 11 QKVLLFIFVIALCCCIISMATDPYLFGKYNSLNMKLYTAFLIIGIVALIVVVLLEMLRAFISSVRSNGSIQIVGIVAMVIAAVCLIIACAVYNDGNVPYGWTVAGCTLVIEAVVIILITH 130
BLAST of SMED30011235 vs. Planmine SMEST
Match: SMESG000015390.1 (SMESG000015390.1) HSP 1 Score: 93.5893 bits (231), Expect = 1.382e-24 Identity = 58/123 (47.15%), Postives = 88/123 (71.54%), Query Frame = 3 Query: 144 MTTLTVRQLLIFVYIVSFVTLIIGIATEPQNFNVNSSSRAKAYAAFQXXXXXXXXXXXXXXXXXAFTSAVKDNRTVQLISTVFMVIACVSTVIACAVYSAYHFPYGWTVAACTLVIEALFIFI 512 M T+++ ++ + ++I+SF II I T+ + + S R KAY AF +IG++SLG+V+++EIL F + DNR +Q++S FMVI V+ +IACA+ HFPYGWTVA+CTL++EA+FIFI Sbjct: 1 MVTVSIGKVSLTIFILSFACAIIAICTDAGKLH-SYSDRDKAYGAFLIIGIISLGIVVVMEILLNFIHSFTDNRIIQILSLSFMVIGGVALIIACAICFPMHFPYGWTVASCTLLMEAIFIFI 122
BLAST of SMED30011235 vs. Planmine SMEST
Match: SMESG000015329.1 (SMESG000015329.1) HSP 1 Score: 92.0485 bits (227), Expect = 7.100e-24 Identity = 52/124 (41.94%), Postives = 86/124 (69.35%), Query Frame = 3 Query: 144 MTTLTVRQLLIFVYIVSFVTLIIGIATEPQNFNVNSSSRAKAYAAFQXXXXXXXXXXXXXXXXXAFTSAVKDNRTVQLISTVFMVIACVSTVIACAVYSAYHFPYGWTVAACTLVIEALFIFIV 515 M + ++++ ++ +S V II IAT+ F+ S R KAY +F +I ++SLG+V+ +E+L F ++ +NR +Q++S FMV+A VS +I+C++YS H PYGWTVA+CTL++E + IF+V Sbjct: 1 MVKIAPPKIMLIIFAMSLVCAIIAIATDSSLFSY--SDRNKAYGSFLIIAIISLGIVLFIELLLNFVGSLSENRIMQILSIAFMVLAGVSLIISCSIYSTSHMPYGWTVASCTLIMEGILIFLV 122 The following BLAST results are available for this feature:
BLAST of SMED30011235 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30011235 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30011235 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30011235 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30011235 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30011235 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30011235 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30011235 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30011235 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30011235 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30011235 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30011235 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30011235 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30011235 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 >SMED30011235 ID=SMED30011235|Name=SMED30011235|organism=Schmidtea mediterranea sexual|type=transcript|length=602bpback to top protein sequence of SMED30011235-orf-1 >SMED30011235-orf-1 ID=SMED30011235-orf-1|Name=SMED30011235-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=144bp MKIYSESYRNSNKMTTLTVRQLLIFVYIVSFVTLIIGIATEPQNFNVNSSback 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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